bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discrimination between human populations using a small number of differentially methylated CpG sites: a preliminary study using lymphoblastoid cell lines and peripheral blood samples of European and Chinese origin
Authors: Daca-Roszak Patrycja , Jaksik Roman , Paczkowska Julia , Witt Michał , Ziętkiewicz Ewa 
Published: October 2020

Abstract
Background
Epigenetics is one of the factors shaping natural variability observed among human populations. A small proportion of heritable inter-population differences are observed in the context of both the genome-wide methylation level and the methylation status of individual CpG sites. It has been demonstrated that a limited number of carefully selected differentially methylated sites may allow discrimination between main human populations. However, most of the few published results have been performed exclusively on B-lymphocyte cell lines.

Results
The goal of our study was to identify a set of CpG sites sufficient to discriminate between populations of European and Chinese ancestry based on the difference in the DNA methylation profile not only in cell lines but also in primary cell samples. The preliminary selection of CpG sites differentially methylated in these two populations (pop-CpGs) was based on the analysis of two groups of commercially available ethnically-specific B-lymphocyte cell lines, performed using Illumina Infinium Human Methylation 450 BeadChip Array. A subset of 10 pop-CpGs characterized by the best differentiating criteria (|Mdiff| > 1, q < 0.05; lack of the confounding genomic features), and 10 additional CpGs in their immediate vicinity, were further tested using pyrosequencing technology in both B-lymphocyte cell lines and in the primary samples of the peripheral blood representing two analyzed populations. To assess the population-discriminating potential of the selected set of CpGs (further referred to as “composite pop (CEU-CHB)-CpG marker”), three classification methods were applied. The predictive ability of the composite 8-site pop (CEU-CHB)-CpG marker was assessed using 10-fold cross-validation method on two independent sets of samples.

Conclusions
Our results showed that less than 10 pop-CpG sites may distinguish populations of European and Chinese ancestry; importantly, this small composite pop-CpG marker performs well in both lymphoblastoid cell lines and in non-homogenous blood samples regardless of a gender.
Predicting and clustering plant CLE genes with a new method developed specifically for short amino acid sequences
Authors: Zhang Zhe , Liu Lei , Kucukoglu Melis , Tian Dongdong , Larkin Robert M. , Shi Xueping , Zheng Bo 
Published: October 2020

Abstract
Background
The CLV3/ESR-RELATED (CLE) gene family encodes small secreted peptides (SSPs) and plays vital roles in plant growth and development by promoting cell-to-cell communication. The prediction and classification of CLE genes is challenging because of their low sequence similarity.

Results
We developed a machine learning-aided method for predicting CLE genes by using a CLE motif-specific residual score matrix and a novel clustering method based on the Euclidean distance of 12 amino acid residues from the CLE motif in a site-weight dependent manner. In total, 2156 CLE candidates—including 627 novel candidates—were predicted from 69 plant species. The results from our CLE motif-based clustering are consistent with previous reports using the entire pre-propeptide. Characterization of CLE candidates provided systematic statistics on protein lengths, signal peptides, relative motif positions, amino acid compositions of different parts of the CLE precursor proteins, and decisive factors of CLE prediction. The approach taken here provides information on the evolution of the CLE gene family and provides evidence that the CLE and IDA/IDL genes share a common ancestor.

Conclusions
Our new approach is applicable to SSPs or other proteins with short conserved domains and hence, provides a useful tool for gene prediction, classification and evolutionary analysis.
Image and fractal analysis as a tool for evaluating salinity growth response between two Salicornia europaea populations
Authors: Cárdenas-Pérez S. , Piernik A. , Ludwiczak A. , Duszyn M. , Szmidt-Jaworska A. , Chanona-Pérez J. J. 
Published: October 2020

Abstract
Background
This study describes a promising method for understanding how halophytes adapt to extreme saline conditions and to identify populations with greater resistance. Image and colour analyses have the ability to obtain many image parameters and to discriminate between different aspects in plants, which makes them a suitable tool in combination with genetic analysis to study the plants salt tolerance. To the best of our knowledge, there are no publications about the monitoring of halophytic plants by non-destructive methods for identifying the differences between plants that belong to different maternal salinity environments. The aim is to evaluate the ability of image analysis as a non-destructive method and principal component analysis (PCA) to identify the multiple responses of two S. europaea populations, and to determine which population is most affected by different salinity treatments as a preliminary model of selection.

Results
Image analysis was beneficial for detecting the phenotypic variability of two S. europaea populations by morphometric and colour parameters, fractal dimension (FD), projected area (A), shoot height (H), number of branches (B), shoot diameter (S) and colour change (ΔE). S was found to strongly positively correlate with both proline content and ΔE, and negatively with chlorophyll content. These results suggest that proline and ΔE are strongly linked to plant succulence, while chlorophyll decreases with increased succulence. The negative correlation between FD and hydrogen peroxide (HP) suggests that when the plant is under salt stress, HP content increases in plants causing a reduction in plant complexity and foliage growth. The PCA results indicate that the greater the stress, the more marked the differences. At 400 mM a shorter distance between the factorial scores was observed. Genetic variability analysis provided evidence of the differences between these populations.

Conclusions
Our non-destructive method is beneficial for evaluating the halophyte development under salt stress. FD, S and ΔE were relevant indicators of plant architecture. PCA provided evidence that anthropogenic saline plants were more tolerant to saline stress. Furthermore, random amplified polymorphic DNA analysis provided a quick method for determining genetic variation patterns between the two populations and provided evidence of genetic differences between them.
Clinical characteristics and laboratory indicator analysis of 67 COVID-19 pneumonia patients in Suzhou, China
Authors: Wang Yi , Yao Lin , Zhang Jian-Ping , Tang Pei-Jun , Ye Zhi-Jian , Shen Xing-Hua , Xu Jun-Chi , Wu Mei-Ying , Yu Xin 
Published: October 2020

Abstract
Background
Sudden exacerbations and respiratory failure are major causes of death in patients with severe coronavirus disease 2019(COVID-19) pneumonia, but indicators for the prediction and treatment of severe patients are still lacking.

Methods
A retrospective analysis of 67 collected cases was conducted and included approximately 67 patients with COVID-19 pneumonia who were admitted to the Suzhou Fifth People’s Hospital from January 1, 2020 to February 8, 2020. The epidemiological, clinical and imaging characteristics as well as laboratory data of the 67 patients were analyzed.

Results
The study found that fibrinogen (FIB) was increased in 45 (65.2%) patients, and when FIB reached a critical value of 4.805 g/L, the sensitivity and specificity、DA, helping to distinguish general and severe cases, were 100 and 14%、92.9%, respectively, which were significantly better than those for lymphocyte count and myoglobin. Chest CT images indicated that the cumulative number of lung lobes with lesions in severe patients was significantly higher than that in general patients (P < 0.05), and the cumulative number of lung lobes with lesions was negatively correlated with lymphocyte count and positively correlated with myoglobin and FIB. Our study also found that there was no obvious effect of hormone therapy in patients with severe COVID-19.

Conclusions
Based on the retrospective analysis, FIB was found to be increased in severe patients and was better than lymphocyte count and myoglobin in distinguishing general and severe patients. The study also suggested that hormone treatment has no significant effect on COVID-19.
Changes in 3-month mineral and bone disorder patterns were associated with all-cause mortality in prevalent hemodialysis patients with secondary hyperparathyroidism
Authors: Kato Chihiro , Fujii Naohiko , Miyakoshi Chisato , Asada Shinji , Onishi Yoshihiro , Fukuma Shingo , Nomura Takanobu , Wada Michihito , Fukagawa Masafumi , Fukuhara Shunichi , Akizawa Tadao 
Published: October 2020

Abstract
Background
There is limited evidence on the association between short-term changes in mineral and bone disorder parameters and survival in maintenance hemodialysis patients.

Methods
We investigated the association between changing patterns of phosphorus, calcium and intact parathyroid hormone levels and all-cause mortality in hemodialysis patients with secondary hyperparathyroidism. Each parameter was divided into three categories (low [L], middle [M] and high [H]), and the changing patterns between two consecutive visits at 3-month intervals were categorized into nine groups (e.g., L-L and M-H). The middle category was defined as 4.0–7.0 mg/dL for phosphorous, 8.5–9.5 mg/dL for calcium and 200–500 pg/mL for intact parathyroid hormone. Adjusted incidence rates and rate ratios were analyzed by weighted Poisson regression models accounting for time-dependent exposures.

Results
For phosphorus, shifts from low/high to middle category (L-M/H-M) were associated with a lower mortality compared with the L-L and H–H groups, whereas shifts from middle to low/high category (M-L/M-H) were associated with a higher mortality compared with the M-M group. For calcium, shifts from low/middle to high category (L–H/M-H) were associated with a higher mortality compared with the L-L and M-M groups, whereas shifts from high to middle category (H-M) were associated with a lower mortality compared with the H–H group. For intact parathyroid hormone, shifts from low to middle category (L-M) were associated with a lower mortality compared with the L-L group.

Conclusions
Changes in the 3-month patterns of phosphorus and calcium toward the middle category were associated with lower mortality. Our study also suggests the importance of avoiding hypercalcemia.
Venetoclax and alvocidib are both cytotoxic to acute myeloid leukemia cells resistant to cytarabine and clofarabine
Authors: Nishi Rie , Shigemi Hiroko , Negoro Eiju , Okura Miyuki , Hosono Naoko , Yamauchi Takahiro 
Published: October 2020

Abstract
Background
Cytarabine (ara-C) is the major drug for the treatment of acute myeloid leukemia (AML), but cellular resistance to ara-C is a major obstacle to therapeutic success. The present study examined enhanced anti-apoptosis identified in 3 newly established nucleoside analogue-resistant leukemic cell line variants and approaches to overcoming this resistance.

Methods
HL-60 human AML cells were used to develop the ara-C– or clofarabine (CAFdA)-resistant variants. The Bcl-2 inhibitor venetoclax and the Mcl-1 inhibitor alvocidib were tested to determine whether they could reverse these cells’ resistance.

Results
A 10-fold ara-C-resistant HL-60 variant, a 4-fold CAFdA-resistant HL-60 variant, and a 30-fold CAFdA-resistant HL-60 variant were newly established. The variants demonstrated reduced deoxycytidine kinase and deoxyguanosine kinase expression, but intact expression of surface transporters (hENT1, hENT2, hCNT3). The variants exhibited lower expression of intracellular nucleoside analogue triphosphates compared with non-variant HL-60 cells. The variants also overexpressed Bcl-2 and Mcl-1. Venetoclax as a single agent was not cytotoxic to the resistant variants. Nevertheless, venetoclax with nucleoside analogs demonstrated synergistic cytotoxicity against the variants. Alvocidib as a single agent was cytotoxic to the cells. However, alvocidib induced G1 arrest and suppressed the cytotoxicity of the co-administered nucleoside analogs.

Conclusions
Three new nucleoside analogue-resistant HL-60 cell variants exhibited reduced production of intracellular analogue triphosphates and enhanced Bcl-2 and Mcl-1 expressions. Venetoclax combined with nucleoside analogs showed synergistic anti-leukemic effects and overcame the drug resistance.
Identification of common signatures in idiopathic pulmonary fibrosis and lung cancer using gene expression modeling
Authors: Leng Dong , Yi Jiawen , Xiang Maodong , Zhao Hongying , Zhang Yuhui 
Published: October 2020

Abstract
Background
Idiopathic pulmonary fibrosis (IPF) is associated with an increased risk for lung cancer, but the underlying mechanisms driving malignant transformation remain largely unknown. This study aimed to identify differentially expressed genes (DEGs) distinguishing IPF and lung cancer from healthy individuals and common genes driving the transformation from healthy to IPF and lung cancer.

Methods
The gene expression data for IPF and non-small cell lung cancer (NSCLC) were retrieved from the Gene Expression Omnibus (GEO) database. The DEG signatures were identified via unsupervised two-way clustering (TWC) analysis, supervised support vector machine analysis, dimensional reduction, and mutual exclusivity analysis. Gene enrichment and pathway analyses were performed to identify common signaling pathways. The most significant signature genes in common among IPF and lung cancer were further verified by immunohistochemistry.

Results
The gene expression data from GSE24206 and GSE18842 were merged into a super array dataset comprising 86 patients with lung disorders (17 IPF and 46 NSCLC) and 51 healthy controls and measuring 23,494 unique genes. Seventy-nine signature DEGs were found among IPF and NSCLC. The peroxisome proliferator-activated receptor (PPAR) signaling pathway was the most enriched pathway associated with lung disorders, and matrix metalloproteinase-1 (MMP-1) in this pathway was mutually exclusive with several genes in IPF and NSCLC. Subsequent immunohistochemical analysis verified enhanced MMP1 expression in NSCLC associated with IPF.

Conclusions
For the first time, we defined common signature genes for IPF and NSCLC. The mutually exclusive sets of genes were potential drivers for IPF and NSCLC.
Relationship between formulaic breast volume and risk of breast cancer based on linear measurements
Authors: Li Xiaoxia , Zhou Chunlan , Wu Yanni , Chen Xiaohong 
Published: October 2020

AbstractBackgroundWhether breast volume is a risk factor for breast cancer is controversial. This study aimed to evaluate whether a significant association between breast volume and risk of breast cancer, based on linear measurements, was present by applying propensity score matching (PSM).MethodsThe study was designed as a hospital-based case-control study. Between March 2018 and May 2019, 208 cases and 340 controls were retrospectively reviewed. Information on menarche, smoking, feeding mode, oral contraceptives, reproductive history and family history was obtained through a structured questionnaire. Breast volume was calculated using a formula based on linear measurements of breast parameters. Cox regression and PSM were used to estimate odds ratios and 95% confidence intervals for breast cancer using risk factors adjusted for potential confounders.ResultsThere was a significant difference in breast volume between the two groups before propensity score matching (P = 0.014). Binary logistic regression showed that the risk of breast cancer was slightly higher in the case group with larger breast volumes than in the control group(P = 0.009, OR = 1.002, 95%CI:1.000 ~ 1.003). However, there was no significant statistical difference between the two groups using an independent sampleMann-Whitney Utest (P = 0.438) or conditional logistic regression (P = 0.446).ConclusionsAfter PSM for potential confounding factors, there is no significant difference in breast volume estimated by BREAST-V formula between the case group and the control group. The risk of breast cancer may not be related to breast volume in Chinese women.
Evaluations of knowledge, skills and practices of insulin storage and injection handling techniques of diabetic patients in Ethiopian primary hospitals
Authors: Netere Adeladlew Kassie , Ashete Eyayaw , Gebreyohannes Eyob Alemayehu , Belachew Sewunet Admasu 
Published: October 2020

Abstract
Background
Insulin is an effective therapeutic agent in the management of diabetes, but also sensitive to the external environment. Consequently, diabetic patients’ adherence to insulin delivery recommendations is critical for better effectiveness. Patients’ lack of knowledge, skill and irrational practices towards appropriate insulin delivery techniques may end up in therapeutic failure and increase costs of therapy. The aim of this study was to evaluate patients’ knowledge, skills and practices of insulin storage and injection techniques.

Methods
An interview-based cross-sectional study was conducted through purposive selection of participants in Northwest Ethiopian primary hospitals from March 1 to May 30, 2019. Levels of knowledge were assessed with right or wrong responses, while practice was measured by using a 4-point Likert scale structured questionnaire collected via face-to-face interviews. Likewise, a five-point observational (demonstration) techniques checklist employed to assess patients’ skills.

Results
Among 194 patients approached, 166 participants completed the survey giving a response rate of 85.6%. More than half of the respondents (54.8%) were males and the mean age (±SD) was 38.5 ± 13.8 years. The overall patients’ median knowledge and practice levels on insulin storage and handling techniques were moderately adequate (64.3%) and fair (55.4%), respectively. In patients’ skill assessments, 94.6% correctly showed injection sites, 70% indicated injection site rotations, and 60.75% practiced injection site rotations. Education (P < 0.001), duration of insulin therapy (P = 0.008), and duration of diabetes (P = 0.014) had significant impact on knowledge level. Education (P < 0.001), occupation (P < 0.001), duration of insulin therapy (P = 0.001), duration of diabetes (P = 0.036) and patients’ knowledge level (P < 0.001) were found to have a significant effects on the patients’ practice levels. A Mann-Whitney U test also disclosed that residency, ways to get insulin and mocked injection technique during the first training had significant effects on patients’ knowledge levels.

Conclusion
The current study revealed that patients had moderately adequate knowledge and fair practice levels on insulin storage and handling techniques. However, patients missed important insulin administration skills. This study highlights the need of regular public health education so as to enhance the patients’ knowledge, skill and practice levels on insulin handling techniques.
Trajectories of vital status parameters and risk of mortality among acute organophosphorus poisoning patients – a latent class growth analysis
Authors: Farooqui Waqas Ahmed , Uddin Mudassir , Qadeer Rashid , Shafique Kashif 
Published: October 2020

Abstract
Background
Acute organophosphorus (OP) poisoning is one of the major causes of mortality among patients presenting to emergency departments in developing countries. Although various predictors of mortality among OP poisoning patients have been identified, the role of repeated measurements of vital signs in determining the risk of mortality is not yet clear.
Therefore, the present study examined the relationship between trajectories of vital signs and mortality among OP poisoning patients using latent class growth analysis (LCGA).

Methods
This was a retrospective cohort study using data for 449 OP poisoning patients admitted to Civil-Hospital Karachi from Aug’10 to Sep’16. Demographic data and vital signs, including body temperature, blood pressure, heart rate, respiratory rate, and partial-oxygen pressure, were retrieved from medical records. The trajectories of vital signs were formed using LCGA, and these trajectories were applied as independent variables to determine the risk of mortality using Cox-proportional hazards models. P-values of < 0.05 were considered statistically significant.

Results
Data for 449 patients, with a mean age of 25.4 years (range 13–85 years), were included. Overall mortality was 13.4%(n = 60). In trajectory analysis, a low-declining systolic blood pressure, high-declining heart rate trajectory, high-remitting respiratory rate trajectory and normal-remitting partial-oxygen pressure trajectory resulted in the greatest mortality, i.e. 38.9,40.0,50.0, and 60.0%, respectively, compared with other trajectories of the same parameters. Based on multivariable analysis, patients with low-declining systolic blood pressure were three times [HR:3.0,95%CI:1.2–7.1] more likely to die compared with those who had a normal-stable systolic blood pressure. Moreover, patients with a high-declining heart rate were three times [HR:3.0,95%CI:1.5–6.2] more likely to die compared with those who had a high-stable heart rate. Patients with a high-remitting respiratory rate were six times [HR:5.7,95%CI:1.3–23.8] more likely to die than those with a high-stable respiratory rate. Patients with normal-remitting partial oxygen pressure were five times [HR:4.7,95%CI:1.4–15.1] more likely to die compared with those who had a normal-stable partial-oxygen pressure.

Conclusion
The trajectories of systolic blood pressure, heart rate, respiratory rate and partial-oxygen pressure were significantly associated with an increased risk of mortality among OP poisoning patients.
Implementing social accountability for contraceptive services: lessons from Uganda
Authors: Boydell Victoria , Nulu Nanono , Hardee Karen , Gay Jill 
Published: October 2020

Abstract
Background
Growing evidence shows that social accountability contributes to improving health care services, with much promise for addressing women’s barriers in contraceptive care. Yet little is known about how social accountability works in the often-complex context of sexual and reproductive health, particularly as sex and reproduction can be sensitive topics in the open and public formats typical of social accountability. This paper explores how social accountability operates in the highly gendered and complex context of contraceptive care.

Methods
This exploratory research uses a case study approach to provide a more grounded understanding of how social accountability processes operate in the context of contraceptive information and services. We observed two social accountability projects that predominantly focused on contraceptive care in Uganda over a year. Five instruments were used to capture information from different source materials and multiple respondents. In total, one hundred and twenty-eight interviews were conducted and over 1000 pages of project documents were collected. Data were analyzed and compiled into four case studies that provide a thick description of how these two projects operated.

Results
The case studies show the critical role of information, dialogue and negotiation in social accountability in the context of contraceptive care. Improved community and health system relationships, community empowerment, provider and health system responsiveness and enhanced availability and access to services were reported in both projects. There were also changes in how different actors related to themselves and to each other, and contraceptive care, a previously taboo topic, became a legitimate area for public dialogue.

Conclusion
The study found that while social accountability in the context of contraceptive services is indeed sensitive, it can be a powerful tool to dissolving resistance to family planning and facilitating a more productive discourse on the topic.