bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous Heart-kidney Transplant With Planned Delayed Implantation of the Kidney Graft After Ex Vivo Perfusion
Authors: Lutz Andrew J. , Nagaraju Santosh , Sharfuddin Asif A. , Garcia Jose P. , Saleem Kashif , Mangus Richard S. , Goggins William C. 
Published: June 2023

Background.
Simultaneous heart-kidney transplant (SHK) is an established option for patients with severe heart failure and chronic kidney disease. Recent studies in simultaneous liver-kidney transplantation demonstrate favorable outcomes achieved by delaying implantation of the kidney for over 24 h. This report describes a case series of consecutive patients listed for SHK who had planned delayed implantation of the kidney graft.

Methods.
This case series represents a retrospective analysis of SHK patients extracted from the transplant database at a single center.

Results.
There were 7 patients who underwent SHK during the study period. In all cases, kidney grafts were maintained on hypothermic ex vivo pulsatile perfusion for delayed implantation (mean cold ischemia 53 h [range, 31–69]). The first 5 patients had 100% 1-y heart and kidney graft survival with good function. Patient 6 was unstable on extracorporeal membrane oxygenation post–heart transplant. The kidney was implanted at 69 h, and the patient died soon thereafter. Patient 7 was also unstable on extracorporeal membrane oxygenation after heart transplant. The decision was made to implant the kidney into a backup kidney recipient. The heart transplant recipient subsequently died several days later, whereas the kidney was successfully transplanted in the alternate candidate.

Conclusions.
This case series highlights the potential utility of delayed kidney implantation in SHK patients. SHK with delayed renal transplant may provide an improved physiologic environment for renal transplant, which may result in improved early renal graft function. Delayed kidney transplant also provides the opportunity to transplant the kidney graft into an alternate candidate.
OrthoFx Rescue Aligner: A Mid-Course Correction during Orthodontic Clear Aligner Therapy
Authors: Chwa Evan , Alqazaha Tamara , Sanchez Flavio José Castelli , Kusnoto Budi , Elnagar Mohammed H. 
Published: June 2023

AbstractOver the last few decades, there has been a significant increase in the number of patients seeking orthodontic treatment due to the esthetics of clear aligners. However, clear aligners rely on accurate tracking and if not achieved, can lead to frustrations.Data from 60 comprehensive clear aligner patients were analyzed. The OrthoFX Rescue Aligner intervened in the cases that were not tracking to get the patient back on track. The Rescue Aligner is designed to quickly and cost-effectively correct treatment lag up to a four to eight weeks deviation. The hyper elastic rescue aligners could produce movement ranges up to at least 0.5mm per tray.This retrospective study indicates the potential for further prospective clinical and laboratory studies with improved methods such as 3D superimposition, remote monitoring as well as calibrated inter and intra observer visual inspection methods for better assessment on tracking of each tooth per aligner.
Sub-Concussive Head Impacts From Heading Footballs Do Not Acutely Alter Brain Excitability As Compared to a Control Group
Authors: Hamel R. , Waltzing B. M. , Massey T. , Blenkinsop J. , McConnell L. , Osborne K. , Sesay K. , Stoneman F. , Carter A. , Maaroufi H. , Jenkinson N. 
Published: June 2023

AbstractBackgroundRepeated sub-concussive head impacts are a growing brain health concern, but the possible mechanisms of trauma and plausible biomarkers remain elusive. One impediment is the lack of an experimental model to study the effects of sub-concussive head impacts on the brain.ObjectivesThis work’s objective was to provide an experimental model to study the acute effects of sub-concussive head impacts on the brain. To do so, this study aimed to replicate previous work from Di Virgilio et al. (2016) showing that head impacts from heading footballs acutely alter brain excitability by increasing corticomotor inhibition.MethodsScores from the Rivermead Post-Concussion Questionnaire and measurements of cortical silent period (CSP) duration – obtained using transcranial magnetic stimulation to assess corticomotor inhibition in the central nervous system – were taken before and after participants performed 20 football headings (Headings; n = 30) or control (Control; n = 30).ResultsThe results revealed increased headaches and dizziness symptoms in the Headings as compared to the Control group, revealing the qualitative experience of head impacts. The results then revealed that CSP duration similarly lengthened in both the Headings and Control groups, suggesting that head impacts did not cause the increased corticomotor inhibition.ConclusionsThe results show that head impacts from football headings did not acutely alter corticomotor inhibition as compared to a control group that did not experience head impacts, suggesting that excitability changes do not reflect acute sub-concussive brain injuries. Nonetheless, this work suggests that football headings can be used as an experimental model to study the effects of sub-concussive head impacts on brain health. Future work could use the present procedures to investigate additional biomarkers of brain injury.
Accurate identification of structural variations from cancer samples
Authors: Li Le , Hong Chenyang , Xu Jie , Chung Claire Yik-Lok , Leung Alden King-Yung , Boncan Delbert Almerick T. , Cheng Lixin , Lo Kwok-Wai , Lai Paul B. S. , Wong John , Zhou Jingying , Cheng Alfred Sze-Lok , Chan Ting-Fung , Yue Feng , Yip Kevin Y. 
Published: June 2023

AbstractStructural variations (SVs) are commonly found in cancer genomes. They can cause gene amplification, deletion, and fusion, among other functional consequences. With an average read length of hundreds of kilobases, nano-channel-based optical DNA mapping is powerful in detecting large SVs. However, existing SV calling methods are not tailored for cancer samples, which have special properties such as mixed cell types and sub-clones. Here we propose the COMSV method that is specifically designed for cancer samples. It shows high sensitivity and specificity in benchmark comparisons. Applying to cancer cell lines and patient samples, COMSV identifies hundreds of novel SVs per sample.
Measuring Social Determinants of Health in theAll of UsResearch Program: Technical Document
Authors: Tesfaye Samantha , Cronin Robert , Lopez-Class Maria , Chen Qingxia , Foster Christopher S. , Gu Callie , Guide Andrew , Hiatt Robert A. , Johnson Angelica , Joseph Christine LM , Khatri Parinda , Lim Sokny , Litwin Tamara R. , Munoz Fatima A. , Ramirez Andrea , Sansbury Heather , Schlundt David G. , Viera Emma N. , Dede-Yildirim Elif , Clark Cheryl R. 
Published: June 2023

AbstractBackgroundTo advance precision medicine and improve population health, theAll of UsResearch Program aims to collect data, including a survey of social determinants of health (SDOH), from over 1 million participants. This report (1) outlines the process used to construct theAll of UsSDOH survey and (2) presents the psychometric characteristics and scoring recommendations for SDOH survey measures.MethodsA consensus process was used to select a definition of SDOH and conceptual frameworks to develop inclusion and exclusion criteria and priorities for construct consideration. Cognitive interviewing was used to provide an assessment of SDOH survey item performance in English and Spanish.Scales and scored items were constructed in alignment with validated literature. Item non-response was calculated, and Cronbach ‘s alpha was used to analyze the psychometric properties of each scale, overall and by demographic characteristics. Multivariable logistic regression models were used to examine if demographic categories were associated with item non-response.ResultsTwenty-nine percent (N=117,783) ofAll of Usparticipants submitted SDOH survey data by June 30, 2022. Among those who provided any SDOH survey data, item non-response was infrequent, with most scales having less than 5% incalculable scores due to item non-response. Item non-response varied most along the lines of racial identity, educational attainment, and the language in which the survey was administered (Spanish or English). In our regression models, for most scales, patterns of missing data due to item non-response were seen by racial identity, educational attainment, income level, and age. Internal consistency reliability was greater than 0.80 for almost all scales, with variability by racial identity, educational attainment, and the language of survey administration.ConclusionThe SDOH survey demonstrated good to excellent reliability across several measures of SDOHs and within multiple population groups that are underrepresented in biomedical research. Bias due to survey non-response and item non-response should be monitored and addressed as the survey is fielded more completely.
Evidence for deliberate burial of the dead byHomo naledi
Authors: Berger Lee R , Makhubela Tebogo , Molopyane Keneiloe , Krüger Ashley , Randolph-Quinney Patrick , Elliott Marina , Peixotto Becca , Fuentes Agustín , Tafforeau Paul , Beyrand Vincent , Dollman Kathleen , Jinnah Zubair , Gillham Angharad Brewer , Broad Kenneth , Brophy Juliet , Chinamatira Gideon , Dirks Paul H. M. , Feuerriegel Elen , Gurtov Alia , Hlophe Nompumelelo , Hunter Lindsay , Hunter Rick , Jakata Kudakwashe , Jaskolski Corey , Morris Hannah , Pryor Ellie , Mpete Maropeng , Roberts Eric , Smilg Jacqueline S. , Tsikoane Mathabela , Tucker Steven , van Rooyen Dirk , Warren Kerryn , Wren Colin D. , Kissel Marc , Spikins Penny , Hawks John 
Published: June 2023

AbstractIn this study we describe new results of excavations in the Dinaledi Subsystem of the Rising Star cave system, South Africa. In two areas within the Hill Antechamber and the Dinaledi Chamber this work uncovered concentrations of abundantHomo naledifossils including articulated, matrix-supported skeletal regions consistent with rapid covering by sediment prior to the decomposition of soft tissue. We additionally re-examine the spatial positioning of skeletal material and associated sediments within the Puzzle Box area, from which abundantH. nalediremains representing a minimum of six individuals were recovered in 2013 and 2014. Multiple lines of evidence exclude the hypothesis that skeletal remains from these three areas come from bodies that decomposed on the floor of the chamber or within a shallow depression prior to burial by sediments. The spatial positioning of skeletal material, the topography of the subsystem, and observations on sediments within and surrounding features exclude the hypothesis that rapid burial by sediment was a result of gravity-driven slumping or spontaneous movement of sediments. We present a minimal hypothesis of hominin cultural burial and test the evidence from all three areas, finding that this hypothesis is most compatible with the pattern of evidence. These results suggest that mortuary behavior including cultural burial was part of the repertoire ofHomo naledi.
Identification of differentially expressed genes and enriched pathways in inflammatory bowel disease using bioinformatics and next generation sequencing data analysis
Authors: Vastrad Basavaraj , Vastrad Chanabasayya 
Published: June 2023

AbstractInflammatory bowel disease (IBD) is the most common chronic digestive disorders and inflammation in the gastrointestinal tract globally that is characterized by episodes of abdominal pain, diarrhea, bloody stools and weight loss. However, the pathophysiologic mechanisms of IBD have not been thoroughly investigated. To explore potential targets for treatment of IBD, we reorganized and analyzed next generation sequencing (NGS) dataset (GSE186507). The R package DESeq2 tool was used to screen for differentially expressed genes (DEGs) between IBD and normal control samples. We used the g:Profiler database to perform Gene Ontology (GO) enrichment analysis and the REACTOME for pathway enrichment analysis. Protein-protein interaction (PPI) network construction and module analysis were performed to elucidate molecular mechanisms of DEGs and screen hub genes. Then miRNA-hub gene regulatory network and TF-hub gene regulatory network of these hub genes were visualized by Cytoscape. We also validated the identified hub genes via receiver operating characteristic (ROC) curve analysis. A total of 957 DEGs (478 up regulated genes and 479 down regulated genes) were detected in NGS dataset. And they were mainly enriched in the terms of multicellular organismal process, response to stimulus, GPCR ligand binding and immune system. Based on the data of PPI network, miRNA-hub gene regulatory network and TF-hub gene regulatory network the top hub genes were ranked, including IL7R, ERBB2, SMAD1, RPS26, TLE1, HNF4A, CDKN1A, SRPK1, H3C12 and SFN. In conclusion, the identified DEGs, particularly the hub genes, strengthen the understanding of the development and progression of IDB, and certain novel genes might be used as candidate target molecules to diagnose, monitor and treat IDB.
A guide to computational cotranscriptional folding featuring the SRP RNA
Authors: Badelt Stefan , Lorenz Ronny 
Published: June 2023

AbstractAlthough RNA molecules are synthesized via transcription, little is known about the general impact of cotranscriptional folding in vivo. We present different computational approaches for the simulation of changing structure ensembles during transcription, including interpretations with respect to experimental data from literature. Specifically, we analyze different mutations of the E.coli SRP RNA, which has been studied comparatively well in previous literature, yet the details of which specific metastable structures form, as well as when they form are still under debate. Here, we combine thermodynamic and kinetic, deterministic and stochastic models with automated and visual inspection of those systems to derive the most likely scenario of which substructures form at which point during transcription. The simulations do not only provide explanations for present experimental observations, but also suggest previously unnoticed conformations that may be verified through future experimental studies.
A similarity matrix for preserving haplotype diversity among parents in genomic selection
Authors: Musa Abdulraheem A. , Reinsch Norbert 
Published: June 2023

AbstractMendelian sampling variability (MSV), determined by the heterozygosity and linkage phases of the parental haplotypes, quantifies the chance of producing offspring with high breeding values. Recent genomic selection criteria combine expected breeding values with MSV to maximize the chance of producing offspring with exceptional breeding values. These criteria, however, tend to select similar parents with high variability potential. Therefore, a measure of haplotype similarity is required to avoid this tendency and preserve diversity. Here, we derive this measure by pairing all potential gametes from two parents based on their segregating marker patterns. Subsequently, a similarity measure between two parents is defined as the absolute value of the covariance between the additive values of the paired gametes on a chromosome. A similarity matrix with absolute covariances as off-diagonal elements and MSVs as diagonal elements summarizes all pairwise similarities between parents. A parent’s similarity to itself equals its MSV. High similarity indicates that the parents share many heterozygous markers with large effects on a trait in the same linkage phase. The concept generalizes to multiple chromosomes, an aggregate genotype with multiple traits, and similarity between zygotes. We demonstrated the properties of the similarity matrix using empirical data. Through simulations, we showed that incorporating the matrix into genomic selection preserves up to 1630% more genetic variability and yields up to 7% more genetic gain relative to index selection in the long term. Although further research is needed, our results show that including similarity matrices preserves haplotype diversity and improves long-term genomic selection.
NINJ1 mediates plasma membrane rupture through formation of nanodisc-like rings
Authors: David Liron , Borges Jazlyn P , Hollingsworth L. Robert , Volchuk Allen , Jansen Isabelle , Steinberg Benjamin E , Wu Hao 
Published: June 2023

SUMMARYThe membrane proteins Ninjurin1(NINJ1) and Ninjurin2 (NINJ2) are upregulated by nerve injury to increase cell adhesion and promote axonal growth in neurons. NINJ1, but not NINJ2, has also been shown to play an essential role in pyroptosis by promoting plasma membrane rupture downstream of gasdermin D (GSDMD) pore formation, as well as in lytic cell death mediated by other pathways. Recombinant NINJ1 and NINJ2 purified in detergent show irregular rings of various diameters as well as curved filaments. While NINJ1 and NINJ2 both formed ring-like structures when mixed with liposomes, strikingly, only NINJ1, but not NINJ2, ruptures liposome membranes, leading to their dissolution. Because of the better feasibility, we determined the cryo-EM structure of NINJ1 ring segments from detergent by segmenting the irregular rings into shorter fragments. Each NINJ1 subunit contains a transmembrane (TM) helical hairpin (α3 and α4) that likely mediates NINJ1 membrane localization, as well as the side-by-side interaction between adjacent subunits. There are two extracellular domain amphipathic helices (α1 and α2), among which α1 crosses over to the neighboring subunit at the outside facing surface of the ring, to link NINJ1 subunits together into chains. As such, the inner face of the rings is hydrophobic whereas the outer face of the rings is hydrophilic and should repel membranes. Live cell imaging of NINJ1-deficient THP-1 cells reconstituted with NINJ1-eGFP uncovers the pinching off of NINJ1 rings from the cell surface and the loss of NINJ1 to the culture supernatant in oligomerized forms upon inflammasome activation. Formation of rings is also confirmed by super-resolution imaging of endogenous NINJ1 using anti-NINJ1 antibody. These data suggest that membrane insertion of amphipathic helices and formation of rings with a hydrophilic outer surface underlie the mechanism for NINJ1 to pinch off membranes as if it were a nanodisc-forming amphipathic polymer, leading to membrane rupture and lysis during cell death.
Improving anxiety research: novel approach to reveal trait anxiety through summary measures of multiple states
Authors: Varga Zoltán K , Pejtsik Diána , Tóth Máté , Balogh Zoltán , Aliczki Manó , Szente László , Balla Gyula Y , Kontra Levente , Eckert Zsófia , Szebik Huba , Borhegyi Zsolt , Mikics Éva 
Published: June 2023

AbstractThe reliability and validity of preclinical anxiety testing is essential for translating animal research into clinical use. However, the commonly used anxiety tests lack inter-test correlations and face challenges with repeatability. While translational animal research should be able to capture stable individual anxiety traits, the current approach employs a single type of test at a single time that only measures transient states of animals, heavily influenced by experimental conditions. Here, we propose a validated, optimized test battery capable of reliably capturing trait anxiety in rats and mice of both sexes. Instead of developing novel tests, we combined widely used tests (elevated plus-maze, open field and light-dark test) to provide instantly applicable adjustments for better predictive validity. We repeated these tests three times to capture behaviour across multiple challenges, which we combined to generate summary measures (SuMs). Our approach resolved between-test correlation issues and provided better predictions for subsequent outcomes under anxiogenic conditions or fear conditioning. SuMs were also able to reveal differences in anxiety in an etiological stress model. Finally, we tested our method’s efficacy in discovering anxiety-related molecular pathways through RNA sequencing of the medial prefrontal cortex. Using SuMs, we identified four-times more molecular correlates of trait anxiety as compared to transient anxiety states, pointing out novel functional gene clusters. Furthermore, 16% of these molecular correlates of anxiety were replicated in amygdalar samples, as well. In summary, we provide a novel approach to capture trait anxiety in rodents, offering improved predictions for potential therapeutic targets for personalized medicine.
A novel monocarboxylate transporter involved in 3-hydroxykynurenine transport for ommochrome coloration
Authors: Uchiyama Hirosumi , Takasu Yoko , Moriyama Minoru , Yoshitake Kazutoshi , Uchiyama Hironobu , Iizuka Tetsuya , Uchino Keiro , Okude Genta , Banno Yutaka , Kuwazaki Seigo , Yamamoto Kimiko , Yajima Shunsuke , Sezutsu Hideki , Tamura Toshiki , Futahashi Ryo , Osanai-Futahashi Mizuko 
Published: June 2023

AbstractOmmochromes are widespread pigments in invertebrates utilized for screening pigments in compound eyes and for reddish coloration in epidermis and wings. Ommochromes are derived from 3-hydroxykynurenine (3OHK), which is incorporated into cells from hemolymph or synthesized from tryptophan within cells. While the synthetic pathway from tryptophan to 3OHK has been well characterized, the gene responsible for cellular uptake of 3OHK has been poorly understood. In the silkwormBombyx mori, adult compound eyes and eggs contain a mixture of ommochrome pigments. By using positional cloning method, we found that a novel monocarboxylate transporter, 3-hydroxykynurenine transporter (3OHKT), is responsible for the recessive mutantmaternal brown of Tsujita(b-t) ofB. mori. Inb-tmutant, the color of the eggs is light brown, whereas the color of the compound eyes is normal, and we identified a 2-kb deletion in3OHKTgene. TALEN-mediated knockout of3OHKTgene produced the same coloration phenotype asb-tmutant, and the complementation test betweenb-tmutant and3OHKTknockout strain proved that3OHKTis responsible forb-tphenotype. 3OHKT protein was localized in the cellular membrane, and LC-MS analysis indicated that the uptake of 3OHK from hemolymph into the ovary was suppressed in theb-tmutant. Moreover, we confirmed that3OHKTgene is specifically expressed at the reddish region and the time of pigmentation in the pupal wing of nymphalid butterflies. RNA interference of3OHKTprevented reddish pigmentation in wings, highlighting its general involvement in ommochrome-based pigmentation other than compound eyes.SignificanceOmmochromes are widely distributed pigments in invertebrates and are synthesized from intracellular tryptophan or 3-hydroxykynurenine (3OHK). Ommochrome-based red markings on butterfly wings are often used for sexual selection, warning colors and mimicry. Most genes involved in the ommochrome synthesis pathway have been elucidated from analyses of eye color mutants inDrosophila. However, this study reveals that the ommochrome synthesis pathway has a different genetic repertoire depending on the tissues, and that the novel monocarboxylate transporter identified in this study has a major role in ommochrome pigmentation other than in compound eyes. In particular, our results suggest that classical ommochrome-related genes are rarely involved in the wing pigmentation of the nymphalid butterflies.