bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections
Authors: Franco-Duran Jorge , Crossa José , Chen Jiafa , Hearne Sarah Jane 
Published: November 2019

AbstractBackgroundGermplasm banks maintain collections representing the most comprehensive catalogue of native genetic diversity available for crop improvement. Users of germplasm banks are interested in a fixed number of samples representing as broadly as possible the diversity present in the wider collection. A relevant question is whether it is necessary to develop completely independent germplasm samples or it is possible to select nested sets from a pre-defined core set panel not from the whole collection. We used data from 15,384, maize landraces stored in the CIMMYT germplasm bank to study the impact on 8 diversity criteria and the sample representativeness of: (1) two core selection strategies, a statistical sampling (DM), or a numerical maximization method (CH); (2) selecting samples of varying sizes; and (3) selecting samples of different sizes independently of each other or in a nested manner.ResultsSample sizes greater than 10% of the whole population size retained more than 75% of the polymorphic markers for all selection strategies and types of sample; lower sample sizes showed more variability (instability) among repetitions; the strongest effect of sample size was observed on the CH-independent combination. Independent and nested samples showed similar performance for all the criteria for the DM method, but there were differences between them for the CH method. The DM method achieved better approximations to the known values in the population than the CH method; 2-d multidimensional scaling plots of the collection and samples highlighted tendency of sample selection towards the extremes of diversity in the CH method, compared with sampling more representative of the overall genotypic distribution of diversity under the DM method.ConclusionsThe use of core subsets of size greater than or equal to 10% of the whole collection satisfied well the requirement of representativeness and diversity. Nested samples showed similar diversity and representativeness characteristics as independent samples offering a cost effective method of sample definition for germplasm banks. For most criteria assessed the DM method achieved better approximations to the known values in the whole population than the CH method, that is, it generated more statistically representative samples from collections.
Perioperative poor grip strength recovery is associated with 30-day complication rate after cardiac surgery discharge in middle-aged and older adults - a prospective observational study
Authors: Fu Liyuan , Zhang Yuanyuan , Shao Bohan , Liu Xiangjing , Yuan Bo , Wang Zhengqing , Chen Tienan , Liu Zhigang , Liu Xiaocheng , Guo Qi 
Published: November 2019

Abstract
Background
Although perioperative care during heart surgery has improved considerably, the rate of postoperative complications has remained stable. It has not been concluded how to better apply grip strength to clinical, postoperative complications. So our study aimed at researching the best way for using grip value for predicting early postoperative complications.

Methods
A total of 212 patients with mean age 63.8 ± 6.3 who underwent cardiac surgery participated in our study. We analyzed the ROC curve of grip strength, grip/weight and grip recovery with complications, found the best cutoff point. Logistic regression confirmed the association between grip strength grouping and complications.

Results
We found that 36 patients had 30-day complications. EuroSCORE were 2.15 ± 1.52 and 2.42 ± 1.58 between normal and complication groups, respectively. The area under the receiver-operating characteristic curve (AUC) of grip recovery take the most area (0.837, p < 0.001), and the cutoff point was 83.92%. In logistic regression, lower grip recovery has higher risk impact on 30-day complications for 25.68 times than normal group, after adjusted surgery-related factors. After regrouped characteristic information by grip recovery cutoff point, we found that percentage of the estimated 6 min walk distance (41.5 vs 48.3, p = 0.028) and hospitalization time (7.2 vs 6.1, p = 0.042) had worse trends in lower recovery group.

Conclusions
Poor grip recovery may be related to higher risk of postoperative complications within 30 days after discharge in middle-aged and older people independent of surgical risk. The results of this study provide a reference for the development of rehabilitation programs in the early postoperative recovery, and may also be a prognostic indicator for postoperative high-risk groups.

Trial registration
Our research was registered on Research Registry website, the registry number was ChiCTR1800018465. Date: 2018/9/20. Status: Successful.
A comparison of machine learning techniques for classification of HIV patients with antiretroviral therapy-induced mitochondrial toxicity from those without mitochondrial toxicity
Authors: Lee Jong Soo , Paintsil Elijah , Gopalakrishnan Vivek , Ghebremichael Musie 
Published: November 2019

AbstractBackgroundAntiretroviral therapy (ART) has significantly reduced HIV-related morbidity and mortality. However, therapeutic benefit of ART is often limited by delayed drug-associated toxicity. Nucleoside reverse transcriptase inhibitors (NRTIs) are the backbone of ART regimens. NRTIs compete with endogenous deoxyribonucleotide triphosphates (dNTPs) in incorporation into elongating DNA chain resulting in their cytotoxic or antiviral effect. Thus, the efficacy of NRTIs could be affected by direct competition with endogenous dNTPs and/or feedback inhibition of their metabolic enzymes. In this paper, we assessed whether the levels of ribonucleotides (RN) and dNTP pool sizes can be used as biomarkers in distinguishing between HIV-infected patients with ART-induced mitochondrial toxicity and HIV-infected patients without toxicity.MethodsWe used data collected through a case-control study from 50 subjects. Cases were defined as HIV-infected individuals with clinical and/or laboratory evidence of mitochondrial toxicity. Each case was age, gender, and race matched with an HIV-positive without evidence of toxicity. We used a range of machine learning procedures to distinguish between patients with and without toxicity. Using resampling methods like Monte Carlok-fold cross validation, we compared the accuracy of several machine learning algorithms applied to our data. We used the algorithm with highest classification accuracy rate in evaluating the diagnostic performance of 12 RN and 14 dNTP pool sizes as biomarkers of mitochondrial toxicity.ResultsWe used eight classification algorithms to assess the diagnostic performance of RN and dNTP pool sizes distinguishing HIV patients with and without NRTI-associated mitochondrial toxicity. The algorithms resulted in cross-validated classification rates of 0.65–0.76 for dNTP and 0.72–0.83 for RN, following reduction of the dimensionality of the input data. The reduction of input variables improved the classification performance of the algorithms, with the most pronounced improvement for RN. Complex tree-based methods worked the best for both the deoxyribose dataset (Random Forest) and the ribose dataset (Classification Tree and AdaBoost), but it is worth noting that simple methods such as Linear Discriminant Analysis and Logistic Regression were very competitive in terms of classification performance.ConclusionsOur finding of changes in RN and dNTP pools in participants with mitochondrial toxicity validates the importance of dNTP pools in mitochondrial function. Hence, levels of RN and dNTP pools can be used as biomarkers of ART-induced mitochondrial toxicity.
Risk-adjusted CUSUM control charts for shared frailty survival models with application to hip replacement outcomes: a study using the NJR dataset
Authors: Begun Alexander , Kulinskaya Elena , MacGregor Alexander J 
Published: November 2019

Abstract
Background
Continuous monitoring of surgical outcomes after joint replacement is needed to detect which brands’ components have a higher than expected failure rate and are therefore no longer recommended to be used in surgical practice. We developed a monitoring method based on cumulative sum (CUSUM) chart specifically for this application.

Methods
Our method entails the use of the competing risks model with the Weibull and the Gompertz hazard functions adjusted for observed covariates to approximate the baseline time-to-revision and time-to-death distributions, respectively. The correlated shared frailty terms for competing risks, corresponding to the operating unit, are also included in the model. A bootstrap-based boundary adjustment is then required for risk-adjusted CUSUM charts to guarantee a given probability of the false alarm rates. We propose a method to evaluate the CUSUM scores and the adjusted boundary for a survival model with the shared frailty terms. We also introduce a unit performance quality score based on the posterior frailty distribution. This method is illustrated using the 2003-2012 hip replacement data from the UK National Joint Registry (NJR).

Results
We found that the best model included the shared frailty for revision but not for death. This means that the competing risks of revision and death are independent in NJR data. Our method was superior to the standard NJR methodology. For one of the two monitored components, it produced alarms four years before the increased failure rate came to the attention of the UK regulatory authorities. The hazard ratios of revision across the units varied from 0.38 to 2.28.

Conclusions
An earlier detection of failure signal by our method in comparison to the standard method used by the NJR may be explained by proper risk-adjustment and the ability to accommodate time-dependent hazards. The continuous monitoring of hip replacement outcomes should include risk adjustment at both the individual and unit level.
True and false positive rates for different criteria of evaluating statistical evidence from clinical trials
Authors: van Ravenzwaaij Don , Ioannidis John P. A. 
Published: November 2019

Abstract
Background
Until recently a typical rule that has often been used for the endorsement of new medications by the Food and Drug Administration has been the existence of at least two statistically significant clinical trials favoring the new medication. This rule has consequences for the true positive (endorsement of an effective treatment) and false positive rates (endorsement of an ineffective treatment).

Methods
In this paper, we compare true positive and false positive rates for different evaluation criteria through simulations that rely on (1) conventional p-values; (2) confidence intervals based on meta-analyses assuming fixed or random effects; and (3) Bayes factors. We varied threshold levels for statistical evidence, thresholds for what constitutes a clinically meaningful treatment effect, and number of trials conducted.

Results
Our results show that Bayes factors, meta-analytic confidence intervals, and p-values often have similar performance. Bayes factors may perform better when the number of trials conducted is high and when trials have small sample sizes and clinically meaningful effects are not small, particularly in fields where the number of non-zero effects is relatively large.

Conclusions
Thinking about realistic effect sizes in conjunction with desirable levels of statistical evidence, as well as quantifying statistical evidence with Bayes factors may help improve decision-making in some circumstances.
B-cell acute lymphoblastic leukemia in an elderly man with plasma cell myeloma and long-term exposure to thalidomide and lenalidomide: a case report and literature review
Authors: Sinit Ryan B. , Hwang Dick G. , Vishnu Prakash , Peterson Jess F. , Aboulafia David M. 
Published: November 2019

Abstract
Background
The advent of the immunomodulatory imide drugs (IMiDs) lenalidomide and thalidomide for the treatment of patients with plasma cell myeloma (PCM), has contributed to more than a doubling of the overall survival of these individuals. As a result, PCM patients join survivors of other malignancies such as breast and prostate cancer with a relatively new clinical problem – second primary malignancies (SPMs) – many of which are a result of the treatment of the initial cancer. PCM patients have a statistically significant increased risk for acute myeloid leukemia (AML) and Kaposi sarcoma. IMiD treatment has also been associated with an increased risk of myelodysplastic syndrome (MDS), AML, and squamous cell carcinoma of the skin. However, within these overlapping groups, acute lymphoblastic leukemia (ALL) is much less common.

Case presentation
Herein, we describe an elderly man with PCM and a 14-year cumulative history of IMiD therapy who developed persistent pancytopenia and was diagnosed with B-cell acute lymphoblastic leukemia (B-ALL). He joins a group of 17 other patients documented in the literature who have followed a similar sequence of events starting with worsening cytopenias while on IMiD maintenance for PCM. These PCM patients were diagnosed with B-ALL after a median time of 36 months after starting IMiD therapy and at a median age of 61.5 years old.

Conclusions
PCM patients with subsequent B-ALL have a poorer prognosis than their de novo B-ALL counterparts, however, the very low prevalence rate of subsequent B-ALL and high efficacy of IMiD maintenance therapy in PCM should not alter physicians’ current practice. Instead, there should be a low threshold for bone marrow biopsy for unexplained cytopenias.
Vaccine confidence in China after the Changsheng vaccine incident: a cross-sectional study
Authors: Liu Baohua , Chen Ruohui , Zhao Miaomiao , Zhang Xin , Wang Jiahui , Gao Lijun , Xu Jiao , Wu Qunhong , Ning Ning 
Published: November 2019

Abstract
Background
China’s achievements in immunization are being threatened by a vaccine crisis. This paper aims to investigate vaccine confidence in China after the Changsheng vaccine incident and attempts to identify the factors contributing to it.

Methods
An online cross-sectional investigation was conducted from 1 to 25 September 2018. Descriptive analysis and logistic regression were performed to examine the associations between socio-demographic factors, cognition and attitudes towards the Changsheng vaccine incident and vaccine confidence.

Results
We included 1115 respondents in the final analysis, and found that approximately 70% (783) of the respondents did not have vaccine confidence. More than half of the respondents (54.53%) were dissatisfied with the government’s response measures to the Changsheng vaccine incident. The logistic regression model indicated that vaccine confidence was positively associated with the degree of satisfaction with the government’s response measures (OR = 1.621, 95% CI = 1.215–2.163), attitudes towards the risks and benefits of vaccination (OR = 1.501, 95% CI = 1.119–2.013), concerns about vaccine safety (OR = 0.480, 95% CI = 0.317–0.726), and vaccine efficacy (OR = 0.594, 95% CI = 0.394–0.895).

Conclusions
A majority of the respondents held negative attitudes towards vaccines after the Changsheng vaccine incident. A coordinated effort is required to restore public confidence in vaccines, especially in China, where a nationwide mandatory immunization policy is implemented. To end dissent towards inoculation, a series of actions is crucial and multiple parties should work together to advance efforts and explore the possibility of establishing an open and transparent regulatory system.
Determinants of breast self-examination practice among women in Surabaya, Indonesia: an application of the health belief model
Authors: Dewi Triana Kesuma , Massar Karlijn , Ruiter Robert A. C. , Leonardi Tino 
Published: November 2019

Abstract
Background
Breast cancer has become one of the most common causes of mortality among Indonesian women. Many women in Indonesia present with late-stage breast cancer, negatively affecting prognosis and treatment outcomes. Better prognosis of breast cancer will be achieved if it is diagnosed in an earlier stage, thus efforts to detect breast cancer earlier are important. Breast Self-Examination (BSE) is considered as an important first step to encourage women to actively be responsible for their own health, especially for women in low-and middle-income countries with limited resources and access to other forms of preventive healthcare (e.g., screening programs). The present study aimed to predict BSE practice among women in Surabaya, Indonesia using the Health Belief Model (HBM).

Methods
This investigation was a cross-sectional survey which was distributed among 1967 women aged 20–60 years. The Indonesian version of Champion’s Health Belief Model Scale (I-CHBMS) was used to explain self-reported BSE practice. Logistic regression analysis was used to examine the association of HBM variables with BSE practice.

Results
44.4% of the respondents indicated they had performed BSE. Further, the results indicated that the HBM variables were significantly associated with BSE practice. Specifically, higher perceived benefits and self-efficacy, lower perceived barriers and less cues to action were unique correlates of BSE practice. The result also showed that perceived severity and susceptibility were not associated with BSE practice.

Conclusion
This study indicated that several HBM constructs significantly associated with BSE practice among Indonesian women, suggesting that BSE health education programs should emphasize the perceived benefits of BSE, focus on increasing women’s self-efficacy to address and overcome perceived barriers in performing BSE, and help them in identifying personally relevant cues to action.
Retrorectal adenocarcinoma arising from tailgut cysts: a rare case report
Authors: Li Wei , Li Jian , Yu Ke , Zhang Kai , Li Jiannan 
Published: November 2019

AbstractBackgroundTailgut cysts arise from the remnants of the tailgut during the embryonic period. Although malignant transition of tailgut cysts is very rarely observed in the clinic, this congenital condition should be carefully monitored for early diagnosis and appropriate treatment, especially when the tailgut cysts are malignant.Case presentationHere, we report the case of a 33-year-old man with retrorectal adenocarcinoma originating from the tailgut cysts. Magnetic resonance imaging (MRI) showed many cystic masses in the posterior rectal space, the largest of which was approximately 100 mm × 59 mm × 53 mm in size and compressed the rectum. The patient underwent surgical resection of the masses located in the retrorectal and anterior sacral spaces. Histological and immunohistological examinations confirmed adenocarcinoma transition of the tailgut cysts. The patient recovered well and was discharged 10 days after surgery.ConclusionsWe have reported a rare case of retrorectal adenocarcinoma originating from tailgut cysts. MRI, histological, and immunohistological examinations are vital for the diagnosis of tailgut cysts. Complete surgical resection of the tumor should be better performed.
Fracture behavior of root-amputated teeth at different amount of periodontal support – a preliminary in vitro study
Authors: Szabó Balázs , Garoushi Sufyan , Braunitzer Gábor , Szabó P. Balázs , Baráth Zoltán , Fráter Márk 
Published: November 2019

AbstractBackgroundThe purpose of this study was to evaluate the effect of the amount of periodontal support on the fracture resistance of root-amputated maxillary molar teeth restored with either direct class. I. restorations or class II. mesio-occluso-distal (MOD) indirect overlay restorations with cuspal coverage.MethodsSixty sound maxillary first molars were collected and randomly divided into four groups. In Groups 1 and 2, MOD cavities were prepared and all cusps were reduced by 2 mm, whereas in Group 3 and 4, only a conservative Class I. cavity was prepared. Subsequently, root canal treatment was performed and the mesio-buccal roots were amputated. Groups 1 and 2 were restored with indirect composite overlay, while Groups 3 and 4 received direct composite fillings. After restoration, teeth were embedded as follows: Groups 1 and 3: normal bone level, Groups 2 and 4: furcation involvement. The specimens were submitted to static fracture resistance testing. Fracture thresholds and fracture patterns were measured and evaluated.ResultsGroup 1 had the highest fracture resistance (2311,6 N) among the restored groups and showed statistically significant difference compared to Group 2 (p = 0.038) and Group 4 (p = 0.011). There was no statistically significant difference in terms of fracture resistance between the rest of the groups. In terms of the fracture patterns, Group 3 was characterized by the highest percentage (60%) of mostly favorable fractures, while the rest of the groups showed predominantly unfavorable ones.ConclusionsThe amount of periodontal support seems to influence the fracture resistance of root-amputated and restored maxillary molars.
Tong-Xie-Yao-Fang improves intestinal permeability in diarrhoea-predominant irritable bowel syndrome rats by inhibiting the NF-κB and notch signalling pathways
Authors: Hou Qiuke , Huang Yongquan , Zhu Zhaoyang , Liao Liu , Chen Xinlin , Han Quanbin , Liu Fengbin 
Published: November 2019

Abstract
Background
Tong-Xie-Yao-Fang (TXYF) has been shown to be effective in diarrhoea-predominant irritable bowel syndrome (IBS-D) patients. However, the underlying mechanism remains to be clarified. The aim of this study was to investigate the efficacy and related mechanisms of TXYF in an IBS-D rat model.

Methods
The IBS-D rat model was established with 4% acetic acid and evaluated by haematoxylin-eosin (HE) staining. Then, IBS-D rats were divided into control, TXYF and rifaximin groups and treated intragastrically with normal saline, TXYF and rifaximin, respectively, for 14 days. The following indicators were measured before and after treatment: defecation frequency, faecal water content (FWC) and colorectal distension (CRD). Histopathological changes in the distal colon were observed after treatment. The expression of OCLN and ZO1 in the distal colon of IBS-D rats reflected the intestinal mucosal permeability, as measured by qRT-PCR, western blot, and enzyme-linked immunosorbent assays (ELISAs). The NF-κB and Notch signalling pathways and inflammation-related factors were investigated.

Results
After treatment with TXYF, the defecation frequency, FWC and CRD were significantly lower than those in the model group (P < 0.05). HE staining showed that colonic epithelial cells (CECs) in the IBS-D rats displayed significant oedema, impaired intestinal mucosal integrity and an increased influx of inflammatory cells. A significant reduction in granulocyte and CEC oedema was observed after the administration of TXYF and rifaximin compared to that of the model group and blank group (P < 0.05). TXYF significantly upregulated the expression of OCLN and ZO-1 and downregulated inflammation-related factors (IL-6, IL-1β, and TNF-α and the chemokine KC) in IBS-D rats compared to those in the model group rats (P < 0.05). In terms of the NF-κB and Notch signalling pathways, the expression of NICD, p-ERK, Hes-1 and p-P65 decreased significantly in the TXYF and rifaximin groups, while the expression of ATOH1 increased significantly compared to that in the model group (P < 0.05).

Conclusion
TXYF can effectively improve intestinal permeability and enhance intestinal mucosal barrier function, which may be related to inhibition of the inflammatory cascade and the NF-κB and Notch signalling pathways.