bluuebunny/crossref_metadata_2025_split huggingface dataset:
Who Do We Fail to Rescue after Pancreatoduodenectomy? Outcomes Among >4000 Procedures Expose Windows of Opportunity
Authors: Kinny-Köster Benedict , Halm Darius , Tran Duc , Kaiser Jörg , Heckler Max , Hank Thomas , Hinz Ulf , Berchtold Christoph , Al-Saeedi Mohammed , Roth Susanne , Mehrabi Arianeb , Marchegiani Giovanni , Büchler Markus W. , Loos Martin 
Published: July 2024

Objective:
Our investigation on in-hospital mortality after 4474 pancreatoduodenectomies aimed to identify time-dependent risks as well as windows of opportunity to rescue patients from complications.

Background:
Pancreatoduodenectomy is generally considered a safe procedure with a 1-10% perioperative mortality based on complexity and surgical volume. Yet, patients are susceptible for life-threatening complications particularly with extended resections. Recognition of distinct vulnerabilities over time while patients recover is required to permit focused monitoring, sophisticated resource allocation, and greatest surgical safety.

Methods:
Patients who deceased in-hospital after pancreatoduodenectomy between 2003-2021 were retrieved from the institutional pancreatectomy registry and analyzed in detail with respect to their postoperative course.

Results:
Among 4474 pancreatoduodenectomies, 156 patients deceased in-hospital (3.5%). When assessing root causes of mortality, we observed 3 different clusters of complications which were postpancreatectomy-specific (47.4%), visceral vasculature-associated (25.6%), or cardiopulmonary in origin (23.7%). The median times of root cause onset in the 3 categories were postoperative day (POD) 9, POD 4.5 (P=0.008) and POD 3 (P<0.001), and medians of in-hospital mortality were POD 31, POD 18 (P=0.009) and POD 8 (P<0.001), respectively. Intervals between root cause onset and mortality varied with medians of 23 days, 11 days (P=0.017), and 1 days (P<0.001). The 3 categories were similarly distributed between different types of surgical complexity.

Conclusion:
Postpancreatectomy-specific complications prompt almost half of in-hospital mortalities after pancreatoduodenectomy, with rather long intervals for interventions to prevent failure to rescue. In contrast, visceral vasculature-related events and cardiopulmonary complications dominate early in-hospital mortalities with short intervals until mortality, demanding rigorous management of such events or preoperative conditioning. These data externally validate a previous high-volume initiative and highlight distinct windows of opportunity to optimize perioperative safety.
Optimizing DCD Liver Grafts With Prolonged Warm Ischemic Time Using Stabilized Plasmin in a Static Cold Storage Orthotopic Rat Liver Transplant Model
Authors: Kahan Riley , Abraham Nader , Zhang Min , Novokhatny Valery , Alderete Isaac , Cray Paul , Chen Fengming , Gao Qimeng , Cywinska Greta , Neill Ryan , Nakata Kentaro , Hassan Ahmed , Rush Caroline , Penaflor Jude , Pollara Justin J. , Hartwig Matthew G. , Hughes Benjamin , Barbas Andrew S. 
Published: July 2024

Background.
The clinical success of liver transplantation has led to increased demand, requiring further expansion of the donor pool. Therapeutic interventions to optimize organs from donation after circulatory death (DCD) have significant potential to mitigate the organ shortage. Dysfunction in DCD liver grafts is mediated by microvascular thrombosis during the warm ischemic period, and strategies that reduce this thrombotic burden may improve graft function. We hypothesized that the administration of the fibrinolytic enzyme plasmin to the donor organ during the cold storage period would reduce the thrombotic burden and improve DCD liver graft function.

Methods.
In 2 separate cohorts, 32 syngeneic orthotopic rat liver transplants were performed in Lewis rats. Livers were procured from donors with 45 min of warm ischemic injury. Liver grafts were flushed with histidine-tryptophan-ketoglutarate preservation solution mixed with either plasmin (experimental group) or albumin (control group). All investigators were blinded to treatment group. After preparing the liver for implant using a modified cuff technique, the liver was stored for 1 h by static cold storage at 4 °C. Immediately before implantation, the liver graft was flushed, and this effluent was analyzed for fibrin degradation products to determine graft clot burden. Twenty-four hours following transplantation, animals were euthanized, and samples were collected.

Results.
Recipient survival was significantly higher for DCD liver grafts treated with plasmin compared with control. Moreover, histology of liver graft tissue immediately before implant reflected significantly reduced congestion in plasmin-treated livers (score, mean ± SD: 0.73 ± 0.59 versus 1.12 ± 0.48; P = 0.0456). The concentration of fibrin degradation products in the final flush before implantation was significantly reduced in plasmin-treated livers (743 ± 136 versus 10 919 ± 4642 pg/mL; P = 0.0001), reflecting decreased clot burden in the graft.

Conclusions.
The present study demonstrates that plasmin improves survival and may reduce thrombotic burden in DCD liver grafts with prolonged warm ischemic injury, meriting further study.
IDO+ Endothelial Cells in Glomeruli of Kidney Transplantation Patients With Glomerulitis
Authors: Hendriks Sanne H. , Heidt Sebastiaan , Krop Juliette , IJsselsteijn Marieke E. , Eggermont Jeroen , Kers Jesper , Reinders Marlies E.J. , Koning Frits , van Kooten Cees 
Published: July 2024

Background.
Kidney transplantation is the preferred treatment option for patients with end-stage renal disease. However, long-term graft survival remains a challenge. The enzyme indoleamine 2,3 dioxygenase (IDO) has been reported to have immunomodulatory effects with IDO transcripts being elevated in both antibody-mediated rejection and T cell–mediated rejection.

Methods.
A metal-conjugated antibody panel for the staining of kidney biopsies was developed, allowing the visualization of 41 structural and immune markers on a single tissue slide to gain in-depth insight into the composition and localization of the immune cell compartment. Staining was applied to week 4 and 24 protocol biopsies of 49 patients as well as on 15 indication biopsies of the TRITON study and 4 additional transplantation biopsies with glomerulitis.

Results.
A highly distinctive and specific glomerular IDO expression was observed in biopsies from 3 of 49 patients in imaging mass cytometry. Immunohistochemistry confirmed IDO expression in glomeruli of 10 of 10 cases with glomerulitis. IDO was found to be expressed by CD31+ glomerular endothelial cells, accompanied by the presence of granzyme-B+Tbet+CD7+CD45RA+ natural killer cells and CD68+ macrophages. Furthermore, a proportion of both the immune cells and endothelial cells expressed Ki-67, indicative of cell proliferation, which was not observed in control glomeruli.

Conclusions.
Our results show glomerular IDO expression in transplanted kidneys with glomerulitis, which is accompanied by increased numbers of natural killer cells and macrophages and likely reflects local immune activation.
Normothermic Machine Perfusion Is Associated With Improvement in Mortality and Graft Failure in Donation After Cardiac Death Liver Transplant Recipients in the United States
Authors: Okumura Kenji , Dhand Abhay , Misawa Ryosuke , Sogawa Hiroshi , Veillette Gregory , Nishida Seigo 
Published: July 2024

Background.
Use of normothermic machine perfusion (NMP) may help to expand the liver transplantation (LT) donor pool by potentially increasing the utilization of donation after circulatory death (DCD) organs. The aim of this study was to assess the impact of NMP on LT from DCD organs.

Methods.
Data among DCD adult LT recipients in the United Network for Organ Sharing between January 2016 and December 2022 were analyzed. Outcomes were compared between 2 groups: NMP versus non-MP using propensity score matching.

Results.
During the study period, 4217 DCD LT recipients (NMP: 257 and non-MP: 3960) were identified. compared with non-MP, DCD LT recipients in NMP group were older (median recipient age: 61 versus 59 y, P = 0.013), had lower model for the end-stage liver disease score, longer wait time (126 versus 107 d, P = 0.028), and received organs from older donors (median age: 42 versus 38 y, P < 0.01) with longer preservation time (9.9 versus 5.3 h, P < 0.001). Two-year overall survival (NMP 94.4% versus non-MP 89.7%, P = 0.040) and 2-y graft survival (NMP 91.3% versus non-MP 84.6%, P = 0.017) were better in the NMP group. After propensity score matching, 2-y overall survival (NMP 94.2% versus non-MP 88.0%, P = 0.023) and graft survival (NMP 91.3% versus non-MP 81.6%, P = 0.004) were better in the NMP group. On multivariable cox regression analysis, NMP was an independent factor of protection against mortality (hazard ratio, 0.43; 95% confidence interval: 0.20-0.91; P = 0.029) and against graft failure (hazard ratio, 0.26; 95% confidence interval: 0.11-0.61; P = 0.002).

Conclusions.
Use of NMP for LT from DCD donors was associated with improved posttransplant patient and graft survival.
<xhtml:span xmlns:xhtml="http://www.w3.org/1999/xhtml" xml:lang="en">Comparative analysis of virulence gene profiles of&#160;Escherichia coli&#160;from human and non-human sources&#160;in Rivers State, Nigeria
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Authors: Abeni Barira Azeez , Frank-Peterside Nnenna , Otokunefor Kome 
Published: July 2024

Traditionally, the presence of virulence features have been thought to be a key factor in differentiating pathogenic from commensal strains. An understanding of virulence potential of Escherichia coli isolates from various sources is essential to help shed light on potential contamination/transmission rates between the various sources. This study was therefore aimed at exploring the occurrence of specific virulence genes and gene profiles associated with Escherichia coli from human and non-human sources in Rivers State, Nigeria.
Two hundred samples from human (urine and feces) and non-human (soil and poultry droppings) sources (50 each) were analyzed using standard microbiological procedures. DNA was extracted from isolates presumptively identified as Escherichia coli using PrestoTM Mini gDNA Bacteria-Kit Quick protocol following the manufacturer’s instructions. Isolate identities were confirmed using E. coli specific 16S rRNA primers and confirmed isolates screened for the presence of six virulence genes (Afimbriae binding adhesin (afa), type 1 fimbriae (fimH), P-fimbrial Usher Protein (papC)), iron acquisition systems: aerobactin (aer), Cytotoxic necrotizing factor I (cnf1) and alpha hemolysin (hly).
Results showed that all isolates haboured at least one of the tested virulence genes, with fimH (97%) as the most prevalent virulence gene and papC the least commonly occurring (35%). A higher occurrence of virulence genes was noted in non-human isolates though hly and cnf were not detected at all in any of the isolates studied (0%). Ten different profiles were observed with the afaCc-aer-fimH profile the most commonly occurring virulence gene profile in general (33.3%). For non-human isolates however, the aer-afaCc-fimH-papC was the most commonly occurring profile (42.9%).
This study shows that the test Escherichia coli from human and non-human sources do not carry distinct virulence gene profiles. Studies on a larger subset of isolates would however be necessary to determine if indeed the virulence genes tested for in this study really cannot be used to tell whether an isolate is from a human source or not in the South-South of Nigeria.
Comparative evaluation of Drosophila melanogaster and Drosophila simulans larva against environmental chemicals
Authors: Khan Nisha , Rani Usha , Bhan Veer , Singh Ravinder , Singh Amit , Mohan Man , Singh Raj , Khan Anish 
Published: July 2024

ABSTRACT
Background: Drosophila genus comprises of ~1600 species but predictable to have several thousands in number. D. melanogaster (DMG) Meigen and D. simulans (DSI) are also closely related to each other but morphologically have difference to each other. Both are cosmopolitan flies that are mostly found in the India and south-east Asian regions and resident in ours surrounding and eat to ripened fruits.
Methodology: As compared to DSI, DMG is consideration to be progression modified to decaying, overripe and fermented fruits that released huge quantity of ethanol (EtOH), acetic-acid (AA), methanol (MeOH) and ethyl-acetate (EtOAc) chemicals. We explored the survival rate of DMG and DSI larva at various concentrations (ranging from 2-10%) of EtOH, AA, MeOH and EtOAc while inhibitory concentration 50 (IC50) was calculated and compare tolerance power and susceptibility of both against these chemicals.
Results: Firstly, a statistically significant (p>0.01) differences was observed between survival rate of DMG and DSI larva against 10% of EtOH (37.4 vs. 25.1%), AA (34.9 vs. 23.2%), MeOH (32.5 vs. 19.9%) and EtOAc (26.9 vs. 17.6%), respectively. Secondly, IC50 values of both larva of flies were found statistically significant (p>0.01) at 10% EtOH (DMG: 5.8-6.8 vs. DSI: 3.9-5.0%) and EtOAc (DMG: 3.8-4.8 vs. DSI: 2.3-3.6%). Thus we found a descending order of IC50 values as: EtOH>AA>MeOH>EtOAc for both flies. While survival rate and sensitivity order was found same but mortality and resistivity order (i.e. EtOAc>MeOH>AA>EtOH) are reciprocal to survival rate and sensitivity.
Conclusion: To considering DMG and DSI larva’s have diverse habitats, ecological, physiological differences but DMG larva might exhibit higher susceptibility toward non-toxic chemicals released from fermenting and decaying fruits as compared to DSI larva. Hence, we found that DMG larva is more susceptible, tolerable against EtOH, AA, MeOH and EtOAc chemicals than larva of DSI.
Single-cell RNA sequencing of the holothurian regenerating intestine reveals the pluripotency of the coelomic epithelium
Authors: Medina-Feliciano Joshua G. , Valentín-Tirado Griselle , Luna-Martínez Kiara , Beltran-Rivera Alejandra , Miranda-Negrón Yamil , García-Arrarás José E. 
Published: July 2024

AbstractIn holothurians, the regenerative process following evisceration involves the development of a “rudiment” or “anlage” at the injured end of the mesentery. This regenerating anlage plays a pivotal role in the formation of a new intestine. Despite its significance, our understanding of the molecular characteristics inherent to the constituent cells of this structure has remained limited. To address this gap, we employed state-of-the-art scRNA-seq and HCR-FISH analyses to discern the distinct cellular populations associated with the regeneration anlage. Through this approach, we successfully identified thirteen distinct cell clusters. Among these, two clusters exhibit characteristics consistent with putative mesenchymal cells, while another four show features akin to coelomocyte cell populations. The remaining seven cell clusters collectively form a large group encompassing the coelomic epithelium of the regenerating anlage and mesentery. Within this large group of clusters, we recognized previously documented cell populations such as muscle precursors, neuroepithelial cells and actively proliferating cells. Strikingly, our analysis provides data for identifying at least four other cellular populations that we define as the precursor cells of the growing anlage. Consequently, our findings strengthen the hypothesis that the coelomic epithelium of the anlage is a pluripotent tissue that gives rise to diverse cell types of the regenerating intestinal organ. Moreover, our results provide the initial view into the transcriptomic analysis of cell populations responsible for the amazing regenerative capabilities of echinoderms.
Decoding imaginary handwriting trajectories with shape and time distortion loss for brain-to-text communication
Authors: Xu Guangxiang , Wang Zebin , Xu Kedi , Zhu Junming , Zhang Jianmin , Wang Yueming , Hao Yaoyao 
Published: July 2024

AbstractThe potential to decode handwriting trajectories from brain signals has yet to be fully explored in clinical brain-computer interfaces (BCIs). One of challenges remains that the clinical BCIs mostly rely on imaginary movement due to motor deficit of the subject, which often leads to misalignment with neural activity and impedes accurate decoding. Here, we recorded intracortical neural signals from a paralyzed patient during imaginary handwriting of Chinese characters, from which the trajectories of handwriting were reconstructed and translated into texts using machine learning approach. We introduced an innovated decoding framework that incorporates a novel loss function, DILATE, to accommodate both shape and temporal distortions between movement and neural activity to account for the misalignment issue. Our method reconstructed closely resembled and human-recognizable handwriting trajectories, outperforming the conventional mean square error loss by 10% of recognition rate. Moreover, the new decoding framework enabled effective multi-day data fusion, resulting in further 15% enhancement. With a dynamic time warping approach, the recognition rate achieved up to 91.1% within a 1000-character database. Additionally, we applied our method to a previous subject who imaged handwriting of English letters, showcasing its capability for single-trail trajectory reconstruction and 13.5% higher recognition outcomes. Altogether, these findings demonstrated a new decoding scheme for BCIs that could accurately reconstruct the imaginary handwriting trajectory. This advancement paves the way for a universal brain-to-text communication system that is applicable to any written language, marking a significant leap forward in the field of neural decoding and BCI technology.
Outbreak-associatedSalmonellaBaildon found in wastewater demonstrates how sewage monitoring can supplement traditional disease surveillance
Authors: M’ikanatha Nkuchia M. , Goldblum Zoe S. , Cesari Nicholas , Nawrocki Erin M. , Fu Yezhi , Kovac Jasna , Dudley Edward G. 
Published: July 2024

AbstractNon-typhoidalSalmonellais a common cause of gastroenteritis worldwide, but current non-typhoidalSalmonellasurveillance is suboptimal. Here we evaluated the utility of wastewater monitoring to enhance surveillance for this foodborne pathogen. In June 2022, we tested composite raw sewage collected twice a week from two treatment plants in central Pennsylvania for non-typhoidalSalmonellaand characterized isolates using whole genome sequencing. We recovered 43Salmonellaisolates from wastewater samples, differentiated by genomic analysis into seven serovars: 16 Panama (37.2%), 9 Senftenberg (20.9%), and 8 Baildon (18.6%), 3 or fewer for four other serovars. We assessed genetic relatedness and epidemiologic links between non-typhoidalSalmonellaserovars from wastewater and isolates from patients with salmonellosis. AllS.Baildon serovars from wastewater were genetically and epidemiologically associated with a known salmonellosis outbreak.S.Baildon from wastewater and 42 outbreak-related isolates in the national outbreak detection database had the same core genome multilocus sequence typing and code differed by no or one single polynucleotide polymorphisms. One of the 42 outbreak-related isolates was obtained from a patient residing in the wastewater sample collection catchment area, which serves approximately 17000 people.S.Baildon is a rare serovar (reported in <1% cases nationally over five years). Our study underscores the value of monitoring sewage from a defined population to supplement traditional surveillance methods for evidence ofSalmonellainfections and to determine the extent of outbreaks.Importance statementDuring the COVID-19 pandemic, surveillance for SARS-CoV-2 in wastewater was a powerful tool for assessing community burden days ahead of traditional reporting. Here, we show that domestic sewage monitoring is useful for surveillance for a foodborne pathogen.Salmonella entericawas detected in samples from two wastewater treatment plants in central Pennsylvania during June 2022. Using whole genome sequencing, we demonstrated that isolates of variantS. Baildon clustered with those from an outbreak that occurred in a similar time frame. Case reports were primarily from Pennsylvania, and one individual lived within the treatment center catchment area. This study provides support for the utility of domestic sewage surveillance in assisting public health agencies identify communities impacted by infectious diseases.
Online unsupervised performance-based cognitive testing: a feasible and reliable approach to scalable cognitive phenotyping of Parkinson’s patients
Authors: Balit Nasri , Sun Sophie , Zhang Yilin , Sharp Madeleine 
Published: July 2024

AbstractIntroductionA better understanding of the heterogeneity in the cognitive and mood symptoms of Parkinson’s disease will require research conducted in large samples of patients. Fully online and remote research assessments present interesting opportunities for scaling up research but the feasibility and reliability of remote and fully unsupervised performance-based cognitive testing in individuals with Parkinson’s disease is unknown. This study aims to establish the feasibility and reliability of this testing modality in Parkinson’s patients.MethodsSixty-seven Parkinson’s patients and 36 older adults completed two sessions of an at-home, online battery of five cognitive tasks and three self-report questionnaires. Feasibility was established by examining completion rates and data quality. Test-retest reliability was evaluated using the Intraclass Correlation Coefficient (ICC (2,1)).ResultsOverall completion rates and data quality were high with few participant exclusions across tasks. With regards to test-retest reliability, intraclass correlation coefficients were quite variable across measures extracted from a task as well as across tasks, but at least one standard measure from each task achieved moderate to good reliability levels. Self-report questionnaires achieved a higher test-retest reliability than cognitive tasks. Feasibility and reliability were similar between Parkinson’s patients and older adults.ConclusionThese results demonstrate that remote and unsupervised testing is a feasible and reliable method of measuring cognition and mood in Parkinson’s patients that achieves levels of test-retest reliability that are comparable to those reported for standard in-person testing.
ATG5 is dispensable for ATG8ylation of cellular proteins
Authors: Ketteler Robin , Kiso Koshiro , von Chamier Lucas , Agrotis Alexander 
Published: July 2024

AbstractProtein ATG8ylation refers to a post-translational modification involving covalent attachment of ubiquitin-like autophagy-related protein ATG8 (LC3/GABARAP) to other cellular proteins, with reversal mediated by ATG4 proteases. While lipid ATG8ylation is important for autophagosome formation and mechanistically well-characterized, little is known about the mechanism of protein ATG8ylation. Here, we investigated the conjugation machinery of protein ATG8ylation in CRISPR/Cas9-engineered knockout human cell lines, utilizing a deconjugation-resistant (Q116P G120) form of MAP1LC3B. We report that protein ATG8ylation requires the E1-like activating enzyme ATG7 and E2-like conjugating enzyme ATG3, in common with ATG8 lipidation. However, in contrast, the E3-like ATG12-ATG5-ATG16L1 complex involved in lipidation is dispensable for protein ATG8ylation, since ATG5 knockout cells can form ATG8ylated protein conjugates. Further, we uncover that ATG7 itself is a target of ATG8ylation. Overall, our work provides crucial insight into the mechanism of protein ATG8ylation, distinguishing it from ATG8 lipidation, which will aid investigating its functional role.