Miracle-dz/UniFAR-FTUs huggingface dataset:
Photoactive Yellow Protein Represents a Distinct, Evolutionarily Novel Family of PAS Domains

Photoactive yellow protein is a model bacterial photoreceptor. For many years, it was considered a prototypical model of the ubiquitous PAS domain superfamily. Here, we show that, in fact, the PYP family is evolutionarily novel, restricted to a few bacterial phyla and distinct from other PAS domains. We also reveal the diversity of PYP-containing signal transduction proteins and their potential mechanisms. ABSTRACT Photoactive yellow protein (PYP) is a model photoreceptor. It binds a p-coumaric acid as a chromophore, thus enabling blue light sensing. The first discovered single-domain PYP from Halorhodospira halophila has been studied thoroughly in terms of its structural dynamics and photochemical properties. However, the evolutionary origins and biological role of PYP homologs are not well understood. Here, we show that PYP is an evolutionarily novel domain family of the ubiquitous PAS (Per-Arnt-Sim) superfamily. It likely originated from the phylum Myxococcota and was then horizontally transferred to representatives of a few other bacterial phyla. We show that PYP is associated with signal transduction either by domain fusion or by genome context. Key cellular functions modulated by PYP-initiated signal transduction pathways likely involve gene expression, motility, and biofilm formation. We identified three clades of the PYP family, one of which is poorly understood and potentially has novel functional properties. The Tyr42, Glu46, and Cys69 residues that are involved in p-coumaric acid binding in the model PYP from H. halophila are well conserved in the PYP family. However, we also identified cases where substitutions in these residues might have led to neofunctionalization, such as the proposed transition from light to redox sensing. Overall, this study provides definition, a newly built hidden Markov model, and the current genomic landscape of the PYP family and sets the stage for the future exploration of its signaling mechanisms and functional diversity. IMPORTANCE Photoactive yellow protein is a model bacterial photoreceptor. For many years, it was considered a prototypical model of the ubiquitous PAS domain superfamily. Here, we show that, in fact, the PYP family is evolutionarily novel, restricted to a few bacterial phyla and distinct from other PAS domains. We also reveal the diversity of PYP-containing signal transduction proteins and their potential mechanisms.
IL-33 attenuates cardiac remodeling following myocardial infarction via inhibition of the p38 MAPK and NF-κB pathways

An interested reader of an article published in the journal Circulation Research [Krishnamurthy P, Rajasingh J, Lambers E, Qin G, Losordo DW and Kishore R: L‑10 inhibits inflammation and attenuates left ventricular remodeling after myocardial infarction via activation of STAT3 and suppression of HuR. Circ Res 104: e9‑18, 2008] drew to our attention that data featured in their paper had appeared subsequently in the abovementioned article by Yin et al in Molecular Medicine Reports in 2014. Specifically, Fig. 1 in the Mol Med Rep paper included the same histograms as those featured in Fig. 2 in the Circ Res paper; Fig. 2 in the Mol Med Rep paper contained data derived from Fig. 1 in the Circ Res paper; and Figs. 3‑5 in both papers shared a substantial amount of the same data. Following an internal investigation, the Journal was able to confirm that this accusation of plagiarism was well‑founded. On those grounds, the Editor of Molecular Medicine Reports has decided to retract this paper. The authors were asked for an explanation to account for these concerns, but the Editorial Office did not receive a reply. The Editor deeply regrets the grievance that this matter has caused to the authors of the previously published article, and also any inconvenience caused to the readership of the Journal.
Adsorption of rhodamine 6G and choline on gold electrodes: a molecular dynamics study

The adsorption of analyte molecules on nano-optoelectrodes (e.g. a combined nanoantenna and nanoelectrode device) significantly affects the signal characteristics in surface-enhanced Raman scattering (SERS) measurements. Understanding how different molecules adsorb on electrodes and their electrical potential modulation helps interpret SERS measurements better. We use molecular dynamics simulations to investigate the adsorption of prototypical analyte molecules (rhodamine 6G and choline) on gold electrodes with negative, neutral, and positive surface charges. We show that both molecules can readily adsorb on gold surfaces at all surface charge densities studied. Nevertheless, the configurations of the adsorbed molecules can differ for different surface charge densities, and adsorption can also change a molecule’s conformation. Rhodamine 6G molecules adsorb more strongly than choline molecules, and the adsorption of both molecules is affected by electrode charge in 0.25 M NaCl solutions. The mechanisms of these observations are elucidated, and their implications for voltage-modulated SERS measurements are discussed.
MILLIMETER EMISSION STRUCTURE IN THE FIRST ALMA IMAGE OF THE AU Mic DEBRIS DISK

We present 1.3 mm ALMA Cycle 0 observations of the edge-on debris disk around the nearby, ∼10 Myr old, M-type star AU Mic. These observations obtain 0. ″6 (6 AU) resolution and reveal two distinct emission components: (1) the previously known dust belt that extends to a radius of 40 AU and (2) a newly recognized central peak that remains unresolved. The cold dust belt of mass ∼1 MMoon is resolved in the radial direction with a rising emission profile that peaks sharply at the location of the outer edge of the “birth ring” of planetesimals hypothesized to explain the midplane scattered light gradients. No significant asymmetries are discerned in the structure or position of this dust belt. The central peak identified in the ALMA image is ∼6 times brighter than the stellar photosphere, which indicates an additional emission process in the inner regions of the system. Emission from a stellar corona or activity may contribute, but the observations show no signs of temporal variations characteristic of radio-wave flares. We suggest that this central component may be dominated by dust emission from an inner planetesimal belt of mass ∼0.01 MMoon, consistent with a lack of emission shortward of 25 μm and a location ≲3 AU from the star. Future millimeter observations can test this assertion, as an inner dust belt should be readily separated from the central star at higher angular resolution.
Electroacupuncture reduces blood glucose by regulating intestinal flora in type 2 diabetic mice

The development of diabetes is closely related to the gut microbiota in recent studies, which can be influenced by intestinal motility. A few studies report that electroacupuncture (EA) can lower blood glucose. EA can promote colonic motility and influence gut microbes. In this study, we explored the effect of the EA on blood glucose level in mice with type 2 diabetes (T2D) and its mechanism.
Genome Sequences of Arthrobacter globiformis B-2979 Phages GlobiWarming and TaylorSipht

Phages GlobiWarming and TaylorSipht are siphoviruses isolated on Arthrobacter globiformis B-2979. GlobiWarming has a 42,691 bp long genome that encodes 74 genes, whereas TaylorSipht has a 39,051 bp genome that encodes 65 genes. Both phages encode functions typical of temperate phages, with each including an immunity repressor, integrase, and excise. ABSTRACT Phages GlobiWarming and TaylorSipht are siphoviruses isolated on Arthrobacter globiformis B-2979. GlobiWarming has a 42,691 bp long genome that encodes 74 genes, whereas TaylorSipht has a 39,051 bp genome that encodes 65 genes. Both phages encode functions typical of temperate phages, with each including an immunity repressor, integrase, and excise.
Chromospheric Sunspot Oscillations in H-alpha and Ca II 8542A

We study chromospheric oscillations including umbral flashes and running penumbral waves in a sunspot of active region (AR) using scanning spectroscopy in H-alpha and Ca II 8542A, with the Fast Imaging Solar Spectrograph (FISS) at the 1.6 meter New Solar Telescope at Big Bear Solar Observatory. A bisector method is applied to spectral observations to construct chromospheric Doppler velocity maps. Temporal sequence analysis of these shows enhanced high-frequency oscillations inside the sunspot umbra in both lines. Their peak frequency gradually decreases outward from the umbra. The oscillation power is found to be associated with magnetic-field strength and inclination, with different relationships in different frequency bands.
Global optimization for nonconvex optimization problems

Duality is one of the most successful ideas in modern science [46] [91]. It is essential in natural phenomena, particularly, in physics and mathematics [39] [94] [96]. In this thesis, we consider the canonical duality theory for several classes of optimization problems. The first problem that we consider is a general sum of fourth-order polynomial minimization problem. This problem arises extensively in engineering and science, including database analysis, computational biology, sensor network communications, nonconvex mechanics, and ecology. We first show that this global optimization problem is actually equivalent to a discretized minimal potential variational problem in large deformation mechanics. Therefore, a general analytical solution is proposed by using the canonical duality theory. The second problem that we consider is a nonconvex quadratic-exponential optimization problem. By using the canonical duality theory, the nonconvex primal problem in n-dimensional space can be converted into a one-dimensional canonical dual problem, which is either a concave maximization or a convex minimization problem with zero duality gap. Several examples are solved so as to illustrate the applicability of the theory developed. The third problem that we consider is quadratic minimization problems subjected to either box or integer constraints. Results show that these nonconvex problems can be converted into concave maximization dual problems over convex feasible spaces without duality gap and the Boolean integer programming problem is actually equivalent to a critical point problem in continuous space. These dual problems can be solved under certain conditions. Both existence and uniqueness of the canonical dual solutions are presented. A canonical duality algorithm is presented and applications are illustrated. The fourth problem that we consider is a quadratic discrete value selection problem subjected to inequality constraints. The problem is first transformed into a quadratic 0-1 integer programming problem. The dual problem is thus constructed by using the canonical duality theory. Under appropriate conditions, this dual problem is a maximization problem of a concave function over a convex continuous space. Theoretical results show that the canonical duality theory can either provide a global optimization solution, or an optimal lower bound approximation to this NP-hard problem. Numerical simulation studies, including some relatively large scale problems, are carried out so as to demon-
Suppression of Methicillin-Resistant Staphylococcus aureus and Reduction of Other Bacteria by Black Soldier Fly Larvae Reared on Potato Substrate

Larvae of black soldier flies, Hermetia illucens, may be used to provide an environmentally sustainable and economically viable method for biological conversion of animal and plant wastes into ingredients of animal feeds on an industrial scale. However, contamination of harvested larvae by pathogenic microorganisms inhabiting decaying substrates may be a serious problem for wide-scale adoption of this technology. ABSTRACT Larvae of black soldier flies, Hermetia illucens, are increasingly used for biological conversion of animal and plant wastes into ingredients of animal feeds on an industrial scale. The presence of pathogenic microorganisms in harvested larvae may be a serious problem for wide-scale adoption of this technology. Fortunately, black soldier fly larvae may have some antimicrobial properties. Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterium associated with various environments that can be pathogenic to humans and farmed animals. We tested whether black soldier fly larvae suppress MRSA on potato substrate. Autoclaved potatoes containing black soldier fly larvae (P+BSFL), potatoes inoculated with MRSA and containing black soldier fly larvae (P+MRSA+BSFL), and potatoes inoculated with MRSA (P+MRSA) were incubated in glass jars. Substrate samples were taken after 3 and 7 days of incubation and plated on Trypticase soy agar (TSA) and Staphylococcus medium 110 agar (SA) to quantify total bacteria and MRSA, respectively. DNA was extracted from potato substrates on both days and sequenced to assess bacterial and fungal diversity using 515F/806R and internal transcribed spacer (ITS) 1/2 primers, respectively, and QIIME 2.0 software. Both total bacterial and MRSA-specific CFU were reduced in the presence of black soldier fly larvae, with a larger reduction for the latter. Twenty-five bacterial genera and 3 fungal genera were detected. Twenty bacterial genera were shared among the treatments and the days, but their relative abundances often varied. Among the most abundant genera, only Enterococcus and Lactococcus were universally present. Our findings confirm antimicrobial properties of black soldier fly larvae. IMPORTANCE Larvae of black soldier flies, Hermetia illucens, may be used to provide an environmentally sustainable and economically viable method for biological conversion of animal and plant wastes into ingredients of animal feeds on an industrial scale. However, contamination of harvested larvae by pathogenic microorganisms inhabiting decaying substrates may be a serious problem for wide-scale adoption of this technology. Fortunately, black soldier fly larvae may have some antimicrobial properties, including suppression of several common pathogens. Our study showed that such a suppression applies to methicillin-resistant Staphylococcus aureus, which is a ubiquitous bacterium pathogenic to animals (including humans).
A Reflexive Lens on Preparing and Conducting Semi-structured Interviews with Academic Colleagues

In qualitative research, researchers often conduct semi-structured interviews with people familiar to them, but there are limited guidelines for researchers who conduct interviews to obtain curriculum-related information with academic colleagues who work in the same area of practice but at different higher education institutions. Using a pragmatic constructivist stance, we address the practicalities of conducting semi-structured interviews with fellow educators who work in the same area of professional practice, where the researcher has to address the dual roles of “insider” and “outsider” as well as that of researcher and participant. Interviewing academic colleagues offers a unique opportunity for rich data collection, but researchers should adopt a flexible conversational style during interviewing within research parameters and be acutely aware of their positionality and fluidity of roles. This article contributes to existing knowledge by drawing on the work of previous scholars in various areas of research and research methodology thereby offering a practical and theoretical perspective on conducting qualitative research interviewing in higher education institutions where the role of researcher and participant can become blurred. These guidelines and insights will also benefit researchers who conduct research with peers who work together in the same area of expertise, in similar contexts and with whom there are varying levels of working relationships.
Sticky Mittens Training to Improve Reaching Skills and Manual Exploration of Full-Term and At-Risk Infants: A Systematic Review

Abstract Aim To systematically review evidence of the effectiveness of sticky mittens training to improve reaching skills and manual exploration of full-term and at-risk infants and optimal training dosage. Methods The Cochrane Collaboration and Preferred Reporting Items for Systematic Reviews and Meta-Analyses guided this systematic review. The electronic search was performed from September 2017 to August 2021 on PubMed, Scopus, Science Direct, and Cochrane databases. Eligibility criteria followed PICO terms: clinical trials investigating the effects of sticky mittens training on reaching skills and manual exploration of full-term and at-risk infants. PEDro scale and GRADE assessed methodological quality and quality of evidence, respectively. Results Eight studies (313 children) were included. Five studies found statistically significant differences between experimental and control groups (62.6%). One study presented high methodological quality. Evidence synthesis showed very low and low evidence of the beneficial effects of sticky mittens training in full-term and at-risk infants, respectively. Conclusions Findings suggest that sticky mittens training facilitates reaching skills and manual exploration. However, results should interpretation with caution because studies targeted full-term infants. Future research should focus on infants at risk or with motor impairments since sticky mittens training seems to show positive effects and is easy to apply.
The Role of HIV Partner Services in the Modern Biomedical HIV Prevention Era: A Network Modeling Study

HIV partner services has low estimated impact on population-level HIV prevention without substantial improvements to both partner identification and delivery of HIV screening, antiretroviral therapy, and preexposure prophylaxis to partners. Background HIV partner services can accelerate the use of antiretroviral-based HIV prevention tools (antiretroviral therapy [ART] and preexposure prophylaxis [PrEP]), but its population impact on long-term HIV incidence reduction is challenging to quantify with traditional partner services metrics of partner identified or HIV screened. Understanding the role of partner services within the portfolio of HIV prevention interventions, including using it to efficiently deliver antiretrovirals, is needed to achieve HIV prevention targets. Methods We used a stochastic network model of HIV/sexually transmitted infection transmission for men who have sex with men, calibrated to surveillance-based estimates in the Atlanta area, a jurisdiction with high HIV burden and suboptimal partner services uptake. Model scenarios varied successful delivery of partner services cascade steps (newly diagnosed “index” patient and partner identification, partner HIV screening, and linkage or reengagement of partners in PrEP or ART care) individually and jointly. Results At current levels observed in Atlanta, removal of HIV partner services had minimal impact on 10-year cumulative HIV incidence, as did improving a single partner services step while holding the others constant. These changes did not sufficiently impact overall PrEP or ART coverage to reduce HIV transmission. If all index patients and partners were identified, maximizing partner HIV screening, partner PrEP provision, partner ART linkage, and partner ART reengagement would avert 6%, 11%, 5%, and 18% of infections, respectively. Realistic improvements in partner identification and service delivery were estimated to avert 2% to 8% of infections, depending on the combination of improvements. Conclusions Achieving optimal HIV prevention with partner services depends on pairing improvements in index patient and partner identification with maximal delivery of HIV screening, ART, and PrEP to partners if indicated. Improving the identification steps without improvement to antiretroviral service delivery steps, or vice versa, is projected to result in negligible population HIV prevention benefit.
Development and validation of a prediction model for persistent functional impairment among older ICU survivors

Critical illness often leads to persistent functional impairment among older Intensive Care Unit (ICU) survivors. Identification of high‐risk survivors prior to discharge from their ICU hospitalization can facilitate targeting for restorative interventions after discharge, potentially improving the likelihood of functional recovery. Our objective was to develop and validate a prediction model for persistent functional impairment among older adults in the year after an ICU hospitalization.
Fundamentals behind the specificity of Cysteinyl‐tRNA synthetase: MD and QM/MM joint investigations

Cysteinyl‐tRNA synthetase (CysRS) catalyzes the aminoacylation reaction of cysteine to its cognate tRNACys in the first step of protein translation. It is found that CysRS is different from other aaRSs as it transfers cysteine without the need for an editing reaction, which is not applicable in the case of serine despite the similarity in their structures. Surprisingly, the reasons why CysRS has high amino acid specificity are not clear yet. In this research, the binding configurations of Cys‐AMP and its near‐cognate amino acid Ser‐AMP with CysRS are compared by Molecular Dynamics (MD). The results reveal that CysRS screens the substrate Cys‐AMP to a certain extent in the process of combination and recognition, thus providing a guarantee for the high selectivity of the next reaction. While Ser‐AMP is in a folded state in CysRS. In the meanwhile, the interaction between Cys‐AMP and Zn963 in CysRS is much stronger than Ser‐AMP. The substrate‐assisted aminoacylation mechanism in CysRS is also explored by Quantum Mechanics/Molecular Mechanics (QM/MM) modeling. According to the QM/MM potential energies, the energy barrier of TSCys‐AMP is 91.75 kJ/mol, while that of TSSer‐AMP is close to 150 kJ/mol. Based on thermochemistry calculations, it is found that the product of Cys‐AMP is more stable than the reactant. In contrast, Ser‐AMP has a reactant that is more stable than its product. As a result, it reflects that the specificity of CysRS originates from both the kinetic and thermodynamical perspectives of the reaction. Our investigations demonstrate comprehensively on how CysRS recognizes and catalyzes the substrate Cys‐AMP, hoping to provide some guidance for researchers in this area.