Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of stocking density on performance of snubnose pompano juvenile (Trachinotus blochii) reared in recirculating system

Received 22 Feb 2021 Revised 21 May 2021 Accepted 04 Jun 2021 This study aimed to determine appropriate densities for rearing pompano juvenile (Trachinotus blochii) in a recirculating system. Four treatments of stocking density were evaluated including 500, 1.000, 1.500, and 2.000 inds/m in triplicate. The experimental system for pompano rearing was designed with 120-L tanks connected to 1 settling tank, 1 filter tank, 1 stone filter tank (contained 250 L of filter volume for each tank). The system was fulfilled with marine water at 30 ‰ of salinity and aerated continuously. Pompano were initially stocked at 0.07 ± 0.03 g/fish of body weight and daily fed using commercial pellet contained 55% of crude protein. After 30 days of rearing, the fish stocked at 1.000 individuals/m showed the best results in growth rate (0.060 g/day of DWG and 10.97 %/day of SGR) and was significantly higher than the treatment stocked at 1,500 and 2,000 inds/m (p < 0.05), however, no significant difference was observed between 1,000 and 500 treatments (p > 0.05). Keywords
ARBUSCULAR MYCORRHIZAL FUNGAL COMMUNITIES IN PASTURE AND TROPICAL RIPARIAN FOREST ECOSYSTEMS IN GUAJARÁ-MIRIM, RONDÔNIA, BRAZIL

Understanding the dynamics of soil organisms in natural environments can be very useful for determining the quality of forest and agricultural ecosystems. The hypothesis of this work is that the FMA community varies depending on the land use system and seasonality. This study aimed to assess arbuscular mycorrhizal fungal (AMF) communities in pasture and regenerating riparian forest (Forest) sites in Guajará-Mirim, Rondônia, Brazil. Ten soil samples were randomly collected from each ecosystem in three seasons (2018 dry and rainy seasons and 2019 dry season). AMF species richness (SR), frequency, spore density, Shannon–Wiener (H’) diversity index, Simpson’s dominance index, and ideal sample size were determined. Species richness varied among sites and seasons, with a tendency toward higher richness in pasture soil in the 2018 dry season. The dominant AMF species in both ecosystems were Glomus macrocarpum and Acaulospora mellea. The pasture site in the 2018 dry season had higher AMF diversity (H’) than the riparian forest in the 2018 rainy season and the 2019 dry season. The complete linkage distance between the pasture site in the 2019 dry season and all other sites/seasons was 100%. More than 10 soil samples are needed to accurately determine the richness of AMF species in pasture and riparian forest sites in Guajará-Mirim, Brazil.
Changes in brain morphometry after motor rehabilitation in chronic stroke

Abstract Purpose Recent studies have revealed structural changes after motor rehabilitation, but its morphological changes related to upper limb motor behaviours have not been studied exhaustively. Therefore, we aimed to map the grey matter (GM) changes associated with motor rehabilitation after stroke using voxel-based morphometry (VBM), deformation-based morphometry (DBM), and surface-based morphometry (SBM). Methods Forty-one patients with chronic stroke received twelve sessions of low-frequency repetitive transcranial magnetic stimulation plus intensive occupational therapy. MRI data were obtained before and after the intervention. Fugl-Meyer Assessment and Wolf Motor Function Test-Functional Ability Scale were assessed at the two-time points. We performed VBM, DBM, and SBM analyses using T1-weighted images. A correlation analysis was performed between cortical thickness in motor areas and clinical outcomes. Results Clinical outcomes significantly improved after the intervention. VBM showed significant GM volume changes in ipsilesional and contralesional primary motor regions. DBM results demonstrated GM changes contralesionally and ipsilesionally after the intervention. SBM results showed significant cortical thickness changes in posterior visuomotor coordination, precentral, postcentral gyri of the ipsilesional hemisphere and contralesional visuomotor area after the intervention. A combination of threshold p < . 05, False Discovery Rate and p < . 001 (uncorrected) were considered significant. In addition, cortical thickness changes of the ipsilesional motor areas were significantly correlated with the clinical outcome changes. Conclusions We found GM structural changes in areas involved in motor, visuomotor and somatosensory functions after the intervention. Furthermore, our findings suggest that structural plasticity changes in chronic stroke could occur in the ipsilesional and contralesional hemispheres after motor rehabilitation.
Assessment of Disease Activity and Complications in Patients of Pulmonary Tuberculosis by High Resolution Computed Tomography

Background: Tuberculosis (TB) is a global health problem and the second most common infectious cause of death. High-resolution computed tomography (HRCT) is far more superior to chest radiography as well as conventional CT for analyzing the pulmonary parenchyma. This study aimed to evaluate the role of HRCT in pulmonary tuberculosis (PTB) with respect to disease activity and complication after anti-tubercular therapy (ATT). Methods: This prospective observational study was conducted in the Department of Radiodiagnosis, Teerthanker Mahaveer Medical College & Research Centre (TMMC&RC) for a period of 1.5 years. A total of 50 cases of newly diagnosed TB were included in the study and a standard six-month ATT was given to the patients. Pulmonary involvement was evaluated by HRCT (128 slice multi-detector PHILIPS INGENUITY CT scanner), twice for each patient (first scan after diagnosis and second after treatment completion). The acquired HRCT images were reconstructed on a highresolution lung algorithm and parenchymal, bronchial, and extra parenchymal findings were recorded systematically. Results: Out of the 50 patients, 5 died within two months of the initiation of treatment and four were lost to follow-up. Thus, post treatment follow-up sample sizewas reduced to 41 patients. Ill-defined nodules (96%), tree-in-bud pattern (74%), consolidation (86%), cavitary lesions (98%), and ground glass opacities (58%) were the main imaging features of active cases of TB on HRCT. Resolution to thin-walled cavitary lesions (36.5%), bronchiectasis (41.5%), and fibrotic (parenchymal) bands (66%) were common complications or sequelae which were observed after completion of treatment. How to cite this article: Ashwani Jain, Ankur Malhotra, Deepti Arora, Mazher Maqusood, and Sunil Kumar (2021) “Assessment of Disease Activity and Complications in Patients of Pulmonary Tuberculosis by High Resolution Computed Tomography,” Sudan Journal of Medical Sciences, vol. 16, Issue no. 2, pages 159–177. DOI 10.18502/sjms.v16i2. 9286 Page 159 Corresponding Author: Dr. Ankur Malhotra, Associate Professor; Department of Radiodiagnosis, Teerthanker Mahaveer Medical College & Research Centre (TMMC&RC), Moradabad, Uttar Pradesh244001, India. Contact no.: +918394097126 email: drankur.m7@gmail.com Received 12 March 2021 Accepted 18 June 2021 Published 30 June 2021 Production and Hosting by
Quantification of the pace of biological aging in humans through a blood test: the DunedinPACE DNA methylation algorithm

Measures to quantify changes in the pace of biological aging in response to intervention are needed to evaluate geroprotective interventions for humans. Here, we report an advance on our original method (Belsky et al. 2020). We used data from the Dunedin Study 1972-3 birth cohort tracking within-individual decline in 19 organ-system integrity indicators across four timepoints spanning two decades to model Pace of Aging. We distilled two-decade Pace of Aging into a single-time-point DNA-methylation blood-test using elastic-net regression and DNA-methylation data restricted to exclude probes with low test-retest reliability. The resulting measure, DunedinPACE, showed high test-retest reliability, was associated with functional decline, morbidity, and mortality, and indicated accelerated Pace of Aging in young adults with childhood adversity across five datasets. DunedinPACE effect-sizes were similar to GrimAge-clock effect-sizes and larger than those for other benchmark DNA-methylation-clocks. DunedinPACE is a novel blood biomarker of the pace of aging for gerontology and geroscience
A New World Monkey Resembles Human in Bitter Taste Receptor Evolution and Function via a Single Parallel Amino Acid Substitution

Abstract Bitter taste receptors serve as a vital component in the defense system against toxin intake by animals, and the family of genes encoding these receptors has been demonstrated, usually by family size variance, to correlate with dietary preference. However, few systematic studies of specific Tas2R to unveil their functional evolution have been conducted. Here, we surveyed Tas2R16 across all major clades of primates and reported a rare case of a convergent change to increase sensitivity to β-glucopyranosides in human and a New World monkey, the white-faced saki. Combining analyses at multiple levels, we demonstrate that a parallel amino acid substitution (K172N) shared by these two species is responsible for this functional convergence of Tas2R16. Considering the specialized feeding preference of the white-faced saki, the K172N change likely played an important adaptive role in its early evolution to avoid potentially toxic cyanogenic glycosides, as suggested for the human TAS2R16 gene.
Overfeeding Saturated Fat Increases LDL (Low-Density Lipoprotein) Aggregation Susceptibility While Overfeeding Unsaturated Fat Decreases Proteoglycan-Binding of Lipoproteins

Supplemental Digital Content is available in the text. Objective: We recently showed that measurement of the susceptibility of LDL (low-density lipoprotein) to aggregation is an independent predictor of cardiovascular events. We now wished to compare effects of overfeeding different dietary macronutrients on LDL aggregation, proteoglycan-binding of plasma lipoproteins, and on the concentration of oxidized LDL in plasma, 3 in vitro parameters consistent with increased atherogenicity. Approach and Results: The participants (36 subjects; age, 48±10 years; body mass index, 30.9±6.2 kg/m2) were randomized to consume an extra 1000 kcal/day of either unsaturated fat, saturated fat, or simple sugars (CARB) for 3 weeks. We measured plasma proatherogenic properties (susceptibility of LDL to aggregation, proteoglycan-binding, oxidized LDL) and concentrations and composition of plasma lipoproteins using nuclear magnetic resonance spectroscopy, and in LDL using liquid chromatography mass spectrometry, before and after the overfeeding diets. LDL aggregation increased in the saturated fat but not the other groups. This change was associated with increased sphingolipid and saturated triacylglycerols in LDL and in plasma and reduction of clusterin on LDL particles. Proteoglycan binding of plasma lipoproteins decreased in the unsaturated fat group relative to the baseline diet. Lipoprotein properties remained unchanged in the CARB group. Conclusions: The type of fat during 3 weeks of overfeeding is an important determinant of the characteristics and functional properties of plasma lipoproteins in humans. Registration: URL: http://www.clinicaltrials. gov; Unique identifier NCT02133144.
Choledochoduodenostomy Versus Hepaticogastrostomy in Endoscopic Ultrasound-guided Drainage for Malignant Biliary Obstruction: A Meta-analysis and Systematic Review

Objectives: This study aimed to estimate the safety and efficacy of endoscopic ultrasound-guided choledochoduodenostomy (EUS-CDS) and endoscopic ultrasound-guided hepaticogastrostomy (EUS-HGS) for malignant biliary obstruction. Methods: We conducted a literature search using PubMed, Embase, Web of Science, the Cochrane Central Register of Controlled Trials, and ClinicalTrials.gov. Studies that compared EUS-CDS and EUS-HGS were included in this study. Results: Thirteen studies were eligible for inclusion. The technical [odds ratio (OR): 0.95; 95% confidence interval (CI): 0.51-1.74) and clinical (OR: 1.13; 95%CI: 0.66-1.94) success rates of EUS-CDS were comparable to those of EUS-HGS. However, EUS-CDS had less reintervention (OR: 0.31; 95%CI: 0.16-0.63) and stent obstruction (OR: 0.48; 95%CI: 0.21-0.94) than EUS-HGS. Both groups had similar adverse events (OR: 1.00; 95%CI: 0.70-1.43) and overall survival (hazard ratio: 1.07; 95%CI: 0.58-1.97). Conclusions: EUS-CDS and EUS-HGS have comparable technical and clinical success rates, adverse events, and overall survival. However, EUS-CDS has less reintervention and stent obstruction.
Effects of the short‐ and long‐term accumulation of detritus in larval habitats on life history traits of Aedes aegypti in temperate Argentina

Aedes aegypti larvae that develop in containers largely depend on plant detritus as a source of nutritional resources. However, few studies have evaluated the performance of immature individuals under natural amounts and quality of this food source. Here, we aimed to assess the effect of the variation in the accumulation time and amount of detritus on life history traits of Ae. aegypti under semi‐field conditions. Ae. aegypti larvae were raised with detritus collected in different sites to represent natural variability in its amount, simulating short (28 days) and long (70 days) accumulation. A control with optimal food conditions (yeast) was included. Survival, development time and wing length of adults were compared among treatments. Survival was relatively high in all treatments. Development time was similar among treatments but significantly longer and more variable in containers with the lowest detritus amounts. Wing lengths were smaller in the treatments with detritus than in the control, especially in females. The results support the hypothesis that, in a temperate region, Ae. aegypti larvae may have a nutritional limitation, at least in some containers, and emphasize the importance of performing experiments that simulate the environmental conditions to which individuals are exposed in nature.
Clinical significance of new‐onset atrial fibrillation in patients with hypertrophic cardiomyopathy

There is limited information about the clinical significance of atrial fibrillation (AF), particularly new‐onset AF, in patients with hypertrophic cardiomyopathy (HCM) in a community‐based patient cohort. This study was carried out to clarify the prevalence and prognostic impact of AF in Japanese HCM patients.
In-silico strategies to combat COVID-19: A comprehensive review

ABSTRACT The novel coronavirus SARS-CoV-2 since its emergence at Wuhan, China in December 2019 has been creating global health turmoil despite extensive containment measures and has resulted in the present pandemic COVID-19. Although the virus and its interaction with the host have been thoroughly characterized, effective treatment regimens beyond symptom-based care and repurposed therapeutics could not be identified. Various countries have successfully developed vaccines to curb the disease-transmission and prevent future outbreaks. Vaccination-drives are being conducted on a war-footing, but the process is time-consuming, especially in the densely populated regions of the world. Bioinformaticians and computational biologists have been playing an efficient role in this state of emergency to escalate clinical research and therapeutic development. However, there are not many reviews available in the literature concerning COVID-19 and its management. Hence, we have focused on designing a comprehensive review on in-silico approaches concerning COVID-19 to discuss the relevant bioinformatics and computational resources, tools, patterns of research, outcomes generated so far and their future implications to efficiently model data based on epidemiology; identify drug targets to design new drugs; predict epitopes for vaccine design and conceptualize diagnostic models. Artificial intelligence/machine learning can be employed to accelerate the research programs encompassing all the above urgent needs to counter COVID-19 and similar outbreaks.
Discovery of novel inhibitors of SARS-CoV-2 main protease

Abstract Corona Virus Disease 2019 (COVID-19), referred to as ‘New Coronary Pneumonia’, is a type of acute infectious disease caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. Mpro is one of the main targets for treating COVID-19. The current research on Mpro mainly focuses on the repurposing of old drugs, and there are only a few novel ligands that inhibit Mpro. In this research, we used computational free energy calculation to screen a compound library against Mpro, and discovered four novel compounds with the two best compounds (AG-690/13507628 and AG-690/13507724) having experimental measured IC50 of just under 3 μM and low cell toxicity. Detailed decomposition of the interactions between the inhibitors and Mpro reveals key interacting residues and interactions that determine the activity. The results from this study should provide a basis for further development of anti-SARS-CoV-2 drugs. Communicated by Ramaswamy H. Sarma
Evaluation of the Antibacterial Potential of Essential Oil and Extract of Apium graveolens L. as an Environmentally Friendly Technology Against Helicobacter pylori

The hygiene hypothesis links the environmental and microbial exposure in early life to the prevalence of atopy, allergy, and asthma. Helicobacter pylori infection is typically acquired in childhood and the acquisition is associated with poor household hygiene. In this study, the current knowledge on the activity of essential oils and extract of Apium graveolens L. (celery seeds) and their derivatives against H. pylori was reviewed. Celery seeds were prepared at the Pharmaceutical Farm (Babol, Mazandaran) of Iran. The essential oils were extracted by a Clevenger approach and analyzed using GC-MS, and maceration method was used to prepare the extract. H. pylori bacteria were isolated by the cultivation of gastric biopsy removed from the patient who had gastric ulcer. The antibacterial activities of both essential oils and extract against H. pylori were evaluated by agar dilution method, and the corresponding MIC (minimum inhibitory concentration) and MBC (minimum bactericidal concentration) values were determined for each sample. The results showed that the main components in celery seed essential oils were α-pinene (20.25%), β-pinene (16.62%), and Sabinene (7.81%). Among different samples, essential oils of celery seed exhibited better effect on H. pylori with MIC value of 1.56 mg/mL and MBC value of 3.12 mg/mL. Methanol and water extracts of celery seed showed MIC values of 0.38 mg/mL and 0.78 mg/mL and MBC values of 1.56 mg/mL and 6.25 mg/ mL, respectively (P≤0.005). The results of this study indicated that all the samples had antibacterial effect against H. pylori due to antibacterial components.
Paclitaxel-loaded PLGA microspheres with a novel morphology to facilitate drug delivery and antitumor efficiency

The aim of this study was to develop a novel morphological paclitaxel (PTX) loaded poly(lactide-co-glycolide) (PLGA) microspheres (MS) delivery system to enhance drug delivery and antitumor efficiency as well as reduce drug administration frequency. Therefore, different morphological types of PTX-PLGA-MS were prepared using a modified solvent evaporation technique. Morphology analysis confirmed the successful preparation of the smooth PTX-PLGA-MS with internal sporadic porosity, and the novel rough PTX-PLGA-MS with microporous surface and porous internal structures. The PTX drugs were distributed in the readily bioavailable state (amorphous) in PTX-loaded MS, which allowed fast drug release from MS following intratumoral administration. The drug entrapment and release behaviors indicated that the rough MS could provide enough hydrophobic space for PTX-loading and deep surface folds for fast matrices degradation, thus achieving a higher drug-loading efficiency (17.8%) and a rapid sustained drug release effect. Furthermore, the rough MS showed strengthened in vitro anti-hepatoma efficiency than that of free PTX and smooth MS. The in vivo studies indicated remarkable antitumor activity of rough MS (tumor inhibition rate = 58.33%) for at least 13 days after a single injection, which was because the rapid sustained-release drugs could induce the pro-apoptosis gene and protein expressions, cause extensive tumor cell apoptosis, and reduce the toxicity to normal tissues. In conclusion, the rough PTX-PLGA-MS drug delivery system with outstanding tumor growth inhibition effect could serve as a promising treatment for liver tumor.
Comprehensive analysis of pan‐cancer reveals potential of ASF1B as a prognostic and immunological biomarker

Anti‐silencing function 1 (ASF1) is a conserved histone H3–H4 chaperone protein. ASF1B, a paralog of ASF1, acts by promoting cell proliferation and influencing cell cycle progression. Although there is some evidence demonstrating that ASF1B plays a key role in the development, progression, and prognosis of certain cancers, there are no pan‐cancer analyses of ASF1B.
Pathological findings identified during the posterior approach to the spinal accessory nerve after high-energy trauma

The spinal accessory to suprascapular nerve transfer is a key procedure for restoring shoulder function in upper brachial plexus injuries and is typically undertaken via an anterior approach. The anterior approach may miss injury to the suprascapular nerve about the suprascapular notch, which may explain why functional outcomes are often limited. In 2014 we adopted a posterior approach to enable better visualization of the suprascapular nerve at the notch. Over the next 6 years we have used this approach for 20 explorations after high-energy trauma. In 7/20 we identified abnormalities at the level of the suprascapular ligament, which we would not have identified with an anterior approach: there were two ruptures, two neuromas-in-continuity and three cases of scar encasement, necessitating neurolysis. Nerve transfer could be undertaken distal to the suprascapular notch, bypassing the site of injury. These pathological findings support the wider adoption of the posterior approach in cases of high-energy trauma. Level of evidence: IV
Implantable vagus nerve stimulator settings and short‐term adverse effects in epileptic dogs

Abstract Background Implantable vagus nerve stimulation (VNS) devices can be used to treat epilepsy in dogs. Adverse effects and short‐term complications associated with delivering suggested therapeutic electrical stimulation (>1.5 mA) are not well‐described. Objectives To compare complications and adverse effects observed with standard and rapid protocols of current increase. Animals Sixteen client‐owned dogs with idiopathic epilepsy. Methods Nonrandomized, nonblinded prospective cohort study. Surgical complications, stimulation‐related adverse effects, modifications to stimulator settings, number of hospital visits, and time to reach 1.5 mA stimulation current without intolerable adverse effects were described in dogs receiving current increases every 1 to 3 weeks (slow ramping) and dogs receiving current increases every 8 to 12 hours (fast ramping). Results Self‐resolving surgery site seromas formed in 6 dogs. No other surgical complications were observed. Fourteen dogs reached 1.5 mA. Coughing (11/14 dogs; 5 slow, 6 fast ramping) was the most common adverse effect. Intolerable coughing that limited current increases despite changing other stimulus parameters occurred in 6/7 of the fast‐ramping group and in none of the slow‐ramping group. Median time to 1.5 mA was 72 days (range, 28‐98) in the slow‐ramping group and 77 days (range, 3‐152) in the fast‐ramping group. Median number of clinic visits was 6 for the slow‐ramping group (range, 5‐6) and 3 for the fast‐ramping group (range, 1‐7). Conclusions and Clinical Importance Coughing is a common adverse effect of VNS in dogs and generally is well tolerated, particularly if current is increased slowly and other stimulation parameters are adapted for effect.