gebhart/patrepeval huggingface dataset:
A molecular sensor system based on genetically engineered alkaline phosphatase. (1995)

Binding and signaling proteins based on Escherichia coli alkaline phosphatase (AP; EC 3.1.3.1) were designed for the detection of antibodies. Hybrid proteins were constructed by using wild-type AP and point mutants of AP [Asp-101 --> Ser (D101S) and Asp-153 --> Gly (D153G)]. The binding function of the hybrid proteins is provided by a peptide epitope inserted between amino acids 407 and 408 in AP. Binding of anti-epitope antibodies to the hybrid proteins modulates the enzyme activity of the hybrids; upon antibody binding, enzyme activity can increase to as much as 300% of the level of activity in the absence of antibody or can decrease as much as 40%, depending on the presence or absence of the point mutations in AP. The fact that modulation is altered from inhibition to activation by single amino acid changes in the active site of AP suggests that the mechanism for modulation is due to structural alterations upon antibody binding. Modulation is a general phenomenon. The properties of the system are demonstrated by using two epitopes, one from the V3 loop of human immunodeficiency virus type 1 gp120 protein and one from hepatitis C virus core protein, and corresponding monoclonal antibodies. The trend of modulation is consistent for all hybrids; those in wild-type AP are inhibited by antibody, while those in the AP mutants are activated by antibody. This demonstrates that modulation of enzyme activity of the AP-epitope hybrid proteins is not specific to either a particular epitope sequence or a particular antibody-epitope combination.
Disease-Suppressive Soil and Root-Colonizing Bacteria (1982)

Soils in many areas suppress certain plant diseases. Understanding the basis for this disease suppressiveness could lead to improved plant health in less favorable areas. Some forms of disease suppression may be caused by bacteria in the genus Pseudomonas which aggressively colonize root surfaces. Increased plant growth and yield are closely associated with the capacity of some of these bacteria to produce iron-binding compounds called siderophores. This article addresses the biological characteristics of these soil-bome root epiphytes, their contribution to plant health, and their potential use in biotechnology.
Engineering of an Escherichia coli Strain for the Production of 3-Methyl-1-Butanol (2008)

3-Methyl-1-butanol is a potential fuel additive or substitute. Previously this compound was identified in small quantities in yeast fermentation as one of the fusel alcohols. In this work, we engineered an Escherichia coli strain to produce 3-methyl-1-butanol from glucose via the host's amino acid biosynthetic pathways. Strain improvement with the removal of feedback inhibition and competing pathways increased the selectivity and productivity of 3-methyl-1-butanol. This work demonstrates the feasibility of production of 3-methyl-1-butanol as a biofuel and shows promise in using E. coli as a host for production.
Third generation cephalosporins as a risk factor for Clostridium difficile-associated disease: a four-year survey in a general hospital (1989)

The main clinical features of patients who developed pseudomembranous colitis (PMC) or Clostridium difficile-associated diarrhoea (CDAD) during their stay at the S. Anna General Hospital, Como, over the period February 1984 to May 1988, are reported. Forty patients developed either CDAD (ten cases) or PMC (30 cases). Twenty-seven (65.7%) had undergone surgery and 32 (80.0%) had received prolonged antibiotic treatment. Three patients (7.5%) were given three doses only of ceftriaxone. Five patients (12.5%) had not received any antibiotic treatment; but three were nursed in a bed next to a patient with PMC-CDAD. The number of cases diagnosed were correlated retrospectively with the cumulative consumption of different groups of antibiotics on wards in which PMC or CDAD occurred. A significant difference (P less than 0.01) between third generation cephalosporins (16 cases) and ureidopenicillins (one case), was found. Twenty-five patients were treated with oral vancomycin. Two died of the underlying disease and 23 were cured. The disease recurred clinically in three, and follow-up cultures were positive in another asymptomatic case. Fifteen patients (all PMC cases) were treated with oral teicoplanin. All were clinically cured and remained asymptomatic and all but one were also cleared of C. difficile. No adverse reactions were observed in patients given either drug. Third generation cephalosporins, even when administered as short-term perioperative prophylaxis, but not ureidopenicillins, are significantly associated with C. difficile-related diseases. Teicoplanin proved to be very effective and safe in the treatment of PMC, and should be further evaluated there.
Formation of Lactyl-Coenzyme A and Pyruvyl-Coenzyme A from Lactic Acid byEscherichia coli (1965)

Megraw, Robert E. (Albert Einstein Medical Center, Philadelphia, Pa.), Henry C. Reeves, and Samuel J. Ajl. Formation of lactyl-coenzyme A and pyruvyl-coenzyme A from lactic acid by Escherichia coli. J. Bacteriol. 90:984-988. 1965.-Cell extracts of propionate-adapted Escherichia coli were found to contain a lactyl-coenzyme A (CoA) synthetase which catalyzes the formation of the CoA thiolester from lactate, CoA, and cofactors. The extracts also catalyzed the nicotinamide adenine dinucleotide-dependent oxidation of lactyl-CoA. The product of this oxidation was identified chromatographically as pyruvyl-CoA.
Paclitaxel Gelatin Nanoparticles for Intravesical Bladder Cancer Therapy (2011)

Constant drug release from paclitaxel gelatin nanoparticles may overcome the problem of drug dilution by newly produced urine and the sustained drug levels in tumors may decrease treatment frequency.
Evaluation on Masks with Exhaust Valves and with Exhaust Holes fromPhysiological and Subjective Responses (2008)

The purpose of this study was to compare the effects of wearing different kinds of masks on the ear canal temperature, heart rate, clothing microclimate, and subjective perception of discomfort. Ten subjects performed intermittent exercise on a treadmill while wearing the protective masks in a climatic chamber controlled at an air temperature of 25 degrees C and a relative humidity of 70%. Two types of mask-mask A, with exhaust valves and mask B, with exhaust holes-were used in the study. The results of this study indicated: (1) The subjects had a tendency toward lower maximum heart rate when wearing mask A than when wearing mask B. (2) Temperatures and absolute humidities (the outer surface of mask, the microclimate inside the mask, the chest wall skin and microclimate) of mask A were significantly lower than those of mask B. (3) The ear canal temperature increased significantly in mask B as compared to that in mask A. (4) The ear canal temperature showed significant augmentation along with increased temperature and humidity inside the mask microclimate. The mask microclimate temperature also affected significantly the chest microclimate temperature. (5) Mask A was rated significantly lower for perception of humidity, heat, breath resistance, tightness, unfitness, odor, fatigue, and offered less overall discomfort than mask B. (6) Subjective preference for mask A was higher. (7) The ratings of subjective overall discomfort showed significant augmentation along with increased wetness and fatigue. We discuss how the ventilation properties of masks A and B induce significantly different temperature and humidity in the microclimates of the masks and the heat loss of the body, which have profound influences on heart rate, thermal stress, and subjective perception of discomfort.
EDEM As an Acceptor of Terminally Misfolded Glycoproteins Released from Calnexin (2003)

Terminally misfolded proteins in the endoplasmic reticulum (ER) are retrotranslocated to the cytoplasm and degraded by proteasomes through a mechanism known as ER-associated degradation (ERAD). EDEM, a postulated Man8B-binding protein, accelerates the degradation of misfolded proteins in the ER. Here, EDEM was shown to interact with calnexin, but not with calreticulin, through its transmembrane region. Both binding of substrates to calnexin and their release from calnexin were required for ERAD to occur. Overexpression of EDEM accelerated ERAD by promoting the release of terminally misfolded proteins from calnexin. Thus, EDEM appeared to function in the ERAD pathway by accepting substrates from calnexin.
Receptor for Advanced Glycation End Products and Age-Related Macular Degeneration (2004)

Immunolocalization of RAGE in RPE and photoreceptors coincided with AGE deposits and macular disease in aged, early AMD, and GA retinas. Further, AGE stimulated RAGE-mediated activation of cultured ARPE-19 cells in a dose-dependent fashion. AGE accumulation, as occurs with normal aging and in disease, may induce receptor-mediated activation of RPE/photoreceptor cells, contributing to disease progression in the aging human retinas.
Automated analysis of digital oximetry in the diagnosis of obstructive sleep apnoea (2000)

In a population of patients suspected of having OSA, off line automated analysis of the oximetry signal provides a close estimate of AHI as well as excellent diagnostic sensitivity and specificity for OSA.
Localization and Developmental Regulation of a Dispersed Gene Family 1 Protein in Trypanosoma cruzi (2009)

The dispersed gene family 1 (DGF-1) is the fifth largest gene family in the Trypanosoma cruzi genome, with over 500 members (11). Many of the predicted DGF-1 protein products have several transmembrane domains and N-glycosylation and phosphorylation sites and were thought to localize in the plasma membrane. Here, we report that affinity-purified antibodies against a region of one of these proteins (DGF-1.2) localized it intracellularly in different stages of the parasite. DGF-1.2 is more abundant in the amastigote stage than in trypomastigotes and epimastigotes, as detected by immunofluorescence and Western blot analyses. The protein changed localization during intracellular or extracellular differentiation from the trypomastigote to the amastigote stage, where it finally localized to small bodies in close contact with the inner side of the amastigote plasma membrane. DGF-1.2 did not colocalize with markers of other subcellular organelles, such as acidocalcisomes, glycosomes, reservosomes, lipid droplets, or endocytic vesicles. During extracellular differentiation, the protein was detected in the culture medium from 0 to 22 h, peaking at 14 h. The presence of DGF-1.2 in the differentiation culture medium was confirmed by mass spectrometry analysis. Finally, when epimastigotes were subjected to starvation, there was a decrease in the labeling of the cells and, in Western blots, the appearance of bands of lower molecular mass, suggesting its cleavage. These results represent the first report of direct immunodetection and developmental expression and secretion of a DGF-1 protein.
Inhibition of pseudomonal ulceration in rabbit corneas by a synthetic matrix metalloproteinase inhibitor. (1996)

Pseudomonal protease activity in culture broth consisted predominantly of metalloproteinases and were effectively inhibited by Galardin in vitro. Topical treatment with Galardin prevented destruction of rabbit corneas by bacterial products present in culture broth, and it delayed corneal destruction after injection of PA bacteria. Galardin may be a useful adjuvant when corneal destruction proceeds despite prompt antibiotic treatment.
SOX10 Expression in Malignant Melanoma, Carcinoma, and Normal Tissues (2013)

Sry-related HMg-Box gene 10 (SOX10) is a nuclear transcription factor that plays an important role in melanocytic cell differentiation. It has been shown to be a sensitive marker of melanoma including spindle and desmoplastic subtypes. We assessed its frequency of expression in melanoma, carcinoma, benign nevi, and non-neoplastic tissues with routine immunohistochemistry for SOX10. The 109 primary melanoma included 49 epithelioid, 19 spindle cell, 22 desmoplastic, and 19 mixed spindle cell/desmoplastic melanoma. All primary, except 8 desmoplastic melanoma, and 11 metastatic melanoma were strongly and diffusely nuclear SOX10-positive. Six desmoplastic melanoma had ≤10% cells positive, and 2 were <50% positive, all of 3+ intensity. Eighteen of 149 (12%) breast carcinoma were SOX10-positive. All 24 ovarian, 23 endometrial, 26 lung, and 25 colon carcinoma were SOX10-negative. All 43 benign nevi, 18 dysplastic nevi, 68 non-neoplastic and benign skins, and all 56 non-neoplastic breast tissue were SOX10-positive. The sensitivity and specificity for SOX10 in the diagnosis of melanoma are 1.0 and 0.93, respectively; the positive and negative predictive values are 0.87 and 1.0, respectively. SOX10 is a sensitive, specific marker for melanoma. As benign nevi also express SOX10, it cannot be used to differentiate between benign and malignant pigmented skin lesions. Only a small number of breast carcinoma (12%), and breast lobules, express SOX10; no carcinoma of the ovary, endometrium, lung, or colon expressed SOX10.
Geographical survey of beta S-globin gene haplotypes: evidence for an independent Asian origin of the sickle-cell mutation. (1986)

The haplotypes of 152 beta S-chromosomes were characterized in six different population groups. The chromosomes of individuals from Nigeria and from the southwest of the Arabian peninsula have the haplotype - - - - + + - + previously found in west African, Jamaican, and U.S. American blacks, whereas those from the eastern oases of Saudi Arabia and from the west and the east coast of India showed a different haplotype not found in Africa (+ + - + + + + -). These data are most consistent with an independent Asian origin of the sickle-cell mutation and provide further information about the geographic distribution of beta S-haplotypes in the Old World. The distribution of the Asian beta S-haplotype corresponds to the reported geographic distribution of a mild clinical phenotype of homozygous SS disease.
Robust treatment of simultaneous collisions (2008)

Robust treatment of complex collisions is a challenging problem in cloth simulation. Some state of the art methods resolve collisions iteratively, invoking a fail-safe when a bound on iteration count is exceeded. The best-known fail-safe rigidifies the contact region, causing simulation artifacts. We present a fail-safe that cancels impact but not sliding motion, considerably reducing artificial dissipation. We equip the proposed fail-safe with an approximation of Coulomb friction, allowing finer control of sliding dissipation.
Tactical driver behavior prediction and intent inference: A review (2011)

Drawing upon fundamental research in human behavior prediction, recently there has been a research focus on how to predict driver behaviors. In this paper we review the field of driver behavior and intent prediction, with a specific focus on tactical maneuvers, as opposed to operational or strategic maneuvers. The aim of a driver behavior prediction system is to forecast the trajectory of the vehicle prior in real-time, which could allow a Driver Assistance System to compensate for dangerous or uncomfortable circumstances. This review provides insights into the scope of the problem, as well as the inputs, algorithms, performance metrics, and shortcomings in the state-of-the-art systems.
Application of the needle optimization technique to the design of optical coatings (1996)

The authors' experience with the application of the needle optimization technique to the design of optical coating is summarized. A physical interpretation of the technique is provided, and its main features are identified. Guidelines on the application of the needle optimization technique to various types of design problems are given.
The Nucleotide Sequence of the Equine Herpesvirus 4 Thymidine Kinase Gene (1990)

We have determined the genomic location and nucleotide sequence of the equine herpesvirus 4 thymidine kinase (TK) gene. The gene is positioned at approximately 0.48 map units within the long unique component of the genome and is flanked by genes encoding a herpes simplex virus 1 (HSV-1) UL24 homologue and glycoprotein H. The predicted protein is composed of 352 amino acids, has an Mr of 38,800 and exhibits 36% identity to the predicted TK of HSV-1.
Melatonin protects SHSY5Y neuroblastoma cells from cobalt‐induced oxidative stress, neurotoxicity and increased β‐amyloid secretion (2001)

Heavy metals are increasingly being implicated as causative agents in neurodegenerative diseases such as Alzheimer's disease (AD). Cobalt, a positively charged transition metal, has previously been shown to be in elevated levels in the brain of AD patients compared with age-matched controls. In this study, we investigate the effects of cobalt as an inducer of oxidative stress/cell cytotoxicity and the resultant metabolic implications for neural cells. We show that cobalt is able to induce cell cytotoxicity (reduced MTT metabolism) and oxidative stress (reduced cellular glutathione). The pre-treatment of cells with the pineal indoleamine melatonin, prevented cell cytotoxicity and the induction of oxidative stress. Cobalt treatment of SHSY5Y cells increased the release of beta-amyloid (Abeta) compared with untreated controls (ratio Abeta 40/42). Melatonin pre-treatment reversed the deleterious effects of cobalt. These findings are significant as cobalt is an essential nutritional requirement, usually bound to cobalamin (vitamin B12), for all animals which in the unbound form could lead to neurotoxicity.
Properties of the collagenous domain of the alpha 3(IV) chain, the Goodpasture antigen, of lens basement membrane collagen. Selective cleavage of alpha (IV) chains with retention of their triple helical structure and noncollagenous domain (1991)

A third chain, alpha 3(IV), of basement membrane collagen was recently discovered and was identified as the primary target for the autoantibodies of patients with Goodpasture syndrome (Saus, J., Wieslander, J., Langeveld, J. P. M., Quinones, S., and Hudson, B. G. (1988) J. Biol. Chem. 263, 13374-13380). In the present study, this chain was excised in the form of a truncated promoter by cleavage of basement membrane with Pseudomonas aeruginosa elastase and characterized. The triple helical structure and NC1 domain were retained. Elastase selectively cleaved at a site within the triple helical domain of the alpha 3 chain that is distinct from the cleavage site of the alpha 1 and alpha 2 chains. The truncated alpha 3 chain was found to contain 1460 residues, of which 1225 comprise the collagenous domain, and is cross-linked within this domain by disulfide bonds, forming a high Mr complex (greater than 300,000). Truncated protomers with a length of 340 nm corresponding to the theoretical length for the truncated alpha 3 chain were observed by electron microscopy as suprastructures in which the triple helical domains of three protomers were interwined. These protomers were also connected to each other and to the 140-nm protomers that appear to be comprised of the alpha 1 and alpha 2 chains. These results extended the known length of the alpha 3 chain by about 1000 residues and suggested that protomers of this chain self-associate through interactions between their triple helical domains and between their NC1 domains.
No Significant Molecular Response in Polycythemia Vera Patients Treated with Imatinib or Interferon alpha. (2005)

Abstract Imatinib mesylate and interferon alpha (rIFNa) have both been reported to induce remission in patients with polycythemia vera (PV), but until recently it has not been possible generally to gauge the depth of these responses due to the absence of a specific cytogenetic or molecular marker of the disease. Here we have used ARMS and pyrosequencing assays to detect and quantify the V617F JAK2 mutation in granulocytes or mononuclear cells from 111 PV patients, of whom 14 were undergoing treatment with imatinib (300–800 mg/day; median follow up 17 months; range 5–31), seven were undergoing treatment with rIFNa (dose range from 2MU three times/week to 3MU/day; median follow up 60 months; range 13–132), and 90 were untreated or treated only by phlebotomy, hydroxyurea or anagrelide (control group). Clinical responses in the 14 imatinib treated cases were none (NR; n=3), partial (PR; n=9) or complete (CR; n=2); responses in the seven rIFNa treated cases were PR (n=1) or CR (n=6). The V617F mutation was detected in all cases undergoing treatment with imatinib or rIFNa and in 82 (91%) of the control PV cases. The median percentage of mutated JAK2 alleles (%V617F) did not differ significantly between the imatinib treated cases (median 59%, range 8–91), the rIFNa treated cases (median 27%, range 19–87) or the V617F positive cases from the control group (median 53%, range 5–100). In the imatinib group, the median %V617F for cases with NR, PR and CR were 72% (44–89; n=3), 60% (30–91; n=9) and 15% (8 and 21; n=2), respectively. In the rIFNa treated group the single case with a PR had 87% V617F compared to a median of 26% (19–39) for the six cases in CR. Pretreatment samples were available for 9 of the imatinib treated cases. Of these, all seven of the NR or PR cases showed a marginal increase (median 1.2 fold, range 1.0–1.5) in the percentage of V617F alleles on treatment. In contrast, the two CR patients showed a 2–3 fold reduction in %V617F on treatment. We conclude that although PV patients may benefit from treatment with imatinib or rIFNa, molecular analysis indicates that responses are modest.
Standards for the diagnosis and treatment of patients with COPD: a summary of the ATS/ERS position paper (2004)

The Standards for the Diagnosis and Treatment of Patients with COPD document 2004 updates the position papers on chronic obstructive pulmonary disease (COPD) published by the American Thoracic Society (ATS) and the European Respiratory Society (ERS) in 1995 1, 2. Both societies felt the need to update the previous documents due to the following. 1) The prevalence and overall importance of COPD as a health problem is increasing. 2) There have been enough advances in the field to require an update, especially adapted to the particular needs of the ATS/ERS constituency. 3) It allows for the creation of a “live” modular document based on the web; it should provide healthcare professionals and patients with a user friendly and reliable authoritative source of information. 4) The care of COPD should be comprehensive, is often multidisciplinary and rapidly changing. 5) Both the ATS and the ERS acknowledge the recent dissemination of the Global Initiative of Obstructive Lung Disease (GOLD) 3 as a major worldwide contribution to the battle against COPD. However, some specific requirements of the members of both societies require adaptation of the broad GOLD initiative. Those requirements include specific recommendations on oxygen therapy, pulmonary rehabilitation, noninvasive ventilation, surgery in and for COPD, sleep, air travel, and end-of-life. In addition, special emphasis has been placed on issues related to the habit of smoking and its control.

### Goals and objectives

The main goals of the updated document are to improve the quality of care provided to patients with COPD and to develop the project using a disease-oriented approach. To achieve these goals, both organisations have developed a modular electronic web-based document with two components. 1) A component for health professionals that intends to: raise awareness of COPD; inform on the latest advances in the overall pathogenesis, diagnosis, monitoring and management of COPD; and …