bluuebunny/crossref_metadata_2025_split huggingface dataset:
LogicNet: probabilistic continuous logics in reconstructing gene regulatory networks
Authors: Malekpour Seyed Amir , Alizad-Rahvar Amir Reza , Sadeghi Mehdi 
Published: July 2020

Abstract
Background
Gene Regulatory Networks (GRNs) have been previously studied by using Boolean/multi-state logics. While the gene expression values are usually scaled into the range [0, 1], these GRN inference methods apply a threshold to discretize the data, resulting in missing information. Most of studies apply fuzzy logics to infer the logical gene-gene interactions from continuous data. However, all these approaches require an a priori known network structure.

Results
Here, by introducing a new probabilistic logic for continuous data, we propose a novel logic-based approach (called the LogicNet) for the simultaneous reconstruction of the GRN structure and identification of the logics among the regulatory genes, from the continuous gene expression data. In contrast to the previous approaches, the LogicNet does not require an a priori known network structure to infer the logics. The proposed probabilistic logic is superior to the existing fuzzy logics and is more relevant to the biological contexts than the fuzzy logics. The performance of the LogicNet is superior to that of several Mutual Information-based and regression-based tools for reconstructing GRNs.

Conclusions
The LogicNet reconstructs GRNs and logic functions without requiring prior knowledge of the network structure. Moreover, in another application, the LogicNet can be applied for logic function detection from the known regulatory genes-target interactions. We also conclude that computational modeling of the logical interactions among the regulatory genes significantly improves the GRN reconstruction accuracy.
High prevalence of t895 and t9364 spa types of methicillin-resistant Staphylococcus aureus in a tertiary-care hospital in Mexico: different lineages of clonal complex 5
Authors: Negrete-González C. , Turrubiartes-Martínez E. , Galicia-Cruz O. G. , Noyola D. E. , Martínez-Aguilar G. , Pérez-González L. F. , González-Amaro R. , Niño-Moreno P. 
Published: July 2020

Abstract
Background
Staphylococcus aureus is a leading cause of broad-spectrum infections both in the community and within healthcare settings. Methicillin-resistant Staphylococcus aureus (MRSA) has become a global public health issue. The aim of this study was to examine the clinical and molecular characteristics of Staphylococcus aureus isolates and to define the population structure and distribution of major MRSA clones isolated in a tertiary-care hospital in Mexico.

Results
From April 2017 to April 2018, 191 Staphylococcus aureus isolates were collected. The frequency of MRSA was 26.7%; these strains exhibited resistance to clindamycin (84.3%), erythromycin (86.2%), levofloxacin (80.3%), and ciprofloxacin (86.3%). The majority of MRSA strains harbored the SCCmec type II (76.4%) and t895 (56.8%) and t9364 (11.7%) were the most common spa types in both hospital-associated MRSA and community-associated MRSA isolates. ST5-MRSA-II-t895 (New York /Japan clone) and ST1011-MRSA-II-t9364 (New York /Japan-Mexican Variant clone) were the most frequently identified clones. Furthermore, different lineages of Clonal Complexes 5 (85.4%) and 8 (8.3%) were predominantly identified in this study.

Conclusion
Our study provides valuable information about the epidemiology of MRSA in a city of the central region of Mexico, and this is the first report on the association between t895 and t9364 spa types and ST5 and ST1011 lineages, respectively. These findings support the importance of permanent surveillance of MRSA aimed to detect the evolutionary changes of the endemic clones and the emergence of new strains.
Redox control in the pathophysiology of influenza virus infection
Authors: Chen Ker-Kong , Minakuchi Moeko , Wuputra Kenly , Ku Chia-Chen , Pan Jia-Bin , Kuo Kung-Kai , Lin Ying-Chu , Saito Shigeo , Lin Chang-Shen , Yokoyama Kazunari K. 
Published: July 2020

AbstractTriggered in response to external and internal ligands in cells and animals, redox homeostasis is transmitted via signal molecules involved in defense redox mechanisms through networks of cell proliferation, differentiation, intracellular detoxification, bacterial infection, and immune reactions. Cellular oxidation is not necessarily harmful per se, but its effects depend on the balance between the peroxidation and antioxidation cascades, which can vary according to the stimulus and serve to maintain oxygen homeostasis. The reactive oxygen species (ROS) that are generated during influenza virus (IV) infection have critical effects on both the virus and host cells. In this review, we outline the link between viral infection and redox control using IV infection as an example. We discuss the current state of knowledge on the molecular relationship between cellular oxidation mediated by ROS accumulation and the diversity of IV infection. We also summarize the potential anti-IV agents available currently that act by targeting redox biology/pathophysiology.
A middle-aged male patient with de Winter syndrome: a case report
Authors: Lu Bo , Fu Deyu , Zhou Xunjie , Gui Mingtai , Yao Lei , Li Jianhua 
Published: July 2020

Abstract
Background
De Winter syndrome accounts for approximately 2% of all patients with acute anterior myocardial infarction admitted to the emergency department, and is characterized by severe stenosis of the left anterior descending coronary artery (LAD). The ECG changes are not recognized by ECG software, and poor understanding of the syndrome among physicians may lead to misdiagnosis, delayed reperfusion, and mortality.

Case presentation
A 51-year-old male patient presented with a newly developed ECG pattern suggestive of de Winter Syndrome. Coronary angiography revealed anterior myocardial infarction. Based on the ECG and clinical manifestations, the patient was diagnosed with de Winter syndrome and underwent timely percutaneous coronary intervention to revascularize the left anterior descending artery (LAD). The patient showed good outcomes and no complications at 4 months after the operation.

Conclusions
This case highlights the importance of being aware of the possibility of de Winter syndrome in patients with symptoms of myocardial infarction but atypical ECG in order to conduct early revascularization and treatments.
Quick and effective improvement of leucine enriched dietary supplement on malnutrition in acute stroke patients receiving enteral tube feeding
Authors: Mori Takahisa , Yoshioka Kazuhiro 
Published: July 2020

Abstract
Background
Malnutrition often occurs in acute stroke patients receiving enteral tube feeding (ETF). Unless malnutrition is improved, their clinical outcome is poor. However, strategies to improve malnutrition in these patients have not been established. Branched-chain amino acids (BCAA) may enhance protein synthesis and attenuate inflammation. Our study aimed to investigate whether a leucine enriched BCAA dietary supplement (LEBDs) could quickly increase serum levels of albumin (Alb) or transthyretin (TTR) and decrease high-sensitivity C-reactive protein (CRP) in the development of severe malnutrition within a few days after stroke onset compared to standard BCAA dietary supplement (SBDs).

Methods
We retrospectively included acute stroke patients who: 1) were admitted between August 2016 and July 2017; 2) underwent ETF for 7 days or longer after admission, and 3) underwent blood examination of Alb, TTR, and CRP on admission, the fifth day and the seventh day. We defined severe malnutrition as severe hypoproteinemia: decrease of TTR to less than 15 mg/dl on the 5th day. In LEBDs and SBDs groups, patients started to receive a dietary supplement containing leucine of 1.44 and 0. 72 g twice a day on the fifth day, respectively. We evaluated Alb (g/dl), TTR (mg/dl), and CRP (mg/dl) on admission, the fifth day, and the seventh day.

Results
Twenty-nine patients met our inclusion criteria:15 in LEBDs and 14 in SBDs. In LEBDs and SBDs groups, the median Alb was 3.5 and 3.3 g/dl, TTR was 12.7 and 10.7 mg/dl, and CRP was 1.02 and 0.673 mg/dl on admission, respectively. In LEBDs, the median Alb and TTR decreased to 2.6 g/dl and 11.9 mg/dl, and CRP increased to 5.337 mg/dl on the fifth day. On the 7th day, TTR increased, and CRP decreased, although Alb did not improve. In SBDs, the median Alb and TTR decreased to 2.6 g/dl and 9.7 mg/dl, and CRP increased to 4.077 mg/dl on the fifth day. On the 7th day, Alb, TTR, and CRP did not improve.

Conclusion
In acute stroke patients receiving leucine enriched BCAA dietary supplement, quick improvements in transthyretin and CRP were observed.
Comparison of hierarchical EMAX and NDLM models in dose-response for early phase clinical trials
Authors: Huang Xiaqing , Gajewski Byron J. 
Published: July 2020

Abstract
Background
Phase II clinical trials primarily aim to find the optimal dose and investigate the relationship between dose and efficacy relative to standard of care (control). Therefore, before moving forward to a phase III confirmatory trial, the most effective dose is needed to be identified.

Methods
The primary endpoint of a phase II trial is typically a binary endpoint of success or failure. The EMAX model, ubiquitous in pharmacology research, was fit for many compounds and described the data well, except for a single compound, which had nonmonotone dose–response (Thomas et al., Stat Biopharmaceutical Res. 6:302-317 2014). To mitigate the risk of nonmonotone dose response one of the alternative options is a Bayesian hierarchical EMAX model (Gajewski et al., Stat Med. 38:3123-3138 2019). The hierarchical EMAX adapts to its environment.

Results
When the dose-response curve is monotonic it enjoys the efficiency of EMAX. When the dose-response curve is non-monotonic the additional random effect hyperprior makes the hierarchical EMAX model more adjustable and flexible. However, the normal dynamic linear model (NDLM) is a useful model to explore dose-response relationships in that the efficacy at the current dose depends on the efficacy of the previous dose(s). Previous research has compared the EMAX to the hierarchical EMAX (Gajewski et al., Stat Med. 38:3123-3138 2019) and the EMAX to the NDLM (Liu et al., BMC Med Res Method 17:149 2017), however, the hierarchical EMAX has not been directly compared to the NDLM.

Conclusions
The focus of this paper is to compare these models and discuss the relative merit for each of their uses for an ongoing early phase dose selection study.
A grading system from health to death using routine experimental indicators based on the pre-chronic disease status theory
Authors: Guang Yang , Yuzhong Li , Hui Liu 
Published: July 2020

Abstract
Background
To establish a system for assessing pre-chronic disease status (PCDS) whereby changes in biomolecule levels occur before the appearance of physical damage to body organs. We based our study on the common biomarkers of aging, disease and end-of-life processes.

Methods
The red blood cell count as well as levels of albumin, creatinine and aspartate aminotransferase were used as indicators for measurement. The basic premise for determining PCDS was that the measured value was outside the reference range for a healthy individual. A binary outcome was determined according to reference range given by the laboratory undertaking the measurements. The Biological Age Index (BAI) was used to ascertain PCDS.

Results
The four indictors that we chose were sensitive for end-of-life and aging. The BAI score for each age group increased significantly with increasing age. The BAI score of patients with cardiac disease, cerebrovascular disease, cancer or chronic obstructive pulmonary disease were mostly higher than those in healthy age-matched people.

Conclusion
A system for assessing PCDS centered on biomolecular detection and independent of the pathologic diagnosis could be effective.
Whole exome sequencing identified mutations causing hearing loss in five consanguineous Pakistani families
Authors: Zhou Yingjie , Tariq Muhammad , He Sijie , Abdullah Uzma , Zhang Jianguo , Baig Shahid Mahmood 
Published: July 2020

Abstract
Background
Hearing loss is the most common sensory defect, and it affects over 6% of the population worldwide. Approximately 50–60% of hearing loss patients are attributed to genetic causes. Currently, more than 100 genes have been reported to cause non-syndromic hearing loss. It is possible and efficient to screen all potential disease-causing genes for hereditary hearing loss by whole exome sequencing (WES).

Methods
We collected 5 consanguineous pedigrees from Pakistan with hearing loss and applied WES in selected patients for each pedigree, followed by bioinformatics analysis and Sanger validation to identify the causal genes.

Results
Variants in 7 genes were identified and validated in these pedigrees. We identified single candidate variant for 3 pedigrees: GIPC3 (c.937 T > C), LOXHD1 (c.6136G > A) and TMPRSS3 (c.941 T > C). The remaining 2 pedigrees each contained two candidate variants: TECTA (c.4045G > A) and MYO15A (c.3310G > T and c.9913G > C) for one pedigree and DFNB59 (c.494G > A) and TRIOBP (c.1952C > T) for the other pedigree. The candidate variants were validated in all available samples by Sanger sequencing.

Conclusion
The candidate variants in hearing-loss genes were validated to be co-segregated in the pedigrees, and they may indicate the aetiologies of hearing loss in such patients. We also suggest that WES may be a suitable strategy for hearing-loss gene screening in clinical detection.
Renal histology in diabetic nephropathy predicts progression to end-stage kidney disease but not the rate of renal function decline
Authors: Misra Paraish S. , Szeto Stephen G. , Krizova Adriana , Gilbert Richard E. , Yuen Darren A. 
Published: July 2020

Abstract
Background
While histopathologic changes correlate with functional impairment in cross-sectional studies of diabetic nephropathy (DN), whether these findings predict future rate of kidney function loss remains uncertain. We thus sought to examine the relationship between kidney histopathology, incidence of end-stage kidney disease (ESKD), and rate of estimated glomerular filtration rate (eGFR) loss in DN.

Methods
In this longitudinal cohort study, we studied 50 adults diagnosed with biopsy-proven DN. We analyzed the histopathologic parameters of each patient’s kidney biopsy, as defined by the Renal Pathology Society classification system for DN, and tracked all available eGFR measurements post-biopsy. We additionally collected baseline clinical parameters (at the time of biopsy), including eGFR, albumin-to-creatinine ratio (ACR), and hemoglobin A1c. Multivariable linear regression was used to assess the relationship between histologic and clinical parameters at the time of the biopsy and eGFR slope. Kaplan-Meier curves and Cox regression were used to evaluate the association between histologic and clinical parameters and ESKD incidence.

Results
Progression to ESKD was associated with worsening interstitial fibrosis score (p = 0.05), lower baseline eGFR (p = 0.02), higher ACR (p = 0.001), and faster eGFR decline (p < 0.001). The rate of eGFR decline did not associate with any histologic parameter. Baseline ACR was the only studied variable correlating with eGFR slope (rho = − 0.41).

Conclusions
Renal histology predicts ultimate progression to ESKD, but not the rate of progression. Future work is required to identify novel predictors of rapid functional decline in patients with diabetic nephropathy.
Clinical effect and safety of continuous renal replacement therapy in the treatment of neonatal sepsis-related acute kidney injury
Authors: Cai Cheng , Qiu Gang , Hong Wenchao , Shen Yunlin , Gong Xiaohui 
Published: July 2020

Abstract
Background
Sepsis is the leading cause of acute kidney injury (AKI) in the neonatal intensive care unit (NICU). The aim of the study is to explore the efficacy and security of continuous renal replacement therapy (CRRT) in the treatment of neonatal sepsis-related AKI.

Method
Totally12 sepsis-related AKI neonates treated with CRRT were hospitalized in the NICU of Shanghai Children’s Hospital between November 2012 and November 2019, and the clinical data of these 12 cases were retrospectively analyzed. Renal function, acid-base balance, electrolytes, blood pressure and hemodynamics indexes were recorded before CRRT initiation, 12/24/48 h after CRRT initiation and at the end of CRRT respectively. The efficacy of CRRT was evaluated and the clinical outcome was observed in these 12 sepsis-related AKI neonates. Repeated measurement analysis of variance was used for statistical analysis of the data.

Result
(1) Continuous veno-venous hemodialysis filtration (CVVHDF) was used in 12 cases of sepsis-related AKI neonates. There were 6 cases with oliguria, 3 cases with fluid overload (FO), 3 cases with septic shock. The duration of CRRT was 49 ~ 110 h, average (76.2 ± 23.5) h. (2) The blood pressure (BP) of 12 sepsis -related AKI neonates could reach the normal level (40–60 mmHg) 12 h after CRRT initiation, and the normal BP level could be maintained during the CRRT treatment. After 12 h CRRT, the blood pH value increased to the normal range (7.35 ~ 7.45). After 12 h CRRT treatment, the oxygenation index of 12sepsis-related AKI neonates could reach 200 mmHg. After 24 h CRRT treatment, it could rise to more than 300 mmHg. Serum potassium, serum urea nitrogen and serum creatinine levels decreased significantly 12 h after CRRT initiation, and reached the normal range 24 h after CRRT initiation. The urine volume significantly increased 24 h after CRRT initiation. (3) Venous catheterization was performed successfully in all sepsis-related AKI neonates. We observed 2 cases of thrombocytopenia, 1 case of obstruction and 1 case of hypotension in the course of CRRT. There were no complications such as hypothermia, hemorrhage, thrombosis and infection.11 neonates were cured and discharged. One neonate was treated with CRRT and passed through the oliguria stage of AKI, but died after the parents gave up the treatment.

Conclusions
It is safe and effective to treat neonatal sepsis-related AKI with CRRT, which should be an effective measure for the treatment of sepsis-related AKI neonates.
Local tirofiban infusion for remnant stenosis in large vessel occlusion: tirofiban ASSIST study
Authors: Kim Yong-Won , Sohn Sung-Il , Yoo Joonsang , Hong Jeong-Ho , Kim Chang-Hyun , Kang Dong-Hun , Kim Yong-Sun , Lee Seong-Joon , Hong Ji Man , Choi Jin Wook , Hwang Yang-Ha , Lee Jin Soo 
Published: July 2020

Abstract
Background
Compared with embolic occlusions, intracranial atherosclerotic stenosis (ICAS)-related large vessel occlusions (LVOs) often require rescue treatment following mechanical thrombectomy (MT). Herein, we hypothesized that local tirofiban infusion can be effective and safe for remnant stenosis in LVO during endovascular treatment and can improve clinical outcomes.

Methods
This observational multicenter registry study (January 2011 to February 2016) included patients with ICAS who underwent endovascular treatment for LVO within 24 h after stroke onset. An underlying fixed focal stenosis at the occlusion site observed on cerebral angiography during and after MT was retrospectively determined as a surrogate marker of ICAS. Procedural and clinical outcomes were compared between the tirofiban and non-tirofiban groups.

Results
Of 118 patients, 59 received local tirofiban infusion. Compared to the non-tirofiban group, patients were older (non-tirofiban group versus tirofiban group; median, 63 years vs. 71 years, p = 0.015) and the onset-to-puncture time was longer (median, 275 min vs. 395 min, p = 0.036) in the tirofiban group. The median percent of residual stenosis prior to rescue treatment tended to be higher in the tirofiban group (80 [71–86] vs. 83 [79–90], p = 0.056). Final reperfusion success (modified Treatment In Cerebral Ischemic 2b–3) was more frequent (42.4%vs. 86.4%, p = 0.016) and post-procedure parenchymal hematoma type 2 and/or thick subarachnoid hemorrhages were less frequent (15.3%vs. 5.1%, p = 0.068) in the tirofiban group. The frequency of favorable outcomes 3 months after endovascular treatment (modified Rankin Scale 0–2) was significantly higher in the tirofiban group (32.2% vs. 52.5%, p = 0.025), and tirofiban administration was an independent predictor of favorable outcomes (odds ratio, 2.991; 95% confidence interval, 1.011–8.848; p = 0.048).

Conclusions
Local tirofiban infusion can be a feasible adjuvant treatment option for patients with ICAS-LVO.
Experiences of an earthquake during pregnancy, antenatal mental health and infants’ birthweight in Bhaktapur District, Nepal, 2015: a population-based cohort study
Authors: Khatri Goma Kumari , Tran Thach Duc , Baral Sushil , Fisher Jane 
Published: July 2020

Abstract
Background
Infant birthweight is an important public health indicator that is a proxy of maternal and baby’s health. Earthquakes can cause acute distress, but can also contribute to chronic stress through long-term disruptions to social, economic and domestic circumstances. The aims of this study were to examine the direct effect of earthquake experiences on the birthweight of infants of women who experienced the 2015 Nepal Earthquakes during pregnancy and whether mental health mediated this relationship.

Methods
This is a prospective, population-based cohort study. Pregnant women in Bhaktapur District, Nepal who had experienced the 2015 earthquakes after conception were recruited. Baseline data were collected in structured individual interviews. Follow up was a short telephone interview two weeks after the baby’s birth. Infant birthweight recorded on the hospital-issued birth certificate. The direct effect of earthquake experiences on birthweight and the indirect effect via antenatal common mental disorders (CMDs) were tested using Sobel tests simultaneously.

Results
In total 497/498 women contributed baseline data and 469 (94.4%) women also provided the birth weight of their infants. In total 6% of infants had low birth weight (< 2.5 kg). The earthquake experiences did not have a significant direct effect on birthweight (p = 0.116). However, the effect of earthquake experiences had a significant indirect effect on infant birthweight via CMDs. When 15 covariates were controlled, women who had moderate to severe earthquake experiences had an increase of 1.58 scores of antenatal CMD symptoms that resulted in their babies being 20.50 g lighter than those who had low earthquake experiences (p = 0.026).

Conclusions
The findings from this study indicate that the relationship is mediated by the mental health of women during pregnancy. Data demonstrate that the mental health of women who are pregnant should be prioritised in post-disaster management not only because of the burden experienced by women but also because of the risk for the growth and development of their babies.