Miracle-dz/UniFAR-FTUs huggingface dataset:
HYPOXIA INDUCES APOPTOSIS BY CASPASE ACTIVATION ACCOMPANYING CYTOCHROME C RELEASE FROM MITOCHONDRIA IN MC3T3E1 OSTEOBLASTS. p38 MAPK IS RELATED IN HYPOXIA-INDUCED APOPTOSIS

The aim of this study is to elucidate the possible mechanism of apoptosis in response to hypoxia in MC3T3E1 osteoblasts. MC3T3E1 osteoblasts under hypoxic conditions (2% oxygen) resulted in apoptosis in a time-dependent manner estimated by DNA fragmentation assay and nuclear morphology stained with fluorescent dye, Hoechst 33258. Pretreatment with Z-VAD-FMK, a pan-caspase inhibitor, or Z-DEVD-CHO, a specific caspase-3 inhibitor, completely suppressed the DNA ladder in response to hypoxia. An increase in caspase-3-like protease (DEVDase) activity was observed during apoptosis, but no caspase-1 activity (YVADase) was detected. To confirm what caspases are involved in apoptosis, western blot analysis was performed using anticaspase-3 or -6 antibody. The 10-kDa protein, corresponding to the active products of caspase-3 and the 10-kDA protein of the active protein of caspase-6 were generated in hypoxia-challenged cells in which processing of the full length form of caspase-3 and -6 was evident. With a time course similar to this caspase-3 and -6 activation was evident, hypoxic stress caused the cleavage of lamin A, typical of caspase-6 activity. In addition, the stress elicited the release of cytochrome c into the cytosol during apoptosis. Furthermore, we have observed that pre-treatment with SB203580, a selective p38 MAP kinase (p38 MAPK) inhibitor, attenuated the hypoxia-induced apoptosis. The addition of SB203580 suppressed caspase-3 and -6-like protease activity by hypoxia up to 50%. In contrast, PD98059 had no effect on the hypoxia-induced apoptosis. To confirm the involvement of MAP kinase, JNK/SAPK, ERK, or p38 kinase assay was performed. Although p38 MAPK was activated in response to hypoxic treatment, the other MAP kinase -JNK/SAPK or ERK- was not or modestly activated. These results suggest that p38 MAPK positively regulates hypoxia-induced apoptosis in MC3T3E1 osteoblasts.
Auditory Spatial Recalibration in Congenital Blind Individuals

Blind individuals show impairments for auditory spatial skills that require complex spatial representation of the environment. We suggest that this is partially due to the egocentric frame of reference used by blind individuals. Here we investigate the possibility of reducing the mentioned auditory spatial impairments with an audio-motor training. Our hypothesis is that the association between a motor command and the corresponding movement's sensory feedback can provide an allocentric frame of reference and consequently help blind individuals in understanding complex spatial relationships. Subjects were required to localize the end point of a moving sound before and after either 2-min of audio-motor training or a complete rest. During the training, subjects were asked to move their hand, and consequently the sound source, to freely explore the space around the setup and the body. Both congenital blind (N = 20) and blindfolded healthy controls (N = 28) participated in the study. Results suggest that the audio-motor training was effective in improving space perception of blind individuals. The improvement was not observed in those subjects that did not perform the training. This study demonstrates that it is possible to recalibrate the auditory spatial representation in congenital blind individuals with a short audio-motor training and provides new insights for rehabilitation protocols in blind people.
The Impact of Mislabelling on the Performance and Interpretation of Defect Prediction Models

The reliability of a prediction model depends on the quality of the data from which it was trained. Therefore, defect prediction models may be unreliable if they are trained using noisy data. Recent research suggests that randomly-injected noise that changes the classification (label) of software modules from defective to clean (and vice versa) can impact the performance of defect models. Yet, in reality, incorrectly labelled (i.e., mislabelled) issue reports are likely non-random. In this paper, we study whether mislabelling is random, and the impact that realistic mislabelling has on the performance and interpretation of defect models. Through a case study of 3,931 manually-curated issue reports from the Apache Jackrabbit and Lucene systems, we find that: (1) issue report mislabelling is not random; (2) precision is rarely impacted by mislabelled issue reports, suggesting that practitioners can rely on the accuracy of modules labelled as defective by models that are trained using noisy data; (3) however, models trained on noisy data typically achieve 56%-68% of the recall of models trained on clean data; and (4) only the metrics in top influence rank of our defect models are robust to the noise introduced by mislabelling, suggesting that the less influential metrics of models that are trained on noisy data should not be interpreted or used to make decisions.
Nerve conduction studies in diabetic neuropathy

To the Editor: The article by Chaudhry et al [1] addresses the reliability of nerve conduction studies (NCS) in patients with diabetic neuropathy. Perhaps the authors would consider providing additional information regarding the coefficient of variation, the standard deviation/mean, of their findings. Unlike ANOVA, the coefficient of variation can be readily understood by nonstatisticians and easily performed. It describes reliability in absolute numbers suitable …
The Effect of Epidermal Structures on Leaf Spectral Signatures of Ice Plants (Aizoaceae)

Epidermal structures (ES) of leaves are known to affect the functional properties and spectral responses. Spectral studies focused mostly on the effect of hairs or wax layers only. We studied a wider range of different ES and their impact on spectral properties. Additionally, we identified spectral regions that allow distinguishing different ES. We used a field spectrometer to measure ex situ leaf spectral responses from 350 nm–2500 nm. A spectral library for 25 species of the succulent family Aizoaceae was assembled. Five functional types were defined based on ES: flat epidermal cell surface, convex to papillary epidermal cell surface, bladder cells, hairs and wax cover. We tested the separability of ES using partial least squares discriminant analysis (PLS-DA) based on the spectral data. Subsequently, variable importance (VIP) was calculated to identify spectral regions relevant for discriminating our functional types (classes). Classification performance was high, with a kappa value of 0.9 indicating well-separable spectral classes. VIP calculations identified six spectral regions of increased importance for the classification. We confirmed and extended previous findings regarding the visible-near-infrared spectral region. Our experiments also confirmed that epidermal leaf traits can be classified due to clearly distinguishable spectral signatures across species and genera within the Aizoaceae.
New Genes from Old: Redeployment of dUTPase by Herpesviruses

ABSTRACT Published work (D. J. McGeoch, Nucleic Acids Res. 18:4105-4110, 1990; J. E. McGeehan, N. W. Depledge, and D. J. McGeoch, Curr. Protein Peptide Sci. 2:325-333, 2001) has indicated that evolution of dUTPase in the class of herpesviruses that infect mammals and birds involved capture of a host gene followed by a duplication event that resulted in a coding region comprising two fused dUTPase domains. Some of the conserved residues required for enzyme activity were then lost, resulting in a dUTPase containing a single active site with different elements contributed by each half of the protein. Further conserved residues were lost in one subfamily (the Betaherpesvirinae), yielding a protein that is related to herpesvirus dUTPases but has a different and as yet unrecognized function. Evidence from sequence similarities and structural predictions now indicates that several additional genes were derived from the herpesvirus dUTPase gene, probably by duplication. These are UL31, UL82, UL83, and UL84 in human cytomegalovirus (and counterparts in other members of the Betaherpesvirinae) and ORF10 and ORF11 in human herpesvirus 8 (and counterparts in other members of the Gammaherpesvirinae). The findings clarify the evolutionary history of these genes and provide novel insights for structural and functional studies.
Managing student transition from conventional to open schooling: a case study of Namibia

The provision of school equivalency programme through Open and Distance Learning (ODL) has gained momentum in the 21 st century through the establishment of open schools. The latter have now become the model of choice for young people and adults who do not want to pursue their secondary education journey through the conventional delivery system. Moreover, shrinking financial resources have made it impossible for governments, especially in the developing world to expand education through the conventional system. Although open schools have made progress in increasing access, low throughput rates and high dropout rates remain the key challenges. The purpose of this study was to explore the experiences and perceptions of learners when migrating from the conventional school system to ODL in general, and to the Namibian College of Open Learning (NAMCOL) in particular. The study mainly focused on the senior secondary learners who transferred from the formal schools to NAMCOL to upgrade their grades. Moore’s (1993) theory of transactional distance and Tinto’s (1997a) theory of academic and social integration were used as the reference theoretical framework. A multi method research design was applied in data collection. The results of the study identified a gap between the learners’ expectations and the high ODL expectations and its demands. The learners w ho participated in the study displayed a marginal understanding of the ODL mode of delivery. The study established certain factors that impede or accelerate the integration process and also identified technology mediated services as well as capacity building for staff as measures to facilitate learner integration in the ODL mode of delivery. The study reaffirms that meeting learners’ academic, social and psychological needs are important for successful learner integration. The findings have implications for policy makers, ODL practitioners and learners on the development of the most effective measures of increasing learner integration into open schools.
Mesh Adaptive Direct Search Algorithms for Constrained Optimization

This paper addresses the problem of minimization of a nonsmooth function under general nonsmooth constraints when no derivatives of the objective or constraint functions are available. We introduce the mesh adaptive direct search (MADS) class of algorithms which extends the generalized pattern search (GPS) class by allowing local exploration, called polling, in an asymptotically dense set of directions in the space of optimization variables. This means that under certain hypotheses, including a weak constraint qualification due to Rockafellar, MADS can treat constraints by the extreme barrier approach of setting the objective to infinity for infeasible points and treating the problem as unconstrained. The main GPS convergence result is to identify limit points $\hat{x}$, where the Clarke generalized derivatives are nonnegative in a finite set of directions, called refining directions. Although in the unconstrained case, nonnegative combinations of these directions span the whole space, the fact that there can only be finitely many GPS refining directions limits rigorous justification of the barrier approach to finitely many linear constraints for GPS. The main result of this paper is that the general MADS framework is flexible enough to allow the generation of an asymptotically dense set of refining directions along which the Clarke derivatives are nonnegative. We propose an instance of MADS for which the refining directions are dense in the hypertangent cone at $\hat{x}$ with probability 1 whenever the iterates associated with the refining directions converge to a single $\hat{x}$. The instance of MADS is compared to versions of GPS on some test problems. We also illustrate the limitation of our results with examples.
Method for Rapidly Assessing the Overtopping Risk of Bridges Due to Flooding over a Large Geographic Region

Hydraulic events are a leading cause of bridge failures. While these hydraulic events are accounted for in bridge design, changing environmental and land use conditions require continual updating of this risk. For example, after a bridge has been constructed, streamflow can change in unanticipated ways as a result of land use changes, geomorphic changes, and climate change. The objective of this research was to create a screening method able to quickly and inexpensively estimate overtopping risk across a collection of bridges based on the current streamflow conditions. The method uses a geographic information system, nationally available and standardized datasets, and recent regression equations to quantify bridge vulnerability to overtopping for flooding with varying return periods. This screening method could also be used to assist decision makers in updating the Waterway Adequacy field in the National Bridge Inventory, which indicates the overtopping risk of bridges. The method was applied to a portion of the Hampton Roads region of Virginia, United States that includes 475 bridges. The results of the analysis, when combined with transportation data for bridges, aid decision makers to assign further resources to complete more detailed analyses of bridges identified as being at risk for overtopping.
Interpretable Semantic Vectors from a Joint Model of Brain- and Text- Based Meaning

Vector space models (VSMs) represent word meanings as points in a high dimensional space. VSMs are typically created using a large text corpora, and so represent word semantics as observed in text. We present a new algorithm (JNNSE) that can incorporate a measure of semantics not previously used to create VSMs: brain activation data recorded while people read words. The resulting model takes advantage of the complementary strengths and weaknesses of corpus and brain activation data to give a more complete representation of semantics. Evaluations show that the model 1) matches a behavioral measure of semantics more closely, 2) can be used to predict corpus data for unseen words and 3) has predictive power that generalizes across brain imaging technologies and across subjects. We believe that the model is thus a more faithful representation of mental vocabularies.
Tlx3 Function in the Dorsal Root Ganglion is Pivotal to Itch and Pain Sensations

Itch, a sensation eliciting a desire to scratch, is distinct from but not completely independent of pain. Inspiring achievements have been made in the characterization of itch-related receptors and neurotransmitters, but the molecular mechanisms controlling the development of pruriceptors remain poorly understood. Here, our RNAseq and in situ hybridization data show that the transcription factor Tlx3 is required for the expression of a majority of itch-related molecules in the dorsal root ganglion (DRG). As a result, Tlx3F/F;Nav1.8-cre mice exhibit significantly attenuated acute and dry skin-induced chronic itch. Furthermore, our study indicates that TRPV1 plays a pivotal role in the chronic itch evoked by dry skin and allergic contact dermatitis (ACD). The mutants also display impaired response to cold and inflammatory pain and elevated response to capsaicin, whereas the responses to acute mechanical, thermal stimuli and neuropathic pain remain normal. In Tlx3F/F;Nav1.8-cre mice, TRPV1 is derepressed and expands predominantly into IB4+ non-peptidergic (NP) neurons. Collectively, our data reveal a molecular mechanism in regulating the development of pruriceptors and controlling itch and pain sensations.
Effects of Pre-treatments and Drying Methods on Chemical Composition, Microbial and Sensory Quality of Orange-Fleshed Sweet Potato Flour and Porridge

This study was aimed to evaluate the effect of pre-treatments and drying methods on the chemical composition (proximate composition, β-carotene content and phytochemicals), functional properties, microbial and sensory of orange-fleshed sweet potato flour and porridge. Physical (blanching) and chemical (1% salt, 0.5% citric acid solution soaked for 20 min) of the sliced OFSP followed by drying (sun, solar and fluidized bed dried) with complete randomized design for chemical composition, functional properties, and microbial load analysis and randomized complete block design was used for sensory analysis. The moisture (4 - 8%), protein (4 - 8%), fat (0.9 - 2.5), ash (4 - 8%), fiber (3.5 - 7%), total carbohydrates (80 - 84%) measured as a function of treatment and drying. The energy contribution of OFSP was determined by difference of the proximate excluding the fiber (352.9-365.6kcal/100g). The salt treated and FB dried had significantly lowest moisture content and highest ash content, citric acid treated and FB dried had significantly highest protein content and gross energy, control and FB dried had significantly highest fiber content, control and sun dried had significantly highest fat content and blanched and FB dried had significantly highest total carbohydrates. The β-carotene (82 -127μg/g), tannin (74 -108mg/100g) and phytate content (51 - 98mg/100g) was measured. Blanched and FB dried was observed better in retention of β-carotene and reduction of phytochemicals (tannin and phytate). The salt treated and FB dried was measured increment with WAC, viscosity and lowest LGC, blanched and FB had highest OAC and high bulk density in the control. The microbial analysis showed OFSP porridge within microbiological acceptable limit. The sensory acceptability showed OFSP was accepted in all sensory attributes. In conclusion, the blanching and FB drying techniques were the best approach in retaining the nutrients.
Contemporary outcomes after surgical aortic valve replacement with bioprostheses and allografts: a systematic review and meta-analysis†

Many observational studies have reported outcomes after surgical aortic valve replacement (AVR), but there are no recent systematic reviews and meta-analyses including all available bioprostheses and allografts. The objective of this study is to provide a comprehensive and up-to-date overview of the outcomes after AVR with bioprostheses and allografts reported in the last 15 years. We conducted a systematic literature review (PROSPERO register: CRD42015017041) of studies published between 2000–15. Inclusion criteria were observational studies or randomized controlled trials reporting on outcomes of AVR with bioprostheses (stented or stentless) or allografts, with or without coronary artery bypass grafting (CABG) or valve repair procedure, with study population size n ≥ 30 and mean follow-up length ≥5 years. Fifty-four bioprosthesis studies and 14 allograft studies were included, encompassing 55 712 and 3872 patients and 349 840 and 32 419 patient-years, respectively. We pooled early mortality risk and linearized occurrence rates of valve-related events, reintervention and late mortality in a random-effects model. Sensitivity, meta-regression and subgroup analyses were performed to investigate the influence of outliers on the pooled estimates and to explore sources of heterogeneity. Funnel plots were used to investigate publication bias. Pooled early mortality risks for bioprostheses and allografts were 4.99% (95% confidence interval [CI], 4.44–5.62) and 5.03% (95% CI, 3.61–7.01), respectively. The late mortality rate was 5.70%/patient-year (95% CI, 4.99–5.62) for bioprostheses and 1.68%/patient-year (95% CI, 1.23–2.28) for allografts. Pooled reintervention rates for bioprostheses and allografts were 0.75%/patient-year (95% CI, 0.61–0.91) and 1.87%/patient-year (95% CI, 1.52–2.31), respectively. There was substantial heterogeneity in most outcomes. Meta-regression analyses identified covariates that could explain the heterogeneity: implantation period, valve type, patient age, gender, pre-intervention New York Heart Association class III/IV, concomitant CABG, study design and follow-up length. There is possible publication bias in all outcomes. This comprehensive systematic review and meta-analysis provides an overview of the outcomes after AVR with bioprostheses and allografts reported during the last 15 years. The results of this study can support patients and doctors in the prosthetic valve choice and can be used in microsimulation models to predict patient outcomes and estimate the cost-effectiveness of AVR with bioprostheses or allografts compared with current and future heart valve prostheses.
Skin Color Detecting Based on Clustering in YCgCb Color Space Under Complicated Background

As everyone knows nature exists a lot of colors similar as skin color, such as sand, sand beach, soil, stone, cement road, wood, bole, filemot leaves, and so on. The above mentioned things are similar to skin color and exist largely in our images. So they bring many difficulties to detect human face color. And the problem hasn’t been solved completely. In this paper we present a circular fitting of distribution of Cg-Cb color space. And we combine a red Gaussian model in Cg-Cb color space aim to make the method of circular model more ideal. The experimental results show that our method can wipe off most of the non-skin color and reserve the skin color perfectly under complicated background than many former methods.
Moderating diets to feed the future

Population growth, dietary changes, and increasing biofuel use are placing unprecedented pressure on the global food system. While this demand likely cannot be met by expanding agricultural lands, much of the world's cropland can attain higher crop yields. Therefore, it is important to examine whether increasing crop productivity to the maximum attainable yield (i.e., yield gap closure) alone can substantially improve food security at global and national scales. Here we show that closing yield gaps through conventional technological development (i.e., fertilizers and irrigation) can potentially meet future global demand if diets are moderated and crop‐based biofuel production is limited. In particular, we find that increases in dietary demand will be largely to blame should crop production fall short of demand. In converting projected diets to a globally adequate diet (3000 kcal/cap/d; 20% animal kcal) under current agrofuel use, we find that 1.8–2.6 billion additional people can be fed in 2030 and 2.1–3.1 billion additional people in 2050, depending on the extent to which yields can improve in those periods. Therefore, the simple combination of yield gap closure and moderating diets offers promise for feeding the world's population but only if long‐term sustainability is the focus.