Miracle-dz/UniFAR-FTUs huggingface dataset:
A mutation in Drosophila Aldolase Causes Temperature-Sensitive Paralysis, Shortened Lifespan, and Neurodegeneration

We describe the characterization of m4, an autosomal recessive, temperature-sensitive paralytic mutant in Drosophila that is associated with shortened lifespan and neurodegeneration. Deletion mapping places the mutation in the gene encoding the glycolytic enzyme, Aldolase. The mutant enzyme contains a single amino acid substitution, which results in decreased steady-state levels of Aldolase with a consequent reduction in adenosine triphosphate (ATP) levels. Transgenic-rescue experiments with a genomic construct containing the entire Aldolase gene confirm that paralysis, reduced lifespan, and neurodegeneration all result from the same mutation. Tissue-specific rescue and RNA interference (RNAi) knockdown experiments indicate that Aldolase function (and presumably glycolysis) is important both in neurons and in glia for normal lifespan and neuronal maintenance over time. Impaired glycolysis in neurons can apparently be rescued in part by glycolytically active glia. However, this rescue may depend on the exact physiological state of the neurons and may also vary in different subsets of neurons. Further studies of m4 and related mutants in Drosophila should help elucidate the connections between energy production and utilization in glia and neurons and lead to better understanding of how metabolic defects impair neuronal function and maintenance.
Sensitivity of serum tissue transglutaminase antibodies for endomysial antibody positive and negative coeliac disease.

BACKGROUND Serum antibodies to tissue transglutaminase (tTGA) are reported to have high sensitivity and specificity for coeliac disease and to correlate closely with endomysial antibodies (EmA). We assessed their performance in a coeliac population with a high proportion of EmA-negative patients, who have been under-represented in previous studies. METHODS We used a commercial ELISA kit to test for IgA class tTGA in sera from a population of 73 untreated coeliac patients with normal serum IgA and a high percentage (19%) EmA-negative, taking 58 patients with normal duodenal biopsies as controls. EmA was measured using indirect immunofluorescence. RESULTS Forty-six (63%) patients with villous atrophy (VA) had both tTGA and EmA. However, when considered separately, sensitivities of tTGA and EmA for VA were similar (75% versus 81%) and both had high specificity (98% versus 97%). As 9 patients were tTGA-positive only and 13 had EmA only, selection of patients for biopsy on the presence of either antibody would have had a sensitivity of 93% (68 of 73), with 5 (7%) patients seronegative for both. CONCLUSION Although the ELISA tTGA assay is more convenient than EmA testing, it offers no advantages in sensitivity or specificity if used in isolation. However, incomplete concordance between EmA and tTGA positivity means that combination screening with both assays offers higher sensitivity, as almost a third of patients have only one antibody. As some coeliac patients with normal serum IgA are negative for both antibodies, biopsies should still be performed in seronegative individuals deemed at high risk for coeliac disease.
Combined feature level and score level fusion Gabor filter-based multiple enrollment fingerprint recognition

Minutiae-based fingerprint matching methods suffer difficulty in automatically extracting all minutiae points due to failure to detect the complete ridge structures of a fingerprint, as well as describing all the local ridge structures as minutiae points. These make matching a difficult process for example, the case where two fingerprints have different numbers of uncaptured minutiae points and hence negatively affecting recognition performance, matching speed and memory consumption. Gabor filter-based matching methods can capture both the local and global details of a fingerprint which qualifies them to be a possible alternative due to their rich features. This paper presents a Combined Feature Level and Score Level Fusion Gabor filter-based approach; the first of the kind to implement a verification multiple enrollment based fingerprint recognition system. We compared the Combined Feature Level and Score Level Fusion Gabor filter-based multiple enrollment fingerprint recognition method with a spectral minutiae-based method using two fingerprint databases; FVC 2000-DB2-A and FVC 2006-DB2-A. Our results indicate that there is a significant percentage increase brought about by the combined feature level and Score Level fusion Gabor filter-based matching approach in comparison to the famous minutiae-based matching approach. The percentage increases in the FVC 2000-DB2-A were 86.45%, 98.01% and 87.82%, while those in the FVC 2006-DB2-A were 79.71%, 97.07% and 85.88% respectively for recognition performance improvement, matching speed improvement and memory consumption reduction. The outstanding results attained from the proposed approach leave no room for deployment in real world multiple enrollment fingerprint recognition applications that require better recognition performance, good matching speed and reduced memory consumption.
Glycogen Synthase Kinase-3β Stabilizes the Interleukin (IL)-22 Receptor from Proteasomal Degradation in Murine Lung Epithelia*

Background: Signaling through the IL-22 axis is essential for immunity, yet there is little known about its regulation. Results: The IL-22R is phosphorylated by GSK-3β that stabilizes the receptor from degradation to control cell repair. Conclusion: Protein stability of IL-22R, modulated by GSK-3β, is a key mechanism impacting cell repair. Significance: Levels of IL-22R protein controlled by GSK-3β may be important for intervention. Signaling through the interleukin (IL)-22 cytokine axis provides essential immune protection in the setting of extracellular infection as part of type 17 immunity. Molecular regulation of IL-22 receptor (IL-22R) protein levels is unknown. In murine lung epithelia, IL-22R is a relatively short-lived protein (t½ ∼1.5 h) degraded by the ubiquitin proteasome under normal unstimulated conditions, but its degradation is accelerated by IL-22 treatment. Lys449 within the intracellular C-terminal domain of the IL-22R serves as a ubiquitin acceptor site as disruption of this site by deletion or site-directed mutagenesis creates an IL-22R variant that, when expressed in cells, is degradation-resistant and not ubiquitinated. Glycogen synthase kinase (GSK)-3β phosphorylates the IL-22R within a consensus phosphorylation signature at Ser410 and Ser414, and IL-22 treatment of cells triggers GSK-3β inactivation. GSK-3β overexpression results in accumulation of IL-22R protein, whereas GSK-3β depletion in cells reduces levels of the receptor. Mutagenesis of IL-22R at Ser410 and Ser414 results in receptor variants that display reduced phosphorylation levels and are more labile as compared with wild-type IL-22R when expressed in cells. Further, the cytoskeletal protein cortactin, which is important for epithelial spreading and barrier formation, is phosphorylated and activated at the epithelial cell leading edge after treatment with IL-22, but this effect is reduced after GSK-3β knockdown. These findings reveal the ability of GSK-3β to modulate IL-22R protein stability that might have significant implications for cytoprotective functions and therapeutic targeting of the IL-22 signaling axis.
Mixed-Effects Modeling and Nonreductive Explanation

This essay considers a mixed-effects modeling practice and its implications for the philosophical debate surrounding reductive explanation. Mixed-effects modeling is a species of the multilevel modeling practice, where a single model incorporates simultaneously two (or even more) levels of explanatory variables to explain a phenomenon of interest. I argue that this practice makes the position of explanatory reductionism held by many philosophers untenable because it violates two central tenets of explanatory reductionism: single-level preference and lower-level obsession.
Compressive sensing based microarray image acquisition

This paper implements Orthogonal Matching Pursuit (OMP) algorithm for reconstruction of Microarray Images based on the compressive sensing paradigm. Gaussian and Bernoulli random patterns are used to capture the scene. A Monte Carlo simulation is performed to calculate the peak signal to noise ratio, relative error and universal quality index of the red and green channels of the image independently. Since images are not sparse but rather compressible, the paper seeks to reconstruct approximately 90 percent of the energy using Discrete Cosine Transform (DCT) as the basis. This paper successfully proposes the use of post processing for quality improvement rather than increase in measurements. Post processing using median filter can account for a reduction of 200 samples per block. The results obtained show that, both the sensing matrices tested are equally good with Bernoulli pattern having the advantage of being sparse.
Turmeric and Curcumin as Topical Agents in Cancer Therapy

An ethanol extract of turmeric (« Curcuma longa ») as well as an ointment of curcumin (its active ingredient) were found to produce remarkable symptomatic relief in patients with external cancerous lesions. Reduction in smell were noted in 90 % of the cases and reduction in itching in almost all cases. Dry lesions were observed in 70 % of the cases, and a small number of patients (10 %) had a reduction in lesion size and pain. In many patients the effect continued for several months. An adverse reaction was noticed in only one of the 62 patients evaluated.
Equilibrium-Informed Trading with Relative Performance Measurement

This article analyzes the informative trading of professional money managers within a rational-expectations equilibrium model in which managers care about their performance relative to their peer group. I find that the existence of uninformed managers causes informed managers with relative performance concerns to trade less informatively, engendering less informative prices. When managers are differentially informed, they need to forecast the average performance based on private signals, and each manager may place more weight on the private signal if the signal provides good information about the average performance. The price aggregates those signals and thus becomes more informative.
Mobile Government Services: An Empirical Analysis of Mobile Government Attractiveness

ABSTRACT The development of modern information and communication technology (ICT) fundamentally impacts the way citizens and governments interact with each other. In this context, mobile ICT is an essential driver for governments around the world to provide public services to citizens and organizations. Against this background, mobile government has significantly increased in importance for practitioners and has become a fruitful field of scientific research. Given the lack of empirical research on the attractiveness of mobile government, this study examines the key determinants of mobile government attractiveness.
First positive reactions to cannabis constitute a priority risk factor for cannabis dependence.

AIM To assess the association between first reactions to cannabis and the risk of cannabis dependence. DESIGN A cross-sectional population-based assessment in 2007. SETTING A campus in a French region (Champagne-Ardennes). PARTICIPANTS A total of 1472 participants aged 18-21 years who reported at least one life-time cannabis consumption, of 3056 students who were screened initially [the Susceptibility Addiction Gene Environment (SAGE) study]. MEASUREMENTS Positive and negative effects of first cannabis consumptions, present cannabis dependence and related risk factors were assessed through questionnaires. FINDINGS The effects of first cannabis consumptions were associated dose-dependently with cannabis dependence at age 18-21 years, both according to the transversal approach of the SAGE study and to the prospective cohort of the Christchurch Health and Development Study (CHDS) assessed at the age of 25 years. Participants of the SAGE study who reported five positive effects of their first cannabis consumption had odds of life-time cannabis dependence that were 28.7 (95% confidence interval: 14.6-56.5) higher than those who reported no positive effects. This association remains significant after controlling for potentially confounding factors, including individual and familial variables. CONCLUSIONS This study suggests an association between positive reactions to first cannabis uses and risk of life-time cannabis dependence, this variable having a central role among, and through, other risk factors.
Comparison of Xe‐CT/CBF and quantitative ECD‐SPELT

We compared stable xenon enhanced X‐ray computed tomography (Xe‐CT) with Technetium‐99m ethylsteinate dimer single‐photon emission computed tomography (ECD‐SPECT) in 12 patients. We evaluated the cerebral blood flow (CBF) values in the territory of the anterior, middle and posterior cerebral artery, and in the thalamus. The CBF values were higher in ECD‐SPECT than in Xe‐CT except for the values of the thalamus. The posterior cerebral artery territory showed a lower correlation and the thalamus had no correlation between two methods. We discussed causes of these differences.
On coordinate systems and the representation of articulatory movements.

Hypothetical examples are used to demonstrate how certain quantitative characterizations of kinematic events can be affected by the placement and orientation of reference axes against which measurements are made. The variation in coordinate systems among a representative sample of recent publications describing speech movements and postures is summarized, and a standard, easily defined coordinate system for future descriptions is proposed. Interpretative benefits associated with the proposed representational standard are noted.
MRI Based Bayesian Personalization of a Tumor Growth Model

The mathematical modeling of brain tumor growth has been the topic of numerous research studies. Most of this work focuses on the reaction-diffusion model, which suggests that the diffusion coefficient and the proliferation rate can be related to clinically relevant information. However, estimating the parameters of the reaction-diffusion model is difficult because of the lack of identifiability of the parameters, the uncertainty in the tumor segmentations, and the model approximation, which cannot perfectly capture the complex dynamics of the tumor evolution. Our approach aims at analyzing the uncertainty in the patient specific parameters of a tumor growth model, by sampling from the posterior probability of the parameters knowing the magnetic resonance images of a given patient. The estimation of the posterior probability is based on: 1) a highly parallelized implementation of the reaction-diffusion equation using the Lattice Boltzmann Method (LBM), and 2) a high acceptance rate Monte Carlo technique called Gaussian Process Hamiltonian Monte Carlo (GPHMC). We compare this personalization approach with two commonly used methods based on the spherical asymptotic analysis of the reaction-diffusion model, and on a derivative-free optimization algorithm. We demonstrate the performance of the method on synthetic data, and on seven patients with a glioblastoma, the most aggressive primary brain tumor. This Bayesian personalization produces more informative results. In particular, it provides samples from the regions of interest and highlights the presence of several modes for some patients. In contrast, previous approaches based on optimization strategies fail to reveal the presence of different modes, and correlation between parameters.
Preservation of Ovarian Function and Minimizing Premature Ovarian Failure during Chemotherapy Using Gonadotropin-Releasing Hormone Analogs

Evaluation of: Del Mastro L, Boni L, Michelotti A et al. Effect of the gonadotropin-releasing hormone analogue triptorelin on the occurrence of chemotherapy-induced early menopause in premenopausal women with breast cancer: a randomized trial. JAMA 306(3), 269–276 (2011). This study is a randomized, open-label, Phase III trial, conducted in 16 Italian centers that enrolled 281 patients between 2003 and 2008. The recruited patients were prospectively and randomly allocated to either chemotherapy alone or combined with monthly triptorelin gonadotropin-releasing hormone analog, started before chemotherapy and repeated every month throughout chemotherapy. The clinical and tumor characteristics of the patients in the control or treatment groups were similar. A total of 12 months after ending chemotherapy, the premature ovarian failure rate was 25.9% in the chemotherapy-alone group versus 8.9% in the chemotherapy and gonadotropin-releasing hormone analog group, an absolute difference of −17% (95% CI: −26 to −7.9%; p < 0.001). The odds ratio for treatment-induced premature ovarian failure was 0.28 (95% CI: 0.14–0.59; p < 0,001). The authors concluded that use of gonadotropin-releasing hormone analog chemotherapy in premenopausal breast cancer patients can significantly reduce the occurrence of chemotherapy-induced early menopause.
Nonreligious coping and religious coping as predictors of expressed emotion in relatives of patients with schizophrenia

Expressed emotion (EE) is a measure of the amount of criticism and emotional over involvement expressed by a key relative towards a relative with a disorder or illness. Research has established that living in a high EE environment, which is characterised by increased levels of critical and emotionally exaggerated communication, leads to a poorer prognosis for patients with a mental illness when compared to low EE environments. Despite evidence that EE is a strong predictor of the course of the illness, there continue to be questions concerning why some family members express excessive levels of high EE attitudes about their mentally ill relatives while others do not. Based on indirect evidence from previous research, the current study tested whether religious and nonreligious coping serve as predictors of EE. A sample of 72 family members of patients with schizophrenia completed an EE interview, along with questionnaires assessing situational nonreligious coping and religious coping. In line with the hypotheses, results indicated that nonreligious coping predicted EE. Specifically, less use of adaptive emotion-focused coping predicted high EE. Also consistent with predictions, maladaptive religious coping predicted high EE above and beyond nonreligious coping.
Expression analysis in response to drought stress in soybean: Shedding light on the regulation of metabolic pathway genes

Metabolomics analysis of wild type Arabidopsis thaliana plants, under control and drought stress conditions revealed several metabolic pathways that are induced under water deficit. The metabolic response to drought stress is also associated with ABA dependent and independent pathways, allowing a better understanding of the molecular mechanisms in this model plant. Through combining an in silico approach and gene expression analysis by quantitative real-time PCR, the present work aims at identifying genes of soybean metabolic pathways potentially associated with water deficit. Digital expression patterns of Arabidopsis genes, which were selected based on the basis of literature reports, were evaluated under drought stress condition by Genevestigator. Genes that showed strong induction under drought stress were selected and used as bait to identify orthologs in the soybean genome. This allowed us to select 354 genes of putative soybean orthologs of 79 Arabidopsis genes belonging to 38 distinct metabolic pathways. The expression pattern of the selected genes was verified in the subtractive libraries available in the GENOSOJA project. Subsequently, 13 genes from different metabolic pathways were selected for validation by qPCR experiments. The expression of six genes was validated in plants undergoing drought stress in both pot-based and hydroponic cultivation systems. The results suggest that the metabolic response to drought stress is conserved in Arabidopsis and soybean plants.
Posttranslational Regulation of Circadian Transcriptional Clock (NPAS2)/BMAL1 Complex by Cryptochromes

Mammalian CLOCK(NPAS2), BMAL1 and CRYPTOCHROMEs are core components of the circadian oscillatory mechanism. The active CLOCK/BMAL1 or NPAS2/BMAL1 complexes regulate expression of numerous genes including two Cryptochromes. The products of these genes, CRY1 and CRY2, in turn repress CLOCK/BMAL1 transcriptional activity by an unknown mechanism. We have examined the effect of CRYPTOCHROMEs on posttranslational modifications and intracellular distribution of endogenous and ectopically expressed CLOCK(NPAS2) and BMAL1 proteins. We found that ectopic coexpression with CRY led to stabilization and nuclear accumulation of unphosphorylated forms of the proteins, which directly correlated with the inhibition of their transcriptional activity. This effect was CRY-specific, as other known repressors of CLOCK/BMAL1 and NPAS2/BMAL1 transcriptional activity were not able to induce similar effects. CRYs had no effect on CLOCK(NPAS2)/BMAL1 complex formation or its ability to bind DNA. Altogether, these results demonstrate that CRYs regulate the functional activity of circadian transcriptional complex at the posttranslational level. Importantly, the posttranslational modifications and intracellular distribution of CLOCK and BMAL1 proteins were critically impaired in the tissues of mice with targeted disruption of both Cry genes, thus confirming the suggested role of CRY in clock function in vivo. Based on these findings we propose a modified model of the circadian transcriptional control, which implies CRY-mediated periodic rotation of transcriptionally active and inactive forms of CLOCK/BMAL1 on the promoter. This model provides mechanistic explanation for previously reported dual functional activity of CLOCK/BMAL1 and highlights the involvement of the circadian system in modulating the organism’s response to various types of genotoxic stress, including chemotherapy and radiation.
Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data

Environmental DNA (eDNA) metabarcoding is increasingly used to study the present and past biodiversity. eDNA analyses often rely on amplification of very small quantities or degraded DNA. To avoid missing detection of taxa that are actually present (false negatives), multiple extractions and amplifications of the same samples are often performed. However, the level of replication needed for reliable estimates of the presence/absence patterns remains an unaddressed topic. Furthermore, degraded DNA and PCR/sequencing errors might produce false positives. We used simulations and empirical data to evaluate the level of replication required for accurate detection of targeted taxa in different contexts and to assess the performance of methods used to reduce the risk of false detections. Furthermore, we evaluated whether statistical approaches developed to estimate occupancy in the presence of observational errors can successfully estimate true prevalence, detection probability and false‐positive rates. Replications reduced the rate of false negatives; the optimal level of replication was strongly dependent on the detection probability of taxa. Occupancy models successfully estimated true prevalence, detection probability and false‐positive rates, but their performance increased with the number of replicates. At least eight PCR replicates should be performed if detection probability is not high, such as in ancient DNA studies. Multiple DNA extractions from the same sample yielded consistent results; in some cases, collecting multiple samples from the same locality allowed detecting more species. The optimal level of replication for accurate species detection strongly varies among studies and could be explicitly estimated to improve the reliability of results.