bluuebunny/crossref_metadata_2025_split huggingface dataset:
The medieval Mongolian roots of Y-chromosomal lineages from South Kazakhstan
Authors: Zhabagin Maxat , Sabitov Zhaxylyk , Tarlykov Pavel , Tazhigulova Inkar , Junissova Zukhra , Yerezhepov Dauren , Akilzhanov Rakhmetolla , Zholdybayeva Elena , Wei Lan-Hai , Akilzhanova Ainur , Balanovsky Oleg , Balanovska Elena 
Published: October 2020

Abstract
Background
The majority of the Kazakhs from South Kazakhstan belongs to the 12 clans of the Senior Zhuz. According to traditional genealogy, nine of these clans have a common ancestor and constitute the Uissun tribe. There are three main hypotheses of the clans’ origin, namely, origin from early Wusuns, from Niru’un Mongols, or from Darligin Mongols. We genotyped 490 samples of South Kazakhs by 35 Y-chromosomal SNPs (single nucleotide polymorphism) and 17 STRs (short tandem repeat). Additionally, 133 samples from citizen science projects were included into the study.

Results
We found that three Uissun clans have unique Y-chromosomal profiles, but the remaining six Uissun clans and one non-Uissun clan share a common paternal gene pool. They share a high frequency (> 40%) of the C2*-ST haplogroup (marked by the SNP F3796), which is associated with the early Niru’un Mongols. Phylogenetic analysis of this haplogroup carried out on 743 individuals from 25 populations of Eurasia has revealed a set of haplotype clusters, three of which contain the Uissun haplotypes. The demographic expansion of these clusters dates back to the 13-fourteenth century, coinciding with the time of the Uissun’s ancestor Maiky-biy known from historical sources. In addition, it coincides with the expansion period of the Mongol Empire in the Late Middle Ages. A comparison of the results with published aDNA (ancient deoxyribonucleic acid) data and modern Y haplogroups frequencies suggest an origin of Uissuns from Niru’un Mongols rather than from Wusuns or Darligin Mongols.

Conclusions
The Y-chromosomal variation in South Kazakh clans indicates their common origin in 13th–14th centuries AD, in agreement with the traditional genealogy. Though genetically there were at least three ancestral lineages instead of the traditional single ancestor. The majority of the Y-chromosomal lineages of South Kazakhstan was brought by the migration of the population related to the medieval Niru’un Mongols.
Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units
Authors: Joos Lisa , Beirinckx Stien , Haegeman Annelies , Debode Jane , Vandecasteele Bart , Baeyen Steve , Goormachtig Sofie , Clement Lieven , De Tender Caroline 
Published: October 2020

AbstractBackgroundMicroorganisms are not only indispensable to ecosystem functioning, they are also keystones for emerging technologies. In the last 15 years, the number of studies on environmental microbial communities has increased exponentially due to advances in sequencing technologies, but the large amount of data generated remains difficult to analyze and interpret. Recently, metabarcoding analysis has shifted from clustering reads using Operational Taxonomical Units (OTUs) to Amplicon Sequence Variants (ASVs). Differences between these methods can seriously affect the biological interpretation of metabarcoding data, especially in ecosystems with high microbial diversity, as the methods are benchmarked based on low diversity datasets.ResultsIn this work we have thoroughly examined the differences in community diversity, structure, and complexity between the OTU and ASV methods. We have examined culture-based mock and simulated datasets as well as soil- and plant-associated bacterial and fungal environmental communities. Four key findings were revealed. First, analysis of microbial datasets at family level guaranteed both consistency and adequate coverage when using either method. Second, the performance of both methods used are related to community diversity and sample sequencing depth. Third, differences in the method used affected sample diversity and number of detected differentially abundant families upon treatment; this may lead researchers to draw different biological conclusions. Fourth, the observed differences can mostly be attributed to low abundant (relative abundance < 0.1%) families, thus extra care is recommended when studying rare species using metabarcoding. The ASV method used outperformed the adopted OTU method concerning community diversity, especially for fungus-related sequences, but only when the sequencing depth was sufficient to capture the community complexity.ConclusionsInvestigation of metabarcoding data should be done with care. Correct biological interpretation depends on several factors, including in-depth sequencing of the samples, choice of the most appropriate filtering strategy for the specific research goal, and use of family level for data clustering.
Intravesical dexmedetomidine instillation reduces postoperative catheter-related bladder discomfort in male patients under general anesthesia: a randomized controlled study
Authors: Chen Hong , Wang Bin , Li Qin , Zhou Juan , Li Rui , Zhang Ye 
Published: October 2020

AbstractBackgroundThe catheter-related bladder discomfort (CRBD) of male patients is a common clinical problem, albeit lacking effective solutions. The present study aimed to investigate whether intravesical dexmedetomidine instillation alleviates the postoperative urinary discomfort in male patients with catheter under general anesthesia.MethodsThis single-blinded, prospective, randomized study included a total of 167 male patients American Society of Anesthesiologists (ASA) physical status I-II scheduled for surgery under general anesthesia were allocated to two groups: 84 in the dexmedetomidine group and 83 in the control group. Dexmedetomidine group patients received intravesical instillation of the drug 0.5 μg/kg and normal saline 20 mL, while the control group received intravesical instillation of 20 mL normal saline. The catheter was clamped for 30 min after intravesical instillation for all patients. CRBD scores and urethra pain numerical rating scale (NRS) scores were measured at admittance to post-anesthesia care unit (PACU) (T0), intravesical instillation (T1), 30 min (T2), 60 min (T3), 2 h (T4) after intravesical instillation, discharged from PACU (T5), and 6 h (T6) and 24 h (T7) after the operation. Patient satisfaction at discharge from PACU and 24 h post-operation were compared between the two groups.ResultsCRBD scores and urethra pain NRS scores after 30 min of intravesical dexmedetomidine instillation to 24 h post-operation were significantly lower than the control group (p < 0.001), and patient satisfaction was higher at discharge from PACU and 24 h post-operation (p < 0.001). No differences were detected in Steward score out of PACU (p = 0.213) and from the time of the end of operation to fully awake (p = 0.417).ConclusionIntravesical dexmedetomidine instillation reduces postoperative urinary discomfort and urethra pain and improves satisfaction in male patients under general anesthesia.Trial registrationChinese Clinical Trial Registry (No.ChiCTR1800016429), date of registration 1st June 2018.
Advanced hepatic vasculobiliary imaging segmentation and 3D reconstruction as an aid in the surgical management of high biliary stenosis
Authors: Pereira da Silva Nuno , Abreu Inês , Serôdio Marco , Ferreira Luís , Alexandrino Henrique , Donato Paulo 
Published: October 2020

Abstract
Background
Three-dimensional (3D) models are increasingly used to help surgeons, guiding them through the complex hepatic vasculobiliary anatomy. The biliary tract is a relatively untapped territory with only a few case reports described in medical literature. Our aim is to present an innovative 3D reconstruction methodology for biliary imaging and surgical planning, applied to a case of iatrogenic biliary stricture, with fusion of segmented CT and MRI images.

Case presentation
A selected case of Bismuth type III iatrogenic biliary stenosis for 3D planning. CT and MR studies were acquired with dedicated protocols for segmentation. Two radiologists performed segmentation and 3D model post-processing, fusing both imaging techniques to faithfully render the anatomical structures. Measurements of anatomical landmarks were taken in both the CT/MRI and the 3D model to assure its accuracy and differences in measurement were calculated. The 3D model replicates anatomical structures and pathology with high accuracy, with only 2.2% variation between STL, CT and MRI measurements. The model was discussed with the surgical team and used in the surgical planning, improving confidence in this delicate procedure, due to the detailed prior knowledge of the patient's anatomy.

Conclusion
Three-dimensional reconstructions are a rapidly growing area of research with a significant impact in the personalized and precision medicine. The construction of 3D models that combine vascular and biliary anatomy, using different imaging techniques, respectively CT and MRI, will predictably contribute to a more rigorous planning of complex liver surgeries.
Understanding the molecular association between hyperkalemia and lung squamous cell carcinomas
Authors: Meng Xianping , Lu Hongyan , Jiang Xia , Huang Bin , Wu Song , Yu Guiping , Cao Hongbao 
Published: October 2020

Abstract
Background
Previous studies indicated a strong association between hyperkalemia and lung squamous cell carcinomas (LSCC). However, the underlying mechanism is not fully understood so far.

Methods
Literature-based data mining was conducted to identify genes, molecule, and cell processes linked to both hyperkalemia and LSCC. Pathway analysis was performed to explore the interactive network, common-target network, and common-regulator network for both disorders. Then, a mega-analysis using 11 independent LSCC RNA expression datasets (358 LSCCs and 278 healthy controls) was performed to test the hypothesis that genes influencing hyperkalemia may also play roles in LSCC.

Results
There was a significant overlap between the genes implicated with both diseases (20 genes, p-value = 4.98e-15), which counts for 16% of all hyperkalemia genes (125 genes). Network analysis identified 12 molecules as common targets for hyperkalemia and LSCC, and 19 molecules as common regulators. Moreover, 19 molecules were identified within an interactive network, through which hyperkalemia and LSCC could exert influence on each other. In addition, meta-analysis identified one hyperkalemia promoter, SPP1, as a novel contributor for LSCC (LFC = 2.64; p-value = 2.81e-6). MLR analysis suggests geographical region as an influential factor for the expression levels of SPP1 in LSCC patients (p value = 0.036, 0.054).

Conclusion
Our results showed that there was a common molecular basis for the pathology of both hyperkalemia and LSCC, and that genes promoting hyperkalemia might also play roles in the development of LSCC. However, this study did not suggest hypercalcemia as a casual factor for LSCC.
Genetic polymorphisms of PIP5K2A and course of schizophrenia
Authors: Poltavskaya Evgeniya G. , Fedorenko Olga Yu. , Vyalova Natalya M. , Kornetova Elena G. , Bokhan Nikolay A. , Loonen Anton J. M. , Ivanova Svetlana A. 
Published: October 2020

Abstract
Background
Schizophrenia is a severe highly heritable mental disorder. The clinical heterogeneity of schizophrenia is expressed in the difference in the leading symptoms and course of the disease. Identifying the genetic variants that affect clinical heterogeneity may ultimately reveal the genetic basis of the features of schizophrenia and suggest novel treatment targets. PIP5K2A (Phosphatidylinositol-4-Phosphate 5-Kinase Type II Alpha) has been investigated as a potential susceptibility gene for schizophrenia.

Methods
In this work, we studied the possible association between eleven polymorphic variants of PIP5K2A and the clinical features of schizophrenia in a population of 384 white Siberian patients with schizophrenia. Genotyping was carried out on QuantStudio 5 Real-Time PCR System with a TaqMan Validate SNP Genotyping Assay (Applied Biosystems, USA).

Results
PIP5K2A rs8341 (χ2 = 6.559, p = 0.038) and rs946961 (χ2 = 5.976, p = 0.049) showed significant association with course of schizophrenia (continuous or episodic). The rs8341*CT (OR = 1.63, 95% CI: 1.04–2.54) and rs946961*CC (OR = 5.17, 95% CI: 1.20–22.21) genotypes were associated with a continuous type of course, while the rs8341*TT genotype (OR = 0.53, 95% CI: 0.29–0.97) was associated with an episodic type of course of schizophrenia. Therefore rs8341*TT genotype presumably has protective effect against the more severe continuous course of schizophrenia compared to the episodic one.

Conclusions
Our experimental data confirm that PIP5K2A is a genetic factor influencing the type of course of schizophrenia in Siberian population. Disturbances in the phosphatidylinositol pathways may be a possible reason for the transition to a more severe continuous course of schizophrenia.
Effect of brain-computer interface training based on non-invasive electroencephalography using motor imagery on functional recovery after stroke - a systematic review and meta-analysis
Authors: Kruse Antje , Suica Zorica , Taeymans Jan , Schuster-Amft Corina 
Published: October 2020

Abstract
Background
Training with brain-computer interface (BCI) technology in the rehabilitation of patients after a stroke is rapidly developing. Numerous RCT investigated the effects of BCI training (BCIT) on recovery of motor and brain function in patients after stroke.

Methods
A systematic literature search was performed in Medline, IEEE Xplore Digital Library, Cochrane library, and Embase in July 2018 and was repeated in March 2019. RCT or controlled clinical trials that included BCIT for improving motor and brain recovery in patients after a stroke were identified. Data were meta-analysed using the random-effects model. Standardized mean difference (SMD) with 95% confidence (95%CI) and 95% prediction interval (95%PI) were calculated. A meta-regression was performed to evaluate the effects of covariates on the pooled effect-size.

Results
In total, 14 studies, including 362 patients after ischemic and hemorrhagic stroke (cortical, subcortical, 121 females; mean age 53.0+/− 5.8; mean time since stroke onset 15.7+/− 18.2 months) were included. Main motor recovery outcome measure used was the Fugl-Meyer Assessment. Quantitative analysis showed that a BCI training compared to conventional therapy alone in patients after stroke was effective with an SMD of 0.39 (95%CI: 0.17 to 0.62; 95%PI of 0.13 to 0.66) for motor function recovery of the upper extremity. An SMD of 0.41 (95%CI: − 0.29 to 1.12) for motor function recovery of the lower extremity was found. BCI training enhanced brain function recovery with an SMD of 1.11 (95%CI: 0.64 to 1.59; 95%PI ranging from 0.33 to 1.89). Covariates such as training duration, impairment level of the upper extremity, and the combination of both did not show significant effects on the overall pooled estimate.

Conclusion
This meta-analysis showed evidence that BCI training added to conventional therapy may enhance motor functioning of the upper extremity and brain function recovery in patients after a stroke. We recommend a standardised evaluation of motor imagery ability of included patients and the assessment of brain function recovery should consider neuropsychological aspects (attention, concentration). Further influencing factors on motor recovery due to BCI technology might consider factors such as age, lesion type and location, quality of performance of motor imagery, or neuropsychological aspects.

Trial Registration
PROSPERO registration: CRD42018105832.
Artificial neural networks improve LDCT lung cancer screening: a comparative validation study
Authors: Hsu Yin-Chen , Tsai Yuan-Hsiung , Weng Hsu-Huei , Hsu Li-Sheng , Tsai Ying-Huang , Lin Yu-Ching , Hung Ming-Szu , Fang Yu-Hung , Chen Chien-Wei 
Published: October 2020

AbstractBackgroundThis study proposes a prediction model for the automatic assessment of lung cancer risk based on an artificial neural network (ANN) with a data-driven approach to the low-dose computed tomography (LDCT) standardized structure report.MethodsThis comparative validation study analysed a prospective cohort from Chiayi Chang Gung Memorial Hospital, Taiwan. In total, 836 asymptomatic patients who had undergone LDCT scans between February 2017 and August 2018 were included, comprising 27 lung cancer cases and 809 controls. A derivation cohort of 602 participants (19 lung cancer cases and 583 controls) was collected to construct the ANN prediction model. A comparative validation of the ANN and Lung-RADS was conducted with a prospective cohort of 234 participants (8 lung cancer cases and 226 controls). The areas under the curves (AUCs) of the receiver operating characteristic (ROC) curves were used to compare the prediction models.ResultsAt the cut-off of category 3, the Lung-RADS had a sensitivity of 12.5%, specificity of 96.0%, positive predictive value of 10.0%, and negative predictive value of 96.9%. At its optimal cut-off value, the ANN had a sensitivity of 75.0%, specificity of 85.0%, positive predictive value of 15.0%, and negative predictive value of 99.0%. The area under the ROC curve was 0.764 for the Lung-RADS and 0.873 for the ANN (P = 0.01). The two most important predictors used by the ANN for predicting lung cancer were the documented sizes of partially solid nodules and ground-glass nodules.ConclusionsCompared to the Lung-RADS, the ANN provided better sensitivity for the detection of lung cancer in an Asian population. In addition, the ANN provided a more refined discriminative ability than the Lung-RADS for lung cancer risk stratification with population-specific demographic characteristics. When lung nodules are detected and documented in a standardized structured report, ANNs may better provide important insights for lung cancer prediction than conventional rule-based criteria.
Effects of Body Mass Index (BMI), demographic and socioeconomic factors on organized physical activity (OPA) participation in children aged 6-15 years: a cross-sectional study comparing primary and secondary school children in Greece
Authors: Carayanni Vilelmine , Vlachopadopoulou Elpis , Koutsouki Dimitra , Bogdanis Gregory C. , Psaltopoulou Theodora , YannisManios  , Karachaliou Feneli , Hatzakis Angelos , Michalacos Stefanos 
Published: October 2020

Abstract
Background
The aim of the present study was to examine the influence of body mass index category, as well as of demographic and socioeconomic factors on the participation in organized physical activity (OPA) of schoolchildren attending primary and secondary school in Greece. Furthermore, to compare the difference between the two levels.

Methods
This is a cross-sectional study conducted on a representative elementary and secondary school cohort, derived using stratification and probability proportional to size (PPS) methodology. The final sample included 18,264 subjects, aged 6 to 15 years.
Parents of all students and students of secondary schools fulfilled validated questionnaires evaluating socioeconomic status, and participation to OPA. International Obesity Task Force (IOTF) cut offs were used to classify the children. Univariate and multivariate logistic models examined factors associated with OPA. All analyses were stratified by school level.

Results
Sport participation was not reported in 37.7 and 54.4% of primary and secondary schoolchildren respectively. Having BMI within normal range, being male, having parents participating in an organized activity and a high socio-economic status seem to encourage participation in OPA in both school levels.

Conclusions
Children with normal BMI are more likely to participate in OPA. Parents as role model as well as higher socioeconomic status of the family emerge as important influencers. Participation in OPA declines as students enter secondary school. Interventions focusing on increasing physical education and activity into school daily program should be tailored to the specific needs of different weight categories and can possibly eliminate the impact of SES inequalities.
Women’s healthcare decision-making capacity and HIV testing in sub-Saharan Africa: a multi-country analysis of demographic and health surveys
Authors: Seidu Abdul-Aziz , Oduro Joseph Kojo , Ahinkorah Bright Opoku , Budu Eugene , Appiah Francis , Baatiema Linus , Ameyaw Edward Kwabena , Sambah Francis 
Published: October 2020

Abstract
Background
Global commitment to stop Human Immunodeficiency Virus (HIV) and ensure access to HIV treatment calls for women empowerment, as these efforts play major roles in mother-to-child transmission. We examined the association between women’s healthcare decision-making capacity and uptake of HIV testing in sub-Saharan Africa.

Methods
We used data from the current Demographic and Health Surveys (DHS) of 28 countries in sub-Saharan Africa, conducted between January 1, 2010 and December 31, 2018. At the descriptive level, we calculated the prevalence of HIV testing in each of the countries. This was followed by the distribution of HIV testing across the socio-demographic characteristics of women. Finally, we used binary logistic regression assess the likelihood of HIV testing uptake by women’s health care decision-making capacity and socio-demographic characteristics. The results were presented as Crude Odds Ratios (COR) and Adjusted Odds Ratios (AOR) with their corresponding 95% confidence intervals signifying precision. Statistical significance was set at p-value < 0.05.

Results
We found that prevalence of HIV testing uptake in the 28 sub-Saharan African countries was 64.4%, with Congo DR having the least (20.2%) and the highest occurred in Rwanda (97.4%). Women who took healthcare decisions alone [COR = 3.183, CI = 2.880–3.519] or with their partners [COR = 2.577, CI = 2.335–2.844] were more likely to test for HIV, compared to those whose healthcare decisions were taken by others, and this persisted after controlling for significant covariates: [AOR = 1.507, CI = 1.321–1.720] and [AOR = 1.518, CI = 1.334–1.728] respectively.

Conclusion
Sub-Saharan African countries intending to improve HIV testing need to incorporate women’s healthcare decision-making capacity strategies. These strategies can include education and counselling. This is essential because our study indicates that the capacity of women to make healthcare decisions has an association with decision to test for their HIV status.