bluuebunny/crossref_metadata_2025_split huggingface dataset:
Life-course socioeconomic disadvantage and lung function: a multicohort study of 70 496 individuals
Authors: Rocha Vânia , Fraga Sílvia , Moreira Carla , Carmeli Cristian , Lenoir Alexandra , Steptoe Andrew , Giles Graham , Goldberg Marcel , Zins Marie , Kivimäki Mika , Vineis Paolo , Vollenweider Peter , Barros Henrique , Stringhini Silvia 
Published: November 2020

BackgroundLung function is an important predictor of health and a marker of physical functioning at older ages. This study aimed to quantify the years of lung function lost according to disadvantaged socioeconomic conditions across the life-course.MethodsThis multicohort study used harmonised individual-level data from six European cohorts with information on life-course socioeconomic disadvantage and lung function assessed by forced expiratory volume in 1 s (FEV1) and forced vital capacity (FVC). 70 496 participants (51% female) aged 18–93 years were included. Socioeconomic disadvantage was measured in early life (low paternal occupational position), early adulthood (low educational level) and adulthood (low occupational position). Risk factors for poor lung function (e.g.smoking, obesity, sedentary behaviour, cardiovascular and respiratory diseases) were included as potential mediators. The years of lung function lost due to socioeconomic disadvantage were computed at each life stage.ResultsSocioeconomic disadvantage during the life-course was associated with a lower FEV1. By the age of 45 years, individuals experiencing disadvantaged socioeconomic conditions had lost 4–5 years of healthy lung functionversustheir more advantaged counterparts (low educational level −4.36 (95% CI −7.33–−2.37) for males and −5.14 (−10.32–−2.71) for females; low occupational position −5.62 (−7.98–−4.90) for males and −4.32 (−13.31–−2.27) for females), after accounting for the risk factors for lung function. By the ages of 65 years and 85 years, the years of lung function lost due to socioeconomic disadvantage decreased by 2–4 years, depending on the socioeconomic indicator. Sensitivity analysis using FVC yielded similar results to those using FEV1.ConclusionLife-course socioeconomic disadvantage is associated with lower lung function and predicts a significant number of years of lung function loss in adulthood and at older ages.
Validation of the Bronchiectasis Impact Measure (BIM): a novel patient-reported outcome measure
Authors: Crichton Megan L. , Dudgeon Emily K. , Shoemark Amelia , Chalmers James D. 
Published: November 2020

IntroductionExisting quality-of-life and symptom tools used in bronchiectasis trials are either not disease specific or are complex and have not been consistently responsive. We developed a simple patient-reported visual analogue outcome measure, the Bronchiectasis Impact Measure (BIM), for use in clinical research, including clinical trials.MethodsPatients with bronchiectasis attending a tertiary referral clinic in the east of Scotland were invited to complete the BIM questionnaire and the quality-of-life bronchiectasis questionnaire at baseline with repeat questionnaires after 2 weeks and 6 months. We assessed internal consistency, test–retest reliability, construct validity and responsiveness by evaluating change during an acute exacerbation.Results173 patients were included. The eight domains (cough, sputum, breathlessness, tiredness, activity, general health, control, exacerbations) showed excellent internal consistency (Cronbach's α 0.93). The intraclass correlation coefficient demonstrated excellent reliability over a 2-week period: cough (0.79, 95% CI 0.70–0.85), sputum (0.86, 95% CI 0.80–0.90), dyspnoea (0.82, 95% CI 0.74–0.87), tiredness (0.88, 95% CI 0.82–0.91), activity (0.84, 95% CI 0.77–0.89), general health (0.81, 95% CI 0.74–0.87), control (0.83, 95% CI 0.75–0.88) and exacerbation (0.71, 95% CI 0.60–0.79). Domains correlated strongly with bronchiectasis severity and exacerbation history. Both distribution and patient-based methods estimated the minimal clinically important difference for each domain as 1.5 points on a 10-point scale. Statistically significant changes in all BIM domains were observed during an acute exacerbation.ConclusionThe BIM is a simple patient-reported outcome. This study validates the internal consistency, reliability, construct validity and response of the tool at acute exacerbation. Further validation of the tool is now required.
Construction of anti-codon table of the plant kingdom and evolution of tRNA selenocysteine (tRNASec)
Authors: Mohanta Tapan Kumar , Mishra Awdhesh Kumar , Hashem Abeer , Abd_Allah Elsayed Fathi , Khan Abdul Latif , Al-Harrasi Ahmed 
Published: November 2020

Abstract
Background
The tRNAs act as a bridge between the coding mRNA and incoming amino acids during protein translation. The anti-codon of tRNA recognizes the codon of the mRNA and deliver the amino acid into the protein translation chain. However, we did not know about the exact abundance of anti-codons in the genome and whether the frequency of abundance remains same across the plant lineage or not.

Results
Therefore, we analysed the tRNAnome of 128 plant species and reported an anti-codon table of the plant kingdom. We found that CAU anti-codon of tRNAMet has highest (5.039%) whereas GCG anti-codon of tRNAArg has lowest (0.004%) abundance. However, when we compared the anti-codon frequencies according to the tRNA isotypes, we found tRNALeu (7.808%) has highest abundance followed by tRNASer (7.668%) and tRNAGly (7.523%). Similarly, suppressor tRNA (0.036%) has lowest abundance followed by tRNASec (0.066%) and tRNAHis (2.109). The genome of Ipomoea nil, Papaver somniferum, and Zea mays encoded the highest number of anti-codons (isoacceptor) at 59 each whereas the genome of Ostreococcus tauri was found to encode only 18 isoacceptors. The tRNASec genes undergone losses more frequently than duplication and we found that tRNASec showed anti-codon switch during the course of evolution.

Conclusion
The anti-codon table of the plant tRNA will enable us to understand the synonymous codon usage of the plant kingdom and can be very helpful to understand which codon is preferred over other during the translation.
NGS-Integrator: An efficient tool for combining multiple NGS data tracks using minimum Bayes’ factors
Authors: Wen Bronte , Jung Hyun Jun , Chen Lihe , Saeed Fahad , Knepper Mark A. 
Published: November 2020

Abstract
Background
Next-generation sequencing (NGS) is widely used for genome-wide identification and quantification of DNA elements involved in the regulation of gene transcription. Studies that generate multiple high-throughput NGS datasets require data integration methods for two general tasks: 1) generation of genome-wide data tracks representing an aggregate of multiple replicates of the same experiment; and 2) combination of tracks from different experimental types that provide complementary information regarding the location of genomic features such as enhancers.

Results
NGS-Integrator is a Java-based command line application, facilitating efficient integration of multiple genome-wide NGS datasets. NGS-Integrator first transforms all input data tracks using the complement of the minimum Bayes’ factor so that all values are expressed in the range [0,1] representing the probability of a true signal given the background noise. Then, NGS-Integrator calculates the joint probability for every genomic position to create an integrated track. We provide examples using real NGS data generated in our laboratory and from the mouse ENCODE database.

Conclusions
Our results show that NGS-Integrator is both time- and memory-efficient. Our examples show that NGS-Integrator can integrate information to facilitate downstream analyses that identify functional regulatory domains along the genome.
Identification of high-copy number long terminal repeat retrotransposons and their expansion in Phalaenopsis orchids
Authors: Hsu Chia-Chi , Chen Shu-Yun , Lai Pei-Han , Hsiao Yu-Yun , Tsai Wen-Chieh , Liu Zhong-Jian , Chung Mei-Chu , Panaud Olivier , Chen Hong-Hwa 
Published: November 2020

Abstract
Background
Transposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations. They represent a great proportion of eukaryotic genomes. The identification and characterization of TEs facilitates understanding the transpositional activity of TEs with their effects on the orchid genome structure.

Results
We combined the draft whole-genome sequences of Phalaenopsis equestris with BAC end sequences, Roche 454, and Illumina/Solexa, and identified long terminal repeat (LTR) retrotransposons in these genome sequences by using LTRfinder and classified by using Gepard software. Among the 10 families Gypsy-like retrotransposons, three families Gypsy1, Gypsy2, and Gypsy3, contained the most copies among these predicted elements. In addition, six high-copy retrotransposons were identified according to their reads in the sequenced raw data. The 12-kb Orchid-rt1 contains 18,000 copies representing 220 Mbp of the P. equestris genome. Southern blot and slot blot assays showed that these four retrotransposons Gypsy1, Gypsy2, Gypsy3, and Orchid-rt1 contained high copies in the large-genome-size/large-chromosome species P. violacea and P. bellina. Both Orchid-rt1 and Gypsy1 displayed various ratios of copy number for the LTR sequences versus coding sequences among four Phalaenopsis species, including P. violacea and P. bellina and small-genome-size/small-chromosome P. equestris and P. ahprodite subsp. formosana, which suggests that Orchid-rt1 and Gypsy1 have been through various mutations and homologous recombination events. FISH results showed amplification of Orchid-rt1 in the euchromatin regions among the four Phalaenopsis species. The expression levels of Peq018599 encoding copper transporter 1 is highly upregulated with the insertion of Orchid-rt1, while it is down regulated for Peq009948 and Peq014239 encoding for a 26S proteasome non-ATP regulatory subunit 4 homolog and auxin-responsive factor AUX/IAA-related. In addition, insertion of Orchid-rt1 in these three genes are all in their intron regions.

Conclusion
Orchid-rt1 and Gypsy1–3 have amplified within Phalaenopsis orchids concomitant with the expanded genome sizes, and Orchid-rt1 and Gypsy1 may have gone through various mutations and homologous recombination events. Insertion of Orchid-rt1 is in the introns and affects gene expression levels.
The attachment process and physiological properties of Escherichia coli O157:H7 on quartz
Authors: Wang Liliang , Wu Yichao , Cai Peng , Huang Qiaoyun 
Published: November 2020

Abstract
Background
Manure application and sewage irrigation release many intestinal pathogens into the soil. After being introduced into the soil matrix, pathogens are commonly found to attach to soil minerals. Although the survival of mineral-associated Escherichia coli O157:H7 has been studied, a comprehensive understanding of the attachment process and physiological properties after attachment is still lacking.

Results
In this study, planktonic and attached Escherichia coli O157:H7 cells on quartz were investigated using RNA sequencing (RNA-seq) and the isobaric tagging for relative and absolute quantitation (iTRAQ) proteomic method. Based on the transcriptomic and proteomic analyses and gene knockouts, functional two-component system pathways were required for efficient attachment; chemotaxis and the Rcs system were identified to play determinant roles in E. coli O157:H7 attachment on quartz. After attachment, the pyruvate catabolic pathway shifted from the tricarboxylic acid (TCA) cycle toward the fermentative route. The survival rate of attached E. coli O157:H7 increased more than 10-fold under penicillin and vancomycin stress and doubled under alkaline pH and ferric iron stress.

Conclusions
These results contribute to the understanding of the roles of chemotaxis and the Rcs system in the attachment process of pathogens and indicate that the attachment of pathogens to minerals significantly elevates their resistance to antibiotics and environmental stress, which may pose a potential threat to public health.
Potential value of guard-wire technology in the interventional treatment for ostial coronary lesions
Authors: Wang Xiaoqiong , Zong Xuemei , Li Bingqiang , Han Zhanying , Duan Xinjie , Li Ying , Zhang Jing , Wang Yaohui , Wang Yaoli 
Published: November 2020

Abstract
Background
To explore potential value of guard-wire technology during percutaneous coronary intervention (PCI) in patients with ostial coronary lesions.

Methods
Patients, who underwent PCI, were collected between October 2011 and March 2017. Of the 141 patients, 63 (44.7%) have ostial lesions, and 78 (55.3%) have distal bifurcation sites. They were divided into group A (n = 71) and group B (n = 70). Group A received PCI after guard-wire technology. Group B were given balloon dilation and stent after placing guide wire through target lesion vessel. X-ray exposure time, contrast agent dosage, total PCI duration, pressure incarceration times, cases of malignant arrhythmia and cases of failed PCI of all patients were analyzed, respectively.

Results
The general clinical characteristics includes patients age, sex ratio, the proportion of complications, smoking ratio and left ventricular ejection fraction of both groups was not significantly different. X-ray exposure time, contrast agent dosage, PCI total time, stent positioning time, pressure infestation frequency, arrhythmia frequency and complication number of group B were higher than those of group A. There is no case of malignant arrhythmia and case of failed PCI in group A, while there were five malignant arrhythmia and four failed PCI in group B. Contrast agent dosage and cases of failed PCI increased in group B compared with group A.

Conclusion
The guard wire technology is safer and more feasible to patients with ostial coronary lesions who underwent PCI.
Tolvaptan therapy of Chinese cirrhotic patients with ascites after insufficient diuretic routine medication responses: a phase III clinical trial
Authors: Tang Jieting , Wang Yongfeng , Han Tao , Mao Qing , Cheng Jun , Ding Huiguo , Shang Jia , Zhang Qin , Niu Junqi , Ji Feng , Chen Chengwei , Jia Jidong , Jiang Xiangjun , Lv Nonghua , Gao Yueqiu , Wang Zhenghua , Wei Zhong , Chen Yingxuan , Zeng Minde , Mao Yimin 
Published: November 2020

Abstract
Background
To determine the safety and efficacy of different doses of tolvaptan for treating Chinese cirrhotic patients with or without hyponatraemia who still had ascites after routine therapy with diuretics.

Methods
In the present placebo-controlled, randomized, double-blinded, multicentre clinical trial, patients with cirrhotic ascites who failed to adequately respond to a combination of an aldosterone antagonist plus an orally administered loop diuretic were randomly placed at a 4:2:1 ratio into 3 groups [the 15 mg/day tolvaptan group (N = 301), 7.5 mg/day tolvaptan group (N = 153) and placebo group (N = 76)] for 7 days of treatment. The effects and safety were evaluated on days 4 and 7. A change in body weight from baseline on day 7 of treatment was the primary endpoint.

Results
The administration of 7.5 or 15 mg/day tolvaptan significantly decreased body weight from baseline on day 7 of treatment compared to that with placebo treatment (P = 0.026; P = 0.001). For the secondary endpoints, changes in abdominal circumference from baseline and improvements in ascites were markedly different in the treatment groups and the placebo group on day 7 (P7.5 = 0.05, P15.0 = 0.002 and P7.5 = 0.037, P15.0 = 0.003), but there was no difference between the 7.5 mg/day and 15 mg/day dosage groups. The 24-h cumulative urine volume was higher in the 7.5 mg/day and 15 mg/day tolvaptan groups than the placebo group (P = 0.002, P < 0.001) and was greater in the 15 mg/day tolvaptan group than the 7.5 mg/day tolvaptan group (P = 0.004). Sodium serum concentrations were higher in patients with hyponatraemia after tolvaptan treatment, with no significant difference between the two dosage groups. The incidence of serious adverse drug reactions was not different between the groups (P = 0.543).

Conclusions
Tolvaptan treatment at 7.5 mg per day might be a good therapeutic choice for Chinese cirrhotic patients with ascites who did not achieve satisfactory clinical responses to previous treatment regimens with combination therapy with an aldosterone antagonist and an orally administered loop diuretic.

Trial registration
NCT01349348. Retrospectively registered May 2011.
Characterization of an N-terminal Nav1.5 channel variant – a potential risk factor for arrhythmias and sudden death?
Authors: Scheiper-Welling Stefanie , Zuccolini Paolo , Rauh Oliver , Beckmann Britt-Maria , Geisen Christof , Moroni Anna , Thiel Gerhard , Kauferstein Silke 
Published: November 2020

Abstract
Background
Alterations in the SCN5A gene encoding the cardiac sodium channel Nav1.5 have been linked to a number of arrhythmia syndromes and diseases including long-QT syndrome (LQTS), Brugada syndrome (BrS) and dilative cardiomyopathy (DCM), which may predispose to fatal arrhythmias and sudden death. We identified the heterozygous variant c.316A > G, p.(Ser106Gly) in a 35-year-old patient with survived cardiac arrest. In the present study, we aimed to investigate the functional impact of the variant to clarify the medical relevance.

Methods
Mutant as well as wild type GFP tagged Nav1.5 channels were expressed in HEK293 cells. We performed functional characterization experiments using patch-clamp technique.

Results
Electrophysiological measurements indicated, that the detected missense variant alters Nav1.5 channel functionality leading to a gain-of-function effect. Cells expressing S106G channels show an increase in Nav1.5 current over the entire voltage window.

Conclusion
The results support the assumption that the detected sequence aberration alters Nav1.5 channel function and may predispose to cardiac arrhythmias and sudden cardiac death.
The effect of the community midwifery model on maternal and newborn health service utilization and outcomes in Busia County of Kenya: a quasi-experimental study
Authors: Shikuku Duncan N. , Tanui Geofrey , Wabomba Mercy , Wanjala Dennis , Friday Josephine , Peru Taphroze , Atamba Evelyne , Sisimwo Kenneth 
Published: November 2020

AbstractBackgroundPoor women in hard-to-reach areas are least likely to receive healthcare and thus carry the burden of maternal and perinatal mortality from complications of childbirth. This study evaluated the effect of an enhanced community midwifery model on skilled attendance during pregnancy/childbirth as well as on maternal and perinatal outcomes against the backdrop of protracted healthcare workers’ strikes in rural Kenya.MethodsThe study used a quasi-experimental (one-group pretest-posttest) design. The study spanned three time periods: December 2016-February 2017 when doctors were on strike (P1), March-May 2017 when no healthcare providers were on strike (P2), and June-October 2017 when nurses/midwives were on strike (P3), which was also the period when the project enhanced the capacity of community midwives (CMs) to provide services at the community level. Analysis entailed comparison of frequencies/means of maternal and newborn health service utilization data across the three periods.ResultsThe monthly average number of clients obtaining services from CMs across the three time periods was: first antenatal care (ANC) (P1-1.8, P2-2.3, P3-9.9), fourth ANC (P1-1.4, P2-1.0, P3-7.1), skilled birth (P1-1.5, P2-1.7, P3-13.1) and the differences in means were statistically significant (p < 0.05). Over the period, the monthly average number of clients obtaining services from health facilities was: first ANC (P1-55.7, P2-70.8, P3-4.0), fourth ANC (P1-29.6, P2-38.1, P3-1.2) and skilled birth (P1-63.1, P2-87.4, P3-5.6),p < 0.05. There were no statistically significant differences in the average number of clients obtaining services from CMs or health facilities between P1 and P2 (p > 0.05). There was, however, a statistically significant increase in the average number of clients obtaining services from CMs in P3 accompanied by a statistically significant decline in the average number of clients obtaining services from health facilities (p < 0.05). First ANC increased by 68%, fourth ANC by 75%, skilled births by 68%, and postnatal care by 33% in P3 (p < 0.0001). There was a non-significant decline in macerated stillbirths and neonatal deaths in P3.ConclusionsThe findings underscore the importance of integrating community-level health service providers (CMs and health volunteers) into the primary health care system to complement service delivery according to their level of expertise, especially in low-resource settings.
Nomogram-derived prediction of pathologic complete response (pCR) in breast cancer patients treated with neoadjuvant chemotherapy (NCT)
Authors: Pu Shengyu , Wang Ke , Liu Yang , Liao Xiaoqin , Chen Heyan , He Jianjun , Zhang Jian 
Published: November 2020

Abstract
Background
Previous research results on the predictive factors of neoadjuvant chemotherapy (NCT) efficacy in breast cancer are inconsistent, suggesting that the ability of a single factor to predict efficacy is insufficient. Combining multiple potential efficacy-related factors to build a model may improve the accuracy of prediction. This study intends to explore the clinical and biological factors in breast cancer patients receiving NCT and to establish a nomogram that can predict the pathologic complete response (pCR) rate of NCT.

Methods
We selected 165 breast cancer patients receiving NCT from July 2017 to May 2019. Using pretreatment biopsy materials, immunohistochemical studies to assess estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER-2), and Ki-67 expression. The correlation between biological markers and pCR was analyzed. These predictors were used to develop a binary logistic regression model with cross-validation and to show the established predictive model with a nomogram.

Results
The nomogram for pCR based on lymphovascular invasion, anemia (hemoglobin≤120 g/L), ER, Ki67 expression levels and NCT regimen had good discrimination performance (area under the curve [AUC], 0.758; 95% confidence interval [CI], 0.675–0.841) and calibration coordination. According to the Hosmer-Lemeshow test, the calibration chart showed satisfactory agreement between the predicted and observed probabilities. The final prediction accuracy of cross-validation was 76%.

Conclusions
We developed a nomogram based on multiple clinical and biological covariations that can provide an early prediction of NCT response and can help to quickly assess the individual benefits of NCT.