bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of Nontuberculous Mycobacteria in a Tertiary Hospital in Beijing, China, January 2013 to December 2018
Authors: HUANG Jing-jing , LI Ying-xing , ZHAO Ying , YANG Wen-hang , XIAO Meng , KUDINHA Timothy , XU Ying-chun 
Published: April 2020

Abstract
Background To investigate the species distribution of non-tuberculous mycobacteria (NTM) among tuberculosis (TB) specimens collected from January 2013 to December 2018 at Peking Union Medical Hospital (Beijing), China. NTM species identification was carried out by DNA microarray chip.
Results Mycobacterial species were detected in 1514 specimens from 1508 patients, among which NTM accounted for 37.3% (565/1514), increasing from a proportion of 15.6% in 2013 to 46.1% in 2018 ( P <0.001). Among the 565 NTM positive specimens, the majority (55.2%) were from female patients. Furthermore, patients aged 45-65 years accounted for 49.6% of the total patients tested. Among 223 NTM positive specimens characterized further, the majority (86.2%) were from respiratory tract, whilst 3.6% and 3.1% were from lymph nodes and pus, respectively. Mycobacterium intracellulare (31.8%) and Mycobacterium chelonae / Mycobacterium abscessus (21.5%) were the most frequently detected species, followed by M. avium (13.5%), M. gordonae (11.7%), M. kansasii (7.6%), and others.
Conclusion The proportion of NTM among mycobacterial species detected in a tertiary hospital in Beijing, China, increased rapidly from year 2013 to 2018. Middle-aged patients are more likely to be infected with NTM, especially females. Mycobacterium intracellulare and Mycobacterium chelonae / Mycobacterium abscessus were the most frequently detected NTM pathogens. Accurate and timely identification of NTM is important for diagnosis and treatment.
CReM: chemically reasonable mutations framework for structure generation
Authors: Polishchuk Pavel 
Published: April 2020

Abstract
Structure generators are widely used in de novo design studies and their performance substantially influences an outcome. Approaches based on the deep learning models and conventional atom-based approaches may result in invalid structures and fail to address their synthetic feasibility issues. On the other hand, conventional reaction-based approaches result in synthetically feasible compounds but novelty and diversity of generated compounds may be limited. Fragment-based approaches can provide both better novelty and diversity of generated compounds but the issue of synthetic complexity of generated structure was not explicitly addressed before. Here we developed a new framework of fragment-based structure generation that, by design, results in the chemically valid structures and provides flexible control over diversity, novelty, synthetic complexity and chemotypes of generated compounds. The framework was implemented as an open-source Python module and can be used to create custom workflows for the exploration of chemical space.
Efficacy of adjuvant radiotherapy for treatment of adrenocortical carcinoma: a retrospective study and an updated meta-analysis
Authors: Zhu Jiawei , Zheng Ziye , Shen Jing , Lian Xin , Miao Zheng , Shen Jie , Zhang Fuquan 
Published: April 2020

Abstract
Background: Adrenocortical carcinoma (ACC) is a rare and highly aggressive malignancy. Surgical resection is the standard treatment for localized ACC, but the local recurrence remains high. Adjuvant radiation (ART) has been proposed as a means to reduce recurrence rates in ACC after surgery with conflicting results from nonrandomized studies. We performed a retrospective study and a meta-analysis to determine the impact of ART on survival outcomes.Methods: A retrospective study of the adrenocortical cancer database in Peking Union Medical College was conducted. We selected postoperative ACC patients with or without ART. A meta-analysis is also performed to compare the outcomes between ART and only surgical resection in ACC patients. The obtained data were analyzed using SPSS 23.0 and Stata 15.0 statistical software. Differences between two groups were compared using the log-rank test for retrospective analysis and estimated by calculating the odds ratio (OR) and 95% confidence interval (CI) for meta-analysis.Results: Of a total of 75 patients available in the database, 12 patients underwent postoperative ART and were matched one to one to patients with only surgical resection. There was no significant difference on overall survival between ART group and control group (log-rank P = 0.149). Locoregional recurrence was diagnosed in 2 of the ART group, and in 4 of the control group (P=0.64). A total of 238 participants were selected for the meta-analysis, of which 111 and 127 patients underwent ART after surgical resection and only surgical resection, respectively. Overall survival is significantly higher in ART group, with an odds ratio (OR) of 2.41 (95% CI of 1.33, 4.38; P = 0.004). Besides, meta-analysis significantly favored ART for locoregional recurrence-free survival and disease-free survival, with an OR of 4.08 and 2.27, respectively. Conclusions: Our results show that compared to only surgical resection, ART is an effective postoperative treatment for ACC.
Development and validation of a new method for visual acuity assesment on tablet in pediatric population: eMOVA test
Authors: STOLL NOEMIE , SPEEG-SCHATZ Claude , Foggia Elsa Di , Sauer Arnaud 
Published: April 2020

Abstract
Background Amblyopia is a major public health problem. Its screening and management require reliable methods of assessing visual acuity. Many tests are available, some of which are used as a reference and the advent of new technologies sees many others whose validity is not proven. The objective of our study was to develop a tablet-based visual acuity test adapted to the pediatric population: the eMOVA test (electronic Measurement Of Visual Acuity). Methods We did a study comparing the eMOVA test with the Rossano-Weiss test. All children aged 3 to 8 attending the ophthalmic and pediatric consultation between September 2016 and June 2017 were included. The results in terms of visual acuity were compared as well as the duration of each test, its comprehension, its acceptability and the attention of the child during the test. Results The eMOVA test overestimated visual acuity by 0.06 logMAR. This difference, statistically significant, was not clinically relevant. The duration of the eMOVA test was longer than the reference test, but it was less painful and more appreciated by children and their parents. Conclusion The e-MOVA test appears as a reliable method of assessing visual acuity that could be used both in consultation and on a larger scale in the context of screening as well as for the care of the most difficult children.
Ordinal outcome analysis improves the detection of between-hospital differences in outcome
Authors: Ceyisakar Iris E. , Leeuwen Nikki van , Dippel Diederik W.J. , Steyerberg Ewout W. , Lingsma Hester F. 
Published: April 2020

Abstract
Background There is a growing interest in assessment of the quality of hospital care, based on outcome measures. Many quality of care comparisons rely on binary outcomes, for example mortality rates. Due to low numbers, the observed differences in outcome are partly subject to chance. Methods We aimed to quantify the gain in efficiency by ordinal instead of binary outcome analyses for hospital comparisons. We analyzed patients with traumatic brain injury (TBI) and stroke as examples. We sampled patients from two trials. We simulated ordinal and dichotomous outcomes based on the modified Rankin Scale (stroke) and Glasgow Outcome Scale (TBI) in scenarios with and without true differences between hospitals in outcome. The potential efficiency gain of ordinal outcomes, analyzed with ordinal logistic regression, compared to dichotomous outcomes, analyzed with binary logistic regression was expressed as the possible reduction in sample size while keeping the same statistical power to detect outliers. In the IMPACT study (8,799 patients in 265 hospitals, mean number of patients per hospital = 36), the analysis of the ordinal scale rather than the dichotomized scale (‘unfavorable outcome’), allowed for up to 32% less patients in the analysis without a loss of power. In the PRACTISE trial (1,657 patients in 12 hospitals, mean number of patients per hospital = 138), ordinal analysis allowed for 13% less patients. Compared to mortality, ordinal outcome analyses allowed for up to 37% to 63% less patients. Conclusion Ordinal analyses provide the statistical power of substantially larger studies which have been analyzed with dichotomization of endpoints. We advise to exploit ordinal outcome measures for hospital comparisons, in order to increase efficiency in quality of care measurements.
Effect of AIDS-defining events at initiation of antiretroviral therapy on long-term mortality of HIV/AIDS patients in southwestern China: a cohort study
Authors: Huang Yunxuan , Zhou Oulu , Zheng Zhigang , Xu Yuexiang , Shao Yi , Qin Chunwei , Qin Fengxiang , Lai Jingzhen , Liu Huifang , Chen Rongfeng , Ye Li , Liang Hao , Qin Xionglin , Jiang Junjun 
Published: April 2020

Abstract
Objective

To evaluate the impact of AIDS-defining events (ADE) on long-term mortality of HIV positive individuals on antiretroviral therapy (ART), a retrospective HIV/AIDS treatment cohort study was performed in southwestern China.

Methods

The cohort was established based on HIV/AIDS patients on ART recruited in Guigang city, Guangxi, China, from January 2004 to December 2018. Participants were divided into ADE and non-ADE groups, and were followed-up every six months to observe treatment outcomes. Comparison of mortality between groups was performed using the log-rank test and Kaplan-Meier analysis. Cox proportional hazard regression was used to explore the risk factors of mortality. 1:1 propensity score matching (PSM) was used to balance confounding factors and adjust the mortality risk.

Results

Of 6,757 participants with 29,096.06 person-years of follow-up, 16.86% (1,139/6,757) belonged to ADE group while the others (83.14%) belonged to the non-ADE group. The most common cause of death by ADE was disseminated mycosis (31.65%), followed by recurrent severe bacterial pneumonia (28.48%), herpes zoster(17.72%), and extra-pulmonary tuberculosis (8.86%). The mortality of the ADE group was significantly higher than that of the non-ADE group [3.45/100 person-years (95% CI: 2.92-3.97) vs. 2.34/100 person-years (95%CI: 2.15-2.52), P<0.001]. The death risk of the ADE group was also higher than that of the non- ADE group [adjusted hazard ratio (aHR) =1.291, 95% CI: 1.061-1.571, P =0.011], which was confirmed by PSM analysis (aHR=1.581, 95% CI: 1.192-2.099, P =0.002). Cox analysis indicated that ADE, older age, male gender, previous non-use of cotrimoxazole, advanced WHO clinical stage, and low baseline CD4+ cell count were the risk factors for death.

Conclusions

Even on ART, the mortality risk of HIV positive individuals with ADE was higher than those without ADE. Active testing, earlier diagnosis, and timely therapy with ART may reduce the death risk of ADE.
Frequently abnormal serum gamma-glutamyl transferase activity is associated with future development of fatty liver: a retrospective cohort study
Authors: Fujii Hideki , Doi Haruna , Ko Tetsuhisa , Fukuma Taito , Kadono Toru , Asaeda Kohei , Kobayashi Reo , Nakano Takahiro , Doi Toshifumi , Nakatsugawa Yoshikazu , Yamada Shinya , Nishimura Takeshi , Tomatsuri Naoya , Sato Hideki 
Published: April 2020

Abstract
BackgroundNonalcoholic fatty liver disease is characterized by excessive hepatic fat accumulation. Some individuals frequently present elevated gamma-glutamyl transferase (GGT) levels without fatty liver ultrasound images and other abnormal liver enzymes levels. However, whether these individuals are at an elevated risk for developing fatty liver is unclear. We compared fatty liver change rates and risk factors between individuals with frequently elevated GGT levels and those with normal levels.MethodsWe designed a retrospective cohort study on the basis of complete medical checkup records. One group of individuals had presented normal serum GGT levels during the observation period (Normal-GGT group, n = 2713). Another group had had abnormal elevated serum GGT levels frequently (Abnormal-GGT group, n = 264). We determined the fatty liver change incident rates before and after propensity score matching. We explored confounding factors affecting fatty changes in each group using univariate and multivariate Cox models.ResultsThe change incidence rates were 5.80/1000 and 10.02/1000 person-years in the Normal-GGT and Abnormal-GGT groups, respectively. After propensity score matching, the incidence rates were 3.08/1000 and 10.18/1000 person-years in the Normal-GGT and Abnormal-GGT groups, respectively (p = 0.026). The factors associated with fatty liver changes in the Normal-GGT group included body mass index (BMI), hemoglobin, alanine aminotransferase (ALT), albumin, triglyceride (TG), fasting blood sugar, and high-density lipoprotein levels. Those in the Abnormal-GGT group were platelet counts and TG. In our multivariable analysis, BMI, ALT, albumin, and TG levels were independent predictors of fatty changes in the Normal-GGT group, and high TG level was the only independent predictor in the Abnormal-GGT group.ConclusionsThe incidence rate of fatty liver change in the Abnormal-GGT group was higher than that in the Normal-GGT group. Consecutive elevated GGT levels increase the risk for fatty liver, and high TG levels in those individuals further independently increase the risk.
Bacillus subtilis HG-15, a Halotolerant Rhizoplane Bacterium, Promotes Growth and Salinity Tolerance in Wheat (Triticum aestivum)
Authors: Ji Chao , Tian Huimei , Wang Xiaohui , Hao Liping , Wang Changdong , Zhou Yanyan , Xu Ruiping , Song Xin , Liu Yue , Du Jianfeng , Liu Xunli 
Published: April 2020

Abstract
Background : Certain plant growth-promoting bacteria (PGPB) reduce salt stress damage in plants. Bacillus subtilis HG-15 is a halotolerant bacterium (able to withstand NaCl concentrations as high as 30%) isolated from the wheat rhizoplane in the Yellow River delta. A qualitative and quantitative investigation of the plant growth-promoting characteristics of this strain confirmed nitrogen fixation, potassium dissolution, and ammonia, plant hormone, 1-aminocyclopropane-1-carboxylic acid deaminase, and proline production abilities. B. subtilis HG-15 colonization of wheat roots, stems, and leaves was examined via scanning electron microscopy , rep-PCR, and double antibiotic screening.Results : Compared with a no B. subtilis HG-15 treatment control, in rhizosphere soil inoculated with the HG-15 strain, the pH (1.08–2.69%), electrical conductivity (3.17–11.48%), and Na + (12.98–15.55%) concentrations significantly decreased ( p < 0.05). Inoculation with the HG-15 strain increased the total N, available N, organic matter, K + , Ca 2+ , and Mg 2+ concentrations in the rhizosphere soil of wheat. Under non-salt stress (0.15% NaCl), low-salt stress (0.25% NaCl), and high-salt stress (0.35% NaCl) conditions, respectively, this strain also significantly increased ( p < 0.05) the dry weight (17.76%, 24.46%, 9.31%), fresh weight (12.80%, 20.48%, 7.43%), plant height (7.79%, 5.86%, 13.13%), root length (10.28%, 17.87%, 48.95%), and other wheat parameters. Through redundancy analysis and Pearson correlation analyses, photosynthesis, biomass accumulation, and osmotic regulation by the wheat plants showed a significant negative correlation with pH, EC, and Na + concentrations in rhizosphere soil.Conclusions : Our results indicated that B . subtilis HG-15 can effectively improve the growth of wheat and elicit induced systemic tolerance in these plant, thus, showing its potential as a microbial inoculant that can protect wheat in salt stress conditions. Furthermore, we determined that the rhizoplane of saline-alkali land plants is an important reservoir for salt-tolerant PGPB.
Population genetic structure and gene flow of rare and endangered Tetraena mongolica Maxim revealed by reduced representation sequencing
Authors: Jin Cheng , Kao Huixia , Dong Shubin 
Published: April 2020

Abstract
BackgroundStudying population genetic structure and gene flow of plant populations and their influence factors is crucial in field of conservation biology, especially rare and endangered plants. Tetraena mongolica Maxim (TM), belong to Zygophyllaceae family, a rare and endangered plant with narrow distribution. Due to excessive logging, urban expansion, industrial development and development of the scenic spot in the last decades, has caused habitat fragments and decline.ResultsIn this study, the genetic diversity, the population genetic structure and gene flow of TM populations were evaluated by reduced representation sequencing technology, a total of more than 133.45 GB high-quality clean reads and 38,097 high-quality SNPs were generated. Analysis based on multiple methods, we found existing TM populations have moderate levels of genetic diversity, very low genetic differentiation and high levels of gene flow between populations. Population structure and principal coordinates analysis showed that 8 TM populations can be divided into two groups, Mantel test detected no significant correlation between geographical distances and genetic distance for the whole sampling. The migration model indicated that the gene flow is more of an north to south migration pattern in history.ConclusionsOur study demonstrate that the present genetic structure is mainly due to habitat fragmentation caused by urban sprawl, industrial development and coal mining. For recommendations of conservation management, all 8 populations should be protected as a whole population, rather than just those in the core area of TM nature reserve, especially the populations near the edge of TM distribution in cities and industrial areas deserve our special protection.
Model to assess workload of village doctors in the National E sential Public Health Services Program in six provinces of China
Authors: Yin Delu , Yin Tao , Yang Huiming , Wang Lihong , Chen Bowen 
Published: April 2020

Abstract
Background: Village doctors face many challenges in providing the National Essential Public Health Service (NEPHS) program, and many factors affect the provision of these services. However, there are no studies (particularly quantitative analyses) regarding the workload of public health services provided by village doctors. In this study, we aimed to develop a quantitative analysis approach to measure the workload of NEPHS provided by village doctors in six provinces of China in 2016. Methods: Based on survey data from 300 town hospital centers (THCs) located in 60 counties in the six selected provinces, we calculated village doctors’ share of workload under the NEPHS using the equivalent value (EV) model. To define the workload and corresponding EV of each NEPHS, a series of five meetings was held with THC managers, public health workers, family physicians, nurses and village doctors. Field observations were conducted to verify the workload and EV of each service. Results: Village doctors’ share of the workload under the NEPHS program was 47.0% across the 300 sampled THCs in six provinces. The village doctors’ workload shares for different NEPHS ranged from 17.1% to 57.0%. The percentage workload undertaken by village doctors under the NEPHS program varied across different provinces, with the highest proportion 63.4% and the lowest 28.5%. Conclusions: The total NEPHS workload assigned to village doctors by THCs in the six sampled provinces exceeded the Chinese government’s requirement of 40%, but the workload proportion in some provinces was less than 40%. We suggest that local governments conduct district-level analysis of the workload among village doctors under the NEPHS program using the EV method, to identify priorities and influencing factors and implement targeted measures to promote health service provision. An EV model of the NEPHS could be built to monitor village doctors’ workload and ensure that assigned workloads are manageable.
Locomotion approach of bipedal robot utilizing passive wheel without swing leg based on stability margin maximization and fall prevention functions
Authors: Kimura Kohei , Imaoka Noriaki , Noda Shintaro , Kakiuchi Yohei , Okada Kei , Inaba Masayuki 
Published: April 2020

Abstract
This paper proposes a locomotion approach of leg-wheel robot utilizing passive wheel attached to the foot of bipedal robot. The key feature of this approach is bipedal mobility without swing leg. This mobility contributes the stability based on expansion of support polygon during locomotion, the robustness for obstacles and stopping to prevent fall, and the adaptability by prevention of body swing sideways. To achieve these, we propose the stability margin maximization to optimize center of gravity projection for support polygon and the fall prevention functions for real environment that is a diﬃcult situation to prevent unexpected fall by the only planning. Finally, we apply the proposed methods to leg-wheel phases through locomotion and verify the contribution by experiments using real bipedal robot.
Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish
Authors: Härer Andreas , Torres-Dowdall Julián , Rometsch Sina J. , Yohannes Elizabeth , Machado-Schiaffino Gonzalo , Meyer Axel 
Published: April 2020

Abstract
Background: Recent increases in understanding the ecological and evolutionary roles of microbial communities has underscored the importance for their hosts’ biology. Yet, little is known about gut microbiota dynamics during early stages of ecological diversification and speciation. We sequenced the V4 region of the 16s rRNA gene to study the gut microbiota of Nicaraguan Midas cichlid fish ( Amphilophus cf. citrinellus ). Specifically, we tested the hypothesis that parallel divergence in trophic ecology in extremely young adaptive radiations from two crater lakes is associated with parallel changes of their gut microbiota.Results: Bacterial communities of fish guts and lake water were highly distinct, indicating that the gut microbiota is shaped by host-specific factors. Among individuals of the same crater lake, differentiation in trophic ecology was weakly associated with gut microbiota differentiation, suggesting that diet, to some extent, affects the gut microbiota. However, differences in trophic ecology were much more pronounced across than within species whereas similar patterns were not observed for taxonomic and functional differences of the gut microbiota. Across the two crater lakes, we could not detect conclusive evidence for parallel changes of the gut microbiota associated with trophic ecology.Conclusions: A lack of clearly differentiated niches during early stages of ecological diversification might result in non-parallel changes of gut microbial communities, as observed in our study system as well as in other recently diverged fish species.