Miracle-dz/UniFAR-FTUs huggingface dataset:
Antibacterial Activity of Defatted and Nondefatted Methanolic Extracts of Aframomum melegueta K. Schum. against Multidrug-Resistant Bacteria of Clinical Importance

The antibacterial activity of the extracts of Aframomum melegueta including n-hexane extract (NHE), nondefatted methanol extract (NDME), and defatted methanol extract (DME) was investigated in this study. The NHE exhibited no antibacterial activity. The DME showed higher antibacterial activity than the NDME against the different isolates. At the highest concentration of 10 mg/mL in agar diffusion, NDME produced inhibition zones ranging from 11 to 29 mm against the microorganisms while DME produced inhibition zones ranging from 20 to 40 mm with the concentration of 10 mg/mL against the microorganisms. 0.1 mg/mL of the DME produced inhibition zones ranging between 12 and 14 mm in Aeromonas hydrophila ATCC 35654 and Pseudomonas aeruginosa ATCC 15442, respectively, while none of the isolates were inhibited by the NDME at a concentration of 1 mg/mL or less. In the agar dilution assay, the MICs of the NDME and DME ranged between 0.31 and 10 mg/mL, but more isolates were inhibited at 0.31 mg/mL of DME than those in NDME. In macrobroth assay, the MICs of the NDME ranged between 0.15 and 5.0 mg/mL and the MBCs ranged between 0.63 and 5.0 mg/mL, and the MICs of the DME ranged between 0.08 and 5.0 mg/mL and the MBCs were between 0.31 and 5.0 mg/mL. This study indicated that DME was more active with higher antibacterial activity than the NDME of this plant, and extracting the fatty portion of plant materials prior susceptibility testing would allow plant extracts to be more effective as well as justifying the use of Aframomum melegueta in traditional medicine for the treatment of bacterial infections.
Cryo-EM structure of the lysosomal chloride-proton exchanger CLC-7 in complex with OSTM1

The chloride-proton exchanger CLC-7 plays critical roles in lysosomal homeostasis and bone regeneration and its mutation can lead to osteopetrosis, lysosomal storage disease and neurological disorders. In lysosomes and the ruffled border of osteoclasts, CLC-7 requires a β-subunit, OSTM1, for stability and activity. Here, we present electron cryomicroscopy structures of CLC-7 in occluded states by itself and in complex with OSTM1, determined at resolutions up to 2.8 Å. In the complex, the luminal surface of CLC-7 is entirely covered by a dimer of the heavily glycosylated and disulfide-bonded OSTM1, which serves to protect CLC-7 from the degradative environment of the lysosomal lumen. OSTM1 binding does not induce large-scale rearrangements of CLC-7, but does have minor effects on the conformation of the ion-conduction pathway, potentially contributing to its regulatory role. These studies provide insights into the role of OSTM1 and serve as a foundation for understanding the mechanisms of CLC-7 regulation.
Dynamic Multi-Swarm Differential Learning Quantum Bird Swarm Algorithm and Its Application in Random Forest Classification Model

Bird swarm algorithm is one of the swarm intelligence algorithms proposed recently. However, the original bird swarm algorithm has some drawbacks, such as easy to fall into local optimum and slow convergence speed. To overcome these short-comings, a dynamic multi-swarm differential learning quantum bird swarm algorithm which combines three hybrid strategies was established. First, establishing a dynamic multi-swarm bird swarm algorithm and the differential evolution strategy was adopted to enhance the randomness of the foraging behavior's movement, which can make the bird swarm algorithm have a stronger global exploration capability. Next, quantum behavior was introduced into the bird swarm algorithm for more efficient search solution space. Then, the improved bird swarm algorithm is used to optimize the number of decision trees and the number of predictor variables on the random forest classification model. In the experiment, the 18 benchmark functions, 30 CEC2014 functions, and the 8 UCI datasets are tested to show that the improved algorithm and model are very competitive and outperform the other algorithms and models. Finally, the effective random forest classification model was applied to actual oil logging prediction. As the experimental results show, the three strategies can significantly boost the performance of the bird swarm algorithm and the proposed learning scheme can guarantee a more stable random forest classification model with higher accuracy and efficiency compared to others.
Cost of Investigating Neurological Disease: Experience of a Tertiary Care Center in Karachi, Pakistan

Introduction: Neurological disorders, structural or functional, are prevalent all over the world and are accompanied by physical and social morbidity. In this study, we aimed to calculate the cost of investigating neurological disorders and compare the costs incurred in a government hospital with that in a private hospital. Materials and Methods: This study was conducted at the Dr. Ruth KM Pfau Civil Hospital, Karachi, Pakistan. One hundred patients were enrolled in the study; 10 each investigated for epilepsy, cerebrovascular accidents (CVAs), headache, neuropathy, myopathy, cranial nerve palsies, movement disorders, demyelinating diseases, central nervous system (CNS) infections, and dementia. Receipts and records in the patients’ medical history were used for the calculation of the cost of procedures, which was then compared with the costs of these investigations in a private hospital. A bottom-up costing approach was taken with individual costs being estimated and then being grouped to calculate the overall economic burden of the disorders. Data were analyzed using IBM SPSS version 23.0. One-way analysis of variance (ANOVA) was done to compare the mean cost (taken by the patient, covered by the government, total cost in the government hospital, and total cost in the private hospital) across diseases in government and private hospitals separately. Pearson correlation and scatter plot were also done to study the cost in private and public hospitals. p-values less than 0.05 were considered statistically significant. The margin of error in the study was 5%. Results: The mean age was 38.2 ± 20.5 years. Some 51% data were received from female samples. The mean income of samples was 13863.6 ± 9715.9 Pakistani Rupees (PKR) or 78.38 ± 58.29 United States Dollars (USD). The mean cost covered by government hospitals was 8866.0 ± 5071.0 PKR (53.19 ± 30.42 USD) per patient, whereas in government hospitals patients were charged on average 2662.9 ± 3774.7 PKR (16 ± 22.65 USD), while in private hospitals patients paid on average 29041.3 ± 12992.6 PKR (174.21 ± 78 USD). Conclusion: The costs of investigations in private hospitals were approximately three times the costs in government hospitals. The maximum cost was generated by patients being investigated for demyelinating disorders. Investigations conducted in government-run hospitals are more cost effective and these institutions should receive increased funding to cater to the maximum number of patients.
Effects of cost surface uncertainty on current density estimates from circuit theory

Background Conservation practitioners are often interested in developing land use plans that increase landscape connectivity, which is defined as the degree to which the landscape facilitates or impedes movement among resource patches. Landscape connectivity is often estimated with a cost surface that indicates the varying costs experienced by an organism in moving across a landscape. True, or absolute costs are rarely known however, and therefore assigning costs to different landscape elements is often a challenge in creating cost surface maps. As such, we consider it important to understand the sensitivity of connectivity estimates to uncertainty in cost estimates. Methods We used simulated landscapes to test the sensitivity of current density estimates from circuit theory to varying relative cost values, fragmentation, and number of cost classes (i.e., thematic resolution). Current density is proportional to the probability of use during a random walk. Using Circuitscape software, we simulated electrical current between pairs of nodes to create current density maps. We then measured the correlation of the current density values across scenarios. Results In general, we found that cost values were highly correlated across scenarios with different cost weights (mean correlation ranged from 0.87 to 0.92). Changing the spatial configuration of landscape elements by varying the degree of fragmentation reduced correlation in current density across maps. We also found that correlations were more variable when the range of cost values in a map was high. Discussion The low sensitivity of current density estimates to relative cost weights suggests that the measure may be reliable for land use applications even when there is uncertainty about absolute cost values, provided that the user has the costs correctly ranked. This finding should facilitate the use of cost surfaces by conservation practitioners interested in estimating connectivity and planning linkages and corridors.
‘They Forget I’m Deaf’: Exploring the Experience and Perception of Deaf Pregnant Women Attending Antenatal Clinics/Care

Background: Antenatal care (ANC) services provide access to integrated health management for several pregnancy related conditions. Unfortunately, deaf pregnant women remain vulnerable during pregnancy due to lack of access as well as communication barriers at antenatal clinics in Nigeria. Objective: The primary aim of this study was to explore the experiences and satisfaction of pregnant deaf women with antenatal care in Nigeria. Methods: This was a qualitative study, conducted among nine deaf pregnant women from two local government areas, attending both private and public health facilities for antenatal care in Ibadan, Oyo State, Nigeria. Data were collected using semi-structured, video recorded one-on-one interviews, with sign language as the medium of communication. The interviews were conducted until saturation of the themes was reached. The recorded interviews were precisely transcribed and thematic analyses were conducted on the data obtained. Findings: The mean age of the participants was 29.5 years. Participants indicated that they had registered/booked for antenatal care in their second trimester. Registration at this stage was regarded as late registration of the pregnancies. Communication difficulties during their ANC (antenatal care) visits, distance and location of the clinics, knowledge and perception of what ANC entailed, finance/cost, and health care professionals’ attitudes towards the participants were the major themes identified for late ANC bookings. Participants who attended privately owned health care facilities for ANC had more satisfaction with ANC care than those attending publicly owned health facilities. Conclusions: Deaf pregnant women were knowledgeable about ANC but registered late for the service, largely due to communication difficulties, distance to the clinic, cost, and the perceived attitudes of the health care workers. There existed a variance in the level of satisfaction of deaf pregnant women who attended private or public health facilities.
Local worlds: Vulnerability and food insecurity in the Eastern Cape province of South Africa

The overwhelming finding is that after more than a decade of democracy, the Eastern Cape (EC) province remains trapped in structural poverty. This shows in all aspects of its demographic, health and socio-economic profiles. Methods, measurements and statistics vary, but from the various studies and data sets one can attest that the majority of the population still lives in poverty. Despite the democratic transformation that began in South Africa in 1994, poverty, unemployment and inequality exist today along with the food insecurity that is symptomatic of them. Food insecurity in South Africa varies across its nine provinces, with the EC province frequently measured as the poorest province in the country. This article examines the extent to which the EC can be defined as vulnerable to food insecurity by using a review of current literature. These vulnerabilities are compounded by the environmental vulnerability factors of climate change and drought, which affect households’ ability to grow food. The elderly and children are affected by life cycle vulnerability factors, with children prone to malnutrition and the elderly unable to work to produce food. Race and gender are associated with vulnerability to food insecurity. Most of the people in the EC who are poor and are African, and a high percentage of women-headed households is poor. The vulnerability factors identified suggest that job creation and agricultural productivity may be useful ways of targeting food insecurity. Interventions need to take local contexts into account and focus on particular communities and their unique needs.
Pseudohypertriglyceridemia: A Novel Case with Important Clinical Implications

Pseudohypertriglyceridemia is an overestimation of serum triglyceride levels that may incorrectly lead to a diagnosis of hypertriglyceridemia. Glycerol kinase deficiency is a condition in which glycerol cannot be phosphorylated to glycerol-3-phosphate, resulting in elevated levels of serum glycerol. Laboratory assays that measure triglycerides indirectly may be affected by elevated glyerol levels and incorrectly report serum tryglyceride levels. We present a case of a novel missense mutation in the GK gene leading to isolated glycerol kinase deficiency and pseudohypertriglyceridemia in a male infant of a mother with gestational diabetes. This paper reviews glycerol kinase deficiency, describes the challenges in diagnosing pseudohypertriglyceridemia, and provides suggestions on improving diagnostic accuracy. Additionally, a potential maternal-fetal interaction between gestational diabetes and glycerol kinase deficiency is discussed.
Étude sur les protéines extracellulaires produites par Streptomyces scabiei souche EF-35 en présence de subérine

Streptomyces scabiei causes common scab, an economically important disease of potato tubers. Some authors have previously suggested that S. scabiei penetration into host plant tissue is facilitated by secretion of esterase enzymes degrading suberin, a lipidic biopolymer of the potato periderm. In the present study, S. scabiei EF-35 showed high esterase activity in suberin-containing media. This strain also exhibited esterase activity in the presence of other biopolymers, such as lignin, cutin or xylan but at a much lower level. In an attempt to identify esterases involved in suberin degradation, translated ORFs of S. scabiei 87-22 were searched for the presence of protein sequences corresponding to extracellular esterases of S. scabiei FL1 and of the fungus Coprinopsis cinerea VTT D041011, that were shown to be produced in the presence of suberin. Two putative extracellular suberinase genes, est A and subl, were identified. The presence of these genes in several actinobacteria was investigated by Southern blot hybridization and both genes were found in most common scab-inducing strains. Moreover, RT-PCR performed with S. scabiei EF-35 showed that est A was expressed in the presence of various biopolymers, including suberin, whereas the subl gene appeared to be specifically expressed in the presence of suberin and cutin.
Perceptions of nurses on access to structural empowerment in a hospital in the Western Cape

Background Structural empowerment is an ever-evolving concept interpreted and applied in many different ways as it focuses on the structures in a healthcare organisation to allow competent nurses to manage empowering opportunities in a professional manner. At a public hospital in the Western Cape, nurses complained about a lack of access to structural empowerment in a hospital, including structures of power, such as clear information, to partake in important decisions. Objectives The purpose of this study was to describe how nurse managers could support nurses in accessing structural empowerment through power resources. Method A quantitative design was followed with a survey. The accessible population in this study was different categories of nurses of professional, enrolled and assistant nurses (N = 200), which were on duty at the time of data gathering. The sample was selected by means of probability sampling (n = 110). An existing instrument based on a five-point Likert scale was distributed that took 45 minutes to complete. Descriptive and inferential statistics were calculated, and the chi-square was used to indicate statistical significance differences among the nursing categories on the items (p < 0.05). Results The general results indicated that the majority of nurses had challenges to access structural empowerment through power sources (information, support and resources). Significant differences were found between nurse categories for having the necessary supplies for the job (p = 0.043) and rewards for unusual job performance (p = 0.023). Those aspects on which no significant differences were found are of utmost importance, as they indicate the urgency of addressing limitations in power sources for all categories of nurses. Conclusion Empowerment can be achieved by enabling access to structural empowerment through power sources (i.e. opportunities, information, resources and support) at different levels for all categories of nurses.
Extracorporeal Shock Waves Increase Markers of Cellular Proliferation in Bronchial Epithelium and in Primary Bronchial Fibroblasts of COPD Patients

Chronic obstructive pulmonary disease (COPD) is due to structural changes and narrowing of small airways and parenchymal destruction (loss of the alveolar attachment as a result of pulmonary emphysema), which all lead to airflow limitation. Extracorporeal shock waves (ESW) increase cell proliferation and differentiation of connective tissue fibroblasts. To date no studies are available on ESW treatment of human bronchial fibroblasts and epithelial cells from COPD and control subjects. We obtained primary bronchial fibroblasts from bronchial biopsies of 3 patients with mild/moderate COPD and 3 control smokers with normal lung function. 16HBE cells were also studied. Cells were treated with a piezoelectric shock wave generator at low energy (0.3 mJ/mm2, 500 pulses). After treatment, viability was evaluated and cells were recultured and followed up for 4, 24, 48, and 72 h. Cell growth (WST-1 test) was assessed, and proliferation markers were analyzed by qRT-PCR in cell lysates and by ELISA tests in cell supernatants and cell lysates. After ESW treatment, we observed a significant increase of cell proliferation in all cell types. C-Kit (CD117) mRNA was significantly increased in 16HBE cells at 4 h. Protein levels were significantly increased for c-Kit (CD117) at 4 h in 16HBE (p < 0.0001) and at 24 h in COPD-fibroblasts (p = 0.037); for PCNA at 4 h in 16HBE (p = 0.046); for Thy1 (CD90) at 24 and 72 h in CS-fibroblasts (p = 0.031 and p = 0.041); for TGFβ1 at 72 h in CS-fibroblasts (p = 0.038); for procollagen-1 at 4 h in COPD-fibroblasts (p = 0.020); and for NF-κB-p65 at 4 and 24 h in 16HBE (p = 0.015 and p = 0.0002). In the peripheral lung tissue of a representative COPD patient, alveolar type II epithelial cells (TTF‐1+) coexpressing c-Kit (CD117) and PCNA were occasionally observed. These data show an increase of cell proliferation induced by a low dosage of extracorporeal shock waves in 16HBE cells and primary bronchial fibroblasts of COPD and control smoking subjects.
Extraction, Characterization, and Antimicrobial Activity of Chitosan from Horse Mussel Modiolus modiolus

Chitin and chitosan have been proved to have enormous applications in biomedical, pharmaceutical, and industrial fields. The horse mussel, Modiolus modiolus, a refuse of the fishery industries at Thondi, is a reserve of rich chitin. The aim of this work is to extract chitosan from the horse mussel and its further characterization using Fourier transform infrared spectroscopy (FTIR), micro-Raman spectroscopy, X-ray diffraction (XRD), and elemental analysis. The result of FTIR studies revealed different functional groups of organic compounds such as out-of-plane bending (564 cm–1), C–O–C stretching (711 cm–1), and CH2 stretching (1174 cm–1) in chitosan. The degree of acetylation of the extracted chitosan was observed to be 57.43%, which makes it suitable as a biopolymer for biomedical applications. Prominent peaks observed with micro-Raman studies were at 484 cm–1 (14,264 counts/s), 2138 cm–1 (45,061 counts/s), and 2447 cm–1 (45,636 counts/s). XRD studies showed the crystalline nature of the polymer, and the maximum peak was observed at 20.04°. Elemental analysis showed a considerable decrease in the percentage of nitrogen and carbon upon the conversion of chitin to chitosan, while chitosan had a higher percentage of hydrogen and sulfur. The antibacterial activities of chitosan from the horse mussel were found to be efficient at a 200 μg/mL concentration against all the bacterial strains tested with a comparatively higher antibacterial activity against Escherichia coli (9 mm) and Bacillus subtilis (8 mm).
Sampling Performance of Multiple Independent Molecular Dynamics Simulations of an RNA Aptamer

Using multiple independent simulations instead of one long simulation has been shown to improve the sampling performance attained with the molecular dynamics (MD) simulation method. However, it is generally not known how long each independent simulation should be, how many independent simulations should be used, or to what extent either of these factors affects the overall sampling performance achieved for a given system. The goal of the present study was to assess the sampling performance of multiple independent MD simulations, where each independent simulation begins from a different initial molecular conformation. For this purpose, we used an RNA aptamer that is 25 nucleotides long as a case study. The initial conformations of the aptamer are derived from six de novo predicted 3D structures. Each of the six de novo predicted structures is energy minimized in solution and equilibrated with MD simulations at high temperature. Ten conformations from these six high-temperature equilibration runs are selected as initial conformations for further simulations at ambient temperature. In total, we conducted 60 independent MD simulations, each with a duration of 100 ns, to study the conformation and dynamics of the aptamer. For each group of 10 independent simulations that originated from a particular de novo predicted structure, we evaluated the potential energy distribution of the RNA and used recurrence quantification analysis to examine the sampling of RNA conformational transitions. To assess the impact of starting from different de novo predicted structures, we computed the density of structure projection on principal components to compare the regions sampled by the different groups of ten independent simulations. The recurrence rate and dependence of initial conformation among the groups were also compared. We stress the necessity of using different initial configurations as simulation starting points by showing long simulations from different initial structures suffer from being trapped in different states. Finally, we summarized the sampling efficiency for the complete set of 60 independent simulations and determined regions of under-sampling on the potential energy landscape. The results suggest that conducting multiple independent simulations using a diverse set of de novo predicted structures is a promising approach to achieve sufficient sampling. This approach avoids undesirable outcomes, such as the problem of the RNA aptamer being trapped in a local minimum. For others wishing to conduct multiple independent simulations, the analysis protocol presented in this study is a guide for examining overall sampling and determining if more simulations are necessary for sufficient sampling.