Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of differentially expressed genes in bacterial and fungal keratitis

Purpose: This study was aimed at identifying differentially expressed genes (DEGs) in bacterial and fungal keratitis. The candidate genes can be selected and quantified to distinguish between causative agents of infectious keratitis to improve therapeutic outcomes. Methods: The expression profile of bacterial or fungal infection, and normal corneal tissues were downloaded from the Gene Expression Omnibus. The limma package in R was used to screen DEGs in bacterial and fungal keratitis. The Co-Express tool was used to calculate correlation coefficients of co-expressed genes. The "Advanced network merge" function of Cytoscape tool was applied to obtain a fusional co-expression network based on bacterial and fungal keratitis DEGs. Finally, functional enrichment analysis by DAVID software and KEGG analysis by KOBAS of DEGs in fusion network were performed. Results: In total, 451 DEGs in bacterial keratitis and 353 DEGs in fungal keratitis were screened, among which 148 DEGs were found only in bacterial keratitis and 50 DEGs only in fungal keratitis. Besides, 117 co-expressed gene pairs were identified among bacterial keratitis DEGs and 87 pairs among fungal keratitis DEGs. In total, nine biological pathways and seven KEGG pathways were screened by analyzing DEGs in the fusional co-expression network. Conclusion: TLR4 is the representative DEG specific to bacterial keratitis, and SOD2 is the representative DEG specific to fungal keratitis, both of which are promising candidate genes to distinguish between bacterial and fungal keratitis.
High Ambient Temperature and Infant Mortality in Philadelphia, Pennsylvania: A Case-Crossover Study.

OBJECTIVE To quantify the association between heat and infant mortality and identify factors that influence infant vulnerability to heat. METHODS We conducted a time-stratified case-crossover analysis of associations between ambient temperature and infant mortality in Philadelphia, Pennsylvania, during the warm months of 2000 through 2015. We used conditional logistic regression models to estimate associations of infant mortality with daily temperatures on the day of death (lag 0) and for averaging periods of 0 to 1 to 0 to 3 days before the day of death. We explored modification of associations by individual and census tract-level characteristics and by amounts of green space. RESULTS Risk of infant mortality increased by 22.4% (95% confidence interval [CI] = 5.0%, 42.6%) for every 1°C increase in minimum daily temperature over 23.9°C on the day of death. We observed limited evidence of effect modification across strata of the covariates. CONCLUSIONS Our results contribute to a growing body of evidence that infants are a subpopulation that is particularly vulnerable to climate change effects. Further research using large data sets is critically needed to elucidate modifiable factors that may protect infants against heat vulnerability. (Am J Public Health. Published online ahead of print December 19, 2019: e1-e7. doi:10.2105/AJPH.2019.305442).
Hexagonal boron nitride synthesized at atmospheric pressure using metal alloy solvents: Evaluation as a substrate for 2D materials.

Hexagonal boron nitride (h-BN) synthesized under high pressure and high temperature (HPHT) has been used worldwide in two-dimensional (2D) materials research as an essential material for constructing van der Waals heterostructures. Here, we study h-BN synthesized with another method, i.e., via synthesis at atmospheric pressure and high temperature (APHT) using a metal alloy solvent. First, we examine the APHT h-BN in a bulk crystal form using cathodoluminescence and find that it does not have carbon-rich domains that inevitably exist in a core region of all the HPHT h-BN crystals. Next, we statistically compare the size of the crystal flakes exfoliated on a SiO2/Si substrate from APHT and HPHT h-BN crystals by employing our automated 2D material searching system. Finally, we provide direct evidence that APHT h-BN can serve as a high-quality substrate for 2D materials by demonstrating high carrier mobility, ballistic transport, and Hofstadter butterfly in graphene and photoluminescence in WS2.
Tofacitinib in combination with methotrexate in patients with rheumatoid arthritis: patient-reported outcomes from the 24-month Phase 3 ORAL Scan study.

OBJECTIVES Tofacitinib is an oral Janus kinase inhibitor for the treatment of rheumatoid arthritis (RA). Here we present data from the completed Phase 3 randomised controlled trial (RCT) ORAL Scan (NCT00847613), which evaluated the impact of tofacitinib on patient-reported outcomes (PROs) through 24 months in patients with active RA and inadequate responses to methotrexate (MTX-IR). METHODS Patients were randomised 4:4:1:1 to receive tofacitinib 5 or 10 mg twice daily (BID), or placebo advanced to tofacitinib 5 or 10 mg, plus background MTX. Patients receiving placebo advanced to tofacitinib at month 3 (non-responders) or month 6 (remaining patients). Mean changes from baseline in PROs, assessed at months 1-24, included Health Assessment Questionnaire-Disability Index, Patient Global Assessment of disease activity (visual analogue scale [VAS]), Patient Assessment of Arthritis Pain (VAS), health-related quality of life (Short Form-36 version 2), Functional Assessment of Chronic Illness Therapy-Fatigue and Medical Outcomes Study-Sleep. RESULTS Overall, 539/797 (67.6%) patients completed 24 months' treatment. At month 3, tofacitinib-treated patients reported signi cant (p<0.05) mean changes from baseline versus placebo across all PROs, and significantly more patients reported improvements ≥ minimum clinically important differences versus placebo. Improvements in PROs with tofacitinib were sustained to month 24. Following advancement to tofacitinib, placebo-treated patients generally reported changes of similar magnitude to tofacitinib-treated patients. CONCLUSIONS Patients with RA and MTX-IR receiving tofacitinib 5 or 10 mg BID plus MTX reported significant and clinically meaningful improvements in PROs versus placebo at month 3, which were sustained through 24 months.
Salt-Templated Construction of Ultrathin Cobalt Doped Iron Thiophosphite Nanosheets toward Electrochemical Ammonia Synthesis.

Exploiting efficient electrocatalysts for electrochemical nitrogen reduction (NRR) is highly desired and deeply meaningful for realizing sustainable ammonia (NH3 ) production under ambient conditions. The Fe protein contains one [Fe4 S4 ] cluster and P cluster, which play an important role for transfer electron during the nitrogen fixing of nitrogenases. Based on the understanding of nitrogenase, the rising-star 2D iron thiophosphite (FePS3 ) nanomaterials may be highly active electrocatalysts toward NRR due to the ideal elemental composition. In this work, 2D FePS3 nanosheets are successfully synthesized by a facile salt-templated method. The FePS3 nanosheets show better electrocatalytic NH3 yield and faradaic efficiency (FE) than Fe2 S3 , which demonstrates that the P element indeed improves the NRR activity of Fe-S. Theoretically, Co incorporation not only effectively prompts the conductivity of FePS3 , but also enhances the catalytic activities of Fe-edge sites. Experimentally, Co-doped FePS3 (Co-FePS3 ) nanosheets exhibit a remarkable electrocatalytic performance toward NRR, such as high NH3 yield rate of 90.6 µg h-1 mgcat -1 , high FE of 3.38%, and an excellent long-term stability. Being the first theoretical and experimental report regarding FePS3 -based electrocatalyst toward NRR, this work represents an important beginning to the family of metal thiophosphite as advanced electrocatalysts toward NRR.
Reliability of Magnetic Resonance Imaging Prediction of Anterior Cruciate Ligament Autograft Size and Comparison of Radiologist and Orthopaedic Surgeon Predictions

Background: In anterior cruciate ligament (ACL) reconstruction, hamstring tendon autografts <8 mm have been associated with increased failure rates. There has been no established modality by which orthopaedic surgeons can preoperatively predict graft sizes. Purpose/Hypothesis: The purposes of this study were to (1) determine whether routine magnetic resonance imaging (MRI) measurement of hamstring tendon cross-sectional area (CSA) can reliably be used by sports medicine fellowship–trained orthopaedic surgeons to predict graft size and (2) determine whether radiologists and sports medicine surgeons are able to discriminate grafts below a predetermined cutoff value. We hypothesized that radiologists will find a correlation between MRI measurement and intraoperative graft size. Similarly, orthopaedic surgeons will be able to correctly estimate the graft size based on MRI measurement. Study Design: Cohort study (diagnosis); Level of evidence, 2. Methods: Included in this study were 30 consecutive patients (15 women and 15 men) (mean age, 23 years [range, 13-43 years]) for whom MRI-determined hamstring tendon CSA and graft size measurements could be compared. Patients were included if they had a preoperative MRI demonstrating acute ACL rupture and were scheduled with 1 of 3 surgeons for a reconstruction performed using the ST and GR tendons. Operative data were collected over 1 year. Sectra imaging software was used to measure the CSA of the semitendinosus (ST) and gracilis (GR) tendons on the preoperative MRIs. Control measurements were performed intraoperatively using a graft sizing block with 0.5-mm increments. Simple linear regression analysis was used to evaluate the ability of MRI measurements to predict autograft size. Logistic regression was used to determine the minimum CSA for a graft of 8 mm. The intraclass correlation coefficient (ICC) was used to evaluate interrater reliability. Results: MRI CSA measurement of the average STGR (ST CSA added to the GR CSA) was a significant predictor of graft size (adjusted R 2 = 0.186; P < .001). The 3 measurements with the strongest correlations with graft size were the ST at the medial femoral condyle (MFC), the STGR at the MFC, and the average STGR. The minimum CSA for the average STGR on MRI to achieve a graft size of 8 mm was 17.168 mm2 (P < .001). The area under the receiver operating characteristic curve was 0.765. The overall ICC was 0.977. Conclusion: Routine preoperative MRI can be used by both radiologists and orthopaedic surgeons to predict the expected ACL autograft size and identify those below a cutoff of 8 mm. This will help in preoperative planning and graft selection.
Differential DNA Methylation Patterns in Patients with Epilepsy due to Malformations of Cortical Development: A Pilot Study

Objective: To study the DNA methylation profiles in brain tissue of patients with refractory epilepsy due to malformations of cortical development (MCDs). Materials and Methods: Clinical, neuroimaging, and pathology characteristics were defined for 13 patients who underwent resective surgery for epilepsy. Methylation analysis was performed using Illumina® 450k Methylation Microarray. Data analysis was completed, and pathway identification was done using the R/Bioconductor package. Results: Genes associated with Ephrin–Reelin pathway, potassium channels, and glutathione metabolism were differentially methylated in the MCD group when compared with patients who had no evidence of MCD. Conclusions: Our preliminary data reveal that epigenetic pathways may have a role in the pathobiogenesis of MCDs.
Risk Scoring Systems to Predict Long-Term Mortality After Carotid Endarterectomy in Asymptomatic Patients: A Systematic Review

The present review was conducted to describe current published risk scoring systems to predict late mortality after carotid endarterectomy (CEA). The aim of the study is to identify simple, clinical, and reproducible tools to predict life expectancy in patients with asymptomatic carotid artery stenosis candidates to CEA and therefore which patients may benefit from surgery, reaching the goal of life expectancy >3 to 5 years, recommended by guidelines. Advantages, disadvantages, feasibility, simplicity, and reproducibility of each selected score were analyzed. Rigorous statistical analysis and validation of the score are essential components to produce a calibrated and usable score. Future studies should address the impact of using these tools in CEA candidates for asymptomatic disease.
The alternative cap-binding complex is required for antiviral defense in vivo

Cellular response to environmental challenges requires immediate and precise regulation of transcriptional programs. During viral infections, this includes the expression of antiviral genes that are essential to combat the pathogen. Transcribed mRNAs are bound and escorted to the cytoplasm by the cap-binding complex (CBC). We recently identified a protein complex consisting of NCBP1 and NCBP3 that, under physiological conditions, has redundant function to the canonical CBC, consisting of NCBP1 and NCBP2. Here, we provide evidence that NCBP3 is essential to mount a precise and appropriate antiviral response. Ncbp3-deficient cells allow higher virus growth and elicit a reduced antiviral response, a defect happening on post-transcriptional level. Ncbp3-deficient mice suffered from severe lung pathology and increased morbidity after influenza A virus challenge. While NCBP3 appeared to be particularly important during viral infections, it may be more broadly involved to ensure proper protein expression.
Identification and frequency of consumption of wild edible plants over a year in central Tunisia: a mixed-methods approach

Abstract Objective: To identify wild plants used as food and assess their frequency of consumption over a year in a region of Tunisia where agriculture is undergoing a major transformation from smallholder farming to an intensive high-input agricultural system. Design: Qualitative ethnobotanical study followed by a survey of women’s frequency of consumption of wild plants conducted using FFQ at quarterly intervals. Setting: Sidi Bouzid governorate of central Tunisia. Participants: Mixed-gender group of key informants (n 14) and focus group participants (n 43). Survey sample of women aged 20–49 years, representative at governorate level (n 584). Results: Ethnobotanical study: thirty folk species of wild edible plants corresponding to thirty-five taxa were identified by key informants, while twenty folk species (twenty-five taxa) were described by focus groups as commonly eaten. Population-based survey: 98 % of women had consumed a wild plant over the year, with a median frequency of 2 d/month. Wild and semi-domesticated fennel (Foeniculum vulgare Mill. and Anethum graveolens) was the most frequently consumed folk species. Women in the upper tertile of wild plant consumption frequency were more likely to be in their 30s, to live in an urban area, to have non-monetary access to foods from their extended family and to belong to wealthier households. Conclusions: In this population, wild edible plants, predominantly leafy vegetables, are appreciated but consumed infrequently. Their favourable perception, however, offers an opportunity for promoting their consumption which could play a role in providing healthy diets and mitigating the obesity epidemic that is affecting the Tunisian population.
Infectivity of Norovirus GI and GII from Bottled Mineral Water during a Waterborne Outbreak, Spain

During a waterborne outbreak of norovirus in Spain, we estimated 50% illness doses for a group of exposed (secretor) persons to be 556 (95% CI 319–957) genome copies/day for norovirus GI and 2,934 (95% CI 1,683–5,044) genome copies/day for norovirus GII. Use of a propidium monoazide viability assay reduced these values.
Flow cytometric significance of cellular alkaline phosphatase activity in acute myeloid leukemia

In this prospective hospital-based cohort study that included 43 newly diagnosed patients with acute myeloid leukemia, flow cytometric cellular alkaline phosphatase (ALP) activity within primitive leukemic cells allowed us to identify two groups of patients at diagnosis according to the numbers of leukemic blasts expressing ≥ 12% of ALP+ cells (27 patients, Group A) and less than 12% of ALP+ cells (16 patients, Group B). Differences in outcome for complete response, relapse or treatment resistance, and exitus were statistically analyzed and were significant, when comparing the two groups. The overall survival (OS) and event-free survival (EFS) differences between Group A and B were statistically significant. The survival of Group A patients was significantly shorter than those for Group B. No significant relationship was detected in outcome when comparing ELN prognostic-risk group based on cytogenetic and molecular profile (patients in the favorable, intermediate, and adverse risk groups). Flow cytometric cellular ALP activity at diagnosis may be used to estimate relapses and disease persistence more accurately. The limitations of our study include the small number of patients enrolled and a short follow-up, due to its prospective nature.
Immunotherapy for the rheumatoid arthritis-associated coronary artery disease: promise and future

Abstract Objective: To review the latest progress on the pathogenic mechanism and management of rheumatoid arthritis (RA)-associated coronary artery disease (CAD), and propose advice on future management optimization as well as prospects for research and development of new therapeutic regimen. Data sources: This study was based on data obtained from PubMed up to May 2019 using various search terms and their combinations, including coronary artery disease, myocardial ischemia, cardiovascular diseases, RA, rheumatic diseases, treatment, therapy, strategies, immunotherapy, inflammation, and anti-inflammation. Study selection: All retrieved literature was scrutinized, most relevant articles about the pathogenic mechanism and clinical management, especially anti-inflammatory therapy of RA-associated CAD were reviewed. Results: RA is an immune-mediated chronic inflammatory disease which has a great social disease burden. In addition to typical arthritic manifestations, RA also affects extra-articular tissues and organs, within which the involvement of the cardiovascular system, especially incorporating CAD, is the leading cause of death for patients with RA. Recently, numerous basic and clinical studies have been carried out on the mechanism of CAD development and progression under the inflammatory cascade of RA. The effect of traditional RA drugs on CAD risk management has been gradually clarified, and more emerging biologic agents are being explored and studied, which have also achieved satisfactory outcomes. Furthermore, with the success of the CANTOS clinical trial, novel anti-inflammatory therapy for the prevention of cardiovascular disease is believed to have a broad prospect. Conclusions: RA is an independent risk factor for CAD, which mainly results from the underlying inflammatory cascade; therefore, anti-inflammatory therapy, especially the emerging novel biologic drugs, is important for CAD management in patients with RA and may also be a promising approach among the general population.
SRD005825 Acts as a Pharmacologic Chaperone of Opsin and Promotes Survival of Photoreceptors in an Animal Model of Autosomal Dominant Retinitis Pigmentosa

Purpose Mutations in RHO, the gene for a rhodopsin, are a leading cause of autosomal dominant retinitis pigmentosa. The objective of this study was to determine if a synthetic retinal analogue (SRD005825) serves as a pharmacologic chaperone to promote appropriate membrane trafficking of a mutant version of human rhodopsin. Methods A tetracycline-inducible cell line was used to produce human wild-type and T17M opsin. A cell-free assay was used to study the impact of SRD005825 on binding of 9-cis-retinal to wild-type opsin. A cell-based assay was used to measure the effect of SRD005825 on the generation of rhodopsin by spectroscopy and Western blot and the transport of rhodopsin to the cell membrane by confocal microscopy. Mice bearing T17M RHO were treated with daily oral doses of SRD005825, and retinal degeneration was measured by spectral-domain optical coherence tomography and, at the conclusion of the experiment, by electroretinography and morphometry. Results SRD005825 competed with 9-cis-retinal for binding to wild-type opsin but promoted the formation of rhodopsin in HEK293 cells and the trafficking of T17M rhodopsin to the plasma membrane of these cells. T17M transgenic mice exhibited rapid retinal degeneration, but thinning of the outer nuclear layer representative of photoreceptor cell bodies was delayed by treatment with SRD005825. Electroretinography a-wave and b-wave amplitudes were significantly improved by drug treatment. Conclusions SRD005825 promoted the reconstitution of mutant rhodopsin and its membrane localization. Because it delayed retinal degeneration in the mouse model, it has potential as a therapeutic for autosomal dominant retinitis pigmentosa. Translational Relevance SRD005825 may be useful as a treatment to delay retinal degeneration in retinitis pigmentosa patients with rhodopsin mutations causing misfolding of the protein.
Patient identified factors influencing decisions to seek fertility care: adaptation of a wellness model

ABSTRACT Objective: To adapt a fertility care wellness model. Background: Despite availability of a range of diagnostic and therapeutic services for infertility, many do not seek care or discontinue care prior to achieving a live birth. Wellness models can inform research on patient decisions to seek and continue fertility care, as many barriers and drivers are represented within the dimensions of wellness. Methods: A mixed-methods online survey was completed by 135 people of reproductive age who experienced infertility in the USA. Outcomes included drivers and barriers to seeking or continuing fertility care. Identified factors were compared by treatment history using chi-square and Fisher’s exact tests. Themes and patterns were identified within 174 responses to 6 open-response items through conventional content analysis. Results: Thematic analysis revealed practical (environmental, financial, and physical) and affective (emotional, social and spiritual) dimensions of wellness in decisions to seek care (67%), with affective rationales more prominent in decisions to return for care (78%). Conclusion: Decisions to seek fertility care and return after failed treatment integrate practical and affective rationales from financial, physical, environmental, emotional, social and spiritual wellness dimensions. Drivers and barriers within these dimensions should be considered to encourage care seeking and improve patient retention.
The mixture toxicity of heavy metals on Photobacterium phosphoreum and its modeling by ion characteristics-based QSAR

Organisms are frequently exposed to mixtures of heavy metals because of their persistence in the environment. The mixture toxicity of heavy metals should therefore be evaluated to perform a rational environmental risk assessment for organisms. In this study, we determined the inhibition toxicity of five heavy metals (Cu2+, Co2+, Zn2+, Fe3+ and Cr3+) and their binary mixtures to Photobacterium phosphoreum (P. phosphoreum). We obtained the following results: (1) the order of individual toxicity was Zn2+>Cu2+>Co2+>Cr3+>Fe3+, and (2) different combined effects (additive, synergistic and antagonistic) were observed in the binary mixtures of heavy metals, with toxicity unit (TU) values ranging from 0.15 to 3.50. To predict the mixture toxicity of heavy metals, we derived the ion characteristic parameters of heavy metal mixtures and explored the ion-characteristic-based quantitative structure–activity relationship (QSAR) model (R2 = 0.750, Q2 = 0.649). The developed QSAR model indicated that the mixture toxicity of heavy metals is related to the change in ionization potential ((ΔIP)mix), the first hydrolysis constant (log(KOH)mix) and the formation constant value (logKfmix).