bluuebunny/crossref_metadata_2025_split huggingface dataset:
Key gene networks that control magnetosome biomineralization in magnetotactic bacteria
Authors: Liu Peiyu , Zheng Yue , Zhang Rongrong , Bai Jinling , Zhu Kelei , Benzerara Karim , Menguy Nicolas , Zhao Xiang , Roberts Andrew P , Pan Yongxin , Li Jinhua 
Published: October 2022

Abstract
Magnetotactic bacteria (MTB) are a group of phylogenetically and morphologically diverse prokaryotes that have the capability of sensing Earth's magnetic field via nanocrystals of magnetic iron minerals. These crystals are enclosed within intracellular membranes or organelles known as magnetosomes and enable a sensing function known as magnetotaxis. Although MTB were discovered over half a century ago, the study of the magnetosome biogenesis and organization remains limited to a few cultured MTB strains. Here, we present an integrative genomic and phenomic analysis to investigate the genetic basis of magnetosome biomineralization in both cultured and uncultured strains from phylogenetically diverse MTB groups. The magnetosome gene contents/networks of strains are correlated with magnetic particle morphology and chain configuration. We propose a general model for gene networks that control/regulate magnetosome biogenesis and chain assembly in MTB systems.
Effect of supplemental vitamin D3 on bone mineral density: a systematic review and meta-analysis
Authors: Kazemian Elham , Pourali Ali , Sedaghat Fatemeh , Karimi Mehrdad , Basirat Vahid , Sajadi Hezaveh Zohreh , Davoodi Sayed Hossein , Holick Michael F 
Published: October 2022

AbstractContextThere is still controversy over the effect of vitamin D3 supplementation on bone health.ObjectiveThe effects of vitamin D3 supplementation on bone mineral density (BMD) and markers of bone turnover, as well as the dose-response relationship between vitamin D3 and bone health in adults, were evaluated.Data SourcesThe PubMed, Scopus, Cochrane, Web of Science, and AGRIS databases were searched for articles published through April 30, 2022. Thirty-nine of the 6409 records identified met the inclusion criteriaData ExtractionData were extracted from articles by 2 authors, and data extraction was cross-checked independently. A random-effects model was used to estimate the pooled effect size and the associated 95%CI for the effect of vitamin D3 for each outcome. A one-stage random-effects dose-response model was used to estimate the dose-response relationship between vitamin D3 supplementation and BMD.Data AnalysisResults of meta-analysis showed a beneficial effect of vitamin D3 at the lumbar spine (standardized mean difference [SMD] = 0.06; 95%CI, 0.01–0.12) and femoral neck (SMD = 0.25; 95%CI, 0.09–0.41). Dose-response analysis revealed a linear relationship between vitamin D3 supplementation doses and BMD at the femoral neck, lumbar spine, and total hip sites. No significant effect of vitamin D3 supplementation on whole-body or total hip BMD was observed (P &gt; 0.05). Vitamin D3 supplementation significantly decreased BMD at both proximal and distal forearm (SMD = −0.16; 95%CI, −0.26 to −0.06). The variables of ethnicity, age, baseline 25-hydroxyvitamin D (25[OH]D), menopause status, vitamin D3 dosing frequency, and bone health status (P interaction = 0.02) altered the effect of vitamin D3 supplementation on BMD. Additionally, a nonlinear relationship between vitamin D3 supplement doses and markers of bone turnover was found.ConclusionA protective effect of vitamin D3 supplementation on BMD of the lumbar spine, femoral neck, and total hip is implicated.Systematic Review RegistrationPROSPERO registration number CRD42017054132.
Transforming Perceptions: The Development of Pre-pack Regulations in England and Wales
Authors: Adebola Bolanle 
Published: October 2022

Abstract
The article systematically assesses the extent to which the Administration (Restrictions on Disposal etc. to Connected Persons) Regulations 2021 achieve the goal of the government to quell the negative perceptions of pre-pack administration. The pre-pack has generated much criticism from disenfranchised groups who regard the practice with much suspicion. These criticisms have triggered questions as to whether and how to structure the regulation of pre-packs.
The article introduces original frames through which to distinguish the competing regulatory visions of the pre-pack, as well as to systematically evaluate the regulatory frameworks that have been introduced. The evaluation reveals a gap between the regulatory visions of the critics and the regulator. This gap has impacted the reception and effectiveness of successive regulatory frameworks. Combining its frames with the expectation gap theory, the article offers a critical assessment of the 2021 reforms, which address most but not all the criticisms of the pre-pack.
The Official Story of the Law
Authors: Baude William , Sachs Stephen E 
Published: October 2022

Abstract
A legal system’s ‘official story’ is its shared account of the law’s structure and sources, which members of its legal community publicly advance and defend. In some societies, however, officials pay lip service to this shared account, while privately adhering to their own unofficial story instead. If the officials enforce some novel legal code while claiming fidelity to older doctrines, then which set of rules—if either—is the law? We defend the legal relevance of the official story, on largely Hartian grounds. Hart saw legal rules as determined by social rules accepted by a particular community. We argue that this acceptance requires no genuine normative commitment; agreement or compliance with the rules might even be feigned. And this community need not be limited to an official class, but includes all who jointly accept the rules. Having rejected these artificial limits, one can take the official story at its word.
Single cell RNA-seq of human cornea organoids identifies cell fates of a developing immature cornea
Authors: Maiti George , Monteiro de Barros Maithê Rocha , Hu Nan , Dolgalev Igor , Roshan Mona , Foster James W , Tsirigos Aristotelis , Wahlin Karl J , Chakravarti Shukti 
Published: October 2022

Abstract
The cornea is a protective and refractive barrier in the eye crucial for vision. Understanding the human cornea in health, disease, and cell-based treatments can be greatly advanced with cornea organoids developed in culture from induced pluripotent stem cells. While a limited number of studies have investigated the single-cell transcriptomic composition of the human cornea, its organoids have not been examined similarly. Here, we elucidated the transcriptomic cell fate map of 4-month-old human cornea organoids and human donor corneas. The organoids harbor cell clusters that resemble cells of the corneal epithelium, stroma, and endothelium, with subpopulations that capture signatures of early developmental states. Unlike the adult cornea where the largest cell population is stromal, the organoids contain large proportions of epithelial and endothelial-like cells. These corneal organoids offer a 3D model to study corneal diseases and integrated responses of different cell types.
Archetypal factorization and gluon poles in semi-exclusive reactions
Authors: Anikin I V , Szymanowski L 
Published: October 2022

Abstract
Within the archetypal factorization procedure, we study the gluon pole contributions manifesting in the nucleon–lepton hard processes of hadron production. We prove the dominant role of gluon pole contributions in such processes. We analyze the different sources of complexity associated with the gluon pole functions. As a practical application, we derive a new single spin asymmetry directly related to the gluon poles that can be studied experimentally.
A genome-wide association study identifying single nucleotide polymorphisms in the PPFIBP2 gene was predictive for interstitial lung disease in rheumatoid arthritis patients
Authors: Hayashi Shinya , Matsubara Tsukasa , Fukuda Koji , Maeda Toshihisa , Funahashi Keiko , Hashimoto Marowa , Takashima Yoshinori , Kikuchi Kenichi , Fujita Masahiro , Matsumoto Tomoyuki , Kuroda Ryosuke 
Published: October 2022

Abstract

Objective
Genetic polymorphisms might serve as useful prognostic markers for the timely diagnosis of RA. The purpose of this study was to identify genomic factors predictive of the occurrence of interstitial lung disease (ILD) in RA by performing a genome-wide association study of genetic variants, including single nucleotide polymorphisms (SNPs).

Methods
The study population included 306 RA patients. All patients were treated with conventional DMARDs, including 6–16 mg MTX per week. Clinical data and venous blood samples were collected from all patients before administration of DMARDs. A total of 278 347 SNPs were analysed to determine their association with ILD occurrence.

Results
Several SNPs were strongly associated with ILD occurrence (P &lt; 10−5). rs6578890, which is located on chromosome 11 in the intronic region of the gene encoding tyrosine phosphatase receptor type F polypeptide-interacting protein-binding protein 2 (PPFIBP2), showed the strongest association with ILD occurrence (odds ratio 4.32, P = 10−7.93).

Conclusion
PPFIBP2 could be a useful genetic marker for occurrence of interstitial pneumonia in RA patients and might help to identify the risk of ILD occurrence before RA treatment, thereby improving patient outcomes.
Obstructive sleep apnea during REM sleep: effects on morning and evening blood pressure
Authors: Falla Catherine , Young Alan , Pope Alun , O’Driscoll Denise M 
Published: October 2022

AbstractStudy ObjectivesObstructive sleep apnea (OSA) is linked to the emergence and progression of cardiovascular complications including hypertension, stroke, arrhythmias, coronary artery disease, and heart failure. Epidemiological studies have reported that hypertension is associated with respiratory events during REM sleep. We examined the relationship between respiratory events during REM and morning and evening hypertensive blood pressure (BP) levels in a clinical sleep population.MethodsThis study included data from in-laboratory diagnostic polysomnographic studies (n = 797) from adults attending for investigation of OSA. Hypertensive BP levels were defined using BP measurements taken in the evening before and morning after polysomnography, and the use of antihypertensive medication. Regression modeling was undertaken to examine the probability of evening and morning hypertensive BP levels according to REM apnea-hypopnea index (AHI), NREM AHI, gender, age, body mass index (BMI), alcohol use, total sleep time (TST), sleep time SpO2 &lt;90%, and smoking status.ResultsThe probability of morning hypertensive BP levels was significantly independently associated with age (p &lt; .001), BMI (p &lt; .001), and REM AHI (p &lt; .001). No significant effect was found for the male gender, NREM AHI, alcohol use, TST, sleep time SpO2 &lt;90%, or smoking (p &gt; .05 for all). The probability of evening hypertensive BP levels was only significantly associated with age (p &lt; .001), male gender (p = .012), BMI (p &lt; .001), and TST (p = .032).ConclusionsRespiratory events during REM sleep are significantly associated with morning hypertensive BP levels. Future research is needed to determine whether treatment of these events can prevent or reverse morning hypertensive BP levels.
Neonatal classic galactosemia—diagnosis, clinical profile and molecular characteristics in unscreened Turkish population
Authors: Çelik Muhittin , Akdeniz Osman , Ozbek Mehmet Nuri , Kirbiyik Ozgur 
Published: October 2022

Abstract

Background
Classic galactosemia (CG) is a rare hereditary disease that can cause serious morbidity and death if it is not diagnosed and treated in early periods of life. Clinical findings usually occur in the neonatal period after the neonate is fed with milk that contains galactose. Most patients are presented with jaundice, hepatomegaly, hypoglycemia and cataracts.

Objective
We aimed to document the clinical, molecular characteristics, regional estimated incidence and time of diagnosis in newborn with CG.

Materials and method
The data of 63 newborn with CG who were diagnosed and followed up between January 2011 and January 2018 were analyzed retrospectively.

Results
During the study period, 63 (33 boys and 30 girls) newborns were diagnosed with CG. The median gestational age was 39 weeks (33–42). Major presenting symptoms were jaundice 90.5% and cataract 41.2%. The mean age at first symptom was 12 ± 7.4 days while the mean age at diagnosis was 18.9 ± 10.6 days. Nearly half of the patients (55.5%) were diagnosed later than the postnatal 15th day. Genetic analysis was performed on 56 patients and homozygous Q188R mutation was found in 92.8%. There were signs of sepsis in 33.3% of the cases. Six patients died due to sepsis. There was consanguinity in 84.1% of the parents and regional estimated incidence was calculated as 1 in 6103 live births.

Conclusion
Q188R mutation was found in 92.8% of our cases. The regional estimated incidence was found as 1 in 6103 live births. Our study strongly supports that galactosemia should be included in the national newborn screening program.
Reading Epilepsy and Language Processing: A Proposed Role for Semantic Salience
Authors: Li Wentao , Seyal Masud 
Published: October 2022

Summary:
Reading epilepsy is a relatively rare reflex epilepsy syndrome that typically presents as orofacial reflex myoclonus triggered by reading. Seizures are thought to be because of activation of hyperexcitable language-related pathways in the dominant hemisphere that subsequently spreads to adjacent motor cortices. More difficult reading tasks are thought to be more provocative of seizures regardless of semantic understanding of the text. The authors sought to better characterize the role of text difficulty and comprehension in triggering seizures in a 27-year-old patient with reading epilepsy. As a part of his epilepsy monitoring unit admission, the patient underwent a series of reading trials with increasing semantic salience and/or difficulty, including pseudo-reading of colors and foreign-language texts, which demonstrated a positive correlation between spike count and clinical events and increasing semantic salience. This suggests that our novel reading task may be able to differentiate between different processes in the reading pathway and that increased semantic relevance of the text, rather than increased difficulty per se, can be associated with increased seizures in reading epilepsy. The authors theorize that this may be associated with his atypical (nondominant) right hemispheric seizure focus and propose that further study of patients with reading epilepsy syndrome may help elucidate the neurobiological networks involved in reading and language processing.
Tonic Seizures in a Patient With Lennox–Gastaut Syndrome Manifest as “Icicles” Rather Than “Flames” on Quantitative EEG Analysis
Authors: Catenaccio Eva , Bennett Mariko L. , Massey Shavonne L. , Abend Nicholas S. , Bergqvist Christina 
Published: October 2022

Summary:
Quantitative analysis of continuous electroencephalography (QEEG) is increasingly being used to augment seizure detection in critically ill patients. Typically, seizures manifest on QEEG as abrupt increases in power and frequency, a visual pattern often called “flames.” Here, we present a case of a 16-year-old patient with intractable Lennox–Gastaut syndrome secondary to a pathogenic variant in the SCN2A gene who had tonic seizures that manifest as abrupt decreases in power on QEEG, a visual pattern we term “icicles.” Recognition of QEEG patterns representative of different seizure types is important as QEEG use becomes more widespread including in pediatric populations.
Time of Sample Collection Critical for Microbiome Replicability
Authors: Allaband Celeste , Lingaraju Amulya , Ramos Stephany Flores , Kumar Tanya , Javaheri Haniyeh , Tiu Maria D. , Machado Ana Carolina Dantas , Richter Roland A. , Elijah Emmanuel , Haddad Gabriel G. , Leone Vanessa A. , Dorrestein Pieter C. , Knight Rob , Zarrinpar Amir 
Published: October 2022

ABSTRACTAlthough many aspects of microbiome studies have been standardized to improve experimental replicability, none account for how the daily diurnal fluctuations in the gut lumen cause dynamic changes in 16S amplicon sequencing. Here we show that sample collection time affects the conclusions drawn from microbiome studies and are larger than the effect size of a daily experimental intervention or dietary changes. The timing of divergence of the microbiome composition between experimental and control groups are unique to each experiment. Sample collection times as short as only four hours apart lead to vastly different conclusions. Lack of consistency in the time of sample collection may explain poor cross-study replicability in microbiome research. Without looking at other data, the impact on other fields is unknown but potentially significant.One-Sentence SummaryIf we are not controlling for host circadian rhythm time in microbiome studies when performing experiments, it is like trying to measure sea level rise while not knowing that tides or waves exist.
Gait speed and individual characteristics can be used to predict specific gait metric magnitudes in neurotypical adults
Authors: Bonilla Yanez Maryana , Kettlety Sarah A. , Finley James M. , Schweighofer Nicolas , Leech Kristan A. 
Published: October 2022

AbstractBackgroundGait biofeedback is commonly used to reduce gait dysfunction in a variety of clinical conditions. In these studies, participants alter their walking to reach the desired magnitude of a specific gait parameter (the biofeedback target) with each step. Biofeedback of parameters such as anterior ground reaction force and step length have been well-studied. Yet, there is no standardized methodology to set the target magnitude of these parameters. Here we present an approach to predict the anterior ground reaction force and step length of neurotypical adults walking at different speeds as a potential method for personalized gait biofeedback.Research questionTo determine if anterior ground reaction force and step lengths achieved during neurotypical walking could be predicted using gait speed and participants’ demographic and anthropomorphic characteristics.MethodsWe analyzed kinetic and kinematic data from 51 neurotypical adults who walked on a treadmill at up to eight speeds. We calculated the average peak anterior ground reaction force and step length of the right lower extremity at each speed. We used linear mixed-effects models to evaluate the effect of speed, leg length, mass, and age on anterior ground reaction force and step length. We fit the model to data from 37 participants and validated predictions from the final models on an independent dataset from 23 participants.ResultsFinal prediction models for anterior ground reaction force and step length both included speed, speed squared, age, mass, and leg length. The models both showed strong agreement between predicted and actual values on an independent dataset.SignificanceAnterior ground reaction force and step length for neurotypical adults can be predicted given an individual’s gait speed, age, leg length, and mass. This may provide a standardized method to personalize targets for individuals with gait dysfunction in future studies of gait biofeedback.
Discovery of prevalent, clinically actionable tumor neoepitopes via integrated biochemical and cell-based platforms
Authors: Gurung Hem , Heidersbach Amy , Darwish Martine , Chan Pamela , Li Jenny , Beresini Maureen , Zill Oliver , Wallace Andrew , Tong Ann-Jay , Hascall Dan , Torres Eric , Chang Andy , Lou Kenny “Hei-Wai” , Abdolazimi Yassan , Moore Amanda , Uche Uzodinma , Laur Melanie , Notturno Richard , Ebert Peter J.R. , Blanchette Craig , Haley Benjamin , Rose Christopher M. 
Published: October 2022

SummaryStrategies for maximizing the potency and specificity of cancer immunotherapies have sparked efforts to identify recurrent epitopes presented in the context of defined tumor-associated neoantigens. Discovering these “neoepitopes” can be difficult owing to the limited number of peptides that arise from a single point mutation, a low number of copies presented on the cell surface, and variable binding specificity of the human leukocyte antigen (HLA) class I complex. Due to these limitations, many discovery efforts focus on identifying neoepitopes from a small number of cancer neoantigens in the context of few HLA alleles. Here we describe a systematic workflow to characterize binding and presentation of neoepitopes derived from 47 shared cancer neoantigens in the context of 15 HLA alleles. Through the development of a high-throughput neoepitope-HLA binding assay, we surveyed 24,149 candidate neoepitope-HLA combinations resulting in 587 stable complexes. These data were supplemented by computational prediction that identified an additional 257 neoepitope-HLA pairs, resulting in a total of 844 unique combinations. We used these results to build sensitive targeted mass spectrometry assays to validate neoepitope presentation on a panel of HLA-I monoallelic cell lines engineered to express neoantigens of interest as a single polypeptide. Altogether, our analyses detected 84 unique neoepitope-HLA pairs derived from 37 shared cancer neoantigens and presented across 12 HLA alleles. We subsequently identified multiple TCRs which specifically recognized two of these neoantigen-HLA combinations. Finally, these novel TCRs were utilized to elicit a T cell response suggesting that these neoepitopes are likely to be immunogenic. Together these data represent a validated, extensive resource of therapeutically relevant neoepitopes and the HLA context in which they can be targeted.
Quantitative analysis of cellular morphology duringin vitrodecidualization
Authors: Ant Luciana , Le Dily François , Beato Miguel , Saragüeta Patricia 
Published: October 2022

AbstractDecidualization is a differentiation process involving shape reorganization from a fibroblast to an epithelioid-like appearance of endometrial stromal cells. Specificities of these cells impede the use of existing automated tools to follow morphological changes during differentiation; we therefore developed a simple but accurate methodology to quantify the phenotypical changes that occur in anin vitrodecidualization system.The approach consists of the analysis of the circularity of the cells directly from light microscopy images. Here, we used this methodology to follow the effects of progesterone or progestin R5020 in combination with estradiol (E2) and cAMP on inducing the decidualization of human endometrial cells. We further implemented a statistical model to detect the differences in the kinetics of decidualization of the two hormonal stimuli before all the cell population acquired the decidual phenotype. We found that 2 days after stimulation are sufficient to detect statistical differences in morphology between decidualization induced and control cells. Here, we detail the model and scripts in order to provide a useful, practical and low cost tool to evaluate morphological aspects of endometrial stromal differentiation.Availability and implementationSee supplementary methodsSupplementary informationSupplementary data is available online.