Miracle-dz/UniFAR-FTUs huggingface dataset:
Nutritional Profile of Phytococktail from Trans-Himalayan Plants

We estimated the nutritive value, vitamin content, amino acid composition, fatty acid content, and mineral profile of a phytococktail comprising sea buckthorn (Hippophae rhamnoides), apricot (Prunus armeniaca), and roseroot (Rhodiola imbricata) from trans-Himalaya. The free vitamin forms in the phytococktail were determined by rapid resolution liquid chromatography/tandem mass spectrometry (RRLC-MS/MS). Vitamin E and B-complex vitamins were detected as the principle vitamins. Reversed-phase high performance liquid chromatography (RP-HPLC) with pre-column derivatization was used for identification and quantification of amino acids. Eight essential and eleven non-essential amino acids were quantified, and the content ranged between 76.33 and 9485.67 µg/g. Among the essential amino acids, L-methionine, L-phenylalanine, L-lysine, L-leucine, and L-histidine were found to be the dominant contributors. We also quantified the fatty acids in the phytococktail by using gas chromatography coupled with a flame ionization detector (GC-FID) with fatty acid methyl esters (FAMEs) derivatization. The analysis revealed the presence of 4 major fatty acids contributing to the total lipid content. Palmitic acid was found to be the rich source of saturated fatty acid (SFA) and constituted ∼31% of the total lipid content. Among the unsaturated fatty acids (UFAs), palmitoleic acid (43.47%), oleic acid (20.89%), and linoleic acid (4.31%) were prominent. The mineral profiling was carried out by inductively coupled plasma optical emission spectrometer (ICP-OES), and it was found to contain a number of important dietary mineral elements. The harsh climatic conditions, difficult terrain, and logistic constraints at high altitude regions of Indian trans-Himalayan cold desert lead to the scarcity of fresh fruits and vegetables. Therefore, the source of multiple vitamins, essential amino acids, fatty acids, and dietary minerals from the phytococktail would provide great health benefit in the stressful environment and could be used as a high value nutritional supplement.
Identification of new channels by systematic analysis of the mitochondrial outer membrane

The mitochondrial outer membrane is essential for communication between mitochondria and the rest of the cell and facilitates the transport of metabolites, ions, and proteins. All mitochondrial outer membrane channels known to date are &bgr;-barrel membrane proteins, including the abundant voltage-dependent anion channel and the cation-preferring protein-conducting channels Tom40, Sam50, and Mdm10. We analyzed outer membrane fractions of yeast mitochondria and identified four new channel activities: two anion-preferring channels and two cation-preferring channels. We characterized the cation-preferring channels at the molecular level. The mitochondrial import component Mim1 forms a channel that is predicted to have an &agr;-helical structure for protein import. The short-chain dehydrogenase-related protein Ayr1 forms an NADPH-regulated channel. We conclude that the mitochondrial outer membrane contains a considerably larger variety of channel-forming proteins than assumed thus far. These findings challenge the traditional view of the outer membrane as an unspecific molecular sieve and indicate a higher degree of selectivity and regulation of metabolite fluxes at the mitochondrial boundary.
Pipelined Query Processing in Coprocessor Environments

Query processing on GPU-style coprocessors is severely limited by the movement of data. With teraflops of compute throughput in one device, even high-bandwidth memory cannot provision enough data for a reasonable utilization. Query compilation is a proven technique to improve memory efficiency. However, its inherent tuple-at-a-time processing style does not suit the massively parallel execution model of GPU-style coprocessors. This compromises the improvements in efficiency offered by query compilation. In this paper, we show how query compilation and GPU-style parallelism can be made to play in unison nevertheless. We describe a compiler strategy that merges multiple operations into a single GPU kernel, thereby significantly reducing bandwidth demand. Compared to operator-at-a-time, we show reductions of memory access volumes by factors of up to 7.5x resulting in shorter kernel execution times by factors of up to 9.5x.
A Method for Detecting Positive Growth Autocorrelation without Marking Individuals

In most ecological studies, within-group variation is a nuisance that obscures patterns of interest and reduces statistical power. However, patterns of within-group variability often contain information about ecological processes. In particular, such patterns can be used to detect positive growth autocorrelation (consistent variation in growth rates among individuals in a cohort across time), even in samples of unmarked individuals. Previous methods for detecting autocorrelated growth required data from marked individuals. We propose a method that requires only estimates of within-cohort variance through time, using maximum likelihood methods to obtain point estimates and confidence intervals of the correlation parameter. We test our method on simulated data sets and determine the loss in statistical power due to the inability to identify individuals. We show how to accommodate nonlinear growth trajectories and test the effects of size-dependent mortality on our method's accuracy. The method can detect significant growth autocorrelation at moderate levels of autocorrelation with moderate-sized cohorts (for example, statistical power of 80% to detect growth autocorrelation ρ 2 = 0.5 in a cohort of 100 individuals measured on 16 occasions). We present a case study of growth in the red-eyed tree frog. Better quantification of the processes driving size variation will help ecologists improve predictions of population dynamics. This work will help researchers to detect growth autocorrelation in cases where marking is logistically infeasible or causes unacceptable decreases in the fitness of marked individuals.
Action Prediction in Younger versus Older Adults: Neural Correlates of Motor Familiarity

Generating predictions during action observation is essential for efficient navigation through our social environment. With age, the sensitivity in action prediction declines. In younger adults, the action observation network (AON), consisting of premotor, parietal and occipitotemporal cortices, has been implicated in transforming executed and observed actions into a common code. Much less is known about age-related changes in the neural representation of observed actions. Using fMRI, the present study measured brain activity in younger and older adults during the prediction of temporarily occluded actions (figure skating elements and simple movement exercises). All participants were highly familiar with the movement exercises whereas only some participants were experienced figure skaters. With respect to the AON, the results confirm that this network was preferentially engaged for the more familiar movement exercises. Compared to younger adults, older adults recruited visual regions to perform the task and, additionally, the hippocampus and caudate when the observed actions were familiar to them. Thus, instead of effectively exploiting the sensorimotor matching properties of the AON, older adults seemed to rely predominantly on the visual dynamics of the observed actions to perform the task. Our data further suggest that the caudate played an important role during the prediction of the less familiar figure skating elements in better-performing groups. Together, these findings show that action prediction engages a distributed network in the brain, which is modulated by the content of the observed actions and the age and experience of the observer.
Construction of Novel Saccharomyces cerevisiae Strains for Bioethanol Active Dry Yeast (ADY) Production

The application of active dry yeast (ADY) in bioethanol production simplifies operation processes and reduces the risk of bacterial contamination. In the present study, we constructed a novel ADY strain with improved stress tolerance and ethanol fermentation performances under stressful conditions. The industrial Saccharomyces cerevisiae strain ZTW1 showed excellent properties and thus subjected to a modified whole-genome shuffling (WGS) process to improve its ethanol titer, proliferation capability, and multiple stress tolerance for ADY production. The best-performing mutant, Z3-86, was obtained after three rounds of WGS, producing 4.4% more ethanol and retaining 2.15-fold higher viability than ZTW1 after drying. Proteomics and physiological analyses indicated that the altered expression patterns of genes involved in protein metabolism, plasma membrane composition, trehalose metabolism, and oxidative responses contribute to the trait improvement of Z3-86. This work not only successfully developed a novel S. cerevisiae mutant for application in commercial bioethanol production, but also enriched the current understanding of how WGS improves the complex traits of microbes.
In Vivo Knockdown of TAK1 Accelerates Bone Marrow Proliferation/Differentiation and Induces Systemic Inflammation

TAK1 (TGF-β Activated Kinase 1) is a MAPK kinase kinase, which activates the p38- and JNK-MAPK and NF-κB pathways downstream of receptors such as Toll-Like-, cytokine- and T-cell and B-cell receptors. Representing such an important node in the pro-inflammatory signal-transduction network, the function of TAK1 has been studied extensively. TAK1 knock-out mice are embryonic lethal, while conditional knock-out mice demonstrated either a pro- or anti-inflammatory function. To study the function of TAK1 protein in the adult immune system, we generated and characterized a transgenic mouse expressing TAK1 shRNA under the control of a doxycycline-inducible promoter. Following treatment of TAK-1 shRNA transgenic mice with doxycycline an effective knockdown of TAK1 protein levels was observed in lymphoid organs and cells in the peritoneal cavity (>50% down regulation). TAK1 knockdown resulted in significant changes in leukocyte populations in blood, bone marrow, spleen and peritoneal cavity. Upon TAK1 knockdown mice demonstrated splenomegaly, signs of systemic inflammation (increased levels of circulating cytokines and increase in cellularity of the B-cell areas and in germinal center development in the follicles) and degenerative changes in heart, kidneys and liver. Not surprisingly, TAK1-Tg mice treated with LPS or anti-CD3 antibodies showed enhanced cytokine/chemokine secretion. Finally, analysis of progenitor cells in the bone marrow upon doxycycline treatment showed increased proliferation and differentiation of myeloid progenitor cells. Given the similarity of the phenotype with TGF-β genetic models, our data suggest that in our model the function of TAK1 in TGF-β signal-transduction is overruling its function in pro-inflammatory signaling.
The Effects of Varying Degree of MWCNT Carboxylation on Bioactivity in Various In Vivo and In Vitro Exposure Models

Functionalization has been shown to alter toxicity of multi-walled carbon nanotube (MWCNT) in several studies. This study varied the degree of functionalization (viz., amount of MWCNT surface carboxylation) to define the relationship between the extent of carboxylation and effects in a variety of in vitro cell models and short-term ex vivo/in vivo particle exposures. Studies with vitamin D3 plus phorbol ester transformed THP-1 macrophages demonstrated that functionalization, regardless of amount, corresponded with profoundly decreased NLRP3 inflammasome activation. However, all MWCNT variants were slightly toxic in this model. Alternatively, studies with A549 epithelial cells showed some varied effects. For example, IL-33 and TNF-α release were related to varying amounts of functionalization. For in vivo particle exposures, autophagy of alveolar macrophages, measured using green fluorescent protein (GFP)- fused-LC3 transgenic mice, increased for all MWCNT tested three days after exposure, but, by Day 7, autophagy was clearly dependent on the amount of carboxylation. The instilled source MWCNT continued to produce cellular injury in alveolar macrophages over seven days. In contrast, the more functionalized MWCNT initially showed similar effects, but reduced over time. Dark-field imaging showed the more functionalized MWCNTs were distributed more uniformly throughout the lung and not isolated to macrophages. Taken together, the results indicated that in vitro and in vivo bioactivity of MWCNT decreased with increased carboxylation. Functionalization by carboxylation eliminated the bioactive potential of the MWCNT in the exposure models tested. The observation that maximally functionalized MWCNT distribute more freely throughout the lung with the absence of cellular damage, and extended deposition, may establish a practical use for these particles as a safer alternative for unmodified MWCNT.
The impacts of community social capital on the life satisfaction of older adults in Hong Kong: the moderator role of intergenerational family capital

Objective: This study examined the moderator role of intergenerational family capital on the relationship between community social capital and life satisfaction of older Chinese adults. Method: The data were derived from a quota sampling of 372 older adults aged 60 and above, who were interviewed at four districts in Hong Kong in 2011. Multiple group analysis was employed to examine the proposed model. Results: For the low family capital group, community social capital was found to be a significant predictor of life satisfaction, even when the well-known covariates were controlled. However, the association between community social capital and life satisfaction was statistically non-significant among the high family capital group. Discussion: The findings highlighted the interplay between community social capital and intergenerational family capital, which supported community social capital replacement theory in understanding the mechanism linking social capital to life satisfaction in older age in a Chinese context. Community social capital can play a compensatory role in maintaining the mental health of older people. It is particularly important for older adults who lack family support and/or suffer from social isolation and loneliness in local communities.
Age-Related Changes following In Vitro Stimulation with Rhodococcus equi of Peripheral Blood Leukocytes from Neonatal Foals

Rhodococcus equi is an intracellular bacterium primarily known as an equine pathogen that infects young foals causing a pyogranulomatuous pneumonia. The molecular mechanisms mediating the immune response of foals to R. equi are not fully elucidated. Hence, global genomic high-throughput tools like gene expression microarrays might identify age-related gene expression signatures and molecular pathways that contribute to the immune mechanisms underlying the inherent susceptibility of foals to disease caused by R. equi. The objectives of this study were 2-fold: 1) to compare the expression profiles at specific ages of blood leukocytes from foals stimulated with virulent R. equi with those of unstimulated leukocytes; and, 2) to characterize the age-related changes in the gene expression profile associated with blood leukocytes in response to stimulation with virulent R. equi. Peripheral blood leukocytes were obtained from 6 foals within 24 hours (h) of birth (day 1) and 2, 4, and 8 weeks after birth. The samples were split, such that half were stimulated with live virulent R. equi, and the other half served as unstimulated control. RNA was extracted and the generated cDNA was labeled with fluorescent dyes for microarray hybridizations using an equine microarray. Our findings suggest that there is age-related differential expression of genes involved in host immune response and immunity. We found induction of genes critical for host immunity against pathogens (MHC class II) only at the later time-points (compared to birth). While it appears that foals up to 8-weeks of age are able to initiate a protective inflammatory response against the bacteria, relatively decreased expression of various other immune-related genes points toward inherent diminished immune responses closer to birth. These genes and pathways may contribute to disease susceptibility in foals if infected early in life, and might thus be targeted for developing preventative or therapeutic strategies.
Effectiveness of Home-Based Cupping Massage Compared to Progressive Muscle Relaxation in Patients with Chronic Neck Pain—A Randomized Controlled Trial

Chronic neck pain is a major public health problem with very few evidence-based complementary treatment options. This study aimed to test the efficacy of 12 weeks of a partner-delivered home-based cupping massage, compared to the same period of progressive muscle relaxation in patients with chronic non-specific neck pain. Patients were randomly assigned to self-directed cupping massage or progressive muscle relaxation. They were trained and asked to undertake the assigned treatment twice weekly for 12 weeks. Primary outcome measure was the current neck pain intensity (0–100 mm visual analog scale; VAS) after 12 weeks. Secondary outcome measures included pain on motion, affective pain perception, functional disability, psychological distress, wellbeing, health-related quality of life, pressure pain thresholds and adverse events. Sixty one patients (54.1±12.7 years; 73.8%female) were randomized to cupping massage (n = 30) or progressive muscle relaxation (n = 31). After treatment, both groups showed significantly less pain compared to baseline however without significant group differences. Significant effects in favor of cupping massage were only found for wellbeing and pressure pain thresholds. In conclusion, cupping massage is no more effective than progressive muscle relaxation in reducing chronic non-specific neck pain. Both therapies can be easily used at home and can reduce pain to a minimal clinically relevant extent. Cupping massage may however be better than PMR in improving well-being and decreasing pressure pain sensitivity but more studies with larger samples and longer follow-up periods are needed to confirm these results. Trial Registration ClinicalTrials.gov NCT01500330
Constraint Neighborhood Projections for Semi-Supervised Clustering

Semi-supervised clustering aims to incorporate the known prior knowledge into the clustering algorithm. Pairwise constraints and constraint projections are two popular techniques in semi-supervised clustering. However, both of them only consider the given constraints and do not consider the neighbors around the data points constrained by the constraints. This paper presents a new technique by utilizing the constrained pairwise data points and their neighbors, denoted as constraint neighborhood projections that requires fewer labeled data points (constraints) and can naturally deal with constraint conflicts. It includes two steps: 1) the constraint neighbors are chosen according to the pairwise constraints and a given radius so that the pairwise constraint relationships can be extended to their neighbors, and 2) the original data points are projected into a new low-dimensional space learned from the pairwise constraints and their neighbors. A CNP-Kmeans algorithm is developed based on the constraint neighborhood projections. Extensive experiments on University of California Irvine (UCI) datasets demonstrate the effectiveness of the proposed method. Our study also shows that constraint neighborhood projections (CNP) has some favorable features compared with the previous techniques.
Surface texture measurement for dental wear applications

The application of surface topography measurement and characterization within dental materials science is highly active and rapidly developing, in line with many modern industries. Surface measurement and structuring is used extensively within oral and dental science to optimize the optical, tribological and biological performance of natural and biomimetic dental materials. Although there has historically been little standardization in the use and reporting of surface metrology instrumentation and software, the dental industry is beginning to adopt modern areal measurement and characterization techniques, especially as the dental industry is increasingly adopting digital impressioning techniques in order to leverage CAD/CAM technologies for the design and construction of dental restorations. As dental treatment becomes increasingly digitized and reliant on advanced technologies such as dental implants, wider adoption of standardized surface topography and characterization techniques will become evermore essential. The dental research community welcomes the advances that are being made in surface topography measurement science towards realizing this ultimate goal.
Overgeneral autobiographical memory and depression in older adults: a systematic review

ABSTRACT Objectives: Overgeneral autobiographical memory (OGM) is a well-researched phenomenon in working age adults with depression. However, the relevance and importance of OGM in older adult depression is not well established. The aim of this review was to synthesise existing literature on OGM and depressive symptoms in older adults under the framework of the Capture and Rumination, Functional Avoidance and Impaired Executive Control (CaR-FA-X) model. Method: Literature searches were conducted using PsychINFO, PubMed and Web of Knowledge. Eighteen articles were reviewed. Results: OGM is elevated in healthy older adults compared to adults of working age, and further elevated in older adults with depression. Evidence supports the role of impaired executive function as a mechanism for OGM in older adults with depression, but no studies measured other components of the CaR-FA-X model (i.e. functional avoidance and rumination). Conclusion: OGM is prevalent in older adults and more so for those with depression; however, there is no clear understanding of the underpinning mechanisms. It is recommended that future research looks at the role of functional avoidance and rumination, and at the use of memory specificity interventions being developed in the working age adult literature.
Histone demethylase KDM5A regulates the ZMYND8–NuRD chromatin remodeler to promote DNA repair

Upon DNA damage, histone modifications are dynamically reshaped to accommodate DNA damage signaling and repair within chromatin. In this study, we report the identification of the histone demethylase KDM5A as a key regulator of the bromodomain protein ZMYND8 and NuRD (nucleosome remodeling and histone deacetylation) complex in the DNA damage response. We observe KDM5A-dependent H3K4me3 demethylation within chromatin near DNA double-strand break (DSB) sites. Mechanistically, demethylation of H3K4me3 is required for ZMYND8–NuRD binding to chromatin and recruitment to DNA damage. Functionally, KDM5A deficiency results in impaired transcriptional silencing and repair of DSBs by homologous recombination. Thus, this study identifies a crucial function for KDM5A in demethylating H3K4 to allow ZMYND8–NuRD to operate within damaged chromatin to repair DSBs.
Composition and magnetic character of nanometre-size Cu precipitates in reactor pressure vessel steels: Implications for nuclear power plant lifetime extension

The sensitivity of positrons to nanometre-size Cu precipitates in Fe alloys has enabled us to apply a novel spin-polarized element-specific method to probe the composition and magnetic character of the precipitates responsible for reactor pressure vessel (RPV) steel embrittlement. The results clearly show that the precipitates are non-magnetic and place an upper limit of about 10at% on their Fe content. The practical implication of this result is that the Cu precipitate contribution to RPV steel embrittlement saturates is not expected to contribute further during lifetime extension. Our study demonstrates that polarized positrons can be used as a powerful probe of the magnetic character of nanoscale materials, even those embedded in a strongly magnetic host.