Miracle-dz/UniFAR-FTUs huggingface dataset:
Toward Improved Optical Transparency of Polyimide Aerogels.

Highly translucent polyimide aerogels were prepared by combining equimolar amounts of pyromellitic dianhydride (PMDA) and 4, 4'-hexafluoroisopropylidene di(phthalic anhydride) (6FDA), 2,2'-dimethylbenzidine (DMBZ), and cross-linking with 1,3,5-benzenetricarbonyl trichloride (BTC). A multivariable statistical design of experiments was used to perform a comparison study between three variables used to fabricate the aerogels: formulated repeat unit (n) of polyimide oligomers, 6FDA fraction of total dianhydride (0 to 50 mol %), and total polymer concentration in solution (7- 10 wt %). Polymers with 25 mol % of 6FDA in the backbone structure, were found to produce polyimide aerogels with high optical transmission and low haze. These aerogels also possessed higher surface areas and very narrow nanoscale pore size distribution. Due to the decreased thermal conductivity with increasing amount of 6FDA in the backbone, these aerogels may find use where the combination of high optical transparency and thermal impedance are desired, such as insulated window panes. To this end, future efforts will focus on reducing the yellow color of the polyimide aerogels.
Device use errors with soft mist inhalers: A global systematic literature review and meta-analysis

Inhaled bronchodilators are the cornerstone of treatment for chronic obstructive pulmonary disease (COPD). Soft mist inhalers (SMIs) are devices that deliver bronchodilators. Although correct device use is paramount to successful medication delivery, patient errors are common. This global systematic literature review and meta-analysis examined device use errors with SMIs among patients with obstructive lung diseases. PubMed, EMBASE, PsycINFO, Cochrane, and Google Scholar were searched to identify studies published between 2010 and 2019 that met the following inclusion criteria: (a) English language; (b) a diagnosis of COPD, bronchitis, or emphysema; and (c) reported device use errors among adults receiving long-acting bronchodilator treatment with Respimat® SMI (i.e. Spiriva®, Stiolto®, Spiolto®, and Striverdi®). Descriptive statistics examined sociodemographics, clinical characteristics, and device use errors. Meta-analysis techniques were employed with random-effects models to generate pooled mean effect sizes and 95% confidence intervals (CIs) for overall and step-by-step errors. The I 2 statistic measured heterogeneity. Twelve studies (n = 1288 patients) were included in this meta-analysis. Eighty-eight percent of patients had COPD, and most had moderate/very severe airflow limitation (Global Initiative for Chronic Obstructive Lung Disease spirometric stages II to IV). Aggregate results revealed that 58.9% (95% CI: 42.4–75.5; I 2 = 92.8%) of patients made ≥1 device use errors. Among 11 studies with step-by-step data, the most common errors were failure to (1) exhale completely and away from the device (47.8% (95% CI: 33.6–62.0)); (2) hold breath for up to 10 seconds (30.6% (95% CI: 17.5–43.7)); (3) take a slow, deep breath while pressing the dose release button (27.9% (95% CI: 14.5–41.2)); (4) hold the inhaler upright (22.6% (95% CI: 6.2–39.0)); and (5) turn the base toward the arrows until it clicked (17.6% (95% CI: 3.0–32.2)). Device use errors occurred in about 6 of 10 patients who used SMIs. An individualized approach to inhalation device selection and ongoing training and monitoring of device use are important in optimizing bronchodilator treatment.
Survival Rates and Associated Factors of Colorectal Cancer Patients in Brunei Darussalam

Background: Colorectal cancer (CRC) is the third most common cancer in both men and women. In most Asian countries, both the incidence and mortality rates of CRC are gradually increasing. In Brunei Darussalam, CRC ranks first and second in lifetime risk among men and women respectively. This study aims to report the overall survival rates and associated factors of CRC in Brunei Darussalam. Methods: This is a retrospective study examining CRC data for the period 2007 to 2017 retrieved from a population based cancer registry in Brunei Darussalam. A total of 728 patients were included in the analysis. Kaplan Meier method was used to estimate survival rates. Univariate analysis using log-rank test was used to examine the differences in survival between groups. Multivariate analysis using Cox PH regression was used to estimate hazard of death and obtain significant predictors that influence CRC patients’ survival. Results: The median survival time for colorectal, colon and rectal cancer patients were 57.0, 85.8 and 40.0 months respectively. The overall 1-, 3- and 5- year survival rates for CRC patients were 78.0%, 57.7% and 49.6% respectively. In univariate analysis, age at diagnosis, ethnicity, cancer stage, tumour location and histology were found to have significant difference in CRC patients’ survival. In the Cox PH analysis, older age (≥70 years), cancer stage, ethnicity and other histological type were determined as associated factors of CRC patients’ survival. Conclusion: This study found the overall 5-year survival rate of CRC in Brunei Darussalam is similar to that in some Asian countries such as Singapore and Malaysia. However, more efforts need to be carried out in order to raise awareness of CRC and improve the survival of CRC patients.
Meta‐analysis on the potential for increasing nitrogen losses from intensifying tropical agriculture

Fertilized temperate croplands export large amounts of reactive nitrogen (N), which degrades water and air quality and contributes to climate change. Fertilizer use is poised to increase in the tropics, where widespread food insecurity persists and increased agricultural productivity will be needed, but much less is known about the potential consequences of increased tropical N fertilizer application. We conducted a meta‐analysis of tropical field studies of nitrate leaching, nitrous oxide emissions, nitric oxide emissions, and ammonia volatilization totaling more than 1,000 observations. We found that the relationship between N inputs and losses differed little between temperate and tropical croplands, although total nitric oxide losses were higher in the tropics. Among the potential drivers we studied, the N input rate controlled all N losses, but soil texture and water inputs also controlled hydrological N losses. Irrigated systems had significantly higher losses of ammonia, and pasture agroecosystems had higher nitric oxide losses. Tripling of fertilizer N inputs to tropical croplands from 50 to 150 kg N ha−1 year−1 would have substantial environmental implications and would lead to increases in nitrate leaching (+30%), nitrous oxide emissions (+30%), nitric oxide (+66%) emissions, and ammonia volatilization (+74%), bringing tropical agricultural nitrate, nitrous oxide, and ammonia losses in line with temperate losses and raising nitric oxide losses above them.
Cardiovascular risk factors as determinants of cerebral blood flow – a cross-sectional and 6-year follow-up study

Abstract Purpose: The parameters of cerebral blood flow are modulated by many factors. The aim of the study was to prospectively assess the relationship between the number of the established cardiovascular risk factors and hemodynamic parameters of cerebral blood flow. Material and methods: The study was cross-sectional baseline and 6-year follow-up data analysis. We analyzed data regarding cardiovascular risk factors, medications use, and ultrasonographically (transcranial Doppler) obtained mean cerebral blood flow velocity (mCBFV), pulsatility (PI), resistance (RI) indexes of middle cerebral artery. Results: After 6.0 ± 0.6 years of follow-up, there was increase in systolic (p = .047), and decrease in diastolic (p = .005) blood pressure, resulting in greater pulse pressure (p < .001). Although intima-media thickness increased during follow-up (p = .019), PI, RI and mCBFV did not differ between baseline and follow-up. In the cohort without follow-up (n = 112), we observed strong association between number of studied cardiovascular risk factors and lower mCBFV, and higher PI and RI (all p < .001), in the cohort with 6 year follow-up (n = 53), we confirmed similar association for mCBFV and PI (p = .002) at baseline, and mCBFV (p = .024) after follow-up. During follow-up, more patients were treated with vasoactive medications (p < .05). Also the median (interquartile range) of total number of taken drugs at follow-up 2 (1–3) was greater than at baseline 1 (0–2), (p < .001). The addition of vasoactive medications during follow-up was associated with increase of the mCBFV (0.012 ± 0.02 m/s, p = .013). Conclusion: The parameters of the cerebral blood flow are adversely influenced by accretion of cardiovascular risk factors, both at baseline and after 6 years of follow-up. The addition of a vasoactive medication during follow-up is associated with an increase of the mCBFV, a possibly beneficial effect.
Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization

Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base‐pair resolution, but the use of short‐read sequencing is limited by repetitive sequences, and long‐read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked‐reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short‐read to linked‐read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short‐read WGS.
Absorption, Biokinetics, and Metabolism of the Dopamine D2 Receptor Agonist Hordenine (N,N-Dimethyltyramine) After Beer Consumption in Humans.

Hordenine, a natural constituent of germinated barley, is a biased agonist of the dopamine D2 receptor. This pilot study investigated the biokinetics of hordenine and its metabolites in four volunteers consuming beer equal to 0.075 mg hordenine/kg body weight. A new UHPLC-ESI-MS/MS method determined maximum plasma concentrations of 12.0-17.3 nM free hordenine after 0-60 min. Hordenine phase-II metabolism was first dominated by sulfation, but later by glucuronidation. The elimination half-lives in plasma were 52.7-66.4 min for free hordenine and about 60/80 min longer for hordenine sulfate and -glucoronide. Urinary excretion peaked 2-3.5 hours after consumption and accumulated to 3.78 µmol within 24 hours corresponding to 9.9% of the ingested dose. The observed hordenine levels in plasma seem too low to provoke direct interaction with the dopamine D2 receptor related to food reward, but synergistic or additive effects with alcohol or N-methyltyramine may occur.
The Feature-Viewer: a visualization tool for positional annotations on a sequence

SUMMARY The Feature-Viewer is a lightweight library for the visualization of biological data mapped to a protein or nucleotide sequence. It is designed for ease of use while allowing for a full customization. The library is already used by several biological data resources and allows intuitive visual mapping of a full spectra of sequence features for different usages. AVAILABILITY AND IMPLEMENTATION The Feature-Viewer is open source, compatible with state-of-the-art development technologies and responsive, also for mobile viewing. Documentation and usage examples are available online.
Sodium adsorption by reusable zeolite adsorbents: integrated adsorption cycles for salinised groundwater treatment

ABSTRACT Using Canadian (CMZ), Bear River (BRZ), and St. Cloud (SCZ) zeolites, this study investigates the application of natural and pre-treated zeolites for Na+ removal from salinised groundwater. Natural BRZ achieved better Na+ removal for initial concentrations of 250–10,000 mg Na+/L and had the highest maximum adsorption capacity (14.3 ± 0.4 mg/g) compared to natural CMZ (5.8 ± 0.5 mg/g) and SCZ (5.6 ± 0.7 mg/g). Natural BRZ exhibited a higher cation exchange capacity (CEC), mineralogical purity, and natural abundance of exchangeable calcium. The natural abundance of Na+ on CMZ and SCZ may have reduced Na+ adsorption. H-form BRZ and H-form CMZ were also prepared through conventional acidic pre-treatment. Acid treatment improved zeolite properties for adsorption (surface area and CEC). Synchrotron-based X-ray scanning transmission microscopy (STXM) indicated that Na+ adsorption sites in the H-form zeolites were associated with the mineral framework. However, sorption effluents were highly acidic (pH ∼2) and Al3+ leached significantly due to the dealumination induced by acid treatment. Alternatively, hard water softening was cyclically integrated with sodium adsorption as a zeolite treatment to generate Ca/Mg-form CMZ. This integration suggested the feasibility of combining CMZ cycles for water softening and sodium reduction for an extended CMZ lifecycle. Natural CMZ was first used to treat hard water, which enriched the CMZ with Ca2+ and Mg2+ and increased its subsequent Na+ removal rate by over 77%, without producing acidic effluents. The Canadian zeolite adsorbed more sodium when water softening was integrated with sodium removal, which is a repeatable dual-treatment. GRAPHICAL ABSTRACT
Broadly neutralizing antibodies for HIV-1: efficacies, challenges and opportunities

ABSTRACT Combination antiretroviral therapy (cART) is effective but not curative, and no successful vaccine is currently available for human immunodeficiency virus-1 (HIV-1). Broadly neutralizing antibodies (bNAbs) provide a new approach to HIV-1 prevention and treatment, and these promising candidates advancing into clinical trials have shown certain efficacies in infected individuals. In addition, bNAbs have the potential to kill HIV-1-infected cells and to affect the course of HIV-1 infection by directly engaging host immunity. Nonetheless, challenges accompany the use of bNAbs, including transient suppression of viraemia, frequent emergence of resistant viruses in rebound viraemia, suboptimal efficacy in virus cell-to-cell transmission, and unclear effects on the cell-associated HIV-1 reservoir. In this review, we discuss opportunities and potential strategies to address current challenges to promote the future use of immunotherapy regimens.
Underglycosylated prion protein modulates plaque formation in the brain.

The prion agent is unique in biology and is comprised of prion protein scrapie (PrPSc), a self-templating conformational variant of the host encoded prion protein cellular (PrPC). The deposition patterns of PrPSc in the CNS can vary considerably from a diffuse synaptic pattern to large plaque-like aggregates. Alterations of PrPC posttranslational processing can change PrPSc deposition patterns; however, the mechanism underlying these observations is unclear. In this issue of the JCI, Sevillano and authors determined that parenchymal PrPSc plaques of the mouse brain preferentially incorporated underglycosylated PrPC that had been liberated from the cell surface by the metalloproteinase, ADAM-10, in combination with heparin sulfate. These results provide mechanistic insight into the formation of PrPSc plaques and suggest that PrP posttranslational modifications direct pathogenicity as well as the rate of disease progression.
A novel protein biochip screening serum anti-sperm antibody expression and natural pregnancy rate in a follow-up study in Chinese infertility

Abstract Production of anti-sperm antibody (ASA) often suffers from autoimmune reaction against sperms in human infertility. The antibodies are measured in both blood and seminal plasma of males. Here, we reported a simple protein biochip methodology that takes advantage of a functionalized self-assembled monolayer modified by N-hydroxysuccinimide (NHS) and enables identification of anti-sperm antibody in Chinese male infertility. To validate this biochip platform, we immobilized purified sperm protein on the biochip surface and tested a variety of parameters in quality controls for the protein assay, respectively. Then, we analyzed serum samples from 368 patients with infertility and 116 healthy donors by means of this biochip simultaneously. We found that positive rate of serum ASA was 20.92% (77/368) in the cases and 1.72% (2/116) in the controls, respectively. Furthermore, we further corroborated the biochip assay in comparison with ELISA method. We found that both methods were compatible for the detection of serum ASA in the patients. In addition, a follow-up study for natural conception in ASA-positive and ASA-negative patients was conducted. The result showed a significant correlation between serum ASA expression and natural pregnancy rate 6.5% in ASA-positive patients while 18.9% in ASA-negative patients, indicating the potential roles of ASA in naturally reproductive processes.
ATP-binding cassette (ABC) import systems of Mycobacterium tuberculosis: target for drug and vaccine development

ABSTRACT Nutrient procurement specifically from nutrient-limiting environment is essential for pathogenic bacteria to survive and/or persist within the host. Long-term survival or persistent infection is one of the main reasons for the overuse of antibiotics, and contributes to the development and spread of antibiotic resistance. Mycobacterium tuberculosis is known for long-term survival within the host, and develops multidrug resistance. Before and during infection, the pathogen encounters various harsh environmental conditions. To cope up with such nutrient-limiting conditions, it is crucial to uptake essential nutrients such as ions, sugars, amino acids, peptides, and metals, necessary for numerous vital biological activities. Among the various types of transporters, ATP-binding cassette (ABC) importers are essentially unique to bacteria, accessible as drug targets without penetrating the cytoplasmic membrane, and offer an ATP-dependent gateway into the cell by mimicking substrates of the importer and designing inhibitors against substrate-binding proteins, ABC importers endeavour for the development of successful drug candidates and antibiotics. Alternatively, the production of antibodies against substrate-binding proteins could lead to vaccine development. In this review, we will emphasize the role of M. tuberculosis ABC importers for survival and virulence within the host. Furthermore, we will elucidate their unique characteristics to discover emerging therapies to combat tuberculosis.
Colocalization of pain and reduced intraepidermal nerve fiber density in individuals with HIV-associated sensory neuropathy

Introduction There is poor correlation between decreases in intra-epidermal nerve fiber density (IENFD) and the presence of pain in HIV-associated sensory neuropathy (HIV-SN) and other painful distal symmetrical polyneuropathies. Objective We investigated whether in individuals with HIV-SN, having pain at the ankle skin biopsy site was associated with lower IENFD compared to when there was no pain at the ankle biopsy site. Methods We recruited 15 individuals with symptomatic HIV-SN. Nine had pain at the site where the ankle biopsy was taken, while six did not. Skin punch biopsies for IENFD quantification were taken from the ankle and the thigh. Contrasts between the two groups were made using the overlap of confidence interval (CI) method. Results IENFD was substantially lower in the group that had pain at the site of the ankle biopsy compared to the other group [6.6 (CI: 5.3 to 7.2) vs. 3.3 (CI: 10.0 to 15.0) fibers/mm]. However, there was no group differences at the thigh biopsy site [15.6 (CI: 15.0 to 15.9) vs 16.2 (CI: 14.5 to 17.8) fibers/mm]. When taking the ratio of ankle IENFD:thigh IENFD, the point estimate for the pain at the ankle group [0.43 (CI: 0.36 to 0.48)] was about half that of the other group [0.81 (CI: 0.68 to 0.87)]. Conclusion Thus, co-localization of pain to the ankle is associated with meaningful decreases in ankle IENFD. Summary Having pain at the ankle biopsy site is associated with lower intra-epidermal nerve fiber density compared to not having pain at the ankle biopsy site.
Phenological responses in a sycamore–aphid–parasitoid system and consequences for aphid population dynamics: A 20 year case study

Species interactions have a spatiotemporal component driven by environmental cues, which if altered by climate change can drive shifts in community dynamics. There is insufficient understanding of the precise time windows during which inter‐annual variation in weather drives phenological shifts and the consequences for mismatches between interacting species and resultant population dynamics—particularly for insects. We use a 20 year study on a tri‐trophic system: sycamore Acer pseudoplatanus, two associated aphid species Drepanosiphum platanoidis and Periphyllus testudinaceus and their hymenopteran parasitoids. Using a sliding window approach, we assess climatic drivers of phenology in all three trophic levels. We quantify the magnitude of resultant trophic mismatches between aphids and their plant hosts and parasitoids, and then model the impacts of these mismatches, direct weather effects and density dependence on local‐scale aphid population dynamics. Warmer temperatures in mid‐March to late‐April were associated with advanced sycamore budburst, parasitoid attack and (marginally) D. platanoidis emergence. The precise time window during which spring weather advances phenology varies considerably across each species. Crucially, warmer temperatures in late winter delayed the emergence of both aphid species. Seasonal variation in warming rates thus generates marked shifts in the relative timing of spring events across trophic levels and mismatches in the phenology of interacting species. Despite this, we found no evidence that aphid population growth rates were adversely impacted by the magnitude of mismatch with their host plants or parasitoids, or direct impacts of temperature and precipitation. Strong density dependence effects occurred in both aphid species and probably buffered populations, through density‐dependent compensation, from adverse impacts of the marked inter‐annual climatic variation that occurred during the study period. These findings explain the resilience of aphid populations to climate change and uncover a key mechanism, warmer winter temperatures delaying insect phenology, by which climate change drives asynchronous shifts between interacting species.
Treatment of Helicobacter pylori infection and its long‐term impacts on gut microbiota

The rising prevalence of antibiotic resistance and the long‐term safety following eradication therapy are important issues in the management of Helicobacter pylori infection. The prevalence of clarithromycin, levofloxacin, and metronidazole resistance of H. pylori has increased to 21%, 27%, and 45%, respectively, in the Asia‐Pacific region. Personalized treatment guided by susceptibility testing may provide a reliably excellent eradication rate in the first‐line treatment but is costly and not widely available. Population‐specific empirical therapy according to the local prevalence of antibiotic resistance may be an alternative strategy. Levofloxacin‐based therapy and bismuth quadruple therapy are the recommended second‐line rescue therapy. Susceptibility testing or genotypic resistance‐guided therapy is the preferred treatment for refractory H. pylori infection, but empirical therapy may be an acceptable alternative. Eradication of H. pylori leads to short‐term perturbation of gut microbiota. The diversity of gut microbiota can be restored months after eradication therapy, but the speed of recovery varies with regimens. The short‐term increases of antibiotic resistance of Escherichia coli and Klebsiella pneumoniae may be restored to basal states months after H. pylori eradication. Future studies that apply in‐depth sequencing, such as shotgun metagenomics sequencing, are needed to clarify whether the compositions of gut microbiota at the species level are fully restored.