gebhart/patrepeval huggingface dataset:
Specification scheme for the visualisation of data structures (1994)

The paper describes a general principle for program visualisation, based on the concept of structure models. We propose a specification scheme that can be used to implement the general principle without requiring a change of the program code. Two aspects of the scheme are discussed in detail; the specification of critical entities and their graphical representations. Its use is illustrated by means of a specification for the visualisation of a program which calculates the convex hull of a finite set of points.
Scanning electrochemical microscopy: A new scanning mode based on convective effects (1994)

Abstract A new measuring technique for the scanning electrochemical microscope (SECM) is presented, which we call picking mode. The influence of the tip‐surface distance on the current signal is separated from the current due to the electrochemical properties of the surface by this new method. Based on convective effects, the fast approach of the tip towards samples revealed a sharp increase of the tip current close to the samples' surface. During this strongly instationary stage, the current is dominated by convective flows and the influence of the electrochemical surface properties is negligible. Using this convective current, the tip‐surface distance can be adjusted within a few microns. In a second step after reaching the steady‐state transport conditions again, the electrochemical processes are characterised by the current at this position. The capability of the new mode is proven by scanning a bended platinum sheet and a PVC sample. The new method enables the separate acquisition of the height profile due to the surface's morphology and of the topology due to local variations of electrochemical properties.
Postmenopausal Hormone Therapy and Risk of Cardiovascular Disease by Age and Years Since Menopause (2007)

clinicaltrials.gov Identifier: NCT00000611.
Reduction of O-LinkedN-Acetylglucosamine-Modified Assembly Protein-3 in Alzheimer’s Disease (1998)

Abnormal protein processing and modification is associated with Alzheimer's disease (AD) pathology. The role of phosphorylation in AD has been studied extensively because the presumed abnormal phosphorylation of tau protein is believed to play a role in the formation of paired helical filaments. Glycosylation with O-linked N-acetylglucosamine (O-GlcNAc) to serine and threonine residues is a dynamic protein modification of intracellular proteins, and it shares similar features with protein phosphorylation. In this study, O-GlcNAc glycosylation of proteins from autopsied human brains with confirmed AD and non-AD age-matched controls was examined. O-GlcNAcylation was demonstrated by labeling protein extracts with [3H]galactose in the presence of galactosyltransferase and subsequent analyses of saccharide-protein linkage and saccharide structure. The number of O-GlcNAc-containing proteins and the overall O-GlcNAc level do not appear to be different between AD and control brain tissues. The only significant change observed is a marked reduction of O-GlcNAcylated clathrin assembly protein-3 (AP-3) in AD. The reduction is more evident in brain neocortical regions, and there appears to be a negative correlation between O-glycosylated AP-3 and the density of neurofibrillary tangles. These data suggest a possible association between the O-glycosylated AP-3 and AD pathology.
Oral Use of Interferon-alpha Delays the Onset of Insulin-Dependent Diabetes Mellitus in Nonobese Diabetes Mice (1999)

Insulin-dependent diabetes mellitus (IDDM) in the nonobese diabetes (NOD) mouse model is thought to be an autoimmune CD4 Th1-like cell-mediated disease. We tested the efficacy of oral use of interferon-alpha (IFN-alpha) therapy on IDDM in NOD mice. Using urine and blood sugar levels as indicators of IDDM, oral administration of murine IFN-alpha (100 IU/body) to NOD mice significantly delayed the onset of symptomatic diabetes. However, oral use of IFN-alpha did not prevent diabetic NOD mice from losing weight once NOD mice were symptomatic, suggesting that orally administered IFN-alpha is a prophylactic rather than therapeutic approach to the management of IDDM.
Nucleotide sequence and deduced functions of a set of cotranscribed genes of Streptomyces coelicolor A3(2) including the polyketide synthase for the antibiotic actinorhodin. (1992)

A 5.3-kb region of the Streptomyces coelicolor actinorhodin gene cluster, including the genes for polyketide biosynthesis, was sequenced. Six identified open reading frames (ORF1-6) were related to genetically characterized mutations of classes actI, VII, IV, and VB by complementation analysis. ORF1-6 run divergently from the adjacent actIII gene, which encodes the polyketide synthase (PKS) ketoreductase, and appear to form an operon. The deduced gene products of ORF1-3 are similar to fatty acid synthases (FAS) of different organisms and PKS genes from other polyketide producers. The predicted ORF5 gene product is similar to type II beta-lactamases of Bacillus cereus and Bacteroides fragilis. The ORF6 product does not resemble other known proteins. Combining the genetical, biochemical, and similarity data, the potential activities of the products of the six genes can be postulated as: 1) condensing enzyme/acyl transferase (ORF1 + ORF2); 2) acyl carrier protein (ORF3); 3) putative cyclase/dehydrase (ORF4); 4) dehydrase (ORF5); and 5) "dimerase" (ORF6). The data show that the actinorhodin PKS consists of discrete monofunctional components, like that of the Escherichia coli (Type II) FAS, rather than the multifunctional polypeptides for the macrolide PKSs and vertebrate FASs (Type I).
Influence ofAr2+in an argon collisional-radiative model (2002)

A nonlinear time-dependent collisional-radiative model for recombining argon is presented. Reactions involving Ar(2)+ are taken into account and their influence is discussed. It is shown that Ar(2)+ may increase the time to reach the quasi-steady-state by a factor of 100. The calculation of the recombination rate coefficient at the quasi-steady-state is presented. An analytical expression is derived and compared with existing literature values. The importance of the increase of the quasi-steady-state time is illustrated by comparisons of excited levels population densities distribution measured in a fast moving plasma where the mechanical time scale is sufficiently short to provide a time-dependent chemistry in a reference frame moving with the flow. The high sensitivity of the results towards the electron number density is pointed out. Finally, the influence of the processes involving Ar(2)+ on the excitation temperature is discussed.
Tear meniscus measurement in the diagnosis of dry eye (1996)

This study has shown tear meniscus assessment to be a useful alternative to existing tests for dry eye.
SPARCS: a web server to analyze (un)structured regions in coding RNA sequences (2013)

More than a simple carrier of the genetic information, messenger RNA (mRNA) coding regions can also harbor functional elements that evolved to control different post-transcriptional processes, such as mRNA splicing, localization and translation. Functional elements in RNA molecules are often encoded by secondary structure elements. In this aticle, we introduce Structural Profile Assignment of RNA Coding Sequences (SPARCS), an efficient method to analyze the (secondary) structure profile of protein-coding regions in mRNAs. First, we develop a novel algorithm that enables us to sample uniformly the sequence landscape preserving the dinucleotide frequency and the encoded amino acid sequence of the input mRNA. Then, we use this algorithm to generate a set of artificial sequences that is used to estimate the Z-score of classical structural metrics such as the sum of base pairing probabilities and the base pairing entropy. Finally, we use these metrics to predict structured and unstructured regions in the input mRNA sequence. We applied our methods to study the structural profile of the ASH1 genes and recovered key structural elements. A web server implementing this discovery pipeline is available at http://csb.cs.mcgill.ca/sparcs together with the source code of the sampling algorithm.
Materials Specificity and Directed Assembly of a Gold‐Binding Peptide (2006)

Adsorption studies of a genetically engineered gold-binding peptide, GBP1, were carried out using a quartz-crystal microbalance (QCM) to quantify its molecular affinity to noble metals. The peptide showed higher adsorption onto and lower desorption from a gold surface compared to a platinum substrate. The material specificity, that is, the preferential adsorption, of GBP1 was also demonstrated using gold and platinum micropatterned on a silicon wafer containing native oxide. The biotinylated three-repeat units of GBP1 were preferentially adsorbed onto gold regions delineated using streptavidin-conjugated quantum dots (SAQDs). These experiments not only demonstrate that an inorganic-binding peptide could preferentially adsorb onto a metal (Au) rather than an oxide (SiO2) but also onto one noble metal (Au) over another (Pt). This result shows the utility of an engineered peptide as a molecular erector in the directed immobilization of a nanoscale hybrid entity (SAQDs) over selected regions (Au) on a fairly complex substrate (Au and Pt micropatterned regions on silica). The selective and controlled adsorption of inorganic-binding peptides may have significant implications in nano- and nanobiotechnology, where they could be genetically tailored for specific use in the development of self-assembled molecular systems.
What is an adult stem cell? (2015)

Tissues may use diverse mechanisms to replace lost cells
Novel Synthesis of Silica‐Coated Ferrite Nanoparticles Prepared Using Water‐in‐Oil Microemulsion (2002)

Ferrite nanoparticles (magnetite (Fe 3 O 4 ) and cobalt‐ferrite (Co x Fe 3− x O 4 )) coated with silica (SiO 2 ) were prepared using water‐in‐oil microemulsion of a polyoxyethylen(15)cetylether/cyclohexene system. Observation via transmission electron microscopy revealed that the ferrite nanoparticles were located nearly at the center of spherical SiO 2 particles. The sizes of Fe 3 O 4 and Co x Fe 3− x O 4 nanoparticles were in the range of 8–12 nm and 10–14 nm, respectively, and the thickness of the SiO 2 layer was ∼14.0 nm. The solid solution of cobalt ions into Fe 3 O 4 to form Co x Fe 3− x O 4 nanoparticles led to an increase in the coercivity of the SiO 2 ‐coated ferrite nanoparticles. The coercivity increased with increasing amounts of added cobalt, obtaining a maximum value of 780 Oe around a Co/Fe ratio of 0.3–0.4.
Endoproteolytic Processing of the Lymphocytic Choriomeningitis Virus Glycoprotein by the Subtilase SKI-1/S1P (2003)

The envelope glycoprotein (GP) of lymphocytic choriomeningitis virus (LCMV) is posttranslationally cleaved into two subunits. We show here that this endoproteolytic processing is not required for transport to the cell surface but is essential for LCMV GP to mediate infectivity of pseudotyped retroviral vectors. By systematic mutational analysis of the LCMV GP cleavage site, we determined that the consensus motif R-(R/K/H)-L-(A/L/S/T/F)(265) is essential for the endoproteolytic processing. In agreement with the identified consensus motif, we show that the cellular subtilase SKI-1/S1P cleaves LCMV GP.
Partial-Match Retrieval Algorithms (1976)

We examine the efficiency of hash-coding and tree-search algorithms for retrieving from a file of k-letter words all words which match a partially-specified input query word (for example, retrieving all six-letter English words of the form S**R*H where “*” is a “don’t care” character). We precisely characterize those balanced hash-coding algorithms with minimum average number of lists examined. Use of the first few letters of each word as a list index is shown to be one such optimal algorithm. A new class of combinatorial designs (called associative block designs) provides better hash functions with a greatly reduced worst-case number of lists examined, yet with optimal average behavior maintained. Another efficient variant involves storing each word in several lists. Tree-search algorithms are shown to be approximately as efficient as hash-coding algorithms, on the average. In general, these algorithms require time about $O(n^{(k - s)/k} )$ to respond to a query word with s letters specified, given a file of nk-letter words. Previous algorithms either required time $O(s \cdot n/k)$ or else used exorbitant amounts of storage.
Differential degeneration of the cerebral microvasculature in Alzheimerʼs disease (1995)

We used immunocytochemical methods to define abnormalities in the cerebral endothelium and the vascular basement membrane in patients with Alzheimer's disease (AD) and in aging control subjects. Double immunostaining with antibodies to the endothelial cell markers CD34 and CD31 revealed an absence of endothelial staining in many capillary profiles that still appeared to retain their basement membranes stained by antibodies to collagen IV. Such differential labeling, clearly suggesting capillaries with collapsed or degenerated endothelium, was frequently (> 90% of cases) evident in AD but relatively lacking in brain regions or other diseases and controls (< 30%) free of amyloid beta (A beta) deposits. We suggest that this profound vascular phenomenon is concomitant with A beta deposition and implies abnormalities in the integrity of brain microvasculature related to neuronal degeneration in AD.
Improved Diagnosis and Prognosis of Mucormyucosis (1986)

Mucormycosis is an uncommon, frequently fatal, fungal infection which rarely arises in otherwise healthy people (15, 18, 92). An underlying disease, frequently diabetes mellitus, is almost always present. It appears stereotypically in different anatomic sites: paranasal, rhinoorbital, rhinocerebral, cerebral, pulmonary, and gastrointestinal areas; and in the soft tissue of the extremities. It can also appear as disseminated disease. Tissue invasion by the hyphae of mucormycosis must be seen microscopically to establish the diagnosis, but culture is required to identify the fungal species involved. A study of 33 cases seen in one hospital over five decades suggests that the incidence of this infection is increasing. There has been a dramatic improvement in outcome, which has been paralleled by a major shift from postmortem to premortem diagnosis. Premortem diagnosis gives the opportunity for metabolic stabilization, surgical excision, and amphotericin-B therapy appropriate to this disease.
Release of vasoactive peptides in the extracerebral circulation of humans and the cat during activation of the trigeminovascular system (1988)

The trigeminal ganglion was activated, in humans by thermocoagulation as part of the treatment of trigeminal neuralgia and in cats by electrical stimulation, and blood samples were taken from the external jugular vein for estimates of plasma levels of substance P and calcitonin gene-related peptide (CGRP). In those patients who were noted at the time of coagulation to have flushed there were marked elevations of the local (cranial) levels of both peptides. However, in the nonflushing patients no changes in the peptide levels were observed. Parallel experiments in the cat revealed that the levels of substance P-like and CGRP-like immunoreactivity were increased during electrical stimulation of the trigeminal ganglion. The observation of elevation of substance P-like and CGRP-like immunoreactivity after activation of the nociceptive afferent system of the head provides new insights into a putative role of peptides in the pathophysiology of migraine and cluster headache, and suggests new areas of possible therapeutic intervention.
XENOGENEIC EXTRACELLULAR MATRIX GRAFTS ELICIT A TH2-RESTRICTED IMMUNE RESPONSE1 (2001)

Porcine extracellular matrix elicits an immune response that is predominately Th2-like, consistent with a remodeling reaction rather than rejection.
New Authentication and Key Agreement Protocol for LTE-WLAN Interworking (2013)

New cellular networks are capable of providing high mobility, whereas WLANs are known for having relatively higher bandwidths. Therefore, interworking cellular networks with WLANs offers ubiquitous data services and relatively high data rates across modern networks. This interworking will enable a user to access new cellular services via a WLAN, while roaming within a range of hotspots. To provide secure 3G-WLAN interworking in the SAE/LTE architecture, Extensible Authentication Protocol-Authentication and Key Agreement (EAP-AKA) is used. However, EAP-AKA has several vulnerabilities. This paper analyzes vulnerabilities in LTE-WLAN interworking and proposes a new authentication and key agreement protocol based on EAP-AKA.
High‐Performance Biodegradable/Transient Electronics on Biodegradable Polymers (2014)

Materials and fabrication approaches that allow integration of biodegradable/transient electronics onto diverse classes of biodegradable substrates are presented in this article. By first depositing, patterning, and etching the materials for the electronics and then integrating them on a substrate of interest, it is possible to use nearly any type of biodegradable material for this purpose. Component and system-level studies of various devices and biodegradable polymers illustrate the capabilities and operational aspects. Dissolution studies and mechanics modeling results highlight different modes for transient behavior.
Membrane-Mediated Extractive Fermentation for Lactic Acid Production from Cellulosic Biomass (1997)

Lactic acid production from cellulosic biomass by cellulase and Lactobacillus delbrueckii was studied in a fermenter-extractor employing a microporous hollow fiber membrane (MHF). This bioreactor system was operated under a fed-batch mode with continuous removal of lactic acid by an in situ extraction. A tertiary amine (Alamine 336) was used as an extractant for lactic acid. The extraction capacity of Alamine 336 is greatly enhanced by addition of alcohol. Long-chain alcohols serve well for this purpose since they are less toxic to micro-organism. Addition of kerosene, a diluent, was necessary to reduce the solvent viscosity. A solvent mixture of 20% Alamine 336, 40% oleyl alcohol, and 40% kerosene was found to be most effective in the extraction of lactic acid. Progressive change of pH from an initial value of 5.0 down to 4.3 has significantly improved the overall performance of the simultaneous saccharification and extractive fermentation over that of constant pH operation. The change of pH was applied to promote cell growth in the early phase, and extraction in the latter phase.
Topical antibiotic therapy for the treatment of experimental Staphylococcus aureus keratitis. (1992)

A rabbit model of Staphylococcus aureus keratitis was developed to study the chemotherapeutic efficacy of ciprofloxacin, vancomycin, and cefazolin. Intrastromal injection of 100 colony forming units of log phase S. aureus ATCC strain 25923 resulted in rapid growth in the cornea, peaking at 10(7) cfu/cornea by 12 hr post-infection. Slit-lamp examination revealed that infected eyes reached 30% of maximum inflammation by 10 hr and 60% by 22 hr post-infection. Antibiotic therapy (one drop every 15 min for 5 hr) was initiated at 4 hr post-infection (experiment 1) or 10 hr post-infection (experiment 2). Another group was initiated at 10 hr post-infection and treated for 10 hr (experiment 3). In experiment 1, treatment from 4-9 hr post-infection with 0.3% ciprofloxacin drops decreased the cfu per cornea 6.1 logs, compared to placebo-treated controls (P = 0.0001), and rendered 50% of inoculated eyes sterile. Vancomycin (5.0%) and cefazolin (5.0%) each lowered the cfu per cornea 4.6 logs (P = 0.0187) but did not sterilize any eyes. In experiment 2, therapy from 10-15 hr post-infection with 0.3% ciprofloxacin reduced the cfu per cornea 0.9 logs (P = 0.0001). Vancomycin (5.0%) and cefazolin (5.0%) decreased the cfu per cornea 0.2 logs (P = 0.3973) and 0.3 logs (P = 0.1307), respectively. In experiment 3, therapy from 10-20 hr post-infection with 0.3% ciprofloxacin reduced the cfu per cornea 3.9 logs (P < 0.0001). In this keratitis model, ciprofloxacin was more effective than vancomycin or cefazolin in killing S. aureus.
Intrapleural Tissue Plasminogen Activator and Deoxyribonuclease for Pleural Infection. An Effective and Safe Alternative to Surgery (2014)

This large series of patients who received intrapleural tPA/DNase therapy provides important evidence that the treatment is effective and safe, especially as a "rescue therapy" in patients who do not initially respond to antibiotics and thoracostomy drainage.
Electroencephalographic Findings in Ornithine Transcarbamylase Deficiency (1999)

A 3-day-old infant presented with anorexia, irritability, hypotonia, and seizures. Blood ammonia was 2115 micromol/L and amino and organic acid analyses were consistent with ornithine transcarbamylase deficiency. Liver biopsy confirmed only 1% enzyme activity. The patient was treated with hemodialysis. An electroencephalogram (EEG) revealed multifocal independent spike-and-sharp-wave discharges. After initial stabilization he was placed on a low-protein diet with citrulline and phenylbutyrate. Conjugating agents (arginine, sodium benzoate, and sodium phenylacetate) have been added during periods of metabolic decompensation. Although developmentally delayed, the patient has shown signs of clinical improvement and EEG activity has likewise improved with only mild background slowing and no evidence of epileptogenic activity at 4 years of age. A second infant presented at 3 days of age with a similar history, blood ammonia of 1382 micromol/L, and metabolic studies indicative of ornithine transcarbamylase deficiency. EEG showed multifocal independent ictal and interictal discharges. Electrographic abnormalities persisted despite lowering of blood ammonia with hemodialysis and conjugating agents. The patient continued to decline clinically and died on the 7th hospital day. EEG changes parallel the clinical course of ornithine transcarbamylase deficiency and may serve as an objective marker of the effectiveness of therapeutic interventions.
Targeting Proteins for Destruction by the Ubiquitin System: Implications for Human Pathobiology (2008)

Cellular proteins are in a dynamic state maintained by synthesis and degradation. The ubiquitin proteolytic pathway is responsible for the degradation of the bulk of cellular proteins including short-lived, regulatory, and misfolded/denatured proteins. Ubiquitin-mediated proteolysis involves covalent attachment of multiple ubiquitin molecules to the protein substrate and degradation of the targeted protein by the 26S proteasome. Recent understanding of the molecular mechanisms involved provides a framework to understand a wide variety of human pathophysiological states as well as therapeutic interventions. This review focuses on the response to hypoxia, inflammatory diseases, neurodegenerative diseases, and muscle-wasting disorders, as well as human papillomaviruses, cervical cancer and other malignancies.