bluuebunny/crossref_metadata_2025_split huggingface dataset:
Obstructive sleep apnea and atrial fibrillation: insights from a bidirectional Mendelian randomization study
Authors: Chen Lu , Sun Xingang , He Yuxian , Lu Yunlong , Zheng Liangrong 
Published: February 2022

Abstract
Background
Observational studies have suggested that obstructive sleep apnea (OSA) is in relation to atrial fibrillation (AF); however, these studies might be confounded and whether the relationship is causal remains unclear. We conducted a bidirectional Mendelian randomization (MR) study to clarify the causal inference between OSA and AF.

Methods
Genetic instruments for OSA and AF were obtained from genome-wide association studies. The fixed-effects inverse-variance weighted (IVW) method was used as the main method, supplemented by several sensitivity analyses. For replication, another AF dataset was used to validate the causal effect of OSA on AF. Furthermore, multivariable MR analyses were performed to obtain direct estimates adjusting for potential confounders.

Results
Genetic liability to OSA was found to be significantly associated with a higher AF risk in the fixed-effects IVW method [odds ratio (OR) 1.210; 95% CI 1.119–1.307; P = 1.51 × 10–6]. The results were consistent in MR sensitivity analyses as well as in replication analyses, and the significance remained after adjusting for potential confounders. In the reverse MR analyses, there was no causal effect of AF on OSA.

Conclusions
Our study strengthened the causal evidence of genetically predicted OSA with a higher AF risk. Early screening and appropriate management of OSA might show anti-arrhythmic benefits.
Clinicopathological and prognostic value of SIRT6 in patients with solid tumors: a meta-analysis and TCGA data review
Authors: Wu Xiaojing , Wang Shuyuan , Zhao Xuanzhu , Lai Sizhen , Yuan Zhen , Zhan Yixiang , Ni Kemin , Liu Zhaoce , Liu Lina , Xin Ran , Zhou Xingyu , Yin Xin , Liu Xinyu , Zhang Xipeng , Cui Wei , Zhang Chunze 
Published: February 2022

Abstract
Purposes
In addition to its role in cellular progression and cancer, SIRT6, a member of nicotinamide adenine dinucleotide (NAD+)-dependent class III deacylase sirtuin family, serves a variety of roles in the body's immune system. In this study, we sought to determine the relationship between the expression of SIRT6 and the clinicopathological outcomes of patients with solid tumours by conducting a meta-analysis of the available data.

Methods
The databases PubMed and ISI Web of Science were searched for relevant literature, and the results were presented here. Using Stata16.0, a meta-analysis was conducted to determine the impact of SIRT6 on clinicopathological characteristics and prognosis in malignancy patients. The results were published in the journal Cancer Research. The dataset from the Cancer Genome Atlas (TCGA) was used to investigate the prognostic significance of SIRT6 in various types of tumors.

Results
The inclusion and exclusion criteria were met by 15 studies. In patients with solid tumours, reduced SIRT6 expression was found to be related with improved overall survival (OS) (HR = 0.66, 95% CI = 0.45–0.97, P < 0.001) as well as improved disease-free survival (DFS) (HR = 0.48, 95% CI = 0.26–0.91, P < 0.001). Low SIRT6 expression was found to be associated with a better OS in breast cancer (HR = 0.49, 95% CI = 0.27–0.89, P = 0.179), but was found to be associated with a worse OS in gastrointestinal cancer (gastric cancer and colon cancer) (HR = 1.83, 95% CI = 1.20–2.79, P = 0.939) after subgroup analysis. In terms of clinicopathological characteristics, SIRT6 expression was found to be linked with distant metastasis (OR = 2.98, 95% CI = 1.59–5.57, P = 0.694). When the data from the TCGA dataset was compared to normal tissue, it was discovered that SIRT6 expression was significantly different in 11 different types of cancers. Meanwhile, reduced SIRT6 expression was shown to be associated with improved OS (P < 0.05), which was consistent with the findings of the meta-analysis. Aside from that, the expression of SIRT6 was found to be associated with both gender and clinical stage.

Conclusion
The overall data of the present meta-analysis indicated that low expression of SIRT6 may predict a favorable survival for patients with solid tumors.
Detection of asymptomatic malaria in Asian countries: a meta-analysis of diagnostic accuracy
Authors: Naing Cho , Htet Norah Htet , Aye Saint Nway , Aung Htar Htar , Tanner Marcel , Whittaker Maxine A. 
Published: February 2022

Abstract
Background
Achieving malaria elimination requires the targeting of the human reservoir of infection, including those patients with asymptomatic infection. The objective was to synthesise evidence on the accuracy of the rapid-onsite diagnostic tests (RDTs) and microscopy for the detection of asymptomatic malaria as part of the surveillance activities in Asian countries.

Methods
This was a meta-analysis of diagnostic test accuracy. Relevant studies that evaluated the diagnostic performance of RDTs and microscopy for detection of asymptomatic malaria were searched in health-related electronic databases. The methodological quality of the studies included was assessed using the QUADAS-2 tool.

Results
Ten studies assessing RDT and/or microscopy were identified. The diagnostic accuracies in all these studies were verified by PCR. Overall, the pooled sensitivities of RDT, as well as microscopy for detection of any malaria parasites in asymptomatic participants, were low, while their pooled specificities were almost ideal. For the detection of Plasmodium falciparum, pooled sensitivity by RDT (59%, 95%CI:16–91%) or microscopy (55%, 95%CI: 25–82%) were almost comparable. For detection of Plasmodium vivax, pooled sensitivity of RDT (51%, 95% CI:7–94%) had also the comparable accuracy of microscopy (54%, 95%CI,11–92%). Of note are the wide range of sensitivity and specificity.

Conclusion
The findings of this meta-analysis suggest that RDTs and microscopy have limited sensitivity and are inappropriate for the detection of asymptomatic Plasmodium infections. Other methods including a combination of PCR-based strategies, Loop-Mediated Isothermal Amplification (LAMP) technique must be considered to target these infections, in order to achieve malaria elimination. However, more data is needed for the wide acceptance and feasibility of these approaches. Studies to explore the role of asymptomatic and sub-patent infections in the transmission of malaria are of critical importance and are recommended.
Three-year evaluation of the nosocomial infections in pediatrics: bacterial and fungal profile and antimicrobial resistance pattern
Authors: Afsharipour Mehrnoush , Mahmoudi Shima , Raji Hojatollahh , Pourakbari Babak , Mamishi Setareh 
Published: February 2022

Abstract
Background
Nosocomial infections (NIs) could lead to considerably higher mortality rates, length of the hospital stays and costs, and represent a serious public health concern worldwide. Besides, the unreasonable use of antibiotics could lead to get resistant to different antibiotics and create limited therapeutic options, increased risks of treatment failure and poor patient management. The current study aimed to evaluate the prevalence and antimicrobial susceptibility of NIs in an Iranian referral pediatrics hospital during 3 years.

Methods
During the 3-year period, all electronic medical records of nosocomial infection episodes in hospitalized patients were retrospectively reviewed. The bacterial and fungal profile and antimicrobial susceptibility profiles of isolates recovered from different samples of patients with NIs were determined.

Results
In this study, a total of 718 patients with NIs was found, among which 61.3% were male (N = 440). The median age of the patients was 2.5 years (IQR: 1 month to 3 years). Klebsiella pneumonia and Candida spp. isolates were the most prevalent microorganisms (N = 125, 17.4%, N = 121, 16.9%, respectively), followed by Pseudomonas aeruginosa (N = 72, 10%) and Coagulase-negative Staphylococci (CoNS) (N = 69, 9.6%). Pseudomonas aeroginusa strains showed high sensitivity to the studied antibiotics. Acinetobacter baumannii strains displayed more than 90% resistance to the almost all antibiotics. All of the tested isolates of S. maltophilia were susceptible to Trimethoprim−sulfamethoxazole (100%) and showed high susceptibility rate to ciprofloxacin (96.4%). Vancomycin resistance was not reported in S. aureus isolates, while 64% of Enterococcus spp. was resistant to vancomycin. The rates of methicillin resistance for S. aureus and CoNS isolates were 45.5% and 85.7%, respectively.

Conclusions
High frequency of antimicrobial resistance to the commonly tested antibiotics is a concerning alarm. Therefore, effective infection control programs and rational antibiotic use policies should be established promptly.
Aberrant salience relationship with first rank symptoms
Authors: Ballerini Andrea , Tortorelli Marta , Marino Paolo , Appignanesi Cristina , Baschirotto Cinzia , Mallardo Luca , Tofani Tommaso , Pietrini Francesco , D’Anna Giulio , Rossi Andrea , Ricca Valdo , Santella Marina 
Published: February 2022

Abstract
Background
Aberrant salience is the incorrect assignment of salience, significance, or value to different innocuous stimuli that might precede the onset of psychotic symptoms. The present study aimed to perform a preliminary evaluation of potentially different correlations between the Aberrant Salience Inventory (ASI) score and dimensional or categorical diagnostic approaches.

Methods
168 adult outpatients with a current psychiatric diagnosis were consecutively enrolled. Patients were evaluated using different psychometric scales. ASI was used to evaluate aberrant salience, and to evaluate the association between ASI scores and first rank symptoms (FRS), and/or with a psychiatric diagnosis. Principal dichotomic clusters of ASI were identified using the Chi-square automatic interaction detection (CHAID) method.

Results
Current (16.76 ± 6.02 vs 13.37 ± 5.76; p = 0.001), lifetime (15.74 ± 6.08 vs 13.16 ± 5.74; p = 0.005) and past (15.75 ± 6.01 vs 13.33 ± 5.80; p = 0.009) FRS were the main clusters dichotomizing ASI. The average ASI score did not significantly differ among patients with different diagnoses.

Conclusions
ASI could be used as a tool to identify psychopathological dimensions, rather than the categorical diagnoses, in the schizophrenic spectrum.
A prognostic model of patients with ovarian mucinous adenocarcinoma: a population-based analysis
Authors: Yang Li , Yu Jinfen , Zhang Shuang , Shan Yisi , Li Yajun , Xu Liugang , Zhang Jinhu , Zhang Jianya 
Published: February 2022

Abstract
Background
Ovarian mucinous carcinoma is a disease that requires unique treatment. But for a long time, guidelines for ovarian serous carcinoma have been used for the treatment of ovarian mucinous carcinoma. This study aimed to construct and validate nomograms for predicting the overall survival (OS) and cancer-specific survival (CSS) in patients with ovarian mucinous adenocarcinoma.

Methods
In this study, patients initially diagnosed with ovarian mucinous adenocarcinoma from 2004 to 2015 were screened from the Surveillance, Epidemiology, and End Results (SEER) database, and divided into the training group and the validation group at a ratio of 7:3. Independent risk factors for OS and CSS were determined by multivariate Cox regression analysis, and nomograms were constructed and validated.

Results
In this study, 1309 patients with ovarian mucinous adenocarcinoma were finally screened and randomly divided into 917 cases in the training group and 392 cases in the validation group according to a 7:3 ratio. Multivariate Cox regression analysis showed that the independent risk factors of OS were age, race, T_stage, N_stage, M_stage, grade, CA125, and chemotherapy. Independent risk factors of CSS were age, race, marital, T_stage, N_stage, M_stage, grade, CA125, and chemotherapy. According to the above results, the nomograms of OS and CSS in ovarian mucinous adenocarcinoma were constructed. In the training group, the C-index of the OS nomogram was 0.845 (95% CI: 0.821–0.869) and the C-index of the CSS nomogram was 0.862 (95%CI: 0.838–0.886). In the validation group, the C-index of the OS nomogram was 0.843 (95% CI: 0.810–0.876) and the C-index of the CSS nomogram was 0.841 (95%CI: 0.806–0.876). The calibration curve showed the consistency between the predicted results and the actual results, indicating the high accuracy of the nomogram.

Conclusion
The nomogram provides 3-year and 5-year OS and CSS predictions for patients with ovarian mucinous adenocarcinoma, which helps clinicians predict the prognosis of patients and formulate appropriate treatment plans.
Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism
Authors: Zhu Yihui , Gomez J. Antonio , Laufer Benjamin I. , Mordaunt Charles E. , Mouat Julia S. , Soto Daniela C. , Dennis Megan Y. , Benke Kelly S. , Bakulski Kelly M. , Dou John , Marathe Ria , Jianu Julia M. , Williams Logan A. , Gutierrez Fugón Orangel J. , Walker Cheryl K. , Ozonoff Sally , Daniels Jason , Grosvenor Luke P. , Volk Heather E. , Feinberg Jason I. , Fallin M. Daniele , Hertz-Picciotto Irva , Schmidt Rebecca J. , Yasui Dag H. , LaSalle Janine M. 
Published: February 2022

Abstract
Background
Autism spectrum disorder (ASD) involves complex genetics interacting with the perinatal environment, complicating the discovery of common genetic risk. The epigenetic layer of DNA methylation shows dynamic developmental changes and molecular memory of in utero experiences, particularly in placenta, a fetal tissue discarded at birth. However, current array-based methods to identify novel ASD risk genes lack coverage of the most structurally and epigenetically variable regions of the human genome.

Results
We use whole genome bisulfite sequencing in placenta samples from prospective ASD studies to discover a previously uncharacterized ASD risk gene, LOC105373085, renamed NHIP. Out of 134 differentially methylated regions associated with ASD in placental samples, a cluster at 22q13.33 corresponds to a 118-kb hypomethylated block that replicates in two additional cohorts. Within this locus, NHIP is functionally characterized as a nuclear peptide-encoding transcript with high expression in brain, and increased expression following neuronal differentiation or hypoxia, but decreased expression in ASD placenta and brain. NHIP overexpression increases cellular proliferation and alters expression of genes regulating synapses and neurogenesis, overlapping significantly with known ASD risk genes and NHIP-associated genes in ASD brain. A common structural variant disrupting the proximity of NHIP to a fetal brain enhancer is associated with NHIP expression and methylation levels and ASD risk, demonstrating a common genetic influence.

Conclusions
Together, these results identify and initially characterize a novel environmentally responsive ASD risk gene relevant to brain development in a hitherto under-characterized region of the human genome.
Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software
Authors: Gardner Paul P. , Paterson James M. , McGimpsey Stephanie , Ashari-Ghomi Fatemeh , Umu Sinan U. , Pawlik Aleksandra , Gavryushkin Alex , Black Michael A. 
Published: February 2022

AbstractBackgroundComputational biology provides software tools for testing and making inferences about biological data. In the face of increasing volumes of data, heuristic methods that trade software speed for accuracy may be employed. We have studied these trade-offs using the results of a large number of independent software benchmarks, and evaluated whether external factors, including speed, author reputation, journal impact, recency and developer efforts, are indicative of accurate software.ResultsWe find that software speed, author reputation, journal impact, number of citations and age are unreliable predictors of software accuracy. This is unfortunate because these are frequently cited reasons for selecting software tools. However, GitHub-derived statistics and high version numbers show that accurate bioinformatic software tools are generally the product of many improvements over time. We also find an excess of slow and inaccurate bioinformatic software tools, and this is consistent across many sub-disciplines. There are few tools that are middle-of-road in terms of accuracy and speed trade-offs.ConclusionsOur findings indicate that accurate bioinformatic software is primarily the product of long-term commitments to software development. In addition, we hypothesise that bioinformatics software suffers from publication bias. Software that is intermediate in terms of both speed and accuracy may be difficult to publish—possibly due to author, editor and reviewer practises. This leaves an unfortunate hole in the literature, as ideal tools may fall into this gap. High accuracy tools are not always useful if they are slow, while high speed is not useful if the results are also inaccurate.
Electrical stimulation to prevent recurring pressure ulcers in individuals with a spinal cord injury compared to usual care: the Spinal Cord Injury PREssure VOLTage (SCI PREVOLT) study protocol
Authors: Wijker Boas J. , de Groot Sonja , van Dongen Johanna M. , van Nassau Femke , Adriaansen Jacinthe J. E. , Achterberg-Warmer Wendy J. , Anema Johan R. , Riedstra Andries T. , van Tulder Maurits W. , Janssen Thomas W. J. 
Published: February 2022

Abstract
Background
Pressure ulcers (PUs) on the buttocks are among the most common secondary complications in individuals with chronic spinal cord injury (SCI). PUs can result from sitting for extended periods, disuse atrophy, increased sitting pressure and reduced circulation. Compared with usual care, activation of paralysed muscles using electrical stimulation (ES) has been shown to markedly increase paralysed muscle mass, improve circulation of skin and muscle and improve sitting pressure distribution. ES might therefore be a useful method to reduce PU incidence.

Methods
A multicentre randomized controlled trial (SCI PREVOLT) will be conducted with an economic and process evaluation alongside. One hundred participants with a SCI in the chronic phase and a minimal incidence of 1 PU in the last 5 years will be recruited from rehabilitation centres across the Netherlands. Participants will be stratified by centre and age and randomized to the intervention or control group. The intervention group will use ES at least 1 h/day during at least 4 times a week for 1 year next to usual care. The control group will only receive usual care. The primary outcome is the incidence of PUs, measured by a blinded person assessing the presence or absence of a PU on the buttocks on a photo made by the participant or his/her caregiver. The incidence of a PU will be evaluated every 2 weeks. Secondary outcomes include interface pressure distribution, blood flow in the profunda femoris artery, muscle thickness of the hamstrings and gluteal muscles and questionnaires about different dimensions of life, e.g. participation and quality of life. Secondary outcomes will be measured at baseline and 3, 6, 9 and 12 months after randomization.

Discussion
This study will assess if electrical stimulation is a (cost-)effective method to prevent PUs and reduce the risk factors of getting PUs. If ES is effective and cost-effective compared with usual care, ES could be implemented in daily treatment of individuals with a SCI.

Trial registration
Netherlands Trials Register NTR NL9469. Registered on 26 May 2021.
Comparison of self-sampling blood collection for N-glycosylation analysis
Authors: Cvetko Ana , Tijardović Marko , Bilandžija-Kuš Iva , Gornik Olga 
Published: February 2022

Abstract
Objective
Self-sampling of capillary blood provides easier sample collection, handling, and shipping compared to more invasive blood sampling via venepuncture. Recently, other means of capillary blood collection were introduced to the market, such as Neoteryx sticks and Noviplex cards. We tested the comparability of these two self-sampling methods, alongside dried blood spots (DBS), with plasma acquired from venepunctured blood in N-glycoprofiling of total proteins. We have also tested the intra-day repeatability of the three mentioned self-sampling methods. Capillary blood collection with Neoteryx, Noviplex and DBS was done following the manufacturers’ instructions and N-glycoprofiling of released, fluorescently labelled N-glycans was performed with ultra-performance liquid chromatography.

Results
Comparability with plasma was assessed by calculating the relative deviance, which was 0.674 for DBS, 0.092 for Neoteryx sticks, and 0.069 for Noviplex cards. In repeatability testing, similar results were obtained, with Noviplex cards and Neoteryx sticks performing substantially better than DBS (CVs = 4.831% and 7.098%, compared to 14.305%, respectively). Our preliminary study on the use of Neoteryx and Noviplex self-sampling devices in glycoanalysis demonstrates their satisfactory performance in both the comparability and repeatability testing, however, they should be further tested in larger collaborations and cohorts.
Bone mineral density in men with de novo metastatic castration-sensitive prostate cancer treated with or without abiraterone plus prednisone in the PEACE-1 phase 3 trial.
Authors: Roubaud Guilhem , Kostine Marie , McDermott Raymond S. , Bernard-Tessier Alice , Maldonado Xavier , Silva Marlon , Flechon Aude , Berthold Dominik R. , Ronchin Philippe , Tombal Bertrand F. , Mourey Loic , Gravis Gwenaelle , Escande Anne , Abadie Lacourtoisie Sophie , Thiery-Vuillemin Antoine , Climent Duran Miguel Angel A. , Ribault Hélène , Bossi Alberto , Foulon Stéphanie , Fizazi Karim 
Published: February 2022

19 Background: Addition of abiraterone plus prednisone (AAP) to androgen deprivation therapy (ADT) with or without docetaxel (D) improved overall survival in men with de novo metastatic castration sensitive prostate cancer in PEACE-1 trial. An analysis of bone mineral density (BMD) was planned by an amendment in the last randomized patients to assess whether addition of AAP increases bone loss. Methods: Patients (pts) were randomized to receive either ADT + D + AAP or ADT + D (and also randomized for radiotherapy given to the prostate). BMD (g/cm2) of the lumbar spine (L), femoral neck (F) and total hip (H) were measured by dual x-ray absorptiometry at baseline, M6, M12 and M24 in both arms. Mean percent change in BMD values from baseline to the different time points were calculated. T-Scores were also assessed. Results: Among the 210 pts with BMD data, 182 (87%) had available data at baseline, 109 (52%) at M6, 94 (45%) at M12, and 109 (52%) at M24: 97 pts were treated with AAP and 98 without. In both arms, the median age was 65 years and 69 pts (71%) were ECOG PS 0. Median body mass index (BMI) was 25.6 and 26.5 kg/m2 in pts treated with or without AAP, respectively. BMD, T score and mean percent change in BMD values are summarized in the Table. Conclusions: This is the first prospective assessment of BMD in a randomized trial, according to an experimental treatment with AAP. Despite a bone loss increase in both arms over time, addition of AAP to ADT+D was associated with no or modest difference in bone loss during the first 2 years, compared to ADT+D. Data including fractures will be presented. Main limitations include the difficulty to reliably assess BMD in men with bone metastases, the limited sample size and the short follow-up (i.e. 2 years). Clinical trial information: NCT01957436. [Table: see text]