Miracle-dz/UniFAR-FTUs huggingface dataset:
An integrated insight into the response of bacterial communities to anthropogenic contaminants in a river: A case study of the Wonderfonteinspruit catchment area, South Africa

Bacterial communities in human-impacted rivers and streams are exposed to multiple anthropogenic contaminants, which can eventually lead to biodiversity loss and function. The Wonderfonteinspruit catchment area is impacted by operational and abandoned gold mines, farms, and formal and informal settlements. In this study, we used 16S rRNA gene high-throughput sequencing to characterize bacterial communities in the lower Wonderfonteinspruit and their response to various contaminant sources. The results showed that composition and structure of bacterial communities differed significantly (P<0.05) between less (downstream) and more (upstream) polluted sites. The taxonomic and functional gene dissimilarities significantly correlated with each other, while downstream sites had more distinct functional genes. The relative abundance of Proteobacteria, Bacteroidetes and Actinobacteria was higher at upstream sites, while Acidobacteria, Cyanobacteria, Firmicutes and Verrucomicrobia were prominent at downstream sites. In addition, upstream sites were rich in genera pathogenic and/or potentially pathogenic to humans. Multivariate and correlation analyses suggest that bacterial diversity was significantly (P<0.05) impacted by pH and heavy metals (cobalt, arsenic, chromium, nickel and uranium). A significant fraction (~14%) of the compositional variation was explained by a combination of anthropogenic inputs, of which mining (~6%) was the main contributor to bacterial community variation. Network analysis indicated that bacterial communities had non-random inter- and intra-phyla associations and that the main taxa showed both positive and negative linkages to environmental parameters. Our results suggest that species sorting, due to environmental parameters, was the main process that structured bacterial communities. Furthermore, upstream sites had higher relative abundances of genes involved in xenobiotic degradation, suggesting stronger removal of polycyclic aromatic hydrocarbons and other organic compounds. This study provides insights into the influences of anthropogenic land use on bacterial community structure and functions in the lower Wonderfonteinspruit.
The Veterans Affairs Low-Vision Visual Functioning Questionnaire-48 (VA LV VFQ-48): Performance of the Italian version

Purpose: The Veterans Affairs Low-Vision Visual Functioning Questionnaire-48 is among the most validated tools to collect patient-reported outcomes in a low-vision population. We have aimed to conduct a pilot validation of the Italian version of the Veterans Affairs Low-Vision Visual Functioning Questionnaire-48. Methods: The Veterans Affairs Low-Vision Visual Functioning Questionnaire-48 was translated using a standardized procedure and then administered to consecutive low-vision patients attending rehabilitation services in three centers. Patients were interviewed by a trained psychologist regarding the individual items of the tool. Results: We included 131 patients with a mean visual acuity of 0.91 logMAR (standard deviation: 0.42 logMAR), mostly affected by age-related macular degeneration. The Veterans Affairs Low-Vision Visual Functioning Questionnaire-48 showed high internal consistency (Cronbach’s alpha: 0.98) and good item-test and item-rest correlation (median: 0.73 and 0.71, respectively). Both the overall score and the subscale (reading, visual motor, mobility and visual information) scores significantly correlated with visual acuity, reading acuity and speed. Reading speed achieved the best absolute correlation with the Veterans Affairs Low-Vision Visual Functioning Questionnaire-48 scores (Spearman r: 0.39–0.49). Conclusion: The Italian version of the Veterans Affairs Low-Vision Visual Functioning Questionnaire-48 is a valid tool to assess patients attending low-vision services. Revising a few items may further improve the tool.
Learning across multi-stimulus enhances target recognition methods in SSVEP-based BCIs

Objective. Latest target recognition methods that are equipped with learning from the subject’s calibration data, represented by the extended canonical correlation analysis (eCCA) and the ensemble task-related component analysis (eTRCA), can achieve extra high performance in the steady-state visual evoked potential (SSVEP)-based brain–computer interfaces (BCIs), however their performance deteriorate drastically if the calibration trials are insufficient. This paper develops a new scheme to learn from limited calibration data. Approach. A learning across multiple stimuli scheme is proposed for the target recognition methods, which applies to learning the data corresponding to not only the target stimulus but also the other stimuli. The resulting optimization problems can be simplified and solved utilizing the prior knowledge and properties of SSVEPs across different stimuli. With the new learning scheme, the eCCA and the eTRCA can be extended to the multi-stimulus eCCA (ms-eCCA) and the multi-stimulus eTRCA (ms-eTRCA), respectively, as well as a combination of them (i.e. ms-eCCA+ms-eTRCA) that incorporates their merits. Main results. Evaluation and comparison using an SSVEP-BCI benchmark dataset with 35 subjects show that the ms-eCCA (or ms-eTRCA) performs significantly better than the eCCA (or eTRCA) method while the ms-eCCA+ms-eTRCA performs the best. With the learning across stimuli scheme, the existing target recognition methods can be further improved in terms of the target recognition performance and the ability against insufficient calibration. Significance. A new learning scheme is proposed towards the efficient use of the calibration data, providing enhanced performance and saving calibration time in the SSVEP-based BCIs.
A Randomized Controlled Trial Comparing Two Lung Expansion Therapies After Upper Abdominal Surgery

BACKGROUND: Lung expansion therapy is often ordered after surgery to improve alveolar ventilation and reduce risks of postoperative pulmonary complications. The impact of lung expansion therapy at altering ventilation in patients who are not intubated has not been described. The primary purpose of this study was to determine if there is a difference in dorsal redistribution of ventilation and incidences of postoperative pulmonary complications when comparing incentive spirometry (IS) with EzPAP lung expansion therapy after upper abdominal surgery. Our a priori null hypothesis was that there are no differences. METHODS: This randomized controlled trial enrolled adult human subjects after upper- abdominal surgery from January 2017 to November 2018. The subjects were allocated to receive IS or EzPAP 3 times a day on postoperative days 1–5. An electrical impedance tomography device was connected to the subjects for a single lung expansion therapy session on postoperative days 1, 3, and 5 to measure the change in post-lung expansion therapy dorsal end-expiratory lung impedance (ΔEELI%). Lung expansion therapy sessions with electrical impedance tomography included 2 min of normal breathing, 3 cycles of 10 breaths, and 2 min of normal breathing after cycle 3. Postoperative pulmonary complications were screened until hospital discharge. Mann-Whitney, chi-square, and Fisher exact tests were applied. Data were reported as count (n), percentage, and median (interquartile range) for primary and secondary outcomes. Alpha (2-tailed) was < 0.05. RESULTS: A total of 112 subjects were enrolled to receive IS (n = 56) or EzPAP (n = 56). Baseline characteristics were equal. Post-lung expansion therapy dorsal ΔEELI% increased for both groups, but the dorsal ΔEELI% for IS versus EzPAP on postoperative day 1 (16% versus 12%, P = .39), postoperative day 3 (6% versus 6%, P = .68), and postoperative day 5 (9% versus 6%, P = .46) was not significantly different. Hospital length of stay (4 d; P = .30) and incidence of postoperative pulmonary complications (3.6% versus 7.1%, P = .19) were similar. CONCLUSIONS: There was no significant post-lung expansion therapy dorsal ΔEELI% or postoperative pulmonary complications among the adults who received IS or EzPAP 3 times a day after upper abdominal surgery. (ClinicalTrials.gov registration NCT02892773.)
Identification of genes mediating branched chain fatty acid elongation

Saturated branched chain fatty acids (BCFA) terminating with either a prop‐2‐yl (iso) or sec‐butan‐2‐yl (anteiso) group are common bioactive food components consumed from beef, fish, and dairy products. Little is known about the endogenous metabolism of BCFA and the enzymes mediating their interconversions. By using transient transfection studies, we report for the first time the substrate specificity of the elongase of very long chain fatty acids (ELOVL)1‐7 toward anteiso‐15:0 and iso‐18:0, and assessed competition between BCFA and normal saturated fatty acids (n‐SFA). ELOVL6 mediates elongation of anteiso‐15:0→anteiso‐17:0, while ELOVL3 is active toward iso‐18:0→iso‐20:0. Competition studies reveal n‐16:0 competes with anteiso‐15:0 for ELOVL6, while n‐18:0 competes with iso‐18:0 for ELOVL3. These competitions for elongation may have implications in specialized tissues where both BCFA and n‐SFA are present at comparable levels.
Near-neighbour optimal outcrossing in the bird-pollinated Anigozanthosmanglesii.

BACKGROUND AND AIMS In plants, the spatial and genetic distance between mates can influence reproductive success and offspring fitness. Negative fitness consequences associated with the extremes of inbreeding and outbreeding suggests that there will be an intermediate optimal outcrossing distance (OOD), the scale and drivers of which remain poorly understood. In the bird-pollinated Anigozanthosmanglesii (Haemodoraceae) we tested i) for the presence of within-population OOD, ii) over what scale it occurs, and iii) for OOD under biologically realistic scenarios of multi-donor deposition associated with pollination by nectar-feeding birds. METHODS We measured the impact of mate distance (spatial and genetic) on seed set, fruit size, seed mass, seed viability, and germination success following hand pollination from i) single donors across 0m (self), <1m, 1-3m, 7-15m, and 50m and ii) a mix of eight donors. Microsatellite loci were used to quantify spatial genetic structure and test for the presence of an OOD by paternity assignment after multi-donor deposition. KEY RESULTS Inter-mate distance had a significant impact on single donor reproductive success, with selfed and nearest neighbour (<1m) pollination resulting in only ca. 50 seeds/fruit, lower overall germination success, and slower germination. Seed set was greatest for inter-mate distance of 1-3m (148 seeds/fruit) thereafter plateauing at approximately 100 seeds/fruit. Lower seed set following nearest neighbour mating was associated with significant spatial genetic autocorrelation at this scale. Paternal success following pollination with multiple sires showed a significantly negative association with increasing distance between mates. CONCLUSIONS Collectively, single- and multi-donor pollinations indicated evidence for a near neighbour OOD within A. manglesii. A survey of the literature suggests that within population OOD may be more characteristic of plants pollinated by birds than those pollinated by insects.
Human platelets and megakaryocytes express defensin alpha 1

Abstract Platelets are anucleate cells that have a role in several innate immune functions, including the secretion of proteins with antimicrobial activity. Several studies have demonstrated the ability of platelets to secrete thrombin-induced platelet microbicidal proteins and antimicrobial peptides, like hBD-1. However, the expression and secretion of defensins of the alpha family by platelets have not been fully elucidated. The aim of this study was to characterize the expression of defensin alpha 1 (DEFA1) in human platelets and megakaryocytes. Our data indicate that DEFA1 mRNA and protein are present in peripheral blood platelets and in the megakaryoblastic leukemia cell line (MEG-01). DEFA1 co-localize with α-granules of platelets and MEG-01 cells, and was also detected in cytoplasm of MEG-01 cells. The assay of our in vitro model of platelet-like particles (PLPs) revealed that MEG-01 cells could transfer DEFA1 mRNA to their differentiated PLPs. Furthermore, platelets secreted DEFA1 into the culture medium when activated with thrombin, adenosine diphosphate, and lipopolysaccharide; meanwhile, MEG-01 cells secreted DEFA1 when activated with thrombopoietin. Platelet’s secreted DEFA1 can rebind to platelet’s surface and have antibacterial activity against the gram-negative bacteria Escherichia coli. In summary, our data indicate that both, human platelets and megakaryocytes, can express and secrete DEFA1. These results suggest a new role of platelets and megakaryocytes in the innate immune response.
Induction of UDP-glucuronosyltransferase by the flavonoids chrysin and quercetin in Caco-2 cells.

PURPOSE Dietary flavonoids have been reported to be potent inhibitors of drug metabolizing enzymes. In the present study we examined the inducing effect of three of these compounds, chrysin, quercetin and genistein, on UDP-glucuronosyltransferase (UGT) in the human intestinal cell line Caco-2. METHODS The induction of UGT by flavonoid pretreatment was studied both in the intact cells and cell homogenates, measured as the glucuronidation of chrysin, and by immunoblot analysis of the UGT 1A protein. RESULTS Exposure of Caco-2 cells to 50 microM chrysin resulted in a 3.8-fold increase in chrysin glucuronidation in intact cells (p < 0.0001) with a 38% decrease in sulfation (p < 0.01). In the cell homogenate the induction was much larger, 14-fold. The induction was slow to develop with maximum induction after 3-4 days. Interestingly, the isoflavonoid genistein was without effect. Immunoblot analysis of Caco-2 cell microsomes with a UGT1A subfamily-selective antibody showed a markedly increased band at about 59 kDa, consistent with induction of one or more UGT1A isoforms. A 5-week exposure of Caco-2 cells to low concentrations (10 microM) of chrysin or quercetin also showed markedly increased glucuronidation activity. CONCLUSIONS Diet-mediated induction of intestinal UGT may be important for the bioavailability of carcinogens and other toxic chemicals as well as therapeutic drugs.
Application of effort parameter to robot gesture motion

Laban Movement Analysis (LMA), proposed by Rudolf von Laban, is widespread method for describing, notating, and interpreting human movement. Effort is one of major components of LMA that is commonly used to scrutinize or analyze the kinetic movement from viewpoint of `dynamic' qualities. Effort comprises four factors and they can provide qualitative parameters about dynamic features of movement for describing a body movement. In this study, we proposed a computational model of Weight and Time Effort, and applied it to robot platforms to develop robot gesture motion diversification method. Experiments with certified movement analysts are conducted to check the validity of our model.
Revisiting “An Exercise in Groundwater Model Calibration and Prediction” After 30 Years: Insights and New Directions

In 1988, an important publication moved model calibration and forecasting beyond case studies and theoretical analysis. It reported on a somewhat idyllic graduate student modeling exercise where many of the system properties were known; the primary forecasts of interest were heads in pumping wells after a river was modified. The model was calibrated using manual trial‐and‐error approaches where a model's forecast quality was not related to how well it was calibrated. Here, we investigate whether tools widely available today obviate the shortcomings identified 30 years ago. A reconstructed version of the 1988 true model was tested using increasing parameter estimation sophistication. The parameter estimation demonstrated the inverse problem was non‐unique because only head data were available for calibration. When a flux observation was included, current parameter estimation approaches were able to overcome all calibration and forecast issues noted in 1988. The best forecasts were obtained from a highly parameterized model that used pilot points for hydraulic conductivity and was constrained with soft knowledge. Like the 1988 results, however, the best calibrated model did not produce the best forecasts due to parameter overfitting. Finally, a computationally frugal linear uncertainty analysis demonstrated that the single‐zone model was oversimplified, with only half of the forecasts falling within the calculated uncertainty bounds. Uncertainties from the highly parameterized models had all six forecasts within the calculated uncertainty. The current results outperformed those of the 1988 effort, demonstrating the value of quantitative parameter estimation and uncertainty analysis methods.
Adaptive protection schemes for the microgrid in a Smart Grid scenario: Technical challenges

Microgrids are gaining attention as an important part of the smart grid, due to their numerous benefits and their ability to operate both in the island mode as well as in the grid connected mode. However, a protection scheme which suits to a microgrid both in the island mode and the grid connected mode of operation is a challenge. The conventional overcurrent protection scheme faces selectivity and sensitivity issues during the grid faults and the microgrid faults, since the fault current level is different in both the cases for the same relay. Various approaches have been implemented in the past to deal with this problem yet the most promising ones are the adaptive protection techniques. The feasibility, reliability and cost benefit issues are some major concerns which are associated with the implementation of the adaptive microgrid protection schemes. This paper presents a critical review of the existing adaptive protection schemes, the technical challenges, if any, and the recent advancement concerning to their suitability to operate in a smart grid scenario.
Add-on angiotensin receptor blockade with maximized ACE inhibition.

BACKGROUND Prolonged angiotensin-converting enzyme (ACE) inhibitor therapy leads to angiotensin I (Ang I) accumulation, which may "escape" ACE inhibition, generate Ang II, stimulate the Ang II subtype 1 (AT1) receptor, and exert deleterious renal effects in patients with chronic renal diseases. We tested the hypothesis that losartan therapy added to a background of chronic (>3 months) maximal ACE inhibitor therapy (lisinopril 40 mg q.d.) will result in additional Ang II antagonism in patients with proteinuric chronic renal failure with hypertension. METHODS Sixteen patients with proteinuric moderately advanced chronic renal failure completed a two-period, crossover, randomized controlled trial. Each period was one month with a two-week washout between periods. In one period, patients received lisinopril 40 mg q.d. along with other antihypertensive therapy, and in the other, losartan 50 mg q.d. was added to the previously mentioned regimen. Hemodynamic measurements included ambulatory blood pressure monitoring (ABP; Spacelabs 90207), glomerular filtration rate (GFR) with iothalamate clearances and cardiac outputs by acetylene helium rebreathing technique. Supine plasma renin activity and plasma aldosterone and 24-hour urine protein were measured in all patients. RESULTS Twelve patients had diabetic nephropathy, and four had chronic glomerulonephritis. The mean age (+/- SD) was 53 +/- 9 years. The body mass index was 38 +/- 5.7 kg/m(2), and all except two patients were males. Seated cuff blood pressure was 156 +/- 18/88 +/- 12 mm Hg. The pulse rate was 77 +/- 11 per min, and the cardiac index was 2.9 +/- 0.5 L/min/m(2). Mean log 24-hour protein excretion/g creatinine or overall ABPs did not change. Mean placebo subtracted, losartan-attributable change in protein excretion was +1% (95% CI, -20% to 28%, P = 0.89). Similarly, the change in systolic ambulatory blood pressure (ABP) was 4.6 mm Hg (-5.7 to 14.9, P = 0.95), and diastolic ABP was 1.5 mm Hg (-4.5 to 7.6, P = 0.59). No change was seen in cardiac output. However, there was a mean 14% increase (95% CI, 3 to 26%, P = 0.017) in GFR attributable to losartan therapy. A concomitant fall in plasma renin activity by 32% was seen (95% CI, -15%, - 45%, P = 0.002). No hyperkalemia, hypotension, or acute renal failure occurred in the trial. These results were not attributable to sequence or carryover effects. CONCLUSIONS Add-on losartan therapy did not improve proteinuria or ABP over one month of add on therapy. Improvement of GFR and fall in plasma renin activity suggest that renal hemodynamic and endocrine changes are more sensitive measures of AT1 receptor blockade. Whether add-on AT1 receptor blockade causes antiproteinuric effects or long-term renal protection requires larger and longer prospective, randomized controlled trials.
Safe anesthesia for office-based plastic surgery: Proceedings from the PRS Korea 2018 meeting in Seoul, Korea

There has been an exponential increase in plastic surgery cases over the last 20 years, surging from 2.8 million to 17.5 million cases per year. Seventy-two percent of these cases are being performed in the office-based or ambulatory setting. There are certain advantages to performing aesthetic procedures in the office, but several widely publicized fatalities and malpractice claims has put the spotlight on patient safety and the lack of uniform regulation of office-based practices. While 33 states currently have legislation for office-based surgery and anesthesia, 17 states have no mandate to report patient deaths or adverse outcomes. The literature on office-base surgery and anesthesia has demonstrated significant improvements in patient safety over the last 20 years. In the following review of the proceedings from the PRS Korea 2018 meeting, we discuss several key concepts regarding safe anesthesia for officebased cosmetic surgery. These include the safe delivery of oxygen, appropriate local anesthetic usage and the avoidance of local anesthetic toxicity, the implementation of Enhanced Recovery after Surgery protocols, multimodal analgesic techniques with less reliance on narcotic pain medications, the use of surgical safety checklists, and incorporating “the patient” into the surgical decision-making process through decision aids.