Miracle-dz/UniFAR-FTUs huggingface dataset:
How Hospitalized Older Adults and Physicians Negotiate Plan-of-Care Decisions during Daily Rounds

ABSTRACT The purpose of this study is to explore how older adults and physicians negotiate the plan of care during daily rounds in the hospital setting. We audio-recorded 40 physician–patient interactions during daily rounds in a small teaching hospital. We analyzed the data using conversation analysis, a qualitative method that examines the turns-of-talk during interactions. We focused the analysis on how physicians introduced the plan of care and how the plan of care was subsequently negotiated with the patient. Physicians often introduced the plan in two different ways that have a persuasive design: leading with evidence and medical expertise or, for sensitive topics in which the plan could be disagreeable, using preplan sequences to delicately introduce the plan of care and assess patient response. Patients negotiated the plan of care by displaying resistance, both passively and actively. Despite patients sharing their evidence for their preferred plan of care in resisting the physician’s plan, physicians often closed the negotiation by reorienting to a different aspect of the plan of care.
Serious health threats of novel adulterants of the street heroin: a report from India during the COVID-19 pandemic

The COVID-19 pandemic and a consequent nationwide lockdown in India for several weeks had restricted the access to street heroin and treatment for substance abuse. Use of cutting agents to increase the volume or psychoactive effect has been widely practised under such circumstances. Our patient with opioid use disorder chased heroin with an unknown cutting agent to enhance psychoactive effect from the limited quantities of heroin. He suffered from an abrupt onset sedation, weakness, postural imbalance, slurred speech, cognitive dysfunctions and disinhibited behaviour. Symptoms rapidly reversed following abstinence and initiation of buprenorphine–naloxone. Gas chromatography-mass spectrometric analysis of the adulterant revealed high concentrations of benzodiazepines and barbiturates, alongside the usual cutting agents—caffeine and acetaminophen. Abrupt reduction in availability of ‘street drugs’ in conjunction with poor healthcare access can lead to the use of novel adulterants with potentially serious clinical and public health implications.
Repetitive Transcranial Magnetic Stimulation for Major Depressive Disorder in Older Adults: Systematic Review and Meta-Analysis.

BACKGROUND Major Depressive Disorder (MDD) in older adults is a serious public health concern. Repetitive transcranial magnetic stimulation (rTMS) is a non-pharmacological intervention approved for Major Depressive Disorder (MDD) treatment in adults, but its value in older adults remains unknown. The present study aims to systematically review and meta-analyze evidence of rTMS efficacy in MDD treatment among older adults. METHODS We systematically reviewed the literature for randomized controlled trials (RCTs) and open-label studies assessing rTMS for the treatment of MDD in patients older than 50 years-old, published until June 2020. Random-effects meta-analyses using standardized mean differences (SMD) were conducted to assess change in depression severity score (primary outcome), while odds-ratios (OR) were used to assess secondary categorical outcomes (response and remission). Additionally, univariate meta-regression analyses were performed to identify potential predictors of change in depression severity scores. RESULTS Fourteen RCTs were included in meta-analyses and 26 studies (10 RCTs and 16 open-label studies) in meta-regression. Active rTMS was significantly superior to sham-treatment for reduction of severity (SMD=0.36; 95%CI=0.13-0.60), as well as response (OR=3.26; 95%CI=2.11-5.04) and remission (OR=4.63; 95%CI=2.24-9.55). Studies were of moderate to high quality, with funnel plots and Egger's regression test not suggestive of publication bias. In meta-regressions, higher mean age and number of sessions were significantly associated to greater improvement. CONCLUSIONS Our results support that rTMS is an effective, safe and well-tolerated treatment for MDD in older adults, and that it should be considered in the treatment of this vulnerable population.
Distant Supervision for Mental Health Management in Social Media: Suicide Risk Classification System Development Study

Background Web-based social media provides common people with a platform to express their emotions conveniently and anonymously. There have been nearly 2 million messages in a particular Chinese social media data source, and several thousands more are generated each day. Therefore, it has become impossible to analyze these messages manually. However, these messages have been identified as an important data source for the prevention of suicide related to depression disorder. Objective We proposed in this paper a distant supervision approach to developing a system that can automatically identify textual comments that are indicative of a high suicide risk. Methods To avoid expensive manual data annotations, we used a knowledge graph method to produce approximate annotations for distant supervision, which provided a basis for a deep learning architecture that was built and refined by interactions with psychology experts. There were three annotation levels, as follows: free annotations (zero cost), easy annotations (by psychology students), and hard annotations (by psychology experts). Results Our system was evaluated accordingly and showed that its performance at each level was promising. By combining our system with several important psychology features from user blogs, we obtained a precision of 80.75%, a recall of 75.41%, and an F1 score of 77.98% for the hardest test data. Conclusions In this paper, we proposed a distant supervision approach to develop an automatic system that can classify high and low suicide risk based on social media comments. The model can therefore provide volunteers with early warnings to prevent social media users from committing suicide.
Response of Methanogen Communities to the Elevation of Cathode Potentials in Bioelectrochemical Reactors Amended with Magnetite

Converting CO2 to CH4 through bioelectrochemistry is a promising approach to the development of green energy biotechnology. This process, however, requires low cathode potentials, which entails a cost. ABSTRACT Electromethanogenesis refers to the process whereby methanogens utilize current for the reduction of CO2 to CH4. Setting low cathode potentials is essential for this process. In this study, we tested if magnetite, an iron oxide mineral widespread in the environment, can facilitate the adaptation of methanogen communities to the elevation of cathode potentials in electrochemical reactors. Two-chamber electrochemical reactors were constructed with inoculants obtained from paddy field soil. We elevated cathode potentials stepwise from the initial −0.6 V versus the standard hydrogen electrode (SHE) to −0.5 V and then to −0.4 V over the 130 days of acclimation. Only weak current consumption and CH4 production were observed in the bioreactors without magnetite. However, significant current consumption and CH4 production were recorded in the magnetite bioreactors. The robustness of electroactivity of the magnetite bioreactors was not affected by the elevation of cathode potentials from −0.6 V to −0.4 V. However, the current consumption and CH4 production were halted in the bioreactors without magnetite when the cathode potentials were elevated to −0.4 V. Methanogens related to Methanospirillum were enriched on the cathode surfaces of magnetite bioreactors at −0.4 V, while Methanosarcina relatively dominated in the bioreactors without magnetite. Methanobacterium also increased in the magnetite bioreactors but stayed off electrodes at −0.4 V. Apparently, the magnetite greatly facilitates the development of biocathodes, and it appears that with the aid of magnetite, Methanospirillum spp. can adapt to the high cathode potentials, performing efficient electromethanogenesis. IMPORTANCE Converting CO2 to CH4 through bioelectrochemistry is a promising approach to the development of green energy biotechnology. This process, however, requires low cathode potentials, which entails a cost. In this study, we tested if magnetite, a conductive iron mineral, can facilitate the adaptation of methanogens to the elevation of cathode potentials. In two-chamber reactors constructed by using inoculants obtained from paddy field soil, biocathodes developed robustly in the presence of magnetite, whereas only weak activities in CH4 production and current consumption were observed in the bioreactors without magnetite. The elevation of cathode potentials did not affect the robustness of electroactivity of the magnetite bioreactors over the 130 days of acclimation. Methanospirillum strains were identified as the key methanogens associated with the cathode surfaces during the operation at high potentials. The findings reported in this study shed new light on the adaptation of methanogen communities to the elevated cathode potentials in the presence of magnetite.
Methodology, selection, and integration of fracture healing assessments in mice

Long bone fractures are one of the most common and costly medical conditions encountered after trauma. Characterization of the biology of fracture healing and development of potential medical interventions generally involves animal models of fracture healing using varying genetic or treatment groups, then analyzing relative repair success via the synthesis of diverse assessment methodologies. Murine models are some of the most widely used given their low cost, wide variety of genetic variants, and rapid breeding and maturation. This review addresses key concerns regarding fracture repair investigations in mice and may serve as a guide in conducting and interpreting such studies. Specifically, this review details the procedures, highlights relevant parameters, and discusses special considerations for the selection and integration of the major modalities used for quantifying fracture repair in such studies, including X‐ray, microcomputed tomography, histomorphometric, biomechanical, gene expression and biomarker analyses.
Closed Genome Sequence of Clostridium botulinum Strain IBCA10-7060 Type Bh

Clostridium botulinum strain IBCA10-7060 was isolated from a stool specimen from an infant botulism patient and is the only Clostridium botulinum strain known that produces botulinum toxin type H. We present here its 4.09-Mbp closed genome sequence. ABSTRACT Clostridium botulinum strain IBCA10-7060 was isolated from a stool specimen from an infant botulism patient and is the only Clostridium botulinum strain known that produces botulinum toxin type H. We present here its 4.09-Mbp closed genome sequence.
Kidney biopsy chronicity grading in antineutrophil cytoplasmic antibody-associated vasculitis

Abstract Background Kidney biopsy is valuable for prognostic assessment of renal outcomes in antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) with glomerulonephritis (AAV-GN) but the impact of chronic changes is not determined. Methods We conducted a retrospective cohort study of myeloperoxidase (MPO)- or proteinase 3 (PR3)-ANCA-positive patients with AAV and active renal disease. We applied the Mayo Clinic Chronicity Score (MCCS) and validated and evaluated its implications on outcome prediction in AAV-GN. Results We analyzed 329 patients with kidney biopsies available to score. The extent of chronicity was graded by MCCS as minimal [102 (31.0%)], mild [106 (32.2%)], moderate [86 (26.1%)] and severe [35 (10.6%)]. The MCCS grades correlated with the degree of renal function impairment at presentation [mean estimated glomerular filtration rate (eGFR) 48.3 versus 29.2 versus 23.7 versus 18.5 mL/min/1.73 m2, respectively; P < 0.0001]. Higher degrees of the individual components of the MCCS (glomerulosclerosis, interstitial fibrosis, tubular atrophy and arteriosclerosis) were associated with lower median eGFR (P < 0.0001) and decreased event-free [kidney failure (KF) and death] survival (P = 0.002, P < 0.0001, P < 0.0001 and P = 0.017, respectively). Patients with lower MCCS grades recovered renal function more frequently (P < 0.0001). Increasing MCCS grades were associated with decreased renal recovery (P = 0.001), more frequent events and shorter time to KF (P < 0.0001), KF and death (P < 0.0001) and death (P = 0.042), independent of the remission induction treatment used (cyclophosphamide or rituximab). The MCCS stratified renal outcomes for each MCCS grade and can be used in clinical practice as a cutoff for KF prediction (MCCS ≥4). Conclusions Chronic changes on kidney histology independently predict renal function, outcomes and response to treatment in AAV-GN.
Genome Mining and Metabolic Profiling Uncover Polycyclic Tetramate Macrolactams from Streptomyces koyangensis SCSIO 5802

We have previously shown deep-sea-derived Streptomyces koyangensis SCSIO 5802 to produce two types of active secondary metabolites, abyssomicins and candicidins. Here, we report the complete genome sequence of S. koyangensis SCSIO 5802 employing bioinformatics to highlight its potential to produce at least 21 categories of natural products. In order to mine novel natural products, the production of two polycyclic tetramate macrolactams (PTMs), the known 10-epi-HSAF (1) and a new compound, koyanamide A (2), was stimulated via inactivation of the abyssomicin and candicidin biosynthetic machineries. Detailed bioinformatics analyses revealed a PKS/NRPS gene cluster, containing 6 open reading frames (ORFs) and spanning ~16 kb of contiguous genomic DNA, as the putative PTM biosynthetic gene cluster (BGC) (termed herein sko). We furthermore demonstrate, via gene disruption experiments, that the sko cluster encodes the biosynthesis of 10-epi-HSAF and koyanamide A. Finally, we propose a plausible biosynthetic pathway to 10-epi-HSAF and koyanamide A. In total, this study demonstrates an effective approach to cryptic BGC activation enabling the discovery of new bioactive metabolites; genome mining and metabolic profiling methods play key roles in this strategy.
Comparisons of Outcomes between Patients with Direct and Indirect Acute Respiratory Distress Syndrome Receiving Extracorporeal Membrane Oxygenation

Acute respiratory distress syndrome (ARDS) is a heterogeneous syndrome caused by direct (local damage to lung parenchyma) or indirect lung injury (insults from extrapulmonary sites with acute systemic inflammatory response), the clinical and biological complexity can have a profound effect on clinical outcomes. We performed a retrospective analysis of 152 severe ARDS patients receiving extracorporeal membrane oxygenation (ECMO). Our objective was to assess the differences in clinical characteristics and outcomes of direct and indirect ARDS patients receiving ECMO. Overall hospital mortality was 53.3%. A total of 118 patients were assigned to the direct ARDS group, and 34 patients were assigned to the indirect ARDS group. The 28-, 60-, and 90-day hospital mortality rates were significantly higher among indirect ARDS patients (all p < 0.05). Cox regression models demonstrated that among direct ARDS patients, diabetes mellitus, immunocompromised status, ARDS duration before ECMO, and SOFA score during the first 3 days of ECMO were independently associated with mortality. In indirect ARDS patients, SOFA score and dynamic compliance during the first 3 days of ECMO were independently associated with mortality. Our findings revealed that among patients receiving ECMO, direct and indirect subphenotypes of ARDS have distinct clinical outcomes and different predictors for mortality.
Characterization of Phytoestrogens in Medicago sativa L. and Grazing Beef Cattle

Phytoestrogens are plant-produced bioactive secondary metabolites known to play an integral role in plant defense that frequently accumulate in times of stress and/or microbial infection. Phytoestrogens typically belong to two distinct chemical classes; flavonoids (isoflavones) and non-flavonoids (lignans and coumestans). Upon consumption by livestock, high concentrations of phytoestrogens can cause long-term disruption in reproduction due to structural similarities with mammalian estrogens and their tendency to bind estrogen receptors. Wide variation in phytoestrogen concentration has been reported in pasture legumes and corresponding silage or hay. Lucerne is a common perennial pasture legume in temperate climates, but information on phytoestrogen production or accumulation in grazing livestock is currently limited. Therefore, metabolic profiling using UHPLC-MS-QToF was performed to identify and quantitate key phytoestrogens in both fresh and dried lucerne fodder from replicated field or controlled glasshouse environments. Phytoestrogens were also profiled in the blood plasma of Angus cattle grazing field-grown lucerne. Results revealed that phytoestrogens varied quantitatively and qualitatively among selected lucerne cultivars grown under glasshouse conditions. Fresh lucerne samples contained higher concentrations of coumestans and other phytoestrogenic isoflavones than did dried samples for all cultivars profiled, with several exceeding desirable threshold levels for grazing cattle. Coumestans and isoflavones profiled in plasma of Angus heifers grazing lucerne increased significantly over a 21-day sampling period following experimental initiation. Currently, threshold concentrations for phytoestrogens in plasma are unreported. However, total phytoestrogen concentration exceeded 300 mg·kg−1 in fresh and 180 mg·kg−1 in dried samples of selected cultivars, suggesting that certain genotypes may upregulate phytoestrogen production, while others may prove suitable sources of fodder for grazing livestock.
Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis

Development of cervical cancer is directly associated with integration of human papillomavirus (HPV) genomes into host chromosomes and subsequent modulation of HPV oncogene expression, which correlates with multi-layered epigenetic changes at the integrated HPV genomes. However, the process of integration itself and dysregulation of host gene expression at sites of integration in our model of HPV16 integrant clone natural selection has remained enigmatic. We now show, using a state-of-the-art ‘HPV integrated site capture’ (HISC) technique, that integration likely occurs through microhomology-mediated repair (MHMR) mechanisms via either a direct process, resulting in host sequence deletion (in our case, partially homozygously) or via a ‘looping’ mechanism by which flanking host regions become amplified. Furthermore, using our ‘HPV16-specific Region Capture Hi-C’ technique, we have determined that chromatin interactions between the integrated virus genome and host chromosomes, both at short- (<500 kbp) and long-range (>500 kbp), appear to drive local host gene dysregulation through the disruption of host:host interactions within (but not exceeding) host structures known as topologically associating domains (TADs). This mechanism of HPV-induced host gene expression modulation indicates that integration of virus genomes near to or within a ‘cancer-causing gene’ is not essential to influence their expression and that these modifications to genome interactions could have a major role in selection of HPV integrants at the early stage of cervical neoplastic progression.
Untargeted Metabolomics Uncovers the Essential Lysine Transporter in Toxoplasma gondii

Apicomplexan parasites are responsible for devastating diseases, including malaria, toxoplasmosis, and cryptosporidiosis. Current treatments are limited by emerging resistance to, as well as the high cost and toxicity of existing drugs. As obligate intracellular parasites, apicomplexans rely on the uptake of many essential metabolites from their host. Toxoplasma gondii, the causative agent of toxoplasmosis, is auxotrophic for several metabolites, including sugars (e.g., myo-inositol), amino acids (e.g., tyrosine), lipidic compounds and lipid precursors (cholesterol, choline), vitamins, cofactors (thiamine) and others. To date, only few apicomplexan metabolite transporters have been characterized and assigned a substrate. Here, we set out to investigate whether untargeted metabolomics can be used to identify the substrate of an uncharacterized transporter. Based on existing genome- and proteome-wide datasets, we have identified an essential plasma membrane transporter of the major facilitator superfamily in T. gondii—previously termed TgApiAT6-1. Using an inducible system based on RNA degradation, TgApiAT6-1 was depleted, and the mutant parasite’s metabolome was compared to that of non-depleted parasites. The most significantly reduced metabolite in parasites depleted in TgApiAT6-1 was identified as the amino acid lysine, for which T. gondii is predicted to be auxotrophic. Using stable isotope-labeled amino acids, we confirmed that TgApiAT6-1 is required for efficient lysine uptake. Our findings highlight untargeted metabolomics as a powerful tool to identify the substrate of orphan transporters.
In vivo hepatoprotective effect of Morinda elliptica stem extract against liver fibrosis induced by thioacetamide

Morinda elliptica L. (Rubiaceae) is a phytomedicinal herb, used to treat gastrointestinal complications in Peninsular Malaysia. The study evaluates the in vivo hepatoprotective activity of ethanolic extract of M. elliptica stem in thioacetamide (TAA) induced liver fibrosis in male Sprague Drawly rats. Thirty adult rats were divided into five groups of six rats each. Rats of the normal control group received intraperitoneal injections (i. p.) of vehicle 10% Tween‐20, 5 ml/kg, and hepatotoxic group 200 mg/kg TAA three times per week respectively. Three supplementary groups were treated with TAA plus daily oral silymarin (50 mg/kg) or M. elliptica (250 or 500 mg/kg). After 8 weeks of treatment, all rats were sacrificed. Liver fibrosis was assessed by gross macroscopic and microscopic tissue analysis, histopathological, and biochemical analysis. The livers of the TAA treated group showed uniform coarse granules, hepatocytic necrosis with lymphocytes infiltration. Contrary, the livers of M. elliptica treated groups (250 and 500 mg/kg) were much smoother and the cell damage was much lesser. The livers of M. elliptica treated groups rats showed elevated activity of SOD and CAT with a significant decrease in MDA level at p < . 0001. The level of liver damage parameters, that is, ALP, ALT, and AST, bilirubin, total protein, and albumin were restored to the normal comparable to silymarin. M. elliptica stem extract significantly promoted normal rat liver architecture with significant perfections in biochemical parameters. The molecular contents of M. elliptica with hepatoprotective influence could be discovered, is the future prospective of this study.