bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene expression profiling of orbital muscles in treatment-resistant ophthalmoplegic myasthenia gravis
Authors: Europa Tarin A. , Nel Melissa , Heckmann Jeannine M. 
Published: December 2020

Abstract
Background
Unbiased in silico approaches applied to genome-wide data prioritized putative functional gene variants associating with treatment-resistant ophthalmoplegic myasthenia gravis (OP-MG). Although altered expression of genes harbouring these variants, or associated pathways, were shown in patient-derived transdifferentiated-myocyte models, gene expression in orbital-derived muscle was required to test the validity of the predictions.

Methods
We sampled orbicularis oculi muscle (OOM) and one paralysed extraocular muscle (EOM) from six individuals with OP-MG during blepharoptosis and re-alignment surgeries, respectively. For controls, the OOMs were sampled from four individuals without myasthenia undergoing surgery for non-muscle causes of ptosis, and one non-paralysed EOM. Using a qPCR array, expression of 120 genes was compared between OP-MG and control OOMs, profiling putative “OP-MG” genes, genes in related biological pathways and genes reported to be dysregulated in MG cases or experimental MG models, and in EOMs of cases with strabismus. Normalization was performed with two stable reference genes. Differential gene expression was compared between OP-MG and control samples using the ΔΔCT method. Co-expression was analysed by pairwise correlation of gene transcripts to infer expression networks.

Results
Overall, transcript levels were similar in OOMs and EOMs (p = 0.72). In OOMs, significant downregulated expression of eight genes was observed in OP-MG cases compared with controls (> twofold; p ≤ 0.016), including TFAM, a mitochondrial transcription factor, and genes related to the following pathways: atrophy signalling; muscle regeneration and contraction; glycogen synthesis; and extracellular matrix remodelling. Several microRNAs, known to be highly expressed in EOMs, are predicted to regulate some of these genes. Co-expression analyses of gene-pairs suggested high interconnectedness of gene expression networks in OP-MG muscle, but not controls (r > 0.96, p < 0.01). Significant inverse directions of gene-pair correlations were noted in OP-MG versus controls OOM networks (r ≥ 0.92, p < 0.001) involving most OP-MG genes overlapping prominently with muscle atrophy/contractility and oxidative metabolism genes.

Conclusions
The gene expression in orbital muscles derived from OP-MG individuals compared with normal controls, support the pathogenic hypothesis previously generated from whole genome sequence analyses. Repression of gene transcripts in OP-MG orbital muscle implicate tissue-specific regulatory mechanisms, which may inform future biomarker discovery approaches.
Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome
Authors: Accorsi Emma K. , Franzosa Eric A. , Hsu Tiffany , Joice Cordy Regina , Maayan-Metzger Ayala , Jaber Hanaa , Reiss-Mandel Aylana , Kline Madeleine , DuLong Casey , Lipsitch Marc , Regev-Yochay Gili , Huttenhower Curtis 
Published: December 2020

AbstractBackgroundStaphylococcus aureusis a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of individuals carryS. aureusasymptomatically in their nares, a risk factor for later infection, and interactions with other species in the nasal microbiome likely modulate its carriage. It is thus important to identify ecological or functional genetic elements within the maternal or infant nasal microbiomes that influenceS. aureusacquisition and retention in early life.ResultsWe recruited 36 mother-infant pairs and profiled a subset of monthly longitudinal nasal samples from the first year after birth using shotgun metagenomic sequencing. The infant nasal microbiome is highly variable, particularly within the first 2 months. It is weakly influenced by maternal nasal microbiome composition, but primarily shaped by developmental and external factors, such as daycare. Infants display distinctive patterns ofS. aureuscarriage, positively associated withAcinetobacterspecies,Streptococcus parasanguinis,Streptococcus salivarius, andVeillonellaspecies and inversely associated with maternalDolosigranulum pigrum. Furthermore, we identify a gene family, likely acting as a taxonomic marker for an unclassified species, that is significantly anti-correlated withS. aureusin infants and mothers. In gene content-based strain profiling, infantS. aureusstrains are more similar to maternal strains.ConclusionsThis improved understanding ofS. aureuscolonization is an important first step toward the development of novel, ecological therapies for controllingS. aureuscarriage.
Developing a core outcome set for the treatment of pregnant women with pregestational diabetes—a study protocol
Authors:   On behalf of the INSPIRED group, Kgosidialwa Oratile , Bogdanet Delia , Egan Aoife , O’Shea Paula M. , Biesty Linda , Devane Declan , Dunne Fidelma 
Published: December 2020

AbstractBackgroundPregestational diabetes mellitus (PGDM) is associated with adverse pregnancy outcomes including increased rates of caesarean section birth, macrosomia, congenital malformation, prematurity, admission to the neonatal intensive care unit and stillbirth. As a result, there has been an increase in interventions to improve outcomes in both mother and infant. To date, meaningful comparisons between these studies are limited due to heterogeneity in outcome selection and reporting. The aim of this study is to develop a core outcome set (COS) for randomised controlled trials evaluating the effectiveness of interventions for the treatment of pregnant women with PGDM.MethodsThe study consists of three steps. The first step is a systematic review of the literature to assess outcomes reported in randomised controlled trials assessing the effectiveness of interventions for the treatment of pregnant women with PGDM. The second step is a three round, online Delphi survey to prioritise these outcomes. In this step, stakeholders (including women with PGDM, healthcare workers, researchers and policymakers) will be asked to rank the importance of outcomes for inclusion in the COS using a 9-point Likert type scale. Outcomes that meet the inclusion criteria after completion of the Delphi surveys will be brought to the consensus meeting. The consensus meeting will be the third and final step, where the COS will be finalised. The consensus meeting will include members from each stakeholder group.DiscussionThis paper describes the process used to develop a COS for the reporting of studies evaluating the effectiveness of interventions in pregnant women with PGDM. The COS will enable greater comparison between and information synthesis across RCTs in the treatment of PGDM. In addition, this COS will also help improve trial reporting and minimise research waste by prioritising the collection and reporting of outcomes that matter to all relevant stakeholder groups.Trial registrationThis COS has been registered with the Core Outcome Measures in Effectiveness Trials (COMET) initiative (http://www.comet-initiative.org/studies/details/1425) on the 4th of November 2019. The systematic review component of this study has also been registered with the International Prospective Register of Systematic Reviews (PROSPERO) (https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42020173549).
Detection of SARS-CoV-2 pneumonia: two case reports
Authors: Seibert Felix S. , Toma Daniela , Bauer Frederic , Paniskaki Krystallenia , Anft Moritz , Rohn Benjamin J. , Wang Simon , Racovitan Diana , Babel Nina , Westhoff Timm H. 
Published: December 2020

Abstract
Background
Developing therapeutic strategies for a SARS-CoV-2 infection is challenging, but first the correct diagnosis has to be made. Unspecific upper and lower respiratory tract symptoms can be misleading; hence, a nasopharyngeal swab test with a real-time reverse-transcription-polymerase chain reaction is of great importance. However, early viral clearing jeopardizes a sound diagnosis of COVID-19.

Case presentation
We report on two Caucasian patients who had negative pharyngeal swab tests at the onset of SARS-CoV-2 pneumonia. In one patient, the virus was not even detectable in bronchoalveolar lavage despite typical radiomorphologic changes.

Conclusions
Negative PCR findings in both the pharynx and bronchoalveolar lavage do not exclude COVID-19 pneumonia. Computed tomography is a crucial diagnostic prerequisite in this context.
Knockdown of Parkinson’s disease-related gene ATP13A2 reduces tumorigenesis via blocking autophagic flux in colon cancer
Authors: Chen Qian , Zhong Li , Zhou Chao , Feng Yan , Liu Quan-xing , Zhou Dong , Lu Xiao , Du Guang-Sheng , Jian Dan , Luo Hao , Wang Dong , Zheng Hong , Qiu Yuan 
Published: December 2020

Abstract
Background
Accumulating evidence shows that Parkinson’s disease is negatively associated with colon cancer risk, indicating that Parkinson’s disease family proteins may be involved in the initiation of colon cancer. Here, we aimed to identify a Parkinson’s disease-related gene involved in colon cancer, elucidate the underlying mechanisms, and test whether it can be used as a target for cancer therapy.

Methods
We first screened colon cancer and normal tissues for differential expression of Parkinson’s disease-associated genes and identified ATP13A2, which encodes cation-transporting ATPase 13A2, as a putative marker for colon cancer. We next correlated ATP13A2 expression with colon cancer prognosis. We performed a series of ATP13A2 knockdown and overexpression studies in vitro to identify the contribution of ATP13A2 in the stemness and invasive capacity of colon cancer cells. Additionally, autophagy flux assay were determined to explore the mechanism of ATP13A2 induced stemness. Finally, we knocked down ATP13A2 in mice using siRNA to determine whether it can be used as target for colon cancer treatment.

Results
Colon cancer patients with high ATP13A2 expression exhibit shorter overall survival than those with low ATP13A2. Functionally, ATP13A2 acts as a novel stimulator of stem-like traits. Furthermore, knockdown of ATP13A2 in HCT116 resulted in decreased levels of cellular autophagy. Additionally, bafilomycin A1, an autophagy inhibitor, reversed the ATP13A2-induced stemness of colon cancer cells. Lastly treatment with ATP13A2 siRNA reduced the volume of colon cancer xenografts in mice.

Conclusions
The PD-associated gene ATP13A2 is involved in colon cancer stemness through regulation of autophagy. Furthermore, ATP13A2 is a novel prognostic biomarker for colon cancer and is a potential target for colon cancer therapy.
Epigenome-wide association study identifies DNA methylation markers for asthma remission in whole blood and nasal epithelium
Authors:   BIOS Consortium, Qi Cancan , Vonk Judith M. , van der Plaat Diana A. , Nieuwenhuis Maartje A. E. , Dijk F. Nicole , Aïssi Dylan , Siroux Valérie , Boezen H. Marike , Xu Cheng-jian , Koppelman Gerard H. 
Published: December 2020

Abstract
Background
Asthma is a chronic respiratory disease which is not curable, yet some patients experience spontaneous remission. We hypothesized that epigenetic mechanisms may be involved in asthma remission.

Methods
Clinical remission (ClinR) was defined as the absence of asthma symptoms and medication for at least 12 months, and complete remission (ComR) was defined as ClinR with normal lung function and absence of airway hyperresponsiveness. We analyzed differential DNA methylation of ClinR and ComR comparing to persistent asthma (PersA) in whole blood samples (n = 72) and nasal brushing samples (n = 97) in a longitudinal cohort of well characterized asthma patients. Significant findings of whole blood DNA methylation were tested for replication in two independent cohorts, Lifelines and Epidemiological study on the Genetics and Environment of Asthma (EGEA).

Results
We identified differentially methylated CpG sites associated with ClinR (7 CpG sites) and ComR (129 CpG sites) in whole blood. One CpG (cg13378519, Chr1) associated with ClinR was replicated and annotated to PEX11 (Peroxisomal Biogenesis Factor 11 Beta). The whole blood DNA methylation levels of this CpG were also different between ClinR and healthy subjects. One ComR-associated CpG (cg24788483, Chr10) that annotated to TCF7L2 (Transcription Factor 7 Like 2) was replicated and associated with expression of TCF7L2 gene. One out of seven ClinR-associated CpG sites and 8 out of 129 ComR-associated CpG sites identified from whole blood samples showed nominal significance (P < 0.05) and the same direction of effect in nasal brushes.

Conclusion
We identified DNA methylation markers possibly associated with clinical and complete asthma remission in nasal brushes and whole blood, and two CpG sites identified from whole blood can be replicated in independent cohorts and may play a role in peroxisome proliferation and Wnt signaling pathway.
Client-side rogue access-point detection using a simple walking strategy and round-trip time analysis
Authors: Kitisriworapan Songrit , Jansang Aphirak , Phonphoem Anan 
Published: December 2020

AbstractTraditional rogue access-point (AP) detection mechanisms are employed in network administration to protect network infrastructure and organization; however, these mechanisms do not protect end users from connecting to a rogue-AP. In this paper, a rogue-AP detection technique on the mobile-user side is proposed. By using a simple method involving walking, the round-trip time (RTT) and the modulation and coding scheme values are obtained, and a more accurate transmission rate for particular RTT values is thereby calculated. Further, the cleansed data are classified using the k-means method and the cumulative distribution function for the detection process. The results demonstrate that a rogue-AP can be detected with an F-measure value of up to 0.9. In the future, the proposed algorithm can be implemented as an application installed on mobile devices so that nontechnical users can detect rogue-APs.
A reverse Hardy–Hilbert-type integral inequality involving one derivative function
Authors: Chen Qian , Yang Bicheng 
Published: December 2020

AbstractIn this article, by using weight functions, the idea of introducing parameters, the reverse extended Hardy–Hilbert integral inequality and the techniques of real analysis, a reverse Hardy–Hilbert-type integral inequality involving one derivative function and the beta function is obtained. The equivalent statements of the best possible constant factor related to several parameters are considered. The equivalent form, the cases of non-homogeneous kernel and some particular inequalities are also presented.
Stabilization of nonlinear systems via aperiodic intermittent stochastic noise driven by G-Brownian motion with application to epidemic models
Authors: Zhong Xiaojing , Deng Feiqi , Zhang Bo , Ouyang Haibin 
Published: December 2020

AbstractTo stabilize a nonlinear system $dx(t)=f(t,x(t))\,dt$
d
x
(
t
)
=
f
(
t
,
x
(
t
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d
t
, we stochastically perturb the deterministic model by using two types of aperiodic intermittent stochastic noise driven by G-Brownian motion. We demonstrate quasi-sure exponential stability for the perturbed system and give the convergence rate, which is related to the control intensity. An application to SIS epidemic model is presented to confirm the theoretical results.
Effect of lemon peel flavonoids on anti-fatigue and anti-oxidation capacities of exhaustive exercise mice
Authors: Bao Guili , Zhang Yinglong , Yang Xiaoguang 
Published: December 2020

AbstractIn this study, lemon peel flavonoids (LPF) were administered to investigate its effect on the anti-fatigue and antioxidant capacity of mice that undergo exercise until exhaustion. LPF (88.36 min in LPFH group mice) significantly increased the exhaustion swimming time compare to the untreated mice (40.36 min), increased the liver glycogen and free fatty acid content in mice and reduce lactic acid and BUN content in a dose-dependent manner. As the concentration of lemon peel flavonoids increased, the serum creatine kinase, aspartate aminotransferase, and alanine aminotransferase levels of mice gradually decreased. LPF increases superoxide dismutase (SOD) and catalase (CAT) levels in mice and reduces malondialdehyde levels in a dose-dependent manner. And LPF raises hepatic tissue SOD, CAT activities and reduces skeletal muscle tissue iNOS, TNF-α levels of mice compared to the control group. LPF also enhanced the expression of copper/zinc-superoxide dismutase (Cu/Zn-SOD), manganese-superoxide dismutase (Mn-SOD), and CAT mRNA in mouse liver tissue. LPF also enhanced the expression of alanine/serine/cysteine/threonine transporter 1 (ASCT1) mRNA and attenuate the expression of syncytin-1, inducible nitric oxide synthase (iNOS), and tumor necrosis factor (TNF)-α in mouse skeletal muscle. According to high-performance liquid chromatography (HPLC) analysis, it was found that LPF contains flavonoids such as rutin, astragalin, isomangiferin, naringin, and quercetin. Our experimental data show that LPF has good anti-fatigue effects and anti-oxidation ability. In summary, LPF has high prospects to be developed and added to nutritional supplements.
COVID-19 cases and testing in 53 prison systems
Authors: Lemasters Katherine , McCauley Erin , Nowotny Kathryn , Brinkley-Rubinstein Lauren 
Published: December 2020

Abstract
Background
COVID-19 has entered United States prison systems at alarming rates. Disparities in social and structural determinants of health disproportionately affect those experiencing incarceration, making them more vulnerable to COVID-19. Additionally, prisons are sites of congregate living, making it impossible to practice social distancing, and most prisons have relied only on incremental measures to reduce risk and spread of COVID-19. To more fully understand the impact that COVID-19 is having on incarcerated populations, it is critical to have systematic data on testing, test positivity, cases, and case fatality. Using data from the COVID Prison Project, we present data on 53 prison systems COVID-19 testing, test positivity, case, and case fatality by state and compare these data with each state’s general population. We do this for the early stages of the pandemic, utilizing data through July 15, 2020.

Results
Many states are not reporting full information on COVID testing with some also not reporting on case fatality. Among those reporting data, there is a wide variation between testing, test positivity, and case rates within prison systems and as compared to the general population. However, when more tests are deployed more cases are identified with the majority of state prisons having higher case rates than their general population.

Conclusions
These findings underscore the need for the implementation and study of COVID-19 mitigation and surveillance strategies to flatten the COVID-19 curve in prisons across the country. We call for future research to build on these data from the COVID Prison Project to protect the health of our nations’ often forgotten residents.
Arabic text summarization using deep learning approach
Authors: Al-Maleh Molham , Desouki Said 
Published: December 2020

AbstractNatural language processing has witnessed remarkable progress with the advent of deep learning techniques. Text summarization, along other tasks like text translation and sentiment analysis, used deep neural network models to enhance results. The new methods of text summarization are subject to a sequence-to-sequence framework of encoder–decoder model, which is composed of neural networks trained jointly on both input and output. Deep neural networks take advantage of big datasets to improve their results. These networks are supported by the attention mechanism, which can deal with long texts more efficiently by identifying focus points in the text. They are also supported by the copy mechanism that allows the model to copy words from the source to the summary directly. In this research, we are re-implementing the basic summarization model that applies the sequence-to-sequence framework on the Arabic language, which has not witnessed the employment of this model in the text summarization before. Initially, we build an Arabic data set of summarized article headlines. This data set consists of approximately 300 thousand entries, each consisting of an article introduction and the headline corresponding to this introduction. We then apply baseline summarization models to the previous data set and compare the results using the ROUGE scale.
Predictive factors for intrauterine insemination outcomes: a review
Authors: Starosta Anabel , Gordon Catherine E. , Hornstein Mark D. 
Published: December 2020

Abstract
Purpose
Intrauterine insemination (IUI) is a frequently utilized method of assisted reproduction for patients with mild male factor infertility, anovulation, endometriosis, and unexplained infertility. The purpose of this review is to discuss factors that affect IUI outcomes, including infertility diagnosis, semen parameters, and stimulation regimens.

Methods
We reviewed the published literature to evaluate how patient and cycle specific factors affect IUI outcomes, specifically clinical pregnancy rate, live birth rate, spontaneous abortion rate and multiple pregnancy rate.

Results
Most data support IUI for men with a total motile count > 5 million and post-wash sperm count > 1 million. High sperm DNA fragmentation does not consistently affect pregnancy rates in IUI cycles. Advancing maternal and paternal age negatively impact pregnancy rates. Paternal obesity contributes to infertility while elevated maternal BMI increases medication requirements without impacting pregnancy outcomes. For ovulation induction, letrozole and clomiphene citrate result in similar pregnancy outcomes and are recommended over gonadotropins given increased risk for multiple pregnancies with gonadotropins. Letrozole is preferred for obese women with polycystic ovary syndrome. IUI is most effective for women with ovulatory dysfunction and unexplained infertility, and least effective for women with tubal factor and stage III-IV endometriosis. Outcomes are similar when IUI is performed with ovulation trigger or spontaneous ovulatory surge, and ovulation may be monitored by urine or serum. Most pregnancies occur within the first four IUI cycles, after which in vitro fertilization should be considered.

Conclusions
Providers recommending IUI for treatment of infertility should take into account all of these factors when evaluating patients and making treatment recommendations.