bluuebunny/crossref_metadata_2025_split huggingface dataset:
PGG.MHC: toward understanding the diversity of major histocompatibility complexes in human populations
Authors: Zhao Xiaohan , Ma Sen , Wang Baonan , Jiang Xuetong ,   The Han100K Initiative, Xu Shuhua 
Published: November 2022

Abstract
The human leukocyte antigen (HLA) system, or the human version of the major histocompatibility complex (MHC), is known for its extreme polymorphic nature and high heterogeneity. Taking advantage of whole-genome and whole-exome sequencing data, we developed PGG.MHC to provide a platform to explore the diversity of the MHC in Asia as well as in global populations. PGG.MHC currently archives high-resolution HLA alleles of 53 254 samples representing 190 populations spanning 66 countries. PGG.MHC provides: (i) high-quality allele frequencies for eight classical HLA loci (HLA-A, -B, -C, -DQA1, -DQB1, -DRB1, -DPA1 and -DPB1); (ii) visualization of population prevalence of HLA alleles on global, regional, and country-wide levels; (iii) haplotype structure of 134 populations; (iv) two online analysis tools including ‘HLA imputation’ for inferring HLA alleles from SNP genotyping data and ‘HLA association’ to perform case/control studies for HLA-related phenotypes and (v) East Asian–specific reference panels for HLA imputation. Equipped with high-quality frequency data and user-friendly computer tools, we expect that the PGG.MHC database can advance the understanding and facilitate applications of MHC genomic diversity in both evolutionary and medical studies. The PGG.MHC database is freely accessible via https://pog.fudan.edu.cn/pggmhc or https://www.pggmhc.org/pggmhc.
Associations Between Race/Ethnicity, Language, and Enrollment on Cancer Research Studies
Authors: Ezeoke Ogochukwu M , Brooks Gary , Postow Michael A , Baxi Shrujal , Young Kim Soo , Narang Bharat , Diamond Lisa C 
Published: November 2022

Abstract

Purpose
The objective of this study was to determine whether differences in patients’ race/ethnicity, preferred language, and other factors were associated with patient enrollment in oncology research studies.

Patients and Methods
We conducted a retrospective cross-sectional analysis of all adults (&gt;18 and ≤90) seen at a large, metropolitan cancer center from 2005 to 2015, examining if enrollment to a research study, varied by race/ethnicity, preferred language, comorbidities, gender, and age.

Results
A total of 233 604 patients were available for initial analysis. Of these, 93 278 (39.9%) were enrolled in a research protocol (therapeutic and non-therapeutic studies). Patients who self-reported their race/ethnicity as Native, Other, Unknown, or Refuse to Answer were less likely to be enrolled on a study. Patients with one or more comorbidities, and those whose preferred language was English, were more likely to be enrolled on a research study. A logistic regression model showed that, although Non-Hispanic Black patients were more likely to have one or more comorbidities and had a higher proportion of their subset selecting English as their preferred language, they were less likely to be enrolled on a study, than our largest population, Non-Hispanic/White patients.

Conclusions
We identified differences in research study enrollment based on preferred language, and within race/ethnicity categories including Native-Populations, Other, Unknown or Refuse to Answer compared to Non-Hispanic/White patients. We also highlighted the lower odds of enrollment among Non-Hispanic/Black patients, in the setting of factors such as comorbidities and English language preference, which were otherwise found to be positive predictors of enrollment. Further investigation is needed to design targeted interventions to reduce disparities in oncology research study enrollment, with particular focus on language diversity.
Is There a Right to Internet Access?
Authors: Cruft Rowan 
Published: November 2022

Abstract
This chapter asks whether the ideas of ‘rights’ and ‘human rights’ are useful concepts for getting to grips with moral questions about internet access. The values served by internet access—democratic participation, freedom of speech, privacy, the welfare state—are often understood in terms of rights, but they are also often taken more communally, as morally grounded fundamentally by their role in constituting an open society that serves us all collectively. Rights approaches highlight the individual right-holder as a party who is ‘wronged’ when a duty is violated. This chapter defends a rights-based approach to moral questions about internet access, and explores the practical implications of this approach for policy and law.
Timing and Petrogenesis of the Permo-Carboniferous Larvik Plutonic Complex, Oslo Rift, Norway: New Insights from U–Pb, Lu-Hf, and O Isotopes in Zircon
Authors: Rämö O Tapani , Andersen Tom , Whitehouse Martin J 
Published: November 2022

AbstractThe Permo-Carboniferous Oslo Rift is a narrow, aborted continental rift with comparatively little extension but voluminous magmatism, developed at a Proterozoic lithospheric discontinuity. On the southern flank of the onshore part of the rift, the multiple intrusive phase Larvik plutonic complex (LPC) encompasses almost the width of the rift with a conspicuous over- to undersaturated assemblage of monzonite (larvikite, tønsbergite) and nepheline syenite (lardalite, foyaite). We present new single-crystal U–Pb–, Lu–Hf–, and O–in–zircon isotope data for the intrusive centers of the complex. U–Pb ages of slightly over- to undersaturated monzonites show a shift in igneous activity from 299 Ma on the eastern edge of the complex to 289 Ma in the west. The western part of the complex is built of two consanguineous magmatic systems with a northward shift in the locus of magmatism, from 296 to 289 Ma (undersaturated monzonite) and 296 to ~288 Ma (nepheline syenite). Moreover, an early oversaturated monzonite was emplaced in the eastern part of the complex at ~302 Ma. The Hf and O isotope composition of the monzonites and nepheline syenites shows little variation with zircon εHf (295 Ma) values of +5.5 to +8 and δ18Ο values of +4.79‰ to +5.49‰. No change in isotope values is observed with varying alkalinity and the Hf and O isotope compositions are interpreted as mantle source values. The source of the precursors of the monzonitic and nepheline syenitic magmas was probably a mildly depleted, sublithospheric peridotite in the lithosphere-asthenosphere boundary zone (at 3–4 GPa). Rhyolite–MELTS modeling implies polybaric fractionation of weakly alkaline basaltic melts from the source having led to an oversaturated/saturated liquid line of descent at ~0.5 GPa and an undersaturated one at ~1 GPa. Magmatism had an imperative role in the evolution of the rift by localizing strain and weakening the lithosphere along the discontinuity. A fractionating crustal melt column was tapped at varying depths in the course of advancing rupturing with no significant mixing of the over- and undersaturated melts, and magma batches were emplaced as sequential nested plutons in response to differential opening of the rift. Among continental saturated-undersaturated alkaline complexes, the LPC may be unique in the emplacement of successive magma batches across a continental rift in the direction of opening, tapping of increasingly deeper parts of the melt column with advancing rifting, and intrusion of two contemporaneous, contrasting magmatic lineages at the end of igneous activity. The marked lithospheric step at the rift locus in the Precambrian basement of southeastern Norway was probably the driving force for the inception and evolution of the Larvik magmatic system.
Testing theoretical frameworks of zooplankton longitudinal distribution in a large reservoir
Authors: Detmer Thomas M , Roberts Hayden , Broadway Kyle , Parkos Joseph , Wahl David 
Published: November 2022

Abstract
Reservoirs are thought to contain three zones (riverine, transition and lacustrine) emerging from environmental gradients from the river to the dam where zooplankton are predicted to peak in the transitional zone. Few high spatial resolution studies, however, have surveyed zooplankton distribution in reservoirs, leading to limited knowledge regarding longitudinal abundance and composition of zooplankton. Using 44 samples from river to dam in a 35.7 km long reservoir, we explore spatial variability in zooplankton density, biomass, composition and relative bottom-up to top-down control. Broadly, density and biomass increased from the river to the dam. Variation occurred in the location and frequency of peaks among groups. Divergence between per unit volume and area within groups highlighted the importance of depth. Richness and turnover between sites were both greatest near the river. The ratio of zooplankton to phytoplankton biomass varied longitudinally, with a low near 20% of the distance from the river to the dam indicating spatial variability in bottom-up versus top-down control. This study highlights the complexity of longitudinal zooplankton composition and distribution in reservoirs and provides insight into reservoir ecosystem complexity and function, with important consequences for water quality, fish distribution, and productivity.
Preventive Effect of an Intervention Program with Increased Physical Activity on the Development of Musculoskeletal Pain in Community-Dwelling Older Adults: A Randomized Controlled Trial
Authors: Hirase Tatsuya , Inokuchi Shigeru , Koshikawa Shota , Shimada Hinata , Okita Minoru 
Published: November 2022

Abstract

Objective
To examine whether compared with a program without increased physical activity, an intervention program with increased physical activity can prevent the development of musculoskeletal pain in community-dwelling older adults.

Design
Randomized controlled trial.

Setting
Japanese community.

Subjects
Seventy-nine older adults without musculoskeletal pain were randomized into two groups: an intervention group (n = 40) that engaged in increased physical activity and an exercise class and a control group (n = 39) that participated only in the exercise class.

Methods
The exercise class consisted of weekly 60-min sessions over 24 weeks. The program to increase physical activity required the participants to record their daily step counts using pedometers. The primary outcome was the development of musculoskeletal pain, and secondary outcomes were physical function, psychological status, cognitive function, and physical activity levels.

Results
Twenty-four weeks after the intervention, the intervention group had a significantly lower prevalence of musculoskeletal pain (12.8%) than the control group (32.4%; P = .040). A time-by-group interaction emerged for cognitive function (P = .01) and physical activity levels (P &lt; .001), both of which favored the intervention group. The intervention group also showed greater improvement in psychological status 24 weeks after the intervention than the control group (P = .018).

Conclusions
The intervention program with increased physical activity prevented the development of musculoskeletal pain and improved cognitive function, physical activity levels, and psychological status more effectively than the program without increased physical activity. Our intervention program may be an effective pain prevention approach for older adults.

Trial registration
UMIN000032768; registered on June 1, 2018.
Antibody-mediated delivery of CRISPR-Cas9 ribonucleoproteins in human cells
Authors: Ubiparipovic Stephanie , Christ Daniel , Rouet Romain 
Published: November 2022

Abstract
The CRISPR genome editing technology holds great clinical potential for the treatment of monogenetic disorders such as sickle cell disease. The therapeutic in vivo application of the technology relies on targeted delivery methods of the Cas9 and gRNA complex to specific cells or tissues. However, such methods are currently limited to direct organ delivery, preventing clinical application. Here, we show that monoclonal antibodies can be employed to deliver the Cas9/gRNA complex directly into human cells via cell-surface receptors. Using the SpyCatcher/SpyTag system, we conjugated the Fab fragment of the therapeutic antibodies Trastuzumab and Pertuzumab directly to the Cas9 enzyme and observed HER2-specific uptake of the ribonucleoprotein in a human HER2 expressing cell line. Following cellular uptake in the presence of an endosomolytic peptide, modest gene editing was also observed. This finding provides a blueprint for the targeted delivery of the CRISPR technology into specific cells using monoclonal antibodies.
The association of new-onset diabetes with subsequent diagnosis of pancreatic cancer—novel use of a large administrative database
Authors: White M J , Sheka A C , LaRocca C J , Irey R L , Ma S , Wirth K M , Benner A , Denbo J W , Jensen E H , Ankeny J S , Ikramuddin S , Tuttle T M , Hui J Y C , Marmor S 
Published: November 2022

Abstract

Background
Screening options for pancreatic ductal adenocarcinoma (PDAC) are limited. New-onset type 2 diabetes (NoD) is associated with subsequent diagnosis of PDAC in observational studies and may afford an opportunity for PDAC screening. We evaluated this association using a large administrative database.

Methods
Patients were identified using claims data from the OptumLabs® Data Warehouse. Adult patients with NoD diagnosis were matched 1:3 with patients without NoD using age, sex and chronic obstructive pulmonary disease (COPD) status. The event of PDAC diagnosis was compared between cohorts using the Kaplan–Meier method. Factors associated with PDAC diagnosis were evaluated with Cox’s proportional hazards modeling.

Results
We identified 640 421 patients with NoD and included 1 921 263 controls. At 3 years, significantly more PDAC events were identified in the NoD group vs control group (579 vs 505; P &lt; 0.001). When controlling for patient factors, NoD was significantly associated with elevated risk of PDAC (HR 3.474, 95% CI 3.082–3.920, P &lt; 0.001). Other factors significantly associated with PDAC diagnosis were increasing age, increasing age among Black patients, and COPD diagnosis (P ≤ 0.05).

Conclusions
NoD was independently associated with subsequent diagnosis of PDAC within 3 years. Future studies should evaluate the feasibility and benefit of PDAC screening in patients with NoD.
B-cell receptor profiling before and after IVIG monotherapy in newly diagnosed idiopathic inflammatory myopathies
Authors: Anang Dornatien C , Walter Hannah A W , Lim Johan , Niewold Ilse , van der Weele Linda , Aronica Eleonora , Eftimov Filip , Raaphorst Joost , van Schaik Barbera D C , van Kampen Antoine H C , van der Kooi Anneke J , de Vries Niek 
Published: November 2022

Abstract

Objective
To unravel B-cell receptor (BcR) characteristics in muscle tissues and peripheral blood and gain more insight into BcR repertoire changes in peripheral blood in idiopathic inflammatory myopathies (IIMs), and study how this correlates to the clinical response to IVIG.

Methods
Nineteen treatment-naive patients with newly diagnosed IIM were prospectively treated with IVIG monotherapy. RNA-based BcR repertoire sequencing was performed in muscle biopsies collected before, and in peripheral blood (PB) collected before and nine weeks after IVIG treatment. Results were correlated to patients’ clinical improvement based on the total improvement score (TIS).

Results
Prior to IVIG treatment, BcR clones found in muscle tissue could be retrieved in peripheral blood. Nine weeks after IVIG treatment, new patient-specific dominant BcR clones appeared in peripheral blood while pre-treatment dominant BcR clones disappeared. The cumulative frequency of all dominant BcR clones before treatment was significantly higher in individuals who responded to IVIG compared with those who did not respond to IVIG, and correlated with a higher CK. During follow-up, a decrease in the cumulative frequency of all dominant clones correlated with a higher TIS.

Conclusion
In treatment-naive patients with newly diagnosed IIM, muscle tissue and peripheral blood share expanded BcR clones. In our study a higher cumulative frequency of dominant BcR clones in blood before treatment was associated with a higher CK and better treatment response, suggesting that response to IVIG may depend on the composition of the pre-treatment BcR repertoire.
Relevance of leukaemia inhibitory factor to anti-melanoma differentiation-associated gene 5 antibody-positive interstitial lung disease
Authors: Ichimura Yuki , Ikei Hiroyuki , Konishi Risa , Zeniya Moko , Okai Takahiro , Nomura Toshifumi , Negishi Kousuke , Okiyama Naoko 
Published: November 2022

Abstract

Objectives
Anti-melanoma differentiation-associated gene 5 (MDA5) antibody-positive rapidly progressive interstitial lung disease (RP-ILD) is a life-threatening disease, the aetiology of which remains unclear. To detect potential diagnostic markers, a transcriptome analysis of the lung sample from a patient with anti-MDA5 antibody-positive RP-ILD was performed.

Methods
RNA sequencing analyses of an autopsy lung sample from a 74-year-old woman with anti-MDA5 antibody-positive RP-ILD was performed and compared with an age- and sex-matched normal lung sample. Genes with changes of gene expression ≥5-fold were considered differentially expressed genes and analysed by Metascape. The levels of leukaemia inhibitory factor (LIF) were measured in the serum samples from 12 cases of anti-MDA5 antibody-positive ILD, 12 cases of anti-aminoacyl tRNA synthetase (ARS) antibody-positive ILD, 10 cases of anti-transcription intermediary factor 1γ/anti-Mi-2 antibody DM and 12 healthy volunteers.

Results
Gene ontology enrichment analysis on the RNA sequencing data showed a strong association with antigen binding. Upregulated expressions of IL-1β, IL-6 and LIF were also detected. Serum LIF levels were significantly elevated in anti-MDA5 antibody-positive ILD patients {median 32.4 pg/ml [interquartile range (IQR) 13.2–125.7]} when compared with anti-ARS antibody-positive ILD patients [4.9 pg/ml (IQR 3.1–19.7), P &lt; 0.05] and DM patients [5.3 pg/ml (IQR 3.9–9.7), P &lt; 0.05].

Conclusion
Our present study suggested that upregulation of LIF might be a new potential disease marker specific for anti-MDA5 antibody-positive ILD.
EXAMINATION OF LENS EXPOSURE DOSES OF CARDIOLOGISTS, NEUROSURGEONS AND RADIOLOGISTS IN INTERVENTIONAL RADIOLOGY
Authors: Osawa Mitsuharu , Tawada Yuka , Kaneda Naoki , Fujita Naotoshi , Koyama Shuji 
Published: November 2022

Abstract
The International Commission on Radiological Protection (ICRP) 118th recommendation significantly reduced the threshold dose for cataract development from 8 to 0.5 Gy. Equivalent dose limits for the crystalline lenses of radiation workers are being reviewed for individual countries. Interventional radiology (IR) procedures are less invasive than surgery and have become widespread; however, there are concerns about exposure not only to patients but also to staff, including operators. Therefore, in this study, we used a human phantom to measure the near-lens dose of the operators (cardiologists, neurosurgeons and radiologists) and estimated the operator’s lens dose for every major procedure in each clinical department; this was found to vary. Owing to the different imaging and fluoroscopy conditions of each department, and the varying ratio of fluoroscopy to radiography, it is necessary to measure the lens dose for each condition, as in this study. In addition, this study explains the differences between the protective effect of various safety equipment and the appropriate use of protective plates; it can contribute to the reduction of lens doses for operators.
ESTIMATION OF PROTECTION FACTORS FOR SURROGATE VEHICLE MODELS IN ENVIRONMENTAL CONTAMINATION SCENARIOS
Authors: Dalak Sena , Asano Ethan , Dewji Shaheen 
Published: November 2022

Abstract
In the event of a nuclear or radiological incident involving the release of radioactive material, it may be critical to estimate doses to individuals who are transported through contaminated areas by vehicles. The radiation protection factor (RPF) for vehicles can be calculated to determine the level of shielding protection by the vehicle from external radiation sources. Prior studies evaluating RPFs demonstrate a lack of realistic vehicle configurations and the results cannot be extended directly to scenarios where a vehicle is surrounded by a contaminated environmental field. In this work, sex-averaged effective dose-rate coefficients were computed employing International Commission on Radiological Protection Publication 103 recommendations for radionuclides of interest and used to calculate the RPF as the ratio of unshielded to shielded dose for various radionuclides of interest in consequence management scenarios. Comparisons to dose reduction factors calculated using environmental measurement data from the 2011 Fukushima Daiichi nuclear incident were conducted to benchmark to experimental field measurements.
Social Work and Social Justice: A Conceptual Review
Authors: Atteberry-Ash Brittanie E 
Published: November 2022

Abstract
As a profession, social work has codified within its ethical guidance and educational policies a commitment to social justice. While a commitment to social justice is asserted in several of our profession’s guiding documents, social work continues to lack consensus on both the meaning and merit of social justice, resulting is disparate and sometimes discriminatory practice even under a “social justice” label. This study examines how social justice has been operationalized in social work via a conceptual review of the literature. Findings show that social work leans heavily on John Rawls’s definition of social justice, Martha Nussbaum’s and Amartya Sen’s capabilities approach, and the definition of social justice included in The Social Work Dictionary. Unfortunately, none of these adequately align with the National Association of Social Workers’ Code of Ethics, which drives the profession. This conceptual review is a call to social workers to join together in defining the guiding principle of the profession.
Respiratory syncytial virus: host genetic susceptibility and factors associated with disease severity in a cohort of pediatric patients
Authors: I. G. Giamberardino Heloisa , O. Pacheco Ana P , Pereira Luciane A , Debur Maria do Carmo , Genehold Gustavo , Raboni Sonia M 
Published: November 2022

Abstract

Background
Respiratory syncytial virus (RSV) infections are the leading cause of hospitalization in young children. We assessed the epidemiology, severity, clinical characteristics, molecular profile and genetic factors of RSV infections compared to acute respiratory illness (ARI) caused by other respiratory viruses.

Methods
Prospective cohort study was conducted from 2017 to 2018 with children under 2 years old hospitalized with ARI. Detection of respiratory viruses was carried out using RT-PCR. RSVs were genotyped via nucleotide sequencing, and host interleukin 28B (IL28B) single nucleotide polymorphisms (SNPs) were determined using SNP TaqMan® Genotyping Assays.

Results
A total of 468 children were included; 288 (61.5%) had an infection by a single virus: 202 (70.1%) cases by RSV followed by rhinovirus 36 (12.5%) and influenza 16 (5.6%). Of the RSV cases, 36% were genotyped with a higher prevalence of RSV B (62.1%). The RSV group presented median age of 2.7 months (1.6–6.8), higher frequency in: intensive care unit admission (p = 0.004), mechanical ventilation use (p = 0.018), wheezing (p &lt; 0.001), antimicrobial use (p &lt; 0.001) and low oxygen saturation (p &lt; 0.001). Prematurity (27.2%) was the most frequent comorbidity. RSV patients without comorbidities demonstrated a higher frequency in the combination of IL28B rs12979860 CT/IL28B rs8099917 TG and IL28B rs12979860 TT/IL28B rs8099917 TT genotypes. Viral coinfection was detected in 27 (5.7%) children, with the most frequent being RSV and rhinovirus (14.2%).

Conclusions
This study highlighted the burden of RSV infection in children under 2 years of age, without comorbidities, with a higher need for pediatric ICU admission. Some IL28B allele combinations had a significant association with RSV frequency of infections.