Literatura académica sobre el tema "Shade Tree Laboratories"

Background: Tissue counter analysis is an image analysis tool designed for the detection of structures in complex images at the macroscopic or microscopic scale. As a basic principle, small square or circular measuring masks are randomly placed across the image and image analysis parameters are obtained for each mask. Based on learning sets, statistical classification procedures are generated which facilitate an automated classification of new data sets.Objective: To evaluate the influence of the size and shape of the measuring masks as well as the importance of feature selection, statistical procedures and technical preparation of slides on the performance of tissue counter analysis in microscopic images. As main quality measure of the final classification procedure, the percentage of elements that were correctly classified was used.Study design: H&E‐stained slides of 25 primary cutaneous melanomas were evaluated by tissue counter analysis for the recognition of melanoma elements (section area occupied by tumour cells) in contrast to other tissue elements and background elements. Circular and square measuring masks, various subsets of image analysis features and classification and regression trees compared with linear discriminant analysis as statistical alternatives were used. The percentage of elements that were correctly classified by the various classification procedures was assessed. In order to evaluate the applicability to slides obtained from different laboratories, the best procedure was automatically applied in a test set of another 50 cases of primary melanoma derived from the same laboratory as the learning set and two test sets of 20 cases each derived from two different laboratories, and the measurements of melanoma area in these cases were compared with conventional assessment of vertical tumour thickness.Results: Square measuring masks were slightly superior to circular masks, and larger masks (64 or 128 pixels in diameter) were superior to smaller masks (8 to 32 pixels in diameter). As far as the subsets of image analysis features were concerned, colour features were superior to densitometric and Haralick texture features. Statistical moments of the grey level distribution were of least significance. CART (classification and regression tree) analysis turned out to be superior to linear discriminant analysis. In the best setting, 95% of melanoma tissue elements were correctly recognized. Automated measurement of melanoma area in the independent test sets yielded a correlation ofr=0.846 with vertical tumour thickness (p< 0.001), similar to the relationship reported for manual measurements. The test sets obtained from different laboratories yielded comparable results.Conclusions: Large, square measuring masks, colour features and CART analysis provide a useful setting for the automated measurement of melanoma tissue in tissue counter analysis, which can also be used for slides derived from different laboratories.

Abstract Background: Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a highly aggressive hematologic malignancy with a historical overall survival (OS) of ~8-14 months from diagnosis and no approved therapies or standard of care. Tagraxofusp (Elzonris™; SL-401) is a novel targeted therapy directed to the interleukin-3 receptor-α (CD123), a target expressed on BPDCN and other malignancies. Tagraxofusp was granted Breakthrough Therapy Designation for the treatment of patients with BPDCN, and a rolling Biologics License Application (BLA) submission to the U.S. Food and Drug Administration (FDA) was completed in June 2018. Detailed results from the pivotal trial of tagraxofusp in BPDCN will be presented. Methods: This pivotal Phase 2 clinical trial is a multicenter, open label, non-randomized, single-arm trial designed to determine safety and efficacy of tagraxofusp in patients with BPDCN. In Stage 1 (lead-in), first line (1L) and relapsed/refractory (r/r) patients with BPDCN received tagraxofusp as a daily IV infusion at 7, 9, or 12 mcg/kg/day on days 1-5 of a 21-day cycle. Patients with BPDCN enrolled in subsequent stages received tagraxofusp at the dose determined in Stage 1 (12 mcg/kg). Stage 2 (expansion) enrolled 1L and r/r patients, and Stage 3 (pivotal, confirmatory) enrolled only 1L patients. Results: 45 patients with BPDCN (Stages 1 and 2, n=32; Stage 3, n=13) were enrolled at 7 sites in the US, including 32 (71%) patients as 1L. Median age was 70 years (range, 22-84); 82% male. Median follow-up for all 1L patients treated at 12 mcg/kg (n=29) was 13.8 months (range 0.2-37.4+). The most common treatment-related adverse events (TRAEs) at 12 mcg/kg in 148 patients treated in four clinical trials with tagraxofusp were transaminitis (44%), hypoalbuminemia (44%), and thrombocytopenia (26%). Capillary leak syndrome (CLS), all grades, occurred in 17% of patients across all indications at 12 mcg/kg; 0.7% (1/148) and 1.6% (3/182) of cases resulted in death across all indications at 12 mcg/kg and all doses, respectively. The Stage 3 pivotal cohort met its primary endpoint with a 54% (7/13) rate of CR+CRc (95% CI: 25.1, 80.8). Across Stages 1, 2 and 3, in 1L patients dosed at 12 mcg/kg (n=29), ORR was 90% (26/29) with a 72% (21/29) rate of CR+CRc+CRi (ORR=overall response rate; CR=complete response; CRc=clinical CR: absence of gross disease with minimal residual skin abnormality; CRi=CR with incomplete hematologic recovery). 45% (13/29) of first-line patients treated with 12 mcg/kg were bridged to stem cell transplant (SCT) (10 allo+3 auto). In r/r patients, ORR was 69% (9/13) with a 38% (5/13) rate of CR+CRc+CRi. Additional patient follow-up will be provided. Conclusions: The pivotal trial of tagraxofusp was the largest prospectively designed, multi-center trial specifically dedicated to patients with BPDCN. This study has met its primary endpoint, and also demonstrated high response rates that were generally achieved early in the course of treatment and maintained over multiple cycles of therapy. Safety profile demonstrated most common toxicities of transaminitis, hypoalbuminemia, and thrombocytopenia; occurrence of CLS was the most serious TRAE, which was overall manageable in this population. Patients with BPDCN are being enrolled in an additional cohort, Stage 4, to ensure ongoing access. Tagraxofusp is also being evaluated in other trials including in patients with chronic myelomonocytic leukemia (CMML) and myelofibrosis (MF). Disclosures Pemmaraju: celgene: Consultancy, Honoraria; SagerStrong Foundation: Research Funding; stemline: Consultancy, Honoraria, Research Funding; cellectis: Research Funding; novartis: Research Funding; abbvie: Research Funding; samus: Research Funding; daiichi sankyo: Research Funding; plexxikon: Research Funding; Affymetrix: Research Funding. Lane:N-of-one: Consultancy; Stemline Therapeutics: Research Funding. Sweet:Agios: Consultancy; Jazz: Speakers Bureau; BMS: Honoraria; Novartis: Consultancy, Honoraria, Speakers Bureau; Novartis: Consultancy, Honoraria, Speakers Bureau; Astellas: Consultancy; Celgene: Honoraria, Speakers Bureau; Jazz: Speakers Bureau; Astellas: Consultancy; BMS: Honoraria; Phizer: Consultancy; Agios: Consultancy; Celgene: Honoraria, Speakers Bureau; Phizer: Consultancy. Stein:Amgen Inc.: Speakers Bureau; Celgene: Speakers Bureau. Vasu:Boehringer Ingelheim Inc: Membership on an entity's Board of Directors or advisory committees. Blum:Tolero: Research Funding; Forma: Research Funding; Astellas: Consultancy; Xencor: Research Funding; Boehringer Ingelheim: Research Funding; Pfizer: Consultancy. Rizzieri:Gilead: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Arog: Consultancy, Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy, Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy; Teva: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Incyte: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Jazz: Consultancy, Membership on an entity's Board of Directors or advisory committees; Pfizer: Consultancy, Membership on an entity's Board of Directors or advisory committees. Wang:Pfizer: Consultancy, Membership on an entity's Board of Directors or advisory committees; Jazz: Speakers Bureau; Novartis: Speakers Bureau; Novartis: Speakers Bureau; Jazz: Speakers Bureau; Abbvie: Consultancy, Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy; Pfizer: Consultancy, Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy; Abbvie: Consultancy, Membership on an entity's Board of Directors or advisory committees. Duvic:Guidepoint Global: Consultancy; Eisai: Research Funding; Allos: Research Funding; Clinical Care Options: Consultancy; Array Biopharma: Consultancy, Honoraria; Spatz Foundation: Research Funding; Defined Health: Consultancy; Medivir AB: Membership on an entity's Board of Directors or advisory committees; MiRagen Therapeutics: Consultancy; MEDACorp: Consultancy; Taiwan Liposome Company LTD: Consultancy; Medscape: Other: Speaker/Preceptor; Concert Pharmaceuticals, Inc.: Consultancy; Kyowa Hakko Kirin, Co: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Huya Bioscience Int'l: Consultancy; Shape: Research Funding; Kiniksa Pharmaceuticals: Consultancy; Soligenix, Inc.: Membership on an entity's Board of Directors or advisory committees, Research Funding; Forty Seven, Inc.: Membership on an entity's Board of Directors or advisory committees; Celgene Corp: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Cell Medica Inc.: Consultancy, Honoraria; Dr. Reddy's Laboratories (A.K.A. Promius Pharma): Consultancy; Huron Consulting Group: Consultancy; Aclaris Therapeutics Int'l Ltd.: Honoraria, Membership on an entity's Board of Directors or advisory committees; UT MD Anderson Cancer Center: Employment; The Lynx Group: Consultancy; Evidera, Inc.: Consultancy; Mallinckrddt Pharmaceuticals (formerly Therakos): Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; American Council on Extracorporeal Photopheresis (ACE): Membership on an entity's Board of Directors or advisory committees; Millennium Pharmaceuticals, Inc.: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Tetralogics: Research Funding; Precision Oncology, LLC: Membership on an entity's Board of Directors or advisory committees; Oncoceuticals: Research Funding; Jonathan Wood & Associates: Other: Speaker; Seattle Genetics: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Rhizen Pharma: Research Funding. Spence:Stemline Therapeutics: Consultancy. Shemesh:Stemline Therapeutics: Employment, Equity Ownership. Brooks:Stemline Therapeutics: Employment, Equity Ownership. Bergstein:Stemline Therapeutics: Employment, Equity Ownership. Chen:Stemline Therapeutics: Employment, Equity Ownership. Dunn:Stemline Therapeutics: Employment, Equity Ownership. McDonald:Stemline Therapeutics: Employment, Equity Ownership. Sloan:Stemline Therapeutics: Consultancy. Konopleva:Stemline Therapeutics: Research Funding.

Introduction: There are numerous methods of isolating and detecting organisms that are similar and closely related; one of the most reliable method is molecular typing of 16S rRNA. Apart from being omnipresent as a multigene family, or operons; it is evolutionarily stable; the 16S rRNA gene (1,500 bp) is large enough for informatics purposes.
 Materials and Method: This study employed molecular sequencing of 16S rRNA by Sanger method to reveal the specific organisms’ nucleotides and blasting (BLASTn) to show the similarities between the resulting organisms and existing organisms. The 16S rRNA remains the best choice of identification process for bacteria because of its distinguishing sizes and evolutionary stability.
 Results: All isolates were Gram positive rods and were positive in Biochemical tests such as oxidase, catalase, citrate, and protease but were in turn negative in coagulase and indole test tests. On sensitivity test; 80% of all the isolates were resistant to common antibiotics except ciprofloxacin and ceftriaxone. Based on the sequence difference in the variable region (V1) of 16S rRNA as observed from the molecular sequencing results; four isolates out of ten were identified. Six were different strains of B cereus. Others isolates include: wiedmannii, thuringensis, toyonensis and pseudomycoides. Sequence analysis of the primer annealing sites showed that there is no clear‐cut difference in the conserved region of 16S rRNA, and in the gyrB gene, between B. cereus and B. thuringiensis strains. Phylogenetic analysis showed that four isolates showed high similarity to each other; hence the limited number of deletions when subjected to alignments by maximum neighborhood joining parsimony using MEGA X software. B. toyonensis, B. wiedmannii and thuringensis were distantly related.
 Introduction
 Authors Pathogens cause illness and death in some countries and it also causes infections and gastrointestinal diseases in other countries thereby causing public health concern. Pathogens are organisms capable of causing diseases. Reliable methods are needed for the detection of pathogens due to pathogen evolution as a result of new human habits or new industrial practices.
 
 Microbial classification of organisms ranges from genus to specie level depending upon the technique used either phenotypic or genotypic. Presently, molecular methods now obtain advances to allow utilization in microbiology [1]. There are numerous molecular methods which are of fast and simple application to the detection of pathogen. Among the pathogens involved in human health, Bacillus cereus is interesting due to their ability to survive in various habitats [2].
 The genus Bacillus is aerobic or facultative anaerobic bacteria, gram positive spore forming rod shaped bacteria. Which can be characterized by two morphological forms, the vegetative cell which range from 1.02 to 1.2 um in width and from 3.0 to 5.0 in length, it can be straight or slightly curve, motile or non-motile, and the endospore (the non-swelling sporangium). The genus Bacillus is been characterized by the presence of endospore, which is not more than one per cell and they are resistant to many adverse environmental conditions such as heat, radiation, cold and disinfectants. It can also respire either in the presence or absence of oxygen [3]. Cell diameter of Bacillus cereus, sporangium and catalase test do not allow differentiation, where as important in differentiation among B. anthracis, B. cereus, B. thuringiensis can be considered by parasporal crystals and the presence of capsule. [4] Showed a B. thuringiensis strain capable of producing a capsule resembling that of B. anthracis. Most species of the genus display a great kind in physiological characteristics such as degradation of cellulose, starch, pectin, agar, hydrocarbons, production of enzymes and antibiotics and other characteristic such as acidophile, alkalinophile, psychrophile, and thermophile's which allows them to adapt to various environmental conditions [5]. In differentiating between species of the genus Bacillus it was difficult at early attempts when endospore formation and aerobic respiration were the main character used for classification. As reported by many authors that at molecular method level, the differentiation between B. thuringiensis and B. cereus is also very difficult.
 
 cereus can survive at the temperature between 4°c and 55°c. The mesophile strains can grow between the temperature of 10°c and 42°c, while psychotropic strains can survive at 4°c, whereas other strains are able to grow at 52 to 55°c. B. cereus vegetative cells grow at pH between 1.0 and 5.2. Heat resistant strain can survive and multiply in wet low acid foods in temperature ranging from 5 to 52°c. The survivability of B. cereus spores at 95°c decreases when the pH level decreases from 6.2 to 4.7 [6]. B. cereus can grow in the presence of salt with concentration up to 7.5% depending on the pH value.
 thuringiensis possesses a protein crystal that is toxic to insects. This toxin protein was first known as parasporal crystalline inclusion but was later referred to as π - endotoxin or in other ways known as insecticidal crystal protein [7]. Strains of B. thuringiensis bacteria possess a wide range of specificity in various orders of insects such as Lepidoptera, dipteral, coleoptera. These strains of bacteria produce crystalline proteins known as cry protein during sporulation. When B. thuringiensis infects an insects, it will cause the insect to loose appetite, enhances slow movement and over time the insect will die due to crystals of proteins that have been dissolved in the insect's stomach.
 
 In the cultivation of vegetable crops, the plant can be attack by many types of pests. Hence, in overcoming pest attacks farmers often use pesticides that contain active synthetic materials. Many negative effects arise from the folly use of chemical pesticides. Among the negative effect is the increase of pest population, resistance, death of natural enemy population and increase in residue level on Agricultural product which makes it unsafe for public consumption [8]. Therefore, it is necessary to find an alternative method in the control of crop pest. The best alternative that can be done is to replace the chemical insecticide with biological control which involves the use of living things in the form of microorganisms. In these profiling microbial communities, the main objective is to identify which bacteria and how much they are present in the environments. Most microbial profiling methods focus on the identification and quantification of bacteria with already sequenced genomes. Further, most methods utilize information obtained from entire genomes. Homology-based methods such as [1–4] classify sequences by detecting homology in reads belonging to either an entire genome or only a small set of marker genes. Composition-based methods generally use conserved compositional features of genomes for classification and as such they utilize less computational resources.Using the 16S rRNA gene instead of whole genome information is not only computational efficient but also economical; Illumina indicated that targeted sequencing of a focused region of interest reduces sequencing costs and enables deep sequencing, compared to whole-genome sequencing. On the other hand, as observed by [8], by focusing exclusively on one gene, one might lose essential information for advanced analyses. We, however, will provide an analysis that demonstrates that at least in the context of oral microbial communities, the 16S rRNA gene retains sufficient information to allow us detect unknown bacteria
 [9, 10]. This study aimed at employing 16S rRNA as an instrument of identification of seemingly close Bacillus species.
 Abbreviations
 BLAST, Basic Local Alignment sequence Tools; PCR, Polymerase Chains reactions; rRNA, ribosomal RNA;
 Material and methods
 T Sample collection. Soil samples were collected from three sources from Rice, Sugar Cane, vegetables and abandoned farmland in January 2019. The samples were labeled serially from Sample 1 to Sample 10 (S1 to S10).
 Bacterial culture: A serial dilution of 10 folds was performed. Bacterial suspension was diluted (10-10) with saline water and 100 μl of bacterial suspension werespread on Nutrient Agar plate and incubated for 24 hours. Bacterial colonies were isolated and grown in Nutrient Broth and nutrient agar. Other microbiological solid agar used include: Chocolate, Blood Agar, EMB, MacConkey, Simon citrate, MRS Agar. Bacteria were characterized by conventional technique by the use of morphological appearance and performance on biochemical analysis [11].
 Identification of bacteria:The identification of bacteria was based on morphological characteristics and biochemical tests carried out on the isolates. Morphological characteristics observed for each bacteria colony after 24 h of growth included colony appearance; cell shape, color, optical characteristics, consistency, colonial appearance and pigmentation. Biochemical characterizations were performed according to the method of [12]
 Catalase test: A small quantity of 24 h old culture was transferred into a drop of 3% Hydrogen peroxide solution on a clean slide with the aid of sterile inoculating loop. Gas seen as white froth indicates the presence of catalase enzyme [13] on the isolates.
 DNA Extraction Processes
 The extraction processes was in four phase which are:
 Collection of cell, lyses of cell, Collection of DNA by phenol, Concentration and purification of DNA.
 Collection of cell: the pure colonyof the bacteria culture was inoculated into a prepared sterile nutrient broth. After growth is confirmed by the turbidity of the culture, 1.5ml of the culture was taken into a centrifuge tube and was centrifuge at 5000 rpm for 5 minutes; the supernatant layer was discarded leaving the sediment.
 Lyses of cell: 400 microns of lyses buffer is added to the sediment and was mixed thoroughly and allow to stand for five minutes at room temperature (25°c). 200 microns of Sodium Dodecyl Sulfate (SDS) solution was added for protein lyses and was mixed gently and incubated at 65°c for 10 minutes.
 Collection of DNA by phenol; 500 microns of phenol chloroform was added to the solution for the separation of DNA, it was mixed completely and centrifuge at 10,000 rpm for 10 minutes. The white pallet seen at the top of the tube after centrifugation is separated into another sterile tube and 1micron of Isopropanol is added and incubated for 1hour at -20°c for precipitation of DNA. The DNA is seen as a colorless liquid in the solution.
 Concentration and purification of DNA: the solution was centrifuge at 10,000 rpm for 10 minutes. The supernatant layer was discarded and the remaining DNA pellets was washed with 1micron of 17% ethanol, mixed and centrifuge at 10,000 rpm for 10 minutes. The supernatant layer was discarded and air dried. 60 micron TE. Buffer was added for further dissolving of the DNA which was later stored at -40°c until it was required for use [14].
 PCR Amplification 
 This requires the use of primers (Forward and Reverse), polymerase enzyme, a template DNA and the d pieces which includedddATP, ddGTP and ddTTP, ddNTP. All this are called the master mix. 
 The PCR reactions consist of three main cycles.
 The DNA sample was heated at 940c to separate the two template of the DNA strand which was bonded by a hydrogen bond. Once both strand are separated the temperature is reduced to 570c (Annealing temperature). This temperature allows the binding of the forward and reverse primers to the template DNA. After binding the temperature is raised back to 720c which leads to the activation of polymerase enzyme and its start adding d NTPs to the DNA leading to the synthesize of new strands. The cycles were repeated several times in order to obtain millions of the copies of the target DNA [15].
 Preparation of Agarose Gel
 One gram (1 g) of agarose for DNA was measured or 2 g of agarose powdered will be measured for PCR analysis. This done by mixing the agarose powder with 100 ml 1×TAE in a microwaveable flask and microwaved for 1-3 minutes until the agarose is completely dissolved (do not over boil the solution as some of the buffer will evaporate) and thus alter the final percentage of the agarose in the gel. Allow the agarose solution to cool down to about 50°c then after five minutes 10µL was added to EZ vision DNA stain. EZ vision binds to the DNA and allows one to easily visualize the DNA under ultra violet (UV) light. The agarose was poured into the gel tray with the well comb firmly in place and this was placed in newly poured gel at 4°c for 10-15 mins or it sit at room temperature for 20-30 mins, until it has completely solidified[16].
 Loading and Running of samples on Agarose gel
 The agarose gel was placed into the chamber, and the process of electrophoresis commenced with running buffer introduced into the reservoir at the end of the chamber until it the buffer covered at least 2millimeter of the gel. It is advisable to place samples to be loaded in the correct order according to the lanes they are assigned to be running. When loading the samples keep the pipette tip perpendicular to the row of the wells as by supporting your accustomed hand with the second hand; this will reduce the risk of accidentally puncturing the wells with the tip. Lower the tip of the pipette until it breaks the surface of the buffer and is located just above the well. Once all the samples have been loaded it is advised to always avoid any movement of the gel chamber. This might result in the sample spilling into adjacent well. Place the lid on the gel chamber with the terminal correctly positioned to the matching electrodes on the gel chamber black to black and red to red. Remember that DNA is negatively charged hence the movement of the electric current from negatively charged to the positively charged depending on the bandwidth in Kilobytes. Once the electrode is connected to the power supply, switch ON the power supply then set the correct constant voltage (100) and stopwatch for proper time. Press the start button to begin the flow of current that will separate the DNA fragment.After few minutes the samples begins to migrate from the wells into the gel. As the DNA runs, the diaphragm moves from the negative electrode towards the positive electrode [17].
 PCR mix Components and Sanger Sequencing
 This is made up of primers which is both Forward and Reverse, the polymerase enzyme (Taq), a template DNA and the pieces of nucleotides which include: ddNTP, ddATP, ddGTP and ddTTP. Note that the specific Primer’s sequences for bacterial identification is: 785F 5' (GGA TTA GAT ACC CTG GTA) 3', 27F 5' (AGA GTT TGA TCM TGG CTC AG) 3', 907R 5' (CCG TCA ATT CMT TTR AGT TT) 3', 1492R 5' (TAC GGY TAC CTT GTT ACG ACT T) 3' in Sanger Sequencing techniques.
 BLAST
 The resulting genomic sequence were assembled and submitted in GenBank at NCBI for assignment of accession numbers. The resultant assertion numbers were subjected to homology search by using Basic Local Alignment Search Tool (BLAST) as NCBI with the assertion number MW362290, MW362291, MW362292, MW362293, MW362294 and MW362295 respectively. Whereas, the other isolates’ accession numbers were retrieved from NCBI GenBank which are:AB 738796.1, JH792136.1, MW 015768.1 and MG745385.1.MEGA 5.2 software was used for the construction of phylogenetic tree and phylogenetic analysis.
 All the organisms possess 100% identities, 0% gaps and 0.0% E.value which indicated that the organisms are closely related to the existing organisms. The use of 16S rRNA is the best identification process for bacteria because 16S rRNA gene has a distinguishing size of about 500 bases until 1500bp. Rather than using 23S rRNA which is of higher variation, The 16S rRNA is adopted in prokaryotes. 18S rRNA is used for identification in Eukaryotes
 Results
 The results of both the conventional morphological and cultural identification was correlated with the molecular sequencing results. Six isolates were confirmed B. cereus species while the other four isolates were. B. wiedmannii, B. thuringiensis, B. toyonensis and B. pseudomycoides.The 16S rRNA sequence of six isolates MW 362290.1- MW362295.1 were assigned accession numbers and deposited in the GenBank while the other four sequences were aligned to those available in the NCBI database. The alignment results showed closely relatedness to LT844650.1with an identity of 100% to 92.2% as above. The six isolates of Bacillus cereus great evolutionary relatedness as shown in the phylogenetic tree constructed using MEGA X software.
 Results
 The results of both the conventional morphological and cultural identification was correlated with the molecular sequencing results. Six isolates were confirmed B. cereus species while the other four isolates were. B. wiedmannii, B. thuringiensis, B. toyonensis and B. pseudomycoides.The 16S rRNA sequence of six isolates MW 362290.1- MW362295.1 were assigned accession numbers and deposited in the GenBank while the other four sequences were aligned to those available in the NCBI database. The alignment results showed closely relatedness to LT844650.1with an identity of 100% to 92.2% as above. The six isolates of Bacillus cereus great evolutionary relatedness as shown in the phylogenetic treeconstructed using MEGA X software.
 Discussion
 The results obtained in this study is consistent with the previous studies in other countries22,23 The results of the phylogenetic analysis of the 16S rRNA isolate of in this study was similar to the housekeeping genes proposed by [18, 19]. In comparing this study with the earlier study, B. cereus group comprising other species of Bacillus was hypothesized to be considered to form a single species with different ecotypes and pathotype. This study was able to phenotypically differentiated B. thuringiensis, B. pseudomycoides, B. toyonensis, B. wiedmannii and B. cereus sensu strito. Despite differences at the colonial appearance level, the 16S rRNA sequences have homology ranging from 100% to 92% providing insufficient resolution at the species level [6, 7, 18].After analysis through various methods, the strain was identified as Gram-positive bacteria of Bacillus cereus with a homology of 99.4%. Cohan [20] demonstrated that 95–99% of the similarity of 16S rRNA gene sequence between two bacteria hints towards a similar species while >99% indicates the same bacteria.The phylogenetic tree showed that B. toyonensis, B. thuringiensis and B. wiedmanniiare the outgroups of B. cereus
 group while B. pseudomycoides are most closely related to B. cereus group [19, 21, 22].
 Conclusion
 In the area of molecular epidemiology, genotypic typing method has greatly increased our ability to differentiate between micro-organisms at the intra and interspecies levels and have become an essential and powerful tool. Phenotypic method will still remain important in diagnostic microbiology and genotypic method will become increasingly popular.
 After analysis through various methods, the strain was identified as Gram-positive bacteria of Bacillus cereus with a homology of between 100% and 92.3%.
 Acknowledgments
 Collate acknowledgments in a separate section at the end of the article before the references, not as a footnote to the title. Use the unnumbered Acknowledgements Head style for the Acknowledgments heading. List here those individuals who provided help during the research. 
 Conflicts of interest
 The Authors declare that there is no conflict of interest.
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The field of genomic epidemiology is rapidly growing as many jurisdictions begin to deploy whole-genome sequencing (WGS) in their national or regional pathogen surveillance programmes. WGS data offer a rich view of the shared ancestry of a set of taxa, typically visualized with phylogenetic trees illustrating the clusters or subtypes present in a group of taxa, their relatedness and the extent of diversification within and between them. When methicillin-resistant Staphylococcus aureus (MRSA) arose and disseminated widely, phylogenetic trees of MRSA-containing types of S. aureus had a distinctive ‘comet’ shape, with a ‘comet head’ of recently adapted drug-resistant isolates in the context of a ‘comet tail’ that was predominantly drug-sensitive. Placing an S. aureus isolate in the context of such a ‘comet’ helped public health laboratories interpret local data within the broader setting of S. aureus evolution. In this work, we ask what other tree shapes, analogous to the MRSA comet, are present in bacterial WGS datasets. We extract trees from large bacterial genomic datasets, visualize them as images and cluster the images. We find nine major groups of tree images, including the ‘comets’, star-like phylogenies, ‘barbell’ phylogenies and other shapes, and comment on the evolutionary and epidemiological stories these shapes might illustrate. This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.

Elevation gradients provide natural laboratories for investigating tropical tree ecophysiology in the context of climate warming. Previously observed trends with increasing elevation include decreasing stem diameter growth rates (GR), increasing leaf mass per area (LMA), higher root-to-shoot ratios (R:S), increasing leaf δ13C, and decreasing leaf δ15N. These patterns could be driven by decreases in temperature, lower soil nutrient availability, changes in species composition, or a combination thereof. We investigated whether these patterns hold within the genus Flindersia (Rutaceae) along an elevation gradient (0–1,600 m) in the Australian Wet Tropics. Flindersia species are relatively abundant and are important contributors to biomass in these forests. Next, we conducted a glasshouse experiment to better understand the effects of temperature, soil nutrient availability, and species on growth, biomass allocation, and leaf isotopic composition. In the field, GR and δ15N decreased, whereas LMA and δ13C increased with elevation, consistent with observations on other continents. Soil C:N ratio also increased and soil δ15N decreased with increasing elevation, consistent with decreasing nutrient availability. In the glasshouse, relative growth rates (RGR) of the two lowland Flindersia species responded more strongly to temperature than did those of the two upland species. Interestingly, leaf δ13C displayed an opposite relationship with temperature in the glasshouse compared with that observed in the field, indicating the importance of covarying drivers in the field. Leaf δ15N increased in nutrient-rich compared to nutrient-poor soil in the glasshouse, like the trend in the field. There was a significant interaction for δ15N between temperature and species; upland species showed a steeper increase in leaf δ15N with temperature than lowland species. This could indicate more flexibility in nitrogen acquisition in lowland compared to upland species with warming. The distinguishing feature of a mountaintop restricted Flindersia species in the glasshouse was a very high R:S ratio in nutrient-poor soil at low temperatures, conditions approximating the mountaintop environment. Our results suggest that species traits interact with temperature and nutrient availability to drive observed elevation patterns. Capturing this complexity in models will be challenging but is important for making realistic predictions of tropical tree responses to global warming.

Abstract Summary Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together with different and sometimes ad hoc, analytical procedures for generating genome sequences. A fully integrated analytical process for raw sequence to consensus genome determination, suited to outbreaks such as the ongoing COVID-19 pandemic, is critical to provide a solid genomic basis for epidemiological analyses and well-informed decision making. We have developed a web-based platform and integrated bioinformatic workflows that help to provide consistent high-quality analysis of SARS-CoV-2 sequencing data generated with either the Illumina or Oxford Nanopore Technologies (ONT). Using an intuitive web-based interface, this workflow automates data quality control, SARS-CoV-2 reference-based genome variant and consensus calling, lineage determination and provides the ability to submit the consensus sequence and necessary metadata to GenBank, GISAID and INSDC raw data repositories. We tested workflow usability using real world data and validated the accuracy of variant and lineage analysis using several test datasets, and further performed detailed comparisons with results from the COVID-19 Galaxy Project workflow. Our analyses indicate that EC-19 workflows generate high-quality SARS-CoV-2 genomes. Finally, we share a perspective on patterns and impact observed with Illumina versus ONT technologies on workflow congruence and differences. Availability and implementation https://edge-covid19.edgebioinformatics.org, and https://github.com/LANL-Bioinformatics/EDGE/tree/SARS-CoV2. Supplementary information Supplementary data are available at Bioinformatics online.

Thuja is one of the ornamental plants used for landscaping parks and health resorts. The plant is distinguished by a pyramidal and conical crown shape and the presence of many thin branches with scale-shaped needles, green all year round. In addition, this plant has a number of antimicrobial properties, which affects the popularity of the plant in landscaping the health resort territory (Bakht et al. 2020, Chindyaeva et al. 2020). In January 2020, symptomatic Thuja plants were observed in Southern Kazakhstan. Symptoms included distortion of the crown. External examination of the trees revelaed the presence of white fluffy mycelium on Thuja branches. The branches acquired a yellow color with a necrotic lesion developing below the affected area. Samples of infected branches from different Thuja trees (n = 13) were collected. The infected branches were cut into small pieces (5 × 5 mm), washed in 70% ethanol for 30 min, and then rinsed three times with sterile distilled water. Later, these pieces were placed on Sabouraud's medium (Laboratorios Conda S.A., Spain) and incubated at 28°C for 7 days. Yellow-green colonies grew from the pieces of wood. The colonies had a light gray-whitish aerial mycelium. Conidia (n = 35) were pale to dark brown in color, irregular and ellipsoid to ovoid conical in shape. The size of the conidia varied from 5 to 25 µm × 6 to 12 µm (n = 40) with longitudinal and transverse septations. These morphological characters were previously described and corresponded to the Alternaria alternata (Simmons et al. 2007). Genomic DNA was extracted from mycelium using the liquid nitrogen and phenol-chloroform extraction method (Butler 2012). A 568 bp product of the Alt a1 gene and 472 bp product of the calmodulin protein-coding gene was amplified using following primer pairs Alt-for/Alt-rev (Hong et al. 2005) and CALDF1/CALDR1, respectively (Lawrence et al. 2013) (Integrated DNA Technologies, Inc., Coralville, IA, USA). The PCR reaction was done in a SimpliAmp thermal cycler (Applied biosystems, Waltham, MA, USA) under the following conditions: initial denaturation at 94 °C for 1 min, 35 cycles at 94°C for 30 s to denature, 57°C for 1 min for annealing, and 72°C for 1 min for extension. A final extension step at 72°C for 10 min was also included. The sequencing was done using BigDye® Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems) and the sequence was deposited in GenBank with accession no. OL542696 calmodulin). These sequences were compared with other sequences in the GenBank by using the BLAST analysis (MZ222274.1 and MN473132.1). The phylogenetic analysis was carried out with MEGA 6 software (The Pennsylvania State University, University Park, PA, USA). To confirm the pathogenicity, 10 thuja branches from healthy trees from another area without visible pathologies were inoculated with a suspension of conidia (100 conidia/ml; obtained from 2-week-old cultures). Control samples were inoculated with sterile distilled water. The inoculated branches were placed in sterile plastic containers to maintain high humidity and incubated for 10 days at 28°C. After 7 days, irregular shaped lesions and fungal growth was observed at the site of inoculation. The affected area gradually increased in size with simioar symptomatology to that described above. Re-isolation of the pathogen and identification based on morphological features and sequencing confirmed the presence of the A. alternata pathogen. To our knowledge, this is the first report of A. alternata causing branches of thuja in Kazakhstan. Thuja is a rare plant species for this region; the cost and care are expensive. This case will allow timely diagnosis of the disease caused by Alternaria spp. in the future. It is necessary to develop preventive measures and a protocol for the treatment of thuja from a fungal infection. Bakht, J., 2020. Antibacterial activity of the crude extracts from medicinally important Thuja occidentalis. Pak J Pharm Sci. 33(2): 627-630. PMID: 32276908. Butler, J.M., 2012. Chapter 2 - DNA extraction methods. pp. 29-47 in Butler JM (Ed) Advanced topics in forensic DNA typing: Methodology. San Diego, Academic Press. doi: 10.1016/C2011-0-04189-3. Chindyaeva., L.N., et al. 2020. Comparative assessment of the phytoncidity of woody plants in the selection of species for landscaping: the possibility of use in sanatorium-and-spa practice. Vopr Kurortol Fizioter Lech Fiz Kult. 97(4): 44-51. Russian. doi: 10.17116/kurort20209704144. Hong, S.G. et al. 2005. Alt a1 allergen homologs from Alternaria and related taxa: analysis of phylogenetic content and secondary structure. Fungal Genet Biol 42:119-129. doi:10.1016/j.fgb.2004.10.009 Lawrence, D.P. et al. 2013. The sections of Alternaria: formalizing species-group concepts. Mycologia 105: 530-546. DOI: 10.3852/12-249. Simmons, E. G., 2007. Alternaria: An Identification Manual. CBS, Fungal Biodiversity Center, Utrecht, Netherlands.

Dish Stirling power generation systems have been identified by DOE, Sandia National Laboratories, and Stirling Energy Systems (SES) as having the capability of delivering utility-scale renewable energy to the nation’s electrical grid. SES has proposed large plants, 20,000 units or more (0.5 GW rated power) in one place, in order to rapidly ramp up production automation. With the large capital investment needed in such a plant it becomes critical to optimize the system at the field level, as well as at the individual unit level. In this new software model, we provide a tool that predicts the annual and monthly energy performance of a field of dishes, in particular taking into account the impact of dish-to-dish shading on the energy and revenue streams. The Excel-based model goes beyond prior models in that it incorporates the true dish shape (flexible to accommodate many dish designs), multiple-row shading, and a revenue stream model that incorporates time-of-day and time-of-year pricing. This last feature is critical to understanding key shading tradeoffs on a financial basis. The model uses TMY or 15-minute meteorological data for the selected location. It can incorporate local ground slope across the plant, as well as stagger between the rows of dish systems. It also incorporates field-edge effects, which can be significant on smaller plants. It also incorporates factors for measured degraded performance due to shading. This tool provides one aspect of the decision process for fielding many systems, and must be combined with land costs, copper layout and costs, and O&M predictions (driving distance issues) in order to optimize the loss of power due to shading against the added expense of a larger spatial array. Considering only the energy and revenue stream, the model indicates that a rectangular, unstaggered field layout maximizes field performance. We also found that recognizing and accounting for true performance degradation due to shading significantly impacts plant production, compared with prior modeling attempts.

Abstract Flat rheology drilling fluids are synthetic-based fluids designed to provide better drilling performance with flat rheological properties for deep water and/or cold environments. The detailed mud properties are mainly measured in laboratories and are often measured twice a day in the field. This prevents real-time mud performance optimization and negatively affects the decisions. If the real-time estimation of mud properties, which affects decision-making in time, is absent, the ROP may slow down, and serious drilling problems and severe economic losses may take place. Consequently, it is important to evaluate the mud properties while drilling to capture the dynamics of mudflow. Unlike other mud properties, mud density (MD) and Marsh funnel viscosity (MFV) are frequently measured every 15–20 minutes in the field. The objective of this work is to predict the rheological properties of the flat rheology drilling fluids in real-time using machine learning (ML). A proposed approach is followed to firstly predict the viscometer readings at 300 and 600 RPM (R600 and R300) and then calculate the other mud properties using the existing equations in the literature. For forecasting the viscometer readings, the created model using the decision trees (DT) demonstrated good accuracy. The results revealed a maximum average absolute percentage error (AAPE) below 4.5% and a correlation coefficient (R) of greater than 0.97. The estimated rheological properties showed a good matching with the actual values with low errors. Introduction Drilling fluid or mud is a mixture of a base fluid and additional ingredients in certain proportions used while drilling. Several materials are added to adjust the mud properties such as, but are not limited to, the weighting agents for density, the fluid loss control materials, and viscosifiers for controlling the rheological properties (e.g., plastic viscosity (PV), yield point (YP), and gel strength). Despite mud represents 5% to 15% of total drilling costs, it may cause most of drilling problems. Drilling fluids are put to even greater strain by high-angle wells, high temperatures, and lengthy horizontal sections across pay zones (Bloys et al., 1994). Newtonian and non-Newtonian are the main two types of fluids. Newtonian fluid is characterized by a constant viscosity at a certain temperature and pressure. Non-Newtonian fluid such as most drilling fluids and cement slurries has viscosities that rely on shear rates for certain pressure and temperature (Rabia, 2002). Drilling fluids are mainly classified as water-based mud (WBM) or oil-based mud (OBM). OBM typically contains a base oil representing the external continuous phase; a saline aqueous solution representing the internal phase, emulsifiers at the interface, and other additives for suspension, weighting materials, oil-wetting, fluid loss, and rheology control additives. Oil based drilling fluids have two main categories which are invert-emulsion and all-oil drilling fluids (Alsabaa et al., 2020). An invert emulsion mud contains about 50:50 to about 95:5 by volume oil to water ratio. An all-oil mud contains 100% oil; that is, there is no aqueous internal phase. The invert emulsion mud is used to tackle some drilling problems like shale instability, minimize damage to water zones, and, and protect the casing and tubing against corrosion (Gray and Grioni, 1969; Growcock et al., 1994). The invert emulsion mud is characterized by its low toxicity and the brine is added to control the salinity to prevent water molecules from invading the formations (Hossain and Al-Majed, 2015). The invert emulsion drilling fluid is mainly used to drill the HPHT wells owing to its thermal stability which outperforms the WBM and can be used in drilling up to 400 ℉ (Lee et al., 2012).