bluuebunny/crossref_metadata_2025_split huggingface dataset:
Graft-derived cfDNA Monitoring in Plasma and Bile During Normothermic Machine Perfusion in Liver Transplantation Is Feasible and a Potential Tool for Assessing Graft Viability
Authors: Cox Daniel R.A. , Lee Eunice , Wong Boris K.L. , McClure Tess , Zhang Fan , Goh Su Kah , Vago Angela , Jackett Louise , Fink Michael , Jones Robert , Perini Marcos V. , Dobrovic Alexander , Testro Adam , Starkey Graham , Muralidharan Vijayaragavan 
Published: October 2023

Background.
Ex vivo normothermic machine perfusion (NMP) is an organ preservation technique that enables an extended assessment of graft suitability before liver transplantation (LT). Established monitoring protocols used during NMP vary significantly in their assessment of transplant suitability when applied to the same grafts. Graft-derived cell-free DNA (gdcfDNA) analysis is an emerging tool for monitoring graft health post-transplantation. We investigated the feasibility of monitoring gdcfDNA during NMP for LT in a proof-of-concept, observational study.

Methods.
Serial plasma and bile samples were collected during NMP for 10 consecutive grafts, at 15 min post–machine reperfusion and then 2-h intervals. Digital polymerase chain reaction was used to quantify gdcfDNA at each time point.

Results.
Five grafts were suitable for LT, there were no cases of primary nonfunction or death in the recipients. gdcfDNA was quantified in all bile and plasma samples (n > 100). In plasma, gdcfDNA concentrations climbed post–machine reperfusion until 4.25 h (median 2.25 h = 15.98 × 106 copies/mL, 4.25 h = 40.21 × 106 copies/mL). gdcfDNA levels then diverged significantly when comparing the viable and non-viable graft groups (6.25 h, median viable: 117.15 × 106 copies/mL versus non-viable: 16.72 × 106 copies/mL, P = 0.01). These opposing trends correlated in each graft and in all cases with the viable/non-viable outcome. There was a trend of gradual decline in bile gdcfDNA from viable grafts post–machine reperfusion; discarded grafts showed more variable patterns of release.

Conclusions.
gdcfDNA analysis during NMP is a feasible and potential tool to inform viability assessment during NMP for LT. Bile gdcfDNA monitoring offers the prospect of an objective means to assess the degree of biliary injury associated with organ procurement.
Incoherent feedback from coupled amino acids and ribosome pools generates damped oscillations in growing E. coli
Authors: Droghetti Rossana , Fuchs Philippe , Iuliani Ilaria , Firmano Valerio , Tallarico Giorgio , Calabrese Ludovico , Grilli Jacopo , Sclavi Bianca , Ciandrini Luca , Lagomarsino Marco Cosentino 
Published: October 2023

AbstractCurrent theories of bacterial growth physiology demonstrate impressive predictive power but are often phenomenological, lacking mechanistic detail. Incorporating such details would significantly enhance our ability to predict and control bacterial growth under varying environmental conditions. The “Flux Controlled Regulation” (FCR) model serves as a reference framework, linking ribosome allocation to translation efficiency through a steady-state assumption. However, it neglects ppGpp-mediated nutrient sensing and transcriptional regulation of ribosomal operons. Here, we propose a mechanistic model that extends the FCR framework by incorporating three key components: (i) the amino acid pool, (ii) ppGpp sensing of translation elongation rate, and (iii) transcriptional regulation of protein allocation by ppGpp-sensitive promoters. Our model aligns with observed steady-state growth laws and makes testable predictions for unobserved quantities. We show that during environmental changes, the incoherent feedback between sensing and regulation generates oscillatory relaxation dynamics, a behavior that we support by new and existing experimental data.
Phase-changing citrate macromolecule combats oxidative pancreatic islet damage, enables islet engraftment and function in the omentum
Authors: Burke Jacqueline A. , Zhu Yunxiao , Zhang Xiaomin , Rios Peter D. , Joshi Ira , Lopez Daisy , Nasir Hafsa , Roberts Sharon , Rodriguez Quetzalli , McGarrigle James , Cook David , Oberholzer Jose , Luo Xunrong , Ameer Guillermo A. 
Published: October 2023

AbstractClinical outcomes for total-pancreatectomy followed by intraportal islet autotransplantation (TP-IAT) to treat chronic pancreatitis (CP) patients are suboptimal due to the inflammatory state of the patient’s pancreas, oxidative tissue damage during the isolation process, and the harsh engraftment conditions in the liver’s vasculature, which include ischemia-reperfusion injury, and instant blood–mediated inflammatory reactions. We describe the use of the thermoresponsive, antioxidant macromolecule poly(polyethylene glycol citrate-co-N-isopropylacrylamide) (PPCN) to protect islet redox status and functionin vitroandin vivoand to create a viable extrahepatic islet engraftment site in the abdomen. PPCN in aqueous media transitions from a liquid to an elastic hydrogel when exposed to body temperature via temperature-induced macromolecular self-assembly. Islets entrapped in the PPCN hydrogel and exposed to oxidative stress remain functional and support long-term euglycemia, in contrast to islets entrapped in a biologic scaffold (BS). When applied to the omentum of non-human primates (NHPs), PPCN is well-tolerated, safe, and mostly resorbed without fibrosis at 3 months post-implantation. To obtain autologous islets, a partial pancreatectomy was performed, followed by STZ administration to induce diabetes and destroy any remaining endogenous islets. Application of the autologous islets to the momentum using PPCN restored normoglycemia with minimal insulin requirements for over 100 days. These results support the use of PPCN as a scaffold for minimally invasive delivery of islets to the omentum of pancreatitis patients and highlight the importance of scaffold antioxidant properties as a new mechanism to protect islet function and maximize long-term autologous graft performance.One Sentence SummaryOmentum islet transplantation using a thermoresponsive, antioxidative polymer supports autologous islet viability and function in nonhuman primates.
Ornaments for Accurate and Efficient Allele-Specific Expression Estimation with Bias Correction
Authors: Adduri Abhinav , Kim Seyoung 
Published: October 2023

AbstractAllele-specific expression has been used to elucidate various biological mechanisms, such as genomic imprinting and gene expression variation caused by genetic changes incis-regulatory elements. However, existing methods for obtaining allele-specific expression from RNA-seq reads do not adequately and efficiently remove various biases, such as reference bias, where reads containing the alternative allele do not map to the reference transcriptome, or ambiguous mapping bias, where reads containing the reference allele map differently from reads containing the alternative allele. We present Ornaments, a computational tool for rapid and accurate estimation of allele-specific expression at unphased heterozygous loci from RNA-seq reads while correcting for allele-specific read mapping bias. Ornaments removes reference bias by accounting for personalized transcriptome, and ambiguous mapping bias by probabilistically assigning reads to multiple transcripts and variant loci they map to. Ornaments is a lightweight extension of kallisto, a popular tool for fast RNA-seq quantification, that improves the efficiency and accuracy of WASP, a popular tool for bias correction in allele-specific read mapping. Our experiments on simulated and human lymphoblastoid cell-line RNA-seq reads with the genomes of the 1000 Genomes Project show that Ornaments is as efficient as kallisto, an order of magnitude faster than WASP, and more accurate than WASP and kallisto. In addition, Ornaments detected genes that are imprinted at transcript level with higher sensitivity, compared to WASP that detected the imprinted signals only at gene level.
Genome-wide association study of prostate-specific antigen levels in 392,522 men identifies new loci and improves cross-ancestry prediction
Authors: Hoffmann Thomas J , Graff Rebecca E , Madduri Ravi K , Rodriguez Alex A , Cario Clinton L , Feng Karen , Jiang Yu , Wang Anqi , Klein Robert J , Pierce Brandon L , Eggener Scott , Tong Lin , Blot William , Long Jirong , Goss Louisa B , Darst Burcu F , Rebbeck Timothy , Lachance Joseph , Andrews Caroline , Adebiyi Akindele O , Adusei Ben , Aisuodionoe-Shadrach Oseremen I , Fernandez Pedro W , Jalloh Mohamed , Janivara Rohini , Chen Wenlong C , Mensah James E , Agalliu Ilir , Berndt Sonja I , Shelley John P , Schaffer Kerry , Machiela Mitchell J , Freedman Neal D , Huang Wen-Yi , Li Shengchao A , Goodman Phyllis J , Till Cathee , Thompson Ian , Lilja Hans , Ranatunga Dilrini K , Presti Joseph , Van Den Eeden Stephen K , Chanock Stephen J , Mosley Jonathan D , Conti David V , Haiman Christopher A , Justice Amy C , Kachuri Linda , Witte John S 
Published: October 2023

AbstractWe conducted a multi-ancestry genome-wide association study of prostate-specific antigen (PSA) levels in 296,754 men (211,342 European ancestry; 58,236 African ancestry; 23,546 Hispanic/Latino; 3,630 Asian ancestry; 96.5% of participants were from the Million Veteran Program). We identified 318 independent genome-wide significant (p≤5e-8) variants, 184 of which were novel. Most demonstrated evidence of replication in an independent cohort (n=95,768). Meta-analyzing discovery and replication (n=392,522) identified 447 variants, of which a further 111 were novel. Out-of-sample variance in PSA explained by our genome-wide polygenic risk scores ranged from 11.6%-16.6% in European ancestry, 5.5%-9.5% in African ancestry, 13.5%-18.2% in Hispanic/Latino, and 8.6%-15.3% in Asian ancestry, and decreased with increasing age. Mid-life genetically-adjusted PSA levels were more strongly associated with overall and aggressive prostate cancer than unadjusted PSA. Our study highlights how including proportionally more participants from underrepresented populations improves genetic prediction of PSA levels, offering potential to personalize prostate cancer screening.
Race, Hypertensive Disorders of Pregnancy and Outcomes in Peripartum Cardiomyopathy
Authors: Polsinelli Vincenzo B. , Koczo Agnes , Johnson Amber E. , Elkayam Uri , Cooper Leslie , Gorcsan John , Briller Joan , Fett James , McNamara Dennis M. ,   the IPAC investigators
Published: October 2023

AbstractIntroductionBlack women with peripartum cardiomyopathy (PPCM) have a high prevalence of hypertensive disorders of pregnancy (HDP) and worse clinical outcomes compared with other races. We examined the role of HDP and race on myocardial recovery in women with PPCM.MethodsA total of 100 women were enrolled into the Investigation in Pregnancy Associated Cardiomyopathy (IPAC) study. A hypertensive disorder of pregnancy (HDP) was defined as a gestational hypertension and preeclampsia, chronic hypertension was not included in the HDP subgroup. Left ventricular ejection fraction (LVEF) was assessed by echocardiography at entry, 6, and 12-months post-partum (PP). Clinical outcomes including persistent cardiomyopathy (LVEF≤35%), left ventricular assist device, (LVAD), transplantation, or death at 12-months were examined with and without HDP and between Black and non-Black subsets of women.ResultsMean age in IPAC was 30±6 years, with a baseline LVEF of 35±10%. In Black women, those with HDP were more likely to present earlier (days PP HDP: 35±20 vs 54±27 days, P=0.03) compared to women without HDP. There was no difference in LVEF at study entry, but better recovery with HDP at 6 (HDP:0.52±0.11 vs no HDP:0.40±0.14, P=0.03) and 12-months (HDP:0.53±0.10 vs no HDP:0.40±0.16, P=0.02). At 12-months, Black women had a lower LVEF than non-Black women (P=0.007), driven by worse recovery in Black women without HDP (P=0.002). Black women with HDP had a similar LVEF to non-Black women (P=0.31).ConclusionsIn women with PPCM, HDP among Black women was associated with earlier presentation and better recovery compared to Black women without HDP.
Individual-level deviations from normative brain morphology in violence, psychosis, and psychopathy
Authors: Haukvik Unn K , Wolfers Thomas , Tesli Natalia , Bell Christina , Hjell Gabriela , Fischer-Vieler Thomas , Bang Nina , Melle Ingrid , Andreassen Ole A , Rasmussen Kirsten , Agartz Ingrid , Westlye Lars T , Friestad Christine , Rokicki Jaroslav 
Published: October 2023

AbstractBackgroundNeuroimaging research has shown brain morphological abnormalities associated with violence and psychosis, but individual differences are substantial and results not consistent across studies. Recently developed normative modeling of brain MRI-features provides a possibility to parse this heterogeneity by mapping inter-individual brain characteristics, which has not yet been explored in forensic psychiatry.MethodsWe explored brain heterogeneity in persons with a history of severe violence with or without a schizophrenia spectrum disorder (HoV, n=58), non-violent patients with schizophrenia spectrum disorders (SSD-NV, n=138), and healthy non-violent controls (HC) from lifetime normative trajectories of cortical thickness, surface area, and subcortical volumes. Normative models were based on Freesurfer derived regions of interest from 58,836 individuals (ages 2-100) from 82 sites. Group differences and associations between brain deviations and psychopathy traits (PCL-R scores) were investigated.ResultsAcross groups, we found an overall heterogeneous pattern of individual-level deviations, with a significantly higher frequency of extreme negative deviations in HoV (p=.020,d=.31) and SSD-NV (p=.019,d=.48), than HC. Group differences were mostly present in subcortical volumes and cortical area, but not thickness, with significant regional group-level differences within the subcallosal and insular cortices, and the cerebellum, and no significant associations to psychopathy traits.ConclusionBy applying normative modeling, this proof-of-concept study demonstrates the heterogeneous pattern of brain morphometry deviations associated with violence and psychosis. While the results warrant replication, studies addressing individual brain deviations may contribute to improved understanding of the complex underpinnings of violence in forensic psychiatry.
Reliability of high-quantity human brain organoids for modeling microcephaly, glioma invasion, and drug screening
Authors: Ramani Anand , Pasquini Giovanni , Gerkau Niklas J. , Vinchure Omkar Suhas , Gabriel Elke , Rothenaigner Ina , Lin Sean , Altinisk Nazlican , Rathinam Dhanasekaran , Mirsaidi Ali , Goureau Olivier , Giorgio Lucia Ricci-Vitiani , d’alessandris Q. , Pallini Roberto , Wollnik Bernd , Muotri Alysson , Jurisch-Yaksi Nathalie , Rose Christine R. , Busskamp Volker , Hadian Kamyar , Gopalakrishnan Jay 
Published: October 2023

SUMMARYBrain organoids offer unprecedented insights into brain development and disease modeling and hold promise for drug screening. Significant hindrances, however, are morphological and cellular heterogeneity, inter-organoid size differences, cellular stress, and poor reproducibility. Here, we describe a method that reproducibly generates thousands of organoids across multiple iPSC lines. These High Quantity brain organoids (Hi-Q brain organoids) exhibit reproducible cytoarchitecture, cell diversity, and functionality, are free from ectopically active cellular stress pathways, and allow cryopreservation and re-culturing. Using patient-derived Hi-Q brain organoids, we recapitulated distinct forms of microcephaly pathogenesis: primary microcephaly due to a mutation in centrosomal CDK5RAP2 and progeria-associated microcephaly in Cockayne syndrome. When modeling glioma invasion, hi-Q brain organoids displayed a similar invasion pattern for a given patient-derived glioma cell line. This enabled a medium-throughput screen to identify Selumetinib and Fulvestrant, which also perturbed glioma invasion in vivo. Thus, the Hi-Q approach can easily be adapted to reliably harness brain organoids’ utility for personalized disease modeling and drug discovery.
The N-terminal region of DNMT3A combines multiple chromatin reading motifs to guide recruitment
Authors: Wapenaar Hannah , Clifford Gillian , Rolls Willow , Burdett Hayden , Zhang Yujie , Deák Gauri , Zou Juan , Taylor Mark R. D. , Mills Jacquie , Watson James A. , Kumar Dhananjay , Das Alakta , Valsakumar Devisree , Bramham Janice , Voigt Philipp , Wilson Marcus D. 
Published: October 2023

AbstractDNA methyltransferase 3A (DNMT3A) plays a critical role in establishing and maintaining DNA methylation patterns. However, the mechanisms underlying DNMT3A recruitment to and function within different chromatin environments remain unclear. Using a combination of biochemical and structural approaches we find that DNMT3A interacts using multiple interfaces with chromatin; directly binding generic nucleosome features as well as site-specific post-translational histone modifications. The N-terminal region, unique to the DNMT3A1 isoform, is essential for these interactions and stabilises H3K36me2-nucleosome recruitment. Intriguingly, in the same region critical for nucleosome binding we also map a ubiquitylation-dependent recruitment motif (UDR). The UDR binds specifically to ubiquitylated H2AK119, explaining the previously observed recruitment to Polycomb-occupied heterochromatin. A cryo-EM structure of DNMT3A1-DNMT3L with a modified nucleosome reveals that the UDR interacts with the nucleosome surface including the acidic patch. Previously unexplained disease-associated mutations are present in the UDR and ablate nucleosome interactions. This leads to an increased understanding of how DNMT3A1 recruitment occurs in the genome and highlights the importance of multivalent binding of DNMT3A to histone modifications and the nucleosome.
Economic-financial performance and value creation in the Brazilian construction industry
Authors: Jordão Ricardo Vinícius Dias , Costa Davidson Junio 
Published: October 2023

PurposeThis paper aims to analyze the economic-financial performance (EFP) and value creation (VC) in the Brazilian construction industry.Design/methodology/approachBased on the theories of strategy and finance, a quantitative-qualitative, descriptive and explanatory and applied study was carried out, contrasting the performance of the Direcional company and the civil construction industry – both listed on the Brazilian Stock Exchange and the Over-the-Counter Market (B3)FindingsThe analysis of the EFP in the Brazilian construction industry shows that EZTEC, Helbor, Trisul and Direcional were the companies with the best EFP in the period. The analysis of the Economic Value Added (EVA®, henceforth EVA), as a VC metric and basis for assessing the relative technical efficiency score by Data Envelopment Analysis (DEA®, henceforth DEA), revealed that the companies Direcional, EZTEC, MRV and CR2 were considered efficient throughout the period covered. The multicriteria methodology for empirical testing of the EFP and VC allowed not only contrasts Direcional's results with the other companies of the construction industry but also offered a complementary tool for comparative analysis of enterprises of different sizes, structures and realities.Research limitations/implicationsRegardless of any contextual limitations, from a theoretical point of view, the research not only helps fill the research gap aforementioned but also expands knowledge on the topic and demonstrates how this multi-criteria methodology (integrating DEA and EVA) can be used to assess EFP and VC in addition to traditional tools. However, this new approach evaluates, at the same time, corporate and sectorial effectiveness by contrasting the efficiency and efficacy (simultaneously) in the generation of performance and value of a company in relation to the industry.Practical implicationsSignificant implications for managerial practice could be noted by offering a tool to improve company performance and creating a competitive benchmarking process for analysts, investors, managers, financing agencies, shareholders, policymakers and business owners, as well as organizations and sectors in similar situations – who need to assess the EFP and VC holistically and improve their decision-making processes.Originality/valueThe uniqueness and innovation of this research come from the original multi-criteria methodology developed, applied and validated for analysis of EFP and VC. This methodology was operationalized through DEA applied to the companies' EVA, making it possible to compare corporate results and those of the whole industry in a balanced way – an unexplored issue in the literature, especially in emerging economies, opening several avenues for future research.
The formation of citizens' intentions to purchase prefabricated housing in China: the integrating theory of planned behavior and norm activation model
Authors: Zhou Zhenzong , Shen Geoffrey , Xue Jin , Sun Chengshuang , Liu Yongyue , Cong Weiyi , Yu Tao , Wang Yaowu 
Published: October 2023

PurposeThis study aims to develop an improved understanding of the formation of citizens' purchase intention to increase the adoption of prefabricated housing (PH).Design/methodology/approachAn integrative model of the theory of planned behavior (TPB) and norm activation model (NAM) was proposed based on previous studies. To verify the conceptual model, an analysis was conducted after data collection from a questionnaire survey. Lastly, findings were presented by explaining the formation of purchase intention in the egoistic and altruistic contexts. Practical implications were likewise discussed.FindingsFindings manifest that citizens' purchase intention is influenced by egoistic and altruistic cognitions. An effective strategy is to show citizens the pro-environmental features of PH to promote its adoption because they value the environmental performance of housing. Meanwhile, consumers' social fitness also plays an essential role in decision-making, and the dual contradiction in the PH market is revealed.Originality/valueThis study extends the knowledge of psychological decision-making theories in the field of purchase intention toward PH by proposing an integrative framework of TPB and NAM. Results indicate a systematic and comprehensive understanding of consumers' decision-making in the PH domain. Moreover, results of this research contribute to specifying and refining the applicable contexts of TPB and NAM by adding two antecedents: subjective knowledge and environmental concern. This research contributes to the literature by being one of the first to investigate purchase intention toward a high-cost product with invisible technological innovation.