gebhart/patrepeval huggingface dataset:
Distinct Secondary Structures of the Leucine-rich Repeat Proteoglycans Decorin and Biglycan (1999)

Biglycan and decorin have been overexpressed in eukaryotic cells and two major glycoforms isolated under native conditions: a proteoglycan substituted with glycosaminoglycan chains; and a core protein form secreted devoid of glycosaminoglycans (Hocking, A. M., Strugnell, R. A., Ramamurthy, P., and McQuillan, D. J. (1996) J. Biol. Chem. 271, 19571-19577; Ramamurthy, P., Hocking, A. M., and McQuillan, D. J. (1996) J. Biol. Chem. 271, 19578-19584). Far-UV CD spectroscopy of decorin and biglycan proteoglycans indicates that, although they are predominantly beta-sheet, biglycan has a significantly higher content of alpha-helical structure. Decorin proteoglycan and core protein are very similar, whereas the biglycan core protein exhibits closer similarity to the decorin glycoforms than to the biglycan proteoglycan form. However, enzymatic removal of the chondroitin sulfate chains from biglycan proteoglycan does not induce a shift to the core protein structure, suggesting that the final form is influenced by polysaccharide addition only during biosynthesis. Fluorescence emission spectroscopy demonstrated that the single tryptophan residue, which is at a conserved position at the C-terminal domain of both biglycan and decorin, is found in similar microenvironments. This indicates that in this specific domain the different glycoforms do exhibit apparent conservation of structure. Exposure of decorin and biglycan to 10 M urea resulted in an increase in fluorescent intensity, which indicates that the emission from tryptophan in the native state is quenched. Comparison of urea-induced protein unfolding curves provide further evidence that decorin and biglycan assume different structures in solution. Decorin proteoglycan and core protein unfold in a manner similar to a classic two-state model, in which there is a steep transition to an unfolded state between 1 and 2 M urea. The biglycan core protein also shows a similar steep transition. However, biglycan proteoglycan shows a broad unfolding transition between 1 and 6 M urea, probably indicating the presence of stable unfolding intermediates.
Inhibition of alcoholic fermentation by substrate and ethanol (1980)

Abstract The effect of ethanol and sugars on rates of fermentation was studied. We used a strain of Canadida pseudotropicalis . The specific rate of fermentation was determined by using the Warburg manometer. The effect of ethanol was formulated as an exponential function of ethanol concentration, but the empirical constant was different when glucose or lactose was used as a substrate. The effects of both ethanol and substrate were formulated. It was demonstrate that when lactose and glucose were present in the medium with a small amount of alcohol, a synergistic effect on the rate of fermentation appeard. This phenomenon considerably limits the rate of fermentation.
Cancer Detection at your Fingertips: Smartphone-Enabled DNA Testing (2018)

High molecular weight cell-free DNA (hmw cfDNA) found in biological fluid, such as blood, is a promising biomarker for cancer detection. Due to the abundance of background apoptotic cell-free DNA in blood, quantifying the native concentration of hmw cfDNA using existing methods is technically challenging, time consuming, and expensive. We have developed a novel technology which utilizes Alternating Current Electrokinetics (ACE) to isolate hmw cfDNA directly from blood. Furthermore, we integrated this technology into a handheld device which utilizes a smartphone for power, instruction transmission, optical detection, image processing, and data transmission. The detection of hmw cfDNA in blood plasma demonstrated the performance of the device. We are continuing development of this device as a future point of care in vitro diagnostic.
The 5'-flanking region of the rat synapsin I gene directs neuron-specific and developmentally regulated reporter gene expression in transgenic mice. (1993)

The expression of the synapsin I gene is neuron-specific and developmentally regulated. As a step toward characterizing the molecular mechanisms that are responsible for its transcriptional regulation in vivo, we have generated transgenic mice that carry the chloramphenicol acetyltransferase (CAT) receptor gene under the control of approximately 4,300 nucleotides of 5'-flanking sequence of the rat synapsin I gene. In four independent transgenic mouse lines, high level CAT expression is observed specifically in the brain and other neural tissues. Two of these lines also exhibit notable CAT expression in testis. The transgene is expressed at similar levels in many different regions of the central nervous system. Immunohistochemical staining detects the CAT marker protein in various cell populations of neuronal morphology within the brain and the spinal cord. Transgene expression is developmentally regulated in a way that correlates well with the expression of the endogenous synapsin I gene. Both follow a characteristic, biphasic postnatal time course with a maximum around day 20. We conclude that the DNA region investigated contains cis-regulatory elements sufficient to drive the expression of a reporter gene in a spatial and temporal pattern that resembles the expression of the endogenous synapsin I gene.
<title>Tunable Diode Laser Measurements Of Carbon Monoxide In Engine Exhaust</title> (1983)

In the past few years we have made several studies of carbon monoxide (CO) in automotive exhaust with lead-salt tunable diode lasers. The laser system has several advantages over conventional exhaust analysis instrumentation including a fast response time (25 milliseconds) and the ability to measure CO in the presence of water vapor without interference. These studies were done using an engine dynamometer with a 5.7 &ell; V-8 engine. Initially, the CO was measured before and after the exhaust catalytic converter during step changes in the air-fuel ratio to study the dynamic response of the converter. The converter responded differently when the air-fuel ratio was switched from lean to rich than it did when switched from rich to lean. This behavior was attributed to chemical storage effects on the converter bed, among other factors. Next, the engine was closed-loop controlled at a given CO concentration level using the diode laser as a CO sensor rather than the conven-tional oxygen sensor. Limit cycle oscillations of the closed-loop system were substantially reduced by this method. Finally, a linearized model of the engine&apos;s CO emissions was developed based on the TDL measurements of CO during oscillation of the air-fuel ratio at different engine operating conditions.
Cutting Edge: Role of C-C Chemokine Receptor 5 in Organ-Specific and Innate Immunity to Cryptococcus neoformans (1999)

After intratracheal inoculation of the AIDS-associated pathogen Cryptococcus neoformans, 12-wk survival was >90% for CCR5+/+ mice but <25% for CCR5-/- mice. There were no defects in lung leukocyte recruitment (wk 5), pulmonary clearance, or delayed-type hypersensitivity in CCR5-/- mice. However, CCR5-/- mice had defects in leukocyte recruitment into the brain and, strikingly, in elimination of cryptococcal polysaccharide from the brain. In nonimmune CCR5-/- mice, there was a significant defect in macrophage recruitment after challenge with shed cryptococcal products (C. neoformans filtrate Ag) but not other nonspecific stimuli. Thus, CCR5 plays specific roles in innate immunity and organ-specific leukocyte trafficking during host defense against C. neoformans.
The Scalable Tree Protocol-a cache coherence approach for large-scale multiprocessors (2003)

The problem of cache coherence in large-scale shared-memory multiprocessors has been addressed using directory-schemes. Two problems arise when the number of processors increases: the network latency increases and the implementation cost must be kept acceptable. The authors present a tree-based cache coherence protocol called the scalable tree protocol (STP). They show that it can be implemented at a reasonable implementation cost and that the write latency is logarithmic to the size of the sharing set. How to maintain an optimal tree structure and how to handle replacements efficiently are critical issues the authors address for this type of protocol. They compare the performance of the STP with that of the scalable coherent interface (SCI) (IEEE standard P1596) by considering a classical matrix-oriented algorithm targeted for large-scale parallel processing. They show that the STP manages to reduce the execution time considerably by reducing the write latency.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An algorithm for computing nucleic acid base‐pairing probabilities including pseudoknots (2004)

Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of physically relevant pseudoknots. Here, we present a method for computing base-pairing probabilities starting from the output of this partition function algorithm. The approach relies on the calculation of recursion probabilities that are computed by backtracking through the partition function algorithm, applying a particular transformation at each step. This transformation is applicable to any partition function algorithm that follows the same basic dynamic programming paradigm. Base-pairing probabilities are useful for analyzing the equilibrium ensemble properties of natural and engineered nucleic acids, as demonstrated for a human telomerase RNA and a synthetic DNA nanostructure.
Decreased type VI adenylyl cyclase mRNA concentration and Mg2+-dependent adenylyl cyclase activities and unchanged type V adenylyl cyclase mRNA concentration and Mn2+-dependent adenylyl cyclase activities in the left ventricle of rats with myocardial infarction and longstanding heart failure (1999)

Longstanding LV hypertrophy and failure resulting from MI in rats is not associated with altered expression of the most abundant, type V, AC mRNA isoform, whereas that of type VI is decreased. The lack of change in Mn(2+)-dependent AC activities in the LV of F rats suggests that this decrease has no functional consequence on overall AC activity and that decreased Mg(2+)-dependent activities are related to alterations occurring upstream.
An assessment and evaluation of computer science education (2003)

This research shows an audience of fellow computer science teachers that there is benefit in testing college student's scientific reasoning skills and that the students increase their logical thinking skills in computer science classes when they are presented with real world problems, engaged in group activities, and given hands-on experiments.Students' scientific reasoning skills from several different computer science courses are analyzed and tested before and after taking the computer science course to measure their improvement in logical thinking. The higher order thinking skills test results are compared, and the overall class and individual student improvement between the classes that use different teaching strategies are analyzed. Also, the test results are compared with students' ability to perform adequately in a computer science course. This information is valuable to advisors when placing students in computer science courses.In the assessments of students' entering knowledge and evaluations of students' thinking improvement, the students' individual higher order thinking skills as well as their overall level of cognitive development are analyzed. Through the analysis of their individual skills and level of thinking, one can expand conclusions about the students' and teacher's performance over time.
Relationships among capsular structure, phagocytosis, and mouse virulence in Klebsiella pneumoniae (1995)

Klebsiella pneumoniae strains of the K2 capsular serotype are usually highly virulent in mice, which is in contrast to the low virulence of most other serotypes. Here we used a genetic approach to examine the relative contribution of capsule type to the virulence of K. pneumoniae in mice. We used wild-type strains expressing capsular polysaccharide (CPS) serotypes K2 (strain KPA1) and K21a (strains KPB1 and KPC1), which were then used to construct capsule-switched derivatives. The close proximity of the cps gene cluster to selectable his markers made it possible to mobilize the cps genes by conjugation from one serotype (donor) to another (recipient) and to obtain recombinants in which interserotype switching had occurred by reciprocal recombination. Each capsule-switched derivative examined of the KPA and KPC strain backgrounds produced a CPS that was immunologically and structurally identical to that of the donor. Strain background was confirmed by demonstrating restriction fragment length polymorphism patterns identical to those of the respective recipients. The parent strains were then compared with capsule-switched recombinants for phenotypic properties associated with virulence. Clearance from the bloodstreams of mice was rapid in serotype K21a strains of either wild-type or recombinant origin, whereas K2 strains remained viable in the blood during the period examined. These differences appeared to be dependent upon the CPS type but independent of strain background. Binding to macrophages was higher in K21a strains than in those with the K2 capsule and was also independent of the strain background. Both blood clearance and macrophage-binding activities were completely inhibited by yeast mannan, suggesting that they were mediated via the macrophage mannose receptor. The K2 parent strain was highly virulent to mice (50% lethal dose [LD50], 3 x 10(3)), while the K21a parent strains demonstrated low virulence (LD50, > 2 x 10(8)). Interestingly, the virulence of recombinant KPC10(cpsK2), originally of the KPC1(cpsK21a) background, was intermediate (LD50, 4 x 10(5)). In contrast, both cpsK21a recombinants of the originally virulent KPA1 (cpsK2) background became nearly avirulent (LD50, > 2 x 10(8)). Six additional serotypes (K12, K24, K32, K55, K62, and K67) were examined, and all showed a positive correlation between the ability of the Klebsiella serotype to interact with a human mannose receptor, as expressed by Cos I cell recombinants, and the LD50 of the serotype. These results suggest that expression of a capsule which is recognized by the mannose receptor markedly affects the interaction with macrophages and blood clearance.(ABSTRACT TRUNCATED AT 400 WORDS)
Engineered Escherichia coli with Periplasmic Carbonic Anhydrase as a Biocatalyst for CO2Sequestration (2013)

Carbonic anhydrase is an enzyme that reversibly catalyzes the hydration of carbon dioxide (CO2). It has been suggested recently that this remarkably fast enzyme can be used for sequestration of CO2, a major greenhouse gas, making this a promising alternative for chemical CO2 mitigation. To promote the economical use of enzymes, we engineered the carbonic anhydrase from Neisseria gonorrhoeae (ngCA) in the periplasm of Escherichia coli, thereby creating a bacterial whole-cell catalyst. We then investigated the application of this system to CO2 sequestration by mineral carbonation, a process with the potential to store large quantities of CO2. ngCA was highly expressed in the periplasm of E. coli in a soluble form, and the recombinant bacterial cell displayed the distinct ability to hydrate CO2 compared with its cytoplasmic ngCA counterpart and previously reported whole-cell CA systems. The expression of ngCA in the periplasm of E. coli greatly accelerated the rate of calcium carbonate (CaCO3) formation and exerted a striking impact on the maximal amount of CaCO3 produced under conditions of relatively low pH. It was also shown that the thermal stability of the periplasmic enzyme was significantly improved. These results demonstrate that the engineered bacterial cell with periplasmic ngCA can successfully serve as an efficient biocatalyst for CO2 sequestration.
Transcranial Magnetic Stimulation in Mania: A Controlled Study (1998)

The therapeutic effect of transcranial magnetic stimulation in mania may show laterality opposite to its effect in depression.
Insulin Response in Relation to Insulin Sensitivity (2009)

Black South African women are more insulin resistant than their white counterparts but compensate by increasing their insulin response to maintain normal glucose levels, suggesting an appropriate beta-cell response for the level of insulin sensitivity.
Synthesis of 3-aryl-1,4-benzoxathianes: application to the preparation of a sweet compound (1994)

Attempts to prepare 3-phenyl-1,4-benzoxathiane by acid-catalysed ring-closure of 2-(2-hydroxyphenylthio)-2-phenylethanol gave instead 2-phenyl-1,4- benzoxathiane, via a rearrangement probably involving an episulfonium ion. The first synthesis of 3-aryl-1,4-benzoxathianes was obtained by N-bromosuccinimide-promoted oxidative rearrangement of 1,3-oxathiolanes derived from cyclohexanone. The application of this route to the synthesis of 3-(3-hydroxy-4-methoxyphenyl)-1,4-benzoxathiane, a compound ca. 2000 times as sweet as sucrose, is reported.
Pain as a channelopathy (2010)

Mendelian heritable pain disorders have provided insights into human pain mechanisms and suggested new analgesic drug targets. Interestingly, many of the heritable monogenic pain disorders have been mapped to mutations in genes encoding ion channels. Studies in transgenic mice have also implicated many ion channels in damage sensing and pain modulation. It seems likely that aberrant peripheral or central ion channel activity underlies or initiates many pathological pain conditions. Understanding the mechanistic basis of ion channel malfunction in terms of trafficking, localization, biophysics, and consequences for neurotransmission is a potential route to new pain therapies.
Evidence of multiple extracellular phospholipase activities of Aspergillus fumigatus (1996)

Extracellular phospholipase activity has been implicated in the pathogenesis of several bacterial infections. Recently, extracellular phospholipase activity has been proposed as a virulence factor in the opportunistic yeast Candida albicans. Aspergillus fumigatus is the most pathogenic member of its genus, responsible for > 90% of infections. Previously, no specific virulence factors have been determined. We investigated the ability of A. fumigatus to produce extracellular phospholipases at 37 degrees C. Fast atom bombardment was used to compare lipid-containing media before and at 5-h intervals during shaking culture of A. fumigatus. Lipids were extracted and analyzed. Many anions corresponding to phospholipid breakdown products were identified. Specific anion species identified indicated phospholipase A, B, C (PLC), and D activities. PLC activity was further investigated by using the synthetic substrate p-nitrophenylphosphorylcholine. PLC activity was initially observed after 30 h of growth and accumulated in broth cultures up to 50 h. At 55 h, there was a sharp increase in PLC activity which coincided with cultures reaching the stationary phase. Activity of the PLC was measured at different temperatures, with greater activity occurring at 37 degrees C than at lower temperatures. Phospholipases could represent a virulence determinant in A. fumigatus.
Neural Networks and Diagnosis in the Clinical Laboratory: State of the Art (1992)

Journal Article Neural Networks and Diagnosis in the Clinical Laboratory: State of the Art Get access Domenic V Cicchetti Domenic V Cicchetti West Haven VA Medical Center and Yale University 950 Campbell Ave. West Haven, CT 06516 Search for other works by this author on: Oxford Academic Google Scholar Clinical Chemistry, Volume 38, Issue 1, 1 January 1992, Pages 9–10, https://doi.org/10.1093/clinchem/38.1.9 Published: 01 January 1992
Fluorescence Detection of Specific Sequence of Nucleic Acids by Oxazole Yellow-Linked Oligonucleotides. Homogeneous Quantitative Monitoring of In Vitro Transcription (1996)

We have developed a fluorescent DNA probe, oxazole yellow (YO)-linked oligonucleotide complementary to a target DNA/RNA, which can enhance the fluorescence on hybridizing with a target nucleotide. We demonstrated the applicability of the YO-linked oligonucleotide probe to real-time monitoring of the in vitro transcription process of a plasmid DNA constructed containing the 5'-terminus non-coded region of hepatitis C virus RNA. In the process of in vitro transcription in the presence of YO-linked complementary oligonucleotide, the fluorescence of the reaction mixture showed a time-dependent linear increase corresponding to the generated target RNA product.
Pharmacological Treatment of Alzheimer Disease (2011)

Pharmacological options are presently available for the symptomatic treatment of AD. These treatments provide mild but sustained benefits. Before disease-modifying approaches become available, optimizing the use of the available treatment options is crucial.
Nature’s molecular sponges: Small heat shock proteins grow into their chaperone roles (2010)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Microinjection of a rabbit beta-globin gene into zygotes and its subsequent expression in adult mice and their offspring. (1981)

We have transferred a gene coding for rabbit beta-globin into the male pronucleus of mouse zygotes by direct microinjection. Some of these zygotes developed into mature mice which contained this gene and appeared to be producing a rabbit globin. Evidence for the presence of the gene in these animals was provided by Southern blot hybridization analysis. Evidence for the expression of the rabbit gene in these transformed mice and their offspring was provided by hemoglobin isoelectric focusing analysis and specific serological reactivity between mouse anti-rabbit hemoglobin antiserum and a hemolysate from the mice that developed from the microinjected zygotes. The use of this zygote transformation may allow the introduction and expression of a broad range of genetic elements in mammals.