bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climate and Morphology Drive Breeding Periods in Frogs
Authors: Juarez Bryan H , O’Connell Lauren A 
Published: July 2022

AbstractAimClimate can have profound effects on reproductive behavior and physiology, especially in ectothermic animals. Breeding periods in amphibians have received little attention despite amphibian reliance on climate and water due to their reproductive biology and ecological diversity. The aim of this study is to determine how global climate impacts breeding periods in ectothermic animals through physiology, body size, and microhabitat.LocationAll continents, except Antarctica.Time periodBreeding periods and climate both dating as far back as 1970.Major taxa studied497 (7%) anuran species of 41 (76%) families.MethodsWe used phylogenetic comparative methods to analyze a global dataset of frog breeding periods, climate, body size, and microhabitat for 497 species.ResultsWe found support for a global latitudinal gradient of breeding periods which are longer in the warmer, wetter tropics while shorter in the colder, dryer temperate zone. Latitudinal and non-latitudinal global patterns of breeding period were composites of the same patterns in the temperate and tropical zones. However, the effect of climate and body size in each zone is unique. Breeding periods displayed weak phylogenetic signal and were similar across microhabitats.Main conclusionsBreeding periods show a global latitudinal gradient but this concept breaks down within the tropical zone. Our results are consistent with the importance of physiology in driving breeding periods and we describe how breeding period and body size may exhibit trade-offs which make latitudinal gradients context-dependent. Our results set within an ecophysiological framework have broad implications for understanding reproductive diversity in other ectothermic organisms.
Independent evolution of influenza A virus H1N1 in pigs in Guatemala
Authors: Ortiz Lucia , Geiger Ginger , Ferreri Lucas , Moran David , Alvarez Danilo , Gonzalez-Reiche Ana Silvia , Mendez Dione , Rajao Daniela , Cordon-Rosales Celia , Perez Daniel R. 
Published: July 2022

AbstractCommercial swine farms provide unique systems for interspecies transmission of influenza A viruses (FLUAVs) at the animal-human interface. Bidirectional transmission of FLUAVs between pigs and humans plays a significant role in the generation of novel strains that become established in the new host population. Active FLUAV surveillance was conducted for two years on a commercial pig farm in Southern Guatemala with no history of FLUAV vaccination. Nasal swabs (n=2,094) from fattening pigs (6 to 24 weeks old) with respiratory signs were collected from May 2016 to February 2018. Swabs were screened for FLUAV by RRT-PCR and full virus genomes of FLUAV-positive swabs were sequenced by next-generation sequencing (NGS). FLUAV prevalence was 12.0% (95% CI: 10.6% – 13.4%) with two distinct periods of high infection. All samples were identified as FLUAVs of the H1N1 subtype within the H1 swine clade 1A.3.3.2 and whose ancestors are the human origin 2009 H1N1 influenza pandemic virus (H1N1 pdm09). Compared to the prototypic reference segment sequence, 10 amino acid signatures were observed on relevant antigenic sites on the hemagglutinin. We also found that Guatemalan swine-origin FLUAVs show independent evolution from other H1N1 pdm09 FLUAVs circulating in Central America. The zoonotic risk of these viruses remains unknown, but strongly calls for continued FLUAV surveillance in pigs in Guatemala.ImportanceDespite increased surveillance efforts, the epidemiology of FLUAVs circulating in swine in Latin America remains understudied. For instance, the 2009 H1N1 influenza pandemic strain (H1N1 pdm09) emerged in Mexico, but its circulation remained undetected in pigs. In Central America, Guatemala is the country with the largest swine industry. We found a unique group of H1N1 pdm09 sequences that suggests independent evolution from similar viruses circulating in Central America. These viruses may represent the establishment of a novel genetic lineage with the potential to reassort with other co-circulating viruses, and whose zoonotic risk remains to be determined.
Highly pathogenic avian influenza H5N1 virus infections in wild red foxes (Vulpes vulpes) show neurotropism and adaptive virus mutations
Authors: Bordes Luca , Vreman Sandra , Heutink Rene , Roose Marit , Venema Sandra , Pritz-Verschuren Sylvia B E , Rijks Jolianne M , Gonzales José L , Germeraad Evelien A , Engelsma Marc , Beerens Nancy 
Published: July 2022

ABSTRACTDuring the 2020-2022 epizootic of highly pathogenic avian influenza virus (HPAI) several infections of mammalian species were reported in Europe. In the Netherlands, HPAI H5N1 virus infections were detected in three wild red foxes (Vulpes vulpes) that were submitted with neurological symptoms between December 2021 and February 2022. Histopathological analysis demonstrated the virus was mainly present in the brain, with limited or no detection in the respiratory tract and other organs. Phylogenetic analysis showed the three fox viruses were not closely related, but were related to HPAI H5N1 clade 2.3.4.4b viruses found in wild birds. In addition, limited virus shedding was detected suggesting the virus was not transmitted between the foxes. Genetic analysis demonstrated the presence of mammalian adaptation E627K in the polymerase basic two (PB2) protein of the two fox viruses. In both foxes the avian (PB2-627E) and the mammalian (PB2-627K) variant were present as a mixture in the virus population, which suggests the mutation emerged in these specific animals. The two variant viruses were isolated and virus replication and passaging experiments were performed. These experiments showed mutation PB2-627K increases replication of the virus in mammalian cell lines compared to the chicken cell line, and at the lower temperatures of the mammalian upper respiratory tract. This study showed the HPAI H5N1 virus is capable of adaptation to mammals, however more adaptive mutations are required to allow efficient transmission between mammals. Therefore, surveillance in mammals should be expanded to closely monitor the emergence of zoonotic mutations for pandemic preparedness.IMPORTANCEHighly pathogenic avian influenza (HPAI) viruses caused high mortality amongst wild birds in 2021-2022 in the Netherlands. Recently three wild foxes were found to be infected with HPAI H5N1 viruses, likely by feeding on infected birds. Although HPAI is a respiratory virus, in these foxes the viruses were mostly detected in the brain. Two viruses isolated from the foxes contained a mutation that is associated with adaptation to mammals. We show the mutant virus replicates better in mammalian cells than in avian cells, and at the lower body temperature of mammals. More mutations are required before viruses can transmit between mammals, or can be transmitted to humans. However, the infections in mammalian species should be closely monitored to swiftly detect mutations that may increase the zoonotic potential of the HPAI H5N1 viruses as these may threaten public health.
Cysteine dependent conformation heterogeneity of Shigella flexneri autotransporter IcsA and implications in its function
Authors: Qin Jilong , Hong Yaoqin , Morona Renato , Totsika Makrina 
Published: July 2022

AbstractShigella IcsA is a versatile surface virulence factor required for both early and late pathogenesis stages, extracellularly to intracellularly. Despite IcsA serving as a model Type V secretion system (T5SS) autotransporter to study host pathogen interactions, its detailed molecular architecture is poorly understood. Recently, IcsA was found to switch to a different conformation for its adhesin activity upon sensing of the host stimuli by Shigella Type III secretion system (T3SS). Here, we report that the single cysteine residue (C130) near the N-terminus of IcsA passenger has a role in IcsA adhesin activity. We also show that the IcsA passenger (IcsAp) exists in multiple conformations, and the conformation populations are influenced by a central pair of cysteine residues (C375 and C379), which is not previously reported for any Type V autotransporter passengers. Disruption of either or both central cysteine residues alters the exposure of IcsA epitopes to polyclonal anti-IcsA antibodies previously shown to block Shigella adherence, yet without loss of IcsA intracellular functions in actin-based motility (ABM). Anti-IcsA antibody reactivity was restored when the IcsA paired cysteine substitution mutants were expressed in a ∆ipaD background with a constitutively active T3SS, highlighting an interplay between T3SS and T5SS. The work here uncovers a novel molecular switch empowered by a centrally localised, short-spaced cysteine pair in the Type V autotransporter IcsA that ensures conformational heterogeneity to aid IcsA evasion of host immunity.ImportanceShigella species are the leading cause of diarrheal related death globally by causing bacillary dysentery. The surface virulence factor IcsA which is essential for Shigella pathogenesis is a unique multi-functional autotransporter that is responsible for cell adhesion, and actin-based motility, yet detailed mechanistic understanding is lacking. Here, we show that the three cysteine residues in IcsA contribute to the protein’s distinct functions. The N terminus cysteine residue within the IcsA passenger domain plays a role in adhesin function, while a centrally localised cysteine pair provides conformational heterogeneity resulting in IcsA molecules with different reactivity to adhesion-blocking anti-IcsA antibodies. In synergy with the Type III secretion system, this molecular switch preserves biological function in distinct IcsA conformations for cell adhesion, actin-based motility and autophagy escape, providing a potential strategy by which Shigella evade host immunity targeting of this essential virulence factor.
Morphology of proximal and distal human semitendinosus compartments and the effects of distal tendon harvesting for anterior cruciate ligament reconstruction
Authors: Kositsky Adam , Maas Huub , Barrett Rod S. , Kennedy Ben , Stenroth Lauri , Korhonen Rami K. , Vertullo Chris J. , Diamond Laura E. , Saxby David J. 
Published: July 2022

ABSTRACTThe human semitendinosus muscle is characterized by a tendinous inscription separating proximal (STprox) and distal (STdist) neuromuscular compartments. As each compartment is innervated by separate nerve branches, potential exists for the compartments to operate and be controlled independently. However, the morphology and function of each compartment have not been thoroughly examined in a human adult population. Further, the distal semitendinosus tendon is typically harvested for use in anterior cruciate ligament reconstruction (ACLR) surgery, which induces long-term morphological changes to the semitendinosus muscle-tendon unit. It remains unknown if muscle morphological alterations following ACLR are uniform between STproxand STdist. Here, we performed magnetic resonance imaging on ten individuals who had undergone ACLR involving an ipsilateral distal semitendinosus tendon graft 14 ± 6 months prior, extracting morphological parameters of the whole ST muscle and each individual muscle compartment from both the (non-injured) contralateral and surgical legs. In the contralateral non-surgical leg, volume and length of STproxwere lower than STdist. No between-compartment differences in volume or length were found for ACLR legs, likely due to greater shortening of STdistcompared to STproxafter ACLR. The maximal anatomical cross-sectional area of both compartments was substantially smaller on the ACLR leg, but did not differ between STproxand STdiston either leg. The absolute and relative differences in STproxmorphology on the ACLR leg were strongly correlated with the corresponding between-leg differences in STdistmorphological parameters. Specifically, greater morphological differences in one compartment were highly correlated with large differences in the other compartment, and vice versa for smaller differences. These relationships indicate that despite the heterogeneity in compartment length and volume, compartment atrophy is not independent or random. Further, the tendinous inscription endpoints were generally positioned at the same proximodistal level as the compartment maximal anatomical cross-sectional areas, providing a wide area over which the tendinous inscription could mechanically interact with compartments. Overall, results suggest the two human semitendinosus compartments are not mechanically independent.
Pin-pointing the key hubs in the IFN-γ pathway responding to SARS-CoV-2 infection
Authors: Toro Ayelen , Lage-Vickers Sofia , Bizzotto Juan , Vilicich Felipe , Sabater Agustina , Pascual Gaston , Ledesma-Bazan Sabrina , Sanchis Pablo , Ruiz Maria S. , Arevalo Ana P. , Porfido Jorge L. , Seniuk Rocio , Labanca Estefania , Anselmino Nicolas , Navone Nora , Alonso Daniel F. , Vazquez Elba , Crispo Martina , Cotignola Javier , Gueron Geraldine 
Published: July 2022

ABSTRACTInterferon gamma may be a potential adjuvant immunotherapy for COVID-19 patients. In this work, we assessed gene expression profiles associated with the IFN-γ pathway in response to SARS-CoV-2 infection. Employing a case-control study from SARS-CoV-2 positive and negative patients, we identified IFN-γ-associated pathways to be enriched in positive patients. Bioinformatics analyses showed upregulation ofMAP2K6, CBL, RUNX3, STAT1andJAK2in COVID-19 positive vs. negative patients. A positive correlation was observed betweenSTAT1/JAK2, which varied alongside the patient’s viral load. Expression ofMX1, MX2, ISG15andOAS1(4 well-known IFN-stimulated genes (ISGs)) displayed upregulation in COVID-19 positive vs. negative patients. Integrative analyses showcased higher levels of ISGs which were associated with increased viral load andSTAT1/JAK2expression. Confirmation of ISGs up-regulation was performedin vitrousing the A549 lung cell line treated with Poly(I:C), a synthetic analog of viral double-stranded RNA; and in different pulmonary human cell lines and ferret tracheal biopsies infected with SARS-CoV-2. A pre-clinical murine model of coronavirus infection confirmed findings displaying increased ISGs in the liver and lungs from infected mice. Altogether, these results demonstrate the role of IFN-γ and ISGs in response to SARS-CoV-2 infection, highlighting alternative druggable targets that can boost the host response.
Predictive Modelling of Service Pathways to Admission in Psychiatric Residential Treatment Facilities
Authors: Vsevolozhskaya Olga A. , Turner Brian W. , Shimshock Stephen M. , Harp Kathi L.H. , Tong Xiaoran , Lyons John S. 
Published: July 2022

AbstractObjectiveTo develop and test predictive models of admissions to a psychiatric residential treatment facility (PRTF) in transitional age youth using routinely collected health insurance claims and enrollment data.Data SourcesWe used outpatient service and pharmaceutical claims from Medicaid beneficiaries aged 6-to 21-years old in Kentucky for the years 2010-2017.Study DesignWe assessed over 1,250 predictors (derived from Medicaid claims data) prior to the first PRTF admission. An ensemble machine learning (ML) algorithm based on logistic regression models fitted to a random subsample of the original data was used to predict pathways to the first PRTF admission. Discrimination performance of the ML ensemble was evaluated by comparing predictions to actual outcomes and calculating area under the curve (AUC), accuracy, sensitivity, and specificity. Additionally, a multivariate logistic regression model was fit to investigate the contribution of the continuity of mental health care after the initial PRTF admission on the risk of readmission.Data Collection/Extraction MethodsWe identified N = 519,011 unique children and youth with at least one outpatient service or pharmaceutical claim during our study period (January 1, 2010 through December 31, 2017).Principal FindingsFewer than 0.5% of children and youth in Kentucky had an episode of PRTF admission. Despite a very low prevalence of PRTF admission, classification accuracy of the ML ensemble for identifying PRTF youth achieved over 90% accuracy (AUC = 0.96). Factors associated with the initial PRTF admission were having been prescribed anti-psychotic and anti-manic medications, and receiving outpatient psychiatric care. Within six months after the initial PRTF discharge, there was a surprising drop in service utilization with a large proportion of youth not appearing to receive any follow-up care.ConclusionsDespite the fact that admission into a PRTF was a relatively rare event, our findings suggest that it is a predictable event among youth with identified mental health conditions who are receiving care in the community.What is known on this topicAfter psychiatric hospitalization, PRTF treatment is the most expensive and restrictive intervention available to serve children and youth.Previous research examining predictors of PRTF entry using Medicaid reimbursement data showed that clinical factors were strong predictors of hospitalization.What this study addsWe provide a comprehensive analysis of the factors beyond clinical diagnoses that lead to PRTF entry.We also seek to identify whether any specific patterns of service and/or pharmacy claims utilization are associated with reducing the likelihood of readmission.
Autonomous Remotely Controlled Closed System Transgenic Cell Technologies Robot: CRISPR.BOT
Authors: Erkek Fatmanur , Gulden Gamze , Sert Berranur , Yilmaz Menekse Cagla , Odabas Sibel Pinar , Bal Enes , Yelgen Gamze , Teymur Tarik , Ay Yasin , Dogdu Solen , Tiryaki Nulifer Neslihan , Baran Buse , Gelsin Beste , Araz Hasret , Cavrar Ilayda , Tastan Cihan 
Published: July 2022

AbstractIn manually advancing experimental processes, the stages may be long-term and need to be repeated. Human errors with the repetition of the steps turn into a time-consuming and high-cost for the experiment processes. For this reason, autonomous liquid processing systems are promising technologies. However, in addition to the high cost of fully automatic systems, their maintenance is also quite expensive. Furthermore, conventional systems usually require system-specific protocols and laboratory equipment. Here, we aimed to show that the autonomous robotic systems may provide a closed and error-free molecular biology bench to perform genetic engineering automatically, quickly, and practically 7-24. In this way, researchers can save time from repetitive experiment processes and perform BSL3 experiments including pathogens without human contact. In this study, we built CRISPR.BOT robotic systems to perform Green Fluorescent Protein (GFP) encoding plasmid DNA transfer into bacteria, lentiviral transduction of the gene-of-interests including GFP encoding gene and CRISPR-Cas9 with gRNAs genetic editing system to a human cell line. Furthermore, we showed that CRISPR.BOT system achieved to accomplish single-cell subcloning of GFP+ CRISPR-gRNA+ cells with 90-100% purity. This study suggests that CRISPR.BOT-like approaches may reduce manpower in a safely closed bench in which molecular biology and genetic engineering can be done by robots in a closed system without touching pathogenic microorganisms (virus or bacteria, for example, SARS CoV-2 virus). Furthermore, LEGO Mindstorms robots showed to have the potential to be used in daily laboratory routines with their cost-effectiveness reduced by up to 50 times compared to normal commercial robots.
Measuring the threat from a distance: insight into the complexity and perspectives for implementing sentinel plantation to test host range ofXylella fastidiosa
Authors: Casarin Noemi , Hasbroucq Séverine , López-Mercadal Júlia , Miranda Miguel Ángel , Bragard Claude , Grégoire Jean-Claude 
Published: July 2022

AbstractThe sentinel plantation concept consists of assessing the impact of exotic factors, such as pests and pathogens, on plants of interest by planting them out of their native range. This tool is a way to enhance knowledge for pest risk analysis (PRA) by guiding decisions on how quarantine organisms should be regulated and where to focus prevention and surveillance efforts for an early detection. In this study, the sentinel method was used in the case of research onXylella fastidiosa, a plant pathogenic bacterium that has recently been found established in southern Europe, but whose potential impact and possible host range are still poorly documented in northern areas where the bacterium is not known to occur. To improve knowledge on the susceptibility of potential hosts ofX. fastidiosain northern Europe, a sentinel plantation ofPrunus domesticacv. Opal,Quercus petraeaandSalix albawas established in theX. fastidiosa-infected area of Majorca. In order to assess the circulation of the bacterium in the sentinel plot and around it, surveys of the local flora and insect vectors were carried out, as well as the planting of a network of rosemary “spy plants”. Symptomatic monitoring and molecular analyses were performed on the sentinel plants for four years. During these years,X. fastidiosawas never detected in our sentinel plants most likely because of the low infectivity pressure recorded in the surroundings. This study underlines the complexity of conducting sentinel plantation assays combined withX. fastidiosaresearch, highlighting the need for long-term investigation and questioning the efficiency of the sentinel tool. However, this study is placed in perspective with other valuable sentinel plantations. It also highlights the complementarity of the tool and proposes elements to improve or reorient the implementation of future sentinel projects.
Age-associated DNA methylation changes in Xenopus frogs
Authors: Morselli Marco , Bennett Ronan , Shaidani Nikko-Ideen , Horb Marko , Peshkin Leonid , Pellegrini Matteo 
Published: July 2022

AbstractAge-associated changes in DNA methylation have been widely established and characterized in mammals but not yet extended to other species. We present clear evidence that the aquatic vertebrate species Xenopus tropicalis displays clear patterns of age-associated changes in DNA methylation. This observation allows us to leverage the unique resources available for Xenopus to study how DNA methylation relates to other hallmarks of aging. We have generated whole genome bisulfite sequencing (WGBS) profiles in nine samples representing young, mature and old adults and characterize the gene- and chromosome-scale changes. Moreover, we selected a few thousands CpG sites to expand the findings in a larger cohort of individuals through targeted DNA methylation analysis to produce a cost effective epigenetic clock assay.