Miracle-dz/UniFAR-FTUs huggingface dataset:
Biochemical aspects of pathogenic variability in white rust infected Indian mustard

ABSTRACT White rust caused by Albugo candida, an oomycete pathogen, is a devastating disease of Brassica juncea (Indian mustard) worldwide. There is a need to screen virulent white rust isolates to challenge the developed white rust–resistant B. juncea cultivars to screen their resistance potential. The current study explores pathogenic and biochemical response of Indian mustard to white rust isolates collected from three different geographic locations of India. The observations refine our understanding of the disease severity in India. Disease progression and biochemical responses were studied in the cotyledonary as well as true leaf stage of the B. juncea cultivar Varuna at different time points. The biochemical findings highlight the fluctuation of significant biochemical parameters such as total proteins, sugars, and phenols, superoxide dismutase, and hydrogen peroxide during the A. candida infection in B. juncea.
Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis

The goal of this study was to determine the role of resident breast tissue bacteria in breast cancer development. We analyzed breast tissue bacteria in healthy breast tissue and breast tissue donated prior to (precancerous) and after (postcancerous) breast cancer diagnosis. ABSTRACT Microbiota studies have reported changes in the microbial composition of the breast upon cancer development. However, results are inconsistent and limited to the later phases of cancer development (after diagnosis). We analyzed and compared the resident bacterial taxa of histologically normal breast tissue (healthy, H, n = 49) with those of tissues donated prior to (prediagnostic, PD, n = 15) and after (adjacent normal, AN, n = 49, and tumor, T, n = 46) breast cancer diagnosis (n total = 159). DNA was isolated from tissue samples and submitted for Illumina MiSeq paired-end sequencing of the V3-V4 region of the 16S gene. To infer bacterial function in breast cancer, we predicted the functional bacteriome from the 16S sequencing data using PICRUSt2. Bacterial compositional analysis revealed an intermediary taxonomic signature in the PD tissue relative to that of the H tissue, represented by shifts in Bacillaceae, Burkholderiaceae, Corynebacteriaceae, Streptococcaceae, and Staphylococcaceae. This compositional signature was enhanced in the AN and T tissues. We also identified significant metabolic reprogramming of the microbiota of the PD, AN, and T tissue compared with the H tissue. Further, preliminary correlation analysis between host transcriptome profiling and microbial taxa and genes in H and PD tissues identified altered associations between the human host and mammary microbiota in PD tissue compared with H tissue. These findings suggest that compositional shifts in bacterial abundance and metabolic reprogramming of the breast tissue microbiota are early events in breast cancer development that are potentially linked with cancer susceptibility. IMPORTANCE The goal of this study was to determine the role of resident breast tissue bacteria in breast cancer development. We analyzed breast tissue bacteria in healthy breast tissue and breast tissue donated prior to (precancerous) and after (postcancerous) breast cancer diagnosis. Compared to healthy tissue, the precancerous and postcancerous breast tissues demonstrated differences in the amounts of breast tissue bacteria. In addition, breast tissue bacteria exhibit different functions in pre-cancerous and post-cancerous breast tissues relative to healthy tissue. These differences in function are further emphasized by altered associations of the breast tissue bacteria with gene expression in the human host prior to cancer development. Collectively, these analyses identified shifts in bacterial abundance and metabolic function (dysbiosis) prior to breast tumor diagnosis. This dysbiosis may serve as a therapeutic target in breast cancer prevention.
Oral Microbes in Hospital-Acquired Pneumonia: Practice and Research Implications.

BACKGROUND Hospital-acquired pneumonia accounts for 25% of all health care-associated infections and is classified as either ventilator-associated or non-ventilator-associated pneumonia. Hospital-acquired pneumonia most frequently results from aspiration of oropharyngeal secretions into the lungs. Although preventive measures for ventilator-associated pneumonia are well established, few preventive measures exist for the nonventilator type. OBJECTIVE To (1) explore oral microbes associated with ventilator-associated and non-ventilator-associated pneumonia in acutely ill, adult hospitalized patients, and (2) provide evidence-based recommendations for measures to prevent pneumonia in hospitalized patients. METHODS A literature search was conducted using CINAHL, Academic Search Premier, Medline, and the Cochrane Library. RESULTS Ten studies were found that identified common oral microbes in ventilator-associated and non-ventilator-associated pneumonia, including Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus, S aureus, and Streptococcus pneumoniae. Collectively, oral colonization with E coli, P aeruginosa, methicillin-resistant S aureus, and S aureus increased the risk of nonventilator pneumonia. Findings also suggested microaspiration of colonized oral microbes into the lungs. Non-ventilator-associated pneumonia had similar colonization rates of gram-positive and gram-negative bacteria, whereas ventilator-associated pneumonia had greater colonization with gram-negative bacteria. The literature did not indicate a standard of oral care effective in all patient populations. DISCUSSION Oral care is an effective intervention to prevent hospital-acquired pneumonia by reducing pathogenic oral microbial colonization. The impact of different methods and timing of oral care on oral microbes should be further explored, particularly in patients not receiving mechanical ventilation. CONCLUSIONS Findings reaffirm the importance of consistent oral care in hospitalized patients. In addition, practices should be different in patients receiving mechanical ventilation versus patients not receiving ventilation. Results may also provide knowledge to inform future preventive measures for pneumonia, particularly for nonventilator pneumonia.
Decision-making and Risky Behavior in Individuals with Attention-Deficit/Hyperactivity Disorder: A 10-year Longitudinal Study

ABSTRACT We assessed 85 children with Attention-Deficit/Hyperactivity Disorder (ADHD) and 50 typically developing children (TD) (Mage = 11.59, 57.8% boys) with the Hungry Donkey Task (HDT) at baseline and 2-year follow-up, and the Iowa Gambling Task at 10-year follow-up (75% retention). Improvement in the proportion of advantageous choices was observed from two- to 10-year follow-up, but the ADHD group improved less and was outperformed by the TD group at the 10-year follow-up. More advantageous choices on the HDT at baseline predicted less risky behavior at 10-year follow-up. Male sex and more inattentive or externalizing symptoms at baseline predicted more risky behavior.
A Subregion of Insular Cortex Is Required for Rapid Taste-Visceral Integration and Consequent Conditioned Taste Aversion and Avoidance Expression in Rats

Abstract Postingestive signals are important for shaping appetitive and consummatory responses, but the brain mechanisms required to assimilate interoceptive events with those at the frontlines of ingestion (taste-guided) are poorly understood. Here, we investigated whether an insular cortex (IC) region, which receives viscerosensory input, including gustatory, is required to modify taste-elicited consummatory reactions in response to a real-time interoceptive change using a serial taste reactivity (TR) test where the rats’ oromotor and somatic reactions to intraoral (IO) infusions of sucrose were periodically assessed over 45 min following lithium chloride (LiCl) administration. Results showed that neurally-intact rats shifted from an ingestive repertoire to an aversive one as LiCl took effect. Overall, this hedonic shift was delayed in rats with bilateral neurotoxic IC lesions. Rats with greater neuronal loss in posterior gustatory IC displayed fewer aversive reactions to sucrose following this initial LiCl injection. We further assessed whether the failure to integrate interoceptive feedback with ongoing taste-guided behavior impaired acquisition and/or expression of conditioned aversion and/or avoidance in these same rats. Although, as a group, LiCl-injected rats with IC lesions subsequently avoided the sugar in a 48-h two-bottle test, their preference for sucrose was significantly greater than that of the LiCl-injected neurally-intact rats. Overall lesion size, as well as proportion of the posterior gustatory and/or anterior visceral IC were each associated with impaired avoidance. These findings reveal new roles for the posterior gustatory and anterior visceral ICs in multisensory integrative function.
Self-reported outcomes are associated with knee strength and functional symmetry in individuals who have undergone ACL reconstruction with hamstring tendon autograft

Background: The aim of this study was to investigate the relationship between selfreported knee outcomes and limb symmetry indices (LSIs) for hip and knee strength, postural control and single leg hop distance in individuals who had undergone an ACL reconstruction with hamstring tendon autograft (HTG). Methods: A total of 72 participants with a history of unilateral ACL reconstruction with HTG (Mean ± SD age, 28.0 ± 7.6 years; height, 178.4 ± 6.7 cm; mass, 76.9 ± 14.9 kg) were included. IKDC, Lysholm, KOOS and TAMPA scores were used to evaluate selfreported outcomes. Concentric and eccentric knee extensor and flexor strength, and hip abductor strength were measured with an isokinetic dynamometer. Postural control was assessed using the modified star excursion balance test and hop performance using the single leg hop test. The relationships between the LSI scores and the performance measures were explored using the Pearson correlation coefficient. Results: The IKDC, Lysholm and KOOS scores were positively correlated with knee extensor and flexor strength LSIs (p<0.05, r=0.34 to r=0.50), and the TAMPA score was negatively correlated with eccentric extensor LSI (p=0.02, r=-0.34). Single leg hop distance LSI was correlated with IKDC and Lysholm scores (p=0.003, r=0.50; p=0.04, r=0.29) respectively, while postural control was only correlated with the KOOS scores (p<0.001, r=0.51 to r=0.52). No correlation was observed between self-reported outcomes and hip abductor strength (p>0.05). Conclusions: Self-reported scores were correlated with knee extensor and flexor strength, postural control and hop performance in individuals who have undergone ACLR with HTG. Compared to Lysholm and TAMPA scores, KOOS and IKDC scores were more likely to be correlated with performance-based outcomes. Therefore, KOOS and IKDC scores may help clinicians in RTS decision making when there is a limited time to perform extensive evaluations or access equipment.
Comparative study on the mental wellbeing among regularly meditating and non-meditating health care personnel in Sri Lanka

Introduction: Meditation holds the potential for reducing occupation related stress. However, the current evidence base is largely limited to studies from the western countries with insufficient assessment of performance outcomes. Objectives: To examine the differences in the level of mental wellbeing and depression between regularly meditating and non-meditating health care personnel primarily from a Buddhist population Methods: This study was a descriptive comparative study among health care workers (n=60), exploring the moderating effect of having participated in a structured Vipassana informed mindfulness mediation programme. Data were collected after six months of meditation following the first training session. Mental wellbeing and depression were assessed using Primary Mental Health Questionnaire (PMHQ) and Centre for Epidemiological Studies-Depression scale (CES-D) respectively. Independent sample t Test and Wilcoxon Rank Sum Test were performed to determine the differences in the status of metal wellbeing and level of depression between regular meditators and non-meditators. Results: Regular meditators showed higher levels of mental wellbeing compared to non-meditators, indicated by a significant difference in PMHQ values (p=0.001); and significantly lower depression levels according to the CES-D scores (p<0.01). Conclusions: Our findings suggest that Vipassana informed mindfulness meditation is associated with improved mental wellbeing and may have profound practical implications among health care professionals. This method with its simple and low-cost approach needs to be tested in other professional groups, to increase the generalizability and applicability
Evaluation of quality of life in multiple sclerosis patients: impact of fatigue, anxiety and depression

| This study aims to assess the perception of quality of life in patients with multiple sclerosis (MS) and to verify if there is an association with fatigue, anxiety and depression. This is a cross-sectional study with a sample composed by 100 individuals with a diagnosis of MS enrolled in the Centro de Referência para Atenção ao Paciente Portador de Doença Desmielinizante do Hospital da Restauração . The Functional Determination Scale for Quality of Life in Multiple Sclerosis (DEFU), the Modified Fatigue Impact Scale (MFIS-BR), and the Hospital Anxiety (HADS-S) and Depression Scale (HADS-D) were applied. Patients with a Primary progressive clinical form presented worse perception of quality of life (66.90±3.47) when compared to the Secondary progressive (71.65±5.92) and Relapse-remitting (79.00±6.62) forms, with Significant difference (p<0.001). There was a strong positive correlation between the DEFU and the MFIS-BR scores (r=0.84), and a strong negative correlation between DEFU and HADS-A (r=−0.85), and DEFU and HADS-D (r=−0.82). The decrease in the perception of quality of life in patients with multiple sclerosis is more critical in progressive forms of the disease and is associated with the presence of fatigue, depression and anxiety.
Phytoremediation of diesel and spent engine oil contaminated soil using Kariya ( Hildergardia barteri Mast . ) seedlings

Using a completely randomized design experiment, the effect of different levels of diesel and spent engine oil contamination (0 mL/kg, 25 mL/kg, 50 mL/kg and 75 mL/kg of soil) on growth performance (seedling height, collar diameter, number of leaves and biomass accumulation) of Hildergardia barteri seedlings were assessed for twelve weeks. The concentration of Lead, Nickel, Copper and Zinc in the plant parts were also determined. Data were analysed using descriptive and inferential statistics at P<0.05 level of significance. There were significant differences in the effects of diesel and spent engine oil on growth performance of seedlings based on contamination levels. Control treatment had the highest height (92.43±5.13 cm), collar diameter (16.23±0.98 mm), number of leaves (11.21±0.47) and total biomass (33.01±12.79 g). Seedlings exposed to 50 mL/kg treatments had the least height (diesel oil: 78.21±7.22 cm; spent engine oil: 79±6.24 cm); those exposed to 75 mL/kg contamination had the least collar diameter (diesel oil: 8.85±1.05 mm, spent engine oil: 12.02±1.01 mm), while seedlings treated with 50 mL/kg diesel oil (2.21±0.37) and 75 mL/kg spent engine oil (4.79±0.55) had the lowest number of leaves. Heavy metal bio-accumulation ranges were: Lead: 0.17-0.39 mg/kg, Nickel: 0.09–0.45 mg/kg, Copper: 0.54–1.08 mg/kg, Zinc: 0.88–1.58 mg/kg. The ability of the seedlings to survive and bio-accumulate heavy metals indicate the potential phytoremediation capabilities of Hildergardia barteri.
The Design of GLR Control Charts for Process Monitoring

Generalized likelihood ratio (GLR) control charts are investigated for two types of statistical process monitoring (SPC) problems. The first part of this dissertation considers the problem of monitoring a normally distributed process variable when a special cause may produce a time varying linear drift in the mean. The design and application of a GLR control chart for drift detection is investigated. The GLR drift chart does not require specification of any tuning parameters by the practitioner, and has the advantage that, at the time of the signal, estimates of both the change point and the drift rate are immediately available. An equation is provided to accurately approximate the control limit. The performance of the GLR drift chart is compared to other control charts such as a standard CUSUM chart and a CUSCORE chart designed for drift detection. We also compare the GLR chart designed for drift detection to the GLR chart designed for sustained shift detection since both of them require only a control limit to be specified. In terms of the expected time for detection and in terms of the bias and mean squared error of the change-point estimators, the GLR drift chart has better performance for a wide range of drift rates relative to the GLR shift chart when the out-of-control process is truly a linear drift. The second part of the dissertation considers the problem of monitoring a linear functional relationship between a response variable and one or more explanatory variables (a linear profile). The design and application of GLR control charts for this problem are investigated. The likelihood ratio test of the GLR chart is generalized over the regression coefficients, the variance of the error term, and the possible change-point. The performance of the GLR chart is compared to various existing control charts. We show that the overall performance of the GLR chart is much better than other options in detecting a wide range of shift sizes. The existing control charts designed for certain shifts that may be of particular interest have several chart parameters that need to be specified by the user, which makes the design of such control charts more difficult. The GLR chart is very simple to design, as it is invariant to the choice of design matrix and the values of in-control parameters. Therefore there is only one design parameter (the control limit) that needs to be specified. Especially, the GLR chart can be constructed based on the sample size of 1 at each sampling point, whereas other charts cannot be applied. Another advantage of the GLR chart is its built-in diagnostic aids that provide estimates of both the change-point and the values of linear profile parameters.
HOLOCENE CLIMATE CHANGES AND CULTURAL RESPONSES IN CENTRAL ASIAN ARID ZONE

The synthesized regionally-averaged temperature-index curve from the entire Altai Mountains within the Central Asian Arid Zone (CAAZ) shows that the Holocene temperature has sensitively responded to the annual solar irradiance. The synthesized regionally-averaged aridity-index curve exhibits a persistent and slight drying trend during the Holocene in high-elevation regions and the effect of permafrost thawing in high-elevation regions was blamed for the drying trend. The persistent wetting trend in low-elevation regions, together with the induced Holocene precipitation increasing trend, seems to be parallel with the increasing trend of the winter precipitation anomaly in Norway, and both (precipitation index in Altai and winter precipitation anomaly in Norway) were probably causally associated with the AMO-like event trend in the North Atlantic Ocean. Being compensatory or supplementary or contradictory with the aforementioned moisture declining trend in high-elevation regions and with the aforementioned moisture rising trend in low-elevation regions, more recent reports show that the averaged light absorbance (a humification proxy) curve from the southern Altai Mountains within the Central Asian Arid Zone (CAAZ) is a bow-shaped one. That is, the highest light absorbance occurred in the middle Holocene (~8200-~4200 cal. yr BP) when regionally-averaged moisture was the lowest under relatively high-temperature conditions. And, this bow-shaped curve is well corroborated by other proxy data from nearby sites. In addition, superimposed on the bow-shaped curve are several major troughs (i.e., wetter intervals). The troughs definitely occurred in following intervals: ~8600-~8400, ~7800-~7400, ~6500-~5300, ~3800-~3200 and ~1900-~1200 cal. yr BP. The δ13C-signified moisture reconstruction in the Yushenkule Peat within the southern Altai Mountains or Chinese Altai revealed four wet stages (~200 BC-~400 AD, ~600-~800 AD, ~1000-~1250 AD, ~1600-2013 AD) and three dry stages (~400-~600 AD, ~800-~1000 AD, ~1250-~1600 AD) during the past ~2200 years. The moisture variations over the past 2200 years seem to have been generally controlled by the mean annual precipitation (MAP) and somewhat modulated by the summer (JJA) temperature reconstructed from the northern Altai Mountains. In general, the climate (temperature, precipitation, and moisture) of the past ~2000 years was modulated by solar activities.
Detection of Cryptosporidium parvum by polymerase chain reaction

Cryptosporidium parvum is a protozoan parasite responsible for the outbreaks of cryptosporidiosis in humans. Several outbreaks of cryptosporidiosis associated with water and raw food occurred. Polymerase chain reaction (PCR) for direct detection of Cryptosporidium parvum oocysts in water, milk and apple juice was developed. Real-time PCR was able to detect 10 2 oocysts/ml in water, milk and apple juice. The sensitivity of PCR methods was improved using nested PCR, in which second round was modified by real-time PCR. In this case, the detection limit of nested PCR was less that 10 1 oocysts/ml of water, milk and apple juice, which compares favourably with the detection limit of the conventional PCR method - 10 3 oocyst/ml after DNA isolation by chaotropic solid phase extraction used in both cases.
Ligand Binding and Structural Properties of Segments of GABAA Receptor a1 Subunit Overexpressed in Escherichia coli*

The g-aminobutyric acid, type A (GABAA), receptor is the target for numerous therapeutic compounds. In the present study, the Gln–Leu, Gln–Arg, Gln– Arg, and Gln–Glu (numbering of bovine precursor protein) segments of its a1 subunit were overexpressed in Escherichia coli, along with Cys–Leu produced previously, for structural analysis by circular dichroism and ligand binding studies by fluorescence spectroscopy. Results showed that the protein segments were rich in b-sheet structures. Binding of the fluorescent benzodiazepine Bodipy-FL Ro-1986 was evident from fluorescence resonance energy transfer and fluorescence anisotropy measurements. The binding affinity was in the micromolar range. The binding was attributable more to Cys–Leu than to Gln–Glu and was inhibited by known central benzodiazepine site ligands. Three point mutations, Y187A, T234A, and Y237A, were found to perturb protein secondary structures. Studies with the single Trp mutants W198Y and W273Y indicated that Trp was closer to the binding site than Trp.