gebhart/patrepeval huggingface dataset:
Simultaneous Enhancement of Thermostability and Catalytic Activity of Phospholipase A 1 by Evolutionary Molecular Engineering (2000)

The thermal stability and catalytic activity of phospholipase A(1) from Serratia sp. strain MK1 were improved by evolutionary molecular engineering. Two thermostable mutants were isolated after sequential rounds of error-prone PCR performed to introduce random mutations and filter-based screening of the resultant mutant library; we determined that these mutants had six (mutant TA3) and seven (mutant TA13) amino acid substitutions. Different types of substitutions were found in the two mutants, and these substitutions resulted in an increase in nonpolar residues (mutant TA3) or in differences between side chains for polar or charged residues (mutant TA13). The wild-type and mutant enzymes were purified, and the effect of temperature on the stability and catalytic activity of the enzymes was investigated. The melting temperatures of the TA3 and TA13 enzymes were increased by 7 and 11 degrees C, respectively, compared with the melting temperature of the wild-type enzyme. Thus, we found that evolutionary molecular engineering was an effective and efficient approach for increasing thermostability without compromising enzyme activity.
A Hardware Pattern Matching Algorithm On A Dataflow (1985)

A hardware pattern matcher is presented, which searches for patterns on a data flow, such as characters read from a disk. The backing up on the data flow, for a general pattern matching, is avoided by means of a set of cells running in parallel. Each cell can search for a pattern independently, but requires only one one-character comparator. The interesting feature of this search hardware is the use of simple priority line which can dynamically allocate these cells.
Catalytic cleavage of the androgen-regulated TMPRSS2 protease results in its secretion by prostate and prostate cancer epithelia. (2001)

We identified TMPRSS2 as a gene that is down-regulated in androgen-independent prostate cancer xenograft tissue derived from a bone metastasis. Using specific monoclonal antibodies, we show that the TMPRSS2-encoded serine protease is expressed as a Mr 70,000 full-length form and a cleaved Mr 32,000 protease domain. Mutation of Ser-441 in the catalytic triad shows that the proteolytic cleavage is dependent on catalytic activity, suggesting that it occurs as a result of autocleavage. Mutational analysis reveals the cleavage site to be at Arg-255. A consequence of autocatalytic cleavage is the secretion of the protease domain into the media by TMPRSS2-expressing prostate cancer cells and into the sera of prostate tumor-bearing mice. Immunohistochemical analysis of clinical specimens demonstrates the highest expression of TMPRSS2 at the apical side of prostate and prostate cancer secretory epithelia and within the lumen of the glands. Similar luminal staining was detected in colon cancer samples. Expression was also seen in colon and pancreas, with little to no expression detected in seven additional normal tissues. These data demonstrate that TMPRSS2 is a secreted protease that is highly expressed in prostate and prostate cancer, making it a potential target for cancer therapy and diagnosis.
The interaction of chalcones with tubulin. (2000)

The chalcone 3,4,3',4',5'-pentamethoxychalcone is a potent cytotoxic agent. A series of chalcones and (E)-4-(4'-hydroxyphenyl)but-3-en-2-one were prepared and assessed for their ability to inhibit cell growth in vitro. The cytotoxicity correlates with their ability to bind to tubulin as measured by immunofluorescence, cell cycle analysis and disruption of microtubule assembly. Some of the chalcones were shown to bind to the type II oestrogen receptor.
Concentrations and Molecular Forms of C-Type Natriuretic Peptide in Brain and Cerebrospinal Fluid (1992)

To develop a radioimmunoassay (RIA) specific for human C-type natriuretic peptide (hCNP), we used a highly specific antiserum raised in rabbits. Quantitative inhibition tests with various natriuretic peptides demonstrated that the 50% inhibitory dose of hCNP was 15 fmol, whereas those of other natriuretic peptides were 10(5)-fold higher, indicating a specificity satisfactory for determining concentrations of hCNP in tissues. Using this antiserum, we detected immunoreactive hCNP (ir-hCNP) in various regions of human brain and spinal cord, as well as in cerebrospinal fluid (CSF). The ir-hCNP concentrations in human neural tissues were approximately 10-fold higher than those of immunoreactive human atrial natriuretic peptide (ir-hANP). The mean (+/- SD) concentration of ir-hCNP (72.0 +/- 17.8 ng/L) in CSF also was 10-fold higher than that of ir-hANP (5.2 +/- 2.1 ng/L). Using gel-permeation chromatography, we identified two molecular forms of ir-hCNP in brain and CSF: a 2-kDa form corresponding to mature hCNP, which is composed of 22 amino acid residues (hCNP-22), and a 5- to 6-kDa form corresponding to an N-terminally extended molecule (hCNP-53). The latter form was predominant in brain; the former was the main constituent of hCNP in CSF. These results support the hypothesis that hCNP is a major natriuretic peptide, is synthesized in human brain, and functions in human central nervous tissues.
Virulence of protein A-deficient and alpha-toxin-deficient mutants of Staphylococcus aureus isolated by allele replacement (1987)

The gene coding for protein A (spa) of Staphylococcus aureus 8325-4 has been inactivated by substituting part of the spa coding sequence for a DNA fragment specifying resistance to ethidium bromide. The in vitro-constructed spa::EtBrr substitution mutation was introduced into the S. aureus chromosome by recombinational allele replacement. Southern blot hybridization showed that the in vitro-constructed mutation was present in the chromosomal spa locus. We have previously reported the inactivation of the alpha-toxin gene (hly) by allele replacement with an in vitro-constructed hly::Emr (erythromycin resistance) mutation (M. O'Reilly, J.C.S. de Azavedo, S. Kennedy, and T.J. Foster, Microb. Pathogen. 1:125-138, 1986). A double Spa- Hly- mutant was constructed by transduction. The virulence of Spa- and Hly- mutants was tested by experimental infection of mice. When subcutaneous injections were given, Hly- mutants formed a flat, darkened lesion, whereas Hly+ strains caused a raised, cream lesion. Alpha-toxin was shown to be a major factor in forming subcutaneous lesions and in causing the death of mice injected intraperitoneally. Spa- mutants were slightly less virulent than their Spa+ counterparts, which suggests that protein A is also a virulence factor of S. aureus.
Intraductal carcinoma of the breast: Follow-up after biopsy only (1982)

Twenty-eight women with ductal carcinoma in situ (DCIS) of the breast treated by biopsy only were identified in a histologic review of 11,760 biopsies performed between 1950 and 1968. Seven of the 25 women followed for more than three years developed invasive breast carcinoma, all in the same breast with a previously detected DCIS. Average follow-up interval for the 18 women not developing invasive carcinoma was 16 years. The invasive carcinomas presented clinically from three to ten years (average, 6.1) after the biopsies demonstrating DCIS. Four women with invasive carcinoma developed distant metastases following mastectomy. This study suggests that 28% of women treated with biopsy only for DCIS presenting as an incidental histologic finding will develop invasive carcinoma in a follow-up period of approximately 15 years.
Infectivity of Cryptosporidium parvum in healthy adults with pre-existing anti-C. parvum serum immunoglobulin G. (1999)

A 50% infectious dose (ID50) of 132 Cryptosporidium parvum oocysts was previously determined in serologically negative individuals (ELISA). In this study, 17 healthy adults with pre-existing anti-C. parvum serum IgG were challenged with 500-50,000 oocysts. Infection and diarrhea were associated with the higher challenge doses. The ID50 was 1,880 oocysts, > 20-fold higher than in seronegative volunteers. Fecal oocysts were detected in only seven (53.8%) of 13 individuals with clinical cryptosporidiosis, indicating that the host response may effectively decrease the number of oocysts produced. Subjects with the highest absorbances prior to challenge had little to no increase in IgG following challenge, whereas volunteers with lower reactivities showed significant postchallenge increases. This suggests that an upper limit of serum IgG was present in some subjects, while others were further stimulated by an additional exposure. These data indicate that prior exposure to C. parvum provides protection from infection and illness at low oocyst doses.
Application of Total Reflection XRF to Elemental Studies of Drinking Water (1997)

The aim of this work was to study the water quality, especially metallic pollution, at water treatment plants and inside buildings. The samples were collected in two regions of Portugal and in one of these regions water collection was also made inside houses chosen according to their type of plumbing, in order to compare its influence on metal concentrations in the drinking water. The analyses were carried out by total-reflection x-ray fluorescence without sample preconcentration. The detection limits were in the range 0.5–1.7 μg l-1 for Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Rb, Sr, Hg and Pb and 4.9–11 μg l-1 for K, Ca, V, Cd, Sb and Ba. © 1997 John Wiley & Sons, Ltd.
Preconditioning limits mitochondrial Ca2+during ischemia in rat hearts: role of KATPchannels (2001)

Prolonged myocardial ischemia results in an increase in intracellular calcium concentration ([Ca(2+)]i), which is thought to play a critical role in ischemia-reperfusion injury. Ischemic preconditioning (PC) improves myocardial function during ischemia-reperfusion, a process that may involve opening mitochondrial ATP-sensitive potassium (K(ATP)) channels. Because pharmacological limitation of mitochondrial calcium concentration ([Ca(2+)]m) overload during ischemia-reperfusion has been shown to improve myocardial function, we hypothesized that PC would reduce [Ca(2+)]m during ischemia-reperfusion and that this effect was mediated by opening mitochondrial K(ATP) channels. Isolated rat hearts were subjected to 25 min of global ischemia and 30 min of reperfusion with or without PC in the presence of mitochondrial K(ATP) channel opening (diazoxide, 100 microM) and blockade [5-hydroxydecanoic acid (5-HD), 100 microM]. Contracture during ischemia (end-diastolic pressure) and functional recovery on reperfusion (developed pressure) were assessed. Total [Ca(2+)]i and [Ca(2+)]m were measured using indo 1 fluorescence. Both PC and diazoxide limited the increase in end-diastolic pressure and resulted in greater functional recovery after 30 min of reperfusion, functional effects that were partially or completely abolished by 5-HD. PC and diazoxide also significantly limited the increase in [Ca(2+)]m during ischemia-reperfusion. In addition, PC lowered [Ca(2+)]i during reperfusion, whereas diazoxide paradoxically resulted in increased [Ca(2+)]i during reperfusion. There was an inverse linear relationship between [Ca(2+)]m and developed pressure during reperfusion. PC limits the ischemia-induced increase in mitochondrial, but not total, [Ca(2+)]i, an effect mediated by opening mitochondrial K(ATP) channels. These data suggest that the lowering of mitochondrial calcium overload is a mechanism of cardioprotection in PC.
The TLR7 Agonist Imiquimod Enhances the Anti-Melanoma Effects of a Recombinant Listeria monocytogenes Vaccine (2005)

Activation of innate immune cells through TLR triggers immunomodulating events that enhance cell-mediated immunity, raising the possibility that ligands to these receptors might act as adjuvants in conjunction with T cell activating vaccines. In this report, topical imiquimod, a synthetic TLR7 agonist, significantly enhanced the protective antitumor effects of a live, recombinant listeria vaccine against murine melanoma. This tumor protective effect was not dependent on direct application to the tumor and was associated with an increase in tumor-associated and splenic dendritic cells. Additionally, the combination of imiquimod treatment with prior vaccination led to development of localized vitiligo. These findings indicate that activation of the innate immune system with TLR ligands stimulates dendritic cell activity resulting in a bypass of peripheral tolerance and enhanced antitumor activity. The results of these studies have broad implications for future designs of immunotherapeutic vaccines against tumors and the treatment of metastatic melanoma.
Hot Spot Effects in Hybrid Circuits (1988)

The temperature field due to a hot spot is investigated using a two-dimensional, an improved two-dimensional, and a three-dimensional analysis. It is shown that if the dimensions of the heat source are less than a critical distance, a two-dimensional approach fails even for substrates with a high-thermal conductivity. A combined model involving a local zooming is proposed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
CORROSION AND MECHANICAL PROPERTIES OF Ti3Al-Nb-Mo COMPOSITES FOR BIO- AND ENVIRONMENTAL MATERIALS PREPARED BY SELF-PROPAGATING HIGH TEMPERATURE REACTION (2002)

TiaAl-Nb-Mo composites were prepared by SHS using initial powder mixtures of Ti-Al-Nb-Mo and their corrosion and mechanical properties were studied to develop bio-and environmental materials. The composites reached 99.8% of theoretical densityafter the direct consolidation. The composites shows equiaxed primary α2 in a matrixof fine secondary α2 plates and ordered B2 (B0) forming a basket weave structure.The strain rate sensitivity (m = dlnσr/dlne) at 2% strain is 0.008. Corrosion po-tential and corrosion rate of the composites formed by SHS were -151.5mVSHE and5.72× 10-8A/cm2 for Ti3Al-10Nb-1.5Mo and -138.4m VSHE and 4.12×10-8cm-2 forTi3Al-12Nb-1.5Mo in a 50% NaOH-10%FeCl3 solution, respectively. Corrosion resis-tance decreased with niobium content in the composites and chloride content in theaqueous solution. Selective corrosion of α2 phase in a matrix occurred in the corrosionenvironment which suggests that the corrosion potential and rate changes are relatedto the niobium content and α2 phase in a matrix.
Inflammation in Chronic Wounds (2016)

Non-healing chronic wounds present a major biological, psychological, social, and financial burden on both individual patients and the broader health system. Pathologically extensive inflammation plays a major role in the disruption of the normal healing cascade. The causes of chronic wounds (venous, arterial, pressure, and diabetic ulcers) can be examined through a juxtaposition of normal healing and the rogue inflammatory response created by the common components within chronic wounds (ageing, hypoxia, ischaemia-reperfusion injury, and bacterial colonisation). Wound bed care through debridement, dressings, and antibiotics currently form the basic mode of treatment. Despite recent setbacks, pharmaceutical adjuncts form an interesting area of research.
Use of an Artificial Neural Network for the Diagnosis of Myocardial Infarction (1991)

An artificial neural network trained to identify myocardial infarction in adult patients presenting to an emergency department may be a valuable aid to the clinical diagnosis of myocardial infarction; however, this possibility must be confirmed through prospective testing on a larger patient sample.
Trafficking of Human Immunodeficiency Virus Type 1-Specific CD8+T Cells to Gut-Associated Lymphoid Tissue during Chronic Infection (2003)

Gut-associated lymphoid tissue (GALT) is a significant but understudied lymphoid organ, harboring a majority of the body's total lymphocyte population. GALT is also an important portal of entry for human immunodeficiency virus (HIV), a major site of viral replication and CD4(+) T-cell depletion, and a frequent site of AIDS-related opportunistic infections and neoplasms. However, little is known about HIV-specific cell-mediated immune responses in GALT. Using lymphocytes isolated from rectal biopsies, we have determined the frequency and phenotype of HIV-specific CD8(+) T cells in human GALT. GALT CD8(+) T cells were predominantly CD45RO(+) and expressed CXCR4 and CCR5. In 10 clinically stable, chronically infected individuals, the frequency of HIV Gag (SL9)-specific CD8(+) T cells was increased in GALT relative to peripheral blood mononuclear cells by up to 4.6-fold, while that of cytomegalovirus (CMV)-specific CD8(+) T cells was significantly reduced (P = 0.012). Both HIV- and CMV-specific CD8(+) T cells in GALT expressed CCR5, but only HIV-specific CD8(+) T cells expressed alpha E beta 7 integrin, suggesting that mucosal priming may account for their retention in GALT. Chronically infected individuals exhibited striking depletion of GALT CD4(+) T cells expressing CXCR4, CCR5, and alpha E beta 7 integrin, but CD4(+)/CD8(+) T-cell ratios in blood and GALT were similar. The percentage of GALT CD8(+) T cells expressing alpha E beta 7 was significantly decreased in infected individuals, suggesting that HIV infection may perturb lymphocyte retention in GALT. These studies demonstrate the feasibility of using tetramers to assess HIV-specific T cells in GALT and reveal that GALT is the site of an active CD8(+) T-cell response during chronic infection.
Hematological and acid-base changes in men during prolonged exercise with and without sodium-lactate infusion (2004)

An emerging technique used for the study of metabolic regulation is the elevation of lactate concentration with a sodium-lactate infusion, the lactate clamp (LC). However, hematological and acid-base properties affected by the infusion of hypertonic solutions containing the osmotically active strong ions sodium (Na(+)) and lactate (Lac(-)) are a concern for clinical and research applications of LC. In the present study, we characterized the hematological and plasma acid-base changes during rest and prolonged, light- to moderate-intensity (55% Vo(2 peak)) exercise with and without LC. During the control (Con) trial, subjects were administered an isotonic, isovolumetric saline infusion. During LC, plasma lactate concentration ([Lac(-)]) was elevated to 4 meq/l during rest and to 4-7 meq/l during exercise. During LC at rest, there were rapid and transient changes in plasma, erythrocyte, and blood volumes. LC resulted in decreased plasma [H(+)] (from 39.6 to 29.6 neq/l) at the end of exercise while plasma [HCO(3)(-)] increased from 26 to 32.9 meq/l. Increased plasma strong ion difference [SID], due to increased [Na(+)], was the primary contributor to decreased [H(+)] and increased [HCO(3)(-)]. A decrease in plasma total weak acid concentration also contributed to these changes, whereas Pco(2) contributed little. The infusion of hypertonic LC caused only minor volume, acid-base, and CO(2) storage responses. We conclude that an LC infusion is appropriate for studies of metabolic regulation.
Cloning and sequence analysis ofgyrAgene ofKlebsiella pneumoniae (1990)

The gene gyrA encoding the DNA gyrase A subunit of Klebsiella pneumoniae has been cloned in the plasmid pBR322. Bases of about 3.5 Kb DNA have been sequenced to locate the gyrA gene. An open reading frame of 2628 nucleotides coding for a 97 KD protein has been identified. Homology to the extent of about 85% was detected at the nucleotide level and about 90% at the amino acid level, when the sequences were compared with that of Escherichia coli gyrA. Some very interesting differences have, however, been found in the promoter region.
Differential expression of the HMG box factors TCF-1 and LEF-1 during murine embryogenesis (1993)

The recent identification of a number of T lymphocyte-specific enhancers has allowed the cloning of several novel transcription factors. Two of these, TCF-1 and LEF-1, contain a virtually identical DNA-binding domain of the High Mobility Group (HMG-1) box type. TCF-1 and LEF-1 originate from a recent gene duplication event as evidenced by comparison with the chicken homologue, chTCF. We have now analyzed the differential expression of these two transcription factors. In a panel of lymphoid cell lines, TCF-1 was exclusively expressed in the T cell lineage. In contrast, LEF-1 mRNA was detected at equivalent levels in pro- and pre-B cells and in all T lineage cells. In situ hybridization on murine embryos revealed that TCF-1 and LEF-1 were widely expressed at day 7.5 of gestation. At later stages, the expression patterns were complex and only partially overlapping. The expression of TCF-1 and LEF-1 coincided until day 10.5, when mRNAs were detected in limb buds, neural crest, pharyngeal arches and nasal process. At later time points (day 13.5 to 14.5), sites of overlapping expression included lung, the urogenital system, tooth buds, thymus and choroid plexus. Unique expression sites for TCF-1 included Reichert's membrane and trophectoderm-derived cells, the ribs and thoracic prevertebrae, craniofacial structures, the adrenal gland and meninges. Unique LEF-1 expression was observed in the tail prevertebrae, brain and inner ear. Postnatally, expression of both genes could only be detected in lymphoid tissues. These observations suggest that TCF-1 and LEF-1 exert differential functions during murine embryogenesis.
Energy-efficient mechanisms for managing thread context in throughput processors (2011)

Modern graphics processing units (GPUs) use a large number of hardware threads to hide both function unit and memory access latency. Extreme multithreading requires a complicated thread scheduler as well as a large register file, which is expensive to access both in terms of energy and latency. We present two complementary techniques for reducing energy on massively-threaded processors such as GPUs. First, we examine register file caching to replace accesses to the large main register file with accesses to a smaller structure containing the immediate register working set of active threads. Second, we investigate a two-level thread scheduler that maintains a small set of active threads to hide ALU and local memory access latency and a larger set of pending threads to hide main memory latency. Combined with register file caching, a two-level thread scheduler provides a further reduction in energy by limiting the allocation of temporary register cache resources to only the currently active subset of threads. We show that on average, across a variety of real world graphics and compute workloads, a 6-entry per-thread register file cache reduces the number of reads and writes to the main register file by 50% and 59% respectively. We further show that the active thread count can be reduced by a factor of 4 with minimal impact on performance, resulting in a 36% reduction of register file energy.