bluuebunny/crossref_metadata_2025_split huggingface dataset:
ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics
Authors: Gschwind Rémi , Ugarcina Perovic Svetlana , Weiss Maja , Petitjean Marie , Lao Julie , Coelho Luis Pedro , Ruppé Etienne 
Published: May 2023

Abstract
Metagenomics can be used to monitor the spread of antibiotic resistance genes (ARGs). ARGs found in databases such as ResFinder and CARD primarily originate from culturable and pathogenic bacteria, while ARGs from non-culturable and non-pathogenic bacteria remain understudied. Functional metagenomics is based on phenotypic gene selection and can identify ARGs from non-culturable bacteria with a potentially low identity shared with known ARGs. In 2016, the ResFinderFG v1.0 database was created to collect ARGs from functional metagenomics studies. Here, we present the second version of the database, ResFinderFG v2.0, which is available on the Center of Genomic Epidemiology web server (https://cge.food.dtu.dk/services/ResFinderFG/). It comprises 3913 ARGs identified by functional metagenomics from 50 carefully curated datasets. We assessed its potential to detect ARGs in comparison to other popular databases in gut, soil and water (marine + freshwater) Global Microbial Gene Catalogues (https://gmgc.embl.de). ResFinderFG v2.0 allowed for the detection of ARGs that were not detected using other databases. These included ARGs conferring resistance to beta-lactams, cycline, phenicol, glycopeptide/cycloserine and trimethoprim/sulfonamide. Thus, ResFinderFG v2.0 can be used to identify ARGs differing from those found in conventional databases and therefore improve the description of resistomes.
FunARTS, the Fungal bioActive compound Resistant Target Seeker, an exploration engine for target-directed genome mining in fungi
Authors: Yılmaz Turgut Mesut , Mungan Mehmet Direnç , Berasategui Aileen , Ziemert Nadine 
Published: May 2023

Abstract
There is an urgent need to diversify the pipeline for discovering novel natural products due to the increase in multi-drug resistant infections. Like bacteria, fungi also produce secondary metabolites that have potent bioactivity and rich chemical diversity. To avoid self-toxicity, fungi encode resistance genes which are often present within the biosynthetic gene clusters (BGCs) of the corresponding bioactive compounds. Recent advances in genome mining tools have enabled the detection and prediction of BGCs responsible for the biosynthesis of secondary metabolites. The main challenge now is to prioritize the most promising BGCs that produce bioactive compounds with novel modes of action. With target-directed genome mining methods, it is possible to predict the mode of action of a compound encoded in an uncharacterized BGC based on the presence of resistant target genes. Here, we introduce the ‘fungal bioactive compound resistant target seeker’ (FunARTS) available at https://funarts.ziemertlab.com. This is a specific and efficient mining tool for the identification of fungal bioactive compounds with interesting and novel targets. FunARTS rapidly links housekeeping and known resistance genes to BGC proximity and duplication events, allowing for automated, target-directed mining of fungal genomes. Additionally, FunARTS generates gene cluster networking by comparing the similarity of BGCs from multi-genomes.
PanDrugs2: prioritizing cancer therapies using integrated individual multi-omics data
Authors: Jiménez-Santos María José , Nogueira-Rodríguez Alba , Piñeiro-Yáñez Elena , López-Fernández Hugo , García-Martín Santiago , Gómez-Plana Paula , Reboiro-Jato Miguel , Gómez-López Gonzalo , Glez-Peña Daniel , Al-Shahrour Fátima 
Published: May 2023

Abstract
Genomics studies routinely confront researchers with long lists of tumor alterations detected in patients. Such lists are difficult to interpret since only a minority of the alterations are relevant biomarkers for diagnosis and for designing therapeutic strategies. PanDrugs is a methodology that facilitates the interpretation of tumor molecular alterations and guides the selection of personalized treatments. To do so, PanDrugs scores gene actionability and drug feasibility to provide a prioritized evidence-based list of drugs. Here, we introduce PanDrugs2, a major upgrade of PanDrugs that, in addition to somatic variant analysis, supports a new integrated multi-omics analysis which simultaneously combines somatic and germline variants, copy number variation and gene expression data. Moreover, PanDrugs2 now considers cancer genetic dependencies to extend tumor vulnerabilities providing therapeutic options for untargetable genes. Importantly, a novel intuitive report to support clinical decision-making is generated. PanDrugs database has been updated, integrating 23 primary sources that support &gt;74K drug–gene associations obtained from 4642 genes and 14 659 unique compounds. The database has also been reimplemented to allow semi-automatic updates to facilitate maintenance and release of future versions. PanDrugs2 does not require login and is freely available at https://www.pandrugs.org/.
ProAct: quantifying the differential activity of biological processes in tissues, cells, and user-defined contexts
Authors: Sharon Moran , Gruber Gil , Argov Chanan M , Volozhinsky Miri , Yeger-Lotem Esti 
Published: May 2023

Abstract
The distinct functions and phenotypes of human tissues and cells derive from the activity of biological processes that varies in a context-dependent manner. Here, we present the Process Activity (ProAct) webserver that estimates the preferential activity of biological processes in tissues, cells, and other contexts. Users can upload a differential gene expression matrix measured across contexts or cells, or use a built-in matrix of differential gene expression in 34 human tissues. Per context, ProAct associates gene ontology (GO) biological processes with estimated preferential activity scores, which are inferred from the input matrix. ProAct visualizes these scores across processes, contexts, and process-associated genes. ProAct also offers potential cell-type annotations for cell subsets, by inferring them from the preferential activity of 2001 cell-type-specific processes. Thus, ProAct output can highlight the distinct functions of tissues and cell types in various contexts, and can enhance cell-type annotation efforts. The ProAct webserver is available at https://netbio.bgu.ac.il/ProAct/.
Miniature RNAs are embedded in an exceptionally protein-rich mitoribosome via an elaborate assembly pathway
Authors: Valach Matus , Benz Corinna , Aguilar Lisbeth C , Gahura Ondřej , Faktorová Drahomíra , Zíková Alena , Oeffinger Marlene , Burger Gertraud , Gray Michael W , Lukeš Julius 
Published: May 2023

Abstract
The mitochondrial ribosome (mitoribosome) has diverged drastically from its evolutionary progenitor, the bacterial ribosome. Structural and compositional diversity is particularly striking in the phylum Euglenozoa, with an extraordinary protein gain in the mitoribosome of kinetoplastid protists. Here we report an even more complex mitoribosome in diplonemids, the sister-group of kinetoplastids. Affinity pulldown of mitoribosomal complexes from Diplonema papillatum, the diplonemid type species, demonstrates that they have a mass of &gt; 5 MDa, contain as many as 130 integral proteins, and exhibit a protein-to-RNA ratio of 11:1. This unusual composition reflects unprecedented structural reduction of ribosomal RNAs, increased size of canonical mitoribosomal proteins, and accretion of three dozen lineage-specific components. In addition, we identified &gt;50 candidate assembly factors, around half of which contribute to early mitoribosome maturation steps. Because little is known about early assembly stages even in model organisms, our investigation of the diplonemid mitoribosome illuminates this process. Together, our results provide a foundation for understanding how runaway evolutionary divergence shapes both biogenesis and function of a complex molecular machine.
Multiregional Population-Based Cohort Study for Evaluation of the Association Between Herpes Zoster and mRNA Vaccinations for Severe Acute Respiratory Syndrome Coronavirus-2: The VENUS Study
Authors: Ishiguro Chieko , Mimura Wataru , Uemura Yukari , Maeda Megumi , Murata Fumiko , Fukuda Haruhisa 
Published: May 2023

Abstract

Background
This study was performed to assess the increased risk of herpes zoster (HZ) associated with mRNA vaccines for coronavirus disease 2019.

Methods
This population-based cohort study was conducted in 4 municipalities in Japan. Individuals covered under public health insurance systems without a history of HZ were followed from October 1, 2020 to November 30, 2021. Incidence rates of HZ within 28 days of BNT162b2 or mRNA-1273 vaccination were compared. Adjusted incidence rate ratios (IRR) and 95% confidence intervals (CI) were estimated using a Poisson regression model, including vaccination status as a time-dependent covariate. Subgroup analyses by sex, age, and municipality were also conducted.

Results
A total of 339 548 individuals (median age, 74 years) were identified. During follow up, 296 242 individuals (87.2%) completed the primary series, among whom 289 213 and 7019 individuals received homologous BNT162b2 and mRNA-1273 vaccines, respectively. The adjusted IRRs of the first and second BNT162b2 vaccinations were 1.05 (95% CI, 0.84–1.32) and 1.09 (95% CI, 0.90–1.32), respectively. No cases of HZ were observed after mRNA-1273 vaccination. In subgroup analysis, the adjusted IRR of the second BNT162b2 vaccination was 2.94 (95% CI, 1.41–6.13) in individuals aged &lt;50 years old.

Conclusions
No increased risk of HZ was found after BNT162b2 vaccination in the overall study population. However, an increased risk was observed in the younger subgroup.
Functional outcomes and health-related quality of life following penile cancer surgery: a comprehensive review
Authors: Croghan Stefanie M , Cullen Ivor M , Raheem Omer 
Published: May 2023

Abstract

Introduction
Organ-sparing surgery (OSS) in penile cancer management aspires to maintain organ form and function and preserve health-related quality of life (HRQoL), yet there is a lack of integrated evidence exploring these outcomes.

Objectives
The aim sought to review HRQoL, functional, aesthetic, and psychological outcomes following OSS or radical penectomy for penile cancer.

Methods
A systematic review of MEDLINE and Cochrane databases included studies reporting on function (sexual, urinary or sensory), genital appearance or HRQoL/psychological well-being following surgical treatment of primary penile cancer. English-language reports (2000-2022), incorporating patient-reported or objective clinical outcome measures, were eligible. Studies of nonsurgical treatment strategies and those in the context of metastatic disease were excluded. Data were compiled and analyzed.

Results
Twenty-six studies were included. Sexual function was the most studied outcome (754 pooled respondents; 19 studies), most frequently with the original 15-item and abridged 5-item International Index of Erectile Function. Preservation of erectile function following OSS is generally described, with some reduction in overall sexual satisfaction cited. Heterogeneous assessment of voiding function with little preoperative evaluation render interstudy comparison difficult. Most patients appear able to void from a standing position following OSS, with spraying the most common symptom. Maintenance of some sensory function is described with both split-thickness skin grafting and urethral glanduloplasty following radical glansectomy. Limited studies suggest reasonable patient satisfaction with genital cosmesis post-OSS. A negative impact on HRQoL is described in most studies following penile cancer surgery, variably correlated with aggressiveness of penile surgery and addition of lymphadenectomy. Anxiety, depression, and reduced self-esteem have been reported in penile cancer survivors. Relationship well-being varies, with some survivors reporting this to be unchanged.

Conclusion
OSS can preserve elements of sexual, urinary, and sensory function, supporting advantages over radical penectomy for eligible patients. However, a comprehensive understanding remains limited due to small, heterogeneous patient cohorts, challenges in obtaining premorbid data, and variability in outcome measures. Standardization of patient-reported outcomes following OSS is desirable.
Accelerating Colorectal Cancer Screening and Follow-up through Implementation Science (ACCSIS) in Appalachia: protocol for a group randomized, delayed intervention trial
Authors: Paskett Electra D , Kruse-Diehr Aaron J , Oliveri Jill M , Vanderpool Robin C , Gray Darrell M , Pennell Michael L , Huang Bin , Young Gregory S , Fickle Darla , Cromo Mark , Katz Mira L , Reiter Paul L , Rogers Melinda , Gross David A , Fairchild Vickie , Xu Wendy , Carman Angela , Walunis Jean M , McAlearney Ann Scheck , Huerta Timothy R , Rahurkar Saurabh , Biederman Erika , Dignan Mark 
Published: May 2023

Abstract
Appalachian regions of Kentucky and Ohio are hotspots for colorectal cancer (CRC) mortality in the USA. Screening reduces CRC incidence and mortality; however, screening uptake is needed, especially in these underserved geographic areas. Implementation science offers strategies to address this challenge. The aim of the current study was to conduct multi-site, transdisciplinary research to evaluate and improve CRC screening processes using implementation science strategies. The study consists of two phases (Planning and Implementation). In the Planning Phase, a multilevel assessment of 12 health centers (HC) (one HC from each of the 12 Appalachian counties) was conducted by interviewing key informants, creating community profiles, identifying HC and community champions, and performing HC data inventories. Two designated pilot HCs chose CRC evidence-based interventions to adapt and implement at each level (i.e., patient, provider, HC, and community) with evaluation relative to two matched control HCs. During the Implementation Phase, study staff will repeat the rollout process in HC and community settings in a randomized, staggered fashion in the remaining eight counties/HCs. Evaluation will include analyses of electronic health record data and provider and county surveys. Rural HCs have been reluctant to participate in research because of concerns about capacity; however, this project should demonstrate that research does not need to be burdensome and can adapt to local needs and HC abilities. If effective, this approach could be disseminated to HC and community partners throughout Appalachia to encourage the uptake of effective interventions to reduce the burden of CRC.
Nursing Students’ Experiences of a Student-Led Collaborative Online International Learning Program
Authors: Malik Gulzar , Johnston Jacqueline , Peddle Monica 
Published: May 2023

Abstract

AIM
The aim of the study was to explore undergraduate nursing and midwifery students’ perspectives of participating in a student-led collaborative online international learning (COIL) program.

BACKGROUND
Research on COIL programs is limited. This program, developed across three global universities, was implemented to provide an internationalization-at-home experience for students during the COVID-19 pandemic.

METHOD
An exploratory descriptive qualitative design was employed using nursing students’ reflections and interviews.

RESULTS
Data analysis revealed four key themes: student-led learning experiences, personal gains, influence on professional practice, and becoming a global citizen. Students’ experiences offer insights into positive aspects of the program and highlight challenges to overcome.

CONCLUSION
The student-led COIL experience increased nursing students’ understanding of the dynamics of culture and nursing practices across different countries. Students’ personal growth and professional gains will potentially prepare them to work in multicultural environments and develop global citizenship attributes.
Epithelialization of Free Flap Vascular Pedicles through the Nasal Cavity after Long-term Follow-up: A Case Report
Authors: Wada Mana , Akita Shinsuke , Yasuda Saori , Ikeda Jun-Ichiro , Mitsukawa Nobuyuki 
Published: May 2023

Summary:
A 59-year-old man with right maxillary cancer presented with a right buccal fistula and an ectropion of the lower eyelid after multidisciplinary treatment. With no suitable vessels in the right face or neck for anastomosis, we planned reconstruction with a free thinned deep inferior epigastric artery perforator flap using the contralateral left facial artery and vein as the recipient. To simulate the length of the vascular pedicle, we used our original software and determined to use the route passing through the nasal cavity. The vascular pedicle was passed through a tunnel from the medial wall of the right maxillary sinus, through the nasal septum and the medial-frontal wall of the left maxillary sinus, to the left facial artery and vein. The flap survived completely, and facial deformity was corrected. At 1 year postoperatively, there had been concerns about the fragility of the vascular pedicle in the nasal cavity and the possibility of easy bleeding. Endoscopic examination revealed that the vascular pedicle in the nasal cavity was covered by fibrous tissue and multirow lineage epithelium, and an excisional biopsy indicated a low possibility of hemorrhage. Cutting off the vascular pedicle to prevent bleeding may not be necessary because the vascular pedicle through the nasal cavity becomes fibrotic and epithelialized in the surrounding area in the long term.
Reengagement strategies for hepatitis C patients lost to follow-up: A randomized clinical trial
Authors: Morales-Arraez Dalia , Hernández-Bustabad Alberto , Reygosa Castro Cristina , Benitez-Zafra Federica , Nicolás-Pérez David , Crespo Orestes , Díaz-Flores Felicitas , Hernández-Guerra Manuel 
Published: May 2023

Background and Aims:
To achieve the World Health Organization’s goal of eliminating HCV by 2030, reengagement of lost to follow-up cases is mandatory. However, there is lack of evidence concerning the best strategy. Our study evaluated the effectiveness, efficiency, predictive factors, and costs of 2 different strategies.

Methods:
We identified patients positive for HCV antibodies without RNA requests from 2005 to 2018. Patients fulfilling trial criteria (NCT04153708) were randomized to (1) phone call or (2) letter of invitation to schedule an appointment, followed by switching strategy.

Results:
Three hundred forty-five patients among 1167 lost to follow-up were identified. An analysis of the first 270 randomized patients (72% male, 51±13 y) showed a higher contact rate in the mail than in the phone call strategy (84.5% vs. 50.3%). In the intention-to-treat analysis, no differences were found related to appointment attendance (26.5% vs. 28.5%). Regarding efficiency, 3.1 letters and 8 phone calls were needed to successfully link 1 patient (p<0.001) but dropped down to 2.3 phone calls if we only considered the first call attempt (p=0.008). Prior specialist’s evaluation and HCV testing in the predirect-acting antiviral era were the only factors associated with no showing up for the appointment. The cost per patient was €621.3 (2.5 quality-adjusted life-years) in the phone call strategy and €611.8 (2.4 quality-adjusted life-years) in the mail letter strategy.

Conclusions:
Reengagement of patients with HCV is feasible, and equally effective with similar costs in both strategies. The mail letter was more efficient, except when only 1 phone call was considered. Prior specialist’s evaluation and testing in the predirect-acting antiviral era were factors associated with nonattendance to the appointment.
Biliary microbial patterns in primary sclerosing cholangitis are linked to poorer transplant-free survival
Authors: Özdirik Burcin , Scherf Maria , Brumercek Ana , Nicklaus Jule M. , Kruis Tassilo , Haber Philipp K. , Pratschke Johann , Tacke Frank , Sigal Michael 
Published: May 2023

Background:
Factors that determine individual disease course of patients with primary sclerosing cholangitis (PSC) are poorly understood. Although an association between gut microbes and disease outcome has been suggested, little is known about the role of microbes in the biliary tract.

Methods:
We analyzed microbial cultures from bile specimens obtained during routine endoscopic retrograde cholangiopancreatography (ERCP) and intraoperatively before liver transplantation in 114 patients with PSC in our tertiary academic center. The presence of bacterial and fungal species was correlated with clinical characteristics and outcome data.

Results:
A total of 87 patients (76%) had positive bile culture results. The presence of concomitant inflammatory bowel disease (IBD) was associated with positive bile culture results in multivariate analysis (OR, 4.707; 95% CI, 1.688–13.128; p=0.003). Enterococcus spp. in the bile was associated with a more frequent occurrence of liver transplantation and/or death (OR, 2.778; 95% CI, 1.147–6.728; p=0.021) and recurrent (≥3) cholangitis episodes (OR, 2.839; 95% CI, 1.037–7.768; p=0.037). Biliary candidiasis was linked to a higher frequency of recurrent (≥3) cholangitis episodes (OR, 5.677; 95% CI, 1.940–16.616; p=0.001). Proton pump inhibitor intake conferred a clinical feature associated with biliary candidiasis in multivariate analysis (OR, 3.559; 95% CI, 1.275–9.937; p=0.016).

Conclusions:
Our data indicate that in patients with PSC, presence of Enterococcus spp. and Candida spp. in bile is associated with an adverse outcome. Concomitant IBD is linked to presence of microbes in bile, and proton pump inhibitor intake is a feature associated with biliary candidiasis in patients with PSC.
Assessment of Protective Action Decision Making during Nuclear Power Plant Biennial Exercises
Authors: Smith Todd , Reese Steven 
Published: May 2023

Abstract
Radiological emergency preparedness for commercial nuclear power plants provides planning for implementing predetermined, prompt protective actions such as evacuation and shelter-in-place. In the event of a significant radiological release, onsite emergency response organizations will notify offsite response organizations and provide a protective action recommendation. The cognizant offsite authority will then make a protective action decision and inform the public of the need to act. Both the protective action recommendation and decision are driven by US Environmental Protection Agency protective action guides. Protective action strategies contain conservatisms and are intended to balance protection against other factors to ensure that actions result in more benefit than harm. But added conservatism can potentially shift the risks to those inherent to the protective action with no added benefit of protection. Protective action recommendations and protective action decisions made during biennial exercises were analyzed to assess how well they comport with the protective action guides. Trends in precautionary actions and the use of potassium iodide were also investigated. The analysis shows that protective action decisions typically exceed the protective action recommendation, resulting in an increase in the number of potential evacuees. However, exercise dose projection data do not appear to support such extensive initial evacuation decisions based on consideration of the protective action guides.