Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of medications during pregnancy and breastfeeding for Crohn’s disease and ulcerative colitis

ABSTRACT Introduction: The peak age of diagnosis of inflammatory bowel disease (IBD) occurs during childbearing years, therefore management of IBD during pregnancy is a frequent occurrence. Maintenance of disease remission is crucial to optimize pregnancy outcomes, and potential maternal or fetal toxicity from medications must be balanced against the risks of untreated IBD. Areas covered: This review summarizes the literature on safety and use of medications for IBD during pregnancy and lactation. Expert opinion: 5-aminosalicylates, corticosteroids and thiopurines are safe for use during pregnancy, while methotrexate and tofacitinib should only be used with extreme caution. Anti-TNF agents (except certolizumab), vedolizumab, ustekinumab and tofacitinib readily traverse the placenta via active transport, therefore theoretically may affect fetal development. Certolizumab only undergoes passive transfer across the placenta, thus has markedly lower cord blood levels making it likely the safest biologic agent for infants. There is reasonable evidence to support the safety of anti-TNF monotherapy and combination therapy during pregnancy and lactation. Vedolizumab and ustekinumab are also thought to be safe in pregnancy and lactation, while tofacitinib is generally avoided due to teratogenic effects in animal studies.
Bioactive edible film based on Konjac glucomannan and probiotic Lactobacillus plantarum strains: Physicochemical properties and shelf life of fresh-cut kiwis.

This study investigates the efficacy of Lactobacillus plantarum strains (L. plantarum LP3, L. plantarum AF1, and L. plantarum LU5) incorporated into a Konjac-based edible coating in order to prevent fungi growth and retain physicochemical characteristics of fresh-cut kiwis kept at 4 °C for 5 days. For this purpose, probiotic survivability, fungi counts, decay percentage, color changes, titratable acidity (TA), total soluble solids (TSS), ascorbic acid content, chlorophyll amount, total phenolics, and DPPH radical scavenging of fresh-cut kiwis were evaluated. Results indicated that the population of L. plantarum strains in all treated groups retained at sufficient amounts of probiotic consumption (above 6 and 7 log CFU/g) at the end of the storage period and L. plantarum LP3 had the highest viability in comparison to other strains. The incorporation of L. plantarum in Konjac coatings markedly reduced the amount of decay and color changes and maintained the chlorophyll and ascorbic acid contents of fresh-cut kiwis compared to control samples. After 5 days of storage, total phenol content and the DPPH antiradical activities of coated kiwi slices treated with probiotics were observed about 1.2 and 10.23 g/kg compared to the pure Konjac-coated (0.84 and 7.6 g/kg) and Konjac-uncoated samples (0.44 and 4.1 g/kg), respectively. No significant difference in TSS and TA of various treatments was detected. Coated kiwi slices loaded with probiotics had higher overall acceptability compared to Konjac-coated and control samples. In addition, probiotic treatment significantly reduced mold and yeast counts compared to the control group. PRACTICAL APPLICATIONS: Recently, edible films have received more consideration as a promising method to enhance the shelf life of fresh-cut fruit. The presence of probiotics in edible films reduces the growth of spoilage microorganisms and improves consumer health. Our findings encourage the application of edible coating incorporated with L. plantarum to design multifunctional foods and preserve the qualities of fresh-cut kiwifruit.
The development of food simulants for microwave oven testing

Summary The microwave heating characteristics of foods vary with temperature, chemical composition, physical state and geometry. The purpose of the food simulates reported in this paper is to provide heating loads that will enable reliable and reproducible characterization of the heating performance of microwave ovens (2.45 GHz), specifically when heating chilled convenience meals. An extensive literature search was done to identify food simulants that had been used to mimic the heating responses of foods when heated both conventionally and in microwave fields. Each prospective food simulant was initially assessed against a set of criteria that included ease of manufacture, stability and formability. Four meals were chosen to represent the range of chilled convenience meals available in the UK. Tests, using continuous fibre-optic temperature measurement during heating, indicated that the meals could be separated into two broad categories according to heating times, i.e. ‘slow’ and ‘fast’ responders. Food simulants were developed for the two food categories. A good match between food simulant and meal was achieved for the main indicators, i.e. temperatures at central and intermediate locations and weight loss. A close match (a difference of 2% between food simulant and meal) was achieved for the centre location, which is important, as this is often the coolest area in the meal after heating in domestic microwave ovens.
Subcooled convective boiling in structured surface microchannels

Experiments are performed to investigate subcooled flow boiling, on side wall cavities with angles of 60°, 90° and 120° with bottom-wall asymmetrical heating, for a microchannel heat sink containing 75 parallel 100 µm × 200 µm channels. The heated surface is made of a Cu metal sheet with/without 2 µm thickness diamond film. Tests and measurements are conducted with de-ionized water, de-ionized water + 1 vol.% MCNT additive solution, FC-72 fluids over a mass velocity range of 820–1600 kg m−2 s, inlet temperatures of 15 (8.6), 25 (13.6), 44 (24.6) and 64 °C (36.6 °C) for DI water (FC-72) and heat fluxes up to 800 W cm−2. Flow morphologies, boiling incipience, two-phase heat transfer coefficients and critical heat fluxes are obtained and presented. Both cavities' structured and sputtered diamond ultrathin film surfaces in nanofluid flow boiling in a microchannel are shown to significantly enhance heat transfer through the promotion of bubble ebullitions and to reduce boiling incipience. A significant increase in critical heat flux (CHF) is also found.
Bioinformatics resources for SARS-CoV-2 discovery and surveillance

Abstract In early January 2020, the novel coronavirus (SARS-CoV-2) responsible for a pneumonia outbreak in Wuhan, China, was identified using next-generation sequencing (NGS) and readily available bioinformatics pipelines. In addition to virus discovery, these NGS technologies and bioinformatics resources are currently being employed for ongoing genomic surveillance of SARS-CoV-2 worldwide, tracking its spread, evolution and patterns of variation on a global scale. In this review, we summarize the bioinformatics resources used for the discovery and surveillance of SARS-CoV-2. We also discuss the advantages and disadvantages of these bioinformatics resources and highlight areas where additional technical developments are urgently needed. Solutions to these problems will be beneficial not only to the prevention and control of the current COVID-19 pandemic but also to infectious disease outbreaks of the future.
The genetic proteome: Using genetics to inform the proteome of mycobacterial pathogens

Mycobacterial pathogens pose a sustained threat to human health. There is a critical need for new diagnostics, therapeutics, and vaccines targeting both tuberculous and nontuberculous mycobacterial species. Understanding the basic mechanisms used by diverse mycobacterial species to cause disease will facilitate efforts to design new approaches toward detection, treatment, and prevention of mycobacterial disease. Molecular, genetic, and biochemical approaches have been widely employed to define fundamental aspects of mycobacterial physiology and virulence. The recent expansion of genetic tools in mycobacteria has further increased the accessibility of forward genetic approaches. Proteomics has also emerged as a powerful approach to further our understanding of diverse mycobacterial species. Detection of large numbers of proteins and their modifications from complex mixtures of mycobacterial proteins is now routine, with efforts of quantification of these datasets becoming more robust. In this review, we discuss the “genetic proteome,” how the power of genetics, molecular biology, and biochemistry informs and amplifies the quality of subsequent analytical approaches and maximizes the potential of hypothesis-driven mycobacterial research. Published proteomics datasets can be used for hypothesis generation and effective post hoc supplementation to experimental data. Overall, we highlight how the integration of proteomics, genetic, molecular, and biochemical approaches can be employed successfully to define fundamental aspects of mycobacterial pathobiology.
Liver stiffness measured by two-dimensional shear-wave elastography predicts hepatic vein pressure gradient at high values in liver transplant candidates with advanced liver cirrhosis

Liver stiffness is a reliable non-invasive predictor of Hepatic Venous Pressure Gradient (HVPG) above 10 mm Hg. However, it failed to predict higher thresholds of HVPG. Our aim was to investigate whether liver stiffness and selected previously published non-invasive blood biomarkers could predict higher HVPG thresholds in liver transplant candidates without ongoing alcohol use. One hundred and nine liver transplant candidates with liver cirrhosis of various aetiologies underwent direct HVPG measurement, liver stiffness measurement by 2D shear-wave elastography (Aixplorer Multiwave, Supersonic Imagine, France) and assessment of blood HVPG biomarkers (osteopontin, VCAM-1, IL-6, TNF-α, IL-1ra/IL-1F3 and ELF score). The correlation between liver stiffness and HVPG was linear up to 30 mm Hg of HVPG (r = 0.765, p < 0.0001). The regression lines had similar slopes for HVPG values below and above 16 mm Hg (p > 0.05) and the correlation in patients with HVPG <16 mm Hg (r = 0.456, p = 0.01) was similar to patients with HVPG ≥ 16 mm Hg (r = 0.499, p < 0.0001). The correlation was similar in the subgroup patients with alcoholic (r = 0.718, p < 0.0001), NASH (r = 0.740, p = 0.008), cryptogenic (r = 0.648, p = 0,0377), cholestatic and autoimmune (r = 0.706, p < 0.0001) and viral cirrhosis (r = 0.756, p < 0.0001). Liver stiffness distinguished patients with HVPG above 16, and 20 mm Hg with AUROCs 0.90243, and 0.86824, sensitivity 0.7656, and 0.7027, and specificity 0.9333, and 0.8750. All studied blood biomarkers correlated better with liver stiffness than with HVPG and their AUROCs did not exceed 0.8 at both HVPG thresholds. Therefore, a composite predictor superior to liver stiffness could not be established. We conclude that liver stiffness is a clinically reliable predictor of higher HVPG thresholds in non-drinking subjects with advanced liver cirrhosis.
Group EMDR Interventions in Adults and Children: A Systematic Review of Randomised and Non-randomised Trials.

This review systematically synthesised existing literature on group protocols of Eye Movement Desensitization and Reprocessing (EMDR) therapy for treating a range of mental health difficulties in adults and children. We conducted database searches on PsychINFO, EMBASE, MEDLINE, Web of Science, The Cochrane Library and Francine Shapiro Library up to May 2020, using PRISMA guidelines. Studies were included if they used at least one standardized outcome measure, if they present a quantitative data on the effect of group EMDR protocols on mental health difficulties and if they were published in English. Twenty-two studies with 1739 participants were included. Thirteen studies examined EMDR Integrative Group Treatment Protocol (IGTP) protocol, 4 studies examined EMDR Group Traumatic Episode Protocol (G-TEP), 4 studies EMDR Integrative Group Treatment Protocol for Ongoing Traumatic Stress and one study considered EMDR Group Protocol with Children. Of the 22 studies included, 12 were one-arm trials and 10 were two-arm trials. We assessed risk of bias using a revised Tool to Assess Risk of Bias in Randomized Trials (ROB 2) and Risk of Bias in Non-randomized Studies of Interventions (ROBINS-I). Overall, the results suggested that Group EMDR protocols might be an effective tool in improving a wide range of mental health-related outcomes including PTSD, depression, and anxiety. However, the included studies are limited to methodological challenges. The limitations and future directions are discussed.
Development of reverse transcription loop-mediated isothermal amplification assays for point-of-care testing of avian influenza virus subtype H5 and H9

Avian influenza (AIV) outbreaks can induce fatal human pulmonary infections in addition to economic losses to the poultry industry. In this study, we aimed to develop a rapid and sensitive point-of-care AIV test using loop-mediated isothermal amplification (LAMP) technology. We designed three sets of reverse transcription LAMP (RT-LAMP) primers targeting the matrix (M) and hemagglutinin (HA) genes of the H5 and H9 subtypes. RT-LAMP targeting the universal M gene was designed to screen for the presence of AIV and RT-LAMP assays targeting H5-HA and H9-HA were designed to discriminate between the H5 and H9 subtypes. All three RT-LAMP assays showed specific amplification results without nonspecific reactions. In terms of sensitivity, the detection limits of our RT-LAMP assays were 100 to 1,000 RNA copies per reaction, which were 10 times more sensitive than the detection limits of the reference reverse‒transcription polymerase chain reaction (RT-PCR) (1,000 to 10,000 RNA copies per reaction). The reaction time of our RT-LAMP assays was less than 30 min, which was approximately four times quicker than that of conventional RT-PCR. Altogether, these assays successfully detected the existence of AIV and discriminated between the H5 or H9 subtypes with higher sensitivity and less time than the conventional RT-PCR assay.
The nature of triple-negative breast cancer classification and antitumoral strategies

Identifying the patterns of gene expression in breast cancers is essential to understanding their pathophysiology and developing anticancer drugs. Breast cancer is a heterogeneous disease with different subtypes determined by distinct biological features. Luminal breast cancer is characterized by a relatively high expression of estrogen receptor (ER) and progesterone receptor (PR) genes, which are expressed in breast luminal cells. In ~25% of invasive breast cancers, human epidermal growth factor receptor 2 (HER2) is overexpressed; these cancers are categorized as the HER2 type. Triple-negative breast cancer (TNBC), in which the cancer cells do not express ER/PR or HER2, shows highly aggressive clinical outcomes. TNBC can be further classified into specific subtypes according to genomic mutations and cancer immunogenicity. Herein, we discuss the brief history of TNBC classification and its implications for promising treatments.
Scaling Relations Related to the Kinetics of Excimer Formation between Pyrene Groups Attached onto Poly(N,N-dimethylacrylamide)s

The fluorescence decays of the pyrene monomer of a series of pyrene-labeled poly(N,N-dimethylacrylamide)s (PyPDMAAm) were acquired in N,N-dimethylformamide (DMF) and acetone with different concentrations of nitromethane and at very low polymer concentration. DMF and acetone are good and mediocre solvents for PyPDMAAm, respectively. Nitromethane is a potent quencher of pyrene. Nitromethane addition to the polymer solution shortens the pyrene lifetime. The fluorescence decays of the quenched and unquenched pyrene-labeled polymers were analyzed with a blob model. Shortening the lifetime of pyrene reduces the volume probed by the dye while it remains excited. For each quencher concentration, the blob volume and size were determined, and scaling laws were shown to hold. The exponents retrieved from the scaling relationships agreed with those reported in polymer science textbooks.
Prediction of hub genes of Alzheimer’s disease using a protein interaction network and functional enrichment analysis

Alzheimer's disease (AD) is a chronic, progressive brain disorder that slowly destroys affected individuals’ memory and reasoning faculties, and consequently, their ability to perform the simplest tasks. This study investigated the hub genes of AD. Proteins interact with other proteins and non-protein molecules, and these interactions play an important role in understanding protein function. Computational methods are useful for understanding biological problems, in particular, network analyses of protein-protein interactions. Through a protein network analysis, we identified the following top 10 hub genes associated with AD: PTGER3, C3AR1, NPY, ADCY2, CXCL12, CCR5, MTNR1A, CNR2, GRM2, and CXCL8. Through gene enrichment, it was identified that most gene functions could be classified as integral to the plasma membrane, G-protein coupled receptor activity, and cell communication under gene ontology, as well as involvement in signal transduction pathways. Based on the convergent functional genomics ranking, the prioritized genes were NPY, CXCL12, CCR5, and CNR2.
Properties of carbonaceous-palladium hydrogen sensor

In this paper we present studies of hydrogen sensors based on nanostructural C-Pd films deposited on alundum substrate with silver or titanium electrodes. These C-Pd films were prepared by PVD method. Films were characterized by SEM and EDS. Sensitivity of films toward hydrogen were measured in specially prepare experimental set-up with small chamber (50ml). Response time was also registered for different percentage of hydrogen / nitrogen mixture (up to 1% of hydrogen).
Comparison of clinical outcomes with and without volar lunate facet fragments in dorsal displaced distal radius fractures

Introduction: Although many clinical studies about distal radius fracture (DRF) accompanied by volar lunate facet fragments (VLFF) have recently been reported, none focus on the direction of displacement of distal fragments. Many previous cases with difficulty in treating DRF with VLFF were volar-displaced fractures. Thus, the postoperative risk for re-displacement is different between volar- and dorsal-displaced fractures with VLFF. The aim of this study is to compare the outcome of dorsal-displaced fractures treated using proximal volar locking plates (PVLP) between those with VLFF and those without, in order to reconsider the indications of distal volar locking plates (DVLP) and investigate the possibility of treating dorsal-displaced DRF with VLFF using PVLP. Methods: The subjects were 122 patients with dorsal-displaced DRFs treated using PVLP (42 males and 80 females, mean age: 59.2 years old). The patients were divided into 13 patients with VLFF group and 109 patients without VLFF group, and the clinical outcomes at 12 months after surgery were compared. Results: No significant difference was noted on any evaluation between the groups. In addition, no postoperative re-displacement of VLFF was observed and bone union was confirmed. Furthermore, no osteoarthritic change was noted in all patients. Conclusions: We confirmed that surgical treatment for dorsal-displaced DRF using PVLP is possible even in cases of DRF with VLFF. In addition, DVLP is an implant with a high complication risk; therefore, it may be necessary to reconsider the use of DVLP for dorsal-displaced DRF with VLFF treatable by PVLP.
Oxozirconium Methacrylate Clusters: Zr6(OH)4O4(OMc)12 and Zr4O2(OMc)12 (OMc = Methacrylate)

The crystalline oxozirconium methacrylate clusters Zr6(O-H)4O4(OMc)12 and Zr4O2(OMc)12 were obtained by reaction of Zr(OnPr)4 with an excess of methacrylic acid and analysed by X-ray diffraction. The oxide and hydroxide groups are in a μ3- bridging mode in both structures, and the methacrylate ligands are chelating or bridging. The zirconium atoms in Zr6(OH)4O4(OMc)12 form an octahedron the cluster having crystalographic C3v symmetry. Each metal atom is square-antiprismatically coordinated by eight oxygen atoms. In Zr4O2(OMc)12, the zirconium atoms have a distorted butterfly arrangement; their coordination geometry is square-antiprismatically coordinated by eight oxygen atomes. In Zr4O2)OMc)12, the zirconium atoms have a distorted butterfly arrangement; their coordination geometry is square-antiprismatic or capped octahedral.
A Nonvolatile Organic Memory Device Using ITO Surfaces Modified by Ag‐Nanodots

We report on a single‐layer organic memory device made of poly(N‐vinylcarbazole) embedded between an Al electrode and ITO modified with Ag nanodots (Ag‐NDs). Devices exhibit high ON/OFF switching ratios of 104. This level of performance could be achieved by modifying the ITO electrodes with some Ag‐NDs that act as trapping sites, reducing the current in the OFF state. Temperature dependence of the electrical characteristics suggest that the current of the low‐resistance state can be attributed to Schottky charge tunnelling through low‐resistance pathways of Al particles in the polymer layer and that the high‐resistance state can be controlled by charge trapping by the Al particles and Ag‐NDs.
Couple Simulation: A Novel Approach for Evaluating Models of Human Mate Choice

Choosing a mate is perhaps the most important decision a sexually reproducing organism makes in its lifetime. And yet, psychologists lack a precise description of human mate choice, despite sustained attention from several theoretical perspectives. Here, I argue this limited progress owes to the complexity of mate choice and describe a new modeling approach, called “couple simulation,” designed to compare models of mate choice by challenging them to reproduce real couples within simulated mating markets. I present proof-of-concept simulations that demonstrate couple simulation can identify a population’s true model of mate choice. Furthermore, I apply couple simulation to two samples of real couples and find that the method (a) successfully reconstructs real-world couples, (b) discriminates between models of mate choice, and (c) predicts a wide range of dimensions of relationship quality. Collectively, these results provide evidence that couple simulation offers a framework useful for evaluating theories of human mate choice.
Cascaded deep transfer learning on thoracic CT in COVID-19 patients treated with steroids

Abstract. Purpose: Given the recent COVID-19 pandemic and its stress on global medical resources, presented here is the development of a machine intelligent method for thoracic computed tomography (CT) to inform management of patients on steroid treatment. Approach: Transfer learning has demonstrated strong performance when applied to medical imaging, particularly when only limited data are available. A cascaded transfer learning approach extracted quantitative features from thoracic CT sections using a fine-tuned VGG19 network. The extracted slice features were axially pooled to provide a CT-scan-level representation of thoracic characteristics and a support vector machine was trained to distinguish between patients who required steroid administration and those who did not, with performance evaluated through receiver operating characteristic (ROC) curve analysis. Least-squares fitting was used to assess temporal trends using the transfer learning approach, providing a preliminary method for monitoring disease progression. Results: In the task of identifying patients who should receive steroid treatments, this approach yielded an area under the ROC curve of 0.85±0.10 and demonstrated significant separation between patients who received steroids and those who did not. Furthermore, temporal trend analysis of the prediction score matched expected progression during hospitalization for both groups, with separation at early timepoints prior to convergence near the end of the duration of hospitalization. Conclusions: The proposed cascade deep learning method has strong clinical potential for informing clinical decision-making and monitoring patient treatment.