bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serum levels of endocannabinoids and related lipids in painful vs painless diabetic neuropathy: results from the Pain in Neuropathy Study
Authors: Bäckryd Emmanuel , Themistocleous Andreas , Stensson Niclas , Rice Andrew S. C. , Tesfaye Solomon , Bennett David L. , Gerdle Björn , Ghafouri Bijar 
Published: August 2023

Abstract
N-arachidonoylethanolamine (also known as anandamide) and 2-arachidonoylglycerol are activators of the cannabinoid receptors. The endocannabinoid system also includes structurally and functionally related lipid mediators that do not target cannabinoid receptors, such as oleoylethanolamide, palmitoylethanolamide, and stearoylethanolamide. These bioactive lipids are involved in various physiological processes, including regulation of pain. The primary aim of the study was to analyze associations between serum levels of these lipids and pain in participants in the Pain in Neuropathy Study, an observational, cross-sectional, multicentre, research project in which diabetic patients with painless or painful neuropathy underwent deep phenotyping. Our hypothesis was that painful neuropathy would be associated with higher levels of the 5 lipids compared with painless neuropathy. Secondary aims were to analyze other patient-reported outcome measures and clinical data in relationship to lipid levels. The lipid mediators were analyzed in serum samples using liquid chromatography tandem mass spectrometry (LC-MS/MS). Serum levels of anandamide were significantly higher in the painful group, but the effect size was small (Cohen d = 0.31). Using cluster analysis of lipid data, patients were dichotomized into a “high-level” endocannabinoid group and a “low-level” group. In the high-level group, 61% of patients had painful neuropathy, compared with 45% in the low-level group (P = 0.039). This work is of a correlative nature only, and the relevance of these findings to the search for analgesics targeting the endocannabinoid system needs to be determined in future studies.
Effects of machine perfusion strategies on different donor types in liver transplantation: a systematic review and meta-analysis
Authors: Liang Aijun , Cheng Weiye , Cao Peihua , Cai ShaoRu , Zhang Linya , Zhong Kebo , Nie Yu 
Published: August 2023

Background:Increasing use of extended-criteria donors (ECD) set higher requirements for graft preservation. Machine perfusion (MP) improves orthotopic liver transplantation (OLT) outcomes but its effects on different donor types remains unclear. Our aim was to assess the effects of hypothermic machine perfusion (HMP), normothermic machine perfusion (NMP), or normothermic regional perfusion (NRP) versus static cold storage (SCS) on different donor types.Materials and Methods:A literature search comparing the efficacy of MP versus SCS in PubMed, Cochrane and EMBASE database was conducted. Meta-analysis was performed to obtain pooled effects of MP on extended criteria donors (ECD), donation after circulatory death (DCD), donor after brainstem death.Results:39 studies were included (9 RCTs and 30 cohort studies). Compared with SCS, HMP significantly reduced the risk of non-anastomotic biliary stricture (NAS) (OR 0.43, 95%CI 0.26-0.72), major complications (OR 0.55, 95%CI 0.39-0.78), early allograft dysfunction (EAD) (OR 0.46, 95%CI 0.32-0.65) and improve one-year graft (OR 2.36, 95%CI 1.55-3.62) in ECD-OLT. HMP also reduced primary nonfunction (PNF) (OR 0.40, 95%CI 0.18-0.92) and acute rejection (OR 0.62, 95%CI 0.40-0.97). NMP only reduced major complications in ECD-OLT (OR 0.56, 95%CI 0.34-0.94), without favorable effects on other complications and survival. NRP lower the overall risk of NAS (OR 0.27, 95%CI 0.11-0.68), PNF (OR 0.43, 95%CI 0.22-0.85), EAD (OR 0.58, 95%CI 0.42-0.80) and meanwhile improved one-year graft survival (OR 2.40, 95%CI 1.65-3.49) in control DCD-OLT.Conclusions:HMP might currently be considered for marginal livers as it comprehensively improves ECD-OLT outcomes. NMP assists some outcomes in ECD-OLT but more evidence regarding NMP-ECD is warrant. NRP significantly improves DCD-OLT outcomes and is recommended where longer non-touch periods exist.
Longitudinal surveillance of three biomarkers to predict recurrence of hepatocellular carcinoma after radical resection
Authors: Tong Jing-shu , Lu Cai-de , Lu Chang-jiang , Zheng Siming , Mao Shu-qi 
Published: August 2023

Background
Radical resection is a curative treatment for patients with hepatocellular carcinoma (HCC), but the incidence of recurrence remains high. We aimed to explore the performance of predicting HCC recurrence by longitudinal surveillance of the protein induced by vitamin K absence (PIVKA-II), alpha- fetoprotein (AFP), and lectin-reactive AFP (AFP-L3) during postoperative follow-up.

Methods
Patients who underwent radical resection for HCC at the Ningbo Medical Centre Lihuili Hospital between January 2015 and December 2020 were included. All enrolled patients regularly monitor PIVKA-II, AFP, AFP-L3 every 3 months during postoperative follow-up. The surveillance performance of PIVKA-II, AFP, AFP-L3 during follow-up for the prediction of HCC recurrence was compared in patients. The generalized estimation equation (GEE) was used to analyze the trends of the tumor biomarkers and interactions with time. Area under the receiver operator characteristic (AUROC) curves, the optimal cut-off value, the sensitivity and specificity were calculated to evaluate the performance of the three biomarkers. The recurrence-free survival (RFS) and overall survival (OS) of patients with any of the elevated biomarkers was analyzed by Kaplan–Meier curves and the log-rank test. Multivariate logistic regression models were used to analyze potential risk factors for recurrence.

Results
The GEE analysis indicated that PIVKA-II, AFP, AFP-L3 in the recurrence patients were higher than the no recurrence patients during follow-up, PIVKA-II and AFP showed increasing trends from 6 months before recurrence. In predicting recurrence, the AUROCs for PIVKA-II, AFP, AFP-L3 and their combination were 0.885, 0.754, 0.781 and 0.885 respectively, the optimal cut-off value for PIVKA-II, AFP, AFP-L3 was 29.5 mAU/ml, 10.7 ng/L, 1.5% respectively. The sensitivity in predicting recurrence for PIVKA-II, AFP, AFP-L3 and combination were 75.0, 54.7, 57.8 and 79.7% respectively. The RFS and the OS of patients with any of the biomarkers elevated during the follow-up was significantly shorter than that without elevated biomarkers (P < 0.001). Multivariate analysis showed that any of the biomarkers elevated was the independent risk factor of recurrence.

Conclusion
Longitudinal surveillance of PIVKA-II, AFP and AFP-L3 can effectively predict recurrence of HCC after operation.
Is histological healing more clinically valuable than endoscopic healing in Crohn’s disease?
Authors: Zhang Ting , Zhang Qi-De , Jin Tian , Li Wen-Jie , Wang Han-Ying , Lu Xiao-Yun , Li Xiu-Qing , Liu Shi-Jia , Yang Bo-Lin 
Published: August 2023

Objectives
Small bowel (SB) endoscopic healing has not been well explored in patients with Crohn’s disease (CD). This study aimed to assess the clinical utility of SB endoscopic mucosal and histological healing in patients with CD.

Methods
In total, 99 patients with CD in clinical–serological remission were retrospectively followed after they underwent colonoscopy and double-balloon enteroscopy. Time until clinical relapse (CD activity index of >150 with an increase of >70 points) and serological relapse (abnormal elevation of C-reactive protein levels) constituted the primary endpoints.

Results
Of the 99 patients, 75 (74.7%) exhibited colonoscopic healing and 43 (43.4%) exhibited SB endoscopic healing. Clinical relapse, serological relapse, hospitalization, and surgery occurred in 8 (18.6%), 11 (25.6%), 11 (25.6%), and 2 (4.6%) patients, respectively. Of the 43 patients who exhibited SB endoscopic healing, 21 (48.8%) achieved histological healing. Clinical relapse, serological relapse, hospitalization, and surgery occurred in 4 (19.0%), 7 (33.3%), 7 (33.3%), and 1 (4.8%) patient, respectively. There was no statistically significant difference in the number of patients who relapsed, were hospitalized, or underwent surgery between those who exhibited histological healing and those who did not.

Conclusion
A substantial number of patients who were in clinical–serological remission did not undergo SB endoscopic healing, and the lesions increased their risk of clinical relapse. Thus, endoscopic healing may be of greater clinical value than histological healing when evaluating the remission of patients with CD.
Real-time assessment of H. pylori during the endoscopic assessment of individuals with gastric intestinal metaplasia: a possible way to reduce the burden of care
Authors: Esposito Gianluca , Libânio Diogo , Ligato Irene , Ramos Silva Diana , Dilaghi Emanuele , Ortigão Raquel , Carabotti Marilia , Chaves Jéssica , Annibale Bruno , Dinis-Ribeiro Mário 
Published: August 2023

Objectives
The management of individuals with gastric intestinal metaplasia (GIM) includes biopsies for its staging and to diagnose Helicobacter pylori (Hp). Advanced-stage GIM can be estimated by endoscopy through EGGIM, and a new device permits the real-time assessment of ammonia for the identification of Hp infection. The aim of this study was to assess the simultaneous use of EGGIM and real-time assessment of ammonia to avoid biopsies and reduce the burden of care in clinical practice.

Methods
A multicentre study involving 101 consecutively enrolled patients [52% male; 65(18–85) years]. During endoscopy, gastric juice was aspirated and analysed; EGGIM was determined in real-time. Targeted biopsies were performed and histopathological assessment was used as gold standard.

Results
Advanced-stage GIM were detected in 14.9% of patients and Hp infection in 18.8%. EGGIM showed for advanced-stage GIM a sensitivity, specificity and NPV of 86.7%, 84.9% and 97.3%, whilst real-time assessment of ammonia, 83.3%, 78.2% and 95.4%, respectively. Gastric juice was insufficient in 5 (5.0%). Overall, 64 (67%) patients were correctly diagnosed by EGGIM and real-time assessment of ammonia. If the 47 (49%) patients negative to both assessments would have avoided biopsies, only 4 (4.2%) would have been missed: two with advanced-stage GIM and two with Hp infection.

Conclusion
The combination of endoscopic assessment and real-time analysis of Hp allows the exclusion of advanced-stage GIM or Hp infection without the need of biopsies in a significant proportion of individuals. This may allow in specific situations to abstain from biopsies reducing the burden of care.
Cultivation-based characterization of biliary microbiota in bile samples collected during routine endoscopic retrograde cholangiography: 10 years of experience at a tertiary center
Authors: Forster Kilian , Klein Friederike , Simon Nicolas , Chhatwal Patrick , Ziesing Stefan , Heidrich Benjamin , Solbach Philipp 
Published: August 2023

Introduction
Bile has long been considered sterile. Recent studies show that bacteria can frequently be detected in bile and certain bacterial species are associated with bile duct-associated liver disease.

Objectives
To detect bacterial species and antibiotic resistance in bile in bile duct-associated liver disease.

Methodology
To evaluate microbiological findings of bile samples obtained during ERCP at a tertiary center from 2009 to 2019.

Results
There were 1885 bile samples from 992 patients examined by cultural microbiological analysis. Germs were detected in 91% of the samples. Most bile samples (n) were obtained from patients who had undergone liver transplantation (LTX; n = 556), followed by patients with primary sclerosing cholangitis (PSC; n = 287). Enterococci were detected in 67% of samples, followed by E. coli (32.2%) and Klebsiella (28.2%). Of 1151 enterococci detected, 13.1% were vancomycin (VRE)s and of 216 staphylococci detected, 10% were ORSA. The proportion of VRE increased with the number of tests performed during ERCPs (P < 0.01; chi-square) and increased 2.5-fold over 10 years, whereas the detection of ORSA remained stable. Patients with cholecystolithiasis were significantly more likely to have evidence of VRE in bile compared to LTX and PSC patients (P = 0.02, P < 0.01; chi-square). The most abundant bacterial genera showed highly statistically significant differences in their levels of liver enzymes and c-reactive protein (P < 0.001).

Conclusion
Knowledge of the bacterial composition of bile in various bile duct-associated liver diseases may allow more targeted antibiotic use in the future.
Acute paraquat poisoning complicated by acute kidney injury and lung fibrosis: a case report from Nepal
Authors: Yadav Rupesh K. , Gurung Shekhar , Karki Saurab , Lama Susan , Tamang Shrejung , Poudel Manish 
Published: August 2023

Introduction and importance:
While incidents are rare elsewhere, paraquat herbicide poisoning is a serious medical issue in some parts of Asia. It can cause the failure of various organs, including the heart, kidneys, liver, adrenal glands, central nervous system, muscles, and spleen. Due to its inherent toxicity and lack of available therapies, paraquat has a very high case fatality rate.

Case presentation:
The authors discuss a case of a 15-year-old female with an alleged history of paraquat ingestion who presented with complaints of vomiting, abdominal pain, and loose stools. Initially, she had gastrointestinal symptoms, but she developed renal failure and respiratory symptoms and died of multiple organ failure.

Clinical discussion:
Acute gastrointestinal tract necrosis and multiorgan failure are the initial effects of paraquat intake, and among those who survive the immediate post-ingestion interval, the lung is the target organ for poisoning. Ingestion of large amounts of liquid concentrates results in fulminant organ failure: pulmonary edema, cardiac, renal, and hepatic failure, and convulsions. The course of treatment can range from supportive care alone to various integration of immune modulation, antioxidant therapy, hemoperfusion, and hemodialysis.

Conclusion:
Patients presenting to the emergency department with an alleged history of ingestion of paraquat poisoning should be admitted even if they have mild symptoms initially. There is no specific antidote available. Early renal failure, along with progressive pulmonary fibrosis, can lead to death.
Standardizing Care of the Late Preterm Infant
Authors: Smith Pamela C. , Yonkaitis Catherine F. , Reigart Melissa M. 
Published: August 2023

Abstract

Background:
Late preterm infants are infants born between 34 and 36 6/7 weeks gestation. Compared to term infants, late preterm infants are at increased risk for breastfeeding difficulties, hypoglycemia, hyperbilirubinemia, and hypothermia due to their relative physiologic and metabolic immaturity.

Problem:
Medical record reviews performed at a level III maternal and newborn hospital in central Illinois revealed only 64% of late preterm infants admitted to the newborn nursery received care per the unit late preterm infant policy. The aim of this quality improvement project was to increase nurse adherence to the policy to 80%.

Methods:
Between May 2022 and September 2022, several interventions were implemented for maternal–child nurses and support clinicians: an education offering, creation of a late preterm infant-specific breastfeeding log, and electronic medical record updates. Post-intervention medical record reviews measured policy adherence through documentation of feeding sessions, hypoglycemia, hypothermia, and hyperbilirubinemia. Descriptive statistics were performed to determine improvement.

Results:
Nurse adherence to the late preterm infant policy increased to 90% over the period of the project.

Clinical Implications:
Late preterm infant care protocols should be in place in all newborn nurseries. Late preterm infant policy adherence can be supported through electronic medical record prompts, use of a late preterm infant-specific breastfeeding log, and continuing education.
Analysis of 3,760 hematologic malignancies reveals rare transcriptomic aberrations of driver genes
Authors: Cao Xueqi , Huber Sandra , Ahari Ata Jadid , Traube Franziska R. , Seifert Marc , Oakes Christopher C. , Secheyko Polina , Vilov Sergey , Scheller Ines , Wagner Nils , Yépez Vicente A. , Blombery Piers , Haferlach Torsten , Heinig Matthias , Wachutka Leonhard , Hutter Stephan , Gagneur Julien 
Published: August 2023

AbstractBackgroundRare oncogenic driver events, particularly affecting the expression or splicing of driver genes, are suspected to substantially contribute to the large heterogeneity of hematologic malignancies. However, their identification remains challenging.MethodsTo address this issue, we generated the largest dataset to date of matched whole genome sequencing and total RNA sequencing of hematologic malignancies from 3,760 patients spanning 24 disease entities. Taking advantage of our dataset size, we focused on discovering rare regulatory aberrations. Therefore, we called expression and splicing outliers using an extension of the workflow DROP (Detection of RNA Outliers Pipeline) and AbSplice, a variant effect predictor that identifies genetic variants causing aberrant splicing. We next trained a machine learning model integrating these results to prioritize new candidate disease-specific driver genes.ResultsWe found a median of seven expression outlier genes, two splicing outlier genes, and two rare splice-affecting variants per sample. Each category showed significant enrichment for already well-characterized driver genes, with odds ratios exceeding three among genes called in more than five samples. On held-out data, our integrative modeling significantly outperformed modeling based solely on genomic data and revealed promising novel candidate driver genes. Remarkably, we found a truncated form of the low density lipoprotein receptorLRP1Btranscript to be aberrantly overexpressed in about half of hairy cell leukemia variant (HCL-V) samples and, to a lesser extent, in closely related B-cell neoplasms. This observation, which was confirmed in an independent cohort, suggestsLRP1Bas a novel marker for a HCL-V subclass and a yet unreported functional role ofLRP1Bwithin these rare entities.ConclusionsAltogether, our census of expression and splicing outliers for 24 hematologic malignancy entities and the companion computational workflow constitute unique resources to deepen our understanding of rare oncogenic events in hematologic cancers.
Migration and the Emergence of Chagas Disease Vectors in the Growing City of El Pedregal, Peru
Authors: Gonçalves Raquel , Hacker Kathryn P. , Condori Carlos , Xie Sherrie , Borrini-Mayori Katty , Riveros Lina Mollesaca , Apaza Roger Quispe , Arratea Manuel Ysidro , Nativio Gustavo , Castillo-Neyra Ricardo , Paz-Soldan Valerie A. , Levy Michael Z. 
Published: August 2023

AbstractThe city of El Pedregal grew out of a desert, following an agricultural irrigation project in Southern Peru. We conducted door-to-door entomological surveys to document the emergence of triatomines and bed bugs into this new urban environment. We inspected 5,191 households forTriatoma infestans(known locally as theChirimacha); 21 (0.41%) were infested. These were extremely spatially clustered (Ripley’s K p-value <0.001 at various spatial scales). Using remote sensing we compared the year of construction of infested to un-infested households and found that infested houses were older than controls (Wilcoxon rank-sum: W=33; p=0.02). We confirmed infestations through a subsequent bed bug specific inspection in 34 households. These households were more spatially disperse across El Pedregal. To gain a better understanding of the context surrounding triatomine infestations, we conducted in-depth interviews with residents to explore their migration histories and previous experiences withChirimachas. Main reasons for migration includes searching for work on land, opportunity to buying a house, and scape adverse climate effects. Permanent migration flow and poor housing conditions create suitable environment for emergence triatomine infestation. We discuss how changes in the landscape could potentially heighten vulnerability to vector-borne illnesses.Author summaryLarge-scale irrigation and changes in land-use have been linked with emergence of infectious disease worldwide. In El Pedregal, Southern Peru, the Majes-Siguas irrigation was designed to supply water to agribusiness companies installed in a desert area. This project has propelled a constant migration flow and the growth of this new city, promoting conditions to emergence ofTriatoma infestans, an insect vector of Chagas disease, as well as bed bugs. Triatomine infestation presented a clustered pattern, its dispersion limited by unoccupied houses. Triatomine infested houses tend to be older than other houses. Bed bug infestations were more spread out, and not related to construction age. Householders’ stories of migration shed light on some of the socioeconomic determinants that promote conditions for infestation. Amongst these, living in poor housing conditions, and the constant migration flow; driven by seeking opportunities to work, to buy a house, or to escape from adverse climate effects in other farming regions. Environmental and socioeconomic impacts of large-scale development disproportionately affect vulnerable populations. Design of surveillance systems that account for these contexts is urgently needed to support early detection and control of emergence of vector-borne diseases.
Sensitivity and consistency of long- and short-read metagenomics and epicPCR for the detection of antibiotic resistance genes and their bacterial hosts in wastewater
Authors: Lou Esther G. , Fu Yilei , Wang Qi , Treangen Todd J. , Stadler Lauren B. 
Published: August 2023

AbstractWastewater surveillance is a powerful tool to assess the risks associated with antibiotic resistance in communities. One challenge is selecting which analytical tool to deploy to measure risk indicators, such as antibiotic resistance genes (ARGs) and their respective bacterial hosts. Although metagenomics is frequently used for analyzing ARGs, few studies have compared the performance of long-read and short-read metagenomics in identifying which bacteria harbor ARGs in wastewater. Furthermore, for ARG host detection, untargeted metagenomics has not been compared to targeted methods such as epicPCR. Here, we 1) evaluated long-read and short-read metagenomics as well as epicPCR for detecting ARG hosts in wastewater, and 2) investigated the host range of ARGs across the WWTP to evaluate host proliferation. Results highlighted long-read revealed a wider range of ARG hosts compared to short-read metagenomics. Nonetheless, the ARG host range detected by long-read metagenomics only represented a subset of the hosts detected by epicPCR. The ARG-host linkages across the influent and effluent of the WWTP were characterized. Results showed the ARG-host phylum linkages were relatively consistent across the WWTP, whereas new ARG-host species linkages appeared in the WWTP effluent. The ARG-host linkages of several clinically relevant species found in the effluent were identified.