gebhart/patrepeval huggingface dataset:
On the Biodegradation of β-Peptides Part of the PhD thesis of J.V.S. Dissertation no. 14298, ETH Zürich, 2001. (2002)

A consortium of microorganisms was established that was able to grow with the beta-tripeptide H-beta-HVal-beta-HAla-beta-HLeu-OH, with the beta-dipeptide H-beta-HAla-beta-HLeu-OH, and with the beta-amino acids H-beta-HAla-OH, H-beta-HVal-OH, and H-beta-HLeu-OH as the sole carbon and energy sources. This growth was achieved after several incubation-transfer cycles with the beta-tripeptide as the substrate. During degradation of the beta-tripeptide H-beta-HVal-beta-HAla-beta-HLeu-OH, the temporary formation of a metabolite was observed. The metabolite was identified as the beta-dipeptide H-beta-HAla-beta-HLeu-OH by nuclear magnetic resonance spectroscopy and mass spectrometry. This result indicates that in the course of the degradation of the beta-tripeptide, the N-terminal beta-HVal residue was cleaved off by a not yet known mechanism. During the subsequent degradation of the beta-dipeptide, formation of additional metabolites could not be detected. The growth-yield coefficients Y(x/s) for growth on the beta-di- and beta-tripeptide both had a value of 0.45. When a 1:1 mixture of the beta-tripeptide and the corresponding alpha-tripeptide H-Val-Ala-Leu-OH was added to the enrichment culture, the alpha-peptide was completely utilized in six days and thereafter growth of the culture stopped. This result indicates that even in beta-peptide enrichment cultures, alpha-peptides are the preferred substrates. Our experiments clearly show for the first time that beta-peptides and beta-amino acids are amenable to biodegradation and that a microbial consortium was able to utilize these compounds as sole carbon and energy sources. Furthermore, the preparation of beta-amino acids, of derivatives thereof, and of beta-di- and beta-tripeptides is described.
Activin A Maintains Self-Renewal and Regulates Fibroblast Growth Factor, Wnt, and Bone Morphogenic Protein Pathways in Human Embryonic Stem Cells (2006)

Human embryonic stem cells (hESCs) self-renew indefinitely while maintaining pluripotency. The molecular mechanism underlying hESCs self-renewal and pluripotency is poorly understood. To identify the signaling pathway molecules that maintain the proliferation of hESCs, we performed a microarray analysis comparing an aneuploid H1 hESC line (named H1T) versus euploid H1 hESC line because the H1T hESC line demonstrates a self-renewal advantage while maintaining pluripotency. We find differential gene expression for the Nodal/Activin, fibroblast growth factor (FGF), Wnt, and Hedgehog (Hh) signaling pathways in the H1T line, which implicates each of these molecules in maintaining the undifferentiated state, whereas the bone morphogenic protein (BMP) and Notch pathways could promote hESCs differentiation. Experimentally, we find that Activin A is necessary and sufficient for the maintenance of self-renewal and pluripotency of hESCs and supports long-term feeder and serum-free growth of hESCs. We show that Activin A induces the expression of Oct4, Nanog, Nodal, Wnt3, basic FGF, and FGF8 and suppresses the BMP signal. Our data indicates Activin A as a key regulator in maintenance of the stemness in hESCs. This finding will help elucidate the complex signaling network that maintains the hESC phenotype and function.
Characterization of Organic Contaminants Outgassed from Materials Used in Semiconductor Fabs/Processing (2003)

As ULSI technology continues to advance, semiconductor manufacturers are facing new contamination control and monitoring challenges, including airborne molecular contamination (AMC). AMC is being recognized as one of the yield limiting factors in newer generation microelectronics fabrication processes. A major AMC source, materials’ outgassing can introduce a variety of organic contaminants into semiconductor fabs, impacting many processes. This paper provides a brief overview of typical organic outgassing contaminants, their sources, process impacts and analytical techniques used to detect these species. In addition, outgassing study results for polycyclodimethylsiloxanes and several other contaminants using thermal desorption‐gas chromatography‐mass spectrometry (TD‐GC‐MS) analysis are employed to demonstrate the relationships among (1) outgassing level and outgassing time (linear), (2) outgassing quantity and the inverse of outgassing temperature (logarithmic), and (3) outgassing quantity and material surface area (linear). A new method, based on gas diffusion conductivity detection, for ammonia and volatile amines’ outgassing analysis is also presented.
Session Initiation Protocol (SIP) Authenticated Identity Body (AIB) Format (2004)

RFC 3261 introduces the concept of adding an S/MIME body to a Session
Initiation Protocol (SIP) request or response in order to provide
reference integrity over its headers. This document provides a more
specific mechanism to derive integrity and authentication properties
from an 'authenticated identity body', a digitally-signed SIP
message, or message fragment. A standard format for such bodies (known
as Authenticated Identity Bodies, or AIBs) is given in this document.
Some considerations for the processing of AIBs by recipients of SIP
messages with such bodies are also given. [STANDARDS-TRACK]
Meaning and measurement of crystallinity in polymers: A Review (1969)

Abstract A useful concept in polymer science is the degree of crystallinity—the fraction of the polymer that exists in a relatively ordered state. Methods of determination of the degree of crystallinity using density, infrared, thermal, N.M.R. and X ‐ray measurements are examined in light of modern notions of the structure of semi ‐crystalline polymers.
Host-Selective Toxins and Disease Specificity: Perspectives and Progress (1993)

Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth–promoting bacteria and fungi in the rhizosphere prime the whole plant body for ...Read More
Avoidance of posterior tectal membranes by temporal retinal axons (1987)

Membrane carpets consisting of alternating membrane stripes were prepared from plasma membranes of anterior and posterior chick optic tectum. Axons from retinal explants extend neurites on these carpets. Axons of the nasal retina do not distinguish between the stripes. Axons of the temporal retina prefer to extend neurites on anterior tectal membranes. Treatment of the membrane fragments with high temperature interferes with the pattern of neurite outgrowth from temporal axons. When growing on carpets consisting of treated anterior and posterior tectal membranes, temporal retinal axons no longer distinguish between the stripes. Treatment of posterior membranes alone is sufficient to abolish the preference of temporal axons to extend neurites on anterior tectal membranes. Treatment of the anterior membranes alone has no effect. This result is best explained by a repulsive component in the posterior tectal membranes. Temporal, but not nasal, axons specifically recognize and avoid that component, with the result that they do not extend neurites on posterior tectal membrane stripes. Once the repulsive component is destroyed, temporal axons are able to extend neurites on posterior tectal membranes.
A dynamic and service-oriented component model for python long-lived applications (2012)

Dynamic runtime adaptations are a key feature for long-running applications. One of the most used languages for writing this kind of applications is Java, due to its reflection features, popularity and dynamism. However, as dynamic scripting languages (such as Python and Javascript) increase in popularity, it is desirable to be able to conceive long-running applications with them too. This paper introduces iPOPO and Pelix, a Python-based service-oriented component model and dynamic service platform respectively, which are inspired on two popular Java technologies for the development of long-running applications: the iPOJO component model and the OSGi Service Platform. To illustrate the approach, a usage of iPOPO and Pelix is presented on the context of mediation software.
Modulation of Th1 and Th2 responses for immunotherapy (2002)

Novel therapeutic agents that differentially modulate immune responses are needed to boost protective immunity against infections and neoplasms and conversely, to suppress inappropriate immune reactions responsible for allergic and autoimmune disorders and the rejection of transplanted organs. One major concept that has guided the search for such agents asserts the existence of at least two types of CD4+ helper T-cells, Th1 and Th2 cells, that differ in their pattern of cytokine production and govern different arms of the immune response. Th1 cells produce IFN-γ, IL-2 and TNF-β and are involved in cell-mediated immune responses that are beneficial in host-defence against intracellular pathogens and malignant cells, but detrimental in mediating autoimmunity. Th2 cells secrete IL-4, IL-5, IL-9, IL-10 and IL-13, which augment antibody responses, including IgE production, and protect against helminth infestations but also cause allergy and asthma. Moreover, Th1 and Th2 responses are mutually antagonistic, such that they normally exist in equilibrium and cross-regulate each other. Alterations of this equilibrium are thought to underlie the etiopathogenesis of many immune-mediated diseases. By selectively targeting either one of these two types of polarised responses, it may therefore, be possible to achieve desired therapeutic effects without broad alterations of the immune system. The various strategies proposed in the patent literature of the last three years to modulate the Th1/Th2 balance are reviewed here. These include procedures that affect the differentiation of Th1 and Th2 cells, their production of effector cytokines and the activity of these cytokines. A profusion of new molecular targets for pharmacologic development has been identified and some attempts at therapeutic manipulation of Th1 and Th2 responses in clinical trials have been encouraging, while others have been disappointing. The emerging notion that Th1 and Th2 responses are themselves controlled by another category of T-cells, called regulatory T-cells, has offered further opportunities for immunotherapeutic intervention in autoimmunity and allergy.
The Association of Microalbuminuria and Mortality in Non—Insulin-Dependent Diabetes Mellitus (1997)

<h3>Objectives:</h3> To critically analyze the literature linking microalbuminuria with total and cardiovascular mortality and cardiovascular morbidity in non—insulin— dependent diabetes mellitus (NIDDM) and to quantify the risk. <h3>Methods:</h3> A combination of retrieval techniques (MEDLINE, SCISEARCH, and handsearching published bibliographies) was used to find all relevant articles based on title and abstract and "Methods" sections. Unpublished data on albumin excretion rate were sought from large NIDDM cohort studies. <h3>Results:</h3> A total of 264 citations were retrieved, of which 11 cohort studies were selected for inclusion in the overview, representing a total of 2138 patients followed up for a mean of 6.4 years. Patient age was similar across cohorts. Duration of NIDDM ranged from newly diagnosed to 13 years. The prevalence of microalbuminuria ranged from 20% to 36% in the 8 cohorts that excluded patients with clinical proteinuria. All studies reported either a trend or a significant association between microalbuminuria and total mortality or cardiovascular morbidity or mortality; the overall odds ratio for death was 2.4 (95% confidence interval, 1.8-3.1) and for cardiovascular morbidity or mortality, 2.0 (95% confidence interval, 1.4-2.7). We found no evidence of reporting bias. <h3>Conclusion:</h3> Microalbuminuria is a strong predictor of total and cardiovascular mortality and cardiovascular morbidity in patients with NIDDM. Arch Intern Med. 1997;157:1413-1418
Planar Wireless Charging Technology for Portable Electronic Products and Qi (2013)

Starting from the basic principles of Tesla's wireless power transfer experiment in the 1890s, this review article addresses the key historical developments of wireless power and its modern applications up to formation of the world's first international wireless power standard “Qi” launched in 2010 for portable electronics. The scientific principles laid down by Nicolas Tesla for wireless power transfer, which still remain valid today, are first explained. Then, modern wireless power applications based on nonradiative (near-field) magnetic coupling for short-range applications are described. Some industrial application examples emerging since the 1960s are highlighted. The article then focuses on the comparison of the horizontal and vertical magnetic flux approaches developed in the early 1990s for low-power planar wireless charging pads. Several critical features such as localized charging, load identification, and freedom of positioning that are essential to wireless charging of portable electronic devices are explained. The core technologies adopted by the Wireless Power Consortium (WPC) for the “Qi” Standard in 2010 are summarized. Finally, the latest research and developments of wireless power transfer for midrange applications based on the domino-resonator concept and their future application potential are described.
Intimin-Mediated Export of Passenger Proteins Requires Maintenance of a Translocation-Competent Conformation (2005)

Intimins from pathogenic bacteria promote intimate bacterial adhesion to epithelial cells. Several structurally similar domains form on the bacterial cell surface an extended rigid rod that exposes the carboxy-terminal domain, which interacts with the translocated intimin receptor. We constructed a series of intimin-derived fusion proteins consisting of carboxy-terminally truncated intimin and the immunoglobulin light-chain variable domain REIv, ubiquitin, calmodulin, beta-lactamase inhibitor protein, or beta-lactamase. By systematically investigating the intimin-mediated cell surface exposure of these passenger domains in the presence or absence of compounds that interfere with outer membrane stability or passenger domain folding, we acquired experimental evidence that intimin-mediated protein export across the outer membrane requires, prior to export, the maintenance of a translocation-competent conformation that may be distinct from the final protein structure. We propose that, during export, competition exists between productive translocation and folding of the passenger domain in the periplasm into a stable conformation that is not compatible with translocation through the bacterial outer membrane. These results may expand understanding of the mechanism by which intimins are inserted into the outer membrane and expose extracellular domains on the cell surface.
A unified compact scalable ΔI/sub d/ model for hot carrier reliability simulation (2003)

A new compact drain current difference (/spl Delta/I/sub d/) model for hot carrier induced circuit reliability simulation is presented in this paper. For the first time, a single equation unifies the subthreshold, linear and saturation regions with high accuracy in both forward and reverse operation modes. It applies to both interface state generation and electron trapping dominant device degradation mechanisms. The model also shows good scalability.
Deletions affecting hemolytic and toxin activities of Bordetella pertussis adenylate cyclase (1990)

The Bordetella pertussis cyaA gene encodes a virulence factor which is a bifunctional protein exhibiting calmodulin-sensitive adenylate cyclase and hemolytic activities (P. Glaser, H. Sakamoto, J. Bellahov, A. Ullmann, and A. Danchin, EMBO J. 7:3997-4004, 1988). We characterized the hemolytic and toxin activities of the 200-kilodalton (kDa) bifunctional (CyaA) protein and showed that, whether cell associated or secreted, the 200-kDa CyaA protein carries hemolytic and toxin functions. The catalytically active 45-kDa form of adenylate cyclase released by proteolytic digestion of the 200-kDa CyaA protein displayed neither hemolytic nor toxin activities. We constructed in-phase deletions in the 3' region of the cyaA gene, which presumably carries the hemolytic determinant, and showed that the resulting proteins exhibited wild-type adenylate cyclase activity and were secreted without processing into culture supernatants. The hemolytic activities of these mutant CyaA proteins were severely reduced, and their toxin activities were abolished. These results suggest that the structural integrity of the 200-kDa CyaA protein is necessary for toxin activity and that distinct structural determinants within the CyaA protein are involved in secretion, pore formation, and entry into target cells.
In Vitro High Throughput Screening of Compounds for Favorable Metabolic Properties in Drug Discovery. (2001)

Drug metabolism can have profound effects on the pharmacological and toxicological profile of therapeutic agents. In the pharmaceutical industry, many in vitro techniques are in place or under development to screen and optimize compounds for favorable metabolic properties in the drug discovery phase. These in vitro technologies are meant to address important issues such as: (1) is the compound a potent inhibitor of drug metabolising enzymes (DMEs)? (2) does the compound induce the expression of DMEs? (3) how labile is the compound to metabolic degradation? (4) which specific enzyme(s) is responsible for the compound's biotransformation? and (5) to which metabolites is the compound metabolized? Answers to these questions provide a basis for judging whether a compound is likely to have acceptable pharmacokinetic properties in vivo. To address these issues on the increasing number of compounds inundating the drug discovery programs, high throughput assays are essential. A combination of biochemical advances in the understanding of the function and regulation of DMEs (in particular, cytochromes P450, CYPs) and automated analytical technologies are revolutionizing drug metabolism research. Automated LC-MS based metabolic stability, fluorescence, radiometric and LC-MS based CYP inhibition assays are now in routine use. Automatible models for studying CYP induction based on enzyme activity, quantitative RT-PCR and reporter gene systems are being developed. We will review the utility and limitations of these HTS approaches and highlight on-going developments and emerging technologies to answer metabolism questions at the different stages of the drug discovery process.
Automatic recognition of keywords in unconstrained speech using hidden Markov models (1990)

The modifications made to a connected word speech recognition algorithm based on hidden Markov models (HMMs) which allow it to recognize words from a predefined vocabulary list spoken in an unconstrained fashion are described. The novelty of this approach is that statistical models of both the actual vocabulary word and the extraneous speech and background are created. An HMM-based connected word recognition system is then used to find the best sequence of background, extraneous speech, and vocabulary word models for matching the actual input. Word recognition accuracy of 99.3% on purely isolated speech (i.e., only vocabulary items and background noise were present), and 95.1% when the vocabulary word was embedded in unconstrained extraneous speech, were obtained for the five word vocabulary using the proposed recognition algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Site-directed mutagenesis of human brain-derived neurotrophic factor gene (1998)

Human brain-derived neurotrophic factor gene was used as template for oligonucleotide based site-directed mutagenesis and PCR. Mutated genes werE confirmed by nucleotide sequence analysis. This lays the foundation of structure and function studies of brain-derived neurotrophic factor.
Sustained exposure to diets with an unbalanced macronutrient proportion alters key genes involved in energy homeostasis and obesity-related metabolic parameters in rats (2014)

We have investigated the effects of long term intake of two unbalanced diets (rich in fat -HF- or protein -HP-) administered under isocaloric conditions to a control balanced diet (pair-feeding) to adult rats. Isocaloric intake of a HF diet did not affect the body weight but increased adiposity, liver-fat deposition, and induced insulin resistance. Gene expression changes in the liver and adipose tissue (increased lipolytic and decreased lipogenic gene expression) could try to compensate for increased adiposity. The HP diet decreased caloric intake, the body weight, the size of subcutaneous adipocytes, and circulating cholesterol. Higher insulin levels apparently not related to insulin resistance were observed. Changes at the gene expression level reflected an adaptation to lower diet carbohydrate content and to the use of amino acids as the energy source. The kidney size increased in HP-fed animals but serum creatinine was not affected. Circulating TNF-alpha levels were higher in both dietary models. Thus, a long-term increase in dietary fat proportion produces alterations related to metabolic syndrome even in the absence of increased body weight, whereas an increase in diet protein content reduces the body weight but alters metabolic parameters and kidney size which could be linked to an increased risk of suffering from different pathologies.
Functional and Structural Aspects of the Epithelial Lymphocyte, with Implications for Coeliac Disease and Tropical Sprue (1985)

Epithelial lymphocytes comprise a compartmentalised and specialised population of presumed effector cells which, in general, express the surface phenotypes (Lyt-2+; OX2+; OKT8+) of suppressor/cytolytic (Ts/c) cells. Granular cells within this population (gEL) morphologically resemble the circulating large granular lymphocytes (LGL) which subserve spontaneous (NK) cytolytic activity. Recent in vitro results indicate that gEL can develop this function after prolonged in vitro culture; the relevance of this, in vivo, remains to be decided. EL also appear to be able to mediate ADCC with sIgA against enteric micro-organisms. This is the kind of integrated activity that might be anticipated from local immunocytes within the intestinal mucosa. Other recent work suggests that gEL are not precursors of mucosal mast cells. EL also appear to be capable of inducing Ia-like expression in surface and crypt enterocytes, a property enjoyed both by highly purified Th, but also Ts/c, cells as well. This raises the interesting prospect that enterocytes may display antigen in macrophage-like fashion to other adjacent cells within the inter-epithelial cell spaces. These latter observations might be more consistent with the presence of 'activated' and 'blast-transformed' lymphocytes in such conditions as coeliac disease and tropical sprue. Another emergent view that demands appropriate attention is that the infiltrate of Ts/c cells into surface, and crypt, epithelium of coeliac mucosa does not necessarily cause injury or damage to the jejunal tissues. Nevertheless the role, either primary or secondary, that EL play either in coeliac disease or tropical sprue still remains obscure.
Comparison of two solutions for acoustic radiation pressure on a sphere (1977)

The expression obtained by Hasegawa and Yosioka [J. Acoust. Soc. Am. 46, 1139–1143 (1969)] for the acoustic radiation pressure on a solid elastic sphere in a plane progressive sound field is reformed into a simpler form, in which the acoustic-radiation-pressure function is represented only in terms of scattering coefficients and the size parameter ka. On the other hand, the extension of the Maidanik calculation [J. Acoust. Soc. Am. 29, 936–940 (1957)] for a fluid sphere to solid elastic spheres is attempted. The result is compared with the former. It is demonstrated that the computational differences are commensurate with the same result.