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Journal articles on the topic 'Pruned median joining networks'

Author: Grafiati

Published: 4 June 2025

Last updated: 1 August 2025

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1

Huber, Katharina T., Vincent Moulton, Peter Lockhart, and Andreas Dress. "Pruned Median Networks: A Technique for Reducing the Complexity of Median Networks." Molecular Phylogenetics and Evolution 19, no. 2 (2001): 302–10. http://dx.doi.org/10.1006/mpev.2001.0935.

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Eberhardt, Ursula, Henry J. Beker, Torbjørn Borgen, Henning Knudsen, Nicole Schütz, and Steen A. Elborne. "A survey of Hebeloma (Hymenogastraceae) in Greenland." MycoKeys 79 (April 19, 2021): 17–118. https://doi.org/10.3897/mycokeys.79.63363.

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This is the first study exclusively dedicated to the study of Hebeloma in Greenland. It is based on almost 400 collections, the great majority of which were collected by three of the co-authors over a period of 40 years and were lodged in the fungarium of the Natural History Museum in Copenhagen. The material was identified using molecular and morphological methods. In total, 28 species were recognized, 27 belonging to three sections, H. sects Hebeloma, Denudata and Velutipes. One species sampled was new to science and is here described as H. arcticum. For all species, a description, a distrib

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Bandelt, H. J., P. Forster, and A. Rohl. "Median-joining networks for inferring intraspecific phylogenies." Molecular Biology and Evolution 16, no. 1 (1999): 37–48. http://dx.doi.org/10.1093/oxfordjournals.molbev.a026036.

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Kong, Sungsik, Santiago J. Sánchez-Pacheco, and Robert W. Murphy. "On the use of median-joining networks in evolutionary biology." Cladistics 32, no. 6 (2015): 691–99. http://dx.doi.org/10.1111/cla.12147.

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Kong, Sungsik, Santiago J. Sánchez-Pacheco, and Robert Murphy. "Median-Joining Networks and Bayesian Phylogenies Often Do Not Tell the Same Story." Bulletin of the Society of Systematic Biologists 2, no. 1 (2023): 1–13. http://dx.doi.org/10.18061/bssb.v2i1.9625.

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Inferring phylogenies among intraspecific individuals often yields unresolved relationships (i.e., polytomies). Consequently, methods that compute distance-based abstract networks, like Median-Joining Networks (MJNs), are thought to be more appropriate tools for reconstructing such relationships than traditional trees. Median-Joining Networks visualize all routes of relationships in the form of cycles, if needed, when traditional approaches cannot resolve them. However, the MJN method is a distance-based phenetic approach that does not involve character transformations and makes no reference t

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Pedder, Hugo, Sofia Dias, Meg Bennetts, Martin Boucher, and Nicky J. Welton. "Joining the Dots: Linking Disconnected Networks of Evidence Using Dose-Response Model-Based Network Meta-Analysis." Medical Decision Making 41, no. 2 (2021): 194–208. http://dx.doi.org/10.1177/0272989x20983315.

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Background Network meta-analysis (NMA) synthesizes direct and indirect evidence on multiple treatments to estimate their relative effectiveness. However, comparisons between disconnected treatments are not possible without making strong assumptions. When studies including multiple doses of the same drug are available, model-based NMA (MBNMA) presents a novel solution to this problem by modeling a parametric dose-response relationship within an NMA framework. In this article, we illustrate several scenarios in which dose-response MBNMA can connect and strengthen evidence networks. Methods We cr

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Wani, Charles E., Ibrahim A. Yousif, Muntasir E. Ibrahim, and Hassan H. Musa. "Molecular Characterization of Sudanese and Southern Sudanese Chicken Breeds Using mtDNA D-Loop." Genetics Research International 2014 (April 24, 2014): 1–8. http://dx.doi.org/10.1155/2014/928420.

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The objective of this study was to assess the genetic relationships and diversity and to estimate the amount of gene flow among the five chicken populations from Sudan and South Sudan and commercial strain of egg line White Leghorn chickens. The chicken populations were genotyped using mtDNA D-loop as a molecular marker. PCR product of the mtDNA D-loop segment was 600 bp and 14 haplotypes were identified. The neighbor-joining phylogenetic tree indicated that the indigenous Sudanese chickens can be grouped into two clades, IV and IIIa only. Median joining networks analysis showed that haplotype

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WERTH, Silke. "Fungal-algal interactions in Ramalina menziesii and its associated epiphytic lichen community." Lichenologist 44, no. 4 (2012): 543–60. http://dx.doi.org/10.1017/s0024282912000138.

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AbstractLichens are a fascinating example of a symbiotic mutualism. It is still uncertain which processes guide fungal-photobiont interactions, and whether they are random or of a more complex nature. Here, the fungal-algal interactions in Ramalina menziesii and co-occurring taxa are analyzed by using DNA sequences of the algal Internal Transcribed Spacer region (ITS), to investigate fungal-algal associations in juvenile R. menziesii and allied species. Algal species were identified by a combination of BLAST searches, median-joining network analysis, and Bayesian phylogenetics. Fungal-algal ne

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Wu, Qi, Wycliff M. Kinoti, Nuredin Habili, Stephen D. Tyerman, Amy Rinaldo, and Fiona E. Constable. "Genetic Diversity of Grapevine Virus A in Three Australian Vineyards Using Amplicon High Throughput Sequencing (Amplicon-HTS)." Viruses 16, no. 1 (2023): 42. http://dx.doi.org/10.3390/v16010042.

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Shiraz disease (SD) is one of the most destructive viral diseases of grapevines in Australia and is known to cause significant economic loss to local growers. Grapevine virus A (GVA) was reported to be the key pathogen associated with this disease. This study aimed to better understand the diversity of GVA variants both within and between individual SD and grapevine leafroll disease (LRD) affected grapevines located at vineyards in South Australia. Amplicon high throughput sequencing (Amplicon-HTS) combined with median-joining networks (MJNs) was used to analyze the variability in specific gen

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Maár, Kitti, Gergely I. B. Varga, Bence Kovács, et al. "Maternal Lineages from 10–11th Century Commoner Cemeteries of the Carpathian Basin." Genes 12, no. 3 (2021): 460. http://dx.doi.org/10.3390/genes12030460.

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Nomadic groups of conquering Hungarians played a predominant role in Hungarian prehistory, but genetic data are available only from the immigrant elite strata. Most of the 10–11th century remains in the Carpathian Basin belong to common people, whose origin and relation to the immigrant elite have been widely debated. Mitogenome sequences were obtained from 202 individuals with next generation sequencing combined with hybridization capture. Median joining networks were used for phylogenetic analysis. The commoner population was compared to 87 ancient Eurasian populations with sequence-based (F

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Lipej, Zoran, Dinko Novosel, Lea Vojta, Besi Roić, Miljenko Šimpraga, and Aleksandar Vojta. "Detection and characterisation of hepatitis E virus in naturally infected swine in Croatia." Acta Veterinaria Hungarica 61, no. 4 (2013): 517–28. http://dx.doi.org/10.1556/avet.2013.031.

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Hepatitis E is a viral zoonotic disease infecting swine worldwide. Since pigs represent a likely animal reservoir for the hepatitis E virus, the epidemiology of naturally occurring hepatitis E was investigated in Croatian swine herds. Nearly all tested animals were seropositive for antibodies against the hepatitis E virus (55/60, 91.7%). Active infection was detected in all age groups by RT-PCR of viral RNA in serum (8/60, 13.3%) and bile samples (3/37, 8.1%), which was further confirmed by histopathological findings of characteristic lesions in the livers of the infected animals. Three new st

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Ahmed, Waqas, Shahab Ansari, Muhammad Hanif, and Akhtar Khalil. "PCA driven mixed filter pruning for efficient convNets." PLOS ONE 17, no. 1 (2022): e0262386. http://dx.doi.org/10.1371/journal.pone.0262386.

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Deployment of the deep neural networks (DNNs) on resource-constrained devices is a challenging task due to their limited memory and computational power. In most cases, the pruning techniques do not prune the DNNs to full extent and redundancy still exists in these models. Considering this, a mixed filter pruning approach based on principal component analysis (PCA) and geometric median is presented. First, a pre-trained model is analyzed by using PCA to identify the important filters for every layer. These important filters are then used to reconstruct the network with a fewer number of layers

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Henriques-Gil, Nuno, María Haro, Fernando Izquierdo, Soledad Fenoy, and Carmen del Águila. "Phylogenetic Approach to the Variability of the Microsporidian Enterocytozoon bieneusi and Its Implications for Inter- and Intrahost Transmission." Applied and Environmental Microbiology 76, no. 10 (2010): 3333–42. http://dx.doi.org/10.1128/aem.03026-09.

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ABSTRACT Enterocytozoon bieneusi is a microsporidian parasite that infects many vertebrate animals, including humans. The rDNA internal transcribed spacer (ITS) shows a hypervariable sequence; however, so far no clear information has been inferred about strain evolution in this species. We reviewed all the sequences described and performed a phylogenetic study. Four groups of sequences strongly differentiated from each other were detected, although most of the isolates (94%) corresponded to group I. The highly diverse sequences of this group were analyzed using median-joining networks. The hos

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Bouabdallah, Selsabil, Diana Alves, and Licínio Manco. "Analysis of Human Y Chromosome Haplogroup E-M81 Sublineages in Portuguese Samples." Human Biology 94, no. 4 (2022): 179–87. http://dx.doi.org/10.1353/hub.2022.a937178.

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abstract: The human Y-chromosome haplogroup E-M81 is predominant in northwestern Africa and almost absent elsewhere, except for the Iberian Peninsula. In the present study, we investigated the internal branches of E-M81 (E1b1b1b1a) in 29 unrelated men from mainland Portugal. All individuals sampled carried the derived allele for the marker M183 (E1b1b1b1a1), and all but two had the derived allele for the marker SM001. Eleven individuals carried the derived allele for the marker Z5009 (E1b1b1b1a1c), and 16 were assigned to the paragroup E-SM001*(xZ5009, PF6794, CTS12227, M165, M5043). Median-jo

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Soberanes-Yepiz, Maritza L., Miriam V. Martín-Manzo, Marcel Martínez-Porchas, et al. "Diversity and genetic structure of <i>Macrobrachium americanum </i>(Bate, 1868) in two geographical areas of Mexico." Revista MVZ Córdoba 30, no. 2 (2025): e3388. https://doi.org/10.21897/rmvz.3388.

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Objetive. Analyze the population genetic with mitochondrial molecular markers (16S mtDNA and COI mtDNA) on the river prawn Macrobrachium americanum, in two different geographic areas of Mexico: Baja California Sur (San Pedro de la Presa and Guamuchil basins) and Guerrero (Aguas Blancas River). Materials and Methods. We calculated the number of haplotypes (H), haplotype diversity (Hd), nucleotide diversity (π), and the number of nucleotide differences (k) for each sampling site using the program Dnasp. To calculate the two phylogenetic networks (COI and 16s rDNA), we used the median-joining imp

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Piboon, Promporn, Napat Kriengsakpichit, Anocha Poommouang, et al. "Relationship of stranded cetaceans in Thai territorial waters to global populations: Mitochondrial DNA diversity of Cuvier's beaked whale, Indo Pacific finless porpoise, pygmy sperm whale, and dwarf sperm whale." Science Progress 105, no. 2 (2022): 003685042211037. http://dx.doi.org/10.1177/00368504221103776.

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Cetaceans inhabit oceans throughout the world. Four specific odontocetes, namely Cuvier's beaked whale ( Ziphius cavirostris), Indo Pacific finless porpoise ( Neophocaena phocaenoides), pygmy sperm whale ( Kogia breviceps), and dwarf sperm whale ( Kogia sima), have occasionally been found stranded along Thailand's coastal waters (the Andaman Sea and the Gulf of Thailand). Although shared haplotypes of each species for many locations have been found, and some species have revealed genetic structure through haplotype networks, cetaceans in Thai waters have never been investigated in terms of com

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Šehović, Emir, Adna Ašić, Mustafa Dogan, Ramazan Tunc, Damir Marjanović, and Serkan Dogan. "NETWORK ANALYSIS ON THE IN SILICO ASSIGNED Y CHROMOSOME HAPLOGROUPS IN WESTERN BALKAN POPULATIONS." Genetics & Applications 1, no. 2 (2018): 36. http://dx.doi.org/10.31383/ga.vol1iss2pp36-43.

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The region of Western Balkans has been inhabited since the Paleolithic era and was the route of the spread of farming from the Middle East to Europe during the Neolithic era. In the present study, Y-STR data from European populations have been used to construct median-joining networks. The study was performed using Whit Athey’s Haplogroup Predictor, Y Utility and Network 4 software packages to predict Y haplogroups, construct networks, perform clustering of closely related Y chromosomes and calculate time estimates between individual nodes. The results of the study imply that geographically cl

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Hong, Feng, Lizhi Gao, Hong-Liang Han, et al. "Population Genetics of Bactrocera minax (Diptera: Tephritidae) in China Based on nad4 Gene Sequence." Insects 10, no. 8 (2019): 236. http://dx.doi.org/10.3390/insects10080236.

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Bactrocera minax (Enderlein) (Diptera: Tephritidae) is an important citrus pest in Asia with a non-uniform distribution. In some locations, it had been reported to occur but was either eradicated or disappeared itself. To understand species dispersal of B. minax, we collected and analyzed 359 individuals from 18 localities in China. One mitochondrial DNA gene fragment (nad4) was used to investigate the genetic diversity and population genetic structure of B. minax. The populations were divided by phylogenetic analyses and statistical parsimony haplotype networks into three branches: a Central

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Bento, Miguel, Sónia Gomes Pereira, Wanda Viegas, and Manuela Silva. "Unravelling the hidden inter and intra-varietal diversity of durum wheat commercial varieties used in Portugal." Plant Genetic Resources: Characterization and Utilization 17, no. 04 (2019): 386–89. http://dx.doi.org/10.1017/s1479262119000133.

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AbstractAssessing durum wheat genomic diversity is crucial in a changing environmental particularly in the Mediterranean region where it is largely used to produce pasta. Durum wheat varieties cultivated in Portugal and previously assessed regarding thermotolerance ability were screened for the variability of coding sequences associated with technological traits and repetitive sequences. As expected, reduced variability was observed regarding low molecular weight glutenin subunits (LMW-GS) but a specific LMW-GS allelic form associated with improved pasta-making characteristics was absent in on

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Kottillil, Sudha, Chetan Rao, Brian W. Bowen, and Kartik Shanker. "Phylogeography of sharks and rays: a global review based on life history traits and biogeographic partitions." PeerJ 11 (June 1, 2023): e15396. http://dx.doi.org/10.7717/peerj.15396.

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Considerable research exists on the life history traits, evolutionary history, and environmental factors that shape the population genetic structure of marine organisms, including sharks and rays. Conservation concerns are particularly strong for this group as they are highly susceptible to anthropogenic stressors due to a combination of life history traits including late maturity and low fecundity. Here, we provide a review and synthesis of the global phylogeography of sharks and rays. We examined existing data for 40 species of sharks belonging to 17 genera and 19 species of rays belonging t

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Fadhlaoui-Zid, Karima, Piero Cossu, Daria Sanna, et al. "Spatial genetic patterns of Octopus vulgaris Mediterranean populations support the hypothesis of a transitional zone across the Siculo-Tunisian Strait." Hydrobiologia 848, no. 18 (2021): 4225–40. http://dx.doi.org/10.1007/s10750-021-04634-6.

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AbstractRecent research hypothesised that the Siculo-Tunisian Strait might fit, at least for some species, the picture of a genetic transitional zone instead of a sharp genetic break between the Western and Eastern Mediterranean basins. The present study aimed at using the common Octopus, Octopus vulgaris as an empirical test-case to evaluate this hypothesis. To accomplish this goal, 458 new sequences of the mitochondrial gene cytochrome c oxidase subunit I were used. Combining the new sequences with those available on public databases, we assembled a dataset containing 920 sequences to invest

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Mitrović, M., Ž. Tomanović, M. Jakovljević, D. Radović, J. Havelka, and P. Stary. "Genetic differentiation ofLiparus glabrirostris(Curculionidae: Molytinae) populations from the fragmented habitats of the Alps and Carpathian Mountains." Bulletin of Entomological Research 106, no. 5 (2016): 651–62. http://dx.doi.org/10.1017/s0007485316000377.

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AbstractPopulations ofLiparus glabrirostris(Curculionidae: Molytinae), a weevil inhabiting higher altitudes of Central Europe, were sampled from 24 localities in the Alps and Carpathian Mountains, and the geographical structuring of genetic variation was analyzed. Comparison of the concatenated mitochondrial cytochrome oxidase subunit I and subunit II sequences revealed consistent genetic divergence between the populations ofL. glabrirostrisfrom different mountain ranges. In phylogenetic analysis using maximum parsimony and median-joining networks, concatenated mitochondrial haplotypes from th

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Adeola, Adeniyi C., Foluke E. Sola-Ojo, Yusuf A. Opeyemi, et al. "Genetic diversity and population structure of muscovy duck (Cairina moschata) from Nigeria." PeerJ 10 (April 15, 2022): e13236. http://dx.doi.org/10.7717/peerj.13236.

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The domestic Muscovy duck (Cairina moschata) provide unique genetic resources patterned by both tropical environmental conditions and human activities, the evaluation of their genetic diversity and population structure will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the variation in mtDNA cytochrome b and nuclear DNA CYP2U1 sequences of 378 Nigerian Muscovy ducks (comprising of 287 de novo and 91 downloaded) plus 80 published sequences of Muscovy ducks from India. The results showed high haplotype diversity (0.800 ± 0.023) among Nigerian Muscovy

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Nasernakhaei, Fatemeh, Mohammad Reza Rahiminejad, Hojjatollah Saeidi, and Manoochehr Tavassoli. "Genetic structure and diversity ofTriticum monococcumssp.aegilopoidesandT. urartuin Iran." Plant Genetic Resources 13, no. 1 (2014): 1–8. http://dx.doi.org/10.1017/s1479262114000549.

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To preliminarily evaluate the genetic diversity of the Iranian diploidTriticumL. gene pool, in this study, a total of 176 individuals belonging toT. monococcumL. ssp.aegilopoides(Link) Thell. andT. urartuThum. ex Gandil. were pre-screened using single-strand conformation polymorphism (SSCP) analysis of theAcc-1andPgk-1loci. A selected set of 76 DNA samples corresponding to the observed SSCP variants were sequenced for both loci and evaluated for nucleotide diversity associated with the taxonomic groups and geographical regions. We found three haplotypes, including one that was new for Iran, at

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Guo, Shenghan, Dali Wang, Zhili Feng, Jian Chen, and Weihong Guo. "Di-CNN: Domain-Knowledge-Informed Convolutional Neural Network for Manufacturing Quality Prediction." Sensors 23, no. 11 (2023): 5313. http://dx.doi.org/10.3390/s23115313.

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In manufacturing, convolutional neural networks (CNNs) are widely used on image sensor data for data-driven process monitoring and quality prediction. However, as purely data-driven models, CNNs do not integrate physical measures or practical considerations into the model structure or training procedure. Consequently, CNNs’ prediction accuracy can be limited, and model outputs may be hard to interpret practically. This study aims to leverage manufacturing domain knowledge to improve the accuracy and interpretability of CNNs in quality prediction. A novel CNN model, named Di-CNN, was developed

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Veģeris, Ivars, Iveta Daukšte, Arta Bārzdiņa, Roger C. Parslow, and Reinis Balmaks. "Prospective paediatric intensive care registry in Latvia: one year outcomes." Acta medica Lituanica 26, no. 1 (2019): 64–71. http://dx.doi.org/10.6001/actamedica.v26i1.3957.

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Background. In Latvia, there is a single eight-bed paediatric intensive care unit (PICU) where all critically ill children are admitted. A recent retrospective audit of the outcomes of paediatric critical care in this unit revealed a high number of unplanned extubations and excess crude mortality. In 2017, our centre joined the UK and Ireland based Paediatric Intensive Care Audit Network (PICANet) as a pilot project to investigate the feasibility of developing a paediatric critical care registry in Latvia and in the Baltic states. Methods. Riga Stradins University Ethics Committee approved the

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Grabowski, Michał, Tomasz Mamos, Karolina Bącela-Spychalska, Tomasz Rewicz, and Remi A. Wattier. "Neogene paleogeography provides context for understanding the origin and spatial distribution of cryptic diversity in a widespread Balkan freshwater amphipod." PeerJ 5 (February 28, 2017): e3016. http://dx.doi.org/10.7717/peerj.3016.

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BackgroundThe Balkans are a major biodiversity and endemism hotspot, worldwide. Among the freshwater biota, amphipods are known for their high cryptic diversity. However, little is known about the temporal and paleogeographic aspects of their evolutionary history. We used paleogeography as a framework for understanding the onset of diversification inGammarus roeselii: (1) we hypothesised that, given the high number of isolated waterbodies in the Balkans, the species is characterised by high level of cryptic diversity, even on a local scale; (2) the long geological history of the region might p

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Yang, Aihong, Yongda Zhong, Shujuan Liu, et al. "New insight into the phylogeographic pattern ofLiriodendron chinense(Magnoliaceae) revealed by chloroplast DNA: east–west lineage split and genetic mixture within western subtropical China." PeerJ 7 (February 1, 2019): e6355. http://dx.doi.org/10.7717/peerj.6355.

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BackgroundSubtropical China is a global center of biodiversity and one of the most important refugia worldwide. Mountains play an important role in conserving the genetic resources of species.Liriodendron chinenseis a Tertiary relict tree largely endemic to subtropical China. In this study, we aimed to achieve a better understanding of the phylogeographical pattern ofL. chinenseand to explore the role of mountains in the conservation ofL. chinensegenetic resources.MethodsThree chloroplast regions (psbJ-petA,rpl32-ndhF, andtrnK5’-matK) were sequenced in 40 populations ofL. chinensefor phylogeog

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Zhang, Yiqun, Guodong Zhao, Ning He, et al. "Robust prediction of immune checkpoint inhibition therapy for non-small cell lung cancer." Journal of Clinical Oncology 38, no. 15_suppl (2020): e15192-e15192. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e15192.

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e15192 Background: Immune checkpoint inhibition (ICI) has been validated and applied in advanced lung cancer patients. However Oonly part of patients response to ICI, thus optimizing ICI would be emergent. Based on public non-small cell lung cancer (NSCLC) cohorts’ data, we expected to build a multivariable model which would improve the efficacy of predicting ICIs response. Methods: 2 NSCLC and 1 pan-cancer cohorts treated with ICIs were collected from cBioPortal (luad_mskcc_2015, n = 203; nsclc_pd1_msk_2018, n = 33; tmb_mskcc_2018, n = 1661, pan-cancer). Another NSCLC cohort (cancer_cell_2018

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Sen, Triparna, Subhamoy Chakraborty, Andrew Elliott, et al. "Unveiling drivers of MHC repression and therapeutic strategies to counter immune evasion in small cell lung cancer." Journal of Clinical Oncology 43, no. 16_suppl (2025): 8091. https://doi.org/10.1200/jco.2025.43.16_suppl.8091.

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8091 Background: Small cell lung cancer (SCLC) is a highly aggressive neuroendocrine malignancy with a median survival of 9–11 months. Despite the addition of immune checkpoint blockade (ICB) to frontline chemotherapy, improvements remain limited. SCLC evades anti-tumor immunity by suppressing major histocompatibility complex class I (MHC-I) and antigen presentation (AP). The variability of MHC repression across molecular subtypes of SCLC and high-grade neuroendocrine tumors is not fully understood. This study analyzed clinical SCLC and neuroendocrine tumor samples to identify molecular subtyp

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Sadovska, Darja, Iveta Ozere, Ilva Pole, et al. "Unraveling tuberculosis patient cluster transmission chains: integrating WGS-based network with clinical and epidemiological insights." Frontiers in Public Health 12 (May 20, 2024). http://dx.doi.org/10.3389/fpubh.2024.1378426.

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BackgroundTuberculosis remains a global health threat, and the World Health Organization reports a limited reduction in disease incidence rates, including both new and relapse cases. Therefore, studies targeting tuberculosis transmission chains and recurrent episodes are crucial for developing the most effective control measures. Herein, multiple tuberculosis clusters were retrospectively investigated by integrating patients’ epidemiological and clinical information with median-joining networks recreated based on whole genome sequencing (WGS) data of Mycobacterium tuberculosis isolates.Methods

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Thammuluri, Rajesh, Ramesh Babu Mallela, Gottala Surendra Kumar, Bellamgubba Anoch, Veera V. Rama Rao M., and Anuj Rapaka. "Adaptive Knowledge-Guided Pruning Algorithm AKGP with Dynamic Weight Allocation for Model Compression." International Journal of Computational and Experimental Science and Engineering 11, no. 1 (2025). https://doi.org/10.22399/ijcesen.944.

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In this paper, we propose the Adaptive Knowledge-Guided Pruning Algorithm (AKGP), a novel approach to model compression that enhances traditional pruning by incorporating a dynamic, data-driven weight allocation strategy during knowledge distillation. Unlike existing methods, such as the Geometric Median-based pruning approach combined with knowledge distillation and quantization proposed. AKGP dynamically balances the influence of teacher networks and real labels based on dataset characteristics. This adaptive strategy ensures that pruned models achieve superior accuracy even at high compress

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Çetintürk, Derya. "Revealing the Genetic Differentiation of Rattus norvegicus (Berkenhout 1769) Populations by Analyzing Two Mitochondrial Markers." Hacettepe Journal of Biology and Chemistry, October 8, 2024. http://dx.doi.org/10.15671/hjbc.1531280.

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Rattus norvegicus (Brown rat) has a great importance for public health and economy because it lives in close association with human populations. However, molecular systematic studies on global populations of R. norvegicus are very few. In this study, sequences obtained from Europe, Asia, Africa, and America regions were analyzed using mitochondrial Cytochrome-b and Cytochrome oxidase-I gene regions and genetic differentiation levels between these populations were revealed. Accordingly, samples belonging to the studied populations did not split in Bayesian Inference trees and Median-joining net

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Mashlawi, Abadi M., Ashwaq M. Al-Nazawi, Elsiddig M. Noureldin, et al. "Molecular analysis of knockdown resistance (kdr) mutations in the voltage-gated sodium channel gene of Aedes aegypti populations from Saudi Arabia." Parasites & Vectors 15, no. 1 (2022). http://dx.doi.org/10.1186/s13071-022-05525-y.

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Abstract Background The Aedes aegypti mosquito is the primary vector for dengue, chikungunya, yellow fever and Zika viruses worldwide. The first record of Ae. aegypti in southwestern Saudi Arabia was in 1956. However, the first outbreak and cases of dengue fever were reported in 1994, and cases have increased in recent years. Vector control for Ae. aegypti mainly uses pyrethroid insecticides in outdoor and indoor space spraying. The constant use of pyrethroids has exerted intense selection pressure for developing target-site mutations in the voltage-gated sodium channel (vgsc) gene in Ae. Aegy

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Çetintürk, D., N. Yiğit, and E. Çolak. "Molecular assessment of the taxonomic status of pine vole species Microtus subterraneus and Microtus majori in southeastern Europe and Turkey." Animal Biodiversity and Conservation, February 20, 2023, 57–69. http://dx.doi.org/10.32800/abc.2023.46.0057.

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Intra– and inter–specific phylogenetic relationships and the taxonomic status of pine vole populations have been controversial for years, and cryptic species are thought to exist, especially concering the species' distribution area. To clarify the taxonomic status of Turkish populations we analysed mitochondrial (cytochrome–b and cytochrome oxidase–I) and nuclear (interphotoreceptor retinoid binding protein) gene markers, adding GenBank data from Europe and Caucasia. Considering the data obtained based on mean genetic distance, genetic diversity and fixation index values, Bayesian trees and Me

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Bouabdallah, Selsabil, Diana Alves, and Licínio Manco. "Analysis of Human Y Chromosome Haplogroup E-M81 Sublineages in Portuguese Samples." Human Biology, June 2024. http://dx.doi.org/10.1353/hub.2017.a931433.

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The human Y-chromosome haplogroup E-M81 is predominant in northwestern Africa and almost absent elsewhere, except for the Iberian Peninsula. In the present study, we investigated the internal branches of E-M81 (E1b1b1b1a) in 29 unrelated men from mainland Portugal. All individuals sampled carried the derived allele for the marker M183 (hg E1b1b1b1a1), and all but two had the derived allele for the marker SM001. Eleven individuals carried the derived allele for the marker Z5009 (hg E1b1b1b1a1c), and 16 were assigned to the paragroup E-SM001*(xZ5009, PF6794, CTS12227, M165, M5043). Median-joinin

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Adwan, G., and G. Omar. "Phenotypic and molecular characterization of fluoroquinolone resistant Pseudomonas aeruginosa isolates in Palestine." Brazilian Journal of Biology 82 (2022). http://dx.doi.org/10.1590/1519-6984.239868.

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Abstract Fluoroquinolones are important antimicrobial agents for the treatment of Pseudomonas infections. A total of 11 isolates of P. aeruginosa were collected from different clinical samples from different medical centers in the North West Bank-Palestine during 2017. In this study, resistance to fluoroquinolones and secretions of β-lactamases were detected by phenotypic methods, while presence of β-lactamase gene sequences and other virulence factors were detected by PCR technique. PCR product for gyrA, parC and parE genes were sequenced for further analyses. The phylogenetic analyses, popul

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Çetintürk, Derya, Nuri Yiğit, Riccardo Castiglia, Gabriele Senczuk, and Ercüment Çolak. "Comparative genetic research on Microtus mystacinus (de Filippi, 1865) distributed in Asia and Europe inferred from mitochondrial (CYTB and COXI) and nuclear (IRBP) gene regions." Animal Biology, June 22, 2022, 1–16. http://dx.doi.org/10.1163/15707563-bja10084.

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Abstract The East European vole Microtus mystacinus is the most widespread vole species in Anatolia. It is also frequently seen in watery habitats in a large area of Eurasia. In this paper, an attempt was made to ascertain the level of genetic differentiation between Anatolian (Asian part of Turkey) and Turkish Thracian (European part of Turkey) populations together with additional data from other parts of Asia and Europe by analysing two mitochondrial (cytochrome-b and cytochrome oxidase subunit I) and one nuclear (interphotoreceptor retinoid binding protein) gene regions. Acquired Bayesian I

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Zhunussova, Aigul, Saltanat Tayshanova, Alizhan Bukayev, et al. "Genetic genealogy of Y-chromosome in the Zhetiru tribe of the Kazakh population from Kazakhstan." Frontiers in Genetics 16 (March 24, 2025). https://doi.org/10.3389/fgene.2025.1516130.

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IntroductionThe Y chromosome, transmitted exclusively through the paternal line, is a well-established tool for verifying genealogical data. The Kazakh tribe Zhetiru in Kazakhstan, comprising seven clans, has conflicting historical and genealogical narratives regarding its origin—either as a union of seven independent clans or as descendants of a single common ancestor. A detailed genetic investigation has not yet addressed this question.Methods350 male volunteers from the Zhetiru tribe were analyzed using 23 Y-STR loci and 17 Y-SNPs. We calculated genetic distances using Arlequin and STRAF, a

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Schromm, T. M., and C. U. Grosse. "From 2D projections to the 3D rotation matrix: an attempt for finding a machine learning approach for the efficient evaluation of mechanical joining elements in X-ray computed tomography volume data." SN Applied Sciences 5, no. 1 (2022). http://dx.doi.org/10.1007/s42452-022-05220-8.

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AbstractDestructive and predominantly manual procedures are commonly used in the automotive industry for the testing of mechanical joints, such as rivets or screws. Combining X-ray computed tomography (CT) and machine learning (ML) bears the potential of a non-destructive and largely automated methodology. Assuming the desired result is a comprehensible and documentable evaluation, three basic steps need to be automatized: First, a joint must be detected and identified as such in a CT scan of the joined parts. Second, the detected region containing the joint is rotated to a predefined orientat

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Halasan, Lorenzo C., Paul John L. Geraldino, and Hsiu-Chin Lin. "First Evidence of Cryptic Species Diversity and Population Structuring of Selaroides leptolepis in the Tropical Western Pacific." Frontiers in Marine Science 8 (October 18, 2021). http://dx.doi.org/10.3389/fmars.2021.756163.

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The yellowstripe scad, Selaroides leptolepis (Carangidae), is an important fish commodity in the Tropical Western Pacific (TWP). It has a latitudinal Pacific range from south of Japan down to northern Australia, with the highest concentration in Southeast Asia. However, its TWP fishing grounds have long been a hotspot of unsustainable exploitations, thus threatening the remaining wild populations. Despite the species’ commercial significance, there is limited understanding of its genetic structure and diversity. Herein, the genetic structure of S. leptolepis was examined using mitochondrial CO

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Muthukumarana, Lihini Sandaleka, Methsala Madurangi Wedage, Samanthika Rathnayake, and Nissanka Kolitha De Silva. "Phylogenetic, phylogeographic and divergence time analysis of Anopheles subpictus species complex using ITS2 and COI sequences." Asian Pacific Journal of Tropical Medicine, April 29, 2024. http://dx.doi.org/10.4103/apjtm.apjtm_790_23.

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Objective: To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles (An.) subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Transcriber Spacer 2 (ITS2) and cytochrome C oxidase I (COI) sequences deposited at the GenBank. Methods: Seventy-five ITS2, 210 COI and 26 concatenated sequences available in the NCBI database were used. Phylogenetic analysis was performed using Bayesian likelihood trees, whereas median-joining haplotype networks and time-scale divergence trees were generated for phylogeographic a

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Wagah, Martin G., Petra Korlević, Christopher Clarkson, Alistair Miles, Mara K. N. Lawniczak, and Alex Makunin. "Genetic variation at the Cyp6m2 putative insecticide resistance locus in Anopheles gambiae and Anopheles coluzzii." Malaria Journal 20, no. 1 (2021). http://dx.doi.org/10.1186/s12936-021-03757-4.

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Abstract Background The emergence of insecticide resistance is a major threat to malaria control programmes in Africa, with many different factors contributing to insecticide resistance in its vectors, Anopheles mosquitoes. CYP6M2 has previously been recognized as an important candidate in cytochrome P450-mediated detoxification in Anopheles. As it has been implicated in resistance against pyrethroids, organochlorines and carbamates, its broad metabolic activity makes it a potential agent in insecticide cross-resistance. Currently, allelic variation within the Cyp6m2 gene remains unknown. Meth

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Reding, Dawn M., Susette Castañeda-Rico, Sabrina Shirazi, et al. "Mitochondrial Genomes of the United States Distribution of Gray Fox (Urocyon cinereoargenteus) Reveal a Major Phylogeographic Break at the Great Plains Suture Zone." Frontiers in Ecology and Evolution 9 (June 8, 2021). http://dx.doi.org/10.3389/fevo.2021.666800.

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We examined phylogeographic structure in gray fox (Urocyon cinereoargenteus) across the United States to identify the location of secondary contact zone(s) between eastern and western lineages and investigate the possibility of additional cryptic intraspecific divergences. We generated and analyzed complete mitochondrial genome sequence data from 75 samples and partial control region mitochondrial DNA sequences from 378 samples to investigate levels of genetic diversity and structure through population- and individual-based analyses including estimates of divergence (FST and SAMOVA), median jo

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Sridhar, Kiran, and Ming Ng. "Hacking for good: Leveraging HackerOne data to develop an economic model of Bug Bounties." Journal of Cybersecurity 7, no. 1 (2021). http://dx.doi.org/10.1093/cybsec/tyab007.

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Abstract We ran a study of bug bounties, programs where gig economy security researchers are compensated for pinpointing and explaining vulnerabilities in company code bases. Bug bounty advocates have argued that they are a cost-effective means for companies of all types to shore up their security posture. Our research—which analyzes a large, proprietary dataset and which leverages instrumental variables to eliminate potential sources of endogeneity—provides empirical support for this assertion. Security researchers have a price elasticity of supply of between 0.1 and 0.2 at the median, indica

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Bradbury, Donna, Rachel M. Binks, Stephen van Leeuwen, et al. "The nuanced nature of mesic refugia in arid landscapes: a tale of two peas." Annals of Botany, October 11, 2022. http://dx.doi.org/10.1093/aob/mcac126.

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Abstract Background and Aims Understanding how genetic diversity is distributed and maintained within species is a central tenet of evolutionary and conservation biology, yet is understudied in arid regions of the globe. In temperate, glaciated environments, high genetic diversity in plant species is frequently found in refugial areas, which are often associated with southern non-glaciated landscapes. In arid, unglaciated environments, landscape features providing mesic conditions are likely to be refugia, although our understanding needs more refinement in these biomes. We test whether refugi

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Zhou, Qi, Jiao Li, Xianguang Guo, et al. "Records of three mammal tick species parasitizing an atypical host, the multi-ocellated racerunner lizard, in arid regions of Xinjiang, China." Parasites & Vectors 14, no. 1 (2021). http://dx.doi.org/10.1186/s13071-021-04639-z.

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Abstract Background Ticks are ectoparasites that feed on blood of a broad taxonomical range of terrestrial and flying vertebrates and are distributed across a wide range of environmental settings. To date, the species identity, diversity, and relationships among the ticks on lizards in China have been poorly understood. Methods In this study, 30 ticks, collected from the multi-ocellated racerunner (Eremias multiocellata) lizard in the Tarim Basin and adjacent Yanqi Basin of the Xinjiang Uygur Autonomous Region in China, were identified by morphological observation and confirmed by DNA-based te

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Jesudoss Chelladurai, Jeba R. J., Theresa A. Quintana, William L. Johnson, Carrie Schmidt, Daniel Righter, and Erin Howey. "Cystic echinococcosis in cattle and sheep caused by Echinococcus granulosus sensu stricto genotypes G1 and G3 in the USA." Parasites & Vectors 17, no. 1 (2024). http://dx.doi.org/10.1186/s13071-024-06192-x.

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Abstract Background Endemic domestic dog-ruminant cycles and human cystic echinococcosis caused by Echinococcus granulosus have been sporadically reported in the United States. However, there is a paucity of molecular data describing the genotypes and haplotypes of this important cestode in domestic ruminant hosts. Methods Ninety-four cysts from the lungs and/or livers of slaughtered beef cattle (76 samples), dairy cows (five samples) and sheep (13 samples) were collected from abattoirs in four states of the USA. Samples were genotyped at two mitochondrial loci, cox1 and nad5. Sequences were u

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Hubbard, Demetria M., Marquita S. Brooks, Suzanne E. Judd, et al. "Abstract P291: Understanding Participant Perspectives Towards the Formation of a National Participant Advisory Board Within the Reasons for Geographic and Racial Differences in Stroke (REGARDS) Study: A Qualitative Study." Circulation 149, Suppl_1 (2024). http://dx.doi.org/10.1161/circ.149.suppl_1.p291.

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Introduction: While participant advisory boards (PABs) are common among public health initiatives and clinical trials, they are less common among national, epidemiologic cohort studies. PABs could add value to researchers and participants alike, but their formation and functioning in this context is less understood. We aimed to elicit the perspectives of participants from the national REasons for Geographic and Racial Differences in Stroke (REGARDS) Study towards the formation of a PAB, which can inform future efforts to form one for this cohort study and others like it. Methods: REGARDS is a

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Robinson, Jessica Yarin. "Fungible Citizenship." M/C Journal 25, no. 2 (2022). http://dx.doi.org/10.5204/mcj.2883.

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Social media companies like to claim the world. Mark Zuckerberg says Facebook is “building a global community”. Twitter promises to show you “what’s happening in the world right now”. Even Parler claims to be the “global town square”. Indeed, among the fungible aspects of digital culture is the promise of geographic fungibility—the interchangeability of location and national provenance. The taglines of social media platforms tap into the social imagination of the Internet erasing distance—Marshall McLuhan’s global village on a touch screen (see fig. 1). Fig. 1: Platform taglines: YouTube, Twit

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