Miracle-dz/UniFAR-FTUs huggingface dataset:
Developing the Person–Environment Apathy Rating for persons with dementia

Objectives: To develop the Person–Environment Apathy Rating (PEAR) scale that measures environmental stimulation and apathy in persons with dementia and to evaluate its psychometrics. Method: The PEAR scale consists of the PEAR-Environment subscale and PEAR-Apathy subscales. The items were developed via literature review, field testing, expert review, and pilot testing. The construct validity and reliability were examined through video observation. The parent study enrolled 185 institutionalized residents with dementia. For this study, 96 videos were selected from 24 participants. The PEAR-Environment subscale was validated using the Ambiance Scale and the Crowding Index. The PEAR-Apathy subscale was validated using the Neuropsychiatric Inventory (NPI)-Apathy, Passivity in Dementia Scale (PDS), and NPI-Depression. Results: The PEAR-Environment subscale and PEAR-Apathy subscales each consists of six items rated on a 1–4 scale. For validity, the Crowding Index slightly, yet significantly, correlated with the PEAR-Environment subscale total score and three of the individual scores. Ambiance Scale scores, both engaging and soothing, did not correlate with the PEAR-Environment subscale. The PEAR-Apathy highly correlated with the PDS and NPI-Apathy and moderately correlated with the NPI-Depression, suggesting good convergent validity and moderate discriminant validity. For reliability, both environment and apathy subscales demonstrated excellent internal consistency. Although facial expression and eye contact showed moderate inter-rater reliability, all other items showed good to excellent inter-rater and intra-rater reliability. Conclusion: This study has successfully developed the PEAR scale and established its psychometrics based on the compatible scales available. The PEAR scale is the first scale that concurrently assesses apathy and environmental stimulation, and is recommended for use in persons with dementia.
Inhibition of the mitochondrial pyruvate carrier protects from excitotoxic neuronal death

Glutamate is the dominant excitatory neurotransmitter in the brain, but under conditions of metabolic stress it can accumulate to excitotoxic levels. Although pharmacologic modulation of excitatory amino acid receptors is well studied, minimal consideration has been given to targeting mitochondrial glutamate metabolism to control neurotransmitter levels. Here we demonstrate that chemical inhibition of the mitochondrial pyruvate carrier (MPC) protects primary cortical neurons from excitotoxic death. Reductions in mitochondrial pyruvate uptake do not compromise cellular energy metabolism, suggesting neuronal metabolic flexibility. Rather, MPC inhibition rewires mitochondrial substrate metabolism to preferentially increase reliance on glutamate to fuel energetics and anaplerosis. Mobilizing the neuronal glutamate pool for oxidation decreases the quantity of glutamate released upon depolarization and, in turn, limits the positive-feedback cascade of excitotoxic neuronal injury. The finding links mitochondrial pyruvate metabolism to glutamatergic neurotransmission and establishes the MPC as a therapeutic target to treat neurodegenerative diseases characterized by excitotoxicity.
Simultaneous dimension reduction and adjustment for confounding variation

Significance With the advancement in high-throughput technologies, analyzing high-dimensional data has become a common task. Dimension reduction methods have been applied to visualize and identify dominant patterns in high-dimensional data. Confounding factors, commonly observed in high-throughput biological experiments, can affect the performance of these methods, and other downstream analysis. Here, we develop a method by coupling dimension reduction with the adjustment for confounder effects. Our method is able to capture the underlying patterns, as demonstrated by a human brain exon array dataset, a model organism ENCODE RNA sequencing dataset, and simulations. Dimension reduction methods are commonly applied to high-throughput biological datasets. However, the results can be hindered by confounding factors, either biological or technical in origin. In this study, we extend principal component analysis (PCA) to propose AC-PCA for simultaneous dimension reduction and adjustment for confounding (AC) variation. We show that AC-PCA can adjust for (i) variations across individual donors present in a human brain exon array dataset and (ii) variations of different species in a model organism ENCODE RNA sequencing dataset. Our approach is able to recover the anatomical structure of neocortical regions and to capture the shared variation among species during embryonic development. For gene selection purposes, we extend AC-PCA with sparsity constraints and propose and implement an efficient algorithm. The methods developed in this paper can also be applied to more general settings. The R package and MATLAB source code are available at https://github.com/linzx06/AC-PCA.
Association between pre-pregnancy weight status and maternal micronutrient status in early pregnancy

Abstract Objective Inadequate maternal micronutrient status during pregnancy can lead to short- and long-term health risks for mother and offspring. The present study investigated the association between pre-pregnancy weight status and micronutrient status during pregnancy. Design Maternal blood samples were collected during early pregnancy (median 13, interquartile range 12–15 weeks) and were assayed for serum folate, ferritin, Fe and vitamin B12. Regression modelling was used to assess the association between pre-pregnancy underweight, normal weight, overweight and obesity, and micronutrient levels, as well as the odds for deficiencies. Setting The Amsterdam Born Children and their Development (ABCD) study, the Netherlands. Subjects Women with singleton pregnancies without diabetes (n 4243). Results After adjustment for covariates, overweight women and obese women had lower (β; 95 % CI) folate (−1·2; −2·2, −0·2 and −2·3; −4·0, −0·7 nmol/l, respectively) and Fe (−1·7; −2·3, −1·1 and −3·6; −4·7, −2·6 μmol/l, respectively) levels than women with normal weight. Furthermore, overweight women had 6 % (95 % CI −9, −3 %) and obese women had 15 % (−19, −10 %), lower vitamin B12 levels, and obese women had 19 % (6, 32 %) higher ferritin levels, than normal-weight women. Obese women had higher odds (OR; 95 % CI) for folate deficiency (2·03; 1·35, 3·06), Fe deficiency (3·26; 2·09, 5·08) and vitamin B12 deficiency (2·05; 1·41, 2·99) than women with normal weight. Underweight was not associated with micronutrient status. Conclusions During early pregnancy, women with pre-pregnancy overweight and obesity had lower serum folate, Fe and vitamin B12 status. This resulted in increased risk of serum folate, Fe and vitamin B12 deficiencies in women with obesity.
Evaluation Of Various Desensitizing Agents In Reducing Dentin Hypersensitivity Using Scanning Electron Microscope: A Comparative In Vitro Study.

Background Dentine hypersensitivity is a common complaint among patients. The acute, non-spontaneous, short or long lasting nature of pain requires a therapeutic mode which would bring about a significant immediate and lasting relief from dentine hypersensitivity. This study compares the efficacy of Diode Laser and desensitizing toothpastes containing Calcium Sodium Phosphosilicate, Pro-Argin and Hydroxyapatite in occluding dentinal tubules using Scanning electron microscopy. Method A total of 25 dentin blocks were obtained from the roots of the single rooted teeth within one month of their extraction and randomly divided into five groups comprising of four test groups and one control group. The dentin blocks were treated with their respective agents and immersed in synthetic saliva for a period of 7 days. The dentin blocks were evaluated using SEM by previously trained examiners. Results All groups showed an increase in the percentage of tubular occlusion at 0, 24, 72, 120and 168 hours. However Calcium Sodium Phosphosilicate showed a significantly greater (p<0.0001) percentage of tubular occlusion as compared to the other groups after seven days. Conclusion All the experimental agents were effective in occluding dentinal tubules as compared to the control group. The percentage (%) of occluded tubules was found to be highest for Calcium Sodium Phosphosilicate as compared to the other groups over a period of 7 days. However further long term studies more studies are required to come to a conclusion.
Prevalence of type 2 diabetes in the Arab world: impact of GDP and energy consumption.

OBJECTIVE Diabetes Mellitus (DM) is a rapidly growing and most challenging health issue of the 21st century. This study aimed to investigate the prevalence of type-2 DM and its association with Gross Domestic Product (GDP) and energy consumption in the Arab world countries. MATERIALS AND METHODS We identified 88 articles through systematic searches including Institute of Scientific Information (ISI) Web of Science, PubMed and EMBASE databases published between 1980-2015. The related literature was searched by using the keywords including diabetes mellitus, prevalence, incidence, epidemiology of type-2 diabetes mellitus (T2DM), and names of the individual Arab world countries. The articles were selected and investigated for the prevalence of T2DM. No limitations were imposed in the design of the study or publication language. Finally, 50 peer-reviewed publications were included and the rest were excluded. RESULTS Arab world countries with the highest prevalence of T2DM are: Kingdom of Saudi Arabia 31.6%, Oman 29%, Kuwait 25.4%, Bahrain 25.0% and United Arab Emirates 25.0%. The lowest prevalence was found in Mauritania (4.7%) and Somalia (3.9%). The highest prevalence was observed in Gulf Cooperation Council (GCC) countries (25.45%) whilst non-GCC countries had the lowest prevalence (12.69%). The combined mean prevalence of T2DM in both GCC and Non-GCC Arab countries was 16.17%. The prevalence of T2DM was found to be significantly associated with higher Gross Domestic Product (GDP) (p=0.020) and energy consumption (p=0.017). CONCLUSIONS In the Arab world, the countries with the highest prevalence of type 2 diabetes mellitus are: Saudi Arabia, Oman, Kuwait, Bahrain and UAE, whilst the countries with the lowest prevalence are Mauritania and Somalia. This prevalence was significantly associated with high GDP per capita and energy consumption. Arab states must incorporate diabetes preventive policies on a war-footing basis to minimize the burden of the disease.
Ecophysiological and Anatomical Mechanisms behind the Nurse Effect: Which Are More Important? A Multivariate Approach for Cactus Seedlings

Background Cacti establish mostly occurs under the canopy of nurse plants which provide a less stressful micro-environment, although mechanisms underlying this process are unknown. The impact of the combination of light and watering treatments on Opuntia streptacantha (Cactaceae) seedlings was examined. Methods/Principal Findings Ecophysiological [titratable acidity, osmotic potential (‘solute potential’, Ψs), relative growth rate (RGR) and their components (NAR, SLA, and LWR)], anatomical (chloroplast density, chloroplast frequency, and cell area), and environmental [photosynthetic photon flux density (PPFD) and air temperature] sets of variables were analyzed, assessing relationships between them and measuring the intensity of the relationships. Three harvests were carried out at days 15, 30, and 45. Ψs and acidity content were the most important responses for seedling establishment. The main anatomical and environmental variables were chloroplast density and water availability, respectively. Opuntia streptacantha seedlings establish better in the shade-watering treatment, due to higher Ψs and acidity, unaffected chloroplasts, and lower PPFD. In addition, the chloroplasts of cells under high-light and non-watering treatment were clumped closer to the center of the cytosol than those under shade-drought, to avoid photoinhibition and/or to better distribute or utilize the penetrating light in the green plant tissue. Conclusions Opuntia seedlings grow better under the shade, although they can tolerate drought in open spaces by increasing and moving chloroplasts and avoiding drastic decreases in their Ψs. This tolerance could have important implications for predicting the impact of climate change on natural desert regeneration, as well as for planning reforestation-afforestation practices, and rural land uses.
Second generation noninvasive fetal genome analysis reveals de novo mutations, single-base parental inheritance, and preferred DNA ends

Significance We explored the limit of noninvasive prenatal testing by performing genome-wide sequencing of maternal plasma DNA at 195× and 270× haploid genome coverages. Combined with the use of a series of bioinformatics filters, fetal de novo mutations could be detected with a positive predictive value that was two orders of magnitude higher than previously reported. A de novo BRAF mutation was noninvasively detected in a case with cardiofaciocutaneous syndrome. The maternal inheritance of the fetus could be ascertained on a genome-wide level without the use of maternal haplotypes, hence greatly increasing the resolution of such analysis. Finally, we showed that certain genomic locations were overrepresented at the ends of plasma DNA fragments with fetal or maternal selectivity. Plasma DNA obtained from a pregnant woman was sequenced to a depth of 270× haploid genome coverage. Comparing the maternal plasma DNA sequencing data with the parental genomic DNA data and using a series of bioinformatics filters, fetal de novo mutations were detected at a sensitivity of 85% and a positive predictive value of 74%. These results represent a 169-fold improvement in the positive predictive value over previous attempts. Improvements in the interpretation of the sequence information of every base position in the genome allowed us to interrogate the maternal inheritance of the fetus for 618,271 of 656,676 (94.2%) heterozygous SNPs within the maternal genome. The fetal genotype at each of these sites was deduced individually, unlike previously, where the inheritance was determined for a collection of sites within a haplotype. These results represent a 90-fold enhancement in the resolution in determining the fetus’s maternal inheritance. Selected genomic locations were more likely to be found at the ends of plasma DNA molecules. We found that a subset of such preferred ends exhibited selectivity for fetal- or maternal-derived DNA in maternal plasma. The ratio of the number of maternal plasma DNA molecules with fetal preferred ends to those with maternal preferred ends showed a correlation with the fetal DNA fraction. Finally, this second generation approach for noninvasive fetal whole-genome analysis was validated in a pregnancy diagnosed with cardiofaciocutaneous syndrome with maternal plasma DNA sequenced to 195× coverage. The causative de novo BRAF mutation was successfully detected through the maternal plasma DNA analysis.
Elastodynamic analysis of anisotropic elastic solid with multiple nanocavities

Abstract 2D elastodynamic problem for a finite elastic anisotropic solid with nanosized cavities is worked out in this paper. The solid under plane strain conditions is subjected to time-harmonic load. The developed computational tool for the steady-state problem is boundary integral equation method based on frequency-dependent fundamental solutions for elastic anisotropic continuum obtained by Radon transform. Accuracy of the dynamic stress concentration factor and displacement components is proven by comparisons with existing in the literature analytical solution and with the results obtained using commercial finite element package. In addition, a parametric study is performed in order to examine the sensitivity of the dynamic stress concentration field to the geometrical configuration of multiple cavities, to the characteristics of the surface elastic properties, to the type of orthotropy and to the dynamic interaction between cavities.
Analysis of self-cleaning and float glass : a comparative study of pollution on the glass surfaces under real life conditions

In order to investigate the self-cleaning efficiency two commercial self-cleaning TiO 2 coated glasses and an uncoated float (reference) glass were exposed to the environment under two different sets of experimental conditions. The first experiment involved the exposure of glass panels in unsheltered conditions for 16 months in France and England. Macroscopic observations were performed monthly by panels often end users and a visual ranking of the samples was given according to standardised guidelines. Haze values were also measured by means of a haze meter. A good correlation between the haze and the visual evaluation of samples was obtained. In general, a lower level of soiling was detected on the self-cleaning glasses. The second exposure experiment was carried out in Paris (France); samples were exposed to sheltered and unsheltered conditions and a survey of particulate pollutants was also performed by means of air filtration. Microscopic characterisation of the deposit was performed by means of different analytical techniques. The relative abundance of deposited carbonaceous species as compared to sulphates, and nitrates was determined as well as the nature of the organic compounds deposited on the glass samples. Frequent dry droplets, observed on the traditional float glass samples, demonstrate the hydrophobicity of the glass surface due to the presence of organic contaminants, while different patterns of dirt deposits were identified on the hydrophilic self-cleaning surfaces. Inorganic salts and organic compounds were identified as the 'glue' that hampers the removal of the particles by rain.
Effects of Different Grazing Intensities on Grassland Production in China: A Meta-Analysis

Background Grazing is one of the main grassland disturbances in China, and it is essential to quantitatively evaluate the effects of different grazing intensities on grassland production for grassland carbon budget and sustainable use. Methods A meta-analysis was conducted to reveal general response patterns of grassland production to grazing in China. We used weighted log response ratio to assess the effect size, and 95% confidence intervals to give a sense of the precision of the estimate. Grazing effects were estimated as a percentage change relative to control (%). Results A total of 48 studies, including 251 data sets, were included in the meta-analysis. Grazing significantly decreased total biomass by 58.34% (95% CI: −72.04%∼−37.94%, CI: Confidence Interval), increased root/shoot ratio by 30.58% and decreased litter by 51.41% (95% CI: −63.31%∼−35.64%). Aboveground biomass and belowground biomass decreased significantly by 42.77% (95% CI: −48.88%∼−35.93%) and 23.13% (95% CI: −39.61%∼−2.17%), respectively. However, biomass responses were dependent on grazing intensity and environmental conditions. Percentage changes in aboveground biomass to grazing showed a quadratic relationship with precipitation in light grazing intensity treatment and a linear relationship in moderate and heavy grazing intensity treatment, but did not change with temperature. Grazing effects on belowground biomass did not change with precipitation or temperature. Compared to the global average value, grazing had greater negative effects on grassland production in China. Conclusions Grazing has negative effects on grassland biomass and the grazing effects change with environmental conditions and grazing intensity, therefore flexible rangeland management tactics that suit local circumstances are necessary to take into consideration for balancing the demand of grassland utilization and conservation.
Lipid-Lowering Therapy With Ezetimibe Decreases Spontaneous Atherothrombotic Occlusions in a Rabbit Model of Plaque Erosion: A Role of Serum Oxysterols

Objective— Plaque erosion is increasing its importance as one of the mechanisms of acute coronary syndromes in this statin era. However, the clinical efficacy of currently used lipid-lowering agents in the prevention of thrombotic complications associated with plaque erosion has not been clarified. Therefore, we examined the therapeutic effects of ezetimibe or rosuvastatin monotherapy on spontaneous atherothrombotic occlusion. Approach and Results— Femoral arteries of Japanese white rabbits, fed a high-cholesterol diet, were injured by balloon catheter, and then angiotensin II was continuously administrated. In 94% of these arteries, spontaneous thrombotic occlusions were observed after 5 weeks (median) of balloon injury. Histochemical analyses indicated that the injured arteries had similar pathological features to human plaque erosions; (1) spontaneous thrombotic occlusion, (2) lack of endothelial cells, and (3) tissue factor expression in vascular smooth muscle cells. Ezetimibe (1.0 mg/kg per day), but not rosuvastatin (0.6 mg/kg per day), significantly decreased thrombotic occlusion of arteries accompanied with accelerated re-endothelialization and the decreases of serum oxysterols despite the comparable on-treatment serum cholesterol levels. The 7-ketocholesterol inhibited the migration of human umbilical vein endothelial cells. Both 7-ketocholesterol and 27-hydroxycholesterol increased tissue factor expression in cultured rat vascular smooth muscle cells. Tissue factor expression was also induced by serum from vehicle- or rosuvastatin-treated rabbits, but the induction was attenuated with serum from ezetimibe-treated rabbits. Conclusions— We have established a novel rabbit model of spontaneous atherothromobotic occlusion without plaque rupture that is feasible to test the therapeutic effects of various pharmacotherapies. Ezetimibe may decrease atherothrombotic complications after superficial plaque erosion by reducing serum oxysterols.
High-Resolution NMR Reveals Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane

Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16), an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the 13C, 15N, 2H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, Cα, and Cβ chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T 1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein.