gebhart/patrepeval huggingface dataset:
Reliable Rateless Wireless Broadcasting With Near-Zero Feedback (2012)

We examine the problem of minimizing feedback in reliable wireless broadcasting by pairing rateless coding with extreme value theory. Our key observation is that, in a broadcast environment, this problem resolves into estimating the maximum number of packets dropped among many receivers rather than for each individual receiver. With rateless codes, this estimation relates to the number of redundant transmissions needed at the source in order for all receivers to correctly decode a message with high probability. We develop and analyze two new data dissemination protocols, called Random Sampling (RS) and Full Sampling with Limited Feedback (FSLF), based on the moment and maximum likelihood estimators in extreme value theory. Both protocols rely on a single-round learning phase, requiring the transmission of a few feedback packets from a small subset of receivers. With fixed overhead, we show that FSLF has the desirable property of becoming more accurate as the receivers' population gets larger. Our protocols are channel-agnostic, in that they do not require a priori knowledge of (i.i.d.) packet loss probabilities, which may vary among receivers. We provide simulations and an improved full-scale implementation of the Rateless Deluge over-the-air programming protocol on sensor motes as a demonstration of the practical benefits of our protocols, which translate into about 30% latency and energy consumption savings. Furthermore, we apply our protocols to real-time (RT) oblivious rateless codes in broadcast settings. Through simulations, we demonstrate a 100-fold reduction in the amount of feedback packets while incurring an increase of only 10%–20% in the number of encoded packets transmissions.
The AmiE aliphatic amidase and AmiF formamidase of <i>Helicobacter pylori</i>: natural evolution of two enzyme paralogues (2001)

Aliphatic amidases (EC 3.5.1.4) are enzymes catalysing the hydrolysis of short-chain amides to produce ammonia and the corresponding organic acid. Such an amidase, AmiE, has been detected previously in Helicobacter pylori. Analysis of the complete H. pylori genome sequence revealed the existence of a duplicated amidase gene that we named amiF. The corresponding AmiF protein is 34% identical to its AmiE paralogue. Because gene duplication is widely considered to be a fundamental process in the acquisition of novel enzymatic functions, we decided to study and compare the functions of the paralogous amidases of H. pylori. AmiE and AmiF proteins were overproduced in Escherichia coli and purified by a two-step chromatographic procedure. The two H. pylori amidases could be distinguished by different biochemical characteristics such as optimum pH or temperature. AmiE hydrolysed propionamide, acetamide and acrylamide and had no activity with formamide. AmiF presented an unexpected substrate specificity: it only hydrolysed formamide. AmiF is thus the first formamidase (EC 3.5.1.49) related to aliphatic amidases to be described. Cys-165 in AmiE and Cys-166 in AmiF were identified as residues essential for catalysis of the corresponding enzymes. H. pylori strains carrying single and double mutations of amiE and amiF were constructed. The substrate specificities of these enzymes were confirmed in H. pylori. Production of AmiE and AmiF proteins is dependent on the activity of other enzymes involved in the nitrogen metabolism of H. pylori (urease and arginase respectively). Our results strongly suggest that (i) the H. pylori paralogous amidases have evolved to achieve enzymatic specialization after ancestral gene duplication; and (ii) the production of these enzymes is regulated to maintain intracellular nitrogen balance in H. pylori.
Source Space Analysis of Event-Related Dynamic Reorganization of Brain Networks (2012)

How the brain works is nowadays synonymous with how different parts of the brain work together and the derivation of mathematical descriptions for the functional connectivity patterns that can be objectively derived from data of different neuroimaging techniques. In most cases static networks are studied, often relying on resting state recordings. Here, we present a quantitative study of dynamic reconfiguration of connectivity for event-related experiments. Our motivation is the development of a methodology that can be used for personalized monitoring of brain activity. In line with this motivation, we use data with visual stimuli from a typical subject that participated in different experiments that were previously analyzed with traditional methods. The earlier studies identified well-defined changes in specific brain areas at specific latencies related to attention, properties of stimuli, and tasks demands. Using a recently introduced methodology, we track the event-related changes in network organization, at source space level, thus providing a more global and complete view of the stages of processing associated with the regional changes in activity. The results suggest the time evolving modularity as an additional brain code that is accessible with noninvasive means and hence available for personalized monitoring and clinical applications.
Selection of GmSWEET39 for oil and protein improvement in soybean (2020)

Soybean [Glycine max (L.) Merr.] was domesticated from wild soybean (G. soja Sieb. and Zucc.) and has been further improved as a dual-use seed crop to provide highly valuable oil and protein for food, feed, and industrial applications. However, the underlying genetic and molecular basis remains less understood. Having combined high-confidence bi-parental linkage mapping with high-resolution association analysis based on 631 whole sequenced genomes, we mapped major soybean protein and oil QTLs on chromosome15 to a sugar transporter gene (GmSWEET39). A two-nucleotide CC deletion truncating C-terminus of GmSWEET39 was strongly associated with high seed oil and low seed protein, suggesting its pleiotropic effect on protein and oil content. GmSWEET39 was predominantly expressed in parenchyma and integument of the seed coat, and likely regulates oil and protein accumulation by affecting sugar delivery from maternal seed coat to the filial embryo. We demonstrated that GmSWEET39 has a dual function for both oil and protein improvement and undergoes two different paths of artificial selection. A CC deletion (CC-) haplotype H1 has been intensively selected during domestication and extensively used in soybean improvement worldwide. H1 is fixed in North American soybean cultivars. The protein-favored (CC+) haplotype H3 still undergoes ongoing selection, reflecting its sustainable role for soybean protein improvement. The comprehensive knowledge on the molecular basis underlying the major QTL and GmSWEET39 haplotypes associated with soybean improvement would be valuable to design new strategies for soybean seed quality improvement using molecular breeding and biotechnological approaches.
Aircraft anti-icing and de-icing techniques and modeling (1996)

Nomenclature Ac = accumulation parameter Cd drag coefficient Ci = lift coefficient Cm = moment coefficient Cp = pressure coefficient c = specific heat at constant pressure, J/(kg-K); airfoil chord, D = propeller diameter, m; flexural stiffness, N-m D drag force, N d = droplet diameter, E = total collection efficiency / = freezing fraction g = acceleration caused from gravity, m/s Hi = ice thickness, Hp = plate thickness, h = airfoil projected height, hc = convective heat transfer coefficient, W/(m-K) hfg = heat of vaporization, J/kg hsi = heat of fusion, J/kg / = airfoil drag constant K = thermal conductivity, W/(m-K); inertia parameter K0 = modified inertia parameter k = roughness diameter, LWC = liquid water content, kg/m M = local Mach number MVD = median volume droplet diameter, = mass, kg ra = mass flow rate, kg/s m' = mass flow rate per unit width, kg/(m-s) m = mass flux, kg/(m-s) n = normal direction P = pressure, Pa p spatial pressure distribution, N/m <2 = heat rate, W q = normal pressure distribution, N/m
Electrically conducting transition metal complexes of tetrathio-oxalate (1985)

Oligomeric complexes of tetrathio-oxalate with NiII, CuII, and PdII have been synthesized to yield materials having high electrical conductivities of up to 20 S cm–1.
Maximum expected F-measure training of logistic regression models (2005)

We consider the problem of training logistic regression models for binary classification in information extraction and information retrieval tasks. Fitting probabilistic models for use with such tasks should take into account the demands of the task-specific utility function, in this case the well-known F-measure, which combines recall and precision into a global measure of utility. We develop a training procedure based on empirical risk minimization / utility maximization and evaluate it on a simple extraction task.
Bioinformatics analysis of the epitope regions for norovirus capsid protein (2013)

The predicted conformational epitope regions of norovirus VP1 mainly concentrated on N-terminal, Middle Part and C-terminal. We find two common epitope regions on sequences for GI and GII genogroup, and also found an exclusive epitope region for GII genogroup. The overlapping with experimental epitopes indicates the important role of latest computational technologies. With the fast development of computational immunology tools, the bioinformatics pipeline will be more and more critical to vaccine design.
<i>IQGAP2</i> inactivation through aberrant promoter methylation and promotion of invasion in gastric cancer cells (2007)

Invasion and metastases of cancer cells are the main causes of treatment failure in cancer. IQ motif-containing GTPase activating protein 1 (IQGAP1), plays pivotal roles in intercellular adhesion, migration, invasion and metastases in various cancer cells. However, the role of another family member, IQGAP2, in carcinogenesis remains unknown. Here, we investigated IQGAP2 functions in gastric cancers. We found that IQGAP2 protein expression was lost in 5 of the 9 gastric cancer cell lines. Through analysis by the methylation-specific PCR, aberrant IQGAP2 methylation was detected in 3 gastric cancer cell lines. IQGAP2 mRNA was found to be activated after 5-aza-2'-deoxycytidine treatment of the methylation-positive cells. Moreover, IQGAP2 methylation was detected in 28 of the 59 (47%) primary gastric cancer tissues, but not in 12 normal gastric mucosa samples. Immunohistochemical staining revealed that 7 of the 8 (88%) gastric cancer tissues without methylation signals displayed IQGAP2 expression, whereas among 10 with methylation signals none expressed IQGAP2 (p = 0.0002), indicating that IQGAP2 methylation is highly associated with loss of the IQGAP2 expression in the primary gastric cancer tissues as well as gastric cancer cell lines. Furthermore, IQGAP2 methylation was also associated with tumor invasion and a poor prognosis. IQGAP2 knockdown with small interfering RNA increased the invasive capacity of a gastric cancer cell line. These results suggest that silencing of IQGAP2 by promoter methylation may contribute to gastric cancer development.
Neutralizing IL-23 Is Superior to Blocking IL-17 in Suppressing Intestinal Inflammation in a Spontaneous Murine Colitis Model (2015)

Our results support clinical studies showing that IL-17 neutralization is not therapeutic but that targeting IL-23 suppresses intestinal inflammation. Effects of IL-23 distinct from its effects on maturation of IL-17A-producing lymphocytes may underlie the protection from inflammatory bowel disease conveyed by hypomorphic IL-23 receptor polymorphisms and contribute to the efficacy of IL-23 neutralizing antibodies in inflammatory bowel disease.
Inflammatory events in severe acute asthma (2004)

Severe acute asthma can be induced by different triggers, allergens, irritants, viruses, etc., which induce inflammation and provoke acute bronchoconstriction. Inflammatory cells, such as activated eosinophils and neutrophils identified in sputum and bronchial lavages (BL) in severe acute asthma from children and adults are associated with increased levels of IL-5, IL-8, and of proinflammatory mediators. Viruses, but also endotoxin or allergen exposure, are able to recruit neutrophils, via an IL-8 production by activated macrophages or epithelial cells. Together, these inflammatory mediators are responsible for the diffuse bronchial inflammation, which involve large and small airways. Activated T cells may also be related to the pathogenesis of severe asthma. An aberrant CD8+ T lymphocyte response in bronchi, with a cytotoxic activity has been associated with fatal asthma. Moreover, the persistence of inflammatory cells in bronchi, particularly neutrophils, which respond poorly to corticosteroids, could be in part responsible for the epithelial damage, the extensive mucus plugging, and the abnormalities of epithelial and endothelial permeability which are associated with severe acute asthma. Further studies are necessary to better identify the implication of this increased bronchial permeability in the persistence of high levels of airway resistance, particularly in patients with status asthmaticus.
Identification of 30 protein species involved in replicative senescence and stress‐induced premature senescence (2002)

Exposure of human proliferative cells to subcytotoxic stress triggers stress-induced premature senescence (SIPS) which is characterized by many biomarkers of replicative senescence. Proteomic comparison of replicative senescence and stress-induced premature senescence indicates that, at the level of protein expression, stress-induced premature senescence and replicative senescence are different phenotypes sharing however similarities. In this study, we identified 30 proteins showing changes of expression level specific or common to replicative senescence and/or stress-induced premature senescence. These changes affect different cell functions, including energy metabolism, defense systems, maintenance of the redox potential, cell morphology and transduction pathways.
PPARγ-mediated insulin sensitization: the importance of fat versus muscle (2005)

Peroxisome proliferator-activated receptor-gamma (PPARgamma) is a nuclear hormone receptor that functions as a transcriptional regulator in a variety of tissues. PPARgamma activation, e.g., through binding of the synthetic glitazones or thiazolidinediones (TZD), results in a marked improvement in type 2 diabetic patients of insulin and glucose parameters resulting from an improvement of whole body insulin sensitivity. The role of different metabolic tissues (fat, skeletal muscle, liver) in mediating PPARgamma function in glucose and insulin homeostasis is still unclear. Recently, the function of PPARgamma in adipose tissue and skeletal muscle has been intensively characterized by using targeted deletion of PPARgamma in those tissues. In those studies, adipose PPARgamma has been identified as an essential mediator for the maintainance of whole body insulin sensitivity. Two major mechanisms have been described. 1) Adipose PPARgamma protects nonadipose tissue against excessive lipid overload and maintains normal organ function (liver, skeletal muscle); and 2) adipose PPARgamma guarantees a balanced and adequate production of secretion from adipose tissue of adipocytokines such as adiponectin and leptin, which are important mediators of insulin action in peripheral tissues. In contrast to studies in adipose-specific PPARgamma-deficient mice, the data in muscle-specific PPARgamma(-/-) mice demonstrate that whole body insulin sensitivity is, at least in part, relying on an intact PPARgamma system in skeletal muscle. Finally, these early and elegant studies using tissue-specific PPARgamma knockout mouse models pinpoint adipose tissue as the major target of TZD-mediated improvement of hyperlipidemia and insulin sensitization.
Nanometric Multiscale Rough CuO/Cu(OH)<sub>2</sub> Superhydrophobic Surfaces Prepared by a Facile One-Step Solution-Immersion Process: Transition to Superhydrophilicity with Oxygen Plasma Treatment (2011)

An inexpensive and facile one-step method to develop a superhydrophobic coating on the copper surface is reported. Superhydrophobic CuO/Cu(OH)2 surfaces were prepared by a simple solution-immersion process at room temperature, without using a low surface energy material. The structure and composition of as-prepared CuO/Cu(OH)2 hierarchical structure were confirmed by X-ray diffraction, micro-Raman spectroscopy, and X-ray photoelectron spectroscopy (XPS). The growth stage was carefully examined by field emission scanning electron microscopy (FESEM), and it was observed that initially Cu(OH)2 nanoneedle arrays were formed on the copper surface and subsequently the CuO microflowers formed on the nanoneedle arrays. The contact angle as a function of immersion time was studied using a contact angle goniometer. The correlation between the microstructure of the immersed copper surface and the contact angle was examined carefully using FESEM and atomic force microscopy (AFM). Our results based on FESEM and AFM studies show that the CuO/Cu(OH)2 coatings demonstrate superhydrophobicity only for an optimal combination of the solid region (i.e., microflowers and nanoneedles) and air pockets (i.e., voids). The maximum static water contact angle on the prepared surface was 159°. The wettability transition of the CuO/Cu(OH)2 surface from superhydrophobicity to superhydrophilicity was studied by the alteration of oxygen plasma treatment and dark storage. The FESEM, AFM, and XPS studies showed that this transformation was mainly due to the morphological changes that occur in addition to the chemical changes taking place on the CuO/Cu(OH)2 surface under the influence of oxygen plasma. XPS analysis demonstrated that the incorporation of oxygen species by oxygen plasma activation accounted for the highly hydrophilic character of the surface.
Natural EUV mask blank defects: evidence, timely detection, analysis and outlook (2010)

A combination of blank inspection (BI), patterned mask inspection (PMI) and wafer inspection (WI) is used to find as many as possible printing defects on two different EUV reticles. These multiple inspections result in a total population of known printing defects on each reticle. The printability of these defects is first confirmed by wafer review on wafers exposed on the full field ASML Alpha Demo Tool (ADT) at IMEC. Subsequently reticle review is performed on the corresponding locations with both SEM (Secondary Electron Microscope) and AFM (Atomic Force Microscope). This review methodology allows to separate absorber related mask defects and multi layer (ML) related mask defects. In this investigation the focus is on ML defects, because this type of reticle defects is EUV specific, and not as evolutionary as absorber defects which can be mitigated in more conventional ways. This work gives evidence of critical printing ML defects of natural origin, both pits as shallow as 3nm and bumps just 3nm high at the surface. Wafer inspection was the first inspection technique to detect these ML-defects with marginal surface height distortion, because both state-of-the-art PMI and especially standard BI on the Lasertec M1350 had failed to detect these defects. Compared to standard BI, the more advanced Lasertec M7360 is found to have much better sensitivity for printing MLdefects and our work so far shows no evidence of printing ML defects missed by this tool. Unfortunately it was also observed that this required sensitivity was only achieved at the cost of an unacceptable nuisance rate, i.e., with a too high number of detections of non-printing defects. Optical blank inspection is facing major challenges : It needs not only to find ML defects with height distortions of 3nm and less (and in theory maybe even 0nm), but also it must be able to disposition between such likely-printing and non-printing defects.
NK-1 receptor antagonists as antitumor drugs: a survey of the literature from 2000 to 2011 (2012)

Chemically diverse NK-1 receptor antagonists have been identified. The antitumor action of these compounds is independent of their chemical structures and such action is associated with their affinity for the NK-1 receptor and with the dose of the antagonist administered. The NK-1 receptor can be considered as a target in cancer treatment and NK-1 receptor antagonists could be considered as new antitumor drugs. The NK-1 receptor antagonist aprepitant is used in clinical practice and exerts an antitumor action against tumor cells in vitro. In the future, such antitumor action should be tested in human clinical trials.
Microwave Loss Measurements of Copper-Clad Superconducting Niobium Microstrip Resonators on Flexible Polyimide Substrates (2016)

In this work, we investigated how different under- and capping layers on patterned Nb films impacted the RF losses of flexible thin-film superconducting microstrip transmission line resonators measured in a frequency range from 2 to 20 GHz. We studied how different thicknesses of Ti(10 and 50 nm) under-layer, used for adhesion, impacts conductor losses. We also studied Cu(20, 50, 100, and 200 nm) capping layers and how they affect conductor loss. These studies were carried out on 20-μm-thick spin-on polyimide (PI-2611) thin films and characterized at various cryogenic temperatures between 1.2 and 4.2 K. The results indicate normal-superconductor (Ti/Nb) and superconductor-normal (Nb/Cu) bilayer structures have increased surface resistance, which leads to an increase in microwave loss when compared to Nb-only signal traces. We quantified this additional loss by extracting resonator quality factors for weakly coupled resonators with various conductor stack-ups. Our experimental results can help inform decisions regarding material stack-ups when designing multiconductor multilayer superconducting flexible cables intended for use with ultralow-temperature electronic systems.
Reagent-Free and Rapid Assessment of T Cell Activation State Using Diffraction Phase Microscopy and Deep Learning (2019)

CD8<sup>+</sup> T cells constitute an essential compartment of the adaptive immune system. During immune responses, naı̈ve T cells become functional, as they are primed with their cognate determinants by the antigen presenting cells. Current methods of identifying activated CD8<sup>+</sup> T cells are laborious, time-consuming and expensive due to the extensive list of required reagents. Here, we demonstrate an optical imaging approach featuring quantitative phase imaging to distinguish activated CD8<sup>+</sup> T cells from naı̈ve CD8<sup>+</sup> T cells in a rapid and reagent-free manner. We measured the dry mass of live cells and employed transport-based morphometry to better understand their differential morphological attributes. Our results reveal that, upon activation, the dry cell mass of T cells increases significantly in comparison to that of unstimulated cells. By employing deep learning formalism, we are able to accurately predict the population ratios of unknown mixed population based on the acquired quantitative phase images. We envision that, with further refinement, this label-free method of T cell phenotyping will lead to a rapid and cost-effective platform for assaying T cell responses to candidate antigens in the near future.