Miracle-dz/UniFAR-FTUs huggingface dataset:
A VERSATILE SUITE OF LABORATORY-NONSPECIFIC SOFTWARE FOR PROCESSING SEDIMENT GRAIN-SIZE DATA

We have designed and written four computer programs to facilitate analysis of sediment grain-size data. These programs: 1) describe distributions within the two classification schemes most commonly used by sedimentologists (SEDCLASS); 2) generate moment and inclusive graphics statistics and extrapolate particle distributions to the clay-colloidal boundary (GSSTAT); 3) plot the data on ternary diagrams (SEDPLOT); and 4) calculate settling velocities based on Stokes Law for gravitational procedures and derive angular velocities or total settling times for particles by centrifuge (CENTRISET). Ancillary files include spreadsheet templates that help users organize sample identifiers, incorporate corrections (e.g. for salt, organics, shell debris), and combine relative percents within the gravel, sand, and fine fractions into complete grain-size distributions. The programs run on Windows 98/2000/XP computers, provide interface windows to facilitate execution, and allow users to select options primarily with mouse- click events, or through interactive dialogue boxes. Detailed schematics of the functions and documentation are available within each program. Input files are expected in comma-delimited ASCII text; detailed error messaging warns the user of potential problems and provides diagnostics. All of the programs in this suite are laboratory nonspecific in that usage is not limited to particular analytical equipment or to any uncommon proprietary formats.
Therapeutic effects of nintedanib are not influenced by emphysema in the INPULSIS trials

Emphysema is a common comorbidity in patients with idiopathic pulmonary fibrosis (IPF) [1–4]. Due to the combination of restrictive and obstructive effects, patients with concomitant IPF and emphysema typically present with normal or elevated forced vital capacity (FVC) but reduced diffusing capacity [5]. Data from retrospective studies have demonstrated that lung function decline is attenuated in patients with IPF who have emphysema [6], with some evidence suggesting a threshold for extent of emphysema beyond which FVC decline is reduced [7]. In post hoc analyses of pooled data from the INPULSIS trials, the treatment effect of nintedanib versus placebo was not influenced by the presence of emphysema (yes versus no) or by FEV1/FVC ratio (≥0.7 to ≤0.8 versus >0.8) at baseline http://ow.ly/Gmwn30nwPY1
Aged garlic extract as an antioxidant in cardiovascular disease

The oxidative modification of LDL by ROS/RNS is recognised as playing an important role in the development and progression of atherosclerosis. Adequate intake of dietary antioxidants such as the antioxidant vitamins, carotenoids, and plant antioxidants such as the polyphenols are important in reducing the risk of development of diseases where the pathogenesis involves free radical-mediated damage to proteins, lipids, and micleic acids. Antioxidants act to prevent oxidative damage by multiple mechanisms. The non-antioxidant beneficial properties of garlic in preventing cardiovascular disease are well documented and include lowering of blood lipids, reducing platelet aggregation and subsequent thrombus formation, and reducing blood pressure. In this study the antioxidant properties of a commercial aged garlic extract (AGE, Kyolice) were investigated. AGE displayed the ability to scavenge superoxide in cell ftee assays, and reduced both 15-lipoxygenase-mediated lipid peroxidation and Cu2ý-mediated lipid peroxidation and protein oxidation of isolated human LDL. Two different mechanisms were identified that may be responsible for the observed reduction in Cuý'-mediated oxidation of LDL in the presence of AGE. The first mechanism is the chelation of Cu2+ and the second mechanism is the partial preservation of the endogenous LDL antioxidant P-carotene. Chromatographic and colourimetric analyses suggested that AGE is a rich source of phenolic compounds and that they may bind or become incorporated within the LDL particle and this may help to explain the efficacy of AGE in preventing LDL oxidation by preserving 0carotene rather than a-tocopherol levels. Smoking is a human syndrome of increased oxidative stress and an important risk factor for the development of atherosclerotic heart disease. Thus the antioxidant properties of AGE were also identified in vivo using non-smoking and smoking human volunteers. A reliable and sensitive novel marker of increased oxidative stress and lipid peroxidation in vivo (8-iso-PGF2(,, ) and the antioxidant capacity of plasma to scavenge superoxide were used to assess the antioxidant effects of AGE. Smokers had elevated plasma and urinary levels of 8-iso-PGF2(,, and a decreased antioxidant capacity of plasma to scavenge superoxide when compared to non-smokers. Dietary supplementation with AGE significantly decreased plasma and urinary 8-iso-PGF2,, levels in smokers and non-smokers and increased the antioxidant capacity of plasma to scavenge superoxide in smokers. These studies demonstrated that AGE is an efficient antioxidant plant extract in vitro and in vivo and may be beneficial in reducing oxidative damage to lipid and proteins and thus prevent or reduce the development and progression of free-radical-mediated diseases such as atherosclerosis.
Current approaches for detection of human T‐lymphotropic virus Type 1: A systematic review

Human T‐lymphotropic virus Type 1 (HTLV‐1) is a retrovirus that is endemic in some regions of the world. It is known to cause several diseases like adult T‐cell leukemia (ATL) and HTLV‐1‐associated myelopathy/tropical spastic paraparesis (HAM/TSP). Serology and molecular methods have been used to detect this virus. Of these, enzyme‐linked immunosorbent assay (ELISA) is used as a primary screening method and this is usually followed by western blotting (WB) and polymerase chain reaction (PCR) methods as confirmatory tests. We conducted a systematic review of the different techniques used in the diagnosis of HTLV‐1 infection.
[Correlation in radiological bone age determination using the Greulich and Pyle method versus automated evaluation using BoneXpert software].

OBJECTIVE To determine the degree of correlation in the radiological bone age assessment using the Greulich and Pyle method versus automated assessment through BoneXpert® software between 2013 and 2016. MATERIAL AND METHOD Correlation study of diagnostic techniques of 1500 carpal X-rays to assess bone age in patients under 16 years of age from Clínica Alemana de Santiago. X-rays with bone age assessment using the Atlas of Greulich and Pyle (GP) by 1 out of 7 pediatric radiologists, were analyzed using the BoneXpert (BE) software for automated bone age assessment. 100 cases were taken at random for analysis/re-analysis using the BoneXpert method to determine its accuracy. The level of correlation of the measurements was analyzed using the correlation coefficient (Pearson's r) and the variability of the measurements using the Bland-Altman analysis. RESULTS 1493 cases were assessed, seven were excluded due to failure in the X-ray technique, 922 females (61.8%), with a median chronological age of 9.96 years and 11.12 years for males (p 0.001). The correlation between manual bone age (GP) and automated bone age using BoneXpert method among radiologists ran ged from 0.91 to 0.93. The Bland-Altman analysis indicated an average difference between manual bone age and bone age using the BoneXpert method of 0.19 years (CI 0.13 to 0.25). In the analysis/ re-analysis of 100 random cases using the BoneXpert software, the correlation was 1.00 (100% accu racy). CONCLUSION The automated analysis using BoneXpert allows for standardized, low-variability, and high-concordance assessment.
Evidence for hidden order in a nonlinear model elastic system

Hidden order may arise in strongly correlated systems even if there is an apparent lack of long-range order as measured by local order parameters. This phenomenon has been essentially associated with topological order in quantum systems. Here, we demonstrate the emergence of hidden order in a 1D non-linear classical mechanical system that supports rotational degrees of freedom. The potential energy of the model system creates a bistable system for which hidden order emerges with the introduction of a biquadratic term. To our surprise, we discover that varying the strength of the biquadratic term leads to four distinct phases quantified by the behaviors of the Néel and string order parameters. Three of these phases are locally disordered. Hidden order is identified by a string order parameter that shows correlations with significantly longer range than the Néel order parameter. The hidden order correlation length diverges as the kinetic energy of the system is lowered with a critical exponent ~0.5. The observation of hidden order in a mechanical system reveals that instability and non-linearity may play critical roles in the generation of nonlocal long-range correlations in apparently locally disordered systems.
Factors that prolong the duration of recovery in acute rhinosinusitis with orbital complications

Abstract Background: Regarding prognostic factors of acute rhinosinusitis (ARS) with orbital complications, there are few studies including adult cases. Objectives: The present study aims to delineate prognostic factors of ARS with orbital complications. Material and methods: We conducted a retrospective analysis of medical records of 21 patients (6 pediatric and 15 adult patients) with ARS with orbital complications. The duration of recovery was defined as the time from initial diagnosis to complete resolution of local findings and all symptoms. Orbital complications due to postoperative cysts or mycosis were excluded. Results: Twenty-one patients comprised 11 males and 10 females. Chandler’s classification showed group I in 4, group II in 8, and group III in 9. None of six pediatric patients required any surgical intervention, whereas five adult patients (23.8%) underwent surgical intervention. The average period of recovery was 8.1 days. In univariate analysis, the duration of recovery was significantly longer among adult cases (p < .01) and cases with Chandler’s groups II–III (p = .019). In multivariate analysis, adult patients had a significantly longer duration of recovery than pediatric patients (p = .027). Conclusion and significance: The present study suggested that ARS with orbital complications may have prolonged clinical course in adults.
A Pragmatic Approach to the Implementation of Osteoarthritis Guidelines Has Fewer Potential Barriers Than Recommended Implementation Frameworks.

Translating evidence-based treatment recommendations and guidelines into feasible delivery in routine care is an essential objective to improve quality of care. Nevertheless, guidelines are underused, and many physical therapists and other professionals continue to offer low-value care modalities, providing the patients with treatment options of little to no benefit. In contrast to low-value interventions, evidence-based treatment guidelines for osteoarthritis (OA) recommend information, exercise, and weight control. The authors discuss the feasibility of a pragmatic approach to implementation of clinical guidelines that facilitates improved quality of care for management of OA. J Orthop Sports Phys Ther 2019;49(1):1-4. doi:10.2519/jospt.2019. 0601.
Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis

Significance Whole-exome sequencing data from patients with monogenic inborn errors identify thousands of genetic variants in each patient, only a few of which are pathogenic. Identifying pathogenic mutations therefore requires the rigorous filtration of variants that are too common in public databases to cause a disease of the observed incidence. We report that a large proportion of the variants common in patient cohorts are paradoxically absent from public databases. We define these nonpathogenic, cohort-specific common variants that cannot be removed from the analysis as a “blacklist. ” We describe these blacklisted variants, demonstrate their usefulness for removing nonpathogenic variants, explain their origin experimentally, and provide a web server and software enabling researchers to automate the creation of their own blacklists. Computational analyses of human patient exomes aim to filter out as many nonpathogenic genetic variants (NPVs) as possible, without removing the true disease-causing mutations. This involves comparing the patient’s exome with public databases to remove reported variants inconsistent with disease prevalence, mode of inheritance, or clinical penetrance. However, variants frequent in a given exome cohort, but absent or rare in public databases, have also been reported and treated as NPVs, without rigorous exploration. We report the generation of a blacklist of variants frequent within an in-house cohort of 3,104 exomes. This blacklist did not remove known pathogenic mutations from the exomes of 129 patients and decreased the number of NPVs remaining in the 3,104 individual exomes by a median of 62%. We validated this approach by testing three other independent cohorts of 400, 902, and 3,869 exomes. The blacklist generated from any given cohort removed a substantial proportion of NPVs (11–65%). We analyzed the blacklisted variants computationally and experimentally. Most of the blacklisted variants corresponded to false signals generated by incomplete reference genome assembly, location in low-complexity regions, bioinformatic misprocessing, or limitations inherent to cohort-specific private alleles (e.g., due to sequencing kits, and genetic ancestries). Finally, we provide our precalculated blacklists, together with ReFiNE, a program for generating customized blacklists from any medium-sized or large in-house cohort of exome (or other next-generation sequencing) data via a user-friendly public web server. This work demonstrates the power of extracting variant blacklists from private databases as a specific in-house but broadly applicable tool for optimizing exome analysis.
Civil Rights Pilgrimage Immersion Experience

The Civil Rights Pilgrimage domestic-intercultural immersion experience provides an opportunity for University of Wisconsin-Eau Claire students to learn about key individuals, events, and other aspects surrounding the American Civil Rights Movement on a national basis. In the winter and spring of 2011, students spent ten days immersed in the Deep South to learn about the Movement, visit major sites of significance to the Movement from the 1950s to the 1970s, and hear firsthand accounts of experiences from people who were active in the Civil Rights Movement. A Women’s Studies course focused on women in the American Civil Rights Movement was offered during both the Winterim 2011 and Spring 2011 academic terms. Students had the option of choosing to take this course concurrently with the Civil Rights Pilgrimage. These were the sixth and seventh Civil Rights Pilgrimages. One of the key goals of the Pilgrimage is to provide students with an opportunity to enhance their multicultural competence and experience diversity in ways not naturally fostered by the community make-up of Eau Claire and the Chippewa Valley. The data collected in this study will become part of a longitudinal research project on the long-term impact of the Civil Rights Pilgrimage on students.
Computer-Mediated Communication for Linguistics and Literacy: Technology and Natural Language Education

Due to the complex diversity and multi-disciplinary nature of computer-mediated communication, a reference source solely dedicated to the subjects direct influence on literacy and language becomes imperative among educators. Computer-Mediated Communication for Linguistics and Literacy: Technology and Natural Language Education fills a void within research due to its clear and direct focus on the interactions between human language and communication technologies. Containing extensive research and analysis, this authoritative collection examines the practical implications and applications of how computers can be used to process natural languages for the design of communication systems and devices.
Alicyclic β- and γ-Amino Acids: Useful Scaffolds for the Stereocontrolled Access to Amino Acid-Based Carbocyclic Nucleoside Analogs

Stereocontrolled synthesis of some amino acid-based carbocyclic nucleoside analogs containing ring C=C bond has been performed on β- and γ-lactam basis. Key steps were N-arylation of readily available β- or γ-lactam-derived amino ester isomers and amino alcohols with 5-amino-4,6-dichloropyrimidine; ring closure of the formed adduct with HC(OMe)3 and nucleophilic displacement of chlorine with various N-nucleophiles in the resulting 6-chloropurine moiety.
Growth Factor–Independent 1 Is a Tumor Suppressor Gene in Colorectal Cancer

Colorectal cancer is the third most common cancer and the third leading cause of cancer death in the United States. Growth factor–independent 1 (GFI1) is a zinc finger transcriptional repressor responsible for controlling secretory cell differentiation in the small intestine and colon. GFI1 plays a significant role in the development of human malignancies, including leukemia, lung cancer, and prostate cancer. However, the role of GFI1 in colorectal cancer progression is largely unknown. Our results demonstrate that RNA and protein expression of GFI1 are reduced in advanced-stage nonmucinous colorectal cancer. Subcutaneous tumor xenograft models demonstrated that the reexpression of GFI1 in 4 different human colorectal cancer cell lines inhibits tumor growth. To further investigate the role of Gfi1 in de novo colorectal tumorigenesis, we developed transgenic mice harboring a deletion of Gfi1 in the colon driven by CDX2-cre (Gfi1F/F; CDX2-cre) and crossed them with ApcMin/+ mice (ApcMin/+; Gfi1F/F; CDX2-cre). Loss of Gfi1 significantly increased the total number of colorectal adenomas compared with littermate controls with an APC mutation alone. Furthermore, we found that compound (ApcMin/+; Gfi1F/F; CDX2-cre) mice develop larger adenomas, invasive carcinoma, as well as hyperplastic lesions expressing the neuroendocrine marker chromogranin A, a feature that has not been previously described in APC-mutant tumors in mice. Collectively, these results demonstrate that GFI1 acts as a tumor suppressor gene in colorectal cancer, where deficiency of Gfi1 promotes malignancy in the colon. Implications: These findings reveal that GFI1 functions as a tumor suppressor gene in colorectal tumorigenesis.
Endoplasmic Reticulum Stress Response of Trabecular Meshwork Stem Cells and Trabecular Meshwork Cells and Protective Effects of Activated PERK Pathway

Purpose This study aimed to investigate the differential responses of trabecular meshwork stem cells (TMSCs) and trabecular meshwork (TM) cells to endoplasmic reticulum (ER) stress inducers. Methods Human TM cells and TMSCs were exposed to tunicamycin, brefeldin A, or thapsigargin. Cell apoptosis was evaluated by flow cytometry. ER stress markers were detected by quantitative PCR, Western blotting, and immunostaining. Morphologic changes were evaluated by transmission electron microscopy. Cells were treated with the PERK inhibitor GSK2606414 or the elF2α dephosphorylation inhibitor Salubrinal together with tunicamycin to evaluate their effects on ER stress. Results Both TMSCs and TM cells underwent apoptosis after 48- and 72-hour treatment with ER stress inducers. ER stress triggered the unfolded protein response (UPR) with increased expression of GRP78, sXBP1, and CHOP, which was significantly lower in TMSCs than TM cells. Swollen ER and mitochondria were detected in both TMSCs and TM cells. Neither GSK2606414 nor salubrinal alone activated UPR. GSK2606414 significantly reduced cell survival rates after tunicamycin treatment, and salubrinal increased cell survival rates. The increased expression of GRP78, sXBP1, CHOP, and GADD34 peaked at 6 or 12 hours and lasted longer in TM cells than TMSCs. Salubrinal treatment dramatically increased OCT4 and CHI3L1 expression in TMSCs. Conclusions In response to ER stress inducers, TMSCs activated a lower level of UPR and lasted shorter than TM cells. Inhibition of elF2α dephosphorylation had a protective mechanism against cell death. Stem cells combined with salubrinal may be a more effective way for TM regeneration in glaucoma.
Plant ISOform sequencing database (PISO): a comprehensive repertory of full‐length transcripts in plants

In higher eukaryotes, alternative splicing (AS) and alternative polyadenylation (APA) events can produce multiple transcript isoforms in the majority of genes, which significantly increase the protein-coding potential of a genome (Pan et al., 2008; Anvar et al., 2018). Different transcript isoforms might encode proteins with different functions or affect the mRNA stability and translational capacity, in some sense AS and APA events can dramatically increase the complexity and flexibility of the entire transcriptome and proteome (Yang et al., 2016; Feng et al., 2015; Li et al., 2017a; Wang et al., 2017a). Many databases contained AS events and transcripts in animals are available in some public resources such as ASTD and MAASE (Zheng et al., 2005), whereas there is no database containing full-length transcripts and AS events in plants up to now. This article is protected by copyright. All rights reserved.
NIPBL: a new player in myeloid cell differentiation

The nucleophosmin 1 gene (NPM1) is the most frequently mutated gene in acute myeloid leukemia. Notably, NPM1 mutations are always accompanied by additional mutations such as those in cohesin genes RAD21, SMC1A, SMC3, and STAG2 but not in the cohesin regulator, nipped B-like (NIPBL). In this work, we analyzed a cohort of adult patients with acute myeloid leukemia and NPM1 mutation and observed a specific reduction in the expression of NIPBL but not in other cohesin genes. In our zebrafish model, overexpression of the mutated form of NPM1 also induced downregulation of nipblb, the zebrafish ortholog of human NIPBL. To investigate the hematopoietic phenotype and the interaction between mutated NPM1 and nipblb, we generated a zebrafish model with nipblb downregulation which showed an increased number of myeloid progenitors. This phenotype was due to hyper-activation of the canonical Wnt pathway: myeloid cells blocked in an undifferentiated state could be rescued when the Wnt pathway was inhibited by dkk1b mRNA injection or indomethacin administration. Our results reveal, for the first time, a role for NIPBL during zebrafish hematopoiesis and suggest that an interplay between NIPBL/NPM1 may regulate myeloid differentiation in zebrafish and humans through the canonical Wnt pathway and that dysregulation of these interactions may drive leukemic transformation.
A Fluorescence Inner-Filter Effect Based Sensing Platform for Turn-On Detection of Glutathione in Human Serum

A novel turn-on fluorescence assay was developed for the rapid detection of glutathione (GSH) based on the inner-filter effect (IFE) and redox reaction. Molybdenum disulfide quantum dots (MoS2 QDs), which have stable fluorescent properties, were synthesized with hydrothermal method. Manganese dioxide nanosheets (MnO2 NSs) were prepared by exfoliating the bulk δ-MnO2 material in bovine serum albumin (BSA) aqueous solution. The morphology structures of the prepared nanoparticles were characterized by transmission electron microscope (TEM). Studies have shown that the fluorescence of MoS2 QDs could be quenched in the presence of MnO2 NSs as a result of the IFE, and is recovered after the addition of GSH to dissolve the MnO2 NSs. The fluorescence intensity showed a good linear relationship with the GSH concentration in the range 20–2500 μM, the limit of detection was 1.0 μM. The detection method was applied to the analysis of GSH in human serum samples. This simple, rapid, and cost-effective method has great potential in analyzing GSH and in disease diagnosis.