bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced recovery after surgery for liver transplantation: a review of recent literature
Authors: Crouch Cara E. , Stewart Erin , Hendrickse Adrian 
Published: November 2023

Purpose of review
This review was created to highlight important articles from the past year related to the evolving field of enhanced recovery after surgery (ERAS) in liver transplantation that are relevant to the transplant anesthesiologist.

Recent findings
The International Liver Transplantation Society (ILTS) recently completed a landmark project, the ERAS4OLT.org project, which culminated in 80 recommendations for ERAS in liver transplantation. These recommendations encompass management for deceased donor recipients, living donor recipients and living donors. This review highlights selected articles relevant to the perioperative management of deceased donor liver transplant recipients.

Summary
Though, there are now published internationally agreed upon recommendations for ERAS topics specific to liver transplantation, there is an obvious need for further investigation into this area to provide high quality evidence to support these recommendations. It is reasonable to utilize these recommendations in ERAS protocols for individual institutions; however, more evidence is needed in several areas to confirm the effects of these protocols on short-term outcomes.
Prevalence of and risk factors for surgical site infections after pancreaticoduodenectomy: a systematic review and meta-analysis
Authors: Hu Hongfei , Zhou Ting , Qiu Yijin , Li Yuxin , Liu Wei , Meng Rui , Zhang Xueke , Ma Aixia , Li Hongchao 
Published: November 2023

Background:
Surgical site infections (SSIs) are one of the most common complications after pancreaticoduodenectomy (PD); however, the global prevalence and risk factors for SSIs after PD remain unknown.

Objectives:
To investigate the prevalence of and risk factors for SSIs after PD.

Methods:
The PubMed, Embase, Cochrane Library, Web of Science, and Science Direct databases were systematically searched from inception to 1 December 2022. Observational studies reporting adjusted odds ratios (ORs) and 95% confidence intervals (CIs) of risk factors for SSIs in patients undergoing PD were included. Two independent reviewers in teams performed data extraction, risk of bias assessment, and level of evidence analysis. The pooled results were estimated using a random-effects model. The I
2 statistic and Q χ
2 statistic were used to assess heterogeneity. Funnel plots, Egger’s regression test, and the trim-and-fill method were used to determine publication bias. The primary outcomes were identifying risk factors for SSIs after PD. The secondary outcomes were the pooled prevalence rates of SSIs.

Results:
A total of 98 704 patients from 45 studies were included, and 80% of the studies were considered high quality. The estimated pooled prevalence of SSIs was 23% (0.19–0.27, I
2=97%). The prevalence of SSIs was found to be higher in Japan and lower in USA. Preoperative biliary stenting, higher body mass index (BMI), longer operation time, postoperative pancreatic fistula, soft pancreatic texture, perioperative blood transfusion, and cardiac disease were identified as significant risk factors for the development of SSIs after PD. Additionally, broad-spectrum antibiotics were a significant protective factor against SSIs. Subgroup analysis and sensitivity analysis showed that the results were robust.

Conclusion and relevance:
The prevalence of SSIs remains high and varies widely among regions. It is necessary to take effective preventive measures and carry out more prospective studies to further verify these results.
Analysis of microRNA expression profiles involved oxidative stress in a deep tissue pressure injury
Authors: Wang Xiaoying , Shan Hui , Zhang Ju 
Published: November 2023

Abstract

Objective:
To investigate the association between oxidative stress and the development of deep tissue pressure injury (DTPI) at the genetic level by analyzing microRNA (miRNA) expression profiles in DTPI tissues.

Methods:
A model of DTPI was established in 3 adult mice and 3 elderly mice, whereas another set of 3 adult mice and 3 elderly mice was used as controls. Wound tissues were stained with hematoxylin and eosin to observe the histologic changes, and total RNA was extracted for high-throughput sequencing. Differentially expressed oxidative stress-related miRNAs were screened, and target genes were predicted using TargetScan (v5.0) and Miranda (v3.3a). Enrichment analysis of these genes was executed using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. Selected differentially expressed miRNAs were further validated by quantitative real-time–polymerase chain reaction.

Results:
The results showed that 128 miRNAs were associated with oxidative stress, among which 86 were downregulated, and 42 were upregulated in the DTPI-elderly group; 21 were differentially expressed in the DTPI-adult group (P < 0.05). Moreover, the miRNA associated with oxidation stress between the two groups was miR-181a-1-3p. Its target genes mainly regulated MAPK and AGE pathways. quantitative real-time–polymerase chain reaction results showed that miR-181a-1-3p and miR-21a-5p were significantly downregulated in DTPI tissues.

Conclusion:
By analyzing miRNA expression profiles related to oxidative stress through a high-throughput sequencing system, this study sheds light on the potential pathologic mechanisms underpinning DTPI.
Racial Disparities in the Genetic Landscape of Acute Myeloid Leukaemia from The Cancer Genome Atlas: Insights from a Bioinformatics Analysis
Authors: Nkhoma Panji , Dzobo Kevin , Kafita Doris , Kwenda Geoffrey , Munsaka Sody , Musalula Sinkala 
Published: November 2023

AbstractAcute myeloid leukaemia (AML) is a heterogeneous disease with complex pathogenesis that affects hematopoietic stem cells. Ethnic and racial disparities have been reported to affect treatment and survival outcomes in AML patients. Here, we analysed clinical and transcriptomic data from The Cancer Genome Atlas (TCGA) to investigate potential differences in the genetic landscape of AML between African and European individuals. We found several differentially expressed mRNA transcripts between the AML of Africans and Europeans. Notably, AML in African patients exhibited enrichment for several pathways, including signalling by G-protein-coupled receptors, oncostatin M, and codeine and morphine metabolism. In contrast, AML in European patients showed enrichment for pathways related to the glial cell-line derived neurotrophic factor/rearranged during transfection signalling axis, gamma-aminobutyric acid receptor activation, and ligand-gated ion transport channels. Additionally, kinase enrichment analysis identified shared and distinct kinases in AML among Africans and Europeans: Africans showed an enrichment of cyclin-dependent kinases, while Europeans exhibited an enrichment of ULK2, CSNK2B, and CAMK1. Our study highlights the potential importance of considering race when evaluating the genetic landscape of AML, which may improve treatment strategies for this disease.
Decomposition of retinal ganglion cell electrical images for cell type and functional inference
Authors: Wu Eric G. , Rudzite Andra M. , Bohlen Martin O. , Li Peter H. , Kling Alexandra , Cooler Sam , Rhoades Colleen , Brackbill Nora , Gogliettino Alex R. , Shah Nishal P. , Madugula Sasidhar S. , Sher Alexander , Litke Alan M. , Field Greg D. , Chichilnisky E.J. 
Published: November 2023

AbstractIdentifying neuronal cell types and their biophysical properties based on their extracellular electrical features is a major challenge for experimental neuroscience and the development of high-resolution brain-machine interfaces. One example is identification of retinal ganglion cell (RGC) types and their visual response properties, which is fundamental for developing future electronic implants that can restore vision. The electrical image (EI) of a RGC, or the mean spatio-temporal voltage footprint of its recorded spikes on a high-density electrode array, contains substantial information about its anatomical, morphological, and functional properties. However, the analysis of these properties is complex because of the high-dimensional nature of the EI. We present a novel optimization-based algorithm to decompose electrical image into a low-dimensional, biophysically-based representation: the temporally-shifted superposition of three learned basis waveforms corresponding to spike waveforms produced in the somatic, dendritic and axonal cellular compartments. Large-scale multi-electrode recordings from the macaque retina were used to test the effectiveness of the decomposition. The decomposition accurately localized the somatic and dendritic compartments of the cell. The imputed dendritic fields of RGCs correctly predicted the location and shape of their visual receptive fields. The inferred waveform amplitudes and shapes accurately identified the four major primate RGC types (ON and OFF midget and parasol cells), a substantial advance. Together, these findings may contribute to more accurate inference of RGC types and their original light responses in the degenerated retina, with possible implications for other electrical imaging applications.
Transcriptomic signatures across a critical sedimentation threshold in a major reef-building coral
Authors: Lock Colin , Gabriel Melissa M. , Bentlage Bastian 
Published: November 2023

AbstractSedimentation is a major cause of global near-shore coral reef decline. While negative impacts of sedimentation on coral reef community composition have been well documented, the effects of sedimentation on coral metabolismin situhave received comparatively little attention. Using transcriptomics, we identified gene expression patterns changing across a previously defined sedimentation threshold that was deemed critical due to changes in coral cover and community composition. We identified genes, pathways, and molecular processes associated with this transition that may allow corals, such asPorites lobata, to tolerate chronic, severe sedimentation and persist in turbid environments. Alternative energy generation pathways may helpPorites lobatamaintain a persistent stress response to survive while light and oxygen availability are diminished. We found evidence for the expression of genes linked to increased environmental sensing and cellular communication that likely allowPorites lobatato efficiently respond to sedimentation stress and associated pathogen challenges. Cell damage increases under stress; consequently, we found apoptosis pathways over-represented under severe sedimentation, a likely consequence of damaged cell removal to maintain colony integrity. The results presented here provide a framework for the response ofPorites lobatato sedimentation stress under field conditions. Testing this framework and its related hypotheses using multi-omics approaches can further our understanding of metabolic plasticity and acclimation potential of corals to sedimentation and their resilience in turbid reef systems.
The impact of SARS-CoV-2 variants on the likelihood of children identified as sources of infection in the NIH workforce: a cohort study
Authors: van Loben Sels Jessica M. , Bailin Heike B. , Bell Michael R. , McCormick-Ell Jessica , Das Sanchita , Roder Allison E. , Ghedin Elodie , McGann Michael , Castel Amanda D. , Rebecca Prevots D. , Kwan Jennifer L. 
Published: November 2023

AbstractBackgroundChildren (<18 years old) were not initially considered significant sources of infection (SOIs) for SARS-CoV-2. Risk mitigation strategies were thus prioritized for adults, and vaccination was inaccessible for children until mid-2021. Emergence of novel variants led to significant increases in COVID-19 cases in both children and adults. Whether these emergence events and increased vulnerability of unvaccinated children had a synergistic effect resulting in increased caseloads in adults requires further exploration.MethodsA retrospective cohort study was conducted among 3,545 workers diagnosed with COVID-19. Case details were compiled during contact investigations. Variants of concern were identified following sequencing of biological samples collected through employer-based testing programs. Logistic regression was performed to compare the odds of having a child SOI based on the dominant variant in the workforce.ResultsOne-fourth (24.5%) of the cohort reported having a child in-residence; 11.2% identified a child as their SOI. In Alpha-dominant months, the odds of having a child SOI were 0.3, and the child SOI was likely older (5-17 years old). The odds of having a child SOI increased to 1.3 and 2.2 in Delta- and Omicron-dominant months, respectively. The odds of having younger child SOIs (<5 years old) were significantly higher in Omicron-dominant months.ConclusionsChildren were highly likely to acquire the virus and posed a significant risk of transmission to their adult caretakers during Delta- and Omicron-dominant months. Without proper mitigation strategies in both the home and the workplace, child-associated transmission can threaten operations in the forms of staff shortages.What is already known on this topicIncreases in transmission trends related to SARs-CoV-2 Variants of Concern have been documented in the literature at the population level and in workplaces.What this study addsThis study looks more closely at the role that children played in transmission to adult workers, and therefore their potential to seed transmission outside of the home. This interface of transmission has been neglected in the literature but is key for future policy development.How this study might affect research, practice, or policyTransmission of SARS-CoV-2 from children to their caretakers may cause significantly increased odds of infection in a worker population. This may have second order effects for staffing, particularly in workgroups with employees of childbearing age. Employers should consider this in the design of their policies for continuity of operations, telework, and leave.
Quantifying18F-Fluorodeoxyglucose Uptake in Perianal Fistulas on PET/CT: A Retrospective Analysis
Authors: Huang Katherine , Garuba Favour , Ganapathy Aravinda , Bishop Grace , Zhang Hanjing , Lovato Adriene , Itani Malak , Viswanath Satish E. , Fraum Tyler J. , Deepak Parakkal , Ballard David H. 
Published: November 2023

AbstractRationale and ObjectivesThe use of18F-fluorodeoxyglucose positron emission tomography-computed tomography (FDG-PET/CT) in assessing inflammatory diseases has shown significant promise. Uptake patterns in perianal fistulas, which may be an incidental finding on PET/CT, have not been purposefully studied. Our aim was to compare FDG uptake of perianal fistulas to that of the liver and anal canal in patients who underwent PET/CT for hematologic/oncologic diagnosis or staging.Materials and MethodsWe retrospectively identified patients who underwent FDG- PET/CT imaging between January 2011 and May 2023, where the report described a perianal fistula or abscess. PET/CTs of patients included in the study were retrospectively analyzed to record the maximum standardized uptake value (SUVmax) of the fistula, abscess, anal canal, rectum, and liver. Fistula-to-liver and Fistula-to-anus SUVmaxratios were calculated. We statistically compared FDG activity among the fistula, liver, and anal canal. We also assessed FDG activity in patients with vs. without anorectal cancer, as well as across different St. James fistula grades.ResultsThe study included 24 patients with identifiable fistulas. Fistula SUVmax(mean=10.8±5.28) was significantly higher than both the liver (mean=3.09±0.584, p<0.0001) and the anal canal (mean=5.98± 2.63, p=0.0005). Abscess fistula SUVmaxwas 15.8 ± 4.91. St. James grade 1 fistulas had significantly lower SUVmaxcompared to grades 2 and 4 (p= 0.0224 and p=0.0295 respectively). No significant differences existed in SUVmaxratios between anorectal and non-anorectal cancer groups.ConclusionPerianal fistulas have increased FDG avidity with fistula SUVmaxvalues that are significantly higher than the anal canal.
Transcriptomic changes during the replicative senescence of human articular chondrocytes
Authors: Atasoy-Zeybek Aysegul , Hawse Gresin P. , Nagelli Christopher V. , De Padilla Consuelo Lopez , Abdel Matthew P. , Evans Christopher H. 
Published: November 2023

AbstractOsteoarthritis (OA) is a degenerative joint disease and a leading cause of disability worldwide. Aging is a major risk factor for OA, but the specific mechanisms underlying this connection remain unclear. Although chondrocytes rarely divide in adult articular cartilage, they undergo replicative senescencein vitrowhich provides an opportunity to study changes related to aging under controlled laboratory conditions. In this pilot study, we performed bulk RNA sequencing on early- and late-passage human articular chondrocytes to identify transcriptomic changes associated with cellular aging. Chondrocytes were isolated from the articular cartilage of three donors, two with OA (age 70-80 years) and one with healthy cartilage (age 26 years). Chondrocytes were serially passaged until replicative senescence and RNA extracted from early- and late-passage cells. Principal component analysis of all genes showed clear separation between early- and late- passage chondrocytes, indicating substantial age-related differences in gene expression. Differentially expressed genes (DEGs) analysis confirmed distinct transcriptomic profiles between early- and late-passage chondrocytes. Hierarchical clustering revealed contrasting expression patterns between the two isolates from osteoarthritic samples and the healthy sample. Focused analysis of DEGs on transcripts associated with turnover of the extra-cellular matrix and the senescence-associated secretory phenotype (SASP) showed consistent downregulation of Col2A1 and ACAN, and upregulation of MMP19, ADAMTS4, and ADAMTS8 in late passage chondrocytes across all samples. SASP components including IL-1α, IL-1β, IL-6, IL-7, p16INK4A(CDKN2A) and CCL2 demonstrated significant upregulation in late passage chondrocytes originally isolated from OA samples. Pathway analysis between sexes with OA revealed shared pathways such as extracellular matrix (ECM) organization, collagen formation, skeletal and muscle development, and nervous system development. Sex-specific differences were observed, with males showing distinctions in ECM organization, regulation of the cell cycle process as well as neuron differentiation. In contrast, females exhibited unique variations in the regulation of the cell cycle process, DNA metabolic process, and the PID-PLK1 pathway.
Genetic requirement ofdact1/2to regulate noncanonical Wnt signaling andcalpain 8during embryonic convergent extension and craniofacial morphogenesis
Authors: Carroll Shannon H. , Schafer Sogand , Kawasaki Kenta , Tsimbal Casey , Julé Amélie M. , Hallett Shawn A. , Li Edward , Liao Eric C. 
Published: November 2023

AbstractWnt signaling plays crucial roles in embryonic patterning including the regulation of convergent extension during gastrulation, the establishment of the dorsal axis, and later, craniofacial morphogenesis. Further, Wnt signaling is a crucial regulator of craniofacial morphogenesis. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled. However, the distinct relative functions of Dact1 and Dact2 during embryogenesis remain unclear. We found thatdact1anddact2genes have dynamic spatiotemporal expression domains that are reciprocal to one another suggesting distinct functions during zebrafish embryogenesis. Bothdact1anddact2contribute to axis extension, with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to thewnt11f2mutant. Utilizing single-cell RNAseq and an established noncanonical Wnt pathway mutant with a shortened axis (gpc4), we identifieddact1/2specific roles during early development. Comparative whole transcriptome analysis between wildtype andgpc4and wildtype anddact1/2compound mutants revealed a novel role fordact1/2in regulating the mRNA expression of the classical calpaincapn8. Over-expression ofcapn8phenocopiesdact1/2craniofacial dysmorphology. These results identify a previously unappreciated role ofcapn8and calcium-dependent proteolysis during embryogenesis. Taken together, our findings highlight the distinct and overlapping roles ofdact1anddact2in embryonic craniofacial development, providing new insights into the multifaceted regulation of Wnt signaling.
GADY algorithm: Towards an evolutionary protocol for bottom-up design of synthetic bacteria
Authors: Iñiguez Ulises Sánchez , Villaescusa Sara Lledó , Lahoz-Beltra Rafael 
Published: November 2023

AbstractSynthetic biology applications are currently based on the programming of bacteria with tailor-made circuits designedad hocby applying a top-down strategy. We introduce a novel algorithm oriented to design synthetic bacteria according to a bottom-up approach, i.e. via an ‘evolutionary programming’ algorithm. The proposed algorithm has been referred to as GADY: an acronym forGet signal,Antidote,Die when a killer gene is expressed, emitsYellow fluorescence. We include in this technical note a script of the algorithm in Gro cellular programming language, programming a colony of synthetic bacteria and illustrating its usefulness in a case of bioremediation or elimination of a strain of pathogenic bacteria.
A multi-faceted analysis of synapses reveals the role of neuroligin-1 cleavage in presynaptic vesicle accumulation in the lateral amygdala
Authors: Thomas Connon I. , Anderson Jordan R. , Alexis Arman , Guerrero-Given Debbie , Chavez Abigail , McNabb Micaiah C. , Unal Bengi , Ehlers Michael D. , Bolton McLean M. , Kamasawa Naomi 
Published: November 2023

AbstractNeuroligin-1 (NLGN1) is a cell adhesion molecule found at excitatory glutamatergic synapses in the brain which regulates synaptic function and maturation. Extracellular cleavage of NLGN1 by proteases has been shown to control vesicle release in cultured neurons, but nothing is known about the underlying changes to synapse structure that accompany this, or how synapse function is affected in brain tissue. We found that prevention of NLGN1 cleavage through mutation to the extracellular stalk domain increases synaptic vesicle docking and miniature excitatory post-synaptic current frequency at synapses of the lateral amygdala. Using a novel volume electron microscopy (vEM) analysis pipeline based on deep learning extraction of thousands of synapses and vesicles clouds and subsequent spatial analyses, we found that the total pool of synaptic vesicles shifts closer to the synapse in mutants. Furthermore, we observed an increased frequency of incomplete synapses that lack vesicle accumulation, pointing towards disruption of synaptic pruning and accumulation of putatively non-functioning synapses. Our study provides evidence of a structural and functional role of NLGN1 cleavage in native brain tissue, and establishes a foundation for vEM analysis of synapse-vesicle spatial relationships in other animal models of dysfunction and disease.