Miracle-dz/UniFAR-FTUs huggingface dataset:
Escherichia coli and Pseudomonas aeruginosa lipopolysaccharide O‐antigen ligases share similar membrane topology and biochemical properties

WaaL is an inner membrane glycosyltransferase that catalyzes the transfer of O‐antigen polysaccharide from its lipid‐linked intermediate to a terminal sugar of the lipid A‐core oligosaccharide, a conserved step in lipopolysaccharide biosynthesis. Ligation occurs at the periplasmic side of the bacterial cell membrane, suggesting the catalytic region of WaaL faces the periplasm. Establishing the membrane topology of the WaaL protein family will enable understanding its mechanism and exploit it as a potential antimicrobial target. Applying oxidative labeling of native methionine/cysteine residues, we previously validated a topological model for Escherichia coli WaaL, which differs substantially from the reported topology of the Pseudomonas aeruginosa WaaL, derived from the analysis of truncated protein reporter fusions. Here, we examined the topology of intact E. coli and P. aeruginosa WaaL proteins by labeling engineered cysteine residues with the membrane‐impermeable sulfhydryl reagent polyethylene glycol maleimide (PEG‐Mal). The accessibility of PEG‐Mal to targeted engineered cysteine residues in both E. coli and P. aeruginosa WaaL proteins demonstrates that both ligases share similar membrane topology. Further, we also demonstrate that P. aeruginosa WaaL shares similar functional properties with E. coli WaaL and that E. coli WaaL may adopt a functional dimer conformation.
Development and Implementation of the World Health Organization Emergency Medical Teams: Minimum Technical Standards and Recommendations for Rehabilitation

Emergency medical teams provide urgent medical and surgical care in emergencies characterized by a surge in trauma or disease. Rehabilitation has historically not been included in the acute phase of care, as teams have either not perceived it as their responsibility or have relied on external providers, including local services and international organizations, to provide services. Low- and middle-income countries, which often have limited rehabilitation capacity within their health system, are particularly vulnerable to disaster and are usually ill-equipped to address the increased burden of rehabilitation needs that arise. The resulting unmet needs for rehabilitation culminate in unnecessary complications for patients, delayed recovery, reduced functional outcomes, and often impede return to daily activities and life roles. Recognizing the systemic neglect of rehabilitation in global emergency medical response, the World Health Organization, in collaboration with key operational partners and experts, developed technical standards and recommendations for rehabilitation which are integrated into the WHO verification process for EMTs. This protocol report presents: 1) the rationale for the development of the standards and accompanying recommendations; 2) the methodology of the development process; 3) the minimum standards and other significant content included in the document; 4) challenges encountered during development and implementation; and 5) current and next steps to continue strengthening the inclusion of rehabilitation in emergency medical response.
Radiotherapy-Controllable Chemotherapy from Reactive Oxygen Species-Responsive Polymeric Nanoparticles for Effective Local Dual Modality Treatment of Malignant Tumors.

Radiotherapy is one of the general approaches to deal with malignant solid tumors in clinical treatment. To improve therapeutic efficacy, chemotherapy is frequently adopted as the adjuvant treatment in combination with radiotherapy. In this work, a reactive oxygen species (ROS)-responsive nanoparticle (NP) drug delivery system was developed to synergistically enhance the antitumor efficacy of radiotherapy by local ROS-activated chemotherapy, taking advantages of the enhanced concentration of reactive oxygen species (ROS) in tumor during X-ray irradiation and/or reoxygenation after X-ray irradiation. The ROS-responsive polymers, poly(thiodiethylene adipate) (PSDEA) and PEG-PSDEA-PEG, were synthesized and employed as the major components assembling in aqueous phase into polymer NPs in which an anticancer camptothecin analogue, SN38, was encapsulated. The drug-loaded NPs underwent structural change including swelling and partial dissociation in response to the ROS activation by virtue of the oxidation of the nonpolar sulfide residues in NPs into the polar sulfoxide units, thus leading to significant drug unloading. The in vitro performance of the chemotherapy from the X-ray irradiation preactivated NPs against BNL 1MEA.7R. 1 murine carcinoma cells showed comparable cytotoxicity to free drug and appreciably enhanced effect on killing cancer cells while the X-ray irradiation being incorporated into the treatment. The in vivo tumor growth was fully inhibited with the mice receiving the local dual modality treatment of X-ray irradiation together with SN38-loaded NPs administered by intratumoral injection. The comparable efficacy of the local combinational treatment of X-ray irradiation with SN38-loaded NPs to free SN38/irradiation dual treatment corroborated the effectiveness of ROS-mediated drug release from the irradiated NPs at tumor site. The IHC examination of tumor tissues confirmed the significant reduction of VEGFA and CD31 expression with the tumor receiving the local dual treatment developed in this work, thus accounting for the absence of tumor regrowth compared to other single modality treatment.
A single high‐fat meal alters human soluble RAGE profiles and PBMC RAGE expression with no effect of prior aerobic exercise

A high‐fat diet can induce inflammation and metabolic diseases such as diabetes and atherosclerosis. The receptor for advanced glycation endproducts (RAGE) plays a critical role in metabolic disease pathophysiology and the soluble form of the receptor (sRAGE) can mitigate these effects. However, little is known about RAGE in the postprandial condition and the effect of exercise in this context. Thus, we aimed to determine the effects of a single high‐fat meal (HFM) with and without prior exercise on peripheral blood mononuclear cell (PBMC) RAGE biology. Healthy males (n = 12) consumed a HFM on two occasions, one without prior exercise and one 16–18 hours following acute aerobic exercise. Total soluble RAGE (sRAGE) and endogenous secretory RAGE (esRAGE) were determined via ELISA and cleaved RAGE (cRAGE) was calculated as the difference between the two. Isolated PBMCs were analyzed for RAGE, ADAM10, TLR4, and MyD88 protein expression and ADAM10 activity. The HFM significantly (P < 0.01) attenuated sRAGE, esRAGE, and cRAGE by 9.7%, 6.9%, and 10.5%, respectively. Whereas, the HFM increased PBMC RAGE protein expression by 10.3% (P < 0.01), there was no meal effect on PBMC TLR4, MYD88, or ADAM10 protein expression, nor ADAM10 activity. There was also no exercise effect on any experimental outcomes. These findings suggest that PBMC RAGE and soluble RAGE may be important in the postprandial response to a HFM, and that prior aerobic exercise does not alter these processes in young healthy adult males. The mechanisms by which a HFM induces RAGE expression and reduces circulating soluble RAGE isoforms requires further study.
Head and neck squamous cell carcinoma drives long interspersed element-1 hypomethylation in the peripheral blood mononuclear cells.

OBJECTIVE Alteration of long interspersed element-1 (LINE-1) methylation in peripheral blood mononuclear cells (PBMCs) has been simultaneously activated to breast carcinogenesis due to its secretion. To evaluate the effect in head and neck squamous cell carcinoma (HNSCC), LINE-1 methylation levels and patterns have been measured both in vitro and in vivo. METHODS Analysis of LINE-1 methylation in cocultured models between HNSCC cell lines and normal PBMCs was performed. The observation of PBMCs of HNSCC patients compared to PBMCs of normal controls was performed using the semiquantitative combined bisulfite restriction analysis technique. RESULTS Downregulation of LINE-1 methylation was significantly found in the PBMCs cocultured with all HNSCC cell lines compared to normal PBMCs. Likewise, a reduction in LINE-1 methylation levels was observed in PBMCs of HNSCC compared to normal PBMCs (p < 0.0001). Receiver operating characteristic analysis demonstrated the potential of the unmethylated alleles (u Cu C) of LINE-1 for distinguishing the PBMCs of HNSCC patients from normal controls with 100% sensitivity and specificity. CONCLUSION Our data supported that the alteration of LINE-1 methylation levels in PBMCs was influenced by HNSCC secretions. Moreover, the unmethylated LINE-1 allele of PBMCs was proved to be an effective tumor marker and possesses a potential as HNSCC diagnostic tool.
Consensus assessment of the contamination level of publicly available cyanobacterial genomes

BACKGROUND Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no data are currently available concerning the quality of publicly available cyanobacterial genomes. RESULTS As reliably detecting contaminants is a complex task, we designed a pipeline combining six methods in a consensus strategy to assess the contamination level of 440 genome assemblies of Cyanobacteria. Two methods are based on published reference databases of ribosomal genes (SSU rRNA 16S and ribosomal proteins), one is indirectly based on a reference database of marker genes (CheckM), and three are based on complete genome analysis. Among those genome-wide methods, Kraken and DIAMOND blastx share the same reference database that we derived from Ensembl Bacteria, whereas CONCOCT does not require any reference database, instead relying on differences in DNA tetramer frequencies. Given that all the six methods appear to have their own strengths and limitations, we used the consensus of their rankings to infer that >5% of cyanobacterial genome assemblies are highly contaminated by foreign DNA (i.e., contaminants were detected by 5 or 6 methods). CONCLUSIONS Our results will help researchers to check the quality of publicly available genomic data before use in their own analyses. Moreover, we argue that journals should make mandatory the submission of raw read data along with genome assemblies in order to facilitate the detection of contaminants in sequence databases.
Artificial Neural Network Based Prediction of Temperature and Flow Profile in Data Centers

Thermal management of data centers continues to be a challenge because of their ever-increasing power densities, due for example to shrinking server footprints. Computational fluid dynamics and heat transfer (CFD/HT) have been used extensively to model thermal transport and air flow in data centers. However, the significant computational costs and time associated with accurate room-level CFD/HT simulations for data centers makes such simulations impractical for real-time prediction and control. Nevertheless, developing an effective control framework for data centers to minimize power consumption requires such real-time prediction of server inlet temperatures and tile flow rates. This paper focuses on the development of artificial neural network (ANN)-based models trained on datasets generated from offline CFD/HT simulations for real-time prediction of temperature and flow distributions in a data center. Using CFD simulation results to train ANN transfers computational complexity from model execution (in CFD) to model setup and development. A physics-based and experimentally validated room-level CFD/HT model was developed using Future Facilities 6Sigma Room. The numerical model of the room housing the data center includes an under- floor supply and ceiling-return cooling configuration and consists of one cold aisle with 12 racks arranged on both sides and three CRAC units around the periphery of the room [1]. For steady state modeling, flow and temperature distributions were obtained for 300 representative cases using CFD/HT simulations and used to train the ANN model using the Levenberg-Marquardt backpropagation algorithm. The multidimensional input parameter space for the simulations was comprised of the computer room air conditioner (CRAC) blower speed (NCRAC), the CRAC return air temperature set point (Ta,ret) and the IT load distribution for the racks ($\dot{Q}_{room}$), while rack inlet temperature (Track inlet) and tile flow rate ($\dot{V}_{tile}$) were the predicted variables. The trained ANN model was tested with 33 test cases obtained from the same multi- dimensional input space. The results show good agreement with CFD simulations with an average error of < 0.6°C in rack inlet temperatures and 0.7 % in tile flow rates. For transient modeling a scenario with cooling failure was considered where first 200 s of data after failure were used for training ANN and subsequent 300 s were used for testing the accuracy of extrapolative predictions. The ANN was compared with the Proper Orthogonal Decomposition (POD) modeling framework in terms of prediction accuracy and computational time for this transient scenario. The validated neural network model can be used to obtain rapid prediction of temperature and flow distributions, and when combined with appropriate control strategy, can be used for real-time control of data centers.
Graft choice for anatomic anterior cruciate ligament reconstruction

Abstract Great controversy over the graft choice has been lasted now. This study compared the second-look evaluation and clinical outcomes of anatomic anterior cruciate ligament reconstruction (ACL-R) using a thin autograft versus a thick hybrid graft. Seventy-six patients with complete follow-up data were categorized into the autograft group (N = 34) and hybrid group (N = 42). The Lysholm score, Tegner activity level, International Knee Documentation Committee (IKDC) Knee Evaluation Form, and KT-1000 test were performed before and at follow-up. Results were compared, and further comparisons were made for grafts thicker than 8.5 mm. The hybrid graft was thicker than the autograft (9.10 ± 0.52 vs 8.57 ± 0.48 mm, P < .001). The KT-1000 test, subjective evaluation, and activity level scores increased significantly between pre- and postoperation for all patients (P < .001). No significant differences were, however, found between the 2 groups. Only grafts thicker than 8.5 mm were selected from the autograft (N = 14) and hybrid (N = 34) groups, the Lysholm, IKDC, and KT-1000 test scores were significantly superior for the autograft than the hybrid graft (P = .021, P = .005, and P = .024, respectively). For anatomic ACL-R, a pure autograft is superior to a hybrid graft of the same diameter. The purity of the autograft was more important than the size, and augmenting allografts may be unnecessary.
EXPOSURE IN VIVO VERSUS PAIN-CONTINGENT PHYSICAL THERAPY IN COMPLEX REGIONAL PAIN SYNDROME TYPE I: A COST-EFFECTIVENESS ANALYSIS

Objectives: The aim of this study was to evaluate the cost-effectiveness of exposure in vivo (EXP, a cognitive-behavioral treatment targeting pain-related fear) in Complex Regional Pain Syndrome Type I (CRPS-I), as compared to pain-contingent physical therapy (PPT). Methods: Data from a randomized controlled trial were used to compare the cost-effectiveness of EXP versus PPT from a societal perspective. Intervention costs, other healthcare costs, costs to patient and family, and productivity losses were included. The main outcomes were changes in the SF-36 physical component scale and quality-adjusted life-years. Changes were followed until 6 months after treatment. Uncertainty was estimated using nonparametric bootstrap analysis, cost-effectiveness acceptability curves and cost-effectiveness planes. Sensitivity analyses were performed to check robustness of findings. Results: Forty-six patients were randomized and thirty-eight completed the study. Over 6 months, EXP resulted in greater improvement in physical health-related quality of life and quality-adjusted life-years than PPT. Despite higher initial treatment costs, EXP showed a tendency to reduce all costs compared with PPT; healthcare costs were significantly reduced. Furthermore, the cost-effectiveness planes were in favor of EXP. Sensitivity analyses, for different program costs and complete cases only, confirmed robustness of these findings. Conclusions: EXP, a cognitive-behavioral treatment, seems more cost-effective than PPT in CRPS patients with pain-related fear. The initial higher costs for EXP are offset by a long-term reduction of costs for healthcare use, and a tendency to lower work absenteeism and reduced societal costs. Due to low sample sizes, replication of findings is required to confirm results.
Cross-sectional survey of the amount of sugar and energy in cakes and biscuits on sale in the UK for the evaluation of the sugar-reduction programme

Objectives To investigate the variation in sugar and energy content of cakes and biscuits available in the UK. Design We carried out a cross-sectional survey in 2016 of 381 cakes and 481 biscuits available in nine main UK supermarkets. Methods The sugar and energy content was collected from product packaging and nutrition labelling of cake and biscuit products. Results The average sugar content in cakes and biscuits was 36.6±7.6 and 30.0±9.2 g/100 g, respectively. The mean energy content was 406±37 for cakes and 484±38 kcal/100 g for biscuits. There was a large variation in sugar and energy content between different cake and biscuit categories and within the same category. 97% of cakes and 74% of biscuits would receive a ‘red’ (high) label for sugar. Conclusions This research makes available baseline data of the cakes and biscuits market in the UK for future evaluation of the recently launched sugar-reduction programme. The study showed that reductions in sugar and energy content of cakes and biscuits are possible, since there was a large variation in sugar and energy content between different cake and biscuit categories and within the same category. A reduction in sugar and energy content, and overall cake and biscuit consumption, can help reduce overall sugar and energy intake in the UK and thus reduce the risk of obesity and dental caries.
Biological Predictors of Clozapine Response: A Systematic Review

Background: Clozapine is the recommended antipsychotic for treatment-resistant schizophrenia (TRS) but there is significant variability between patients in the degree to which clozapine will improve symptoms. The biological basis of this variability is unknown. Although clozapine has efficacy in TRS, it can elicit adverse effects and initiation is often delayed. Identification of predictive biomarkers of clozapine response may aid initiation of clozapine treatment, as well as understanding of its mechanism of action. In this article we systematically review prospective or genetic studies of biological predictors of response to clozapine. Methods: We searched the PubMed database until 20th January 2018 for studies investigating “clozapine” AND (“response” OR “outcome”) AND “schizophrenia. ” Inclusion required that studies examined a biological variable in relation to symptomatic response to clozapine. For all studies except genetic-studies, inclusion required that biological variables were measured before clozapine initiation. Results: Ninety-eight studies met the eligibility criteria and were included in the review, including neuroimaging, blood-based, cerebrospinal fluid (CSF)-based, and genetic predictors. The majority (70) are genetic studies, collectively investigating 379 different gene variants, however only three genetic variants (DRD3 Ser9Gly, HTR2A His452Tyr, and C825T GNB3) have independently replicated significant findings. Of the non-genetic variables, the most consistent predictors of a good response to clozapine are higher prefrontal cortical structural integrity and activity, and a lower ratio of the dopamine and serotonin metabolites, homovanillic acid (HVA): 5-hydroxyindoleacetic acid (5-HIAA) in CSF. Conclusions: Recommendations include that future studies should ensure adequate clozapine trial length and clozapine plasma concentrations, and may include multivariate models to increase predictive accuracy.
Measurement and simulation of wideband channel characterization in the underground tunnel environment

This paper presents the results of propagation measurement performed in the underground tunnel line-of-sight (LOS) environment at 6 GHz. Some radio propagation parameters of tunnel channel are discussed based on both the measured results and the method of shooting and bouncing ray tracing/image (SBR/IM). Omni-directional path loss models, root-mean-square (RMS) delay spread and mean angle of arrival (AOA) statistics are obtained from measured results and simulated results. A good agreement is achieved between the measured results and simulated results, so the correctness of SBR/IM method has been validated. Also, path loss exponents are deduced from the empirical statistical analysis. The analysis of the above-mentioned results may be utilized for the future fifth generation wireless communication system.
Augmented Reality Farm MAPPER Development: Lessons Learned from an App Designed to Improve Rural Emergency Response

ABSTRACT Fire departments have right-of-entry to most commercial industrial sites and preemptively map them to identify the onsite resources and hazards they need to promptly and safely respond to an emergency event. This is not the case for private farms. Emergency responders are blind to resources and hazards prior to arrival and must spend critical minutes locating them during an emergency response at a farm location. The original 2013 Farm Mapping to Assist, Protect and Prepare Emergency Responders (Farm MAPPER) project was undertaken to develop a method to give emergency responders an up-to-date view of on-farm hazard information to safely and efficiently conduct emergency response activities on private agricultural operations. In 2017, an augmented reality version of Farm MAPPER was developed to combine the technological advantages of geographic information system-based data points with a heads-up display and graphical overlay of superimposed hazard imagery and informative icons. The development and testing of this iOS- and Android-ready prototype uncovered lessons learned applicable to other mobile-based apps targeting farmers, ranchers, and rural populations faced with limited or inconsistent mobile internet connectivity.
Perceptions of Romantic Partners’ Responsiveness During a Period of Stressful Uncertainty

Whether awaiting biopsy results, a grade on a midterm, or a decision from a journal editor, people feel distressed as they wait for uncertain news. In the present study, we investigated how people’s perceptions of their romantic partner, specifically their partner’s responsiveness to their support needs, corresponds with key aspects of the waiting experience. In a longitudinal study of 184 law students awaiting their result on the California bar exam, we examined changes in perceived responsiveness over time and associations between perceived responsiveness and expectation management strategies, health, and well-being. Results revealed temporal patterns in perceived responsiveness, with the greatest responsiveness perceived at the start and end of the wait. Perceived responsiveness was also intertwined with efforts to manage one’s expectations while awaiting uncertain news and was associated with more positive emotions, better subjective coping, and greater self-reported sleep quality during the wait.