bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kidney Transplantation From Deceased Donors With Vaccine-induced Immune Thrombocytopenia and Thrombosis: An Updated Analysis of the UK Experience
Authors: Greenhall George H.B. , Ushiro-Lumb Ines , Pavord Sue , Hunt Beverley J. , Sharma Hemant , Mehra Sanjay , Calder Francis , Kessaris Nicos , Kilbride Hannah , Jones Gareth , Motallebzadeh Reza , Arslan Zainab , Marks Stephen D. , Graetz Keith , Pettigrew Gavin J. , Torpey Nicholas , Watson Chris , Roy Debabrata , Casey John , Oniscu Gabriel C. , Currie Ian , Sutherland Andrew , Clancy Marc , Dor Frank , Willicombe Michelle , Sandhu Bynvant , Nath Jay , Weston Charles , van Dellen David , Roberts David J. , Madden Susanna , Ravanan Rommel , Forsythe John , Khurram Muhammad A. , Mohamed Ismail , Callaghan Chris J. 
Published: July 2022

Background.
The emergence and attendant mortality of vaccine-induced immune thrombocytopenia and thrombosis (VITT) as a consequence of vaccination against severe acute respiratory syndrome coronavirus 2 have resulted in some patients with VITT being considered as deceased organ donors. Outcomes after kidney transplantation in this context are poorly described. Because the disease seems to be mediated by antiplatelet factor 4 antibodies, there is a theoretical risk of transmission via passenger leukocytes within the allograft.

Methods.
We analyzed the experience of kidney transplantation from donors with VITT in the United Kingdom between January and June 2021. We followed-up all recipients of kidney-only transplants from donors with VITT to detect major postoperative complications or features of disease transmission and assess graft survival and function.

Results.
There were 16 kidney donors and 30 single kidney transplant recipients in our study period. Of 11 preimplantation biopsies, 4 showed widespread glomerular microthrombi. After a median of 5 mo, patient and graft survival were 97% and 90%, respectively. The median 3-mo estimated glomerular filtration rate was 51 mL/min/1.73 m2. Two recipients had detectable antiplatelet factor 4 antibodies but no evidence of clinical disease after transplantation. Major hemorrhagic complications occurred in 3 recipients, all of whom had independent risk factors for bleeding, resulting in the loss of 2 grafts. The involvement of VITT could not be completely excluded in one of these cases.

Conclusions.
The UK experience to date shows that favorable outcomes are possible after kidney transplantation from donors with VITT but highlights the need for ongoing vigilance for donor-related complications in these patients.
Yerbamate Tea Consumption: A Protective Factor in Parkinson Disease
Authors: Sáenz-Farret Michel , Salinas-Martínez Ana María , Zúñiga-Ramírez Carlos , Amorín-Costábile Ignacio , Maiola Ricardo , Mejía-Rojas Koni Katerin , Galeano Martha Sady , Velázquez Carolina , Ruiz Gabriela , Micheli Federico 
Published: July 2022

Introduction
Little is known about the association between Yerbamate (YMT) tea consumption and Parkinson disease (PD). We determined whether there was an association between YMT tea consumption and PD.

Methods
We conducted a multicenter case-control study in 3 countries (Argentina, Paraguay, and Uruguay). We applied a structured questionnaire about YMT tea consumption history. The survey also included information about factors previously associated with a decreased and increased risk of PD, apart from medical and demographic factors. Odds ratios and 95% confidence intervals were calculated using multivariate unconditional binary logistic regression analysis.

Results
We included 215 cases and 219 controls. The mean age of the cases was 65.6 ± 10.5 years and that of controls was 63.1 ± 10.5 years (P < 0.02). Years of YMT tea consumption, number of liters drunk per day, and amount of YMT used for preparing the infusion were similar between cases and controls (P > 0.05), but not the number of times the YMT was added into the container (P = 0.003) and the YMT tea concentration per serving (P = 0.02). The multivariate analysis showed that YMT tea concentration per serving lowered the risk for PD, independent of potential confounders (odds ratio, 0.62; 95% confidence interval, 0.47–0.84).

Conclusions
This multicenter study highlights the association between an environmental factor, the YMT tea drinking, and PD. Although more evidence from longitudinal studies is needed, the results obtained here points toward a protective effect of the YMT tea concentration per serving on PD.
Disruption of flour beetle microbiota limits experimentally evolved immune priming response, but not pathogen resistance
Authors: Prakash Arun , Agashe Deepa , Khan Imroze 
Published: July 2022

ABSTRACTHost-associated microbiota play a fundamental role in the training and induction of different forms of immunity, including inducible as well as constitutive components. However, direct experiments analysing the relative importance of microbiota during evolution of different immune functions are missing. We addressed this gap by using experimentally evolved lines of Tribolium castaneum that either produced inducible immune memory-like responses (immune priming) or constitutively expressed basal resistance (without priming), as mutually exclusive strategies against Bacillus thuringiensis infection. We disrupted the microbial communities in these evolved lines and estimated the impact on the beetle’s ability to mount a priming response vs basal resistance. Populations that had evolved immune priming lost the ability to mount a priming response upon microbiota disruption. Microbiota manipulation also caused a drastic reduction in their reproductive output and post-infection longevity. In contrast, in pathogen-resistant beetles, microbiota manipulation did not affect post-infection survival or reproduction. The divergent evolution of immune responses across beetle lineages was thus associated with divergent reliance on the microbiome. Whether the latter is a direct outcome of differential pathogen exposure during selection or reflects evolved immune functions remains unclear. We hope that our results will motivate further experiments to understand the mechanistic basis of these complex evolutionary associations between microbiota, host immune strategies, and fitness outcomes.
Paternal transmission of behavioural and metabolic traits induced by postnatal stress to the 5thgeneration in mice
Authors: Boscardin Chiara , Manuella Francesca , Mansuy Isabelle M 
Published: July 2022

ABSTRACTLife experiences and environmental conditions in childhood can change the physiology and behaviour of exposed individuals and in some cases, of their offspring. In rodent models, stress/trauma, poor diet and endocrine disruptors in a parent have been shown to cause phenotypes in the direct progeny, suggesting intergenerational inheritance. A few models also examined transmission to further offspring and suggested transgenerational inheritance, but such multi-generations inheritance is not well characterized. Our previous work in a mouse model of early postnatal stress showed that behaviour and metabolism are altered in the offspring of exposed males up to the 4thgeneration in the patriline and up to the 2ndgeneration in the matriline. The present study examined if in the patriline, symptoms can be transmitted beyond the 4thgeneration. Analyses of the 5thand 6thgeneration of mice revealed that altered risk-taking and glucose regulation caused by postnatal stress are still manifested in the 5thgeneration but are attenuated in the 6thgeneration. Some of the symptoms are expressed in both males and females, but some are sex-dependent and sometimes opposite. These results indicate that postnatal trauma can affect behaviour and metabolism over many generations, suggesting epigenetic mechanisms of transmission.
Efficient Human Germ Cell Specification from Stem Cells via Combinatorial Expression of Transcription Factors
Authors: Kramme Christian , Smela Merrick Pierson , Wolf Bennett , Fortuna Patrick R. , Brixi Garyk , Palepu Kalyan , Dong Edward , Adams Jessica , Bhat Suhaas , Koseki Sabrina , Tysinger Emma , Stan Teodora , Kohman Richie E. , Liu Songlei , Kobayashi Mutsumi , Shioda Toshi , Church George M. , Chatterjee Pranam 
Published: July 2022

AbstractGerm cells are the vehicle of human reproduction, arising early in embryonic development and developing throughout adult life until menopause onset in women. Primordial germ cells are the common precursors of germline cells in both sexes, undergoing sexual specification into oogonia or gonocytes which further develop into oocytes or spermatocytes during development. Methods for recapitulation of primordial germ cell and oogonia formation have been developed extensively in recent decades, but fundamental technical limitations in their methodologies, throughput, and yield limit their utilization. Recently, transcription factor (TF)-based methods for human primordial germ cell-like cell (hPGCLC) formation, mouse meiotic entry, and mouse oocyte maturation have demonstrated the feasibility of gene overexpression screening in identifying potent regulators of germ cell development. Here we screened 47 folliculogenesis-regulating TFs for their role in hPGCLC and oogonia formation, identifying DLX5, HHEX, and FIGLA whose individual overexpression enhances hPGCLC formation from hiPSCs. Additionally, we identify a set of three TFs, ZNF281, LHX8, and SOHLH1, whose combinatorial overexpression drives direct oogonia-like formation from hiPSCs in a four-day, feeder-free monolayer culture condition with additional feeder-free culture capabilities post-isolation. We characterize these TF-based germ cells via gene and protein expression analyses, and demonstrate their broad similarity to in vivo germ cells. Together, these results identify novel regulators of human germ cell development and establish new TF-based tools for human in vitro oogenesis research.
Transcriptome Variant Analysis of Noise Susceptibility in C57BL/6J Mice
Authors: Wang Siyue , Cai Jing , Kong Ligang , Xu Lei , Fan Zhaoming , Wang Haibo 
Published: July 2022

AbstractBackgroundSusceptibility to noise varies dramatically between mice of the same genetic background; however, the underlying molecular mechanism remains unknown.MethodsC57BL/6J (B6) mice of the same sex, age, and strain were exposed to noise of the same intensity and duration, and the auditory brainstem response (ABR) threshold was determined 48 h later. Some mice had significant hearing loss, while some did not; the ABR threshold measured in these two groups of mice was significantly different. The cochlea of the two groups of mice was dissected, and RNA sequencing and analysis were performed. Differentially expressed genes (DEGs) between the two groups were selected, Kyoto Encyclopedia of Genes and Genomes pathway analysis was performed, and protein–protein interaction network maps were listed.ResultsThis study showed that noise exposure of the same intensity and duration caused different degrees of hearing loss in C57BL/6J (B6) mice. This was the result of the up-regulation or down-regulation of many genes, such as Nop2, Bysl, Rrp9, Spsb1, Fbxl20, and Fbxo31. Changes in the transcriptome of these genes may affect cochlear susceptibility to noise.ConclusionThe DEGs identified in this experiment may provide more insight into protocols for gene therapy in the clinical practice of hearing loss.
Contexts enhance ratings of craving and psychophysiological responses of cue-reactivity in tobacco use disorder
Authors: Vollstädt-Klein Sabine , Nees Frauke , Wieland Alfred , Karl Damian , Diener Carsten , Smolka Michael N. , Flor Herta 
Published: July 2022

AbstractIntroductionConfrontation with smoking-related cues can provoke craving and relapse, even after long periods of abstinence. The context of these cues might be important for the elicitation of craving. In this study we examined the effects of social, physical and consumptive contexts on cue-reactivity in smokers using ratings and physiological measures.MethodA total of 22 smokers (12 male, 10 female) with tobacco use disorder (TUD) assessed using a cue-reactivity picture perception paradigm in a laboratory setting. Pictures of smoking in different physical and social contexts and of different phases of the smoking ritual were used. Ratings of cigarette craving, valence and arousal as well as startle reflex modulation, skin conductance responses and heart rate were assessed.ResultsWe observed an increased startle modulation in the bar versus control context and a stronger heart rate deceleration in the social versus neutral context. Social smoking induced more craving than neutral context, and cues from the beginning of the smoking ritual induced more craving than in the terminal phase. Social smoking context was rated as more arousing than neutral context, and cigarettes of the terminal phase of the smoking ritual were rated as least pleasant.ConclusionsThe results indicate that physical, social and consumptive contexts differentially affect cue-reactivity in TUD.ImplicationsCues in contexts lead to more pronounced indicators of craving than cues alone. Thus, contexts should be included in both, the assessment and treatment of TUD.
Mechanisms contributing to differential genetic risks for TREM2 R47H and R62H variants in Alzheimer’s Disease
Authors: Fancy Nurun , Willumsen Nanet , Tsartsalis Stergios , Khozoie Combiz , McGarry Aisling , Muirhead Robert C , Schneegans Eleonore , Davey Karen , Chau Vicky MN , Smith Amy M , Scotton William , Hardy John , Huh Dann , Matthews Paul M , Jackson Johanna S 
Published: July 2022

SUMMARYCoding variants in the microglial TREM2 ectodomain differentially (R47H> R62H) increase the risk of Alzheimer’s disease (AD). To define mechanisms responsible, we characterised neuropathology and transcriptomic responses in heterozygotes for these TREM2 variant alleles (TREM2var) and for common allele homozygotes (CV) in non-diseased and AD brain cortical tissue from 58 donors. Increased neurodegeneration in the TREM2var AD cortex was associated with genotype-dependent reductions in expression of Disease Associated Microglia (DAM) genes and increased expression of complement and Type I and II interferon pathways in microglia, phagocytosis and amyloid binding pathways and Disease Associated Astrocyte (DAA) genes in astrocytes, and growth factor, ubiquitination and apoptotic pathways in neurons. The microglial phenotypes and secondary differences in tissue β-amyloid deposition and in astrocyte and neuronal responses describe a variably partial loss of TREM2 function with variant alleles (R47H>R62H) relative to CV and suggest mechanisms that could account for differences in genetic risks conferred.
Application of Atraumatic Care Philosophy to Children in Hospitals a Literature Review
Authors: Ilmiasih Reni , Ningsih Nurul Syafitri 
Published: July 2022

ABSTRACTBackgroundHospitalization for children has an impact on physical and psychological problems for children and parents. Many interventions can be done to reduce stressors for children or parents in nursing using the philosophy of atraumatic care, but there are not many articles that provide specific identification in the realm of the philosophy of atraumatic care. This study aims to determine the Evidence-Based Practice Nursing (EBPN) atraumatic care carried out by nurses in hospitals.MethodThis research uses the literature study method. The Literature Study stages include problem identification, searching data in 4 databases, namely Pubmed (370 Journals), Proquest (295 Journals), Clinical Key (751 Journals), and Science Direct (573 Journals) with a total of 1,989 journals after that through the screening method, assessment of study quality using the JBI Critical Appraisal Tool which resulted in the final results with 18 journals, after that through data extraction and data analysis methods.ResultsFrom 18 intervention journals to prevent physical and psychological stress, including the use of Virtual Reality (VR), and the use of buzzy and interactive play. Intervention impact separation with the presence of parents and involvement in care. Interventions related to the impact of the foreign environment are by modifying the nurse’s uniform and car orientation of the care environment. Intervention in improving treatment control with PRISM-P and Progressive Muscle Relaxation (PMR) with Guided Imagery (GI).ConclusionAll interventions that are included in the 4 philosophies of atraumatic care, show the results of the effectiveness of the intervention on each principle of atraumatic care. This can be applied to patients, especially children and the elderly according to their condition.
Structural basis for ATG9A recruitment to the ULK1 complex in mitophagy initiation
Authors: Ren Xuefeng , Nguyen Thanh N. , Lam Wai Kit , Buffalo Cosmo Z. , Lazarou Michael , Yokom Adam Lee , Hurley James H. 
Published: July 2022

AbstractThe assembly of the autophagy initiation machinery nucleates autophagosome biogenesis, including in the PINK1- and Parkin-dependent mitophagy pathway implicated in Parkinson’s disease. The structural interaction between the sole transmembrane autophagy protein, ATG9A, and components of the ULK1 complex is one of the major missing links needed to complete a structural map of autophagy initiation. We determined the 2.4 Å x-ray crystallographic structure of the ternary structure of ATG9A C-terminal tail bound to the ATG13:ATG101 HORMA dimer, which is part of the ULK1 complex. We term the interacting portion of the extreme C-terminal part of the ATG9A tail the “HORMA dimer interacting region” (HDIR). This structure shows that the HDIR binds to the HORMA domain of ATG101 by β-sheet complementation such that the ATG9A tail resides in a deep cleft at the ATG13:ATG101 interface. Disruption of this complex in cells impairs damage induced PINK1/Parkin mitophagy mediated by the cargo receptor NDP52.
Accurate protein stability predictions from homology models
Authors: Valanciute Audrone , Nygaard Lasse , Zschach Henrike , Jepsen Michael Maglegaard , Lindorff-Larsen Kresten , Stein Amelie 
Published: July 2022

AbstractCalculating changes in protein stability (ΔΔG) has been shown to be central for predicting the consequences of single amino acid substitutions in protein engineering as well as interpretation of genomic variants for disease risk. Structure-based calculations are considered most accurate, however the tools used to calculate ΔΔGs have been developed on experimentally resolved structures. Extending those calculations to homology models based on related proteins would greatly extend their applicability as large parts of e.g. the human proteome are not structurally resolved. In this study we aim to investigate the accuracy of ΔΔG values predicted on homology models compared to crystal structures. Specifically, we identified four proteins with a large number of experimentally tested ΔΔGs and templates for homology modeling across a broad range of sequence identities, and selected three methods for ΔΔG calculations to test. We find that ΔΔG-values predicted from homology models compare equally well to experimental ΔΔGs as those predicted on experimentally established crystal structures, as long as the sequence identity of the model template to the target protein is at least 40%. In particular, the Rosettacartesian_ddgprotocol is robust against the small perturbations in the structure which homology modeling introduces. In an independent assessment, we observe a similar trend when using ΔΔGs to categorize variants as low or wild-type-like abundance. Overall, our results show that stability calculations performed on homology models can substitute for those on crystal structures with acceptable accuracy as long as the model is built on a template with sequence identity of at least 40% to the target protein.
A glycine zipper motif governs translocation of type VI secretion toxic effectors across the cytoplasmic membrane of target cells
Authors: Ali Jemal , Yu Manda , Sung Li-Kang , Cheung Yee-Wai , Lai Erh-Min 
Published: July 2022

ABSTRACTType VI secretion systems (T6SSs) can deliver diverse toxic effectors into eukaryotic and bacterial cells. Although much is known about the regulation and assembly of T6SS, the translocation mechanism of effectors into the periplasm and/or cytoplasm of target cells remains elusive. Here we use theAgrobacterium tumefaciensDNase effector Tde1 to unravel the mechanism of translocation from attacker to prey. We demonstrate that Tde1 binds to its adaptor Tap1 through the N-terminus, which harbours continuous copies of GxxxG motifs resembling the glycine zipper structure found in proteins involved in the membrane channel formation. Amino acid substitutions on G39xxxG43motif does not affect Tde1-Tap1 interaction and secretion but abolish its membrane permeability and translocation of its fluorescent fusion protein into prey cells. The data suggest that G39xxxG43governs the delivery of Tde1 into target cells by permeabilizing the cytoplasmic membrane. Considering the widespread presence of GxxxG motifs in bacterial effectors and pore-forming toxins, we propose that glycine zipper mediated permeabilization is a conserved mechanism used by bacterial effectors for translocation across target cell membranes.
A needle in a haystack: a new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)
Authors: González-Miguéns Rubén , Cano Emilio , Guillén-Oterino Antonio , Quesada Antonio , Lahr Daniel J.G. , Tenorio-Rodríguez Daniel , de Salvador-Velasco David , Velázquez David , Carrasco-Braganza María Isabel , Patterson R. Timothy , Lara Enrique , Singer David 
Published: July 2022

AbstractEnvironmental DNA-based diversity studies have increased in popularity with the development of high throughput sequencing technologies. This permits the potential simultaneous retrieval of vast amounts of molecular data from many different organisms and species, thus contributing to a wide range of biological disciplines. Environmental DNA protocols designed for protists often focused on the highly conserved small subunit of the ribosome gene, that does not permit species-level assignments. On the other hand, eDNA protocols aiming at species-level assignments allow a fine level ecological resolution and reproducible results. These protocols are currently applied to organisms living in marine and shallow lotic freshwater ecosystems, often in a bioindication purpose. Therefore, in this study, we present a species-level eDNA protocol, designed to explore diversity of Arcellinida (Amoebozoa: Tubulinea) testate amoebae taxa, that is based on mitochondrial cytochrome oxidase subunit I (COI). These organisms are widespread in lentic water bodies and soil ecosystems. We applied this protocol to 42 samples from peatlands, estuaries and soil environments, recovering all the infraorders in Glutinoconcha (with COI data), except for Hyalospheniformes. Our results revealed an unsuspected diversity in morphologically homogeneous groups such as Cylindrothecina, Excentrostoma or Sphaerothecina. With this protocol we expect to revolutionize the design of modern distributional Arcellinida surveys. Our approach involve a rapid and cost effective analysis of testate amoeba diversity living in contrasted ecosystems. Therefore, Arcellinida clade have the potential to be established as a model group for an array of theoretical and applied studies.