bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ex Vivo Surgical Removal Versus Conservative Management of Small Asymptomatic Kidney Stones in Living Donors and Long-term Kidney Transplant Outcomes
Authors: Yin Saifu , Tang Yangming , Zhu Mengli , Zeng Jun , Li Xingxing , Wu Lijuan , Wang Xianding , Song Turun , Lin Tao 
Published: July 2024

Background.
Donors with small asymptomatic kidney stones have been increasingly accepted because of organ shortages and advances in endoscopic urology. This study aims to evaluate and compare long-term living-donor kidney transplant outcomes following ex vivo surgical removal versus conservative management of donors’ gifted asymptomatic stones.

Methods.
Between January 2007 and December 2021, 119 kidney transplant recipients received stone-bearing kidneys, divided into the removal group (N = 63) and observation group (N = 56). We evaluated posttransplant stone events, urinary infections, kidney function, delayed graft function, length of hospital stay, and survival outcomes.

Results.
After a median follow-up of 75.5 mo, the removal group had a 10.9% lower absolute incidence of stone events (7/56 [12.5%] versus 1/63 [1.6%]; hazard ratio, 0.08; 95% confidence interval, 0.01-0.77) and a 14.3% lower absolute incidence of urinary infections (16/56 [28.6%] versus 9/63 [14.3%]; hazard ratio, 0.42; 95% confidence interval, 0.19-0.95) than the observation group. The removal group also showed superior kidney graft function. The 2 groups had comparable length of hospital stay (11.0 versus 12.0 d; P = 0.297) and exhibited similar delayed graft function incidence (1/56 [1.8%] versus 2/63 [3.2%]; P = 1.000) and urinary stricture incidence (1/56 [1.8%] versus 3/63 [4.8%]; P = 0.621). Graft survival (P = 0.350) and patient survival (P = 0.260) were comparable between 2 groups. Subgroup analyses in recipients who received kidneys with stones <4 mm also reported similar results.

Conclusions.
Ex vivo surgical removal might outperform conservative management for donors’ gifted asymptomatic kidney stones, improving long-term transplant outcomes and reducing stone events without increasing perioperative complications, even for stones <4 mm.
A genus-specific nsp12 region impacts polymerase assembly in Alpha- and Gammacoronaviruses
Authors: Hoferle Peter J. , Anderson Thomas K. , Kirchdoerfer Robert N. 
Published: July 2024

AbstractCoronavirus relevancy for human health has surged over the past 20 years as they have a propensity for spillover into humans from animal reservoirs resulting in pandemics such as COVID-19. The diversity within theCoronavirinaesubfamily and high infection frequency in animal species worldwide creates a looming threat that calls for research across all genera within theCoronavirinaesubfamily. We sought to contribute to the limited structural knowledge within theGammacoronavirusgenera and determined the structure of the viral core replication-transcription complex (RTC) from Infectious Bronchitis Virus (IBV) using single-particle cryo-EM. Comparison between our IBV structure with published RTC structures from otherCoronavirinaegenera reveals structural differences across genera. Usingin vitrobiochemical assays, we characterized these differences and revealed their differing involvement in core RTC formation across different genera. Our findings highlight the value of cross-generaCoronavirinaestudies, as they show genera specific features in coronavirus genome replication. A broader knowledge of coronavirus replication will better prepare us for future coronavirus spillovers.
Detection and decontamination of chronic wasting disease prions during venison processing
Authors: Milstein Marissa , Gresch Sarah C. , Schwabenlander Marc D. , Li Manci , Bartz Jason C. , Bryant Damani N. , Christenson Peter R. , Lindsey Laramie L. , Lurndahl Nicole , Oh Sang-Hyun , Rowden Gage R. , Shoemaker Rachel L. , Wolf Tiffany M. , Larsen Peter A. , Lichtenberg Stuart S. 
Published: July 2024

AbstractPrion diseases, including chronic wasting disease (CWD), are caused by prions, which are misfolded aggregates of normal cellular prion protein. Prions possess many characteristics that distinguish them from conventional pathogens, in particular, an extraordinary recalcitrance to inactivation and a propensity to avidly bind to surfaces. In mid to late stages of CWD, prions begin accumulating in cervid muscle tissues. These features collectively create scenarios where occupational hazards arise for workers processing venison and pose risks to consumers through direct prion exposure via ingestion and cross-contamination of food products. In this work, we show that steel and plastic surfaces used in venison processing can be directly contaminated with CWD prions and that cross-contamination of CWD-negative venison can occur from equipment that had previously been used with CWD-positive venison. We also show that several decontaminant solutions (commercial bleach and potassium peroxymonosulfate) are efficacious for prion inactivation on these same surfaces.
Sex-specific perching: Monitoring of artificial plants reveals dynamic female-biased perching behavior in the black soldier fly,Hermetia illucens(Diptera: Stratiomyidae)
Authors: Lemke Noah B , Rollinson Lisa N , Tomberlin Jeffery K 
Published: July 2024

AbstractArtificial perches are implemented by many companies that mass-rear the black soldier fly,Hermetia illucens,to create a more natural breeding environment or provide additional surface area for flies to rest. However, basic information related to perching behavior is lacking. This experiment tested the effect of adding perches to breeding cages on fitness and behavior. Perches were constructed from artificial leaves affixed to wooden dowels inserted into foam blocks, placed in the center of cage floors. The four treatment-levels had an added surface area of 0.00-, 0.04-, 0.26-, and 0.34-m2. Each 0.93-m3cage was supplied with 90 male and 90 female flies, and female thoraxes marked with acrylic paint. Beyond the tested range, a linear model suggests that 1.00-m2additional surface area can accommodate a 1.46-fold increase in flies without negative fitness impacts. Time-series analysis revealed; (a) females utilized perches 1.42-times more often than males across two trials; (b) especially in the morning where the difference could be as high as 2.56-times more than males; (c) this decreased to 0.20-1.57 times more females than males by 1600 h, and (d) this cyclical pattern repeated each day throughout the week with decreasing female-bias, starting from 2.41-times more females on Day 1 to 0.88-1.98-times more females than males on Day 6. These dynamics are likely due to the presence of male flies engaging in aerial contests near lamps providing light needed for mating, especially during early hours and early adulthood, aligning with prior knowledge of black soldier fly mating behavior.LAY SUMMARYFemale black soldier flies perch on artificial plants much more often than males, especially early in the day and early in their reproductive lives, times when males are competing with one another in aerial swarms.
We Are on the Verge of Breakthrough Cures for Type 1 Diabetes, but Who Are the 2 Million Americans Who Have It?
Authors: Smith Rebecca , Eisenberg Samara , Turner-Pfifer Aaron , Le Grand Jacqueline , Pincus Sarah , Omer Yousra , Wang Fei , Pyenson Bruce 
Published: July 2024

ABSTRACTTwo million Americans have Type 1 Diabetes. Innovative treatments have standardized insulin delivery and improved outcomes for patients, but patients’ access to such technologies depends on social determinants of health, including insurance coverage, proper diagnosis, and appropriate patient supports. Prior estimates of US prevalence, incidence, and patient characteristics have relied on data from select regions and younger ages and miss important determinants. By contrast, our research leveraged nationally representative administrative claims datasets to build a nuanced picture of the population with T1DM. Our work also supports future policy and research efforts with 2024, 2029, and 2033 projections of demographic and insurance coverage for people with T1DM.
Evaluation of SARS-CoV-2 antibody response between paired fingerprick (hemaPEN®) and venepuncture collected samples in children and adults
Authors: Mazarakis Nadia , Toh Zheng Quan , Nguyen Jill , Higgins Rachel A. , Rudge James , Whittle Belinda , Woudberg Nicholas J. , Devine Justin , Gooley Andrew , Lapierre Florian , Crawford Nigel W. , Tosif Shidan , Licciardi Paul V 
Published: July 2024

AbstractSerological surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies is important to monitor population COVID-19 immunity. Dried blood spots (DBS) are a valuable method for serosurveys, particularly in remote settings and in children. We compared the measurement of SARS-CoV-2 spike-specific IgG in paired blood samples collected by standard venepuncture (serum) and the hemaPEN® microsampling DBS device from children and adults using an established in-house ELISA. A total of 83 participants (10 months – 65 years of age) with paired serum and hemapen samples were included in the analysis; N=41 adults (36 COVID-positive and 5 COVID-negative) and N=42 children (37 COVID positive and 5 COVID-negative). Moderate-to strong-correlations between paired hemaPEN DBS eluates and serum SARS-CoV-2 IgG antibodies for RBD (r=0.9472, P<.0001) and S1 proteins (r=0.6892, P<.0001) were found. Similar results were observed in both adult and paediatric populations. SARS-CoV-2 spike-specific IgG in hemaPEN DBS samples remained stable for at least 35 weeks at room temperature. HemaPEN samples showed high specificity and sensitivity (100% and 89.89%, respectively) compared with serum. The use of the microsampling hemaPEN device for DBS sample collection is a feasible approach for assessing SARS-CoV-2 antibodies for serosurveillance studies, particularly in remote settings and in children.
Framework for Implementation of Poisson MaxSPRT Technique with Variations for Vaccine Safety
Authors: Samiullah Md , Buttery Jim , Clothier Hazel J. , Yin Jiying , Mallard John , Munakabayo Jeremiah , Kattan Gonzalo Sepulveda , Dimaguila Gerardo Luis 
Published: July 2024

AbstractFor direct, continuous, and sequential drug and vaccine safety surveillance, the Maximized Sequential Probability Ratio Test (MaxSPRT) was developed by the Centers for Disease Control and Prevention (CDC) (Kulldorff et al, 2011). Its predictive value and power to detect signals and the ability to monitor adverse events continuously have made it an emerging technique for vaccine adverse event surveillance. Moreover, being able to use a statistical method e.g. MaxSPRT in the absence of dose distributed denominator is a practical advantage for spontaneous reporting systems to function as stand-alone signal detection systems. In this paper, we present a comprehensive framework for implementing MaxSPRT for vaccine safety surveillance and Poisson data. We analysed the literature regarding MaxSPRT and sequential analysis. Our analysis revealed numerous variations of MaxSPRT, adapted to the specific requirements and objectives of the users. Variations are due to differing types of data and purpose of use, including whether used for epidemiological surveillance or for regulatory monitoring. This paper provides a comprehensive guide for organisations contemplating the implementation of MaxSPRT. It synthesises existing literature on MaxSPRT, identifies variations based on specific requirements, and describes an implementation framework. We offer a detailed explanation of the steps and challenges associated with the implementation of MaxSPRT on the adverse event following immunisation (AEFI) reporting database of Surveillance of Adverse Events Following Vaccination in the Community, Victoria, Australia (SAEFVIC), the largest jurisdictional reporting service by volume in Australia. It also proposes some techniques and measures to deal with the challenges associated with the implementation process.Key PointsMaxSPRT is a powerful method for ongoing vaccine surveillance, offering flexibility to adapt to various situations and data limitations. However, this flexibility can lead to challenges in implementation. Our paper simplifies the MaxSPRT method with clear explanations and step-by-step guidance, addressing potential issues and proposing solutions to improve its use in monitoring vaccine and drug safety.
Discovery and evaluation of novel biomarkers reveal dasatinib as a potential treatment for a specific subtype of Triple-Negative Breast Cancer
Authors: Ortega-Álvarez D , Tébar-García D , Casado-Pelaez M , Castillo-Agea E , Balibrea-Rull J , Olivares-Osuna D , Pérez-Parra D , Guardia C , Musulén E , Vinuesa-Pitarch E , Sánchez-López E , Postigo-Corrales F , Ballana E , Martínez-Cardús A , Margelí M , Esteller M , Fernández-Ruiz PL , Luengo-Gil G , Mereu E , Galán-Moya EM , Rodilla V 
Published: July 2024

AbstractTriple-negative breast cancer (TNBC) represents the most heterogeneous and aggressive subtype of breast carcinomas, characterized by the absence of clinical biomarkers (ERα, PR, and HER2) and the lack of targeted therapies. In this regard, several clinical trials have consistently failed to effectively stratify patients and identify specific treatments that elicit substantial responses. This study aims to pinpoint biomarkers expressed exclusively in the basal mammary epithelial compartment, facilitating a refined subclassification of this breast cancer subtype. Using computational analyses of single-cell RNA sequencing data, we have identified a list of genes associated with basal identity (BC-markers). Histological validation in 137 human samples has enabled us to categorize TNBC patients into BC-positive and BC-negative TNBC subtypes. Significantly, the presence of these markers correlates with a poorer prognosis in TNBC patients. Functional analyses have revealed a pivotal role forTAGLNin cell migration, likely influencing tumor aggressiveness. Further, we discovered that BC-marker expression is associated with the mesenchymal phenotype and increased sensitivity to the tyrosine kinase inhibitor dasatinib, particularly in BC-positive TNBC, suggesting novel therapeutic avenues. In our study,TAGLNemerged as a potential predictive biomarker for dasatinib responsiveness, offering new directions for personalized therapy for TNBC patients.
A Viral-Encoded Homologue of IPS-1 Modulates Innate Immune Signaling During KSHV Lytic Replication
Authors: Miranda Daniel , He Buyuan , Sanchez Julio C. , Sennatti Ashkon , Bontemps Johnny R. , Tran James T. , Tang Wilson S. , Sanchez David Jesse 
Published: July 2024

ABSTRACTModulation of innate immunity is critical for virus persistence in a host. In particular, viral-encoded disruption of type I interferon, a major antiviral cytokine induced to fight viral infection, is a key component in the repertoire of viral pathogenicity genes. We have identified a previously undescribed open reading frame within the Kaposi’s sarcoma-associated herpesvirus (KSHV) genome that encodes a homologue of the human IPS-1 (also referred to as MAVS) protein that we have termed viral-IPS-1 (v-IPS-1). This protein is expressed during the lytic replication program of KSHV, and expression of v-IPS-1 blocks induction of type I interferon upstream of the TRAF3 signaling node including signaling initiated via both the RLR and TLR3/4 signaling axes. This disruption of signaling coincides with destabilization of the cellular innate signaling adaptors IPS-1 and TRIF along with a concatenate stabilization of the TRAF3 protein. Additionally, expression of v-IPS-1 leads to decreased antiviral responses indicating a blot to type I interferon induction during viral infection. Taken together, v-IPS-1 is the first described viral homologue of IPS-1 and this viral protein leads to reprogramming of innate immunity through modulation of type I interferon signaling during KSHV lytic replication.
Unlocking data inKlebsiellalysogens to predict capsular type-specificity of phage depolymerases
Authors: Concha-Eloko Robby , Beamud Beatriz , Domingo-Calap Pilar , Sanjuán Rafael 
Published: July 2024

AbstractViral entry is a critical step in the infection process.Klebsiellaspp. and other clinically relevant bacteria often express a complex polysaccharide capsule that acts as a barrier to phage entry. In turn, mostKlebsiellaphages encode depolymerases for capsule removal. This virus-host arms race has led to extensive genetic diversity in both capsules and depolymerases, complicating our ability to understand their interaction. This study exploits the information encoded inKlebsiellaprophages to model the interplay between the bacteria, the prophages, and their depolymerases, using a graph neural network and a sequence clustering-based method. Both approaches showed significant predictive ability for prophages capsular tropism and, importantly, were transferrable to lytic phages. In addition to creating a comprehensive database linking depolymerase sequences to their specific targets, this study demonstrates the predictability of phage-host interactions at the subspecies level, providing new insights for improving the therapeutic and industrial applicability of phages.
Laboratory experiments suggests limited impact of increased nitrogen deposition on snow algae blooms
Authors: Almela Pablo , Elser James J. , Giersch J. Joseph , Hotaling Scott , Rebbeck Victoria , Hamilton Trinity L. 
Published: July 2024

AbstractSnow algal blooms decrease snow albedo and increase local melt rates. However, the causes behind the size and frequency of these blooms are still not well understood. One factor that is likely contributing is nutrient availability, specifically nitrogen (N) and phosphorus (P). However, the nutrient requirements of the taxa responsible for these blooms is not known. Here, we assessed the growth of three commercial strains of snow algae under 24 different nutrient treatments that varied in both absolute and relative concentrations of N and P. After 38 days of incubation, we measured total biomass and cell size and estimated their effective albedo reduction surface (EARS). Snow algal strains tended to respond similarly and achieved bloom-like cell densities over a wide range of NP conditions. However, the molar ratio of N:P at which maximum biomass was achieved was between 4 and 7. Our data indicate a high requirement for P for snow algae and suggest that additional N inputs into the ecosystem may not significantly impact the productivity and abundance of snow algae blooms. This highlights P availability as a critical factor influencing the frequency and extent of snow algae blooms and their potential contribution to snow melt through altered albedo.
Population responses to environmental stochasticity are primarily driven by survival-reproduction trade-offs and mediated by aridity
Authors: Santos Gabriel Silva , Yang Xianyu , L Gascoigne Samuel J , Compagnoni Aldo , Dias André T.C. , Tuljapurkar Shripad , Kajin Maja , Salguero-Gómez Roberto 
Published: July 2024

SummaryForecasting responses of natural populations to increasingly stochastic environments is a major challenge in Ecology and Conservation Biology. We now know that populations can modulate how their vital rates (e.g., survival, reproduction) change through time to minimise the negative impacts of environmental stochasticity. However, despite the important analytical and theoretical advances that have led to this knowledge, we still do not know (1) how much this ability of natural populations to buffer against environmental stochasticity can vary in nature, nor (2) the drivers of these strategies, with likely candidates including the environmental regimes themselves, as well as the life history traits and phylogenetic ancestry of the species of interest. To address these questions, we parameterised a Bayesian generalised linear mixed model with high-resolution vital rate data from 134 natural populations across 89 species of plants and animals. We show that population responses to environmental stochasticity vary three orders of magnitude along a ‘demographic buffering continuum’. Furthermore, the position of a given population along said continuum is predicted by a survival-reproduction trade-off and by the degree of aridity the population experiences. Our findings open a promising avenue of research to improve ecological forecasts and management of natural populations in the Anthropocene.
Multiscale mechanics drive functional maturation of the vertebrate heart
Authors: Andrews Toby G R , Cornwall-Scoones Jake , Ramel Marie-Christine , Gupta Kirti , Briscoe James , Priya Rashmi 
Published: July 2024

AbstractHow simple tissue primordia sculpt complex functional organs, robustly and reproducibly, remains elusive. As the zebrafish embryo grows into a larva, to improve its heart function, the embryonic myocardial wall transforms into an intricate 3D architecture, composed of an outer compact layer enveloping an inner layer of multicellular trabecular ridges. How these tissue layers acquire their characteristic form suited for their function remains an open question. Here, we find that multiscale mechanochemical coupling and an emergent tissue-scale morphological transition steer functional maturation of the developing zebrafish heart. Single-celled trabecular seeds recruit outer compact layer cells to mature into clonally heterogenous multicellular ridges, thereby amplifying cardiac contractile forces. In response, remaining compact layer cells are stretched, which impedes their further recruitment, thereby constraining trabecular ridge density. Concomitantly, Notch-dependent actomyosin dampening triggers a sharp transition in myocardial tissue area, activating rapid organ growth that expands blood filling capacity. Thus, multiscale self-organizing interactions optimize heart size and contractile efficiency to support embryonic life.
Structures of the multi-domain oxygen sensor DosP: remote control of a c-di-GMP phosphodiesterase by a regulatory PAS domain
Authors: Wu Wenbi , Kumar Pankaj , Brautigam Chad A. , Tso Shih-Chia , Baniasadi Hamid R. , Kober Daniel L. , Gilles-Gonzalez Marie-Alda 
Published: July 2024

AbstractThe heme-based direct oxygen sensor DosP degrades c-di-GMP, a second messenger nearly unique to bacteria. In stationary phaseEscherichia coli, DosP is the most abundant c-di-GMP phosphodiesterase. Ligation of O2to a heme-binding PAS domain (hPAS) of the protein enhances the phosphodiesterase through an allosteric mechanism that has remained elusive. We determined six structures of full-length DosP in its aerobic or anaerobic conformations, with or without c-di-GMP. DosP is an elongated dimer with the regulatory heme and phosphodiesterase separated by nearly 180 Å. In the absence of substrate, regardless of the heme status, DosP presents an equilibrium of two distinct conformations. Binding of substrate induces DosP to adopt a single, ON-state or OFF-state conformation depending on its heme status. Structural and biochemical studies of this multi-domain sensor and its mutants provide insights into signal regulation of second-messenger levels.
Supervised Automation of Cell Counting in Confocal Microscopic Cochlear Imaging Datasets Using Macro in Imaris
Authors: Rahman Muhammad Taifur , Khan Nashwaan Ali , Mokbul Mobin Ibne , Razu Ibrahim , Fatima Shakila Mahmuda , Lira Samia Sultana , Garcia Cristina , Eckard Peter , Hansen Marlan R 
Published: July 2024

SummaryAnalyzing confocal microscopic data of biological samples using the Imaris software poses challenges due to its time-consuming nature involving tedious multiple steps and possibility of human errors. Here, we developed a supervised automation protocol to minimize manual input in cell and spot counting on confocal images obtained from mouse cochlear sections. The protocol increases efficiency by incorporating image recognition and object-oriented macros. Moreover, the protocol being adaptable allows scientists in diverse other fields to customize it for their specific needs.Graphical Abstract