ResearchPad - biology-and-life-sciences https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[The fast and the frugal: Divergent locomotory strategies drive limb lengthening in theropod dinosaurs]]> https://www.researchpad.co/article/elastic_article_14509 Limb length, cursoriality and speed have long been areas of significant interest in theropod paleobiology, since locomotory capacity, especially running ability, is critical in the pursuit of prey and to avoid becoming prey. The impact of allometry on running ability, and the limiting effect of large body size, are aspects that are traditionally overlooked. Since several different non-avian theropod lineages have each independently evolved body sizes greater than any known terrestrial carnivorous mammal, ~1000kg or more, the effect that such large mass has on movement ability and energetics is an area with significant implications for Mesozoic paleoecology. Here, using expansive datasets that incorporate several different metrics to estimate body size, limb length and running speed, we calculate the effects of allometry on running ability. We test traditional metrics used to evaluate cursoriality in non-avian theropods such as distal limb length, relative hindlimb length, and compare the energetic cost savings of relative hindlimb elongation between members of the Tyrannosauridae and more basal megacarnivores such as Allosauroidea or Ceratosauridae. We find that once the limiting effects of body size increase is incorporated there is no significant correlation to top speed between any of the commonly used metrics, including the newly suggested distal limb index (Tibia + Metatarsus/ Femur length). The data also shows a significant split between large and small bodied theropods in terms of maximizing running potential suggesting two distinct strategies for promoting limb elongation based on the organisms’ size. For small and medium sized theropods increased leg length seems to correlate with a desire to increase top speed while amongst larger taxa it corresponds more closely to energetic efficiency and reducing foraging costs. We also find, using 3D volumetric mass estimates, that the Tyrannosauridae show significant cost of transport savings compared to more basal clades, indicating reduced energy expenditures during foraging and likely reduced need for hunting forays. This suggests that amongst theropods, hindlimb evolution was not dictated by one particular strategy. Amongst smaller bodied taxa the competing pressures of being both a predator and a prey item dominant while larger ones, freed from predation pressure, seek to maximize foraging ability. We also discuss the implications both for interactions amongst specific clades and Mesozoic paleobiology and paleoecological reconstructions as a whole.

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<![CDATA[Two new sponge species (Demospongiae: Chalinidae and Suberitidae) isolated from hyperarid mangroves of Qatar with notes on their potential antibacterial bioactivity]]> https://www.researchpad.co/article/elastic_article_14508 This study presents the taxonomic description of two new sponge species that are intimately associated with the hyperarid mangrove ecosystem of Qatar. The study includes a preliminary evaluation of the sponges’ potential bioactivity against pathogens. Chalinula qatari sp. nov. is a fragile thinly encrusting sponge with a vivid maroon colour in life, often with oscular chimneys and commonly recorded on pneumatophores in the intertidal and shallow subtidal zone. Suberites luna sp. nov. is a massive globular-lobate sponge with a greenish-black colour externally and a yellowish orange colour internally, recorded on pneumatophores in the shallow subtidal zone, with large specimens near the seagrass ecosystem that surrounds the mangrove. For both species, a drug extraction protocol and an antibacterial experiment was performed. The extract of Suberites luna sp. nov. was found to be bioactive against recognized pathogens such as Staphylococcus epidermidis, Staphylococcus aureus and Enterococcus faecalis, but no bioactive activity was recorded for Chalinula qatari sp. nov. This study highlights the importance of increasing bioprospecting effort in hyperarid conditions and the importance of combining bioprospecting with taxonomic studies for the identification of novel marine drugs.

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<![CDATA[<i>Escherichia coli</i> ST131 clones harbouring AggR and AAF/V fimbriae causing bacteremia in Mozambican children: Emergence of new variant of <i>fimH27</i> subclone]]> https://www.researchpad.co/article/elastic_article_14507 Escherichia coli ST131 has emerged as a globally disseminated multi-drug resistant clone associated with extra-intestinal infections acquired in the community or hospital. In Manhiça district, E. coli is among the top five leading bloodstream pathogens in children. We characterized E. coli strains causing bacteremia in young children in a rural hospital of Mozambique, providing novel information on the occurrence of a new subclone of ST131 harboring both ExPEC and EAEC related genes and belonging to commonly reported O25:H4 and other serotypes. These data suggest the need for further understanding of pathogenesis and clinical impact of this new entity to inform prompt recognition and appropriate treatment.

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<![CDATA[A conformation-based intra-molecular initiation factor identified in the flavivirus RNA-dependent RNA polymerase]]> https://www.researchpad.co/article/elastic_article_14506 The function of a protein is often dictated by a single defined fold, which in turn is determined by its amino acid sequences. However, multiple global conformations can be utilized by a protein to fulfill distinct functions under different circumstances. The flavivirus NS5 protein, a natural fusion of an N-terminal methyltransferase (MTase) and a C-terminal RNA-dependent RNA polymerase (RdRP), may be such an example. Previously reported NS5 crystal structures exhibit two apparently different global conformations. In this work, we demonstrate that both conformations are conserved in the flaviviruses and important for virus proliferation, but only one of them is clearly relevant to RdRP catalysis, in particular at the early stages of the RNA synthesis.

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<![CDATA[Inference on dengue epidemics with Bayesian regime switching models]]> https://www.researchpad.co/article/elastic_article_14505 Dengue, a mosquito-borne infectious disease caused by the dengue viruses, is present in many parts of the tropical and subtropical regions of the world. All four serotypes of dengue viruses are endemic in Singapore, an equatorial city-state. Frequent outbreaks occur, sometimes leading to national epidemics. However, few studies have attempted to characterize breakpoints which precede large rises in dengue case counts. In this paper, Bayesian regime switching (BRS) models were employed to infer epidemic and endemic regimes of dengue transmissions, each containing regime specific processes which drive the growth and decline of dengue cases, estimated using a custom built multi-move Gibbs sampling algorithm. Assessments against various baseline showed that BRS performs better in characterizing dengue transmissions. The dengue regimes estimated by BRS are characterized by their persistent nature. Next, climate analysis showed no short nor long term associations between classified regimes with climate. Lastly, fitting BRS to simulated disease data generated from a mechanistic model, we showed links between disease infectivity and regimes classified using BRS. The model proposed could be applied to other localities and diseases under minimal data requirements where transmission counts over time are collected.

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<![CDATA[Interplay between axonal Wnt5-Vang and dendritic Wnt5-Drl/Ryk signaling controls glomerular patterning in the <i>Drosophila</i> antennal lobe]]> https://www.researchpad.co/article/elastic_article_14504 During brain development, the processes of nerve cells, axons and dendrites, grow over long distances to find and connect with each other to form synapses in precise locations. Understanding the mechanisms that control the growth of these neurites is important for understanding normal brain functions like neuronal plasticity and neural diseases like autism. Although much progress has been made by studying the development of axons and dendrites separately, the mechanisms that guide neuronal processes to their final locations are still incompletely understood. In particular, careful observation of converging pre- and postsynaptic processes suggests that their targeting may be coordinated. Whether the final targeting of axons and dendrites are functionally linked and what molecular mechanisms may be involved are unknown. In this paper we show that, in the developing Drosophila olfactory circuit, coalescing axons and dendrites respond to the extracellular Wnt5 signal in a codependent manner. We demonstrate that the converging axons and dendrites contribute different signaling components to the Wnt5 pathway, the Vang Gogh and Derailed transmembrane receptors respectively, which allow Wnt5 to coordinately guide the targeting of the neurites. Our work thus reveals a novel mechanism of neural circuit patterning and the molecular mechanism that controls it.

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<![CDATA[An Out-of-Patagonia migration explains the worldwide diversity and distribution of <i>Saccharomyces eubayanus</i> lineages]]> https://www.researchpad.co/article/elastic_article_14503 Lager yeast history has intrigued scientists for decades. The recent isolation of S. eubayanus, the lager yeast ancestor, represents an unprecedented opportunity to extend our knowledge on yeast phylogeography and the origins of the S. pastorianus lager hybrid. However, the genetic, phenotypic and evolutionary history of this species remains poorly known. Our work demonstrates that S. eubayanus isolates from Patagonia have the greatest genetic diversity, comprising the largest number of lineages within a single geographic region and experienced ancestral and recent admixture between lineages, likely suggesting co-occurrence in Patagonia. Importantly, some isolates exhibited significant phenotypic differences for traits such as high temperature and ethanol tolerance, together with fermentation performance, demonstrating their potential in the brewing industry for the generation of new styles of lager beers. Furthermore, our results support the idea of colonization from peripheral glacial refugia from the South, as responsible for the high genetic diversity observed in southern Chilean Patagonia. Our results allow hypothesizing a successful physiological adjustment of the species to the local conditions in Patagonia, explaining its wide distribution in the southern hemisphere.

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<![CDATA[Identification and detection of a novel point mutation in the Chitin Synthase gene of <i>Culex pipiens</i> associated with diflubenzuron resistance]]> https://www.researchpad.co/article/elastic_article_14502 Diflubenzuron is one of the main larvicides used for the control of the West Nile Virus vector Culex pipiens in the Mediterranean. However, the efficiency of control is now under threat due to the selection of insecticide resistance. Two point mutations were previously identified at the Chitin synthase and shown to confer low and high levels of resistance and a diagnostic was developed to monitor the trait. This study reports the identification of a third mutation associated with high levels of diflubenzuron resistance in Italy. This mutation was also detected in France, whereas no resistance mutations were found in Cx. pipiens mosquitoes sampled from Greece, Portugal and Israel. The findings are of major concern for mosquito control programs in S. Europe, which rely on the use of a limited number of larvicides.

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<![CDATA[Distribution pattern of Tugai forests species diversity and their relationship to environmental factors in an arid area of China]]> https://www.researchpad.co/article/elastic_article_14501 Ecological restoration of degraded riparian Tugai forests is a key driver to combat desertification in arid regions. Previous studies have focused mainly on changes in groundwater as the underlying mechanisms of Tugai forest’s decline. We evaluated species composition and diversity of Tugai forest and their relationship to groundwater, soil salinity, and soil nutrient. Using 73 quadrats (100 m × 100 m) from 13 transects located perpendicularly to river in the upper reaches of the Tarim River. Eighteen plant species belonging to sixteen genera and eight families were recorded, and the dominant species included Populus euphratica, Phragmites communis, and Tamarix ramosissima. Three P. euphratica stand ages were detected: young stand, mature stand, and old stand. There were significant differences in species diversity, groundwater depth, groundwater salinity, distance from the quadrat to the river channel, soil moisture content, pH, electrical conductivity, total salt, Cl, SO42−, Ca2−, Mg2+, Na+, K+, soil organic carbon, and soil organic matter across the stand ages. Seven species were identified as indicators of the three stand ages. Redundancy analysis indicated that the Tugai forest diversity indices were negatively correlated with groundwater depth, groundwater salinity, and distance from the river, and positively associated with electrical conductivity, total salt, pH, Cl, SO42−, CO32−, soil organic matter, soil organic carbon, and soil moisture content. Plant diversity was the highest at 3–6 m groundwater depth, followed by 0–3 m and then 6–9 m, with the lowest recorded at > 9 m. The appropriate groundwater depth for herbs was about 1–4 m, whereas the depth for trees and shrubs was about 3–6 m. The groundwater depth < 6 m was deemed suitable for the growth of desert riparian forests. This results provide a scientific reference for the ecological restoration and protection for Tugai forests in arid areas.

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<![CDATA[Ontogenetic changes in energetic reserves, digestive enzymes, amino acid and energy content of <i>Lithodes santolla</i> (Anomura: Lithodidae): Baseline for culture]]> https://www.researchpad.co/article/elastic_article_14500 The southern king crab (SKC) Lithodes santolla is an important commercial species in southern South America. Fishing pressure has caused the deterioration of its stocks. Currently, culture techniques are being developed for producing SKC juveniles to enhance the natural population and to recover the fishing stock. Therefore, it is necessary to know about physiology, energetic and nutritional requirements for SKC maintenance in hatchery. Thus, this study aims to evaluate the biochemical and physiological changes in the midgut gland, muscle and hemolymph of juveniles, pre-adults and adults of wild SKC. The energetic reserves, digestive enzymes activity, amino acid profile and energy were quantified in twelve juveniles, ten pre-adult, and ten adult crabs. Juveniles showed high glycogen and low lipids in the midgut gland, and low proteins and low lactate in muscle. In the hemolymph, juveniles had high lipids. Pre-adults had high glycogen and lipids in the midgut gland, and both high protein and lactate in muscle. In the hemolymph, pre-adults had high lipids. Adults had low glycogen and high lipids in midgut gland, and both high proteins and high lactate in muscle. In hemolymph, adults had high glucose and lactate. Juveniles and pre-adults had high proteinase activity, whereas adults had high lipase activity. Major essential amino acids of SKC were arginine, methionine, and tryptophan, and the non-essential amino acids were glycine, aspartic acid and glutamic acid. On another hand, SKC had similar energy in the midgut gland and muscle, regardless of the ontogenetic stage. Moreover, we demonstrated that the biochemical energy calculation underestimates the actual measured values by a calorimeter. Thus, our results help to understand the physiological changes, energetic and nutritional requirements of L. santolla, and this study is a baseline for research on diet formulation for maintaining this species under culture conditions.

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<![CDATA[Dialysis timing may be deferred toward very late initiation: An observational study]]> https://www.researchpad.co/article/elastic_article_14499 The optimal timing to initiate dialysis among patients with an estimated glomerular filtration rate (eGFR) of <5 mL/min/1.73 m2 is unknown. We hypothesized that dialysis initiation time can be deferred in this population even with high uremic burden. A case-crossover study with case (0–30 days before dialysis initiation [DI]) and control (90–120 days before DI) periods was conducted in 1,079 hemodialysis patients aged 18–90 years at China Medical University Hospital between 2006 and 2015. The uremic burden was quantified based on 7 uremic indicators that reached the predefined threshold in case period, namely hemoglobin, serum albumin, blood urea nitrogen, serum creatinine, potassium, phosphorus, and bicarbonate. Dialysis timing was classified as standard (met 0–2 uremic indicators), late (3–5 indicators), and very late (6–7 indicators). Median eGFR-DI of the 1,079 patients was 3.4 mL/min/1.73 m2 and was 2.7 mL/min/1.73 m2 in patients with very late initiation. The median follow-up duration was 2.42 years. Antibiotics, diuretics, antihypertensive medications, and non-steroidal anti-inflammatory drugs (NSAIDs) were more prevalently used during the case period. The fully adjusted hazards ratios of all-cause mortality for the late and very late groups were 0.97 (95% confidence interval 0.76–1.24) and 0.83 (0.61–1.15) compared with the standard group. It is safe to defer dialysis initiation among patients with chronic kidney disease (CKD) having an eGFR of <5 mL/min/1.73 m2 even when patients having multiple biochemical uremic burdens. Coordinated efforts in acute infection prevention, optimal fluid management, and prevention of accidental exposure to NSAIDs are crucial to prolong the dialysis-free survival.

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<![CDATA[The degradation-promoting roles of deubiquitinases Ubp6 and Ubp3 in cytosolic and ER protein quality control]]> https://www.researchpad.co/article/elastic_article_14498 The quality control of intracellular proteins is achieved by degrading misfolded proteins which cannot be refolded by molecular chaperones. In eukaryotes, such degradation is handled primarily by the ubiquitin-proteasome system. However, it remained unclear whether and how protein quality control deploys various deubiquitinases. To address this question, we screened deletions or mutation of the 20 deubiquitinase genes in Saccharomyces cerevisiae and discovered that almost half of the mutations slowed the removal of misfolded proteins whereas none of the remaining mutations accelerated this process significantly. Further characterization revealed that Ubp6 maintains the level of free ubiquitin to promote the elimination of misfolded cytosolic proteins, while Ubp3 supports the degradation of misfolded cytosolic and ER luminal proteins by different mechanisms.

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<![CDATA[A content analysis-based approach to explore simulation verification and identify its current challenges]]> https://www.researchpad.co/article/elastic_article_14497 Verification is a crucial process to facilitate the identification and removal of errors within simulations. This study explores semantic changes to the concept of simulation verification over the past six decades using a data-supported, automated content analysis approach. We collect and utilize a corpus of 4,047 peer-reviewed Modeling and Simulation (M&S) publications dealing with a wide range of studies of simulation verification from 1963 to 2015. We group the selected papers by decade of publication to provide insights and explore the corpus from four perspectives: (i) the positioning of prominent concepts across the corpus as a whole; (ii) a comparison of the prominence of verification, validation, and Verification and Validation (V&V) as separate concepts; (iii) the positioning of the concepts specifically associated with verification; and (iv) an evaluation of verification’s defining characteristics within each decade. Our analysis reveals unique characterizations of verification in each decade. The insights gathered helped to identify and discuss three categories of verification challenges as avenues of future research, awareness, and understanding for researchers, students, and practitioners. These categories include conveying confidence and maintaining ease of use; techniques’ coverage abilities for handling increasing simulation complexities; and new ways to provide error feedback to model users.

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<![CDATA[Changes and prognostic values of tumor-infiltrating lymphocyte subsets after primary systemic therapy in breast cancer]]> https://www.researchpad.co/article/elastic_article_14496 Tumor-infiltrating lymphocyte (TIL) levels have prognostic and predictive values in treatment-naïve breast cancers. However, there have been controversies regarding TIL subset changes and their clinical implications in post-treatment breast cancers. This study aimed to explore change and prognostic significance of TIL subset infiltration after primary systemic therapy (PST) in breast cancer. One-hundred-fifty-five patients who had residual disease after anthracycline- or anthracycline plus taxane-based PST were included. The quantities of intratumoral and stromal TIL subsets (CD8+, CD4+, and FOXP3+ TILs) in pre- and post-PST breast cancer samples, as well as changes between them, were analyzed along with their correlations with clinicopathologic features and outcome of patients. As a whole, intratumoral CD8+ and CD4+ TILs increased after PST while stromal TILs decreased. Both intratumoral and stromal FOXP3+ TILs decreased after PST. The chemo-sensitive group [residual cancer burden (RCB) class I and II] showed the same pattern of change in intratumoral CD8+ TILs as the whole group, whereas the chemo-resistant group (RCB class III) showed no significant change in intratumoral CD8+ TIL infiltration after PST. Survival analyses for each TIL subset as well as their ratios revealed that high levels of intratumoral, stromal, and total CD8+ TIL infiltration after PST were independent predictors of longer patient survival. In subgroup analyses, CD8+ TIL infiltration after PST revealed prognostic significance in the chemo-resistant group but not in the chemo-sensitive group. In conclusion, infiltration of CD8+, CD4+, and FOXP3+ TIL changed after PST in the intratumoral and stromal compartments. Especially, increase of intratumoral CD8+ TILs was associated with chemo-responsiveness. Moreover, CD8+ TIL status in residual tumors after PST may be used as a potential prognostic marker in breast cancer patients who receive PST and provide additional prognostic information to chemo-resistant group.

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<![CDATA[Anti-cancer effects of <i>Bifidobacterium</i> species in colon cancer cells and a mouse model of carcinogenesis]]> https://www.researchpad.co/article/elastic_article_14495 Probiotics are suggested to prevent colorectal cancer (CRC). This study aimed to investigate the anticancer properties of some potential probiotics in vitro and in vivo.Materials and methodsAnticancer effects of potential probiotic groups were investigated following of in LS174T cancer cells compared to IEC-18 normal cells. 1. a single strain of Bifidobacterium. breve, 2. a single strain of Lactobacillus. reuteri, 3. a cocktail of 5 strains of Lactobacilli (LC), 4. a cocktail of 5 strains of Bifidobacteria (BC), 5. a cocktail of 10 strains from Lactobacillus and Bifidobacterium (L+B). Apoptosis rate, EGFR, HER-2 and PTGS-2 (COX-2 protein) expression levels were assessed as metrics of evaluating anticancer properties. Effect of BC, as the most effective group in vitro, was further assessed in mice models.ResultsBC induced ~21% and only ~3% apoptosis among LS174T and IEC-18 cells respectively. BC decreased the expression of EGFR by 4.4 folds, HER-2 by 6.7 folds, and PTGS-2 by 20 folds among the LS174T cells. In all these cases, BC did not interfere significantly with the expression of the genes in IEC-18 cells. This cocktail has caused only 1.1 folds decrease, 1.8 folds increase and 1.7 folds decrease in EGFR, HER-2 and PTGS-2 expression, respectively. Western blot analysis confirmed these results in the protein level. BC significantly ameliorated the disease activity index, restored colon length, inhibited the increase in incidence and progress of tumors to higher stages and grades.ConclusionsBC was the most efficient treatment in this study. It had considerable “protective” anti-cancer properties and concomitantly down regulated EGFR, HER-2 and PTGS-2 (COX-2), while having significant anti-CRC effects on CRC mice models. In general, this potential probiotic could be considered as a suitable nutritional supplement to treat and prevent CRC. ]]> <![CDATA[Why do biting horseflies prefer warmer hosts? tabanids can escape easier from warmer targets]]> https://www.researchpad.co/article/elastic_article_14494 Blood-sucking horseflies (tabanids) prefer warmer (sunlit, darker) host animals and generally attack them in sunshine, the reason for which was unknown until now. Recently, it was hypothesized that blood-seeking female tabanids prefer elevated temperatures, because their wing muscles are quicker and their nervous system functions better at a warmer body temperature brought about by warmer microclimate, and thus they can more successfully avoid the host’s parasite-repelling reactions by prompt takeoffs. To test this hypothesis, we studied in field experiments the success rate of escape reactions of tabanids that landed on black targets as a function of the target temperature, and measured the surface temperature of differently coloured horses with thermography. We found that the escape success of tabanids decreased with decreasing target temperature, that is escape success is driven by temperature. Our results explain the behaviour of biting horseflies that they prefer warmer hosts against colder ones. Since in sunshine the darker the host the warmer its body surface, our results also explain why horseflies prefer sunlit dark (brown, black) hosts against bright (beige, white) ones, and why these parasites attack their hosts usually in sunshine, rather than under shaded conditions.

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<![CDATA[Incidence and risk factors for hyperglycemia in pregnancy among nulliparous women: A Brazilian multicenter cohort study]]> https://www.researchpad.co/article/elastic_article_14493 To assess the incidence and risk factors for hyperglycemia in pregnancy in a cohort of Brazilian nulliparous pregnant women.Materials and methodsThis is a secondary analysis of a multicenter cohort study that enrolled 1,008 nulliparous pregnant women at 19–21 weeks. Exclusion criteria included chronic exposure to corticosteroids and previous diabetes. Bivariate and multivariate analyses by Poisson regression were used to identify associated factors.ResultsThe incidence of hyperglycemia in pregnancy was 14.9% (150/1,008), and 94.7% of these cases were gestational diabetes mellitus (142/150). Significant associated factors included a family history of diabetes mellitus, maternal overweight or obesity at enrollment, and previous maternal conditions (polycystic ovarian syndrome, thyroid dysfunctions and hypertensive disorders). A BMI ≥ 26.3Kg/m2 (RRadj 1.87 [1.66–2.10]) and a family history of diabetes mellitus (RRadj 1.71 [1.37–2.15]) at enrollment were independent risk factors for HIP.ConclusionsA family history of diabetes mellitus and overweight or obesity (until 19–21 weeks of gestation) may be used as selective markers for HIP in Brazilian nulliparous women. Given the scarcity of results in nulliparous women, our findings may contribute to determine the optimal diagnostic approach in populations of similar socioeconomic characteristics. ]]> <![CDATA[Prevalence of endosalpingiosis and other benign gynecologic lesions]]> https://www.researchpad.co/article/elastic_article_14492 Endosalpingiosis, traditionally regarded as an incidental pathological finding, was recently reported to have an association with gynecologic malignancies. To determine the prevalence of endosalpingiosis, we evaluated all benign appearing adnexal lesions using the Sectioning and Extensively Examining-Fimbria (SEE-Fim) protocol, and queried the pathology database for the presence of endosalpingiosis, gynecologic malignancy, endometriosis, Walthard nests, and paratubal cysts. Using the SEE-Fim protocol, the prevalence of endosalpingiosis, endometriosis, Walthard nests, and paratubal cysts were 22%, 45%, 33%, and 42% respectively, substantially higher than previously reported. All lesions were observed to increase with age except endometriosis which increased until menopause then decreased dramatically. Among specimens including ovarian tissue, the prevalence of implantation of at least one lesion type was ubiquitous in patients age 51 and older (93%). The clinical significance of endosalpingiosis should be a continued area of research with larger trials assessing prevalence, factors affecting incidence, and association with malignancy. Our findings contribute to elucidating the origin of ectopic lesions and gynecologic disease risk.

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<![CDATA[Evidence of recombination of vaccine strains of lumpy skin disease virus with field strains, causing disease]]> https://www.researchpad.co/article/elastic_article_14489 Vaccination against lumpy skin disease (LSD) is crucial for maintaining the health of animals and the economic sustainability of farming. Either homologous vaccines consisting of live attenuated LSD virus (LSDV) or heterologous vaccines consisting of live attenuated sheeppox or goatpox virus (SPPV/GPPV) can be used for control of LSDV. Although SPPV/GTPV-based vaccines exhibit slightly lower efficacy than live attenuated LSDV vaccines, they do not cause vaccine-induced viremia, fever, and clinical symptoms of the disease following vaccination, caused by the replication capacity of live attenuated LSDVs. Recombination of capripoxviruses in the field was a long-standing hypothesis until a naturally occurring recombinant LSDV vaccine isolate was detected in Russia, where the sheeppox vaccine alone is used. This occurred after the initiation of vaccination campaigns using LSDV vaccines in the neighboring countries in 2017, when the first cases of presumed vaccine-like isolate circulation were documented with concurrent detection of a recombinant vaccine isolate in the field. The follow-up findings presented herein show that during the period from 2015 to 2018, the molecular epidemiology of LSDV in Russia split into two independent waves. The 2015–2016 epidemic was attributable to the field isolate. Whereas the 2017 epidemic and, in particular, the 2018 epidemic represented novel disease importations that were not genetically linked to the 2015–2016 field-type incursions. This demonstrated a new emergence rather than the continuation of the field-type epidemic. Since recombinant vaccine-like LSDV isolates appear to have entrenched across the country’s border, the policy of using certain live vaccines requires revision in the context of the biosafety threat it presents.

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<![CDATA[Codon Pairs are Phylogenetically Conserved: A comprehensive analysis of codon pairing conservation across the Tree of Life]]> https://www.researchpad.co/article/elastic_article_14487 Identical codon pairing and co-tRNA codon pairing increase translational efficiency within genes when two codons that encode the same amino acid are translated by the same tRNA before it diffuses from the ribosome. We examine the phylogenetic signal in both identical and co-tRNA codon pairing across 23 428 species using alignment-free and parsimony methods. We determined that conserved codon pairing typically has a smaller window size than the length of a ribosome, and codon pairing tracks phylogenies across various taxonomic groups. We report a comprehensive analysis of codon pairing, including the extent to which each codon pairs. Our parsimony method generally recovers phylogenies that are more congruent with the established phylogenies than our alignment-free method. However, four of the ten taxonomic groups did not have sufficient orthologous codon pairings and were therefore analyzed using only the alignment-free methods. Since the recovered phylogenies using only codon pairing largely match phylogenies from the Open Tree of Life and the NCBI taxonomy, and are comparable to trees recovered by other algorithms, we propose that codon pairing biases are phylogenetically conserved and should be considered in conjunction with other phylogenomic techniques.

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