Miracle-dz/UniFAR-FTUs huggingface dataset:
Raft‐forming polysaccharides for the treatment of gastroesophageal reflux disease (GORD): Systematic review

Gastroesophageal reflux disease (GORD) is a common condition induced by unwarranted reflux of gastric and duodenal contents into the oesophagus, and insufficient clearance of refluxate from it. Pharmaceutical formulations possessing raft-forming capability offer an excellent alternative to conventional treatment options to treat uncomplicated GORD. These formulations typically contain a polymer, which performs distinctively upon contact with gastric acid and develops a foam-like structure that can float on gastric contents. This review aims to feature research articles and patents that cover this topic. After undergoing a standardised literature search following PRISMA (preferred reporting items for systematic reviews and meta-analyses) guidelines, we have included 38 research articles and 18 patents describing the role of raft-forming polymers in the treatment of GORD. This is a comprehensive review of formulation/testing of raft-forming polymers. As expected, the majority of the studies focused on alginate; however, fewer studies have reported the use of pectin, xanthan gum and raw psyllium fibres (husk). Moreover, it can be concluded from this comprehensive systematic review that a detailed characterisation of raft forming formulations, type and concentration of used active and inactive materials and different formulations factors are essential for the development of successful anti-reflux raft forming formulations.
Effects of Extracorporeal Shockwave Therapy and Hand Massage on Body Composition and Serum Lipids According to Serum Cholesterol Level in Korean Women

Obesity, particularly abdominal obesity, increases the risk of cardiovascular disease (CVD). This study investigates the effects of six-week (twice a week, 12 sessions total) extracorporeal shockwave therapy (SWT) and hand massage therapy (HT) on body composition and serum lipids in overweight and obese Korean women aged between 35 and 59, according to their serum cholesterol level (≥200 mg/dL versus <200 mg/dL). After the program, weights decreased significantly in both the HT Group and SWT Group (p < 0.05); weights of those with cholesterol < 200 mg/dL significantly decreased in the HT Group (p = 0.038), while weights of those with cholesterol ≥ 200 mg/dL significantly decreased in the SWT Group (p = 0.001). BMIs decreased significantly in both the HT Group and the SWT Group (p < 0.05); BMIs of those with cholesterol < 200 mg/dL significantly decreased in the HT Group (p = 0.018), while BMIs of those with cholesterol ≥ 200 mg/dL significantly decreased in the SWT Group (p = 0.001). The body fat percentage of subjects significantly decreased only in the SWT Group (p = 0.027); the waist-hip ratio significantly decreased only in HT Group (p = 0.034). Serum cholesterol levels significantly decreased in those with cholesterol < 200 mg/dL in the HT Group (p < 0.05) and those with cholesterol ≥ 200 mg/dL in SWT Group (p = 0.055). Triglyceride significantly decreased in both those with cholesterol < 200 mg/dL and those with cholesterol ≥ 200 mg/dL, but did not significantly decrease in either subgroup of the HT Group. The study results suggest that SWT is effective in improving body measurements and serum lipids in those with cholesterol ≥ 200 mg/dL, while HT therapy is effective in those with cholesterol < 200 mg/dL. In conclusion, SWT and HT improved abdominal obesity by reducing body weight and waist circumference and helped improving serum lip index, suggesting the benefit for managing body measurements and serum lipids of overweight and obese individuals.
Physical Disability and Its Effective Factors in the Elderly of Khalkhal City

Background: Aging is considered as one of the crucial stages of human development; it is not only the end of life but also is a normal and natural process. The disability is among the consequences of the elderly, which affects the whole process of aging. The present study aimed to determine the rate of physical disability and its effective factors in the elderly in Khalkhal city in 2017. Materials and Methods: This descriptive cross-sectional study was performed on 400 elderly people who referred to Khalkhal health centers, using convenience random sampling. The data collection tool was a short version of the disability scale of the Stanford Health Assessment Questionnaire (HAQ 8-item DI). Result: Our study showed that the total disability score in the elderly was 2.56 ± 5.24 (2.69 ± 5.40 in men and 2.41 ± 5.06 in women). Also, there was a significant relationship between disability score and age, illness history, the frequency of hospitalization, the perception of health, number of children, current occupation, and lifestyle (P-value<0.05). Conclusion: The overall findings of this study indicated the high rate of disability among the elderly in Khalkhal city. Further, men are more likely than women to experience a disability. Therefore, the use of preventive and contributing measures for national aging health programs can improve the quality of life of the elderly.
Review of Chagas Disease and Treatment Obstacles to Eradication

The World Health Organization and the Center for Disease Control reports Chagas disease, or American trypanosomiasis, as a major neglected tropical disease prevalent in 21 endemic Latin American countries. The agent of the disease is a single-celled protozoan parasite, Trypanosoma cruzi, and common modes of transmission include infected feces of a triatomine bug, crossing the placental barrier, and blood products. The two phases of infection are acute and chronic, and the three most affected body systems are cardiovascular, digestive, and nervous. Although research has led to several advances in the knowledge of CD, there are gaps in treatment and epidemiological research, leaving millions of people susceptible to infection.
Reading Scientific Texts: Some Challenges Faced by EFL Readers

This paper looks at the difficulties encountered by five EFL readers as they read and negotiated two scientific texts. Respondents were five first year undergraduates enrolled in a biology degree programme at a public university in Malaysia. Think aloud procedures and retrospective interviews were conducted to identify the obstacles and difficulties faced by the respondents while reading the texts and how they overcame the reading problems. The findings of this study revealed that general English words in the scientific texts posed more problems compared to scientific terminology. Known scientific terminology in a complex sentence was much easier to comprehend compared to complex English sentences with only general English words. This is because, the scientific terminology previously learned in the EFL readers' L1 provided them with a 'window' to other rich information not mentioned in the particular sentence or text.
Evaluation of network architecture and data augmentation methods for deep learning in chemogenomics

Among virtual screening methods that have been developed to facilitate the drug discovery process, chemogenomics presents the particularity to tackle the question of predicting ligands for proteins, at at scales both in the protein and chemical spaces. Therefore, in addition to to predict drug candidates for a given therapeutic protein target, like more classical ligand-based or receptor-based methods do, chemogenomics can also predict off-targets at the proteome level, and therefore, identify potential side-effects or drug repositioning opportunities. In this study, we study and compare machine-learning and deep learning approaches for chemogenomics, that are applicable to screen large sets of compounds against large sets of druggable proteins. State-of-the-art drug chemogenomics methods rely on expert-based chemical and protein descriptors or similarity measures. The recent development of deep learning approaches enabled to design algorithms that learn numerical abstract representations of molecular graphs and protein sequences in an end-to-end fashion, i.e., so that the learnt features optimise the objective function of the drug-target interaction prediction task. In this paper, we address drug-target interaction prediction at the druggable proteome-level, with what we define as the chemogenomic neuron network. This network consists of a feed-forward neuron network taking as input the combination of molecular and protein representations learnt by molecular graph and protein sequence encoders. We first propose a standard formulation of this chemogenomic neuron network. Then, we compare the performances of the standard chemogenomic network to reference deep learning or shallow (machine-learning without deep learning) methods. In particular, we show that such a representation learning approach is competitive with state-of-the-art chemogenomics with shallow methods, but not ultimately superior. We evaluate the most promising neuron network architectures and data augmentation techniques, such as multi-view and transfer learning, to improve the prediction performance of the chemogenomic network. Our results shed new insights on the design of chemogenomics approaches based on representation learning algorithms. Most importantly, we conclude from our observations that a promising research direction is to integrate heterogeneous sources of data such as various bioactivity datasets, or independently, multiple molecule and protein attribute views, instead of focusing on sophisticated, yet intuitively relevant, encoder’s neuron network architecture.
Aquatic weeds diversity of Fatki River in Magura district, Bangladesh

The study was conducted at Fatki River under Magura district to learn the aquatic weeds diversity and abundance. This paper focused on species variation, number of species, water quality parameter and identification of aquatic weeds. It was assessed by collecting samples from Chukinogor Ghat, Kechuadubi and Arpara bazar during May to August, 2016. Aquatic weeds were abundant in rainy season and the semi-aquatic weeds were available almost all the year round. According to this study, total 22 species belonging to 12 orders, 16 families and 21 genuses were found. Again, 46%, 28%, 26% of total aquatic weeds percentages identified from the Chukinogor Ghat, Kechuadubi and Arpara bazar respectively. During this study period, nine species of family Pontederiaceae, Convolvulaceae, Menyanthaceae, Asteraceae, Poaceae, Araceae, Amaranthaceae, Polygonaceae were common in Chukinogor Ghat, Kechuadubi and Arpara bazar. Noticeable species– Lemna minor, Marsilea quadrifolia, Ludwigia palustris, Aeschynomene aspera, Najas graminea, Hydrilla verticillata, Najas guadalupensis, Utricularia inflate were only found in Chukinogor Ghat. This species are easily adapted in large areas. On the other hands, two species were common in Chukinogor Ghat, Kechuadubi – Pistia stratiotes and Equisetum hyemale. Prominent species of Arpara bazar were Cyperus rotundus and Xanthium indicum. Total 11 species of aquatic weeds were mainly recognized from these Kechuadubi, while greatest number was recorded of 20 species from Chukinogor Ghat and 12 species were have its place to Arpara bazar. Management technique and water quality parameters were also studied during study period and the temperature was recorded 29.0-30.00 ºC in Chukinogor Ghat, same as 28.0-320 ºC in Kechuadubi. Furthermore, 29.0-31.00 ºC temperature was found in Arpara bazar. DO levels were stable at ranged from7.0-7.5 ppm in Chukinogor Ghat and 4.7-5.3 ppm was recorded in two experimental Kechuadubi 4.5-5.0 in Arpara bazar respectively. This difference may arise due to the using of aerator in the Chukinogor Ghat same as decomposition, intensity of light in Kechuadubi and Arpara bazar. Transparency was 28-32cm in Chukinogor Ghat, 36-44cm in Kechuadubi, and 38-42 cm in Arpara bazar. Asian Australas. J. Biosci. Biotechnol. 2018, 3 (3), 201-207
Earliest tinamous (Aves: Palaeognathae) from the Miocene of Argentina and their phylogenetic position

Several isolated bones of tinamous from Miocene deposits of Santa Cruz Province (southern Patagonia, Argentina) are the oldest known remains of this paleognath lineage. The specimens include an incomplete coracoid, proximal end of four coracoids, distal ends of two tibiotarsi, and distal ends of two humeri. They represent at least two species but cannot be assigned to any known taxon. A detailed description and phylogenetic interpretation of this material is provided here. Morphological data of the fossils are included in a matrix of 63 osteological characters and 34 terminal taxa incorporating 24 living species of Tinamidae in addition to the fossils under study. The cladistic analysis produced 81 optimal trees, in which the fossils are more closely related to the open-area tinamous (Nothurinae). Placement of the Santa Cruz fossil tinamous between the open-area (Nothurinae) and the forest-dwelling (‘‘Tinaminae’’) tinamous is consistent with the paleoenvironmental conditions inferred from the associated fossil fauna. RESUMEN. Varios fragmentos de huesos de tinámidos de depósitos del Mioceno de la Provincia de Santa Cruz (sur de Patagonia, Argentina), son los restos más antiguos que se conocen de este linaje de paleognatas. Los especı́menes incluyen un coracoides incompleto, extremos proximales de cuatro coracoides, extremos distales de dos tibiotarsos y extremos distales de dos húmeros, cuya descripción e interpretación filogenética son provistas aquı́. Estos especı́menes representan al menos dos especies, las que no pueden ser asignadas a ningún taxón conocido. Los datos morfológicos de los fósiles aquı́ descriptos son incluı́dos en una matriz de 63 caracteres osteológicos y 34 taxones terminales que incluyen 24 especies de tinámidos vivientes además de los fósiles. El análisis cladı́stico produjo 81 árboles óptimos en los cuales los fósiles están más relacionados con los tinámidos de áreas abiertas (Nothurinae). La ubicación de los fósiles de Santa Cruz entre los tinámidos de áreas abiertas (Nothurinae) y los de selva (‘‘Tinaminae’’) es consistente con las condiciones paleoambientales inferidas a partir de la fauna fósil asociada.
Photovoltaic stimulation efficiently evokes network-mediated activity of retinal ganglion cells

Objective Photovoltaic retinal prostheses theoretically offer the possibility of standalone high-resolution electrical stimulation of the retina. However, in artificial vision, achieving locally selective epiretinal stimulation is particularly challenging, on the grounds of axonal activation and electrical cell coupling. Approach Here we show that electrical and photovoltaic stimulation of dystrophic retinal circuits with capacitive-like pulses leads to a greater efficiency for indirect network-mediated activation of retinal ganglion cells. In addition, a biophysical model of the inner retina stimulation is proposed to investigate the waveform and duration commitments in the genesis of indirect activity of retinal ganglion cells. Main results Both in-vitro and in-silico approaches suggest that the application of long voltage pulses or gradual voltage changes are more effective to sustainably activate the inner excitatory and inhibitory layers of the retina, thus leading to a reproducible indirect response. The involvement of the inhibitory feedback from amacrine cells in the forming of indirect patterns represents a novel biological tool to locally cluster the response of the retinal ganglion cells. Significance These results demonstrate that recruiting inner retina cells with epiretinal stimulation enables not only to bypass axonal stimulation but also to obtain a more focal activation thanks to the natural lateral inhibition. In this perspective, the use of capacitive-like waveforms generated by photovoltaic prostheses may allow improving the neural response resolution while standing high-frequency stimulation.
Predicting Synthetic Lethal Interactions using Heterogeneous Data Sources

Motivation A synthetic lethal (SL) interaction is a relationship between two functional entities where the loss of either one of the entities is viable but the loss of both entities is lethal to the cell. Such pairs can be used as drug targets in targeted anticancer therapies, and so, many methods have been developed to identify potential candidate SL pairs. However, these methods use only a subset of available data from multiple platforms, at genomic, epigenomic and transcriptomic levels; and hence are limited in their ability to learn from complex associations in heterogeneous data sources. Results In this paper we develop techniques that can seamlessly integrate multiple heterogeneous data sources to predict SL interactions. Our approach obtains latent representations by collective matrix factorization based techniques, which in turn are used for prediction through matrix completion. Our experiments, on a variety of biological datasets, illustrate the efficacy and versatility of our approach, that outperforms state-of-the-art methods for predicting SL interactions and can be used with heterogeneous data sources with minimal feature engineering. Availability Software available at https://github.com/lianyh Contact vaibhav.rajan@nus.edu. sg
A rule-based data-informed cellular consensus map of the human mononuclear phagocyte cell space

Single-cell genomic techniques are opening new avenues to understand the basic units of life. Large international efforts, such as those to derive a Human Cell Atlas, are driving progress in this area; here, cellular map generation is key. To expedite the inevitable iterations of these underlying maps, we have developed a rule-based data-informed approach to build next generation cellular consensus maps. Using the human dendritic-cell and monocyte compartment in peripheral blood as an example, we performed computational integration of previous, partially overlapping maps using an approach we termed ‘backmapping’, combined with multi-color flow-cytometry and index sorting-based single-cell RNA-sequencing. Our general strategy can be applied to any atlas generation for humans and other species. Graphical Abstract Highlights Defining a consensus of the human myeloid cell compartment in peripheral blood 3 monocytes subsets, pDC, cDC1, DC2, DC3 and precursor DC make up the compartment Distinguish myeloid cell compartment from other cell spaces, e.g. the NK cell space Providing a generalizable method for building consensus maps for the life sciences
Perception of Pain by a Sample of Patients Undergoing Orthodontic Treatment in Sulaimani City

Aims: Orthodontic treatment is known as a painful procedure among patients. They feel varying degrees of pain during orthodontic treatment from the stage of initial examination till the end of the treatment. The aims of this study are to explore pain experience among patients undergoing orthodontic treatment with the fixed appliances by comparing two different arch wires sizes. Materials and Methods: The study group consisted of 60 patients (26 males, 34 females) with a mean age of 17.6 years and 20.5 years consequently. Insertion of either 0.014 or 0.016-inch wire was by random selection of patients. Patients were asked to fill out a series of questionnaires for five consecutive days after the insertion of orthodontic initial arch wire, and after the arch wire activation for 4 hours, 6 hours, 24 hours, and till 5 days. The intensity (weak, mild, moderate, severe, and intensive) of the pain symptoms in connection with ten items (Biting on a hard/soft food, sensitive to hot or cold food/drink, mastication of food, fitting anterior and fitting posterior teeth together, cheeks, lips, and tongue pain) have been evaluated. Results: No significant differences were found between age groups, and between the two arch wire groups. Pain perception was more significant in females than in males and the pain perceived at the anterior teeth was greater than posterior teeth. Pain percentage level increased gradually till reaching the peak within 24 hours after the insertion of arch wire and retained the same level in the 2nd day, then decreased till the 5th day. Perceptions of pain by fitting anterior teeth were exactly the same within the period of the first few hours in both arch wire groups, and decreased over the following hours. Conclusion: No age discrimination was found for perception of pain in the two different arch wire groups, with no significant correlation for the time with initial pain that perceived after the insertion of two different initial arch wire sizes then the intensity of pain reduced over the time. Pain was perceived as being greater at the anterior than the posterior teeth and females experienced more pain than males.
The association of acetylacetate (Acr AB-Tol C) and QepA genes with multiple antibiotic resistance among Escherichia coli clinical isolates

ISSN The role of efflux pumps in antibiotic resistance development among Escherichia coli may have been underappreciated. The objective of this study was assessment the association of AcrAB-TolCeffluxpumps and qepAgenes with resistance tocommonantibiotics among E. coli isolates. A total of 200 E. coli isolates were obtained from diverse samples of inpatients. Minimum inhibitory concentrations and Kirby–Bauer disk diffusion tests were determined for ceftazidime, cefotaxime, imipenem, gentamicin, and tetracycline. The Acr-AB-TolC and qepA genes were amplified using PCR technique and their association with antibiotics was also evaluated using Chi-square test. A majority of isolates (64%) were retrieved from gastrointestinal samples, followedby urinary tract infections (33%), and bloodstream (3%). All the isolates were resistant to ampicillin (100%), followed by cefazolin (59%), and cefoxitin (58%). However, 100% of the isolates showed susceptibility to fosfomycin. The prevalence of acrA, acrB, and qepA genes was 94% (n1⁄4188), 86% (n1⁄4172), and 8% (n1⁄416), respectively. The acrA and acrB were significantly associated with resistance to cefoxitin and cefazolin (P<0.01), ceftazidime (P<0.01), carbapenems (P1⁄40.022), and tetracycline (P1⁄40.0112). In addition, qepA gene was significantly associated with tetracycline resistance (P1⁄40.032). None of the patients had death outcome. A majority of E. coli isolates harbored the AcrAB genes, but qepA was observed among lower number of the isolates. It is notable that three strains lacked the extended spectrum beta-lactamase and carbapenemases and none of multidrug resistant strains carried tet and aminoglycoside modifying enzymes genes. Over-expression of efflux pumps has been increasingly is associated with clinically relevant antibiotic resistance. For this reason, the expression and functionality of efflux pumps should be more investigated profoundly and be compared between drug-resistant and drug-susceptible isolates. Copyright 2020 Wolters Kluwer Health, Inc. All rights reserved.
Sequence-based prediction of olfactory receptor responses

Computational prediction of how strongly an olfactory receptor responds to various odors can help in bridging the widening gap between the large number of receptors that have been sequenced and the small number of experiments measuring their responses. Previous efforts in this area have predicted the responses of a receptor to some odors, using the known responses of the same receptor to other odors. Here we present a method to predict the responses of a receptor without any known responses, by using available data about the responses of other conspecific receptors and their sequences. We applied this method to olfactory receptors in insects Drosophila melanogaster (both adult and larva) and Anopheles gambiae, and to mouse and human olfactory receptors. We found the predictions to be in significant agreement with the experimental measurements. The method also provides clues about the response-determining positions within the receptor sequences.