Miracle-dz/UniFAR-FTUs huggingface dataset:
Machine-Learnt Fragment-Based Energies for Crystal Structure Prediction

Crystal structure prediction involves a search of a complex configurational space for local minima corresponding to stable crystal structures, which can be performed efficiently using atom-atom force fields for the assessment of intermolecular interactions. However, for challenging systems, the limitations in the accuracy of force fields prevents a reliable assessment of the relative thermodynamic stability of potential structures. Here we present a method to rapidly improve force field lattice energies by correcting two-body interactions with a higher level of theory in a fragment-based approach, and predicting these corrections with machine learning. We find corrected lattice energies with commonly used density functionals and second order perturbation theory (MP2) all significantly improve the ranking of experimentally known polymorphs where the rigid molecule model is applicable. The relative lattice energies of known polymorphs are also found to systematically improve towards experimentally determined values and more comprehensive energy models when using MP2 corrections, despite remaining at the force field geometry. Predicting two-body interactions with atom-centered symmetry functions in a Gaussian process is found to give highly accurate results with as little as 10-20% of the training data, reducing the cost of the energy correction by up to an order of magnitude. The machine learning approach opens up the possibility of using fragment-based methods to a greater degree in crystal structure prediction, providing alternative energy models where standard approaches are insufficient.
Multi-Method Study of Electronic Health Records Workflows

EHRs transform work practices in ways that enhance or impede the quality of care. There is a need for in-depth analysis of EHR workflows, particularly in complex clinical environments. We investigated EHR-basedpre-operative workflows by combining findings from 18 interviews, 7 days of observations, and process mining of EHR interactions from 31 personnel caring for 375 patients at one tertiary referral center. We provided high-definition descriptions of workflows and personnel roles. One third (32.2%) of the time with each patient was spent interacting with the EHR and 4.2% using paper-based artifacts. We also mined personnel social networks validating observed personnel's EHR-interactions. When comparing workflows between two similar pre-operative settings at different hospitals, we found significant differences in physical organization, patient workflow, roles, use of EHR, social networks and time efficiency. This study informs Mayo Clinic's enterprise-wide conversion to a single EHR and will guide before and after workflow comparisons.
Ethnic Variations in Systemic Sclerosis Disease Manifestations, Internal Organ Involvement, and Mortality

Objective. A multiethnic systemic sclerosis (SSc) cohort study to evaluate ethnic variations in disease manifestations, internal organ involvement, and survival. Methods. Adults who fulfilled the American College of Rheumatology/European League Against Rheumatism classification criteria for SSc between 1970 and 2017 were included. Self-reported ethnicity was categorized as European-descent white, Afro-Caribbean, Hispanic, Arab, East Asian, South Asian, First Nations, or Persian. The primary outcome was the time from diagnosis to death from all causes. Survival probabilities and median survival times were determined using Kaplan-Meier survival curves. Results. There were 1005 subjects evaluated, the majority of whom were European-descent white (n = 745, 74%), Afro-Caribbean (n = 58, 6%), South Asian (n = 70, 7%), and East Asian (n = 80, 8%). Compared to European-descent white subjects, East Asians less frequently had calcinosis (29% vs 9%, p = 0.002) and esophageal dysmotility (88% vs 69%, p = 0.002); Afro-Caribbeans more frequently had interstitial lung disease (31% vs 53%, p = 0.007); and First Nations subjects more frequently had diffuse cutaneous disease (35% vs 56%, p = 0.02) and diabetes (5% vs 33%, p = 0.03). We found no difference in the short-term survival across ethnicities. Hispanic subjects have better longterm survival (81.3%, 95% CI 63–100) compared to European-descent white subjects (55%, 95% CI 51–60). East Asians appear to have the longest median survival time (43.3 yrs) and Arabs the shortest median survival time (15 yrs). There was no significant difference in median survival times between Afro-Caribbean and European-descent white subjects (22.2 vs 22.6 yrs). Conclusion. Ethnic variations in some SSc disease manifestations are observed. However, this does not result in significant differences in short-term survival but may affect longterm survival.
Selective Decrosslinking in Liquid Crystal Polymer Actuators for Optical Reconfiguration of Origami and Light-Fueled Locomotion.

The ability to optically reconfigure an existing actuator of a liquid crystal polymer network (LCN) so that it can display a new actuation behavior or function is highly desired in developing materials for soft robotics applications. Demonstrated here is a powerful approach relying on selective polymer chain decrosslinking in a LCN actuator with uniaxial LC alignment. Using an anthracene-containing LCN, spatially controlled optical decrosslinking can be realized through photocleavage of anthracene dimers under 254 nm UV light, which alters the distribution of actuation (crosslinked) and non-actuation (decrosslinked) domains and thus determines the actuation behavior upon order-disorder phase transitions. Based on this mechanism, a single actuator having a flat shape can be reconfigured in an on-demand manner to exhibit reversible shape transformation such as self-folding into origami three-dimensional structures. Moreover, using a dye-doped LCN actuator, a light-fueled microwalker can be optically reconfigured to adopt different locomotion behaviors, changing from moving in the laser scanning direction to moving in the opposite direction.
Role of Type I Interferons on Filovirus Pathogenesis

Filoviruses, such as Ebola and Marburg virus, encode viral proteins with the ability to counteract the type I interferon (IFN-I) response. These IFN-I antagonist proteins are crucial to ensure virus replication, prevent an antiviral state in infected and bystander cells, and impair the ability of antigen-presenting cells to initiate adaptive immune responses. However, in recent years, a number of studies have underscored the conflicting data between in vitro studies and in vivo data obtained in animal models and clinical studies during outbreaks. This review aims to summarize these data and to discuss the relative contributions of IFN-α and IFN-β to filovirus pathogenesis in animal models and humans. Finally, we evaluate the putative utilization of IFN-I in post-exposure therapy and its implications as a biomarker of vaccine efficacy.
Secondary impact of a behavioral intervention on dietary quality in preschoolers with obesity

ABSTRACT Dietary habits and obesity are established in early childhood. This secondary data analysis examined changes in dietary quality among treatment-seeking preschoolers with obesity(n=13). 24-hour dietary recall data collected at baseline, post-treatment(6 months), and 6-months post-treatment follow-up(12 months) were analyzed using the Healthy Eating Index(HEI)-2010. Repeated-measures analyses of variance revealed significant improvements in overall dietary quality and reductions in empty calories from baseline to 12 months. Change in overall dietary quality was not associated with change in BMI z-score at either time point. Identifying effective strategies to increase nutrient-dense food groups(e.g., vegetables) is important for maximizing the health impact of preschool obesity interventions.
Multivariate permutation tests for two sample testing in presence of nondetects with application to microarray data

Very often, data collected in medical research are characterized by censored observations and/or data with mass on the value zero. This happens for example when some measurements fall below the detection limits of the specific instrument used. This type of left censored observations is called “nondetects”. Such a situation of an excessive number of zeros in a data set is also referred to as zero-inflated data. In the present work, we aim at comparing different multivariate permutation procedures in two-sample testing for data with nondetects. The effect of censoring is investigated with regard to the different values that may be attributed to nondetected values, both under the null hypothesis and under alternative. We motivate the problem using data from allergy research.
Urine Angiotensin II Signature Proteins as Markers of Fibrosis in Kidney Transplant Recipients.

BACKGROUND Interstitial fibrosis/tubular atrophy (IFTA) is an important cause of kidney allograft loss; however, noninvasive markers to identify IFTA or guide anti-fibrotic therapy are lacking. Using angiotensin-II (AngII) as the prototypical inducer of IFTA, we previously identified 83 AngII-regulated proteins in vitro. We developed mass spectrometry-based assays for quantification of 6 AngII signature proteins (BST1, GLNA, LAMB2, LYPLA1, RHOB and TSP1) and hypothesized that their urine excretion will correlate with IFTA in kidney transplant patients. METHODS Urine excretion of 6 AngII regulated proteins was quantified using selected reaction monitoring (SRM) and normalized by urine creatinine. Immunohistochemistry was used to assess protein expression of TSP1 and GLNA in kidney biopsies. RESULTS The urine excretion rates of AngII-regulated proteins were found to be increased in 15 kidney transplant recipients with IFTA compared to 20 matched controls with no IFTA (mean log2[fmol/µmol of creatinine], BST1: 3.8 vs 3.0, p = 0.03; GLNA: 1.2 vs -0.4, p = 0.03; LAMB2: 6.1 vs 5.4, p = 0.06; LYPLA1: 2.1 vs 0.6, p = 0.002; RHOB: 1.2 vs -0.1, p = 0.006; TSP1_GGV: 2.5 vs 1.9; p = 0.15; TSP1_TIV: 2.0 vs. 0.6; p = 0.0006). ROC curve analysis demonstrated an AUC=0.86 for the ability of urine AngII signature proteins to discriminate IFTA from controls. Urine excretion of AngII signature proteins correlated strongly with chronic interstitial fibrosis/tubular atrophy and total inflammation. In a separate cohort of 19 kidney transplant recipients, the urine excretion of these 6 proteins was significantly lower following therapy with AngII inhibitors (p < 0.05). CONCLUSIONS AngII-regulated proteins may represent markers of IFTA and may guide anti-fibrotic therapies.This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal.
Association of Thyrotropin Concentration with Chronic Kidney Disease in a Japanese General Population Cohort

Background: Previous studies have indicated an association between hypothyroidism and kidney dysfunction; however, few studies have investigated whether thyroid dysfunction is a risk factor for chronic kidney disease (CKD) development. And their result is not consistent. Objectives: We evaluated the association of thyroid dysfunction with CKD prevalence and development by a multivariate logistic regression analysis. Method: In cross-sectional and longitudinal studies, 16,390 subjects and 7,609 subjects, respectively, who underwent annual health check-ups were analyzed. We categorized the subjects into the following 4 groups based on their serum thyrotropin (TSH) concentrations: below-normal (TSH < 0.54 mU/L), lower-normal (0.54–2.40 mU/L), higher-normal (2.41–4.26 mU/L) and above-normal (> 4.26 mU/L). Subjects with eGFR <60 mL/min/1.73 m2 were determined to have CKD. Results: The cross-sectional study revealed a positive correlation between TSH concentration and CKD prevalence. Compared with the lower-normal TSH group, the ORs and 95% CIs of CKD prevalence were 0.61 (0.45–0.82, p = 0.001) for the below-normal group, 1.49 (1.33–1.67, p < 0.001) for the higher-normal group, and 1.90 (1.57–2.30, p < 0.001) for the above-normal group. The longitudinal study revealed that the risk of CKD development within 3 years was significantly higher in the above-normal TSH group than in the lower-normal TSH group (OR 1.58, 95% CI 1.02–2.45, p = 0.04). Conclusions: Our data indicate that higher TSH concentrations are positively correlated with CKD prevalence and that a high TSH concentration is a risk factor for CKD development.
Measuring Antimicrobial Efficacy against Biofilms: a Meta-analysis

Through a statistical meta-analysis of published data on antimicrobial efficacy against biofilms formed by two common bacterial species, it was concluded that the particular experimental method used is the most important factor determining the outcome of the test. An expected dose-response relationship (greater killing with higher doses or longer treatment times) was observed for data sets derived from a single method but was not observed when data from multiple studies using diverse methods were pooled. ABSTRACT Through a statistical meta-analysis of published data on antimicrobial efficacy against biofilms formed by two common bacterial species, it was concluded that the particular experimental method used is the most important factor determining the outcome of the test. An expected dose-response relationship (greater killing with higher doses or longer treatment times) was observed for data sets derived from a single method but was not observed when data from multiple studies using diverse methods were pooled. Method-specific properties such as the surface area/volume ratio, areal biofilm cell density, and microbial species were shown to influence quantitative measurements of biofilm killing. A better appreciation of the method characteristics that affect antibiofilm efficacy tests could aid decision-making related to investment in research and development and regulatory approvals for biofilm control strategies. The following recommendations are offered to those working in research and development related to biofilm control: (i) report the log reduction, surface area/volume ratio, and biofilm areal cell density; (ii) include data for a benchmark agent, making sure that this agent performs competitively at the dose tested; (iii) measure the dose-response relationship, i.e., make measurements at multiple treatment concentrations or dose durations; and (iv) use a standardized method in addition to research methods.
A clinical and genetic study of early‐onset and familial parkinsonism in taiwan: An integrated approach combining gene dosage analysis and next‐generation sequencing

Recent genetic progress has allowed for the molecular diagnosis of Parkinson's disease. However, genetic causes of PD vary widely in different ethnicities. Mutational frequencies and clinical phenotypes of genes associated with PD in Asian populations are largely unknown. The objective of this study was to identify the mutational frequencies and clinical spectrums of multiple PD‐causative genes in a Taiwanese PD cohort.
Sexual dimorphism on aortic remodelling in rats offspring from diabetic mothers and the role of flaxseed oil in this effect

Abstract Diabetes during pregnancy is associated with aortic remodelling in the fetus, stimulating the development of cardiovascular diseases in adult life. However, studies suggest that the use of foods high in omega-3 fatty acid, such as flaxseed oil, may reverse this effect of metabolic programming. This study aimed at investigating whether the effects of diabetes in mothers are passed on to their offspring in a gender-specific manner and whether the flaxseed oil used during pregnancy and lactation reverses or not the possible negative effects of this programming. Diabetic female rats (n = 18) were mated and allocated into three groups (n = 6): high-fat group (HG); flaxseed oil group (FOG) and control group (CG) (nondiabetic rats) during pregnancy and lactation. On the 21st day, male and female pups were weaned on a standard diet until 180 days. Aorta histomorphometry was analysed. Intima-media layer thickness was larger in FOG than CG in male (+15%) and than HG in female (+13.7%). Male FOG (+11.5%) showed higher amount of elastic fibre than CG. Maternal intake of flaxseed oil during pregnancy and lactation of diabetic mothers program the offspring to increase aorta intima-media layer thickness in adulthood and preserves aorta elastic fibres deposition in male offspring.
Genome‐wide DNA methylation investigation of glucocorticoid exposure within buccal samples

Glucocorticoids play a major role in regulating the stress response, and an imbalance of glucocorticoids has been implicated in stress‐related disorders. Within mouse models, CpGs across the genome have been shown to be differentially methylated in response to glucocorticoid treatment, and using the Infinium 27K array, it was shown that humans given synthetic glucocorticoids had DNA methylation (DNAm) changes in blood. However, further investigation of the extent to which glucocorticoids affect DNAm across a larger proportion of the genome is needed.
MR-DWI–Positive Lesions and Symptomatic Ischemic Complications After Coiling of Unruptured Intracranial Aneurysms

Background and Purpose— The aims of this study are to evaluate the risk factors for symptomatic ischemic complication (symptomatic ischemic complication [SIC], transient ischemic attack, or stroke) and microembolisms detected as MR diffusion-weighted imaging (MR-DWI)–positive (DWI(+)) lesions, and the relationship between DWI(+) and SIC after coiling of unruptured intracranial aneurysm. Methods— Between March 2009 and November 2011, 382 unruptured intracranial aneurysms in 343 patients underwent both coiling and posttreatment MR-DWI. The incidence of and risk factors for SIC and DWI(+), and the relationship between DWI(+) and SIC were retrospectively analyzed. Results— The incidence of SIC was 4.1%. The incidence of DWI(+) was 54.5%. The number of DWI(+) lesions was significantly larger in the SIC group, than in the asymptomatic one (12.1±10.4 versus 5.0±8.7, P<0.00). The cutoff value of DWI(+) for predicting SIC was ≥6 (sensitivity 85.7%, specificity 70.7%). The patients with DWI(+) ≥6 was 28.6%. Of the patients with SIC, the patients with DWI(+) ≥6 was 78.6%. Patients aged≥65 years had a trend for SIC, and it was the only independent risk factor for DWI(+) ≥cutoff (n=6; 95%CI, 1.167–3.083). Conclusions— The number of DWI(+) lesions was significantly larger in the SIC group than in the asymptomatic one after coiling of unruptured intracranial aneurysm. Patients aged≥65 had a trend for SIC, and it was the only independent risk factor for the number of DWI(+) ≥cutoff value (n=6) for predicting SIC.
The influence of operator and wheelchair factors on wheelchair propulsion effort

Abstract Purpose: The goal of this study was to evaluate the relative influence of operator and wheelchair factors on propulsion effort during over-ground wheelchair manoeuvres. Method: This observational study included 23 full-time manual wheelchair users and 13 able-bodied subjects. The operator factors included shoulder position, aerobic capacity and propulsion strength. The wheelchair factors included system mass, weight distribution, and frictional loss in straight and turning trajectories. The performance of over-ground manoeuvres was defined as the propulsion effort measured by VO2 as operators propelled along a modified figure-8 course on tile and carpet surfaces. Results: According to our regression model, shoulder position was the only significant contributor within operator factors, whereas weight distribution was the only significant contributor within wheelchair factors in influencing propulsion efforts. When combining operator and mechanical factors in the regression model, weight distribution became the only significant contributor to influence propulsion effort. Conclusion: Weight distribution and shoulder position had a significant influence on propulsion effort. These variables are related to the operator’s relationship to the drive wheels. However, system mass and muscle strength had the least influence on wheelchair manoeuvres. Our finding can help clinicians to improve wheelchair configurations and manufacturers to improve wheelchair design by understanding the importance of shoulder position and weight distribution. Implication for rehabilitation Studying wheelchair manoeuvers by considering both wheelchair and operator factors might provide a unique insight to address the complex interactions among wheelchair designs and users. Propulsion effort decreases as percentage weight is increased on the drive wheels and the shoulder becomes more aligned with the axle position, which highlights the need to optimize wheelchair axle position. Wheelchair configuration, as represented by weight distribution, had a more significant influence on everyday manoeuvre than wheelchair mass does. It is essential for wheelchair users to choose a wheelchair that can match their daily needs and anthropometric measurements for saving propulsion efforts.
Clinical and biological characteristics of adult biphenotypic acute leukemia in comparison with that of acute myeloid leukemia and acute lymphoblastic leukemia: a case series of a Chinese population

Biphenotypic acute leukemia is rare, necessitating large series to provide information on prognosis. In this paper Xu and colleagues review Chinese experience with this conditions. The findings of this study indicate that the prognosis of biphenotypic acute leukemia patients is poor when compared with de novo acute myeloid leukemia or acute lymphoblastic leukemia. See related perspective article on page 891 and related review article on page 984. Background Biphenotypic acute leukemia is a rare disorder that is difficult to diagnose. It displays features of both myeloid and lymphoid lineage. There is still a lack of studies in biphenotypic acute leukemia in a Chinese population. We present here a comprehensive investigation of the clinical and biological characteristics, and outcome of biphenotypic acute leukemia in our hospital in over a seven year period. Design and Methods We retrospectively analyzed 452 adult acute leukemia patients diagnosed according to French-American-British (FAB) classification and biphenotypic acute leukemia diagnosed according to European Group for the Immunological Characterization of Leukemias (EGIL) classification, respectively. Biological characteristics, response to treatment, and outcome were examined in biphenotypic acute leukemia patients and compared with that in acute myeloid leukemia and acute lymphoblastic leukemia patients with complete follow-up profiles diagnosed in the same period. Results Of 452 acute leukemia patients, 21 cases (4.6%) were diagnosed as biphenotypic acute leukemia. Among them, 14 (66.7%) were B lymphoid and myeloid, 5 (23.8%) were T lymphoid and myeloid, one (4.8%) was T/B lymphoid and one (4.8%) was trilineage differentiation. When compared with acute myeloid leukemia and acute lymphoblastic leukemia, patients with biphenotypic acute leukemia showed significantly higher incidence of CD34 antigen expression, unfavorable karyotypes, and extramedullary infiltration (p<0.05). In this cohort of patients with biphenotypic acute leukemia, t(9;22) was the most common abnormality in chromosome structure. The median disease-free survival and overall survival in biphenotypic acute leukemia patients was five months and ten months, respectively, significantly shorter than those in acute myeloid leukemia and acute lymphoblastic leukemia patients (p<0.05). Conclusions The prognosis of biphenotypic acute leukemia patients is poor when compared with de novo acute myeloid leukemia or acute lymphoblastic leukemia. Biphenotypic acute leukemia patients showed a much higher incidence of CD34 antigen expression, complex abnormal karyotype, extramedullary infiltration, relapse, and resistance to therapy after relapse.