Miracle-dz/UniFAR-FTUs huggingface dataset:
Extended-spectrum β-lactamase-producing Gram-negative bacteria causing neonatal sepsis in India in rural and urban settings

Extended-spectrum β-lactamase (ESBL)-producing Gram-negative bacilli (GNB) are of increasing clinical concern in all age groups worldwide. Whilst sepsis continues to be the leading cause of morbidity and mortality in Indian neonates in the community, identification of microbiological attributes in this population is lacking. This population-based study enrolled 1738 infants with a diagnosis of clinical sepsis at four participating centres in India. Each study site conducted Bactec blood culture, identified bacterial species by API test and stored isolates at −70 °C. From 252 GNB isolates, 155 (113 Klebsiella species, 21 Escherichia coli and 21 other) were subjected to drug susceptibility testing, ESBL phenotyping and testing for clonal relatedness of ESBL strains by PFGE. The results demonstrated that Klebsiella species and E. coli are the most common GNB causes of neonatal sepsis in India, and over one-third are ESBL producers in both community and hospital settings. ESBL-producing strains exhibited frequent co-resistance to aminoglycosides and ciprofloxacin, but remained susceptible to imipenem. PFGE analysis revealed extensive genetic diversity within the ESBL-producing isolates, showing multiple profiles (total of 23). Over 40 % of all ESBL-producing isolates formed three pulsed-field profiles (PFP I–III), with PFP-II being the largest cluster (>20 % of all ESBL-producing isolates), sharing strains from two distant locations. Identification of a common clone at two geographically distant centres indicated that predominant clones with increased virulence may exist, even in the absence of any clear outbreak. The presence of ESBL-producing strains in community infants with no prior history of hospitalization or antibiotic use dictates heightened vigilance and further studies on the ecology of these organisms.
Clinical profile and management of aerodigestive foreign bodies in North - western Nigeria

Background: Aeordigestive tract emergences in Nigeria occur in all age groups. They sometimes have dreaded outcome if lodged in air passages. Objective: The aim is to present the results of this problem in a 5-year retrospective survey of cases in the Emergency Unit of the National Ear Care Centre, Kaduna, Nigeria, from January 2009 to December 2013. Methods: Retrieved cases were studied noting the clinical history, examination and intervention. The study included all patients diagnosed with aerodigestive foreign bodies within the period stated. Results: Fifty-seven thousand nine hundred and four patients were studied. Fifteen thousand eight hundred and fifty were emergencies. The hospital prevalence was 0.61% and the average annual incidence was 0.13%, male preponderance with male to female ratio of 2.24-1.00. All patients were symptomatic. Mortality was recorded in one patient who had a co-morbidity of esophageal perforation. Conclusion: Aerodigestive foreign bodies pose a serious challenge in a setting of poor resources and scarcity in diagnostic and interventional facilities
Real‐Time System Identification: An Algorithm for Simultaneous Model Class Selection and Parametric Identification

In this article, a novel Bayesian real‐time system identification algorithm using response measurement is proposed for dynamical systems. In contrast to most existing structural identification methods which focus solely on parametric identification, the proposed algorithm emphasizes also model class selection. By embedding the novel model class selection component into the extended Kalman filter, the proposed algorithm is applicable to simultaneous model class selection and parametric identification in the real‐time manner. Furthermore, parametric identification using the proposed algorithm is based on multiple model classes. Examples are presented with application to damage detection for degrading structures using noisy dynamic response measurement.
Multidestination Pedestrian Flows in Equilibrium: A Cellular Automaton‐Based Approach

This article presents a new simulation approach for multidestination pedestrian crowds in complex environments. The work covers two major topics. In the first part, a novel cellular automaton (CA) model is proposed. The model describes the pedestrian movement by a set of simple rules and produces fundamental diagrams similar to those derived from laboratory experiments. The second topic of this work describes how the CA can be integrated into an iterative learning cycle where the individual pedestrian can adapt travel plans based on experiences from previous iterations. Depending on the setup, the overall travel behavior moves either toward a Nash equilibrium or the system optimum. The functional interaction of the CA with the iterative learning approach is demonstrated on a set of transport paradoxes. Furthermore, time series of speed and density observed in a small‐scale experiment show a general agreement between the CA simulation and laboratory experiments. The scalability of the proposed approach is demonstrated on a large‐scale scenario.
Primary pigmented nodular adrenocortical disease and its associated conditions

Primary pigmented nodular adrenocortical disease, a rare pituitary-independent, adrenal-dependent cause of the Cushing syndrome, is characterized by: (1) hypercortisolism resistant to suppression by dexamethasone or stimulation by metyrapone or corticotropin-releasing hormone; (2) variable findings
Deep Learning‐Based Crack Damage Detection Using Convolutional Neural Networks

A number of image processing techniques (IPTs) have been implemented for detecting civil infrastructure defects to partially replace human‐conducted onsite inspections. These IPTs are primarily used to manipulate images to extract defect features, such as cracks in concrete and steel surfaces. However, the extensively varying real‐world situations (e.g., lighting and shadow changes) can lead to challenges to the wide adoption of IPTs. To overcome these challenges, this article proposes a vision‐based method using a deep architecture of convolutional neural networks (CNNs) for detecting concrete cracks without calculating the defect features. As CNNs are capable of learning image features automatically, the proposed method works without the conjugation of IPTs for extracting features. The designed CNN is trained on 40 K images of 256 × 256 pixel resolutions and, consequently, records with about 98% accuracy. The trained CNN is combined with a sliding window technique to scan any image size larger than 256 × 256 pixel resolutions. The robustness and adaptability of the proposed approach are tested on 55 images of 5,888 × 3,584 pixel resolutions taken from a different structure which is not used for training and validation processes under various conditions (e.g., strong light spot, shadows, and very thin cracks). Comparative studies are conducted to examine the performance of the proposed CNN using traditional Canny and Sobel edge detection methods. The results show that the proposed method shows quite better performances and can indeed find concrete cracks in realistic situations.
Using Classification Techniques for Assigning Work Descriptions to Task Groups on the Basis of Construction Vocabulary

Construction project management produces a huge amount of documents in a variety of formats. The efficient use of the data contained in these documents is crucial to enhance control and to improve performance. A central pillar throughout the project life cycle is the Bill of Quantities (BoQ) document. It provides economic information and details a collection of work descriptions describing the nature of the different works needed to be done to achieve the project goal. In this work, we focus on the problem of automatically classifying such work descriptions into a predefined task organization hierarchy, so that it can be possible to store them in a common data repository. We describe a methodology for preprocessing the text associated to work descriptions to build training and test data sets and carry out a complete experimentation with several well‐known machine learning algorithms.
A role for topoisomerase III in Escherichia coli chromosome segregation

The cellular function of Escherichia coli topoisomerase III remains elusive. We show that rescue of temperature‐sensitive mutants in parE and parC (encoding the subunits of the chromosomal decatenase topoisomerase IV) at restrictive temperatures by high‐copy suppressors is strictly dependent on topB (encoding topoisomerase III). Double mutants of parEΔtopB and parCΔtopB were barely viable, grew slowly, and were defective in chromosome segregation at permissive temperatures. The topB mutant phenotype did not result from accumulation of toxic recombination intermediates, because it was not relieved by mutations in either recQ or recA. In addition, in an otherwise wild‐type genetic background, ΔtopB cells treated with the type II topoisomerase inhibitor novobiocin displayed aberrant chromosome segregation. This novobiocin sensitivity was attributable to an increased demand for topoisomerase IV and is unlikely to define a new role for topoisomerase III; therefore, these results suggest that topoisomerase III participates in orderly and efficient chromosome segregation in E. coli.
Bacterial growth does require peptidoglycan hydrolases

Most bacteria surround their cytoplasmic membrane with a net‐like, elastic heteropolymer, the peptidoglycan sacculus, to protect themselves from bursting due to the turgor and to maintain cell shape. It has been assumed that growing bacteria require peptidoglycan hydrolases to open meshes in the peptidoglycan net allowing the insertion of the newly synthesized material for surface expansion. However, peptidoglycan hydrolases essential for bacterial growth have long remained elusive. In this issue of Molecular Microbiology Singh et al. ( ) report the identification in Escherichia coli of three new DD‐endopeptidases (Spr, YdhO and YebA) which are collectively required for peptidoglycan growth. Cells depleted of the three enzymes fail to incorporate new peptidoglycan, indicating that the cleavage of cross‐links by the new endopeptidases is needed for surface growth of the sacculus. These results are corroborated by recent data showing that Bacillus subtilis cells require the DL‐endopeptidase activity of CwlO or LytE for growth.
A defect in ATP‐citrate lyase links acetyl‐CoA production, virulence factor elaboration and virulence in Cryptococcus neoformans

The interaction of Cryptococcus neoformans with phagocytic cells of the innate immune system is a key step in disseminated disease leading to meningoencephalitis in immunocompromised individuals. Transcriptional profiling of cryptococcal cells harvested from cell culture medium or from macrophages found differential expression of metabolic and other functions during fungal adaptation to the intracellular environment. We focused on the ACL1 gene for ATP‐citrate lyase, which converts citrate to acetyl‐CoA, because this gene showed elevated transcript levels in macrophages and because of the importance of acetyl‐CoA as a central metabolite. Mutants lacking ACL1 showed delayed growth on medium containing glucose, reduced cellular levels of acetyl‐CoA, defective production of virulence factors, increased susceptibility to the antifungal drug fluconazole and decreased survival within macrophages. Importantly, acl1 mutants were unable to cause disease in a murine inhalation model, a phenotype that was more extreme than other mutants with defects in acetyl‐CoA production (e.g. an acetyl‐CoA synthetase mutant). Loss of virulence is likely due to perturbation of critical physiological interconnections between virulence factor expression and metabolism in C. neoformans. Phylogenetic analysis and structural modelling of cryptococcal Acl1 identified three indels unique to fungal protein sequences; these differences may provide opportunities for the development of pathogen‐specific inhibitors.
Evaluation and quantitative analysis of 11 compounds in Morinda officinalis using ultra-high performance liquid chromatography and photodiode array detection coupled with chemometrics.

Morinda officinalis (Rubiaceae) is a traditional Chinese medicine widely used for the treatment of impotence and osteoporosis in clinical therapy. In the present study, a rapid and simple ultra-high performance liquid chromatography with photodiode array detection method was developed and validated for the simultaneous determination of 11 bioactive compounds in M. officinalis. This assay method was validated with respect to linearity (R2 > 0.9991), precision, repeatability, limit of detection, limit of quantification, and accuracy (with observed recovery rates between 94.21 and 100.38%). The quantitative results revealed significant differences in the concentrations of the selected compounds. Additionally, chemometric methods, including hierarchical clustering analysis, principal component analysis, and partial least-squares discriminate analysis, were applied to compare and sort the 25 batches of M. officinalis samples based on the quantitative data of the analytes. All of the samples were clearly divided into two groups: the Hainan samples were successfully discriminated from the samples from other origins. Simultaneous determination of multiple compounds using the proposed method combined with chemometrics could be a viable strategy to compare and evaluate the quality of M. officinalis.
Mitochondrial shape and function in trypanosomes requires the outer membrane protein, TbLOK1

In an RNAi library screen for loss of kinetoplast DNA (kDNA), we identified an uncharacterized Trypanosoma brucei protein, named TbLOK1, required for maintenance of mitochondrial shape and function. We found the TbLOK1 protein located in discrete patches in the mitochondrial outer membrane. Knock‐down of TbLOK1 in procyclic trypanosomes caused the highly interconnected mitochondrial structure to collapse, forming an unbranched tubule remarkably similar to the streamlined organelle seen in the bloodstream form. Following RNAi, defects in mitochondrial respiration, inner membrane potential and mitochondrial transcription were observed. At later times following TbLOK1 depletion, kDNA was lost and a more drastic alteration in mitochondrial structure was found. Our results demonstrate the close relationship between organelle structure and function in trypanosomes.
Ovarian Preservation and Staging in Reproductive-Age Endometrial Cancer Patients

The prognosis for premenopausal women with early stage endometrial carcinoma is favorable, with a 5-year survival rate greater than 90%. For more than 20 years, standard treatment has been aggressive surgical staging consisting of total abdominal hysterectomy and bilateral salpingo-oophorectomy (BSO) with pelvic and paraaortic lymphadenectomy as needed. Surgical staging in premenopausal women is associated with significant morbidity from lymphadenectomy, and long-term adverse effects in cardiovascular and bone health from premature menopause as well as in quality of life. Investigators have explored the possibility of less aggressive treatment in young, early-stage patients with endometrial cancer using a clinical staging regimen that preserves the ovary and employs limited surgical staging. This regimen appears feasible for young women with early stage endometrial cancer—a patient population at low risk of lymph node metastases and distant spread. This retrospective study compared outcomes of complete surgical and clinical staging, including the impact of ovarian preservation in young patients with endometrial carcinoma. Medical charts were reviewed for all patients with endometrial cancer at age 45 or younger diagnosed and treated from 1960 to 2006 at a large university hospital. Data on clinical findings, histology, epidemiology and history were examined and a gynecologic pathologist reviewed the histological slides. The mean age of the 251 study subjects was 41 years (range: 23-45 years). Stage 1 disease was identified in over 75% of the patients. Surgical staging was used in 146 patients (58.2%), whereas clinical staging was performed in 101 patients (40.2%). Most of the 251 patients (80%) had a BSO. Recurrence was diagnosed in less than 3% of the patients. Women with grade 1 disease who underwent surgical staging had a significantly longer overall survival than clinically staged patients (P = 0.003). No difference in disease-free survival, however, was found between the 2 groups. Compared to patients with ovarian preservation, those who underwent a BSO had a trend toward longer disease-free survival when all patients were included. Women with stage I disease who underwent a BSO had a significantly longer disease-free survival (P = 0.013). The investigators conclude from these findings that clinical staging in young women with early stage low-grade endometrial cancer may be a useful alternative in the absence of risk factors to aggressive surgical staging. Strong consideration should be given, however, to include BSO as part of the surgical regimen.
Conflicting roles for a cell surface modification in Salmonella

Chemical modifications of components of the bacterial cell envelope can enhance resistance to antimicrobial agents. Why then are such modifications produced only under specific conditions? Here, we address this question by examining the role of regulated variations in O‐antigen length in the lipopolysaccharide (LPS), a glycolipid that forms most of the outer leaflet of the outer membrane in Gram‐negative bacteria. We determined that activation of the PmrA/PmrB two‐component system, which is the major regulator of LPS alterations in Salmonella enterica serovar Typhimurium, impaired growth of Salmonella in bile. This growth defect required the PmrA‐activated gene wzzst, which encodes the protein that determines long O‐antigen chain length and confers resistance to complement‐mediated killing. By contrast, this growth defect did not require the wzzfepE gene, which controls production of very long O‐antigen, or other PmrA‐activated genes that mediate modifications of lipid A or core regions of the LPS. Additionally, we establish that long O‐antigen inhibits growth in bile only in the presence of enterobacterial common antigen, an outer‐membrane glycolipid that contributes to bile resistance. Our results suggest that Salmonella regulates the proportion of long O‐antigen in its LPS to respond to the different conditions it faces during infection.
Local silencing controls the oxidative stress response and the multidrug resistance in Candida glabrata

In Candida glabrata, the sirtuins Sir2 and Hst1 control the expression of a wide number of genes including adhesins required for host colonization and niacin transporters needed for growth. Given that these sirtuins can be inactivated during infection, we asked if their inhibition could modify the response of C. glabrata to other stressful conditions. Here, we found that deletion of HST1 decreases susceptibility of C. glabrata to fluconazole and hydrogen peroxide. The transcription factor Pdr1 and the ABC transporter Cdr1 mediated the fluconazole resistance phenotype of the hst1Δ cells, whereas the transcriptional activator Msn4 and the catalase Cta1 are necessary to provide oxidative stress resistance. We show that the transcription factor Sum1 interacts with Hst1 and participate in the regulation of these genes. Interestingly, even though C. glabrata and Saccharomyces cerevisiae are closely related phylogenetically, deletion of HST1 decreased susceptibility to fluconazole and hydrogen peroxide only in C. glabrata but not in S. cerevisiae, indicating a different transcriptional control by two similar sirtuins. Our findings suggest that Hst1 acts as a regulator of stress resistance associated‐genes.
Lyme disease spirochaetes possess an aggrecan‐binding protease with aggrecanase activity

Connective tissues are the most common area of colonization for the Lyme disease spirochaete Borrelia burgdorferi. Colonization is aided by the interaction between numerous bacterial adhesins with components of the extracellular matrix (ECM). Here we describe a novel interaction between B. burgdorferi and the major ECM proteoglycan found in joints, aggrecan. Using affinity chromatography and mass spectrometry we identify two borrelial aggrecan‐binding proteins: the known ECM ligand Bgp (BB0588) and an uncharacterized protease BbHtrA (BB0104). Proteinase K studies demonstrate that BbHtrA is surface exposed. Immunoblots using sera from patients with both early and late Lyme disease establish that BbHtrA is expressed during human disease, immunogenic, and conserved in the three major Lyme disease spirochaete species. Consequences of the interaction between aggrecan and BbHtrA were examined by proteolysis assays. BbHtrA cleaves aggrecan at a site known to destroy aggrecan function and which has been previously observed in the synovial fluid of patients with Lyme arthritis. These data demonstrate that B. burgdorferi possess aggrecan‐binding proteins which may provide the organism with additional capability to colonize connective tissues. Moreover, our studies provide the first evidence that B. burgdorferi possess proteolytic activity which may contribute to the pathogenesis of Lyme arthritis.
Target evaluation of the non‐coding csRNAs reveals a link of the two‐component regulatory system CiaRH to competence control in Streptococcus pneumoniae R6

The two‐component regulatory system CiaRH of Streptococcus pneumoniae controls 25 genes, five of which specify homologous small non‐coding csRNAs (cia‐dependent small RNAs). The csRNAs were predicted to act regulatory as base‐pairing sRNAs, but their targets have not been identified. By csRNA gene inactivations we established that the major phenotypes associated with a hyperactive CiaRH system, enhanced β‐lactam resistance and prevention of genetic competence, are dependent on the csRNAs. Computational target predictions and evaluations by translational fusions identified six genes to be under csRNA control: spr0081, spr0371, spr0159, spr0551, spr1097 and spr2043(comC). Measuring the effect of single csRNAs on three targets indicated that they acted additively. One of the targets, comC(spr2043), encoding the precursor of the competence stimulating pheromone CSP, constitutes a link of CiaRH to competence control. Partially disrupting predicted csRNA‐comC complementarity led to strongly diminished repression by the csRNAs and to transformability in a strain with a hyperactive CiaRH. Thus, a hyperactive CiaRH system prevents competence development by csRNA‐dependent post‐transcriptional repression of CSP production. The csRNAs are also involved in competence regulation in the wild‐type strain R6, but their activity is only apparent in the absence of the protease gene htrA, another CiaRH regulon member.