Miracle-dz/UniFAR-FTUs huggingface dataset:
The impact of long-distance mutations on the Ω-loop conformation in TEM type β-lactamases

Abstract β-lactamases are hydrolytic enzymes primarily responsible for occurrence and abundance of bacteria resistant to β-lactam antibiotics. TEM type β-lactamases are formed by the parent enzyme TEM-1 and more than two hundred of its mutants. Positions for the known amino acid substitutions cover ∼30% of TEM type enzyme's sequence. These substitutions are divided into the key mutations that lead to changes in catalytic properties of β-lactamases, and the secondary ones, which role is poorly understood. In this study, Residue Interaction Networks were constructed from molecular dynamic trajectories of β-lactamase TEM-1 and its variants with two key substitutions, G238S and E240K, and their combinations with secondary ones (M182T and Q39K). Particular attention was paid to a detailed analysis of the interactions that affect conformation and mobility of the Ω-loop, representing a part of the β-lactamase active site. It was shown that key mutations weakened the stability of contact inside the Ω-loop thus increasing its mobility. Combination of three amino acid substitutions, including the 182 residue, leads to the release of R65 promoting its new contacts with N175 and D176. As a result, Ω-loop is fixed on the protein globule. The second distal mutation Q39K prevents changes in spatial position of R65, which lead to the weakening of the effect of M182T substitution and the recovery of the Ω-loop mobility. Thus, the distal secondary mutations are directed for recovering the mobility of enzyme disturbed by the key mutations responsible for expansion of substrate specificity. AbbreviationsESBL extended spectrum beta-lactamasesIR inhibitor resistant beta-lactamasesMD molecular dynamicsRIN residue interaction networksRMSD root mean square deviationRMSF root mean square fluctuations. Communicated by Ramaswamy H. Sarma
Frequency of Blood-Brain Barrier Disruption Post-Endovascular Therapy and Multiple Thrombectomy Passes in Acute Ischemic Stroke Patients.

Background and Purpose- The high prevalence of hyperintense acute reperfusion marker (HARM) seen after endovascular therapy is suggestive of blood-brain barrier disruption and hemorrhage risk and may be attributable to multiple thrombectomy passes needed to achieve recanalization. Methods- Patients with acute stroke were included if they were screened from January 2015 through February 2019, received an acute ischemic stroke diagnosis involving the anterior circulation, treated with or without IV tPA (intravenous tissue-type plasminogen activator), consented to the NINDS Natural History Study, and imaged with a baseline magnetic resonance imaging before receiving endovascular therapy. Consensus image reads for HARM and hemorrhagic transformation were performed. Good clinical outcome was defined as 0-2 using the latest available modified Rankin Scale score. Results- Eighty patients met all study criteria and were included in the analyses. Median age was 65 years, 64% female, 51% black/African American, median admit National Institutes of Health Stroke Scale=19, 56% treated with IV tPA, and 84% achieved Thrombolysis in Cerebral Infarction score of 2b/3. Multiple-pass patients had significantly higher rates of severe HARM at 24 hours (67% versus 29%; P=0.001), any hemorrhagic transformation (60% versus 36%; P=0.04) and poor clinical outcome (67% versus 36%; P=0.008). Only age (odds ratio, 1.1; 95% CI, 1.01-1.12; P=0.022) and severe HARM at 24 hours post-endovascular therapy were significantly associated with multiple passes (odds ratio, 7.2; 95% CI, 1.93-26.92; P=0.003). Conclusions- In this exploratory study, multiple thrombectomy passes are independently associated with a significant increase in blood-brain barrier disruption detected at 24 hours. Patients with HARM post-endovascular therapy had a >7-fold increase in the odds of having multiple- versus single-pass thrombectomy. Clinical Trial Registration- URL: https://www.clinicaltrials. gov . Unique identifier: NCT00009243.
Convergent evidence from humans and Drosophila melanogaster implicates the transcription factor MEF2B/Mef2 in alcohol sensitivity.

BACKGROUND Self-rating of the effects of alcohol (SRE) measures level of response to ethanol in humans. Interestingly, there is a positive relationship between the SRE and risk for abusing alcohol, suggesting mechanistic connections between SRE and alcohol abuse. METHODS To identify candidate genes with a role in SRE and alcohol-related behavior more generally, we coupled human genetic analyses with studies in Drosophila melanogaster. We first performed a gene-based analysis of GWAS summary statistics for SRE in the Avon Longitudinal Study of Parents and Children (ALSPAC) sample. Based on prior findings in humans, orthology to fly genes and the availability of genetic reagents, we selected a subset of these genes for studies on ethanol behavior in Drosophila. RESULTS We found 37 genes with nominal associations in our SRE GWAS. We explored the role of 6 orthologous genes in Drosophila ethanol sedation and rapid tolerance. We found that the transcription factor Mef2 is required for normal ethanol sedation in flies. Pan-neuronal expression of two independent Mef2 RNAi transgenes significantly reduced Mef2 expression and made flies resistant to ethanol sedation. Additionally, flies with multiple independent mutant alleles of Mef2 were also resistant to ethanol sedation, confirming a role for Mef2 in this behavior. Altered expression of Mef2 did not change ethanol rapid tolerance or cause a net change in internal ethanol concentrations. CONCLUSIONS Our studies indicate that MEF2B influences SRE in humans and that Mef2 impacts ethanol sedation in Drosophila. This article is protected by copyright. All rights reserved.
Patch Testing with a New Composition of Mercapto Mix: A Multi-centre Study by the Swedish Contact Dermatitis Research Group.

This study investigated whether more patients with contact allergies were detected by patch testing with mercapto mix with a higher concentration of 2-mercaptobenzothiazolinone (MBT) than the commonly used mercapto mix. A total of 3,143 dermatitis patients in 5 Swedish dermatology departments were patch tested with 3 mercapto mixes: MBT 2.0% petrolatum (pet.); mercapto mix 2.0% pet. ; and mercapto mix 3.5% pet. Positive reactions to these mercapto mixes varied between 0-0.50%, 0-0.93%, and 0-1.4%, respectively, in the 5 centres. Numerically, mercapto mix 3.5% pet. detected all positive patients and more patch-test positive patients than did the 2 other substances, but the difference was not statistically significant. The authors recommend replacing mercapto mix 2.0% pet. in the Swedish baseline series with mercapto mix 3.5% pet. , since the latter also detected those patients who would have been missed because MBT 2.0% is not included in the Swedish baseline series.
The Arabidopsis Pleiotropic Drug Resistance Transporters PEN3 and PDR12 Mediate Camalexin Secretion for Resistance to Botrytis cinerea

PEN3 and PDR12 function redundantly to mediate the secretion of camalexin for Arabidopsis resistance to the necrotrophic fungus Botrytis cinerea. Plant defense often depends on the synthesis and targeted delivery of antimicrobial metabolites at pathogen contact sites. The pleiotropic drug resistance (PDR) transporter PENETRATION3 (PEN3)/PDR8 in Arabidopsis (Arabidopsis thaliana) has been implicated in resistance to a variety of fungal pathogens. However, the antimicrobial metabolite(s) transported by PEN3 for extracellular defense remains unidentified. Here, we report that PEN3 functions redundantly with another PDR transporter (PDR12) to mediate the secretion of camalexin, the major phytoalexin in Arabidopsis. Consistent with this, the pen3 pdr12 double mutants exhibit dramatically enhanced susceptibility to the necrotrophic fungus Botrytis cinerea as well as severe hypersensitivity to exogenous camalexin. PEN3 and PDR12 are transcriptionally activated upon B. cinerea infection, and their expression is regulated by the mitogen-activated protein kinase 3 (MPK3) and MPK6, and their downstream WRKY33 transcription factor. Further genetic analysis indicated that PEN3 and PDR12 contribute to B. cinerea resistance through exporting not only camalexin but also other unidentified metabolite(s) derived from Trp metabolism, suggesting that PEN3 and PDR12 have multiple functions in Arabidopsis immunity via transport of distinct Trp metabolic products.
Tamanu oil potentiated novel sericin emulgel of levocetirizine: repurposing for topical delivery against DNCB-induced atopic dermatitis, QbD based development and in vivo evaluation

Abstract The present study was aimed at preparing and evaluating levocetirizine (LCZD) loaded emulgel containing tamanu oil and sericin for atopic dermatitis (AD) therapy. The emulgel envisaged topical delivery of LCZD utilising natural antioxidants for superior therapeutic outcomes when compared with other conventional therapy. Tamanu oil based microemulsion (ME) was optimised utilising Box-Behnken design (BBD). The OPT-ME displayed globule size 379.5 ± 2.33 nm, polydispersity index 0.284, drug loading 0.41 ± 0.01% w/w, entrapment efficiency 94.34 ± 2.11% w/w and drug release 86.24 ± 4.90% respectively over a period of 24 h. The optimised formulation (OPT-ME) was further incorporated into sericin gel to form emulgel (LSE). In vivo pharmacodynamic studies revealed enhanced therapeutic potential of emulgel in terms of reduced scratching frequency and erythema score when compared with conventional gel. The superior therapeutic potential was further witnessed through histopathological and biochemical studies. The emulgel can be an alternative appropriate dosage form for the treatment of AD.
Ligand-guided homology modeling drives identification of novel histamine H3 receptor ligands

In this study, we report a ligand-guided homology modeling approach allowing the analysis of relevant binding site residue conformations and the identification of two novel histamine H3 receptor ligands with binding affinity in the nanomolar range. The newly developed method is based on exploiting an essential charge interaction characteristic for aminergic G-protein coupled receptors for ranking 3D receptor models appropriate for the discovery of novel compounds through virtual screening.
Impact of linker-drug on ion exchange chromatography separation of antibody-drug conjugates

ABSTRACT Charge variants are important attributes of monoclonal antibodies, including antibody-drug conjugates (ADCs), because charge variants can potentially influence the stability and biological activity of these molecules. Ion exchange chromatography (IEX) is widely used for charge variants analysis of mAbs and offers the feasibility of fractionation for in-depth characterization. However, the conjugated linker-drug on ADCs could potentially affect the separation performance of IEX, considering IEX separation relies on surface charge distribution of analyte and involves the interaction between analyte surface and IEX stationary phase. Here, we investigated weak cation exchange chromatography (WCX) for its application in analyzing three ADCs (two broad distribution ADCs and an ADC with controlled conjugation sites) and the 2-drug/4-drug loaded species isolated from the two broad distribution ADCs using hydrophobic interaction chromatography. The major peaks in WCX profile were characterized via fraction collection followed by capillary electrophoresis-sodium dodecyl sulfate or peptide mapping. Results suggested that both the number of drug loads and conjugation sites could impact WCX separation of an ADC. The hypothesis was that the linker drugs could interfere with the ionic interaction between its surrounding amino acids on the mAb surface and column resin, which reduced the retention of ADCs on WCX column in this study. Our results further revealed that WCX brings good selectivity towards positional isomers, but limited resolution for different drug load, which causes the peak compositions of the two broad-distribution ADCs to be highly complex. We also compared results from WCX and imaged capillary isoelectric focusing (icIEF). Results showed that separation in icIEF was less influenced by conjugated linker drugs for the ADCs studied in this work, and better alignment was found between the two techniques for the ADC with controlled conjugate sites. Overall, this work provides insights into the complexity of WCX analysis of ADCs, which should be considered during method development and sample characterization.
A Low-Cost, Wireless, 3-D-Printed Custom Armband for sEMG Hand Gesture Recognition

Wearable technology can be employed to elevate the abilities of humans to perform demanding and complex tasks more efficiently. Armbands capable of surface electromyography (sEMG) are attractive and noninvasive devices from which human intent can be derived by leveraging machine learning. However, the sEMG acquisition systems currently available tend to be prohibitively costly for personal use or sacrifice wearability or signal quality to be more affordable. This work introduces the 3DC Armband designed by the Biomedical Microsystems Laboratory in Laval University; a wireless, 10-channel, 1000 sps, dry-electrode, low-cost (∼150 USD) myoelectric armband that also includes a 9-axis inertial measurement unit. The proposed system is compared with the Myo Armband by Thalmic Labs, one of the most popular sEMG acquisition systems. The comparison is made by employing a new offline dataset featuring 22 able-bodied participants performing eleven hand/wrist gestures while wearing the two armbands simultaneously. The 3DC Armband systematically and significantly (p<0.05) outperforms the Myo Armband, with three different classifiers employing three different input modalities when using ten seconds or more of training data per gesture. This new dataset, alongside the source code, Altium project and 3-D models are made readily available for download within a Github repository.
The Human Cytomegalovirus Chemokine vCXCL-1 Modulates Normal Dissemination Kinetics of Murine Cytomegalovirus In Vivo

An adequate in vivo analysis of HCMV’s viral chemokine vCXCL-1 has been lacking. Here we generate recombinant MCMVs expressing vCXCL-1 to study vCXCL-1 function in vivo using MCMV as a surrogate. We demonstrate that vCXCL-1 increases MCMV dissemination kinetics for both primary and secondary dissemination. Additionally, we provide evidence, that the murine neutrophil is largely a bystander in the mouse’s response to vCXCL-1. We confirm the hypothesis that vCXCL-1 is a HCMV virulence factor. Infection of severely immunocompromised mice with MCMVs expressing vCXCL-1 was lethal in more than 50% of infected animals, while all animals infected with parental virus survived during a 12-day period. This work provides needed insights into vCXCL-1 function in vivo. ABSTRACT Human cytomegalovirus (HCMV) is a betaherpesvirus that is a significant pathogen within newborn and immunocompromised populations. Morbidity associated with HCMV infection is the consequence of viral dissemination. HCMV has evolved to manipulate the host immune system to enhance viral dissemination and ensure long-term survival within the host. The immunomodulatory protein vCXCL-1, a viral chemokine functioning primarily through the CXCR2 chemokine receptor, is hypothesized to attract CXCR2+ neutrophils to infection sites, aiding viral dissemination. Neutrophils harbor HCMV in vivo; however, the interaction between vCXCL-1 and the neutrophil has not been evaluated in vivo. Using the mouse model and mouse cytomegalovirus (MCMV) infection, we show that murine neutrophils harbor and transfer infectious MCMV and that virus replication initiates within this cell type. Utilizing recombinant MCMVs expressing vCXCL-1 from the HCMV strain (Toledo), we demonstrated that vCXCL-1 significantly enhances MCMV dissemination kinetics. Through cellular depletion experiments, we observe that neutrophils impact dissemination but that overall dissemination is largely neutrophil independent. This work adds neutrophils to the list of innate cells (i.e., dendritic and macrophages/monocytes) that contribute to MCMV dissemination but refutes the hypothesis that neutrophils are the primary cell responding to vCXCL-1. IMPORTANCE An adequate in vivo analysis of HCMV’s viral chemokine vCXCL-1 has been lacking. Here we generate recombinant MCMVs expressing vCXCL-1 to study vCXCL-1 function in vivo using MCMV as a surrogate. We demonstrate that vCXCL-1 increases MCMV dissemination kinetics for both primary and secondary dissemination. Additionally, we provide evidence, that the murine neutrophil is largely a bystander in the mouse’s response to vCXCL-1. We confirm the hypothesis that vCXCL-1 is a HCMV virulence factor. Infection of severely immunocompromised mice with MCMVs expressing vCXCL-1 was lethal in more than 50% of infected animals, while all animals infected with parental virus survived during a 12-day period. This work provides needed insights into vCXCL-1 function in vivo.
Antioxidant Activity and Antiproliferative Effects of Lycium barbarum’s (Goji berry) Fractions on Breast Cancer Cell Lines

Abstract Background: Lycium barbarum has gained immense popularity over the past decade because of its antioxidant properties. There are many reports of observed health benefits of juice consumption, including prophylaxis in neoplastic disease and treatment of tumors. Materials and methods: In this study, we isolated three fractions of Lycium barbarum fruits – total water, pectin-free and polysaccharide, and determined their antioxidant activity by ORAC and HORAC assays. We investigated the antiproliferative effects of Lycium barbarum’s pectin-free and polysaccharide fraction on three different breast cell lines - MCF-10A (non-tumorigenic epithelial breast cell line), MCF-7 (breast cancer cell line, estrogen, progesterone receptors +, HER2-), and MDA-MB-231 (breast cancer cell line, triple negative), by the MTT dye reduction assay. Results: The Lycium barbarum’s pectin-free fraction showed concentration-dependent growth inhibition on the three cell lines, moreover, on cancer cells (MCF- 7 and MDA-MB-231) it was significantly more pronounced. The polysaccharide fraction showed negligible activity on the three cell lines, only the highest concentration (1000 μg/mL), suppressed the proliferation of MCF-7 cells. The combination of pectin-free and polysaccharide fraction on MCF-7 did not show the expected synergistic effect. Conclusion: We found a relative correlation between the polyphenolic content of the extracts and the observed effects. The pectin-free extract had the highest content of polyphenols with the best antioxidant and antineoplastic activity against breast cancer cells. Addition of polysaccharide to the pectin-free fraction contributes to its pharmacological activity.
Number Needed to Treat for Recurrent Events

Many clinical investigators find the Number Needed to Treat (NNT) an appealing measure of treatment effect and use it routinely in reporting the results of randomized trials. It is most easily computed and interpreted for trials with binary responses, but attempts have been made to compute NNT-like measures for recurrent event outcomes. We discuss methodological issues concerning the construction of NNT-like measures of treatment effect based on recurrent event outcomes. Rate and mean functions are used to develop nonparametric estimates of NNT-like measures of treatment effect for recurrent events in terms of the number of individuals to be treated to expect to prevent a k and simply to prevent any event. Parametric analyses facilitate the derivation of alternative measures and associated estimates. Applications to a trial of patients with cystic fibrosis are given for illustration. In settings where mortality rates are non-negligible, joint NNT-like measures for the recurrent event and survival processes are required and these are discussed.
Patient experience of hospital screening for Carbapenemase-producing Enterobacteriaceae (CPE): a qualitative study.

AIM The aim of this paper is to explore patients' accounts of screening and being managed for colonisation with the antimicrobial resistant organism, Carbapenemase-producing Enterobacteriaceae (CPE), when in hospital. BACKGROUND Antimicrobial resistance (AMR) has been identified as one of the biggest global health challenges of the 21st Century. As the threat from AMR grows, screening to identify patients who are colonised with resistant organisms such as CPE, is becoming an increasingly important aspect of nursing practice, in order to reduce risk of transmission of infection within hospitals. There is currently little research evidence on the patient experience of hospital management of CPE colonisation. METHODS Qualitative semi-structured telephone interviews were undertaken, using a topic guide. Nine patients participated in the study. The data was analysed thematically and rigour maintained through peer review. The COREQ checklist was used. RESULTS Two main themes were identified: 'I can't make sense of CPE', illustrating limitations in patients' understandings of CPE; and, 'I feel as if they are saying it is my fault', indicating the feelings of responsibility and blame which patients experienced. CONCLUSIONS This paper contributes original evidence to the limited literature on patients' experiences of being colonised with CPE. The findings suggest that support and information provided for patients, by healthcare professionals needs to be based on current evidence-based guidance on the nature of CPE and its implications for patient care, as well as being responsive to patients' emotional needs. RELEVANCE TO CLINICAL PRACTICE This study has international relevance for nursing practice. As the global threat of AMR grows, the demands on health care providers to manage resistant organisms and their implications for patient care within health care settings is increasing. Enabling health care professionals to engage sensitively with patients being managed for colonisation with CPE is paramount to providing patient-centred care. This article is protected by copyright. All rights reserved.
Fast formation of nitro-PAHs in the marine atmosphere constrained in a regional-scale Lagrangian field experiment.

Polycyclic aromatic hydrocarbons (PAHs) and some of their nitrated derivatives, NPAHs, are seemingly ubiquitous in the atmospheric environment. Atmospheric lifetimes may nevertheless vary within a wide range, and be as short as a few hours. The sources and sinks of NPAH in the atmosphere are not well understood. With a Lagrangian field experiment and modeling, we studied the conversion of the semi-volatile PAHs fluoranthene and pyrene into the 2-nitro derivatives 2-nitrofluoranthene and 2-nitropyrene in a cloud-free marine atmosphere on the time scale of hours to one day between a coastal and an island site. Chemistry and transport during several episodes was simulated by a Lagrangian box model i.e., a box model coupled to a Lagrangian particle dispersion model, FLEXPART-WRF. It is found that the chemical kinetic data do capture photochemical degradation of the 4-ring PAHs under ambient conditions on the time scale of hours to one day, while the production of the corresponding NPAH, which sustained 2-nitrofluoranthene/fluoranthene and 2-nitropyrene/pyrene yields of (3.7±0.2) and (1.5± 0.1)%, respectively, is by far underestimated. Predicted levels of NPAH come close to observed ones, when kinetic data describing the reactivity of the OH-adduct were explored by means of theoretically based estimates. Predictions are also underestimated by 1-2 orders of magnitude, when NPAH/PAH yields reported from laboratory experiments conducted under high NOx conditions are adopted for the simulations. It is concluded that NPAH sources effective under low NOx conditions, are largely underestimated.