Miracle-dz/UniFAR-FTUs huggingface dataset:
Hashimoto’s thyroiditis is associated with elevated serum uric acid to high density lipoprotein-cholesterol ratio

Abstract Background. Hashimoto’s thyroiditis (HT) is an auto-immune condition characterized with lymphocytic and fibroblastic infiltration of the thyroid gland. The rate of uric acid and HDL cholesterol – so called as uric acid to HDL ratio (UHR) has been shown to be elevated in inflammatory conditions diseases. We aimed to compare UHR and other laboratory parameters of the patients with HT to those values in healthy controls. Methods. The patients diagnosed with HT by medical history, physical examination, elevated thyroid autoantibodies in serum and characteristic sonographic findings in outpatient internal medicine clinics of our institution were enrolled to the present retrospective study. Age and sex matched healthy volunteers were enrolled as controls. UHR of the HT patients and control subjects were compared. Results. The mean UHR of the HT group was 11% ± 4 %, while UHR of the control group was 8% ± 2% (p<0.001). UHR was significantly and positively correlated with thyroid stimulating hormone (TSH) (r=0.26, p=0.01) and negatively correlated with free T4 (FT4) (r=−0.22, p=0.04) levels. The sensitivity and specificity of the UHR level were greater than 8.3%: were 74% and 52%, respectively (AUC: 0.74, p<0.001, 95% CI: 0.64–0.84). Conclusion. We suggest that UHR is a reliable and useful marker for HT. Therefore, it may be helpful in establishing the diagnosis of HT in addition to other diagnostic tools.
Serum. Levels of Dihydroneopterin and Soluble Cytokine Receptors in Major Depression

The serum levels of dihydroneopterin (NH2), soluble interleukin -6 receptor (sIL-6R), soluble tumor necrosis factor receptor (sTNF-R) type I and type II were measured in 18 patients with major depression before and after drug treatment and in age- and gender-matched healthy controls. The NH2 and sTNF-R type II levels were significantly higher both in untreated and treated patients when compared to the controls. The sTNF-R type I levels were significantly lower in untreated depressed patients than the controls and significantly increased after drug treatment when compared to those prior to treatment.
Genomic features of Mycobacterium avium subsp. hominissuis isolated from pigs in Japan

Mycobacterium avium subsp. hominissuis (MAH) is one of the most important agents causing non-tuberculosis mycobacterial infection in humans and pigs. Genome analysis on MAH of human isolates has been proceeding, however, those of pigs are limited despite its potential source of infection to human. In the current study, we obtained 30 draft genome sequences of MAH of pigs reared in Japan. The 30 draft genomes consisted of 4,848,678 – 5,620,788 bp length, 4,652 – 5,388 coding genes and 46 – 75 (Med: 47) tRNAs. All isolates had restriction modification associated genes and 185 – 222 predicted virulence genes. Two isolates had tRNA arrays and one isolate had a clustered regularly interspaced short palindromic repeat (CRISPR) region. Our results will be useful for evaluation of the ecology of MAH by providing a foundation for genome-based epidemiological studies.
Predicting drug targets by homology modelling of Pseudomonas aeruginosa proteins of unknown function

Efficacies of antibiotics to treat bacterial infections rapidly decline due to antibiotic resistance. This stimulated the development of novel antibiotics, but most attempts failed. As a response, the idea of mining uncharacterised genes of pathogens to identify potential targets for entirely new classes of antibiotics raised. Without knowing the biochemical function of a protein it is difficult to validate its potential for drug targeting; therefore progress in the functional characterisation of bacterial proteins of an unknown function must be accelerated. Here we present a paradigm for comprehensively predicting biochemical functions of a large set of proteins encoded by hypothetical genes in human pathogens, to identify candidate drug targets. A high-throughput approach based on homology modelling with ten templates per target protein was applied on the set of 2103 P. aeruginosa proteins encoded by hypothetical genes. Obtained >21000 homology modelling results and available biological and biochemical information about several thousand templates was scrutinised to predict the function of reliably modelled proteins of unknown function. This approach resulted in assigning, one or often multiple, putative functions to hundreds of enzymes, ligand-binding proteins and transporters. New biochemical functions were predicted for 41 proteins whose essential or virulence-related roles in P. aeruginosa were already experimentally demonstrated. Eleven of them were shortlisted as promising drug targets which participate in essential pathways (maintaining genome and cell wall integrity), virulence-related processes (adhesion, cell motility, host recognition) or antibiotic resistance, which are general drug targets. These proteins are conserved among other WHO priority pathogens but not in humans, therefore they represent high-potential targets for pre-clinical studies. These and many more biochemical functions assigned to uncharacterised proteins of P. aeruginosa, available as PaPUF database may guide the design of experimental screening of inhibitors which is a crucial step toward validation of the most potential targets for the development of novel drugs against P. aeruginosa and other high-priority pathogens.
Deep learning trained on H&E tumor ROIs predicts HER2 status and Trastuzumab treatment response in HER2+ breast cancer

The current standard of care for many patients with HER2-positive breast cancer is neoadjuvant chemotherapy in combination with anti-HER2 agents, based on HER2 amplification as detected by in situ hybridization (ISH) or protein immunohistochemistry (IHC). However, hematoxylin & eosin (H&E) tumor stains are more commonly available, and accurate prediction of HER2 status and anti-HER2 treatment response from H&E would reduce costs and increase the speed of treatment selection. Computational algorithms for H&E have been effective in predicting a variety of cancer features and clinical outcomes, including moderate success in predicting HER2 status. In this work, we present a novel convolutional neural network (CNN) approach able to predict HER2 status with increased accuracy over prior methods. We trained a CNN classifier on 188 H&E whole slide images (WSIs) manually annotated for tumor regions of interest (ROIs) by our pathology team. Our classifier achieved an area under the curve (AUC) of 0.90 in cross-validation of slide-level HER2 status and 0.81 on an independent TCGA test set. Within slides, we observed strong agreement between pathologist annotated ROIs and blinded computational predictions of tumor regions / HER2 status. Moreover, we trained our classifier on pre-treatment samples from 187 HER2+ patients that subsequently received trastuzumab therapy. Our classifier achieved an AUC of 0.80 in a five-fold cross validation. Our work provides an H&E-based algorithm that can predict HER2 status and trastuzumab response in breast cancer at an accuracy that is better than IHC and may benefit clinical evaluations.
Control of Arabidopsis shoot stem cell homeostasis by two antagonistic CLE peptide signalling pathways

Stem cell homeostasis in plant shoot meristems requires tight coordiantion between stem cell proliferation and cell differentiation. In Arabidopsis, stem cells express the secreted dodecapeptide CLAVATA3 (CLV3), which signals through the leucine-rich repeat (LRR)–receptor kinase CLAVATA1 (CLV1) and related CLV1-family members to downregulate expression of the homeodomain transcription factor WUSCHEL (WUS). WUS protein moves from cells below the stem cell domain to the meristem tip and promotes stem cell identity, together with CLV3 expression, generating a negative feedback loop. How stem cell activity in the meristem centre is coordinated with organ initiation and cell differentiation at the periphery is unknown. We show here that the CLE40 gene, encoding a secreted peptide closely related to CLV3, is expressed in the SAM in differentiating cells in a pattern complementary to that of CLV3. CLE40 promotes WUS expression via BAM1, a CLV1-family receptor, and CLE40 expression is in turn repressed in a WUS-dependent manner. Together, CLE40-BAM1-WUS establish a second negative feedback loop. We propose that stem cell homeostasis is achieved through two intertwined pathways that adjust WUS activity and incorporate information on the size of the stem cell domain, via CLV3-CLV1, and on cell differentiation via CLE40-BAM1.
The TR locus annotation and characteristics of Rhinolophus ferrumequinum

T cell antigen receptors (TCRs) in vertebrate could be divided into αβ or γδ, which are encoded by TRA/D, TRG and TRB loci respectively. TCRs play a central role in mammal cellular immunity, which are functionally produced by rearrangement of V gene, D gene, J gene and C gene in the loci. Bat is the only mammal with flying ability, and is considered as the main host of zoonotic virus, which occupies an important position in the field of public health. At present, little is known about the composition of bat TRs gene. According to the whole genome sequencing results of the Rhinolophus ferrumequinum, and referring to the TR/IG annotation rules formulated by IMGT. We make a complete annotation on the TRA/D, TRG and TRB loci of the Rhinolophus ferrumequinum. A total of 128 V segments, 3 D segments, 85 J segments and 6 C segments were annotated, in addition to compared with the known mammalian, the characteristics of the TRs locus and germline genes of the Rhinolophus ferrumequinum were analyzed.
A novel DNA binding mode, conformational change and intramolecular signaling in MutS upon mismatch recognition in replication DNA structures

MutS initiates mismatch repair by recognizing mismatches in newly replicated DNA. Specific interactions between MutS and mismatches within double-stranded DNA promote ADP-ATP exchange and a conformational change into a sliding clamp. Here, we demonstrated that MutS from Pseudomonas aeruginosa associates with primed DNA replication substrates. The predicted structure of this MutS-DNA complex revealed a new DNA binding site, in which Asn 279 and Arg 272 appeared to directly interact with the 3’-OH terminus of primed DNA. Mutation of these residues resulted in a noticeable defect in the interaction of MutS with replication DNA substrates. Remarkably, MutS interaction with a mismatch within primed DNA induced a compaction of the protein structure and impaired the formation of an ATP-bound sliding clamp. Our findings reveal a novel DNA binding mode, conformational change and intramolecular signaling for MutS recognition of mismatches within DNA replication structures.
Remittances and Households within Neoliberalism: A “Triple Movement”

Abstract The article aims at advancing feminist institutional theory by expanding and revising Karl Polanyi’s framework of capitalist development as it applies to remittances and transnational households. The triple movement is offered by Nancy Fraser to revisit Karl Polanyi’s conception of the double-movement from a feminist perspective. It encompasses not only marketization and social protection, but also emancipation from social relations and markets. The article applies this concept to an understanding of remittance-driven labor exports and the formation of transnational households as an emerging institution of social protection. The discussion focuses on labor as a globalized fictitious commodity, global care chains, and the effects of COVID-19. The article points to the centrality of social subordination in marketization of remittances and labor, as well as to the fragility of this approach to social provisioning.
Steam Flash Explosion Assisted Dissolution of Keratin from Feathers

A steam flash explosion (SFE) process followed by alkali extraction was applied for extracting keratin from duck feathers. Duck feathers were exploded at different steam pressures (1.4–2.0 MPa) for 0.5–5 min. Results showed that combined SFE with alkaline treatment could effectively promote the dissolution of feather keratin. The optimal extraction conditions in this study were 0.4% NaOH, a solvent to material ratio of 20:1 (v/w), 25 °C, and 1 h. An extraction rate of feathers of 65.78% and a yield of keratin of 42.78% was obtained when the steam exploded feather (1.6 MPa, 1 min) was treated under the above conditions. The extracted keratin retained most of the protein backbone, with the breakage of disulfide cross-links and hydrogen bonds. It was also found that the dissolution involved the fragmentation of macromolecular chains and a loss of some ordered structure. SFE assisted dissolution of keratin from feathers, without the use of harmful reagents, offers a possibility of large-scale exploitation.
Activated Carbon-Coated Carbon Nanotubes for Energy Storage in Supercapacitors and Capacitive Water Purification

Polypyrrole-coated multiwalled carbon nanotubes (PPy-MWCNT) were used for the fabrication of activated carbon-coated MWCNT doped with nitrogen (N-AC-MWCNT). The conceptually new method for the fabrication of non-agglomerated PPy-MWCNT with good coating uniformity allowed the fabrication of uniform and well-dispersed N-AC-MWCNT with high surface area. The use of N-AC-MWCNT allowed the fabrication of supercapacitor electrodes with high mass loading in the range of 15–35 mg cm–2 and with a high active material to current collector mass ratio of 0.21–0.50. The N-AC-MWCNT electrodes showed excellent electrochemical performance in aqueous 0.5 M Na2SO4 electrolyte. The maximum specific capacitance of 3.6 F cm–2 (103.1 F g–1) was achieved for mass loading of 35 mg cm–2 at a scan rate of 2 mV s–1. The aqueous supercapacitor cells, based on N-AC-MWCNT electrodes, exhibited excellent performance with energy density of 16.1 mWh g–1, power density of 14.4 W g–1, and enlarged voltage window of 1.8 V. The individual ele.
Enhanced tuning efficiency and sensitivity based on mode transition of symmetric cladding modes in fibre Bragg grating overlaid with high refractive nm-thick film

In this paper, we theoretically investigate the tuning characteristics of a four-layer structure optic fibre Bragg grating (FBG) coated with high refractive index (HRI) overlay. The attention is mainly focused on the analysis of the effects of the mode transition and the mode reorganization on the tuning sensitivity to the overlay HRI of the structure. The cladding diameter of FBG is also considered as a parameter for enhancing the sensitivity of FBG to HRI. Moreover, different cladding modes show different sensitivities. For FBG with negative thermo-optical coefficient coating material, the thermal property of the structure could be effectively suppressed by selecting an optimal fibre cladding diameter. The reported results demonstrate the possibility of this structure can be used as thermal-stable tunable all-fibre photonic device, such as filter, modulator and sensing element.
Can Régulation Theory Inform Institutional Analyses of Contemporary Social Provisioning?

Abstract: A focus on institutions is shared by Régulation Theory and Institutional Economics although each holds a different view of the organization of the capitalist economy. It is argued that, despite the lack of definitional clarity of the term “institution,” Régulation Theory provides “institutional insights” which could be usefully deployed by Institutional Economics. It is also posited that both heterodox traditions should more explicitly conceive of institutions to account for phenomena that transcend national borders, and to render explicit the social ontology underpinning an institution’s conceptualization, otherwise the methodological usefulness of this analytical construct to elucidate social reality is reduced.
Do Mothers’ Status, Autonomy, and Parenting Style Influence Their Children’s Initiation Into Smoking and Alcohol Use?

Abstract This study uses the Cebu Longitudinal Health and Nutrition Survey (CLHNS) data set and Cox proportional hazards models to determine whether factors relating to mothers’ status and autonomy, as well as other parenting and socioeconomic/sociodemographic variables, are associated with the early onset of children’s risky behaviors, namely smoking and drinking alcohol. We find that the women empowerment variables, especially those that have direct bearing on the mother–child relationship, have a significant effect in delaying or hastening the onset of risky behavior. Those factors that compete for the time spent in parenting, such as the mother working, hastens their children’s initiation into these risky habits. On the other hand, mothers’ involvement in household decision-making delays smoking in females.
A Bird's-Eye View of Exercise Intervention in Treating Depression Among Teenagers in the Last 20 Years: A Bibliometric Study and Visualization Analysis

Background: Exercise is medicine. Multiple studies on the effects and mechanisms of exercise in treating depression among teenagers and adolescents have been widely reported. However, literature involving scientometric analysis of this topic is sparse. Here, we endeavored to conduct a bibliometric study and visualization analysis to give a bird's-eye view of publications between 2000 and 2020 on exercise therapy treating depression. Methods: Relevant original publications were obtained from the Science Citation Index Expanded in the Web of Science Core Collection (WoSCC) database between 2000 and 2020. CiteSpace (5.7.R 5) and VOSviewer (1.6.16) software were used to perform bibliometric analysis of countries, institutions, categories, journals, authors, references, and keywords involved in this topic. Results: A total number of 975 articles on this field were retrieved from the WoSCC database and we identified an overall increase in the amount of publications over the past two decades, with the United States and Harvard University leading the field. Most related publications were published in the journals with a focus on sport, medicine, rehabilitation, psychology, and health, as represented by the dual-map overlay. A series of authors and co-cited authors were identified as main contributors in the exercise-depression-teenager domain. Three major clusters were explored based on the reference co-citation analysis: “exercise,” “suicide,” and “concussion”. Conclusions: Current concerns and hotspots of exercise intervention in depression treatments were summarized by “individual level,” “social level,” “role of exercise,” and “research quality. ” We considered that the following four directions were potential future perspectives: “research on the effect of specific exercise intervention,” “research on the essence of exercise and sports,” “research on the combination mode of ‘exercise + X',” and “research on the micro and molecular level,” which should receive more attention.
Light-Responsive Micelles Loaded With Doxorubicin for Osteosarcoma Suppression

The enhancement of tumor targeting and cellular uptake of drugs are significant factors in maximizing anticancer therapy and minimizing the side effects of chemotherapeutic drugs. A key challenge remains to explore stimulus-responsive polymeric nanoparticles to achieve efficient drug delivery. In this study, doxorubicin conjugated polymer (Poly-Dox) with light-responsiveness was synthesized, which can self-assemble to form polymeric micelles (Poly-Dox-M) in water. As an inert structure, the polyethylene glycol (PEG) can shield the adsorption of protein and avoid becoming a protein crown in the blood circulation, improving the tumor targeting of drugs and reducing the cardiotoxicity of doxorubicin (Dox). Besides, after ultraviolet irradiation, the amide bond connecting Dox with PEG can be broken, which induced the responsive detachment of PEG and enhanced cellular uptake of Dox. Notably, the results of immunohistochemistry in vivo showed that Poly-Dox-M had no significant damage to normal organs. Meanwhile, they showed efficient tumor-suppressive effects. This nano-delivery system with the light-responsive feature might hold great promises for the targeted therapy for osteosarcoma.
Control of Streptomyces alfalfae XY25T Over Clubroot Disease and Its Effect on Rhizosphere Microbial Community in Chinese Cabbage Field Trials

Clubroot caused by Plasmodiophora brassicae is one of the most destructive diseases in cruciferous crops. Streptomyces alfalfae XY25T, a biological control agent, exhibited great ability to relieve clubroot disease, regulate rhizosphere bacterial and fungal communities in Chinese cabbage, and promote its growth in greenhouse. Therefore, field experiments were carried out to investigate the effects of S. alfalfae XY25T on clubroot and rhizosphere microbial community in Chinese cabbage. Results showed that the control efficiency of clubroot by S. alfalfae XY25T was 69.4%. Applying the agent can alleviate soil acidification; increase the contents of soil organic matter, available nitrogen, available phosphorus, and available potassium; and enhance activities of invertase, urease, catalase, and alkaline phosphatase. During Chinese cabbage growth, bacterial diversity decreased first and then increased, and fungal diversity decreased gradually after inoculation with S. alfalfae XY25T. High-throughput sequencing analysis showed that the main bacterial phyla were Proteobacteria, Bacteroidetes, Acidobacteria, and Planctomycetes, and the major fungal phyla were Ascomycota and Basidiomycota in rhizosphere soil. The dominant bacterial genera were Flavobacterium, Candidatus, Pseudomonas, Stenotrophomonas, Sphingomonas, Flavisolibacter, and Gemmatimonbacteria with no significant difference in abundance, and the major fungal genera were Monographella, Aspergillus, Hypocreales, Chytridiaceae, Fusarium, Pleosporales, Agaricales, Mortierella, and Pleosporales. The significant differences were observed among Pleosporales, Basidiomycota, Colletotrichum, two strains attributed to Agaricales, and another two unidentified fungi by using S. alfalfae XY25T. Moreover, quantitative real-time PCR results indicated that P. brassicae content was significantly decreased after the agent inoculation. In conclusion, S. alfalfae XY25T can affect rhizosphere microbial communities; therefore, applying the agent is an effective approach to reduce the damage caused by clubroot.