Miracle-dz/UniFAR-FTUs huggingface dataset:
SuCComBase: a manually curated repository of plant sulfur-containing compounds

Abstract Plants produce a wide range of secondary metabolites that play important roles in plant defense and immunity, their interaction with the environment and symbiotic associations. Sulfur-containing compounds (SCCs) are a group of important secondary metabolites produced in members of the Brassicales order. SCCs constitute various groups of phytochemicals, but not much is known about them. Findings from previous studies on SCCs were scattered in published literatures, hence SuCComBase was developed to store all molecular information related to the biosynthesis of SCCs. Information that includes genes, proteins and compounds that are involved in the SCC biosynthetic pathway was manually identified from databases and published scientific literatures. Sets of co-expression data was analyzed to search for other possible (previously unknown) genes that might be involved in the biosynthesis of SCC. These genes were named as potential SCC-related encoding genes. A total of 147 known and 92 putative Arabidopsis thaliana SCC-related genes from literatures were used to identify other potential SCC-related encoding genes. We identified 778 potential SCC-related encoding genes, 4026 homologs to the SCC-related encoding genes and 116 SCCs as shown on SuCComBase homepage. Data entries are searchable from the Main page, Search, Browse and Datasets tabs. Users can easily download all data stored in SuCComBase. All publications related to SCCs are also indexed in SuCComBase, which is currently the first and only database dedicated to plant SCCs. SuCComBase aims to become a manually curated and au fait knowledge-based repository for plant SCCs.
DNA methylation-mediated silencing of miR-204 is a potential prognostic marker for papillary thyroid carcinoma

Background Papillary thyroid carcinoma (PTC) is the most common endocrine malignancy and its incidence has increased over the last few decades. The molecular mechanisms underlying PTC tumorigenesis and progression are still unclear. Patients and methods The microRNA (miRNA) expression patterns of PTC were revealed by miRNA microarray analysis and validated with The Cancer Genome Atlas (TCGA) data. Promoter DNA methylation rates of miR-204 were analyzed by Agena Methylation MassAR-RAY analysis and validated with TCGA data. The underlying molecular mechanisms of miR-204 involved in PTC were studied by bioinformatics analyses. Results A total of 181 differentially expressed miRNAs (89 downregulated and 92 upregulated miRNAs) between PTC and normal tissues were detected in this study. We identified miR-204 as one of the most significantly downregulated miRNAs in PTC. Downregulation of miR-204 was related to PTC extrathyroidal extension, high T-stage, lymph metastasis, BRAF V600E mutation, and aggressive tall cell variant. The Agena MassARRAY results indicated that 12 CpG sites located at the promoter of miR-204 were hypermethylated in PTC tissues compared to normal tissues. The promoter methylation rates of miR-204 in PTC were negatively correlated with the expression levels of miR-204 and its host gene TRPM3. Downregulated miR-204 expression was related to several important pathways and mechanisms involved in tumorigenesis and progression. Conclusion Promoter DNA methylation-silenced miR-204 could serve as a potential diagnostic biomarker of PTC. Downregulation of miR-204 may play an important role in PTC via its involvement in many tumor-related pathways. Novel target genes and putative mechanisms of miR-204 in PTC need to be further validated.
Health Literacy and Clear Bedside Communication: A Curricular Intervention for Internal Medicine Physicians and Medicine Nurses

Introduction Communication remains the backbone of patient-provider relationships, and many health outcomes have been directly attributed to both effective and ineffective communication. We developed an educational intervention to improve bedside communication and increase use of health literacy principles, in part as a response to suboptimal inpatient satisfaction scores. Methods Our intervention consisted of a beside communication curriculum among 37 attending medicine physicians, 76 internal medicine residents, and 85 bedside nurses. The 1- to 1.5-hour curriculum included a didactic session to teach health literacy principles, video demonstrations, group discussion, and role-play. Attending physicians' health literacy knowledge, attitudes, and confidence were evaluated using pre- and postsurveys. Evaluation of the curriculum included Likert-type questions and free-text responses. Results Attending physicians' knowledge and confidence improved (74% correct pre, 100% correct post, p < .001; 4.41 pre, 4.68 post, p = .002, respectively). Certain attitude domains also improved, including importance of team introductions and nurse contributions to bedside rounds (p < .001). Both residents and nurses found the curriculum valuable and planned to incorporate it into their bedside rounding. Discussion A brief, low-cost curricular intervention focusing on clear communication skills and health literacy principles resulted in significant improvements in knowledge and attitudes of attending physicians and was readily incorporated by resident physicians and nurses. This curriculum can be easily implemented in a variety of settings to improve bedside patient-physician communication.
Chemical and sensory quality of sorghum-based extruded product supplemented with defatted soy meal flour

Abstract Effects of defatted soy meal flour (0, 10 and 20%), barrel temperature (135, 150 and 165°C) and feed moisture content (15, 18 and 21%) on proximate composition, minerals, antinutritional factors and sensory properties of extruded products were studied using factorial design. Increasing the addition level of defatted soy meal flour to sorghum flour resulted in a significant increase (P < 0.05) in moisture, crude protein, fat, ash, fiber, Ca and Fe content but decrease in carbohydrate content. Barrel temperature of 135, 150 and 165°C caused a significant reduction in tannin content by about 61, 76 and 86%, and in phytic acid content by 24, 35 and 45%, respectively. The mean sensory values of all extrudates were 3.31 for crispness on 5-point hedonic scale, 4.93, 5.76 and 5.16 for color, flavor and overall acceptability on 7-point hedonic scale, respectively; these indicate all extrudates were well liked by the judges.
Enhanced osteoinduction of electrospun scaffolds with assemblies of hematite nanoparticles as a bioactive interface

Purpose Electrospun scaffolds have been studied extensively for their potential use in bone tissue engineering. However, their hydrophobicity and relatively low matrix stiffness constrain their osteoinduction capacities. In the present study, we studied polymer electrospun scaffolds coated with hydrophilic hematite nanoparticles (αFeNPs) constructed using layer-by-layer (LbL) assembly to construct a bioactive interface between the scaffolds and cells, to improve the osteoinduction capacities of the scaffolds. Materials and methods The morphology of the αFeNPs was assessed. Surface properties of the scaffolds were tested by X-ray photoelectron spectroscopy (XPS), surface water contact angle, and in vitro protein adsorption test. The stiffness of the coating was tested using an atomic force microscope (AFM). In vitro cell assays were performed using rat adipose-derived stem cells (ADSCs). Results Morphology characterizations showed that αFeNPs assembled on the surface of the scaffold, where the nano assemblies improved hydrophilicity and increased surface roughness, with increased surface stiffness. Enhanced initial ADSC cell spread was found in the nano assembled groups. Significant enhancements in osteogenic differentiation, represented by enhanced alkaline phosphatase (ALP) activities, elevated expression of osteogenic marker genes, and increased mineral synthesis by the seeded ADSCs, were detected. The influencing factors were attributed to the better hydrophilicity, rougher surface topography, and harder interface stiffness. In addition, the presence of nanoparticles was believed to provide better cell adhesion sites. Conclusion The results suggested that the construction of a bioactive interface by LbL assembly using αFeNPs on traditional scaffolds should be a promising method for bone tissue engineering.
Univariate Community Assembly Analysis (UniCAA): Combining hierarchical models with null models to test the influence of spatially restricted dispersal, environmental filtering, and stochasticity on community assembly

Abstract Identifying the influence of stochastic processes and of deterministic processes, such as dispersal of individuals of different species and trait‐based environmental filtering, has long been a challenge in studies of community assembly. Here, we present the Univariate Community Assembly Analysis (UniCAA) and test its ability to address three hypotheses: species occurrences within communities are (a) limited by spatially restricted dispersal; (b) environmentally filtered; or (c) the outcome of stochasticity—so that as community size decreases—species that are common outside a local community have a disproportionately higher probability of occurrence than rare species. The comparison with a null model allows assessing if the influence of each of the three processes differs from what one would expect under a purely stochastic distribution of species. We tested the framework by simulating “empirical” metacommunities under 15 scenarios that differed with respect to the strengths of spatially restricted dispersal (restricted vs. not restricted); habitat isolation (low, intermediate, and high immigration rates); and environmental filtering (strong, intermediate, and no filtering). Through these tests, we found that UniCAA rarely produced false positives for the influence of the three processes, yielding a type‐I error rate ≤5%. The type‐II error rate, that is, production of false negatives, was also acceptable and within the typical cutoff (20%). We demonstrate that the UniCAA provides a flexible framework for retrieving the processes behind community assembly and propose avenues for future developments of the framework.
Ultrasound and screening tool for dengue fever

We read the publication “Ultrasound is not useful as a screening tool for dengue fever” with great interest. Parmar et al. noted that “increased gall bladder wall thickness, pleural effusion, ascites, hepatomegaly, and splenomegaly are highly suggestive of dengue fever in clinically suspected cases. However, ultrasound should not be used as a screening tool, as negative ultrasound findings cannot rule out dengue fever due to the low sensitivity of this examination [1]”. We would like to share our ideas and experience on using ultrasound for diagnosis of dengue in our setting, tropical Indochina, where dengue is highly prevalent. Ultrasound is not routinely recommended for diagnosis of dengue. The basic screening tool is the tourniquet test, which is helpful for diagnosis of thrombocytopaenia [2]. The abdominal ultrasound investigation in dengue patients usually gives a negative finding. Positive findings are usually observed in severe cases in which a simple clinical examination combining simple laboratory investigations, complete blood count, and dengue immunological test can help in the diagnosis. Also, the mentioned positive findings, such as thickening gall bladder or hepatomegaly, can also be seen in other tropical infections such as viral hepatitis [3]. It can be concluded that ultrasound is not appropriate and not cost effective for screening of dengue fever.
Immunogenicity and protective efficacy of recombinant alkaline shock protein 23 from Staphylococcus aureus in a murine model

The diversity and severity of infections caused and the rapid emergence of antibiotic resistance necessitates the development of a vaccine against Staphylococcus aureus. None of the antigens tried as vaccine candidates so far has been translated into a clinically viable vaccine. Recent research data suggest that antigens with the potential to activate cell mediated immunity along with humoral immunity would be the key to the development of a vaccine. Alkaline shock protein 23, a membrane-anchored protein involved in the stress response, has been identified as a CD4+ T cell antigen from S. aureus. In the present study, we report the evaluation of immunogenicity and protective efficacy of a recombinant alkaline shock protein 23 from S. aureus in mouse models. The gene coding for the protein was cloned and expressed in Escherichia coli, purified using immobilized metal iron affinity chromatography, sequence-confirmed using mass spectrometry and intraperitoneally administered to BALB/c mice. Serum titers of IgG, IgG1, and IgG2a in response to the protein were measured on post-immunization days 21, 35 and 42 using indirect ELISA and compared to control mice injected with PBS. Our results showed that the protein induced significantly higher (p < 0.01) antibody responses in immunized mice compared to the control mice. The mean serum antibody titers of IgG, IgG1 and IgG2a three weeks after the last immunization were found to be 25600, 25600 and 12800 respectively. Moreover, we found that immunization with Asp23 protected mice from a lethal dose of S. aureus strain USA300.
Distribution and diversity patterns of herpetofauna in the Pantabangan-Carranglan Watershed, Nueva Ecija, Caraballo Mountain Range, Philippines

Abstract The recent extensive survey conducted in the Pantabangan-Carranglan Watershed, located in the Caraballo Mountain Range during the rainy season (October to November) resulted in the recording of fifty-nine (59) species of amphibians and reptiles (17 frogs, 14 skinks, 3 agamids, 6 gekkonid lizards, 2 varanids and 17 snakes). Out of 59 species, 42 species were Philippine endemics and 25 species are recorded only from the Luzon faunal region. Habitat analysis and mapping showed seven habitat types including lowland dipterocarp forest, grassland, lower montane forest, upper montane forest, pine forest, agricultural areas and riparian habitats. GIS-based distribution mapping showed that the number of individuals and species are high in forest and associated riparian habitats at mid-elevation (1,000–1,250 m a.s.l.). The distribution pattern in the area is influenced by similarity in microclimatic conditions, availability of resources and niches which species can utilise. Species diversity is centred in mid- to high elevation forest and riparian habitats and in less disturbed areas. Snake diversity is adversely affected by increased disturbance, making them good indicators of the health of an area. The abundance-based Jaccard's Similarity Index showed that connected habitats and elevation gradients have higher species similarity.
Identification of Potent Inhibitors against Aurora Kinase A Using Molecular Docking and Molecular Dynamics Simulation Studies

Aurora kinase A (AURKA) is a normal cell proliferation-inducing enzyme encoded by AURKA gene, with over-expression observed in different types of malignancies. Hence, the goal is to find potential inhibitors against AURKA. In this study, molecular docking, Standard Precision and Extra Precision methods were employed. After the docking study, the ligands showed an extremely low binding score which suggested very high binding affinity of the ligands. Furthermore, Quantum polarized ligand docking (QPLD) was performed to predict the binding status of the molecules. Based on the binding affinity, the top four compounds were chosen for further analysis. The docked complexes were further analyzed in explicit water conditions using 100 ns molecular dynamics simulations and binding free energy calculation. Then, density functional theory (DFT) calculation was used to calculate the molecular properties of the molecules. Finally, systems biology experiments validated the molecular docking and molecular dynamics simulation studies and indicated that quercetin, kaempferol, luteolin and rutin could inhibit the AURKA. The results show that, these four molecules have high binding affinity to the AURKA and significant interactions (LEU139, GLU211and ALA213) were also identified with the hinge region of Aurora kinase A. Thus, LEU139, GLU211, and ALA213 were identified as the crucial protein mechanisms.
Landscape genetics reveal broad and fine‐scale population structure due to landscape features and climate history in the northern leopard frog (Rana pipiens) in North Dakota

Abstract Prehistoric climate and landscape features play large roles structuring wildlife populations. The amphibians of the northern Great Plains of North America present an opportunity to investigate how these factors affect colonization, migration, and current population genetic structure. This study used 11 microsatellite loci to genotype 1,230 northern leopard frogs (Rana pipiens) from 41 wetlands (30 samples/wetland) across North Dakota. Genetic structure of the sampled frogs was evaluated using Bayesian and multivariate clustering methods. All analyses produced concordant results, identifying a major east–west split between two R. pipiens population clusters separated by the Missouri River. Substructuring within the two major identified population clusters was also found. Spatial principal component analysis (sPCA) and variance partitioning analysis identified distance, river basins, and the Missouri River as the most important landscape factors differentiating R. pipiens populations across the state. Bayesian reconstruction of coalescence times suggested the major east–west split occurred ~13–18 kya during a period of glacial retreat in the northern Great Plains and substructuring largely occurred ~5–11 kya during a period of extreme drought cycles. A range‐wide species distribution model (SDM) for R. pipiens was developed and applied to prehistoric climate conditions during the Last Glacial Maximum (21 kya) and the mid‐Holocene (6 kya) from the CCSM4 climate model to identify potential refugia. The SDM indicated potential refugia existed in South Dakota or further south in Nebraska. The ancestral populations of R. pipiens in North Dakota may have inhabited these refugia, but more sampling outside the state is needed to reconstruct the route of colonization. Using microsatellite genotype data, this study determined that colonization from glacial refugia, drought dynamics in the northern Great Plains, and major rivers acting as barriers to gene flow were the defining forces shaping the regional population structure of R. pipiens in North Dakota.
Cathepsin G cleaves and activates IL-36γ and promotes the inflammation of psoriasis

Background IL-36γ is considered to be a valuable biomarker in psoriatic patients, which is expressed as an inactive precursor that needs to be proteolytically processed and activated, and neutrophil-derived proteases seemed to be potent activating enzymes of IL-36γ. Objectives This study aims to investigate the activation of IL-36γ by cathepsin G (CG) and neutrophil elastase (NE). Materials and methods We used inactive recombinant full-length (FL)-IL-36γ with different doses of NE or CG to stimulate HaCaT cells; neutrophil extracellular traps (NETs) were prepared to act on FL-IL-36γ and then stimulate HaCaT cells. Real-time quantitative PCR and ELISA were performed to detect CXCL-1 and CXCL-8 expression. We developed imiquimod-induced psoriasis-like mouse model to evaluate the effect of hypodermic injection of neutrophil-derived protease or its inhibitor. Histopathology and Western blotting were conducted for effect assessment. Results Purified CG cleaved and activated recombinant human FL-IL-36γ to promote CXCL-1 and CXCL-8 expression by human keratinocytes, and NETs activated FL-IL-36γ and the activation was inhibited by serpin A3. CG induced expression of a more truncated IL-36γ in psoriasiform lesion of mice and aggravated the psoriasis-like lesion induced by imiquimod, whereas recombinant serpin A3 alleviated the severity of the psoriasis-like mouse mode. Conclusion CG has the ability to cleave and activate IL-36γ and aggravate imiquimod-induced mouse psoriasiform lesion. Thus, CG-specific inhibitors might be promising therapeutic drugs for psoriasis.
Use of Mastectomy for Overdiagnosed Breast Cancer in the United States: Analysis of the SEER 9 Cancer Registries

Aim We investigated use of mastectomy as treatment for early breast cancer in the US and applied the resulting information to estimate the minimum and maximum rates at which mastectomy could plausibly be undergone by patients with overdiagnosed breast cancer. Little is currently known about overtreatments undergone by overdiagnosed patients. Methods In the US, screening is often recommended at ages ≥40. The study population was women age ≥40 diagnosed with breast cancer in the US SEER 9 cancer registries during 2013 (n=26,017). We evaluated first-course surgical treatments and their associations with case characteristics. Additionally, a model was developed to estimate probability of mastectomy conditional on observed case characteristics. The model was then applied to evaluate possible rates of mastectomy in overdiagnosed patients. To obtain minimum and maximum plausible rates of this overtreatment, we respectively assumed the cases that were least and most likely to be treated by mastectomy had been overdiagnosed. Results Of women diagnosed with breast cancer at age ≥40 in 2013, 33.8% received mastectomy. Mastectomy was common for most investigated breast cancer types, including for the early breast cancers among which overdiagnosis is thought to be most widespread: mastectomy was undergone in 26.4% of in situ and 28.0% of AJCC stage-I cases. These rates are substantively higher than in many European nations. The probability-based model indicated that between >0% and <18% of the study population could plausibly have undergone mastectomy for overdiagnosed cancer. This range reduced depending on the overdiagnosis rate, shrinking to >0% and <7% if 10% of breast cancers were overdiagnosed and >3% and <15% if 30% were overdiagnosed. Conclusions Screening-associated overtreatment by mastectomy is considerably less common than overdiagnosis itself but should not be assumed to be negligible. Screening can prompt or prevent mastectomy, and the balance of this harm-benefit tradeoff is currently unclear.
Theoretical investigation of the structural and spectroscopic properties of expanded metalloporphyrin complexes

The frontier molecular orbitals, UV–Vis absorption spectra, charge transfer (CT) and triplet excited states of 12 expanded D–A porphyrin/benzoporphyrin complexes were investigated using the density functional theory (DFT) method and time-dependent DFT in this work. The results showed that thiophene was an effective fragment for absorption of ‘long wavelength’, while the benzoporphyrin worked on the ‘short wavelength’, which was derived from its saddle-shaped structure; this expanded D–A conjugated system had a mild CT process with anthraquinone/isoindigo as acceptors and a strong CT process with naphtoquinone as acceptor. In addition, based on the simulation of the triplet state, the theoretical phosphorescence wavelength range of this series of derivatives was between 1000 and 1200 nm. This study is expected to assist the design of conjugated porphyrin for the field of porphyrin chemistry.