Miracle-dz/UniFAR-FTUs huggingface dataset:
Marine Water Quality at Diego Garcia: A Preliminary Study of Pollution Levels in Coastal and Lagoon Waters

Diego Garcia is the largest atoll within the Chagos Archipelago in the Indian Ocean. Since the 1960s it has been a military base, populated only by military and support personnel. Infrastructure includes sewage treatment works, a waste disposal facility and an airbase. Lagoon use includes boating and large vessel anchorage. Current pollution levels by inorganic nutrients and other contaminants are unknown. A field study was undertaken in March 2019 to obtain baseline information on key environmental parameters and pollutants for assessing the state of marine water quality. Outside the atoll, three stations were sampled where human impacts were likely to be lowest (two off the north coast, considered as ‘near-pristine’; one on the east coast); one station was sampled in the lagoon mouth; 10 stations were sampled downstream from two sewage outflows. Inside the lagoon, 10 stations were sampled at near-shore sites likely to be directly impacted by activities such as boating and waste management; six stations were sampled in the central or eastern lagoon. In situ sensors were used to estimate temperature, salinity, chlorophyll (as fluorescence) and dissolved oxygen. Discrete water samples were analyzed for nutrients, chemical contaminants, heavy metals and fecal indicator bacteria. Sea surface temperatures were highest (29.5–35 °C) inside the lagoon; salinities were generally higher (> 34.1) outside the lagoon (vs 33.8–34.1 inside). Surface nutrient concentrations at near-pristine stations were undetectable for nitrate and phosphate and averaged 1.39 μM for dissolved inorganic nitrogen (DIN) and 1.73 μM for silicate. Concentrations were higher at most other stations (maximum 5.7 μM DIN, 0.38 μM phosphate, and 9.93 μM silicate), with ammonium contributing most to DIN. In the lagoon, chlorophyll concentrations were relatively low (0.3 – 0.6 μg chl l–1) near the surface and higher (max 0.9 μg chl l–1) at depth. Results suggested low levels of pollution overall. However, levels of nutrients, oxygen deficiency, chemical contaminants (e.g., solvents and DEET) and heavy metals (cadmium, nickel, zinc and copper) at some sites inside the lagoon are a concern due to slow flushing rates and will be used to inform future monitoring and assessment of environmental health at Diego Garcia.
Assembling the Current Pieces: The Puzzle of RNA-Mediated Regulation in Staphylococcus aureus

The success of the major opportunistic human Staphylococcus aureus relies on the production of numerous virulence factors, which allow rapid colonization and dissemination in any tissues. Indeed, regulation of its virulence is multifactorial, and based on the production of transcriptional factors, two-component systems (TCS) and small regulatory RNAs (sRNAs). Advances in high-throughput sequencing technologies have unveiled the existence of hundreds of potential RNAs with regulatory functions, but only a fraction of which have been validated in vivo. These discoveries have modified our thinking and understanding of bacterial physiology and virulence fitness by placing sRNAs, alongside transcriptional regulators, at the center of complex and intertwined regulatory networks that allow S. aureus to rapidly adapt to the environmental cues present at infection sites. In this review, we describe the recently acquired knowledge of characterized regulatory RNAs in S. aureus that are associated with metal starvation, nutrient availability, stress responses and virulence. These findings highlight the importance of sRNAs for the comprehension of S. aureus infection processes while raising questions about the interplay between these key regulators and the pathways they control.
Bioeconomic Analysis of Groufer Fish (Plectropomus leopardus) Utilization in Selayar Archipelago Regency

The main problem in the management of fishery resources is how the fishery resources produce high economic benefit but its sustainability be maintained. This study aims to analyze the actual and optimal production levels of coral trout grouper in Selayar Archipelago Regency. A survey was conducted in Gusung island, Selayar Archipelago Regency by using simple random cluster sampling. The respondents were 32 fisherman who used fishing rods and 29 fisherman who used traps. Analysis of the data using formulas bioeconomy optimal static and dynamic with the help of software MS. Excel and Mapple 18. The results showed that the actual condition of the coral trout grouper utilization in Selayar Archipelago Regency has not experienced overfishing, both biologically and economically. The actual production was 184,57 tons while the optimum production of OSY (Optimum Sustainable Yield) management regime is equal to 213,32 tons. It is necessary to increase the amount of effort from the actual condition was 52.744 trips to the management OSY regime that is 111.339 trips to get the optimum economic rents amounting to 5.937. 435.339
Identification of a Prognostic Signature Associated With the Homeobox Gene Family for Bladder Cancer

Background: Bladder cancer (BLCA) is a common malignant tumor of the genitourinary system, and there is a lack of specific, reliable, and non-invasive tumor biomarker tests for diagnosis and prognosis evaluation. Homeobox genes play a vital role in BLCA tumorigenesis and development, but few studies have focused on the prognostic value of homeobox genes in BLCA. In this study, we aim to develop a prognostic signature associated with the homeobox gene family for BLCA. Methods: The RNA sequencing data, clinical data, and probe annotation files of BLCA patients were downloaded from the Gene Expression Omnibus database and the University of California, Santa Cruz (UCSC), Xena Browser. First, differentially expressed homeobox gene screening between tumor and normal samples was performed using the “limma” and robust rank aggregation (RRA) methods. The mutation data were obtained with the “TCGAmutation” package and visualized with the “maftools” package. Kaplan–Meier curves were plotted with the “survminer” package. Then, a signature was constructed by logistic regression analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using “clusterProfiler. ” Furthermore, the infiltration level of each immune cell type was estimated using the single-sample gene set enrichment analysis (ssGSEA) algorithm. Finally, the performance of the signature was evaluated by receiver-operating characteristic (ROC) curve and calibration curve analyses. Results: Six genes were selected to construct this prognostic model: TSHZ3, ZFHX4, ZEB2, MEIS1, ISL1, and HOXC4. We divided the BLCA cohort into high- and low-risk groups based on the median risk score calculated with the novel signature. The overall survival (OS) rate of the high-risk group was significantly lower than that of the low-risk group. The infiltration levels of almost all immune cells were significantly higher in the high-risk group than in the low-risk group. The average risk score for the group that responded to immunotherapy was significantly lower than that of the group that did not. Conclusion: We constructed a risk prediction signature with six homeobox genes, which showed good accuracy and consistency in predicting the patient’s prognosis and response to immunotherapy. Therefore, this signature can be a potential biomarker and treatment target for BLCA patients.
The Long-Term Effects of Neonatal Inflammatory Pain on Cognitive Function and Stress Hormones Depend on the Heterogeneity of the Adolescent Period of Development in Male and Female Rats

Exposure to stress at an early age programs the HPA axis which can lead to cognitive deficits in adults. However, it is not known whether these deficits emerge in adulthood or are expressed earlier in life. The aims of the study were to investigate (1) the immediate effects of early injury-induced stress in one-day-old (P1) and repeated stress on at P1 and P2 rat pups on plasma corticosterone levels; and (2) examine the subsequent long-term effects of this early stress on spatial learning and memory, and stress reactivity in early P26-34 and late P45-53 adolescent male and female rats. Intra-plantar injection of formalin induced prolonged and elevated levels of corticosterone in pups and impaired spatial learning and short- and long-term memory in late adolescent males and long-term memory in early adolescent females. There were sex differences in late adolescence in both learning and short-term memory. Performance on the long-term memory task was better than that on the short-term memory task for all early adolescent male and female control and stressed animals. Short-term memory was better in the late age control rats of both sexes and for formalin treated females as compared with the early age rats. These results are consistent with an impaired function of structures involved in memory (the hippocampus, amygdala, prefrontal cortex) after newborn pain. However, activation of the HPA axis by neonatal pain did not directly correlate with spatial learning and memory outcomes and the consequences of neonatal pain remain are likely multi-determined.
Plasma Levels of Brain-Derived Neurotrophic Factor and S100B in Relation to Antidepressant Response to Ketamine

Background Evidence demonstrates that brain-derived neurotrophic factor (BDNF) and S100 calcium-binding protein B (S100B) have a pivotal role in the pathogenesis of major depressive disorder (MDD) and they are proposed as predictors of antidepressant response. Ketamine produces rapid antidepressant effects in MDD and pre-clinical studies suggest the necessity of increased BDNF levels for the antidepressant action of ketamine. However, studies observing the change of blood BDNF levels after ketamine intervention are inconsistent and studies about the role of plasma S100B in ketamine administration in MDD patients are lacking. Method We evaluated mature BDNF (mBDNF), S100B levels in plasma and their associations with depression severity in 30 Selective Serotonin Reuptake Inhibitor (SSRI)-resistant MDD patients enrolled in a randomized controlled trial of ketamine compared (n = 20) to a placebo (n = 10) control (saline). Severity of depression was assessed using the Montgomery–Åsberg Depression Rating Scale (MADRS). Results Plasma mBDNF and S100B were not significantly changed after 1–2 days of single ketamine compared to placebo. Plasma mBDNF and S100B levels did not significantly differ in responders compared to non-responders of ketamine treatment. The change of plasma mBDNF levels was positively correlated with the improvement of MADRS score after 1–2 weeks of open-label ketamine treatment (rho = 0.495, p = 0.031), though this change did not survive correction for multiple comparisons. Conclusion These findings do not support the hypothesis that ketamine treatment increases BDNF plasma levels in MDD patients. No effect of ketamine treatment on S100B plasma levels was seen.
Risk and Protective Factors of Lifetime Cocaine-Associated Chest Pain

Introduction: Cocaine users often present with repetitive events of cocaine-associated chest pain (CACP), clinically resembling acute coronary syndromes. The aim of the study is to describe the specific risk factors for CACP. Method: Cocaine users (n = 316) were recruited for a multicenter cross-sectional study. Lifetime CACP history, sociodemographic factors, and lifetime use of cocaine and other substances were assessed. Thirty single nucleotide polymorphisms (SNPs) of NOS3, ROCK2, EDN1, GUCY1A3, and ALDH2 genes, suggested by the literature on coronary spasms, were selected. The associations with CACP history were tested using the chi-square test, Student's t-test and logistic regression. Results: Among the 316 subjects [78.5% men, mean age 37.5 years, (standard-deviation ±8.7)], 190 (60.1%) were daily cocaine users and 103 (32.6%) reported a lifetime CACP history. Among those with a lifetime CACP history, the median was 10 events per individual. In multivariate analysis, lifetime CACP history was associated with daily cocaine use [odds-ratio (OR) 3.24; 95% confidence intervals (1.29–9.33)], rapid route of cocaine use [OR 2.33 (1.20–4.64) vs. intranasal use], and lifetime amphetamine use [daily amphetamine use: OR 2.80 (1.25–6.32) and non-daily amphetamine use: OR 2.14 (1.15–4.04) vs. never used]. Patients with lifetime opioid maintenance treatment (OMT) reported significantly less lifetime CACP history [OR 0.35 (0.16–0.76)]. None of the selected SNPs was associated with CACP history after multiple testing corrections. Conclusions: Clinical variables describing the intensity of stimulant use were positively associated with lifetime CACP history, while OMT was negatively associated with it. Specific harm reduction strategies can target these risk factors.
Emotional Expression in Children With ASD: A Pre-Study on a Two-Group Pre-Post-Test Design Comparing Robot-Based and Computer-Based Training

Several studies have found a delay in the development of facial emotion recognition and expression in children with an autism spectrum condition (ASC). Several interventions have been designed to help children to fill this gap. Most of them adopt technological devices (i.e., robots, computers, and avatars) as social mediators and reported evidence of improvement. Few interventions have aimed at promoting emotion recognition and expression abilities and, among these, most have focused on emotion recognition. Moreover, a crucial point is the generalization of the ability acquired during treatment to naturalistic interactions. This study aimed to evaluate the effectiveness of two technological-based interventions focused on the expression of basic emotions comparing a robot-based type of training with a “hybrid” computer-based one. Furthermore, we explored the engagement of the hybrid technological device introduced in the study as an intermediate step to facilitate the generalization of the acquired competencies in naturalistic settings. A two-group pre-post-test design was applied to a sample of 12 children (M = 9.33; ds = 2.19) with autism. The children were included in one of the two groups: group 1 received a robot-based type of training (n = 6); and group 2 received a computer-based type of training (n = 6). Pre- and post-intervention evaluations (i.e., time) of facial expression and production of four basic emotions (happiness, sadness, fear, and anger) were performed. Non-parametric ANOVAs found significant time effects between pre- and post-interventions on the ability to recognize sadness [t(1) = 7.35, p = 0.006; pre: M (ds) = 4.58 (0.51); post: M (ds) = 5], and to express happiness [t(1) = 5.72, p = 0.016; pre: M (ds) = 3.25 (1.81); post: M (ds) = 4.25 (1.76)], and sadness [t(1) = 10.89, p < 0; pre: M (ds) = 1.5 (1.32); post: M (ds) = 3.42 (1.78)]. The group*time interactions were significant for fear [t(1) = 1.019, p = 0.03] and anger expression [t(1) = 1.039, p = 0.03]. However, Mann–Whitney comparisons did not show significant differences between robot-based and computer-based training. Finally, no difference was found in the levels of engagement comparing the two groups in terms of the number of voice prompts given during interventions. Albeit the results are preliminary and should be interpreted with caution, this study suggests that two types of technology-based training, one mediated via a humanoid robot and the other via a pre-settled video of a peer, perform similarly in promoting facial recognition and expression of basic emotions in children with an ASC. The findings represent the first step to generalize the abilities acquired in a laboratory-trained situation to naturalistic interactions.
Fe b 20 18 DID : Distributed Incremental Block Coordinate Descent for Nonnegative Matrix Factorization

Nonnegative matrix factorization (NMF) has attracted much attention in the last decade as a dimension reduction method in many applications. Due to the explosion in the size of data, naturally the samples are collected and stored distributively in local computational nodes. Thus, there is a growing need to develop algorithms in a distributed memory architecture. We propose a novel distributed algorithm, called distributed incremental block coordinate descent (DID), to solve the problem. By adapting the block coordinate descent framework, closed-form update rules are obtained in DID. Moreover, DID performs updates incrementally based on the most recently updated residual matrix. As a result, only one communication step per iteration is required. The correctness, efficiency, and scalability of the proposed algorithm are verified in a series of numerical experiments.
Effects of perioperative interventions for preventing postoperative delirium

Supplemental Digital Content is available in the text Abstract Background: Postoperative delirium (POD) not only increases the medical burden but also adversely affects patient prognosis. Although some cases of delirium can be avoided by early intervention, there is no clear evidence indicating whether any of these measures can effectively prevent POD in specific patient groups. Objective: The aim of this meta-analysis was to compare the efficacy and safety of the existing preventive measures for managing POD. Methods: The PubMed, OVID (Embase and MEDLINE), Web of Science, and the Cochrane Library databases were searched for articles published before January 2020. The relevant randomized controlled trials (RCTs) were selected based on the inclusion and exclusion criteria. Data extraction and methodological quality assessment were performed according to a predesigned data extraction form and scoring system, respectively. The interventions were compared on the basis of the primary outcome like incidence of POD, and secondary outcomes like duration of delirium and the length of intensive care unit and hospital stay. Results: Sixty-three RCTs were included in the study, covering interventions like surgery, anesthesia, analgesics, intraoperative blood glucose control, cholinesterase inhibitors, anticonvulsant drugs, antipsychotic drugs, sleep rhythmic regulation, and multi-modal nursing. The occurrence of POD was low in 4 trials that monitored the depth of anesthesia with bispectral index during the operation (P < .0001). Two studies showed that supplementary analgesia was useful for delirium prevention (P = .002). Seventeen studies showed that perioperative sedation with α2-adrenergic receptor agonists prevented POD (P = .0006). Six studies showed that both typical and atypical antipsychotic drugs can reduce the incidence of POD (P = .002). Multimodal nursing during the perioperative period effectively reduced POD in 6 studies (P < .00001). Furthermore, these preventive measures can reduce the duration of delirium, as well as the total and postoperative length of hospitalized stay for non-cardiac surgery patients. For patients undergoing cardiac surgery, effective prevention can only reduce the length of intensive care unit stay. Conclusion: Measures including intraoperative monitoring of bispectral index, supplemental analgesia, α2-adrenergic receptor agonists, antipsychotic drugs, and multimodal care are helpful to prevent POD effectively. However, larger, high-quality RCTs are needed to verify these findings and develop more interventions and drugs for preventing postoperative delirium.
Correlation of Serum 25-Hydroxy Vitamin D and Interleukin-17 Levels with Disease Severity in Acne Vulgaris

Background: The association of Vitamin D (vit.D) and Interleukin 17 (IL-17) with acne vulgaris is uncertain in spite of induction of IL-17 by Propionibacterium acnes (P. acnes) and the role of vit.D in various inflammatory skin disorders including acne. The objectives of present study were to evaluate the levels of serum 25-hydroxyvitamin D3 [25(OH)D] and IL-17 in acne patients and age- and sex-matched controls and to compare them with the severity of acne as measured by Global Acne Grading System (GAGS). Methods: The study included 50 patients of acne and 30 healthy controls. Serum 25(OH) D and IL-17 levels were measured using chemiluminescence immunoassay (CLIA) and enzyme-linked immunosorbent assay (ELISA), respectively. Results: Vitamin D deficiency was detected in 28% of patients with acne but only in 6.7% of the healthy controls (P value 0.022). The levels of 25(OH)D were inversely associated with the severity of acne (P < 0.001). The mean serum IL-17 levels were significantly raised (P < 0.001) in acne patients (8.215 ± 5.33 pg/mL) as compared to controls (2.486 ± 2.12 pg/mL). A significant rise in levels of IL-17 was observed with the severity of acne (P < 0.001). Further, a highly significant negative correlation (Correlation Coefficient: -0.668) was noted between serum IL-17 and 25(OH) D levels along with disease severity in acne patients (P value < 0.001). Conclusions: Raised IL-17 levels in acne correlate negatively with vit.D deficiency and both are significantly more prevalent in patients with acne as compared to healthy controls.
A counterfactual simulation model of causation by omission

When do people say that an event that did not happen was a cause? We extend the counterfactual simulation model (CSM) of causal judgment (Gerstenberg, Goodman, Lagnado, & Tenenbaum, 2021) and test it in a series of three experiments that look at people's causal judgments about omissions in dynamic physical interactions. The problem of omissive causation highlights a series of questions that need to be answered in order to give an adequate causal explanation of why something happened: what are the relevant variables, what are their possible values, how are putative causal relationships evaluated, and how is the causal responsibility for an outcome attributed to multiple causes? The CSM predicts that people make causal judgments about omissions in physical interactions by using their intuitive understanding of physics to mentally simulate what would have happened in relevant counterfactual situations. Prior work has argued that normative expectations affect judgments of omissive causation. Here we suggest a concrete mechanism of how this happens: expectations affect what counterfactuals people consider, and the more certain people are that the counterfactual outcome would have been different from what actually happened, the more causal they judge the omission to be. Our experiments show that both the structure of the physical situation as well as expectations about what will happen affect people's judgments.
Monodisperse semiconducting poly(N-methylaniline) microspheres and their electrorheological response

Monodisperse semiconducting poly(N-methylaniline) (PNMA) microspheres with a suitable electrical conductivity were fabricated using a chemical oxidation process and employed in an electrorheological (ER) suspension. Morphological image of the synthesized PNMA microsphere was assessed via scanning electron microscope and transmission electron microscope. Its chemical composition and thermal behavior were determined using Fourier-transform infrared and thermal gravimetric analysis, respectively. Chain-like structure formation under an input electric field in ER fluid containing silicone oil and 10 wt% PNMA microspheres was observed directly with optical microscopy. Viscoelastic characteristics of the ER fluid under an input electric field were evaluated with a rotational rheometer. Yield stress with a power exponent of 1.5 was observed, along with typical solid-like property under electric field. Dielectric behavior of the ER suspension measured was also found to be closely associated with its ER behavior.