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829 results for “Drug resistance”
The repurposing of tebipenem pivoxil as alternative therapy for severe gastrointestinal infections caused by extensively drug resistant Shigella spp.
<p><strong>dataset for The repurposing of tebipenem pivoxil as alternative therapy for severe gastrointestinal infections caused by extensively drug resistant <em>Shigella</em> spp.</strong></p> <p>Elena Fernández Alvaro <sup>1*</sup>, Phat Voong Vinh <sup>2</sup>, Cristina de Cozar <sup>1</sup>, David Wille <sup>1</sup>, Beatriz Urones <sup>1</sup>,</p> <p>Alan Price <sup>1</sup>, Nhu Tran Do Hoang <sup>2</sup>, Tuyen Ha Thanh <sup>2</sup>, Molly McCloskey <sup>3</sup>, Shareef Shaheen<sup> 3</sup>, Denise Dayao<sup> 4</sup>, Jaime de Mercado <sup>1</sup>, Pablo Castañeda <sup>1</sup>, Adolfo García-Perez <sup>1</sup>, Benson Singa <sup>5</sup>, Patricia Pavlinac <sup>6</sup>,</p> <p>Judd Walson<sup>3</sup>, Maria Santos Martínez-Martínez <sup>1</sup>, Samuel L.M. Arnold <sup>3</sup>, Tzipori Saul <sup>4</sup>, Lluis Ballell <sup>1#</sup>,</p> <p>and Stephen Baker <sup>7,8*</sup></p> <p> </p>
SUPPLEMENTARY (For MD) An integrative pan-genome and subtractive proteomics approach for the identification of potential novel therapeutic drug target against antibiotic resistant honeybee pathogen Paenibacillus larvae
<p><strong>Parameters</strong></p><p>Force field: AMBER ff19SB</p><p>Water type: TIP3P</p><p>Ions: NaCl </p><p>Ligand topology force field: GAFF2</p><p>Temperature: 298k</p><p>Pressure: 1 bar</p><p>minimization step: 20000 on 5 nanoseconds</p><p>initial velocity is changed by changing "ntx" and "ig"</p><p>C2: ntx = 5 , ig = 8</p><p>C3: ntx = 2 , ig = 5</p><p> </p><p><strong>Uploads</strong>- </p><p>1. Zip file of all 3 main files</p><p>2. Unzip file of C1 (Trajectory, PDB complex after each 10 ns run, and Mp4 video of Complex)</p><p>3. Zip file of C1</p><p>4. Unzip file of C2 (Trajectory, PDB complex after each 10 ns run, and Mp4 video of Complex)</p><p>5. Zip file of C2</p><p>6. Unzip file of C3 (Trajectory, PDB complex after each 10 ns run, and Mp4 video of Complex)</p><p>7. Zip file of C3</p><p>8. Zip and unzip file of <strong>Initial</strong> PDB of complex prior to MD simulation with <strong>Post</strong> MD PDB (C1, C2, C3)</p><p>9. Zip file of <strong>topology</strong> files for C1, C2, and C3</p>
Caregivers and MDR-TB patients: Dataset for the importance of knowledge and behavior on drug resistance tuberculosis
<p>Multidrug-resistant Tuberculosis (MDR-TB) is a type of Tuberculosis (TB) that is resistant to at least one or more of the main anti-TB drugs, namely Rifampin or Isoniazid, so this infection is more difficult to eliminate. Good knowledge and behavior of caregivers and patients can affect the success of treatment because they tend not to be late in taking treatment. In this data note we provide the details of a research database of 228 MDR-TB caregivers and patients underwent treatment from January 2020 to December 2021 in preferred hospital in West Java, Indonesia. The purposes of this publication are to describe the dataset for external researchers who may be interested in making use of it, and to detail the methods used to obtain the dataset to determine the level of knowledge and behavior of MDR-TB caregivers and patients regarding the disease through a validated questionnaire consisted of the knowledge and behavior distributed to respondents via online and offline.</p>
Alterations of antimicrobial resistance genes in the clinical multi-drug resistance Acinetobacter baumannii isolates in Vietnam
<p><strong>FIGURE 1 </strong>List of antibiotic resistance gene expression.</p> <p><strong>TABLE 1 </strong>Primers used in this study.</p> <p><strong>TABLE 2 </strong>Clinical characteristics of 30 patients with <em>A. baumannii </em>isolates.</p> <p><strong>TABLE 3 </strong>Antimicrobial resistance values of <em>A. baumannii</em> isolated during 2017 to 2019 year in the Military Hospital 103.</p> <p><strong>TABLE 4 </strong>Relationship between genotype and phenotype antimicrobial resistance of isolates in this study.</p> <p><strong>TABLE 5 </strong>List of altered antibiotic resistance genes expression in isolates of <em>A. baumannii</em> (up or down two-fold changes of related genes compare with <em>16S rRNA</em> gene).</p> <p><strong>TABLE 6 </strong>The multiple antimicrobial resistance gene profile of 30 <em>A. baumannii</em> isolates.</p> <p> </p>
Fig. 1 in Detection of Escherichia fergusonii - an emerging pathogen harbouring drug resistant genes from seafood samples of Tamil Nadu, India
Fig. 1 — Gene specific PCR amplification of Escherichia fergusonii (lane 1 – 100 bp DNA ladder, lane 2 – positive control (clinical E. fergusonii), lane 3 – negative control, lane 4 – E011, lane 5 – E060)
Figure 1 in Challenges of drug-resistant malaria
Figure 1. Different proteins present inside the parasitic organelle that contribute to drug resistance in malaria under selective drug pressure and new drugs in development, targeting the same pathway to rescue resistance. PRBC: parasitized red blood cell, ER: endoplasmic reticulum, MT: mitochondria, DHPS: dihydropterate synthetase, DHFR: dihydrofolate reductase, ATPase6: sacro/endoplasmic reticulum calcium dependent ATPase orthologue, CRT: chloroquine resistance transporter, MDR1: multidrug resistance.
dataset for bioRxiv preprint titled 'Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease'
<p>This data supports the Figures in the preprint titled</p> <p><strong>Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease</strong></p> <p><strong>working abstract</strong></p> <p>The HIV-1 protease is one of several common key targets of combination drug therapies for human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS). During the progression of the disease, some individual patients acquire -drug resistance due to mutational hotspots on the viral proteins targeted by combination drug therapies. It has recently been discovered that drug-resistant mutations accumulate on the ‘flap region’ of the HIV-1 protease, which is a critical dynamic region involved in non-specific polypeptide binding during invasion and infection of the host cell. In this study, we utilize machine learning assisted comparative molecular dynamics, conducted at single amino acid site resolution, to investigate the dynamic changes that occur during functional dimerization and polypeptide binding of the main protease. We use a multi-agent machine learning model to identify conserved dynamics of the HIV-1 main protease that are preserved across simian and feline protease orthologs (SIV and FIV). We also investigate changes in dynamics due to common drug-resistant mutations in many patients. We find that a key functional site in the flap region, a solvent-exposed isoleucine (ILE50) and surrounding sites that control flap dynamics is often targeted by drug-resistance mutations, likely leading to malfunctional molecular dynamics affecting the overall flexibility of the flap region. We conclude that better long term patient outcomes may be achieved by designing drugs that target protease regions which are less dependent upon single sites with large functional binding effects.</p>
Data supplement for the paper "An integrated computational strategy to predict personalized cancer drug combinations by reversing drug resistance signatures"
<p>This dataset contains the the following data created for the paper "An integrated computational strategy to predict personalized cancer drug combinations by reversing drug resistance signatures".</p> <p>Data listing:</p> <p>Cell line-specific drug resistance signatures (CDRSR)</p> <p>Patient-specific drug resistance signatures (CTR-DB)</p>
Renal Denervation for Management of Drug-Resistant Hypertension
ClinicalTrials.gov study NCT01505010. IPD Sharing: YES. Countries: 1. Publications: 2.
Comparative assessment of line-probe assays and targeted next-generation sequencing in drug-resistant tuberculosis diagnosis
Open the record for dataset details and reuse information.
Outcomes and adverse events of pre- and extensively drug-resistant tuberculosis patients in Kinshasa, Democratique Republic of the Congo: retrospective cohort study
<p><strong>Abstract</strong></p> <p><strong>Background</strong>: Extensively drug-resistant tuberculosis (XDR TB) is a very serious form of tuberculosis that is burdened with a heavy mortality toll, especially before the advent of new TB drugs. The Democratic Republic of the Congo (DRC) is among the countries most affected by this new epidemic.</p> <p><strong>Methods:</strong> A retrospective analysis was performed of the records of all patients with pre- and extensively drug-resistant tuberculosis hospitalized from January 1, 2015 to December 31, 2017 and monitored for at least 6 months to one year after the end of their treatment in Kinshasa; an individualized therapeutic regimen with bedaquiline for 20 months was built for each patient. The adverse effects were systematically monitored.</p> <p><strong>Results:</strong> Of the 40 laboratory-confirmed patients, 32 (80%) patients started treatment, including 29 preXRB and 3 XDR TB patients. In the eligible group, 3 patients (9.4%) had HIV-TB coinfections. The therapeutic success rate was 53.2%, and the mortality rate was 46.8% (15/32); there were no relapses, failures or losses to follow-up. All coinfected HIV–TB patients died during treatment. The cumulative patient survival rate was 62.5% at 3 months, 53.1% at 6 months and 53.1% at 20 months. The most common adverse events were vomiting, Skin rash, anemia and peripheral neuropathy.</p> <p><strong>Conclusion: </strong>Bedaquiline based treatment improves patient survival in the DRC despite the still high mortality rate. The new anti-tuberculosis<br> drugs are a real hope for the management of Drug Resistant tuberculosis patient and other new therapeutic combinations may improve favorable outcomes.</p>
Data from: Antibacterial activity of graphene oxide nanosheet against multi drug resistant superbugs isolated from infected patients
Graphene oxide (GO) is a derivative of graphene nanosheet which is the most promising material of the decade in biomedical research. In particular, it has been known as an antimicrobial nanomaterial with good biocompatibility. In this study, we have synthesized and characterize GO and checked its antimicrobial property against different Gram-negative and Gram-positive multi drug resistant (MDR) hospital superbugs grown in solid agar-based nutrient plates with and without human serum through the utilization of agar well diffusion method, live/dead fluorescent staining and genotoxicity analysis. The main focus of the antimicrobial activity analysis is to distinguish the killing performance of GO in artificial and blood containing media because after injection into the bloodstream the activity of GO may be modified by adsorption of blood proteins or other biomolecules. No significant changes in antibacterial activity were found in these two different conditions. We also compare the bactericidal capability of GO with some commonly administrated antibiotics and in all cases the degree of inhibition is found to be higher. The data presented here are novel and show that GO is an effective bactericidal agents against different superbugs and can be used as a future antibacterial agent.
Nano MOFs as targeted drug delivery agents to combat antibiotic resistant bacterial infections
<p>The drug resistance of bacteria is a significant threat to human civilization while the action of antibiotics against drug-resistant bacteria is severely limited due to the hydrophobic nature of drug molecules, which unquestionably inhibit its permanency for clinical applications. The antibacterial action of nanomaterials offers major modalities to combat drug resistance of bacteria. The current work reports, the use of nano MOFs encapsulating drug molecules to enhance its antibacterial activity against model drug-resistant free living bacteria and biofilm of the bacteria. We have attached rifampicin (RF), a well-documented antituberculosis drug with tremendous pharmacological significance, into the pore surface of zeolitic imidazolate framework 8 (ZIF8) by a <span><span>simple synthetic procedure</span></span><span>.</span> The synthesized ZIF8 has been characterized using X-ray diffraction (XRD) method before and after drug encapsulation. The electron microscopic strategies such as scanning electron microscope (SEM) and transmission electron microscope (TEM) methods was performed to characterize the binding between ZIF8 and RF. We have also performed picosecond resolved fluorescence spectroscopy to validate the formation of the ZIF8-RF nanohybrids (NHs). The drug release profile experiment demonstrates that ZIF8-RF depicts pH-responsive drug delivery and ideal for targeting bacterial disease corresponding to its inherent acidic nature. Most remarkably, ZIF8-RF gives enhanced antibacterial activity against methicillin-resistant <i>S. aureus</i> (MRSA) bacteria and also prompts entire damage of structurally robust bacterial biofilms. Overall, the present study depicts a detailed physical insight for manufactured antibiotic-encapsulated NHs presenting tremendous antimicrobial activity that can be beneficial for manifold practical applications.</p>
Antibiotics can be used to contain drug-resistant bacteria by maintaining sufficiently large sensitive populations
<p>Standard infectious disease practice calls for aggressive drug treatment that rapidly eliminates the pathogen population before resistance can emerge. When resistance is absent, this elimination strategy can lead to complete cure. However, when resistance is already present, removing drug-sensitive cells as quickly as possible removes competitive barriers that may slow the growth of resistant cells. In contrast to the elimination strategy, the containment strategy aims to maintain the maximum tolerable number of pathogens, exploiting competitive suppression to achieve chronic control. Here we combine <em>in vitro</em> experiments in computer-controlled bioreactors with mathematical modeling to investigate whether containment strategies can delay failure of antibiotic treatment regimens. To do so, we measured the "escape time" required for drug-resistant <em>E. coli</em> populations to eclipse a threshold density maintained by adaptive antibiotic dosing. Populations containing only resistant cells rapidly escape the threshold density, but we found that matched resistant populations that also contain the maximum possible number of sensitive cells could be contained for significantly longer. The increase in escape time occurs only when the threshold density--the acceptable bacterial burden--is sufficiently high, an effect that mathematical models attribute to increased competition. The findings provide decisive experimental confirmation that maintaining the maximum number of sensitive cells can be used to contain resistance when the size of the population is sufficiently large.</p>
A rapid and versatile tool for HIV-1 Drug Resistance Genotyping by Deep Sequencing: supporting dataset
<p>See file `viral_mixes.md` and [manuscript](http://www.sciencedirect.com/science/article/pii/S0166093416301987).</p> <div class="grammarly-disable-indicator"> </div> <div class="grammarly-disable-indicator"> </div>
Evidence for a role of Anopheles stephensi in the spread of drug- and diagnosis-resistant malaria in Africa
<p>Anopheles stephensi, an Asian malaria vector, continues to expand across Africa. The vector is now firmly established in urban settings in the Horn of Africa. Its presence in areas where malaria resurged suggested a possible role in causing malaria outbreaks. Here, using a prospective case–control design, we investigated the role of An. stephensi in transmission following a malaria outbreak in Dire Dawa, Ethiopia in April–July 2022. Screening contacts of patients with malaria and febrile controls revealed spatial clustering of Plasmodium falciparum infections around patients with malaria in strong association with the presence of An. stephensi in the household vicinity. Plasmodium sporozoites were detected in these mosquitoes. This outbreak involved clonal propagation of parasites with molecular signatures of artemisinin and diagnostic resistance. To our knowledge, this study provides the strongest evidence so far for a role of An. stephensi in driving an urban malaria outbreak in Africa, highlighting the major public health threat posed by this fast-spreading mosquito.</p>
Drug sensitive and multidrug-resistant Mycobacterium tuberculosis genotypes from Bulgaria
<p>Dataset of drug sensitive and multidrug-resistant Mycobacteium tuberculosis spoligo- and MIRU-VNTR genotypes from Bulgaria collected between 2008 till 2019.</p>
Resistance to bacteriophage incurs a cost to virulence in drug resistant Acinetobacter baumannii
<p>Introduction<em>: Acinetobacter baumannii</em> is a critical priority pathogen (World Health Organisation) because of the rise in nosocomial<em> </em>infections and its ability to evolve resistance to last resort antibiotics, which makes <em>A. baumannii</em> a priority target for phage therapy. Two strains of a novel, lytic bacteriophage (LemonAid and Tonic) able to infect carbapenem-resistant <em>A. baumannii</em> (strain NCTC 13420), were isolated from environmental water samples collected through a citizen science program.</p> <p>Methods: <em>In vitro </em>and <em>in vivo</em> assays, genomics and microscopy techniques were used to characterise the phages, determine mechanisms of phage resistance and the efficacy of the phages against <em>A. baumannii</em>.</p> <p>Results: <em>A. baumannii </em>developed resistance to both viruses, LemonAid and Tonic. Resistance came at a cost to virulence, with the resistant variants causing significantly reduced mortality in a <em>Galleria mellonella </em>larval <em>in vivo</em> model. A replicated 8bp insertion increased in frequency (~40% higher frequency than in the wildtype) within phage-resistant <em>A. baumannii </em>mutants, putatively resulting in early truncation of a protein of unknown function. Evidence from comparative genomics and an adsorption assay suggests this protein acts as a novel phage receptor site in <em>A. baumannii</em>. We find no evidence linking resistance to changes in capsule structure, a known virulence factor. LemonAid efficiently suppressed growth of <em>A. baumanni</em> <em>in vitro</em> across a wide range of titres. However, <em>in vivo</em>, while survival of <em>A. baumannii</em> infected larvae significantly increased with both remedial and prophylactic treatment with LemonAid (10<sup>7 </sup>PFU/mL), the effect was weak and not sufficient to save larvae from morbidity and mortality.</p> <p>Conclusion: While LemonAid and Tonic did not prove effective as a treatment in a <em>Galleria </em>larvae model, there is potential to harness their ability to attenuate virulence in drug-resistant <em>A. baumannii</em>.</p>
Phenotypic and genotypic analysis of drug resistance in M. tuberculosis isolates in Gansu, China
<p>Tuberculosis has posed a serious threat to human health. It is imperative to investigate the geographic prevalence of tuberculosis and medication resistance, as this information is essential for informing strategies for its prevention and treatment. Drug resistance was identified using a proportion method. Drug-resistant genes and pathways were predicted using whole genome sequencing. The drug resistance range of bedaquiline was identified using the microporous plate two-fold dilution method, and drug resistance genes were studied using sequencing. The study revealed that 19.99% of the tuberculosis cases had multidrug resistance. The genes of<em> M. tuberculosis</em> are predominantly involved in the synthesis of ABC transporters, two-component systems, and bacterial secretion systems, as well as in energy production and conversion, and lipid transport and metabolism. The genes encode for 82.45% of carbohydrate-related enzymes such as glycoside hydrolases, glycosyl transferases, and carbohydrate esterases. The minimum inhibitory concentration (MIC) of bedaquiline against clinical strains was approximately 0.06 μg/mL, with identified mutations in drug-resistant genes Rv0678, atpE, and pepQ, specifically V152A, P62A, and T222N, respectively. The multidrug resistance tuberculosis development was attributed to the strong medication resistance exhibited. It was concluded that tuberculosis had presented a high level of drug resistance. Phenotypic resistance was related to genes, existing potential genetic resistance in <em>M. tuberculosis</em>. Bedaquiline was found to possess effective antibacterial properties against <em>M. tuberculosis</em>.</p>
Figure 2 in Challenges of drug-resistant malaria
Figure 2. Different parameters that contribute to antimalarial resistance.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.