bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is There a Benefit From Islet Autotransplantation in Patients With Type 1 Diabetes Mellitus Undergoing Total Pancreatectomy?
Authors: Mun Kyu Shik , Nathan Jaimie D. , Lin Tom K. , Elder Deborah A. , Jegga Anil G. , Naren Anjaparavanda P. , Abu-El-Haija Maisam 
Published: June 2022

Abstract
Children with acute recurrent and chronic pancreatitis (CP) experience abdominal pain that leads to hospitalizations, opioid dependence, and poor quality of life. Total pancreatectomy with islet autotransplantation (TPIAT) is offered as a surgical option in management of debilitating pancreatitis that fails medical and endoscopic therapy to reduce or eliminate pain. Given that patients with type 1 diabetes mellitus (T1DM) lack insulin-producing β cells, the outcomes from autotransplanting islet isolates back into total pancreatectomy patients with T1DM are not fully known.
We performed TPIAT in 2 CP patients who also had a diagnosis of T1DM for at least 6 years before the operation and evaluated the clinical and laboratory outcomes before and after the operation. Postoperatively both patients' abdominal pain had significantly subsided, they were weaned off opioid medications, and they were able to return to full-time school attendance. In addition, total daily dose of insulin in 1 patient was able to be slightly reduced at 12 months post-TPIAT. We observed in vitro that residual α cells and β cells in T1DM islets were able to secrete a small amount of glucagon and insulin, respectively.
Incidence of Pancreatic Intraepithelial Neoplasia in an Autopsy Series
Authors: Longnecker Daniel S. , Suriawinata Arief A. 
Published: June 2022

Objectives
Pancreatic intraepithelial neoplasia (PanIN) is the currently preferred designation for putative preneoplastic changes in the pancreas. There are few data for the incidence of PanIN in the general population. Our goal was to determine the incidence of PanIN in a large group of pancreases obtained at autopsy.

Methods
Slides stained with hematoxylin and eosin were scanned to count PanIN.

Results
We found multiple PanINs in most pancreases and at least 1 in 86.4% of 154 pancreases when multiple slides (8–12) from each were examined. The average age at autopsy was 62 years, and 90% of the patients were 40 years or older. Several questions were raised by our observations. Should a minimum size be defined for classification as PanIN? Do PanINs occur in lesions that apparently arise from acinar to ductal metaplasia? Does squamous metaplasia in PanIN have any special significance, and do purely squamous lesions have preneoplastic significance?

Conclusions
We conclude that the incidence of PanIN is higher than previously reported.
Brief Report: It's Time to Embed Health-Related Quality of Life Across all Steps of the HIV Care Cascade
Authors: Arora Anish K. , Lessard David , Dubé Karine , Lebouché Bertrand 
Published: June 2022

Background:
Calls for stakeholders across the global HIV landscape to widely and systematically adopt person-centered care and patient-oriented research approaches have been made by HIV scholars, clinicians, patients, and groups such as the Joint United Nations Programme on HIV/AIDS (UNAIDS). Such calls implicitly acknowledge that the end goal of HIV care, research, and advocacy goes beyond HIV viral suppression or undetectability toward ensuring optimal health-related quality of life (HrQoL) for people living with HIV (PLWH). Indeed, global efforts have focused on keeping people alive yet have failed to ensure that they feel alive.

Approach:
In this brief report, we highlight the progress that has been made toward evolving the HIV care cascade to better represent actual experiences of PLWH, especially those that are most vulnerable and marginalized. We then describe what person-centered care, patient-oriented research, and HrQoL are and why they are important for our current context in HIV. We conclude by sharing 2 propositions for the global HIV community to consider moving forward.

Conclusions:
HIV care must not only focus on viral suppression but also better recognize the intersecting and multifaceted challenges faced by PLWH when taking HIV treatment and engaging in care. Evaluating HrQoL at each step of the cascade using validated patient-reported outcome and experience measures would assist in systematically tracking and addressing challenges faced by PLWH. Measures chosen through global consensus may facilitate rigorous comparisons across jurisdictions. Adopting a patient-oriented research paradigm will also be crucial for empowering and meaningfully engaging patients throughout the research process.
The Effect of the Fibrotherapy Intervention Program on the Coping Patterns of Fibromyalgia Patients
Authors: Cohen-Biton Liraz , Buskila Dan , Nissanholtz-Gannot Rachel 
Published: June 2022

Background
Fibromyalgia (FM) syndrome is characterized by physical symptoms such as pain, fatigue, and sleep disorders, as well as mental symptoms that include depression, mental exhaustion, and a sense of hopelessness. The current study focuses on 3 main strategies used by FM patients living in communities in the Gaza Envelope who are under constant security threat: problem-oriented, emotion-oriented, and avoidance.

Methods
The study introduces a groundbreaking intervention program based on a fibrotherapy intervention (FTI) program developed at the Rehabilitation Center “Ezra Le'Marpeh” led by Rabbi Avraham Elimelech Firer. The cohort study sample consists of 96 women who have been diagnosed with FM and have participated in the FTI program for 10 weeks. The study uses mixed methods of quantitative and qualitative analyses in which 16 women from the sample were interviewed. In addition to collecting demographic information and medical data, the study used the Brief Cope questionnaire.

Results
The findings corroborate the hypothesis and show a difference between the coping patterns of FM patients before and after the intervention.

Conclusions
The sharing experience as a part of the FTI program can lead FM patients to adopt positive disease management strategies, which may improve their quality of life.
The Efficacy and Safety of SGLT2 Inhibitor in Diabetic Kidney Transplant Recipients
Authors: Lim Jeong-Hoon , Kwon Soie , Jeon Yena , Kim Young Hoon , Kwon Hyunwook , Kim Yon Su , Lee Hajeong , Kim Yong-Lim , Kim Chan-Duck , Park Sun-Hee , Lee Jong Soo , Yoo Kyung Don , Son Hyung Eun , Jeong Jong Cheol , Lee Jeonghwan , Lee Jung Pyo , Cho Jang-Hee 
Published: June 2022

Background.
The efficacy and safety of sodium-glucose cotransporter 2 inhibitors (SGLT2i) have not been investigated in kidney transplant recipients (KTRs) with diabetes. We evaluated the impact of SGLT2i in a multicenter cohort of diabetic KTRs.

Methods.
A total of 2083 KTRs with diabetes were enrolled from 6 transplant centers in Korea. Among them, 226 (10.8%) patients were prescribed SGLT2i for >90 d. The primary outcome was a composite outcome of all-cause mortality, death-censored graft failure (DCGF), and serum creatinine doubling. An acute dip in estimated glomerular filtration rate (eGFR) over 10% was surveyed after SGLT2i use.

Results.
During the mean follow-up of 62.9 ± 42.2 mo, the SGLT2i group had a lower risk of primary composite outcome than the control group in the multivariate and propensity score-matched models (adjusted hazard ratio, 0.43; 95% confidence interval, 0.24-0.78; P = 0.006 and adjusted hazard ratio, 0.45; 95% confidence interval, 0.24-0.85; P = 0.013, respectively). Multivariate analyses consistently showed a decreased risk of DCGF and serum creatinine doubling in the SGLT2i group. The overall eGFR remained stable without the initial dip after SGLT2i use. A minority (15.6%) of the SGLT2i users showed acute eGFR dip during the first month, but the eGFR recovered thereafter. The risk factors for the eGFR dip were time from transplantation to SGLT2i usage and mean tacrolimus trough level.

Conclusions.
SGLT2i improved a composite of all-cause mortality, DCGF, or serum creatinine doubling in KTRs. SGLT2i can be used safely and have beneficial effects on preserving graft function in diabetic KTRs.
Recognizability bias in citizen science photographs
Authors: Koch Wouter , Hogeweg Laurens , Nilsen Erlend B. , O’Hara Robert B. , Finstad Anders G. 
Published: June 2022

AbstractCitizen science initiatives and automated collection methods increasingly depend on image recognition in order to provide the amounts of observational data research and management needs. Training recognition models, meanwhile, also requires large amounts of data from these sources, creating a feedback loop between the methods and the tools. Species that are harder to recognize, both for humans and machine learning algorithms, are likely to be underreported, and thus be less prevalent in the training data. As a result, the feedback loop may hamper training mostly for species that already pose the greatest challenge. In this study, we trained recognition models for various taxa, and found evidence for a “recognizability bias”, where species that models struggle with are also generally underreported. This has implications for the kind of performance one can expect from future models that are trained with more data, including such challenging species. We consider identification methods that rely on more than photographs alone to be important in improving future identification tools.
Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r
Authors: Boudry Augustin , Darmon Sasha , Duployez Nicolas , Figeac Martin , Geffroy Sandrine , Bucci Maxime , Celli-Lebras Karine , Duchmann Matthieu , Joudinaud Romane , Fenwarth Laurène , Nibourel Olivier , Goursaud Laure , Itzykson Raphael , Dombret Hervé , Hunault Mathilde , Preudhomme Claude , Salson Mikaël 
Published: June 2022

AbstractBackgroundInternal tandem duplications in theFLT3gene, termedFLT3-ITDs, are useful molecular markers in acute myeloid leukemia (AML) for patient risk stratification and follow-up.FLT3-ITDs are increasingly screened through high-throughput sequencing (HTS) raising the need for robust and efficient algorithms. We developed a new algorithm, which performs no alignment and uses little resources, to identify and quantifyFLT3-ITDs in HTS data.ResultsOur algorithm (FiLT3r) focuses on thek-mers from reads coveringFLT3exons 14 and 15. We show that thosek-mers bring enough information to accurately detect, determine the length and quantifyFLT3-ITD duplications. We compare the performances of FiLT3r to state-of-the-art alternatives and to fragment analysis, the gold standard method, on a cohort of 185 AML patients sequenced with capture-based HTS. On this dataset FiLT3r is more precise (no false positive nor false negative) than the other software evaluated. We also assess the software on public RNA-Seq data, which confirms the previous results and shows that FiLT3r requires little resources compared to other software.ConclusionFiLT3r is a free software available athttps://gitlab.univ-lille.fr/filt3r/filt3r. The repository also contains a Snakefile to reproduce our experiments. We show that FiLT3r detects FLT3-ITDs better than other software while using less memory and time.
Characterisation of the immune repertoire of a humanised transgenic mouse through immunophenotyping and high-throughput sequencing
Authors: Richardson E , Binter Š , Kosmac M , Ghraichy M , von Niederhausern V , Kovaltsuk A , Galson J , Trück J , Kelly DF , Deane CM , Kellam P , Watson SJ 
Published: June 2022

AbstractImmunoglobulin loci-transgenic animals are widely used in antibody discovery and increasingly in vaccine response modelling. In this study, we phenotypically characterised B-cell populations from the Intelliselect® Transgenic mouse (Kymouse) demonstrating full B-cell development competence. Comparison of the naïve B-cell receptor (BCR) repertoires of Kymice BCRs naïve human and murine BCR repertoires revealed key differences in germline gene usage and junctional diversification. These differences result in Kymice having CDRH3 length and diversity intermediate between mice and humans. To compare the structural space explored by CDRH3s in each species repertoire, we used computational structure prediction to show that Kymouse naïve BCR repertoires are more human-like than mouse-like in their predicted distribution of CDRH3 shape. Our combined sequence and structural analysis indicates that the naïve Kymouse BCR repertoire is diverse with key similarities to human repertoires, while immunophenotyping confirms that selected naïve B-cells are able to go through complete development.
Use of a ubiquitous gene-editing tool in budding yeast causes off-target repression of neighboring gene protein synthesis
Authors: Powers Emily Nicole , Allcca Lidia Llacsahuanga , Doron-Mandel Ella , Kim Jenny Kim , Jovanovic Marko , Brar Gloria Ann 
Published: June 2022

AbstractPrecision genome-editing approaches have long been available in budding yeast, enabling introduction of gene deletions, epitope tag fusions, and promoter swaps through a selection-based strategy. Such approaches allow loci to be modified without disruption of coding or regulatory sequences of neighboring genes. Use of this approach to delete DBP1 however, led to silencing of expression and the resultant loss of function for the neighboring gene MRP51. We found that insertion of a resistance cassette to delete DBP1, drove a 5’ extended alternative transcript for MRP51 which dampened Mrp51 protein synthesis. Misregulation of MRP51 occurred through an integrated transcriptional and translational repressive long undecoded transcript isoform (LUTI)-based mechanism that was recently shown to naturally regulate gene expression in yeast and other organisms. Cassette-induced MRP51 repression drove all mutant phenotypes we detected in cells deleted for DBP1. Selection cassette-mediated aberrant transcription events are not specific to this locus or a unique cassette but can be prevented by insertion of transcription insulators flanking the cassette. Our study suggests the existence of confounding off-target mutant phenotypes resulting from misregulated neighboring loci following genome edits in yeast. Furthermore, features of LUTI-based regulation are broadly conserved to eukaryotic organisms which indicates the potential that similar misregulation could be unnoticed in other edited organisms as well.
Understanding reported COVID-19 cases in England following changes to testing, between November 2021 and April 2022
Authors: Halford Florence , Nash Sophie , Tessier Elise , Kall Meaghan , Dabrera Gavin 
Published: June 2022

AbstractBackgroundOver the course of the pandemic, testing policies for SARS-CoV-2 have varied considerably in England, particularly in the five months up to 1 April 2022 when free community testing ended. We described the trends and demographics of COVID-19 cases during this period.MethodsCOVID-19 cases reported between 15 November 2021 and 30 April 2022 were extracted and aggregated by testing pillar: Pillar 1 for those tested within the NHS, private or public health laboratories, and Pillar 2 for community testing. COVID-19 cases were described by epi-week, and stratified by test type, age, sex, index of multiple deprivation (IMD), region, and population density. Incidence rates were also calculated and stratified by IMD and region.ResultsOf 10,196,425 COVID-19 cases, 7.3% were reported under Pillar 1 and 92.7% under Pillar 2. From 15 November 2021 to 31 March 2022, most Pillar 2 cases were tested either by polymerase chain reaction (PCR) only or PCR with lateral flow device (LFD) (70.8%) and three in ten cases tested using LFD only. However, between 1 April and 30 April 2022 this rose to nine out of ten cases testing using LFD only. Over the whole period studied and under both pillars, the majority of cases were female (55.2%), resided in the South East (17.0%) and in the age group 30-39 years (18.6%). Trends in IMD and population density varied over the period. When stratifying by IMD the highest case numbers and incidence rates reported under Pillar 1 and NHS were in those in the most deprived quintile. This was also seen for cases reported under Pillar 2 by LFD until 11 January 2022, where a reverse in the trend occurred with the highest cases and rates in the least deprived quintile. This same pattern was observed when describing the cases by population density, with Pillar 2 LFD reported cases being highest in the most densely populated regions until 11 January, from when there was a switch to the highest cases being in the least densely populated regions.ConclusionDifferences and trends were observed in reported COVID-19 cases in England, particularly those tested under Pillar 2 following the introduction of testing policy changes. To better understand the impact of these changes over the course of the COVID-19 pandemic, as well as to predict the impact of future testing policies, it would be beneficial to investigate the accessibility of testing amongst different populations. Currently, Pillar 1 COVID-19 cases are likely to be more representative of symptomatic cases requiring testing for a clinical need, as these are less impacted by variations in testing patterns compared to Pillar 2. However, a limitation of that approach is that use of Pillar 1 alone would be biased towards those more likely to be clinically unwell.
Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa
Authors: Davies Mary-Ann , Morden Erna , Rosseau Petro , Arendse Juanita , Bam Jamy-Lee , Boloko Linda , Cloete Keith , Cohen Cheryl , Chetty Nicole , Dane Pierre , Heekes Alexa , Hsiao Nei-Yuan , Hunter Mehreen , Hussey Hannah , Jacobs Theuns , Jassat Waasila , Kariem Saadiq , Kassanjee Reshma , Laenen Inneke , Roux Sue Le , Lessells Richard , Mahomed Hassan , Maughan Deborah , Meintjes Graeme , Mendelson Marc , Mnguni Ayanda , Moodley Melvin , Murie Katy , Naude Jonathan , Ntusi Ntobeko A. B. , Paleker Masudah , Parker Arifa , Pienaar David , Preiser Wolfgang , Prozesky Hans , Raubenheimer Peter , Rossouw Liezel , Schrueder Neshaad , Smith Barry , Smith Mariette , Solomon Wesley , Symons Greg , Taljaard Jantjie , Wasserman Sean , Wilkinson Robert J. , Wolmarans Milani , Wolter Nicole , Boulle Andrew 
Published: June 2022

AbstractObjectiveWe aimed to compare clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection.MethodsWe included public sector patients aged ≥20 years with laboratory-confirmed COVID-19 between 1-21 May 2022 (BA.4/BA.5 wave) and equivalent prior wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within 21 days of diagnosis) using Cox regression adjusted for demographics, comorbidities, admission pressure, vaccination and prior infection.ResultsAmong 3,793 patients from the BA.4/BA.5 wave and 190,836 patients from previous waves the risk of severe hospitalization/death was similar in the BA.4/BA.5 and BA.1 waves (adjusted hazard ratio (aHR) 1.01; 95% confidence interval (CI) 0.92; 1.12). Both Omicron waves had lower risk of severe outcomes than previous waves. Prior infection (aHR 0.19, 95% CI 0.16; 0.22) and vaccination (aHR 0.24; 95% CI 0.15; 0.39 for boosted vs. no vaccine) were protective.ConclusionDisease severity was similar amongst diagnosed COVID-19 cases in the BA.4/BA.5 and BA.1 periods in the context of growing immunity against SARS-CoV-2 due to prior infection and vaccination, both of which were strongly protective.
Legionella pneumophilaoccurrence in reduced-occupancy buildings in 11 cities during the COVID-19 pandemic
Authors: Dowdell Katherine S. , Greenwald Hannah D. , Joshi Sayalee , Grimard-Conea Marianne , Pitell Sarah , Song Yang , Ley Christian , Kennedy Lauren C. , Vosloo Solize , Huo Linxuan , Haig Sarah-Jane , Hamilton Kerry A. , Nelson Kara L. , Pinto Ameet , Prévost Michele , Proctor Caitlin R. , Raskin Lutgarde M. , Whelton Andrew J. , Garner Emily , Pieper Kelsey J. , Rhoads William J. 
Published: June 2022

AbstractIn spring 2020, reduced water demand was an unintended consequence of COVID-19 pandemic-related building closures. Concerns arose that contaminants associated with water stagnation, such asLegionella pneumophila, could become prevalent. To investigate this potential public health risk, samples from 26 reduced-occupancy buildings across 11 cities in the United States, Canada, and Switzerland were analyzed forL. pneumophilausing liquid culture (Legiolert, n=258) and DNA-based methods (qPCR/ddPCR, n=138).L. pneumophilaculture-positivity was largely associated with just five buildings, each of which had specific design or operational deficiencies commonly associated withL. pneumophilaoccurrence. Samples from free chlorine buildings had higher culture-positivity (37%) than chloramine buildings (1%), and 78% of culture-positive samples occurred when the residual was ≤0.1 mg/L Cl2. Although overall sample positivities using culture- and DNA-based methods were equivalent (34% vs. 35%), there was disagreement between the methods in 13% of paired samples. Few buildings reported any water management activities, andL. pneumophilaconcentrations in flushed samples were occasionally greater than in first-draw samples. This study provides insight into how building plumbing characteristics and management practices contribute toL. pneumophilaoccurrence during low water use periods and can inform targeted prevention and mitigation efforts.Synopsis StatementLegionella pneumophilaoccurrence was evaluated in reduced-occupancy buildings during the COVID-19 pandemic across multiple cities.Graphic for Table of Contents (TOC)