bluuebunny/crossref_metadata_2025_split huggingface dataset:
Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution
Authors: Matsuo Yoshiyuki , Komiya Shinnosuke , Yasumizu Yoshiaki , Yasuoka Yuki , Mizushima Katsura , Takagi Tomohisa , Kryukov Kirill , Fukuda Aisaku , Morimoto Yoshiharu , Naito Yuji , Okada Hidetaka , Bono Hidemasa , Nakagawa So , Hirota Kiichi 
Published: January 2021

Abstract
Background
Species-level genetic characterization of complex bacterial communities has important clinical applications in both diagnosis and treatment. Amplicon sequencing of the 16S ribosomal RNA (rRNA) gene has proven to be a powerful strategy for the taxonomic classification of bacteria. This study aims to improve the method for full-length 16S rRNA gene analysis using the nanopore long-read sequencer MinION™. We compared it to the conventional short-read sequencing method in both a mock bacterial community and human fecal samples.

Results
We modified our existing protocol for full-length 16S rRNA gene amplicon sequencing by MinION™. A new strategy for library construction with an optimized primer set overcame PCR-associated bias and enabled taxonomic classification across a broad range of bacterial species. We compared the performance of full-length and short-read 16S rRNA gene amplicon sequencing for the characterization of human gut microbiota with a complex bacterial composition. The relative abundance of dominant bacterial genera was highly similar between full-length and short-read sequencing. At the species level, MinION™ long-read sequencing had better resolution for discriminating between members of particular taxa such as Bifidobacterium, allowing an accurate representation of the sample bacterial composition.

Conclusions
Our present microbiome study, comparing the discriminatory power of full-length and short-read sequencing, clearly illustrated the analytical advantage of sequencing the full-length 16S rRNA gene.
Prehospital arterial hypercapnia in acute heart failure is associated with admission to acute care units and emergency room length of stay: a retrospective cohort study
Authors: Fabre Mathias , Fehlmann Christophe A. , Gartner Birgit , Zimmermann-Ivoll Catherine G. , Rey Florian , Sarasin François , Suppan Laurent 
Published: January 2021

AbstractBackgroundAcute Heart Failure (AHF) is a common condition that often presents with acute respiratory distress and requires urgent medical evaluation and treatment. Arterial hypercapnia is common in AHF and has been associated with a higher rate of intubation and non-invasive ventilation in the Emergency Room (ER), but its prognostic value has never been studied in the prehospital setting.MethodsA retrospective study was performed on the charts of all patients taken care of by a physician-staffed prehospital mobile unit between June 2016 and September 2019 in Geneva. After approval by the ethics committee, charts were screened to identify all adult patients with a diagnosis of AHF in whom a prehospital arterial blood gas (ABG) sample was drawn. The main predictor was prehospital hypercapnia. The primary outcome was the admission rate in an acute care unit (ACU, composite of intensive care and high-dependency units). Secondary outcomes were ER length of stay (LOS), orientation from ER (intensive care unit, high-dependency unit, general ward, discharge home), intubation rate at 24 h, hospital LOS and hospital mortality.ResultsA total of 106 patients with a diagnosis of AHF were analysed. Hypercapnia was found in 61 (58%) patients and vital signs were more severely altered in this group. The overall ACU admission rate was 48%, with a statistically significant difference between hypercapnic and non-hypercapnic patients (59% vs 33%,p = 0.009). ER LOS was shorter in hypercapnic patients (5.4 h vs 8.9 h,p = 0.016).ConclusionsThere is a significant association between prehospital arterial hypercapnia, acute care unit admission, and ER LOS in AHF patients.
Short chain fatty acids and colon motility in a mouse model of irritable bowel syndrome
Authors: Shaidullov Ilnar F. , Sorokina Dina M. , Sitdikov Farit G. , Hermann Anton , Abdulkhakov Sayar R. , Sitdikova Guzel F. 
Published: January 2021

Abstract
Background
Irritable bowel syndrome (IBS) is defined as a multifactorial disorder associated with visceral hypersensitivity, altered gut motility and dysfunction of the brain-gut axis. Gut microbiota and its metabolites are proposed as possible etiological factors of IBS. Short chain fatty acids (SCFAs) induce both inhibitory and stimulatory action on colon motility, however, their effects on the IBS model were not investigated. The aim of our study was to investigate the level of SFCAs in feces and their effects on colon motility in a mouse model of IBS.

Methods
IBS model was induced in mice by intracolonic infusion of 1% acetic acid during the early postnatal period. Mice colon hypersensitivity was assessed by the threshold of the abdominal withdrawal reflex in response to colorectal distention. Colon contractility was studied using proximal colon specimens in isometric conditions. Transit rates were assessed by the pellet propulsion in the isolated colon. Concentrations of SCFAs in feces were measured using gas–liquid chromatography.

Results
The concentration of SCFAs in feces of IBS model mice was higher compared to the control group. Visceral sensitivity to colorectal distension and colonic transit rate were increased indicating IBS with predominant diarrhea. The frequency and amplitude of spontaneous contractions of proximal colon segments from IBS mice were higher, but carbachol induced contractions were lower compared to control. During acute application of SCFAs (sodium propionate, sodium acetate or butyric acid) dose-dependently (0.5–30 mM) decreased tonic tension, frequency and amplitude of spontaneous and carbachol-evoked contractions. In the mouse IBS group the inhibitory effects SCFAs on spontaneous and carbachol-evoked contractions were less pronounced. At the same time intraluminal administration of butyrate (5 mM) increased the transit rate in the colon of both groups, but its stimulatory effect was more pronounced in mouse IBS model group.

Conclusion
Our data indicate that the increased transit rate in the mouse IBS model group is associated with a disbalance of activating and inhibiting action of SCFAs due to chronically elevated SCFA levels, which may impact the pathogenesis of IBS with predominant diarrhea syndrome.
Development and validation of a novel competing risk model for predicting survival of esophagogastric junction adenocarcinoma: a SEER population-based study and external validation
Authors: Wang Tongbo , Wu Yan , Zhou Hong , Wu Chaorui , Zhang Xiaojie , Chen Yingtai , Zhao Dongbing 
Published: January 2021

Abstract
Background
Adenocarcinoma in Esophagogastric Junction (AEG) is a severe gastrointestinal malignancy with a unique clinicopathological feature. Hence, we aimed to develop a competing risk nomogram for predicting survival for AEG patients and compared it with new 8th traditional tumor-node-metastasis (TNM) staging system.

Methods
Based on data from the Surveillance, Epidemiology, and End Results (SEER) database of AEG patients between 2004 and 2010, we used univariate and multivariate analysis to filter clinical factors and then built a competing risk nomogram to predict AEG cause-specific survival. We then measured the clinical accuracy by comparing them to the 8th TNM stage with a Receiver Operating Characteristic (ROC) curve, Brier score, and Decision Curve Analysis (DCA). External validation was performed in 273 patients from China National Cancer Center.

Results
A total of 1755 patients were included in this study. The nomogram was based on five variables: Number of examined lymph nodes, grade, invasion, metastatic LNs, and age. The results of the nomogram was greater than traditional TNM staging with ROC curve (1-year AUC: 0.747 vs. 0.641, 3-year AUC: 0.761 vs. 0.679, 5-year AUC: 0.759 vs. 0.682, 7-year AUC: 0.749 vs. 0.673, P < 0.001), Brier score (3-year: 0.198 vs. 0.217, P = 0.012; 5-year: 0.198 vs. 0.216, P = 0.008; 7-year: 0.199 vs. 0.215, P = 0.014) and DCA. In external validation, the nomogram also showed better diagnostic value than traditional TNM staging and great prediction accuracy.

Conclusion
We developed and validated a novel nomogram and risk stratification system integrating clinicopathological characteristics for AEG patients. The model showed superior prediction ability for AEG patients than traditional TNM classification.
Immunogenicity and safety of a live herpes zoster vaccine in hematopoietic stem cell transplant recipients
Authors: Chun June Young , Kim Kichun , Lee Min Kyeong , Kang Chang Kyung , Koh Youngil , Shin Dong-Yeop , Hong Junshik , Choe Pyoeng Gyun , Kim Nam Joong , Yoon Sung-Soo , Park Wan Beom , Kim Inho , Oh Myoung-don 
Published: January 2021

Abstract
Background
Herpes zoster (HZ) infection of hematopoietic stem cell transplant (HSCT) patients is of clinical concern. Vaccination could help restore immunity to varicella zoster virus (VZV); however, temporal changes in immunogenicity and safety of live HZ vaccines after HSCT is still unclear. The aim of this study was to elucidate the temporal immunogenicity and safety of the HZ vaccine according to time since HSCT and to determine optimal timing of vaccination.

Methods
Live HZ vaccine was administered to patients 2–5 years or > 5 years post-HSCT. Control groups comprised patients with a hematologic malignancy who received cytotoxic chemotherapy and healthy volunteers. Humoral and cellular immunogenicity were measured using a glycoprotein enzyme-linked immunosorbent assay (gpELISA) and an interferon-γ (IFN-γ) enzyme-linked immunospot (ELISPOT) assay. Vaccine-related adverse events were also monitored.

Results
Fifty-six patients with hematologic malignancy (41 in the HSCT group and 15 in the chemotherapy group) along with 30 healthy volunteers were enrolled. The geometric mean fold rises (GMFRs) in humoral immune responses of the 2–5 year and > 5 year HSCT groups, and the healthy volunteer group, were comparable and significantly higher than that of the chemotherapy group (3.15, 95% CI [1.96–5.07] vs 5.05, 95% CI [2.50–10.20] vs 2.97, 95% CI [2.30–3.83] vs 1.42, 95% CI [1.08–1.86]). The GMFR of cellular immune responses was highest in the HSCT 2–5 year group and lowest in the chemotherapy group. No subject suffered clinically significant adverse events or reactivation of VZV within the follow-up period.

Conclusion
Our findings demonstrate that a live HZ vaccine is immunogenic and safe when administered 2 years post-HSCT.
Hemostasis functions are associated with hemorrhagic transformation in non-atrial fibrillation patients: a case-control study
Authors: Cheng Hao-Ran , Chen Yun-Bin , Zeng Ya-Ying , Ruan Yi-Ting , Yuan Cheng-Xiang , Cheng Qian-Qian , Chen Hui-Jun , Luan Xiao-Qian , Huang Gui-Qian , He Jin-Cai 
Published: January 2021

Abstract
Background
Hemorrhagic transformation (HT) is a serious neurological complication of acute ischemic stroke (AIS) after revascularization. The majority of AIS patients do not have atrial fibrillation (AF) which could also develop into HT. In this study, we aimed to explore whether hemostasis parameters are risk factors of HT in non-AF patients.

Methods
We consecutively enrolled 285 AIS patients with HT. Meanwhile, age- and sex-matched 285 AIS patients without HT were included. The diagnosis of HT was determined by brain CT or MRI during hospitalization. All patients were divided into two subgroups based on the presence of AF and explore the differences between the two subgroups. Blood samples were obtained within 24 h of admission, and all patients were evenly classified into three tertiles according to platelet counts (PLT) levels.

Results
In this study, we found the first PLT tertile (OR = 3.509, 95%CI = 1.268–9.711, P = 0.016) was independently associated with HT in non-AF patients, taking the third tertile as a reference. Meanwhile, we also found mean platelet volume (MPV) (OR = 0.605, 95%CI = 0.455–0.805, P = 0.001) and fibrinogen (FIB) (OR = 1.928, 95%CI = 1.346–2.760, P < 0.001) were significantly associated with HT in non-AF patients. But in AF patients, hemostasis parameters showed no significant difference. Meanwhile, we found the MPV (OR = 1.314, 95%CI = 1.032–1.675, P = 0.027) and FIB (OR = 1.298, 95%CI = 1.047–1.610, P = 0.018) were significantly associated with long-term outcomes in non-AF HT patients.

Conclusions
Low PLT, low MPV, and high FIB levels were independently associated with HT in non-AF patients. Additionally, MPV and FIB levels were significantly associated with unfavorable long-term outcomes in non-AF HT patients. Our study showed that hemostasis functions at admission may be beneficial for clinicians to recognize patients with a high risk of HT at an early stage and improve unfavorable long-term outcomes in non-AF patients.
Assessment of lower urinary tract symptoms during pregnancy: an observational cross-sectional study from Palestine
Authors: Saffarini Jaffar H. , Ahmad Qais T. , Samara Ahmad M. , Jabri Dima S. , Safarini Zaina H. , Banijaber Yousra M. , Jaradat Ahmad , Abushamma Faris , Zyoud Sa’ed H. 
Published: January 2021

Abstract
Background
Women frequently complain of lower urinary tract symptoms (LUTS) during pregnancy due to multiple physiological and potentially pathological changes. Still, there is limited data on the characteristics of LUTS for pregnant women in Palestine. Therefore, this study was designed to assess LUTS among pregnant women in Palestine, in addition to identifying factors that exacerbate LUTS during pregnancy.

Methods
We devised a cross-sectional, questionnaire-based study that used the Urinary Distress Inventory (UDI) and the Incontinence Impact Questionnaire (IIQ) tools to assess LUTS during pregnancy in an antenatal care clinic setting. Multiple linear regressions were conducted to determine variables that significantly related to LUTS (UDI-6 and IIQ-7 scores as dependent variables).

Results
The study recruited 306 pregnant women. Regarding LUTS findings, the participants scored a mean of 31.9 ± 24.9 out of 100 points (6.7 ± 5.2 out of 21) for the IIQ-7 scale and a mean of 31.2 ± 19.2 out of 100 points (5.6 ± 3.4 out of 18) for the UDI-6 scale. Regression analysis showed that older women (p = 0.031), women with a higher body mass index (p < 0.001), and women in the third trimester of pregnancy (p = 0.023), were independently associated with high UDI score. Multiple linear regression analysis showed that obese and overweight patients (p = 0.006) and multiparity (p = 0.026) were independently associated with high IIQ score.

Conclusions
High body mass index is independently associated with both UDI and IIQ scores for LUTS. Several strategies should be arranged to raise the awareness of females of childbearing age in Palestine regarding LUTS during pregnancy and factors which may exacerbate LUTS, such as obesity and multiparity. Thus, preventive measures should be implemented, such as serial assessment of LUTS during antenatal care to respond timely to this frequent problem.
Efficiency of non-invasive prenatal screening in pregnant women at advanced maternal age
Authors: Zhu Hui , Jin Xiaoxiao , Xu Yuqing , Zhang Weihua , Liu Xiaodan , Jin Jinglei , Qian Yeqing , Dong Minyue 
Published: January 2021

Abstract
Background
Non-invasive prenatal screening (NIPS) is widely used as the alternative choice for pregnant women at high-risk of fetal aneuploidy. However, whether NIPS has a good detective efficiency for pregnant women at advanced maternal age (AMA) has not been fully studied especially in Chinese women.

Methods
Twenty-nine thousand three hundred forty-three pregnant women at AMA with singleton pregnancy who received NIPS and followed-up were recruited. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), receiver operating characteristic (ROC) curves and the Youden Index for detecting fetal chromosomal aneuploidies were analyzed. The relationship between maternal age and common fetal chromosomal aneuploidy was observed.

Results
The sensitivity, specificity, PPV, NPV of NIPS for detecting fetal trisomy 21 were 99.11, 99.96, 90.98, and 100%, respectively. These same parameters for detecting fetal trisomy 18 were 100, 99.94, 67.92, and 100%, respectively. Finally, these parameters for detecting trisomy 13 were 100, 99.96, 27.78, and 100%, respectively. The prevalence of fetal trisomy 21 increased exponentially with maternal age. The high-risk percentage incidence rate of fetal trisomy 21 was significantly higher in the pregnant women at 37 years old or above than that in pregnant women at 35 to 37 years old. (Youden index = 37).

Conclusion
It is indicated that NIPS is an effective prenatal screening method for pregnant women at AMA.
Factors influencing stress, anxiety, and depression among Iranian pregnant women: the role of sexual distress and genital self-image
Authors: Keramat Afsaneh , Malary Mina , Moosazadeh Mahmood , Bagherian Nastaran , Rajabi-Shakib Mohammad-Reza 
Published: January 2021

Abstract
Background
Pregnancy is a unique period with the increased likelihood of psychological changes and emotional disturbances such as depression, anxiety, and stress. In this study, we investigated the factors influencing depression, anxiety, and stress in pregnancy and identify their associations with Sexual Distress (SD) and Genital Self-Image (GSI).

Methods
This was a descriptive, correlational, cross-sectional study performed using the two-stage cluster sampling method between September 2019 and January 2020. Overall, 295 pregnant women completed a demographics and obstetric information checklist, Depression Anxiety and Stress Scale-21 (DASS-21), Female Genital Self-Image Scale (FGSI), and Female Sexual Distress Scale-Revised (FSDS-R).

Results
Analysis of Variance (ANOVA) showed significant differences in the mean scores of SD between the groups with varying degrees of depression, anxiety, and stress (P <  0.001) and in the mean score of GSI between the groups with varying degrees of depression (P = 0.01) and anxiety (P <  0.001). In multivariate linear regression analysis, higher (worse) depression, anxiety, and stress scores were found in women with more advanced age and higher SD scores; however, these scores were lower (better) in those with increased gestational age. Lower depression and anxiety scores were associated with moderate satisfaction with income, moderate satisfaction with BI in pregnancy, and lower stress and depression scores were linked to planned pregnancy. Higher (better) GSI score was a predictor of lower depression score, complication in a previous pregnancy was a predictor of higher stress score, and finally, fear of fetal abortion and being a housewife were predictors of a higher anxiety score.

Conclusion
Various factors contribute to the development of antenatal depression, anxiety, and stress. A positive correlation was found between SD and the severity of depression, anxiety, and stress, while a negative correlation was noted between GSI and the severity of depression and anxiety. Therefore, raising awareness regarding SD and GSI through screening and counseling sessions can have beneficial effects for mothers and their fetuses.
Annual trend of neonatal mortality and its underlying causes: population-based study – São Paulo State, Brazil, 2004–2013
Authors: Guinsburg Ruth , Sanudo Adriana , Kiffer Carlos Roberto V , Marinonio Ana Sílvia S , Costa-Nobre Daniela T , Areco Kelsy N , Kawakami Mandira D , Miyoshi Milton H , Bandiera-Paiva Paulo , Balda Rita de Cássia X , Konstantyner Tulio , Morais Liliam CC , Freitas Rosa MV , Teixeira Mônica LP , Waldvogel Bernadette , Almeida Maria Fernanda B 
Published: January 2021

Abstract
Background
Population-based studies analyzing neonatal deaths in middle-income countries may contribute to design interventions to achieve the Sustainable Development Goals, established by United Nations. This study goal is to analyze the annual trend of neonatal mortality in São Paulo State, Brazil, over a 10-year period and its underlying causes and to identify maternal and neonatal characteristics at birth associated with neonatal mortality.

Method
A population-based study of births and deaths from 0 to 27 days between 2004 and 2013 in São Paulo State, Brazil, was performed. The annual trend of neonatal mortality rate according to gestational age was analyzed by Poisson or by Negative Binomial Regression models. Basic causes of neonatal death were classified according to ICD-10. Association of maternal demographic variables (block 1), prenatal and delivery care variables (block 2), and neonatal characteristics at birth (block 3) with neonatal mortality was evaluated by Poisson regression analysis adjusted by year of birth.

Results
Among 6,056,883 live births in São Paulo State during the study period, 48,309 died from 0 to 27 days (neonatal mortality rate: 8.0/1,000 live births). For the whole group and for infants with gestational age 22–27, 28–31, 32–36, 37–41 and ≥ 42 weeks, reduction of neonatal mortality rate was, respectively, 18 %, 15 %, 38 %, 53 %, 31 %, and 58 %. Median time until 50 % of deaths occurred was 3 days. Main basic causes of death were respiratory disorders (25 %), malformations (20 %), infections (17 %), and perinatal asphyxia (7 %). Variables independently associated with neonatal deaths were maternal schooling, prenatal care, parity, newborn sex, 1st minute Apgar, and malformations. Cesarean delivery, compared to vaginal, was protective against neonatal mortality for infants at 22–31 weeks, but it was a risk factor for those with 32–41 weeks.

Conclusions
Despite the significant decrease in neonatal mortality rate over the 10-year period in São Paulo State, improved access to qualified health care is needed in order to avoid preventable neonatal deaths and increase survival of infants that need more complex levels of assistance.