bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transplantation of Organs From DCD and DBD Donors Who Died After Ligature Asphyxiation
Authors: Trotter Patrick B. , Dark John , Fisher Andrew J. , Robb Matthew , Watson Christopher , Neuberger James 
Published: October 2022

Background
The United Kingdom transplant registry data demonstrated similar transplant outcomes for recipients of kidneys from donors who died following ligature asphyxiation and those who received organs from donors dying from other causes. The impact that this donor cause of death has on the outcomes of other solid organ transplant recipients remains uncertain.

Methods
The United Kingdom transplant registry analysis was undertaken to determine transplant outcomes in recipients of lungs, hearts, livers‚ and pancreases from donors who died following ligature asphyxiation.

Results
Between January 01, 2003, and December 31, 2016, 2.7% (n = 521) of all potential United Kingdom donors died following ligature asphyxiation (mostly suicide by hanging). Of these, 416 (79.9%; 197 donation after brain stem death and 219 donation after circulatory death [DCD]) donated an organ for transplantation. These donors provided organs for 574 transplants (66 lung transplants, 75 heart transplants, 279 liver transplants, and 154 pancreas transplants). Patient and graft survival were similar for recipients of both donation after brain stem death and DCD hearts, livers, and pancreases from donors who died following ligature asphyxiation. Unadjusted graft and patient survival were significantly worse for recipients of lungs from DCD donors who died following ligature asphyxiation. This detrimental effect persisted after propensity score matching.

Conclusions
Livers, hearts, and pancreases from donors who die following ligature asphyxiation suffer an additional warm ischemic insult, but this does not negatively impact transplant outcomes. Outcomes for recipients of DCD lungs appear to be significantly worse.
The Conundrum of Patients With Compensated Cirrhosis Requiring Kidney Transplantation; Kidney Alone or Simultaneous Liver Kidney Transplantation
Authors: Dodge Jennifer L. , Lee Brian T. , Kassem Ali Casey Z. , Biggins Scott W. , Rana Prachi A. , Nadim Mitra K. , Asrani Sumeet K. , Fong Tse-Ling 
Published: October 2022

Background.
Patients with compensated cirrhosis and chronic kidney disease are increasing along with demand for simultaneous liver kidney transplant (SLKT) and shortages of organs for transplantation. Although these well-compensated patients may not need a liver organ, the alternative of kidney transplant alone (KTA) poses the risk of liver decompensation. Therefore, we aim to characterize outcomes among patients with compensated cirrhosis and chronic kidney disease listed for SLKT or receiving KTA to inform clinical decisions.

Methods.
The 2-part retrospective study included a national cohort of patients listed for SLKT in United Network for Organ Sharing from January 2003 to June 2019 with Child A cirrhosis, with model for end-stage liver disease <25, and receiving dialysis; and a cohort of patients who underwent KTA from 2004 to 2019 with Child A cirrhosis identified through a 4-center chart review. Waitlist outcomes (SLKT, death, and clinical improvement) and post-KTA liver decompensation and survival were evaluated in the cohorts, respectively.

Results.
In the national SLKT cohort (N = 705, median age 56 y, 68.8% male), 5-y cumulative incidence of SLKT was 43.1%, death 32.1%, and clinical improvement 9.1%. Among SLKT recipients, 36.3% remained Child A without ascites or encephalopathy at transplant. In the local KTA cohort (N = 34, median age 54 y, 79.4% male), none had ascites or hepatic encephalopathy before KTA, but 15 had clinical portal hypertension. Five-y post-KTA incidence of liver decompensation was 36.8%, and survival was 89.2%.

Conclusions.
SLKT may not be necessary for some patients with compensated cirrhosis needing kidney transplant. KTA is safe for selected patients with intact liver biochemical function, even with portal hypertension but without hepatic encephalopathy or ascites.
Geographical variation in implementation of the Pathways to Comorbidity Care program in Australian drug and alcohol services
Authors: Louie Eva , Giannopoulos Vicki , Uribe Gabriela , Wood Katie , Teesson Maree , Childs Steven , Baillie Andrew , Haber Paul S. , Morley Kirsten C. 
Published: October 2022

ABSTRACT

Aim:
Comorbid drug and alcohol and mental health disorders are highly prevalent. Significant gaps in service provision make this problem particularly difficult to address in regional Australia. The Pathways to Comorbidity Care (PCC) program was designed to improve management of comorbidity by outpatient drug and alcohol clinicians in New South Wales, Australia. This paper uses the Consolidated Framework for Implementation Research (CFIR) to evaluate variations in implementation outcomes across geographically diverse services.

Methods:
Twenty clinicians across three drug and alcohol services from metropolitan, outer metropolitan and regional geographic locations were engaged at multiple levels of influence (directors, managers, clinicians) during the implementation of the multimodal PCC training package. The CFIR guided the development of self-report measures and semi-structured interviews evaluating implementation of the PCC training, and disparities in implementation barriers and facilitators were determined.

Results:
Metropolitan clinicians identified less barriers than regional clinicians on several intervention characteristics (adaptability, complexity, design quality and packaging), as well as outer setting (peer pressure), inner setting (implementation climate, staff incentives, leadership engagement, available resources) and process (planning, opinion leaders, executing) domains. Regional clinicians evaluated the networks and communications construct more favourably.

Conclusions:
Specific barriers identified more strongly by regional clinicians included the importance of communication with local clinicians and leadership about the practicalities of incorporating the approach into routine practice (allocation of time, increased accessibility of implementation team). Metropolitan clinicians provided more favourable evaluations of the package design, implementation climate and specific implementation processes such as a clear and informative implementation plan.
Predator-mediated interactions through changes in predator home range size can lead to local prey exclusion
Authors: Beardsell Andréanne , Berteaux Dominique , Dulude-De-Broin Frédéric , Gauthier Gilles , Clermont Jeanne , Gravel Dominique , Bêty Joël 
Published: October 2022

1AbstractThe effects of indirect biotic interactions on species occurrence are difficult to quantify in the wild. In theory, the exclusion of a prey species can occur through the numerical and functional responses of a predator to another prey. Few studies assessed the relative effects of these responses on the net interaction strength between multiple prey sharing common predators, in part because empirically based multi-species functional response models are very rare. To investigate whether the presence of a prey species affects predation rates and population growth rate of another prey species, we used a multi-prey mechanistic model of predation along with a population matrix model. The predation model was parameterized using a combination of behavioral, demographic, and experimental data acquired in an arctic vertebrate community. It includes the arctic fox (Vulpes lagopus), a predator feeding primarily on small mammals as well as eggs of various bird species such as sandpipers and colonial nesting geese. Our results showed that the positive effects of the presence of a goose colony on sandpiper nesting success (due to the handling time of goose eggs by the predator) were outweighed by the negative effect of an increase in fox density. The numerical response of the arctic fox was driven by a reduction in home range size in the goose colony. As a result, the net interaction from the presence of geese was negative. Our results also showed that this interaction could lead to local exclusion of sandpipers over a range of adult sandpiper annual survival observed in the wild, which is coherent with previous observations of their co-distribution. Our approach takes into account diverse proximate mechanisms underpinning interaction strengths in a multi-prey system and generates novel insights on some of the predator behavioral responses that may influence prey coexistence (and the lack of) in vertebrate communities.
Biodiversity-ecosystem function relationships change in sign and magnitude across the Hill diversity spectrum
Authors: Roswell Michael , Harrison Tina , Genung Mark A. 
Published: October 2022

SummaryMotivated by accelerating anthropogenic extinctions, decades of biodiversity-ecosystem function (BEF) experiments show that ecosystem function declines with species loss from local communities. Yet, at the local scale, changes in species’ total and relative abundances are more common than species loss. The consensus best biodiversity measures are Hill numbers, which use a scaling parameter, ℓ, to emphasize rarer versus more common species. Shifting that emphasis captures distinct, function-relevant biodiversity gradients beyond species richness. Here, we hypothesized that Hill numbers that emphasize rare species more than richness does may distinguish large, complex, and presumably higher-functioning assemblages from smaller and simpler ones. In this study, we tested which values of ℓ produce the strongest BEF relationships in community datasets of ecosystem functions provided by wild, free-living organisms. We found that ℓ values that emphasized rare species more than richness does most often correlated most strongly with ecosystem functions. As emphasis shifted to more common species, BEF correlations were often weak and/or negative. We argue that unconventional Hill diversities that shift emphasis towards rarer species may be useful for describing biodiversity change, and that employing a wide spectrum of Hill numbers can clarify mechanisms underlying BEF relationships.
Temperature as a likely driver shaping global patterns in mineralogical composition in bryozoans: Implications for marine calcifiers under Global Change
Authors: Figuerola Blanca , Griffiths Huw J. , Krzeminska Malgorzata , Piwoni-Piorewicz Anna , Iglikowska Anna , Kuklinski Piotr 
Published: October 2022

AbstractThe Southern Ocean is showing one of the most rapid responses to human-induced global change, thus acting as a sentinel of the effects on marine species and ecosystems. Ocean warming and acidification are already impacting benthic species with carbonate skeletons, but the magnitude of these changes to species and ecosystems remains largely unknown. Here we provide the largest carbonate mineralogical dataset to date for Southern Ocean bryozoans, which are diverse, abundant and important as carbonate producers, thus making them excellent for monitoring the effects of ocean warming and acidification. To improve our understanding of how bryozoans might respond to ocean warming and acidification, we assess latitudinal and seafloor temperature patterns of skeletal mineralogy using bryozoan species occurrences together with temperature data for the first time. Our findings, combining new mineralogical data with published data from warmer regions, show that the proportions of high-Mg calcite and bimineralic species increase significantly towards lower latitudes and with increasing seawater temperature. These patterns are consistent with the hypothesis that seawater temperature is likely a significant driver of variations in bryozoan mineralogy at a global scale.
Acoustic and Neurophysiological Aspects of Lombard Effect
Authors: Castro Christian , Rivera Lucia Z , Prado Pavel , Cuadros Jhosmary , Cortés Juan Pablo , Weinstein Alejandro , Espinoza Victor , Zañartu Matías 
Published: October 2022

AbstractPurposeThis study aims to describe variations in acoustic and electroencephalography measures when speaking in the presence of background noise (Lombard effect) in participants with typical voice and normal hearing.MethodTwenty-one participants with typical voices and normal hearing uttered simple vocal tasks in three sequential background conditions: Baseline (in quiet), Lombard (in noise), and Recovery (five minutes after removing the noise). Acoustic and electroencephalography signals were recorded in all conditions. The noise used in the Lombard condition consisted of speech-shaped noise at 80 dB SPL sent by headphones. Acoustic measure, and ERP responses were analyzed.ResultsDuring the Lombard condition, the participants increased the intensity of their voice, accompanied by an increase in CPP, and a decrease in H1-H2. The cortical response was characterized by the increased N1-P2 complex amplitude of the ERP elicited by the subject’s own vocalizations in noise, The source localization showed neural activities in frontal and temporal cortical regions.ConclusionsThe variation in acoustic measures due to the Lombard Effect could be modulated by temporal, and cortical regions.
Nicotine Modifies Responding for Cocaine in a Concurrent Rodent Self-administration Model
Authors: Dawes Monica H. , Estave Paige M. , Albertson Stephen E. , Holleran Katherine M. , Jones Sara R. 
Published: October 2022

AbstractPrevailing preclinical models of cocaine use have not resulted in an FDA-approved treatment for cocaine use disorder, potentially due to a focus on cocaine use in isolation, which may not translate well to polysubstance use in clinical populations. Clinically, nicotine has been shown to increase cocaine’s potency and reinforcing efficacy, but some preclinical studies suggest that non-contingent nicotine exposure is not sufficient to alter cocaine self-administration in rats; therefore, this experiment examined if the addition of nicotine to the cocaine solution would alter self-administration behavior. Male Sprague Dawley rats (N=7) were trained to self-administer cocaine (0.75mg/kg/inf), and tested on a long access, fixed ratio 1 schedule of reinforcement (6 hour sessions, unlimited inf, 5 days), for cocaine alone (0.75mg/kg/inf), followed by cocaine and nicotine (0.75mg/kg/inf cocaine+0.03mg/kg/inf nicotine). Finally, rats responded on a progressive ratio schedule for varied doses of cocaine with and without concurrent nicotine at a consistent dose (1.5, 0.75, 0.375, 0.19mg/kg/inf cocaine± 0.03mg/kg/inf nicotine). Unexpectedly, under long access conditions, rats self-administering cocaine and nicotine responded less than for cocaine alone, and did not escalate responding. However, under progressive ratio conditions, responding for cocaine and nicotine was greater than responding for cocaine alone across low and moderate cocaine doses, and decreased at high cocaine doses, indicating a leftward shift in the dose response curve. Together, these data highlight the importance of evaluating multiple outcome measures in nicotine + cocaine paradigms, and suggest that concurrent self-administration of cocaine and nicotine results in greater motivated responding than for cocaine alone.
Impact of abiotic conditions on Fungal Diversity and Comparative analysis of Soil quality of two distinct locations
Authors: Chauhan Sindhushri , Ganure Parashuram , Dandin Chethan J. 
Published: October 2022

AbstractSoil fertility play a prominent role in biological sustenance in turn fungi are significant participants in bridging biotic and abiotic interactions between the components in the environment, and they involve in breakdown of organic/ inorganic materials during bioleaching/ bioconversion leading to bio-availability and thus recycling of nutrients. Local environmental factors (abiotic), such as the chemical and physical properties of the soil, greatly influence the composition of existing fungal communities and determine the diversity of soil fungi. A correlation study of the micro fungi found in ecologically two different regions (Karnataka state, India) of Uttara Kannada and Chitradurga districts. One being part of India’s Western Ghats, a biologically fertile ecosystem and the other being a dry, arid region of Deccan plateau with scanty rain fall. Soil samples were collected from various geographical locations in order to study and evaluate the role that certain soil physicochemical features play in fungi diversity. According to our findings, soil attributes (fertility) are related to the composition, richness, and diversity of fungi in soils and thus soil’s physico-chemical properties assessed were linked to fungal diversity measurements. This led us to indicate the role of abiotic factors effecting the fungal diversity in soil and their prominent role in soil fertility.Importance of the WorkThis work signifies the role of fungal diversity on soil fertility and the impact of abiotic and physico-chemical soil parameters on the same. Thus the work explores the importance of the each of these components and the wild fungal strain’s participation in value addition to their functional role in breakdown of organic/ inorganic materials during bioleaching/ bioconversion leading to bio-availability and thus recycling of nutrients. The work also highlights soil pH as one of key indicators to define the diversity of soil fungi and can provide a direct correlation between pH, bioconversion and fungal activity/ diversity. This work is first of a kind from southern India connecting the western ghat bio-diversity hot-spot fertile region with the neighbouring barren Bayaluseemae region of Karnataka State, South India with regards to abiotic factors, fungi and fertility.
Generalization and Transfer of Navigation Memory in Honeybees
Authors: Bullinger Eric , Greggers Uwe , Menzel Randolf 
Published: October 2022

AbstractFlying insects like the honeybee learn multiple features of the environment for efficient navigation. Here we ask whether the memory of such features is generalized to novel test conditions. Foraging bees from colonies located in 5 different home areas were tested in a common area for their search flights. Harmonic radar was used to track the search flights of the bees. The test area resembled partly or not at all the layout of landmarks in the respective home areas. Random search as the only guide for searching was excluded by two model calculations. The generalization and transfer effect was quantified by a partial least squares regression analysis of the guiding effect of the ground structures in the test area. Classification was performed with a support vector machine in order to account for optimal hyperplanes. A rank order of well separated clusters was found that partly resemble the graded differences between the ground structures of the home areas and the test area. We conclude that foragers guide their search flights by a generalization and transfer process that is based on their acquired navigation memory. The conclusion is discussed in the context of the learning and generalization process in an insect, the honeybee.SummaryStatementA new test procedure is applied to address the question whether a flying insect, the honeybee, uses a navigation memory that can be generalized to novel environmental conditions.
An EpCAM/Trop2 mechanostat differentially regulates collective behaviour of human carcinoma cells
Authors: Aslemarz Azam , Fagotto-Kaufmann Marie , Ruppel Artur , Fagotto-Kaufmann Christine , Balland Martial , Lasko Paul , Fagotto François 
Published: October 2022

AbstractEpCAM and its close relative Trop2 are well-known markers of carcinoma, but the potential role of these cell surface proteins in cancer metastasis remains unclear. They are known, however, to downregulate myosin-dependent contractility, a key parameter involved in cell adhesion and migration. We investigate here the morphogenetic impact of the high EpCAM and Trop2 levels typically found in epithelial breast cancer cells, using spheroids of MCF7 cells as an in vitro model. Intriguingly, EpCAM depletion stimulated spheroid cohesive spreading, while Trop2 depletion had the opposite effect. Combining cell biological and biophysical approaches, we demonstrate that while EpCAM and Trop2 both contribute to moderate cell contractility, their depletions differentially impact on the process of “wetting” a substrate, here both matrix and neighboring cells, by affecting the balance of cortical tension at cell and tissue interfaces. These distinct phenotypes can be explained by partial enrichment at specific interfaces. Differential distribution and antagonistic loss-of-function phenotypes are also observed in two other breast cancer cell lines with very different characteristics, suggesting that these are general properties of these two regulators. Our data are consistent with a simple model in which the EpCAM-Trop2 pair acts as a mechanostat that tunes local cortical tension, thus influencing a spectrum of adhesive and migratory behaviours.
The origins of haplotype 58 (H58) Salmonella enterica serovar Typhi
Authors: Carey Megan E. , Thi Nguyen To Nguyen , Hoang Nhu Tran Do , Dyson Zoe A. , Duy Pham Thanh , Mylona Elli , Nair Satheesh , Chattaway Marie , Baker Stephen 
Published: October 2022

AbstractAntimicrobial resistance (AMR) poses a serious threat to the clinical management of typhoid fever. AMR in Salmonella Typhi (S. Typhi) is associated with the H58 lineage, which arose comparatively recently before becoming globally disseminated. To better understand when and how this lineage emerged and became dominant, we performed detailed phylogenetic and phylodynamic analyses on contemporary genome sequences from S. Typhi isolated in the period spanning the emergence. Our dataset, which contains the earliest described H58 S. Typhi, indicates that the prototype H58 organisms were multi-drug resistant (MDR). These organisms emerged spontaneously in India in 1987 and became radially distributed throughout South Asia and then globally in the ensuing years. These early organisms were associated with a single long branch, possessing mutations associated with increased bile tolerance, suggesting that the first H58 organism was generated during chronic carriage. The subsequent use of fluoroquinolones led to several independent mutations in gyrA. The ability of H58 to acquire and maintain AMR genes continues to pose a threat, as extensively drug-resistant (XDR; MDR plus resistance to ciprofloxacin and third generation cephalosporins) variants, have emerged recently in this lineage. Understanding where and how H58 S. Typhi originated and became successful is key to understand how AMR drives successful lineages of bacterial pathogens. Additionally, these data can inform optimal targeting of typhoid conjugate vaccines (TCVs) for reducing the potential for emergence and the impact of new drug-resistant variants. Emphasis should also be placed upon the prospective identification and treatment of chronic carriers to prevent the emergence of new drug resistant variants with the ability to spread efficiently.
Statistical phasing of 150,119 sequenced genomes in the UK Biobank
Authors: Browning Brian L. , Browning Sharon R. 
Published: October 2022

AbstractThe first release of UK Biobank whole genome sequence data contains 150,119 genomes. We present an open-source pipeline for filtering, phasing, and indexing these genomes on the cloud-based UK Biobank Research Analysis Platform. This pipeline makes it possible to apply haplotype-based methods to UK Biobank whole genome sequence data. The pipeline uses BCFtools for marker filtering, Beagle for genotype phasing, and tabix for VCF indexing. We used the pipeline to phase 406 million single nucleotide variants on chromosomes 1-22 and X at a cost of 2,309 British pounds. The maximum time required to process a chromosome was 2.6 days. In order to assess phase accuracy, we modified the pipeline to exclude trio parents. We observed a switch error rate of 0.0016 on chromosome 20 in the White British trio offspring. If we exclude markers with nonmajor allele frequency < 0.1% after phasing, this switch error rate decreases by 80% to 0.00032.