bluuebunny/crossref_metadata_2025_split huggingface dataset:
A systematic review and meta-analysis of HLA class II associations in patients with IgG4 autoimmunity
Authors: Panhuber Anja , Lamorte Giovanni , Bruno Veronica , Cetin Hakan , Bauer Wolfgang , Höftberger Romana , Erber Astrid C. , Frommlet Florian , Koneczny Inga 
Published: June 2022

AbstractAutoimmune diseases caused by pathogenic IgG4 subclass autoantibodies (IgG4-AID) include diseases like MuSK myasthenia gravis, pemphigus vulgaris or thrombotic thrombocytopenic purpura. Their etiology is still unknown. Polymorphisms in the human leukocyte antigen (HLA) gene locus, particularly inHLA-DRB1, are known genetic susceptibility factors for autoimmune diseases. We hypothesized a similar role for HLA polymorphisms in IgG4-AID and conducted a systematic review and meta-analysis with case–control studies on IgG4-AID based on MOOSE/ HuGENet guidelines. Genotype (G) and allele (A) frequencies ofHLA-DQB1*05(G: OR 3.8; 95% CI 2.44–5.9;p < 0.00001; A: OR 2.54; 95% CI 1.82–3.55;p < 0.00001) andHLA-DRB1*14(G: OR 4.31; 95% CI 2.82–6.59;p < 0.00001; A: OR 4.78; 95% CI 3.52–6.49;p < 0.00001) and theHLA-DRB1*14-DQB1*05haplotype (OR 6.3; 95% CI 3.28–12.09;p < 0.00001/OR 4.98; 95% CI 3.8–6.53;p < 0.00001) were increased whileHLA-DRB1*13(G: OR 0.48; 95% CI 0.34–0.68;p < 0.0001; A: OR 0.46; 95% CI 0.34–0.62;p < 0.00001) was decreased in IgG4-AID patients. In conclusion, theHLA-DQB1*05,HLA-DRB1*14alleles and theHLA-DQB1*05-DRB1*14haplotype could be genetic risk factors that predispose for the production of pathogenic IgG4 autoantibodies and theHLA-DRB1*13allele may protect from IgG4 autoimmunity.
Effects of rumen undegradable protein sources on nitrous oxide, methane and ammonia emission from the manure of feedlot-finished cattle
Authors: de Melo Coelho Larissa , de Figueiredo Brito Liziane , Messana Juliana Duarte , da Silva Cardoso Abmael , Carvalho Geovany Macêdo , de Nazaré Santos Torres Rodrigo , Carlos Roberta Souto , Malheiros Euclides Braga , da Cruz Mara Cristina Pessôa , Berchielli Telma Teresinha 
Published: June 2022

AbstractThe effects of sources of rumen undegradable protein (RUP) in diets on methane (CH4), nitrous oxide (N2O) and ammonia (NH3) emissions from the manure of feedlot-finished cattle were evaluated. We hypothesized that the use of different RUP sources in diets would reduce N loss via urine and contribute to reduced N2O, CH4 and NH3 emissions to the environment. Nellore cattle received different diets (18 animals/treatment), including soybean meal (SM, RDP source), by-pass soybean meal (BSM, RUP source) and corn gluten meal (CGM, RUP source). The protein source did not affect the N and C concentration in urine, C concentration in feces, and N balance (P > 0.05). The RUP sources resulted in a higher N2O emission than the RDP source (P = 0.030), while BSM resulted in a higher N2O emission than CGM (P = 0.038) (SM = 633, BSM = 2521, and CGM = 1153 g ha−2 N–N2O); however, there were no differences in CH4 and NH3 emission (P > 0.05). In conclusion, the use of RUP in diets did not affect N excretion of beef cattle or CH4 and NH3 emission from manure, but increased N2O emission from the manure.
Discovery of the cyclotide caripe 11 as a ligand of the cholecystokinin-2 receptor
Authors: Taghizadeh Mohammad Sadegh , Retzl Bernhard , Muratspahić Edin , Trenk Christoph , Casanova Emilio , Moghadam Ali , Afsharifar Alireza , Niazi Ali , Gruber Christian W. 
Published: June 2022

AbstractThe cholecystokinin-2 receptor (CCK2R) is a G protein-coupled receptor (GPCR) that is expressed in peripheral tissues and the central nervous system and constitutes a promising target for drug development in several diseases, such as gastrointestinal cancer. The search for ligands of this receptor over the past years mainly resulted in the discovery of a set of distinct synthetic small molecule chemicals. Here, we carried out a pharmacological screening of cyclotide-containing plant extracts using HEK293 cells transiently-expressing mouse CCK2R, and inositol phosphate (IP1) production as a readout. Our data demonstrated that cyclotide-enriched plant extracts from Oldenlandia affinis, Viola tricolor and Carapichea ipecacuanha activate the CCK2R as measured by the production of IP1. These findings prompted the isolation of a representative cyclotide, namely caripe 11 from C. ipecacuanha for detailed pharmacological analysis. Caripe 11 is a partial agonist of the CCK2R (Emax = 71%) with a moderate potency of 8.5 µM, in comparison to the endogenous full agonist cholecystokinin-8 (CCK-8; EC50 = 11.5 nM). The partial agonism of caripe 11 is further characterized by an increase on basal activity (at low concentrations) and a dextral-shift of the potency of CCK-8 (at higher concentrations) following its co-incubation with the cyclotide. Therefore, cyclotides such as caripe 11 may be explored in the future for the design and development of cyclotide-based ligands or imaging probes targeting the CCK2R and related peptide GPCRs.
HER2 G776S mutation promotes oncogenic potential in colorectal cancer cells when accompanied by loss of APC function
Authors: Mitani Yosuke , Ohashi Shinya , Kikuchi Osamu , Nakai Yukie , Ida Tomomi , Mizumoto Ayaka , Yamamoto Yoshihiro , Saito Tomoki , Kataoka Shigeki , Matsubara Junichi , Yamada Atsushi , Kanai Masashi , Matsumoto Shigemi , Sakai Hiroaki , Yoshikawa Kiyotsugu , Nakamura Eijiro , Muto Manabu 
Published: June 2022

AbstractClinical cancer genome sequencing detects oncogenic variants that are potential targets for cancer treatment, but it also detects variants of unknown significance. These variants may interact with each other to influence tumor pathophysiology, however, such interactions have not been fully elucidated. Additionally, the effect of target therapy for those variants also unclarified. In this study, we investigated the biological functions of a HER2 mutation (G776S mutation) of unknown pathological significance, which was detected together with APC mutation by cancer genome sequencing of samples from a colorectal cancer (CRC) patient. Transfection of the HER2 G776S mutation alone slightly increased the kinase activity and phosphorylation of HER2 protein, but did not activate HER2 downstream signaling or alter the cell phenotype. On the other hand, the HER2 G776S mutation was shown to have strong oncogenic potential when loss of APC function was accompanied. We revealed that loss of APC function increased Wnt pathway activity but also increased RAS–GTP, which increased ERK phosphorylation triggered by HER2 G776S transfection. In addition, afatinib, a pan-HER tyrosine kinase inhibitor, suppressed tumor growth in xenografts derived from HER2 G776S-transfected CRC cells. These findings suggest that this HER2 mutation in CRC may be a potential therapeutic target.
Machine learning predictive model for evaluating the cooking characteristics of moisture conditioned and infrared heated cowpea
Authors: Ogundele Opeolu. M. , Akintola Ayooluwa. T. , Fasogbon Beatrice M. , Adebo Oluwafemi.A. 
Published: June 2022

AbstractCowpea is widely grown and consumed in sub-Saharan Africa because of its low cost and high mineral, protein, and other nutritional content. Nonetheless, cooking it takes considerable time, and there have been attempts on techniques for speeding up the cooking process without compromising its nutritious value. Infrared heating has recently been proposed as a viable way of preparing instantized cowpea grains that take a short amount of time to cook while maintaining desired sensory characteristics. Despite this, only a few studies have shown the impact of moisture, temperature, and cooking time on cooking characteristics such as bulk density, water absorption (WABS), and the pectin solubility of infrared heated cowpea precooked using this technology. Artificial neural network was used as a machine learning tool to study the effect of a prediction model on the infrared heating performance and cooking characteristics of precooked cowpea seeds. With R values of 0.987, 0.991, and 0.938 for the bulk density, WABS, and pectin solubility, respectively, the prediction model created in this study utilizing an artificial neural network (a type of machine learning) outperformed the traditional linear, 2-factor interaction, and quadratic models.
Genetic control of rhizosheath formation in pearl millet
Authors: de la Fuente Cantó C. , Diouf M. N. , Ndour P. M. S. , Debieu M. , Grondin A. , Passot S. , Champion A. , Barrachina C. , Pratlong M. , Gantet P. , Assigbetsé K. , Kane N. , Cubry P. , Diedhiou A. G. , Heulin T. , Achouak W. , Vigouroux Y. , Cournac L. , Laplaze L. 
Published: June 2022

AbstractThe rhizosheath, the layer of soil that adheres strongly to roots, influences water and nutrients acquisition. Pearl millet is a cereal crop that plays a major role for food security in arid regions of sub-Saharan Africa and India. We previously showed that root-adhering soil mass is a heritable trait in pearl millet and that it correlates with changes in rhizosphere microbiota structure and functions. Here, we studied the correlation between root-adhering soil mass and root hair development, root architecture, and symbiosis with arbuscular mycorrhizal fungi and we analysed the genetic control of this trait using genome wide association (GWAS) combined with bulk segregant analysis and gene expression studies. Root-adhering soil mass was weakly correlated only to root hairs traits in pearl millet. Twelve QTLs for rhizosheath formation were identified by GWAS. Bulk segregant analysis on a biparental population validated five of these QTLs. Combining genetics with a comparison of global gene expression in the root tip of contrasted inbred lines revealed candidate genes that might control rhizosheath formation in pearl millet. Our study indicates that rhizosheath formation is under complex genetic control in pearl millet and suggests that it is mainly regulated by root exudation.
Time-resolved structure-function coupling in brain networks
Authors: Liu Zhen-Qi , Vázquez-Rodríguez Bertha , Spreng R. Nathan , Bernhardt Boris C. , Betzel Richard F. , Misic Bratislav 
Published: June 2022

AbstractThe relationship between structural and functional connectivity in the brain is a key question in systems neuroscience. Modern accounts assume a single global structure-function relationship that persists over time. Here we study structure-function coupling from a dynamic perspective, and show that it is regionally heterogeneous. We use a temporal unwrapping procedure to identify moment-to-moment co-fluctuations in neural activity, and reconstruct time-resolved structure-function coupling patterns. We find that patterns of dynamic structure-function coupling are region-specific. We observe stable coupling in unimodal and transmodal cortex, and dynamic coupling in intermediate regions, particularly in insular cortex (salience network) and frontal eye fields (dorsal attention network). Finally, we show that the variability of a region’s structure-function coupling is related to the distribution of its connection lengths. Collectively, our findings provide a way to study structure-function relationships from a dynamic perspective.
Chromosome-specific retention of cancer-associated DNA hypermethylation following pharmacological inhibition of DNMT1
Authors: Wiseman Ashley K. , Tiedemann Rochelle L. , Fan Huihui , Shen Hui , Madaj Zachary , McCabe Michael T. , Pappalardi Melissa B. , Jones Peter A. 
Published: June 2022

AbstractThe DNA methylation status of the X-chromosome in cancer cells is often overlooked because of computational difficulties. Most of the CpG islands on the X-chromosome are mono-allelically methylated in normal female cells and only present as a single copy in male cells. We treated two colorectal cancer cell lines from a male (HCT116) and a female (RKO) with increasing doses of a DNA methyltransferase 1 (DNMT1)-specific inhibitor (GSK3685032/GSK5032) over several months to remove as much non-essential CpG methylation as possible. Profiling of the remaining DNA methylome revealed an unexpected, enriched retention of DNA methylation on the X-chromosome. Strikingly, the identified retained X-chromosome DNA methylation patterns accurately predicted de novo DNA hypermethylation in colon cancer patient methylomes in the TCGA COAD/READ cohort. These results suggest that a re-examination of tumors for X-linked DNA methylation changes may enable greater understanding of the importance of epigenetic silencing of cancer related genes.
Targeting LIPA independent of its lipase activity is a therapeutic strategy in solid tumors via induction of endoplasmic reticulum stress
Authors: Liu Xihui , Viswanadhapalli Suryavathi , Kumar Shourya , Lee Tae-Kyung , Moore Andrew , Ma Shihong , Chen Liping , Hsieh Michael , Li Mengxing , Sareddy Gangadhara R. , Parra Karla , Blatt Eliot B. , Reese Tanner C. , Zhao Yuting , Chang Annabel , Yan Hui , Xu Zhenming , Pratap Uday P. , Liu Zexuan , Roggero Carlos M. , Tan Zhenqiu , Weintraub Susan T. , Peng Yan , Tekmal Rajeshwar R. , Arteaga Carlos L. , Lippincott-Schwartz Jennifer , Vadlamudi Ratna K. , Ahn Jung-Mo , Raj Ganesh V. 
Published: June 2022

AbstractTriple-negative breast cancer (TNBC) has a poor clinical outcome, due to a lack of actionable therapeutic targets. Herein we define lysosomal acid lipase A (LIPA) as a viable molecular target in TNBC and identify a stereospecific small molecule (ERX-41) that binds LIPA. ERX-41 induces endoplasmic reticulum (ER) stress resulting in cell death, and this effect is on target as evidenced by specific LIPA mutations providing resistance. Importantly, we demonstrate that ERX-41 activity is independent of LIPA lipase function but dependent on its ER localization. Mechanistically, ERX-41 binding of LIPA decreases expression of multiple ER-resident proteins involved in protein folding. This targeted vulnerability has a large therapeutic window, with no adverse effects either on normal mammary epithelial cells or in mice. Our study implicates a targeted strategy for solid tumors, including breast, brain, pancreatic and ovarian, whereby small, orally bioavailable molecules targeting LIPA block protein folding, induce ER stress and result in tumor cell death.
The Use of Opioids in the Surgical Care of Patients With Orofacial Clefts: A Commentary and Guide to Management
Authors: Randall Ellen , Tran Khoa , Cordes Emma J. , Borschel Gregory H. , Tholpady Sunil S. 
Published: June 2022

Purpose:
This commentary outlines the surgical pathway for patients with cleft lip and/or palate (CLP), identifies risks associated with opioid prescribing in this patient population, and summarizes strategies to safely minimize the need for perioperative opioid prescribing.

Conclusions:
Patients with orofacial clefts, CLP, undergo multiple reconstructive surgeries. The long-term effects of perioperative opioid prescriptions should concern all members of the cleft and craniofacial team. The amount of surgery each patient with a CLP may face varies by patient and can begin in infancy and continue to adulthood. In this commentary, the surgical pathway for CLP is reviewed, and the opioid crisis is addressed in regard to this vulnerable patient group. Solutions for cleft and craniofacial team members from evidence-based literature are summarized to minimize the use of opioids prescribed in this patient population. Approaches to reduce opioid use after CLP surgery are holistic and multidisciplinary.
Fast 3D‐HEVC inter coding using data mining and machine learning
Authors: Zhang Ruyi , Jia Kebin , Yu Yuan , Liu Pengyu , Sun Zhonghua 
Published: June 2022

AbstractThe Three‐Dimensional High Efficiency Video Coding standard is a video compression standard developed based on the two‐dimensional video coding standard HEVC and used to encode multi‐view plus depth format video. This paper proposes an algorithm based on eXtreme Gradient Boosting to solve the problem of high inter‐frame coding complexity in 3D‐HEVC. Firstly, explore the correlation between the division depth of the inter‐frame coding unit and the texture features in the map, as well as the correlation between the coding unit division structure between each map and each viewpoint. After that, based on the machine learning method, a fast selection mechanism for dividing the depth range of the inter‐frame coding tree unit based on the eXtreme Gradient Boosting algorithm is constructed. Experimental results show that, compared with the reference software HTM‐16.0, this method can save an average of 35.06% of the coding time, with negligible degradation in terms of coding performance. In addition, the proposed algorithm has achieved different degrees of improvement in coding performance compared with the related works.
Plasmonic wideband GST‐based switch in the near‐infrared region
Authors: Heidari Saman , Nozhat Najmeh 
Published: June 2022

AbstractIn this paper, we present a GST‐based wideband plasmonic switch. With the excitation of localised surface plasmons and concentration of electric field in the structure, a near‐perfect and wideband absorption is achieved. The switch consists of a GST layer, which acts as a Fabry–Perot cavity. Increasing the temperature and changing the state of GST lead to a high difference between the absorption spectra in amorphous and crystalline states in a wide range of wavelength. Therefore, the switch has a high extinction ratio of 13.71 dB at the wavelength of 1343 nm. Also, the response time of the switch is obtained as 46 fs. The structure has near‐perfect absorption up to the incident angle of about 20°. Moreover, due to the symmetry of structure, the absorption spectrum is independent of polarisation. To show the validity of simulation results, the analytical method of equivalent circuit model is presented. The proposed polarisation‐insensitive switch with high extinction ratio, fast response time and wide bandwidth can be used in photodetectors, plasmonic modulators and logic gates.
Coping with Diffuse Intrinsic Pontine Glioma in Children –
Findings from an Interview Study on Bereaved Parents
Authors: Radlanski Kalinka , Hartwig Maite , Kordes Uwe 
Published: June 2022

Abstract
Background Diffuse midline glioma (DMG) is the most common malignant glioma
in early childhood with median survival of only eleven months. This
retrospective interview study investigates specific coping strategies and needs
of affected parents.
Patients 13 interviews with parents of seven children who died from DMG at
the age of five to 16 years were conducted in 2016.
Method The used method is a problem-oriented guided interview with
consecutive content and evaluating structuring analysis according to
Mayring.
Results Major inductive category was whether the parents had talked to
their children about their upcoming death. All parents stated overall
satisfaction and comfort regarding their palliative care. Lack of psycho-social
support in families was successfully addressed by involving palliative care.
Conclusions Retrospective interview studies in this context are feasible.
Early involvement of the palliative care team may relieve burden from affected
parents. Open communication about death proved helpful for all involved parties,
it may facilitate acceptance of terminal illness and alleviate guilt in
parents.Concepts for an open and empowering communication within families and
between treatment site and families need continuing adjustment. The Palliative
care team may also have a key role regarding early phase trials and molecular
studies.
The Role of Formative Evaluation in Promoting Digitally-based Health Equity and Reducing Bias for Resilient Health Systems: The Case of Patient Portals
Authors: Cresswell Kathrin , Rigby Michael , Georgiou Andrew , Wong Zoie Shui-Yee , Kukhareva Polina , Medlock Stephanie , De Keizer Nicolet F. , Magrabi Farah , Scott Philip , Ammenwerth Elske 
Published: June 2022

Objectives: Patient portals are increasingly implemented to improve patient involvement and engagement. We here seek to provide an overview of ways to mitigate existing concerns that these technologies increase inequity and bias and do not reach those who could benefit most from them.
Methods: Based on the current literature, we review the limitations of existing evaluations of patient portals in relation to addressing health equity, literacy and bias; outline challenges evaluators face when conducting such evaluations; and suggest methodological approaches that may address existing shortcomings.
Results: Various stakeholder needs should be addressed before deploying patient portals, involving vulnerable groups in user-centred design, and studying unanticipated consequences and impacts of information systems in use over time.
Conclusions: Formative approaches to evaluation can help to address existing shortcomings and facilitate the development and implementation of patient portals in an equitable way thereby promoting the creation of resilient health systems.
The International Academy of Health Sciences Informatics: 2021 Update
Authors: Hersh William R. , Haux Reinhold , Huesing Elaine , Ball Marion J. , Kimura Michio , Otero Paula , Detmer Don , Koch Sabine , Saranto Kaija K. , Wright Graham 
Published: June 2022

Objectives: To summarize the activities of the International Academy of Health Sciences Informatics (IAHSI) in 2021 and welcome its 2021 Class of Fellows.
Methods: Report on governance, strategic directions, newly elected fellows, plenary meetings, and other activities of the Academy.
Results: As in 2020, all of the Academy's activities were carried out virtually due to the COVID-19 pandemic. In 2021, new Board members were elected. Strategic activities in data standards and interoperability and in mentorship moved forward. A new class of 26 Fellows was elected, bringing the total membership of the Academy to 204 Fellows from all regions of the world. In addition, a virtual plenary meeting was held.
Conclusions: The Academy has continued to pursue its role as the honorific society globally for biomedical and health informatics. Expansion of strategic activities and membership will continue moving forward.
Achieving Inclusivity by Design: Social and Contextual Information in Medical Knowledge
Authors: Hastings Janna 
Published: June 2022

Objectives: To select, present, and summarize the most relevant papers published in 2020 and 2021 in the field of Knowledge Representation and Knowledge Management, Medical Vocabularies and Ontologies, with a particular focus on health inclusivity and bias.
Methods: A broad search of the medical literature indexed in PubMed was conducted. The search terms 'ontology'/'ontologies' or 'medical knowledge management' for the dates 2020-2021 (search conducted November 26, 2021) returned 9,608 records. These were pre-screened based on a review of the titles for relevance to health inclusivity, bias, social and contextual factors, and health behaviours. Among these, 109 papers were selected for in-depth reviewing based on full text, from which 22 were selected for inclusion in this survey.
Results: Selected papers were grouped into three themes, each addressing one aspect of the overall challenge for medical knowledge management. The first theme addressed the development of ontologies for social and contextual factors broadening the scope of health information. The second theme addressed the need for synthesis and translation of knowledge across historical disciplinary boundaries to address inequities and bias. The third theme encompassed a growing interest in the semantics of datasets used to train medical artificial intelligence systems and on how to ensure they are free of bias.
Conclusions: Medical knowledge management and semantic resources have much to offer efforts to tackle bias and enhance health inclusivity. Tackling inequities and biases requires relevant, semantically rich data, which needs to be captured and exchanged.