Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep Sleep and Parietal Cortex Gene Expression Changes Are Related to Cognitive Deficits with Age

Background Age-related cognitive deficits negatively affect quality of life and can presage serious neurodegenerative disorders. Despite sleep disruption's well-recognized negative influence on cognition, and its prevalence with age, surprisingly few studies have tested sleep's relationship to cognitive aging. Methodology We measured sleep stages in young adult and aged F344 rats during inactive (enhanced sleep) and active (enhanced wake) periods. Animals were behaviorally characterized on the Morris water maze and gene expression profiles of their parietal cortices were taken. Principal Findings Water maze performance was impaired, and inactive period deep sleep was decreased with age. However, increased deep sleep during the active period was most strongly correlated to maze performance. Transcriptional profiles were strongly associated with behavior and age, and were validated against prior studies. Bioinformatic analysis revealed increased translation and decreased myelin/neuronal pathways. Conclusions The F344 rat appears to serve as a reasonable model for some common sleep architecture and cognitive changes seen with age in humans, including the cognitively disrupting influence of active period deep sleep. Microarray analysis suggests that the processes engaged by this sleep are consistent with its function. Thus, active period deep sleep appears temporally misaligned but mechanistically intact, leading to the following: first, aged brain tissue appears capable of generating the slow waves necessary for deep sleep, albeit at a weaker intensity than in young. Second, this activity, presented during the active period, seems disruptive rather than beneficial to cognition. Third, this active period deep sleep may be a cognitively pathologic attempt to recover age-related loss of inactive period deep sleep. Finally, therapeutic strategies aimed at reducing active period deep sleep (e.g., by promoting active period wakefulness and/or inactive period deep sleep) may be highly relevant to cognitive function in the aging community.
Prevalence and Distribution of Schistosomiasis in Afder and Gode Zone of Somali Region, Ethiopia

Background: There is no recent information about the prevalence and distribution of schistosomiasis in the Somali national regional state of Ethiopia. Ethiopia launched the national integrated neglected tropical diseases (NTDs) Master Plan in June 2013. The Master Plan identified mapping NTDs as a prerequisite for launching control programs. Therefore it is important to understand the prevalence and distribution of schistosomiasis in respective regions. Materials and Methods: From February to March 2011, a cross-sectional survey was done in school-aged children from six districts of Afder Gode zone. Urine samples were collected and examined for ova of Schistosoma haematobium using the sedimentation technique and stool samples were collected and examined for S. mansoni using the Kato-Katz technique. A semistructured questionnaire was used to collect sociodemographic characteristics of the participants. Results: Of the 523 children, 513 (98%) of them participated in the study. The prevalence of S. haematobium was 16.0% (95% confidence interval (CI); 12.8-19.2). The rate of the disease was not uniform across the various six communities studied (x2 = 208.8, P < 0.0001). Musthail district had the highest prevalence with 64.2% (95% CI; 60.0-68.3) followed by Kelafo with 11.8% (95% CI; 9.0-14.6). No infections of S. mansoni were found in these settings. There was no difference in the prevalence of infection across age groups. Boys were more likely to be infected by S. haematobium than girls (odds ratio = 1.68; 95% CI: 1.1-2.7). Conclusion: S. haematobium infection is prevalent in the region with varying distribution across the districts. According to the World Health Organization, mass drug administration should be considered in some of the districts.
Atorvastatin Inhibits gp91phox Circulating Levels in Patients With Hypercholesterolemia

Objective—The inhibition of oxidative stress is among the most relevant pleiotropic effects of statins. The mechanism by which statins exert their antioxidant effect in vivo is still undefined. NADPH oxidase is among the most important sources of reactive oxygen species involved in atherosclerotic disease. Methods/Results—We developed an ELISA to evaluate serum levels of soluble-gp91phox, the catalytic core of phagocyte NADPH oxidase. In a cross-sectional study performed in 30 hypercholesterolemic patients and in 20 controls, serum soluble-gp91phox and urinary isoprostane, a marker of oxidative stress, were measured. The 2 variables were also measured in hypercholesterolemic patients, randomized to diet (n=15), or diet plus atorvastatin (10 mg daily, n=15) and followed for 30 days. Compared to controls, hypercholesterolemic patients had higher and significantly correlated (R=0.71; P<0.001) serum soluble-gp91phox (P<0.001) and urinary isoprostanes (P<0.001). After follow-up, the statin-allocated group showed a significant reduction of soluble-gp91phox (−33%, P<0.01), that paralleled that of isoprostanes (−37%, P<0.01) and cholesterol (−25%, P<0.01). The diet-allocated group showed only a weak reduction of cholesterol. Conclusion—Our study demonstrates that statins exert an antioxidant effect via inhibition of soluble gp91phox expression.
Nuffield Centre for Experimental Social Sciences Discussion Paper Series Ethnic Discrimination and Signals of Trustworthiness in an Online Market: Evidence from Two Field Experiments Ethnic Discrimination and Signals of Trustworthiness in an Online Market: Evidence from Two Field Experiments

Results from two field experiments which were designed to identify possible ethnic discrimination on a German internet auction platform are discussed. A first set of results is produced by a secondary analysis of an earlier experiment. The second experiment additionally tests whether costly signals can help to overcome trust problems between buyers and sellers in online markets. The evidence is rather mixed with respect to ethnic discrimination, and it does not support the signaling hypothesis. helpful comments and suggestions. I gratefully acknowledge the very helpful comments and suggestions of two anonymous reviewers.
Evaluation of the mood repair hypothesis of compulsive buying

Compulsive buying (CB) is a proposed disorder of dysregulated buying behaviour that is associated with high rates of Axis I comorbidity, particularly depression and anxiety. It has been proposed that purchasing behaviours may serve as a maladaptive means of alleviating negative affect in vulnerable individuals. The aim of the current study was to experimentally manipulate affect to test this mood repair hypothesis. Compulsive buyers (n = 26) and pathological gamblers (n = 23) diagnosed using structured clinical interviews (SCID) and healthy controls (n = 24) were randomly assigned to either a negative or positive mood-induction procedure (MIP) and participated in an experimental buying task. Results revealed that, irrespective of mood induction condition, compulsive buyers reported a greater urge to acquire items, purchased more items, and spent a greater total amount of money during the buying task when compared to the healthy control group. Compulsive buyers were also faster than pathological gamblers in making decisions to purchase, even after controlling for motor impulsivity (BIS). There was, however, no main effect of mood-induction condition or group by condition interaction. Limitations and future directions are discussed.
Long-term effectiveness of highly active antiretroviral therapy (HAART) in perinatally HIV-infected children in Denmark

The long-term impact of highly active antiretroviral therapy (HAART) on HIV-1 infected children is not well known. The Danish Paediatric HIV Cohort Study includes all patients <16 y of age with HIV-1 infection in Denmark. We report the complete follow-up from 1996 to 2005 of 49 perinatally infected children treated with HAART. Initial HAART included 2 nucleoside reverse-transcriptase inhibitors in combination with either a protease inhibitor (n =38) or a non-nucleoside reverse-transcriptase inhibitor (n =12). 19 (39%) patients were previously treated with mono- or dual therapy. Baseline characteristics were median CD4 percentage 14% and HIV-RNA viral load 4.9 log10. Within the first 12 weeks of therapy approximately 60% achieved HIV-RNA viral load <500 copies/ml, and this remained stable for up to 8 y, although many children changed the components of HAART. The proportion of children with CD4 percentage >25% increased to 60–70% over the y of treatment. For the total cohort, 245 patient-y of observation were available with only 1 death. During our observation period there were no signs of a waning impact. The challenge remains to maintain a high adherence to therapy as the children grow into adolescence and develop more independence from family and health care staff.
Differentially private multi-party high-dimensional data publishing

In this paper, we study the novel problem of publishing high-dimensional data in a distributed multi-party environment under differential privacy. In particular, with the assistance of a semi-trusted curator, the involved parties (i.e., local data owners) collectively generate a synthetic integrated dataset while satisfying ε-differential privacy for any local dataset. To solve this problem, we present a differentially private sequential update of Bayesian network (DP-SUBN) solution. In DP-SUBN, the parties and the curator collaboratively identify the Bayesian network ℕ that best fits the integrated dataset D in a sequential manner, from which a synthetic dataset can then be generated. The fundamental advantage of adopting the sequential update manner is that the parties can treat the statistical results provided by previous parties as their prior knowledge to direct how to learn ℕ. The core of DP-SUBN is the construction of the search frontier, which can be seen as a priori knowledge to guide the parties to update ℕ. To improve the fitness of ℕ and reduce the communication cost, we introduce a correlation-aware search frontier construction (CSFC) approach, where attribute pairs with strong correlations are used to construct the search frontier. In particular, to privately quantify the correlations of attribute pairs without introducing too much noise, we first propose a non-overlapping covering design (NOCD) method, and then introduce a dynamic programming method to find the optimal parameters used in NOCD to ensure that the injected noise is minimum. Through formal privacy analysis, we show that DP-SUBN satisfies ε-differential privacy for any local dataset. Extensive experiments on a real dataset demonstrate that DP-SUBN offers desirable data utility with low communication cost.
Drug survival for azathioprine and enteric‐coated mycophenolate sodium in a long‐term daily practice cohort of adult patients with atopic dermatitis

Results from clinical studies indicate that azathioprine and enteric-coated mycophenolate sodium (EC-MPS) are safe and potent drugs in the treatment of atopic dermatitis (AD). (1-5) However, published data from large groups of non-selected patients is non-existent to date which hampers generalization to daily practice. In addition, head-to-head trials in which azathioprine and EC-MPS are compared, have never been performed. The primary objective was to perform an analysis of drug survival for azathioprine and EC-MPS in a long-term daily practice cohort of patients with AD. The secondary objective was to identify determinants of drug survival. This article is protected by copyright. All rights reserved.
Magic Angle Effect: A Relevant Artifact in MR Neurography at 3T?

BACKGROUND AND PURPOSE: MRN is an emerging diagnostic method for disorders of peripheral nerves. However, it is unclear whether the influence of the MA on intraneural T2 signal is severe enough to provoke false-positive findings. MATERIALS AND METHODS: Twenty-five healthy subjects underwent MRN of the sciatic nerve of the proximal thigh at 3T. The T2app was calculated from a DE-TSE sequence (TR = 3000 ms, TE1 = 12 ms, TE2 = 69 ms) at 7 angles of the sciatic nerve relative to B0 = 0°, 30°, 35°, 40°, 45°, 50°, and 55°. Precise angle adjustments were performed with a dedicated in-bore positioning aid. Qualitative evaluation of intraneural T2-weighted contrast between this group of healthy subjects and 14 patients with neuropathic lesions was performed by comparing CNRs of a TIRM sequence (TR = 5000 ms, TE = 76 ms, TI = 180 ms). RESULTS: In healthy subjects, the prolongation of T2app from 0° to 55° was from 74.5 ± 13.4 to 104.0 ± 16.9 ms (P < .001). The increase in T2app relative to baseline (0°) was 9.6% (30°), 18.4% (35°), 25% (40°), 27.6% (45°), and 37% (55°). Intraneural CNR increased by 1.98 ± 0.69 at 40° and 2.93 ± 0.46 at 55°. Nevertheless, the mean CNR of healthy subjects was substantially lower than that in patients at 40° (P < .0001) and even at the position of maximum MA (55°: 20.6 ± 5.11 versus 52.6 ± 7.12, P < .0001). CONCLUSIONS: Neuropathic lesions are clearly distinguishable from an artificial increase of intraneural T2 by the MA. Even at a maximum MA (55°), the false-positive determination of a neuropathic lesion is unlikely.
Modification of hippocampal excitability in brain slices pretreated with a low nanomolar concentration of Zn2+

Synaptic Zn2+ homeostasis may be changed during brain slice preparation. However, much less attention has been paid to Zn2+ in artificial cerebrospinal fluid (ACSF) used for slice experiments than has been paid to Ca2+. The present study assesses addition of Zn2+ to ACSF, focused on hippocampal excitability after acute brain slice preparation. When the static levels of intracellular Zn2+ and Ca2+ were compared between brain slices prepared with conventional ACSF without Zn2+ and those pretreated with ACSF containing 20 nM ZnCl2 for 1 hr, both levels were almost the same. On the other hand, intracellular Ca2+ levels were significantly increased in the stratum lucidum of the control brain slices after stimulation with high K+, although the increase was significantly suppressed by the pretreatment with ACSF containing Zn2+, suggesting that neuronal excitation is enhanced in brain slices prepared with ACSF without Zn2+. The increase in extracellular Zn2+ level, an index of glutamate release, after stimulation with high K+ was also significantly suppressed by pretreatment with ACSF containing Zn2+. When mossy fiber excitation was assessed in brain slices with FM4‐64, an indicator of presynaptic activity, attenuation of FM 4‐64 fluorescence based on presynaptic activity was suppressed in the stratum lucidum of brain slices pretreated with ACSF containing Zn2+. The present study indicates that hippocampal excitability is enhanced in brain slices prepared with ACSF without Zn2+. It is likely that a low nanomolar concentration of Zn2+ is necessary for ACSF. © 2015 Wiley Periodicals, Inc.
Dimension-Free Iteration Complexity of Finite Sum Optimization Problems

Many canonical machine learning problems boil down to a convex optimization problem with a finite sum structure. However, whereas much progress has been made in developing faster algorithms for this setting, the inherent limitations of these problems are not satisfactorily addressed by existing lower bounds. Indeed, current bounds focus on first-order optimization algorithms, and only apply in the often unrealistic regime where the number of iterations is less than $\mathcal{O}(d/n)$ (where $d$ is the dimension and $n$ is the number of samples). In this work, we extend the framework of (Arjevani et al., 2015) to provide new lower bounds, which are dimension-free, and go beyond the assumptions of current bounds, thereby covering standard finite sum optimization methods, e.g., SAG, SAGA, SVRG, SDCA without duality, as well as stochastic coordinate-descent methods, such as SDCA and accelerated proximal SDCA.
Are KRAS/BRAF Mutations Potent Prognostic and/or Predictive Biomarkers in Colorectal Cancers?

KRAS and BRAF mutations lead to the constitutive activation of EGFR signaling through the oncogenic Ras/Raf/Mek/Erk pathway. Currently, KRAS is the only potential biomarker for predicting the efficacy of anti-EGFR monoclonal antibodies (mAb) in colorectal cancer (CRC). However, a recent report suggested that the use of cetuximab was associated with survival benefit among patients with p.G13D-mutated tumors. Furthermore, although the presence of mutated BRAF is one of the most powerful prognostic factors for advanced and recurrent CRC, it remains unknown whether patients with BRAF-mutated tumors experience a survival benefit from treatment with anti-EGFR mAb. Thus, the prognostic or predictive relevance of the KRAS and BRAF genotype in CRC remains controversial despite several investigations. Routine KRAS/BRAF screening of pathological specimens is required to promote the appropriate clinical use of anti-EGFR mAb and to determine malignant phenotypes in CRC. The significance of KRAS/BRAF mutations as predictive or prognostic biomarkers should be taken into consideration when selecting a KRAS/BRAF screening assay. This article will review the spectrum of KRAS/BRAF genotype and the impact of KRAS/BRAF mutations on the clinicopathological features and prognosis of patients with CRC, particularly when differentiating between the mutations at KRAS codons 12 and 13. Furthermore, the predictive role of KRAS/BRAF mutations in treatments with anti-EGFR mAb will be verified, focusing on KRAS p.G13D and BRAF mutations.
Research Note: A Socioeconomic Index for the INCAP Longitudinal Study 1969–77

In this note, we calculate and describe proxy measures that account for variation in standard of living across subjects in the Institute of Nutrition of Central America and Panama (INCAP) Longitudinal Study (1969–77), at the time of the original intervention. Using principal components analysis, we construct two linear indices from an array of household consumer durable goods and housing characteristics, measured at the nuclear family level in the 1975 cross-sectional census. The two indices perform well on three dimensions. First, they are internally coherent in that average ownership and quality of housing characteristics increase with the principal component score. Second, they are robust in that the different approaches yield similar results, for example, in classifying nuclear families into tertiles. And third, they are consistent in that they yield results similar to scores constructed by previous researchers. The indices can be used as background controls in analyses of the INCAP Longitudinal Study (1969–77) data and subsequent follow-up studies, including the Human Capital Study 2002–04. Several articles presented in this supplement to the Food and Nutrition Bulletin used the 1975 index.
Perfluorooctane sulfonate induces apoptosis in lung cancer A549 cells through reactive oxygen species‐mediated mitochondrion‐dependent pathway

Perfluorooctane sulfonate (PFOS) is a widespread environmental contaminant that is detected in the lung of mammals. The mechanisms underlying PFOS‐induced lung cytotoxicity remain unclear. The main purpose of this study was to evaluate the cytotoxic effects of PFOS on human lung cancer A549 cells and its possible molecular mechanism. A549 cells were treated with PFOS (0, 25, 50, 100 and 200 μm) and the cellular apoptosis, mitochondrial membrane potential as well as intracellular reactive oxygen species were determined. In this study, PFOS induced a dose‐dependent increase in A549 cell toxicity via an apoptosis pathway as characterized by increased percentage of sub‐G1, activation of caspase‐3 and −9, and increased ratio of Bax/bcl‐2 mRNA expression. In addition, there was obvious oxidative stress, represented by decreased glutathione level, increased malondialdehyde level and superoxide dismutase activity. N‐Acetylcysteine, as an antioxidant that is a direct reactive oxygen species scavenger, can effectively block PFOS‐induced reactive oxygen species generation, mitochondrial membrane potential loss and cell apoptosis. These data indicate that PFOS induces apoptosis in A549 cells through a reactive oxygen species‐mediated mitochondrial dysfunction pathway mechanism. Copyright © 2012 John Wiley & Sons, Ltd.
Miniature Language Acquisition: A Touchstone for Cognitive Science

Cognitive Science, whose genesis was interdisciplinary, shows signs of reverting to a disjoint collection of elds. This paper presents a compact, theory-free task that inherently requires an integrated solution. The basic problem is learning a subset of an arbitrary natural language from picture-sentence pairs. We describe a very speci c instance of this task and show how it presents fundamental (but not impossible) challenges to several areas of cognitive science including vision, language, inference and learning.
BIOTECHNOLOGICALLY RELEVANT ENZYMES AND PROTEINS Purification of recombinant aprotinin from transgenic corn germ fraction using ion exchange and hydrophobic interaction chromatography

Plants have attracted interest as hosts for protein expression because of the promise of a large production capacity and a low production cost. However, recovery costs remain a challenge as illustrated for recovery of recombinant aprotinin, a trypsin inhibitor, with removal of native corn trypsin inhibitor from transgenic corn (Azzoni et al. in Biotechnol Bioeng 80:268–276, 2002). When expression is targeted to corn grain fractions, dry milling can separate germ and endosperm fractions. Hence, only the product-containing fraction needs to be extracted, reducing the cost of extraction and the impurity level of the extract. Selective extraction conditions can reduce impurity levels to the point that low-cost adsorbents can result in relatively high purity levels. In this work, we attempted to achieve comparable purity with these lower cost methods. We replaced whole grain extraction and purification of recombinant aprotinin with sequential trypsin affinity and IMAC steps with an alternative of germ fraction extraction and purification with ion exchange and hydrophobic interaction chromatography (HIC). Using germ extraction at acidic pH supplemented with heat precipitation to remove additional host proteins resulted in a higher specific activity feed to the chromatographic steps. The cation exchange step provided 7.6× purification with 76.4% yield and no sodium dodecyl sulfate–polyacrylamide gel electrophoresis detectable native corn trypsin inhibitor. After the HIC step (2.7× step purification with 44.0% yield), the final product had a specific activity that was 75.3% of that of the affinity-purified aprotinin.
Discretization of Linear Fractional Representations of LPV systems

Commonly, controllers for Linear Parameter- Varying (LPV) systems are designed in continuous-time using a Linear Fractional Representation (LFR) of the plant. However, the resulting controllers are implemented on digital hardware. Furthermore, discrete-time LPV synthesis approaches require a discrete-time model of the plant which is often derived from continuous-time first-principle models. Existing discretization approaches for LFRs suffer from disadvantages like alternation of dynamics, complexity, etc. To overcome the disadvantages, novel discretization methods are derived. These approaches are compared to existing techniques and analyzed in terms of approximation error, considering ideal zero-order hold actuation and sampling.