julilili42/papers huggingface dataset:
Characterizing visual performance in mice: An objective and automated system based on the optokinetic reflex.
2013-01-01

Testing optokinetic head or eye movements is an established method to determine visual performance of laboratory animals, including chickens, guinea pigs, mice, or fish. It is based on the optokinetic reflex which causes the animals to track a drifting stripe pattern with eye and head movements. We have developed an improved version of the optomotor test with better control over the stimulus parameters, as well as a high degree of automation. The stripe pattern is presented on computer monitors surrounding the animal. By tracking the head position of freely moving animals in real time, the visual angle under which the stripes of the pattern appeared was kept constant even for changing head positions. Furthermore, an algorithm was developed for automated evaluation of the tracking performance of the animal. Comparing the automatically determined behavioral score with manual assessment of the animals' tracking behavior confirmed the reliability of our methodology. As an example, we reproduced the known contrast sensitivity function of wild type mice. Furthermore, the progressive decline in visual performance of a mouse model of retinal degeneration, rd10, was demonstrated.
Probing the extent of the non-thermal emission from the Vela X region at TeV energies with H.E.S.S.
2013-01-01

Vela X is a region of extended radio emission in the western part of the Vela constellation: one of the nearest pulsar wind nebulae (PWNe), and associated with the energetic Vela pulsar (PSR B0833-45). Extended very-high-energy (VHE) -ray emission (HESS ) was discovered using the H.E.S.S. experiment in 2004. The VHE -ray emission was found to be coincident with a region of X-ray emission discovered with above 1.5 keV (the so-called \\textit{Vela X cocoon}): a filamentary structure extending southwest from the pulsar to the centre of Vela X. A deeper observation of the entire Vela X nebula region, also including larger offsets from the cocoon, has been performed with H.E.S.S. This re-observation was carried out in order to probe the extent of the non-thermal emission from the Vela X region at TeV energies and to investigate its spectral properties. In order to increase the sensitivity to the faint -ray emission from the very extended Vela X region, a multivariate analysis method combining three complementary reconstruction techniques of Cherenkov-shower images is applied for the selection of -ray events. The analysis is performed with the On/Off background method, which estimates the background from separate observations pointing away from Vela X; towards regions free of -ray sources but with comparable observation conditions. The -ray surface brightness over the large Vela X region reveals that the detection of non-thermal VHE -ray emission from the PWN HESS is statistically significant over a region of radius 1.2 around the position = 08 35 00 , = -45 36 00 (J2000).
Rapid Improvement of Hepatic Steatosis after Initiation of Leptin Substitution in a Leptin-Deficient Girl
2013-01-01

&lt;b&gt;&lt;i&gt;Background:&lt;/i&gt;&lt;/b&gt; Leptin deficiency is associated with severe obesity and metabolic disturbances. Increased liver fat content has been reported in only one case beforehand, even though hepatic steatosis is a typical comorbidity of common obesity. It is also frequent in patients with lipodystrophy where it resolves under leptin therapy. &lt;b&gt;&lt;i&gt;Subject and Methods:&lt;/i&gt;&lt;/b&gt; In 2010, we reported a leptin-deficient patient with a novel homozygous mutation in the leptin gene and severe hepatic steatosis. We have now studied serum changes and changes in liver fat content during the substitution with recombinant methionyl human leptin. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; After 23 weeks of leptin substitution, elevated transaminases, total cholesterol and low-density lipoprotein levels normalized. After 62 weeks, homeostasis model assessment of insulin resistance improved from 10.7 to 6.0 and body fat mass dropped from 50.2 to 37.8%. Liver fat content was drastically reduced from 49.7 to 9.4%. The first changes in liver fat content were detectable after 3 days of therapy. &lt;b&gt;&lt;i&gt;Conclusion:&lt;/i&gt;&lt;/b&gt; Our patient showed a remarkable reduction of liver fat content during the treatment with recombinant methionyl human leptin. These changes occurred rapidly after initiation of the substitution, which implies that leptin has a direct effect on hepatic lipid metabolism in humans as it is seen in rodents.
Emerging DPP-4 inhibitors: focus on linagliptin for type 2 diabetes
2013-01-01

The first dipeptidyl-peptidase-IV (DPP-4) inhibitor for the treatment of type 2 diabetes became available in 2006. Since then, the number of DPP-4 inhibitors has increased and DPP-4 inhibitors have developed into an important drug class. DPP-4 inhibitors act by increasing endogenous GLP-1 and GIP concentrations. Via this mechanism, insulin secretion is glucose-dependently stimulated and glucagon secretion inhibited. This results in a low risk for hypoglycemia. Furthermore, DPP-4 inhibitors are weight-neutral. Linagliptin is a novel DPP-4 inhibitor that, in contrast to the other members of this drug class, is eliminated by a biliary/hepatic route rather than by renal elimination. This property allows the use of linagliptin in type 2 diabetic patients with normal kidney function as well as in patients with renal insufficiency without dose adjustments. In comparative clinical studies, linagliptin was noninferior to other established antidiabetic agents, especially to metformin and sulfonylurea. It showed a superior safety profile over glimepiride regarding hypoglycemia, weight gain, a composite cardiovascular endpoint, and stroke. This review gives an overview on the efficacy and safety of linagliptin in comparison to the classical oral antidiabetic drugs as well as to the other DPP-4 inhibitors.
Data Mining and Support Vector Regression Machine Learning in Semiconductor Manufacturing to Improve Virtual Metrology
2013-01-01

Advanced Process Control is an important research area in Semiconductor Manufacturing to improve process stability crucial for product quality. Especially in low-volume-high-mixture fabrication plants, knowledge discovery in databases is extremely challenging due to complex technology mixtures and reduced availability of data for comparable process steps. Thus, actual research focuses on Data Mining using Machine Learning methods to model unknown functional interrelations. High Density Plasma Chemical Vapor Deposition appears to be a process area in semiconductor manufacturing predestinated for application of Data Mining. Promising results have been achieved by implementing statistical models to predict the thickness of dielectric layers deposited onto a metallization layer of the manufactured wafer. This paper describes the approach to predict the layer thickness using a state-of-the-art Machine Learning regression algorithm: Support Vector Regression. The recent extension of Support Vector Machines overcomes pure classification and deals with multivariate nonlinear input data for regression.
Now you see it, now you don't: on emotion, context, and the algorithmic prediction of human imageability judgments
2013-01-01

Many studies have shown that behavioral measures are affected by manipulating the imageability of words. Though imageability is usually measured by human judgment, little is known about what factors underlie those judgments. We demonstrate that imageability judgments can be largely or entirely accounted for by two computable measures that have previously been associated with imageability, the size and density of a word's context and the emotional associations of the word. We outline an algorithmic method for predicting imageability judgments using co-occurrence distances in a large corpus. Our computed judgments account for 58% of the variance in a set of nearly two thousand imageability judgments, for words that span the entire range of imageability. The two factors account for 43% of the variance in lexical decision reaction times (LDRTs) that is attributable to imageability in a large database of 3697 LDRTs spanning the range of imageability. We document variances in the distribution of our measures across the range of imageability that suggest that they will account for more variance at the extremes, from which most imageability-manipulating stimulus sets are drawn. The two predictors account for 100% of the variance that is attributable to imageability in newly-collected LDRTs using a previously-published stimulus set of 100 items. We argue that our model of imageability is neurobiologically plausible by showing it is consistent with brain imaging data. The evidence we present suggests that behavioral effects in the lexical decision task that are usually attributed to the abstract/concrete distinction between words can be wholly explained by objective characteristics of the word that are not directly related to the semantic distinction. We provide computed imageability estimates for over 29,000 words.
A single particle plasmon resonance study of 3D conical nanoantennas
2013-01-01

Metallic nanocones are well-suited optical antennas for near-field microscopy and spectroscopy, exhibiting a number of different plasmonic modes. A major challenge in using nanocones for many applications is maximizing the signal at the tip while minimizing the background from the base. It is shown that nanocone plasmon resonance properties can be shifted over a wide range of wavelengths by variation of the substrate, material, size and shape, enabling potential control over specific modes and field distributions. The individual resonances are identified and studied by correlated single particle dark field scattering and scanning electron microscopy in combination with numerical simulations.
Virtual screening and experimental validation reveal novel small-molecule inhibitors of 14-3-3 protein–protein interactions
2013-01-01

We report first non-covalent and exclusively extracellular inhibitors of 14-3-3 protein-protein interactions identified by virtual screening. Optimization by crystal structure analysis and in vitro binding assays yielded compounds capable of disrupting the interaction of 14-3-3σ with aminopeptidase N in a cellular assay.
Excited random walks: results, methods, open problems.
2013-01-01

on the occasion of his 70-th birthday. We consider a class of self-interacting random walks in deterministic or random environments, known as excited random walks or cookie walks, on the d-dimensional integer lattice. The main purpose of this paper is two-fold: to give a survey of known results and some of the methods and to present several new results. The latter include functional limit theorems for transient one-dimensional excited random walks in bounded i.i.d. cookie environments as well as some zero-one laws. Several open problems are stated. 1. Model Description Random walks (RWs) and their scaling limits are probably the most widely known and frequently used stochastic processes in probability theory, mathematical physics, and applications. Studies of a RW in a random medium are an attempt to understand which macroscopic effects can be seen and modeled by subjecting the RW’s dynamics on a microscopic level to various kinds of noise, for example, allowing it to interact with a random
A functional role of the extracellular domain of Crumbs in cell architecture and apicobasal polarity
2013-01-01

Regulated cell shape changes in epithelial cells, which contribute to most organs and tissues, are at the basis of morphogenesis. Crumbs (Crb) is an essential apical determinant controlling epithelial apicobasal polarity. Here we provide evidence for a novel role of Crb apical localisation and stabilisation in controlling cell shape through apical domain organisation and Adherens Junctions positioning. We find that Crb apical stabilisation requires the extracellular domain. In vivo results suggest that the extracellular domain assists Crb apical stabilisation by mediating Crb-Crb interactions at opposing cell membranes. We further confirm Crb-Crb extracellular interactions by showing that Crb extracellular domain is sufficient to promote cell aggregation in vitro. Furthermore, we report that Crb apical stabilisation mediated by the extracellular domain is also required for Crb apicobasal polarity maintenance. Our results provide new insights into the mechanisms of apicobasal polarity and the cellular mechanisms of tissue architecture.
IκBζ is a regulator for the senescence-associated secretory phenotype in DNA damage- and oncogene-induced senescence
2013-01-01

Cellular senescence, a state of sustained cell cycle arrest, has been identified as an important anti-tumor barrier. Senescent cells secrete various growth factors and cytokines, such as IL6 and IL8, which collectively constitute the senescence-associated secretory phenotype (SASP). The SASP can signal to the tumor environment and elicit the immune-mediated clearance of tumor cells or, depending on the context, could potentially promote tumor progression. Despite the importance of the SASP to tumor biology, its regulation remains rather unknown. Here, we show that IκBζ, an atypical member of the inhibitor of NFκB proteins and selective coactivator of particular NFκB target genes, is an important regulator of SASP expression. Several models of DNA damage- and oncogene-induced senescence revealed a robust induction of IκBζ expression. RNAi-mediated knockdown of IκBζ impaired IL6 and IL8 expression, whereas exogenous IκBζ expression resulted in enhanced SASP cytokine expression. Importantly, during senescence of IκBζ knockout cells induction of IL6 and IL8 but not of the cell cycle inhibitor p21WAF/CIP1 was completely abolished. Thus, we propose a distinguished and hitherto unappreciated role of IκBζ for SASP formation in both DNA damage- and oncogene-induced senescence.
Phylogenetic Inference from Word Lists Using Weighted Alignment with Empirically Determined Weights
2013-01-01

The paper investigates the task of inferring a phylogenetic tree of languages from the collection of word lists made available by the Automated Similarity Judgment Project . This task involves three steps: (1) computing pairwise word distances, (2) aggregating word distances to a distance measure between languages and inferring a phylogenetic tree from these distances, and (3) evaluating the result by comparing it to expert classifications. For the first task, weighted alignment will be used, and a method to determine weights empirically will be presented. For the second task, a novel method will be developed that attempts to minimize the bias resulting from missing data. For the third task, several methods from the literature will be applied to a large collection of language samples to enable statistical testing. It will be shown that the language distance measure proposed here leads to substantially more accurate phylogenies than a method relying on unweighted Levenshtein distances between words.
Mental Strain and Chronic Stress among University Students with Symptoms of Irritable Bowel Syndrome
2013-01-01

Aim . To investigate the degree of mental strain and chronic stress in a German community sample of students with IBS-like symptoms. Methods and Materials . Following an internet-based survey about stress, this study recruited 176 German university students (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mn>23.45</mml:mn><mml:mo>±</mml:mo><mml:mn>2.48</mml:mn></mml:math>years; 48.3% males) with IBS-like symptoms according to Rome III and 181 students without IBS (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M2"><mml:mn>23.55</mml:mn><mml:mo>±</mml:mo><mml:mn>2.82</mml:mn></mml:math>years; 50.3% males) and compared them regarding current mental strain (SCL-90-R) and the extend of chronic stress. Beyond this, IBS subtypes, IBS severity, and health care utilization were assessed. Results . Students fulfilling IBS criteria showed significantly elevated values of mental strain and chronic stress. Nearly 40% of the IBS group (versus 20% of the controls) reached a clinically relevant value on the SCL-90-R global severity scale. IBS subtypes did not differ in terms of mental distress or chronic stress. Somatization, anxiety, and the chronic stressors “work overload,” “social tension,” and “dissatisfaction with job” were most closely connected to IBS symptom severity. Regarding health care utilization, our results show that consulting a physician frequently was not associated significantly with elevated mental strain or chronic stress but with IBS symptom severity. Conclusion . Our data contribute additional evidence to the distinct association between psychological stress and IBS in community samples.
Variations in neuromuscular activity of thigh muscles during whole-body vibration in consideration of different biomechanical variables.
2013-01-01

The intention of this study was to systematically analyze the impact of biomechanical variables in terms of different vibration frequencies, amplitudes and knee angles on quadriceps femoris and hamstring activity during exposure to whole-body vibration (WBV). 51 healthy men and women (age 55 ± 8 years) voluntary participated in the study and were randomly allocated to five different vibration-frequency groups. Each subject performed 9 static squat positions (3 amplitudes x 3 knee angles) on a side alternating vibration platform. Surface electromyography (EMG) was used to record the neuromuscular activity of the quadriceps femoris and hamstring muscles. Maximal voluntary contractions (MVCs) were performed prior to the measurements to normalize the EMG signals. A three-way mixed ANOVA was performed to analyze the different effects of the biomechanical variables on muscle activity. Depending on the biomechanical variables, EMG muscle activity ranged between 18.2 and 74.1 % MVC in the quadriceps femoris and between 5.2 and 27. 3 % MVC in the hamstrings during WBV. The highest levels of muscle activation were found at high frequencies and large amplitudes. Especially in the quadriceps femoris muscle, a WBV frequency of 30 Hz led to a significant increase in muscle activity compared to the other tested frequencies. However, it seems that knee angle is only relevant for the quadriceps femoris muscle. The results of this study should give more information for developing individual training protocols for WBV treatment in different practical applications. Key PointsWBV leads to a higher muscle activity of the quadriceps femoris than of the hamstrings.The maximum levels of muscle activity were significantly reached at high amplitude and high frequency.The knee angle only significantly affects the quadriceps femoris.Certain combinations of the biomechanical variables have similar effects on the level of muscle activity.
Long-term clinical results after cataract surgery with and without capsular tension ring in patients with retinitis pigmentosa: a retrospective study
2013-01-01

Objectives To describe the long-term clinical outcomes after cataract surgery with and without capsular tension ring (CTR) in a group of patients with retinitis pigmentosa (RP). Design A retrospective study. Setting Tertiary referral centre. Participants 52 eyes (46 patients) with RP. Interventions Cataract surgery was undertaken between October 2002 and May 2010. Primary and secondary outcome measures Visual acuity, secondary cataract, capsular contraction syndrome (CCS), intraocular pressure, cystoid macular edema (CME), intraocular lens dislocation and endophthalmitis. Results The mean age at surgery was about 53 years and the overall mean follow-up was 26 months (range 3–60 months). The mean preoperative logarithm of the minimal angle of resolution of the best corrected visual acuity (LogMAR BCVA) in the entire group was 1.45±0.85 (95% CI 1.21 to 1.69) and had increased to 1.32±0.95 (95% CI 1.06 to 1.58, p=0.02). The mean preoperative and the mean postoperative LogMAR BCVA in the non-CTR group (group 1) improved from 1.16±0.8 (95% CI 0.83 to 1.48) to 0.98±0.88 (95% CI 0.62 to 1.33, p=0.02) and in the CTR group (group 2) from 1.74±0.81 (95% CI 1.42 to 2.07) to 1.66±0.90 (95% CI 1.3 to 2.03, p=0.31), respectively. Secondary cataract was observed in a total of 23 eyes (44%), of which 13 (50%) were belonged to group 1 and 10 (38%) to group 2. CCS was seen in a total of two eyes (4%) all under group 1. CME was noted in two eyes (4%), of which one belonged to group 1 and a second one to group 2. Endophthalmitis was not observed in any group. Conclusions Both surgical approaches were beneficial to the RP patients. Eyes under group 2 showed less long-term postoperative complications. This includes secondary cataract and CCS. Eyes under group 1 performed significantly better in respect of visual acuity. Further research would include insights into the genetic subsets.
Decrease of Global Methylation Improves Significantly Hepatic Differentiation of Ad-MSCs: Possible Future Application for Urea Detoxification
2013-01-01

Hepatocyte transplantation is considered to be an alternative to orthotopic liver transplantation. Cells can be used to bridge patients waiting for a donor organ, decrease mortality in acute liver failure, and support metabolic liver diseases. The limited availability of primary human hepatocytes for such applications has led to the generation of alternative hepatocyte-like cells from various adult stem or precursor cells. The aim of this study was to generate hepatocyte-like cells from adipose-derived mesenchymal stem cells (Ad-MSCs) for clinical applications, which are available “off the shelf.” Epigenetic changes in hepatocyte-like cells were induced by 5-azacytidine, which, in combination with other supplements, leads to significantly improved metabolic and enzymatic activities compared to nontreated cells. Cells with sufficient hepatic features were generated with a four-step protocol: 5-azacytidine (step 1); epidermal growth factor (step 2); fibroblast growth factor-4, dexamethasone, insulin-transferrin-sodium-selenite, and nicotinamide (step 3); and hepatocyte growth factor, dexamethasone, insulin-transferrin-sodium-selenite, and nicotinamide (step 4). Generated differentiated cells had higher phase I (CYP1A1/2, CYP2E1, CYP2B6, CYP3A4) and phase II activities compared to the undifferentiated cells. A strong expression of CYP3A7 and a weak expression of 3A4, as well as the important detoxification markers α-fetoprotein and albumin, could also be detected at the mRNA level. Importantly, urea metabolism (basal, NH 4 -stimulated, NH 4 - and ornithine-stimulated) was comparable to freshly isolated human hepatocytes, and unlike cryopreserved human hepatocytes, this activity was maintained after 6 months of cryopreservation. These findings suggest that these cells may be suitable for clinical application, especially for treatment of urea cycle disorders.