gebhart/patrepeval huggingface dataset:
Mechanism of Stabilization of a Bacterial Collagen Triple Helix in the Absence of Hydroxyproline (2007)

The Streptococcus pyogenes cell-surface protein Scl2 contains a globular N-terminal domain and a collagen-like domain, (Gly-Xaa-X'aa)(79), which forms a triple helix with a thermal stability close to that seen for mammalian collagens. Hyp is a major contributor to triple-helix stability in animal collagens, but is not present in bacteria, which lack prolyl hydroxylase. To explore the basis of bacterial collagen triple-helix stability in the absence of Hyp, biophysical studies were carried out on recombinant Scl2 protein, the isolated collagen-like domain from Scl2, and a set of peptides modeling the Scl2 highly charged repetitive (Gly-Xaa-X'aa)(n) sequences. At pH 7, CD spectroscopy, dynamic light scattering, and differential scanning calorimetry of the Scl2 protein all showed a very sharp thermal transition near 36 degrees C, indicating a highly cooperative unfolding of both the globular and triple-helix domains. The collagen-like domain isolated by trypsin digestion showed a sharp transition at the same temperature, with an enthalpy of 12.5 kJ/mol of tripeptide. At low pH, Scl2 and its isolated collagen-like domain showed substantial destabilization from the neutral pH value, with two thermal transitions at 24 and 27 degrees C. A similar destabilization at low pH was seen for Scl2 charged model peptides, and the degree of destabilization was consistent with the strong pH dependence arising from the GKD tripeptide unit. The Scl2 protein contained twice as much charge as human fibril-forming collagens, and the degree of electrostatic stabilization observed for Scl2 was similar to the contribution Hyp makes to the stability of mammalian collagens. The high enthalpic contribution to the stability of the Scl2 collagenous domain supports the presence of a hydration network in the absence of Hyp.
The Analysis of Education Needs of Dietitians and Cooks According to the Type of Hire and Education Background in Contracted Foodservice Management Company (2000)

This study was designed to develop the education and training program of dietitians and cooks in contracted foodservice management company. The instruments were developed by reviewing extensive literatures on education programs and by interviewing with dietitians and cooks who were working in contracted foodservice management company. A total of 400 questionnaires were hand delivered at the fourteen contracted foodservice management companies by designated coordinators. A total of 286 questionnaires were usable; resulting in a 70.0% response rate. Statistics data analysis was completed using the SPSS for frequency analysis, reliability, mean value, t-test and ANOVA. The results of this study were summarized as follows: 1. The dietitians wanted to take a management course. The cooks wanted to take a culinary education. The dietitians and cooks took an emphasis on service education, foodborne illness & HACCP and sanitation & safety. Service as well as the taste of food and sanitation was emphasized according to the flow of customer satisfaction. 2. Contracted foodservice management company should provide dietitians and cooks with an education for the job to accomplish customer satisfactions.
Argon Direct Analysis in Real Time Mass Spectrometry in Conjunction with Makeup Solvents: A Method for Analysis of Labile Compounds (2012)

Helium direct analysis in real time (He-DART) mass spectrometry (MS) analysis of labile compounds usually tends to be challenging because of the occurrence of prominent fragmentation, which obscures the assigning of an ion to an independent species or merely a fragment in a mixture. In the present work, argon DART (Ar-DART) MS in conjunction with makeup solvents has been demonstrated to analyze a variety of labile compounds including nucleosides, alkaloids, glucose, and other small molecules. The results presented here confirm that Ar-DART can generate significantly less energetic ions than conventional He-DART and is able to produce the intact molecular ions with little or no fragmentation in both positive and negative ion modes. Adding a makeup solvent (absolute ethyl alcohol, methanol, fluorobenzene, or acetone) to the argon gas stream at the exit of the DART ion source can result in 1-2 orders of magnitude increase in detection signals. The sensitivity attainable by Ar-DART was found to be comparable to that by He-DART. The investigation of influence of solvents improves our understanding of the fundamental desorption and ionization processes in DART. The practical application of this rapid and high throughput method is demonstrated by the successful analysis of a natural product (Crude Kusnezoff Monkshood) extract, demonstrating the great potential in mixture research.
Recent studies on the biofunctions and biotransformations of curcumin (2000)

Curcumin is a major component of Curcuma species, which is commonly used as a yellow coloring and flavoring agent in foods. Curcumin has shown anti-carcinogenic activity in animals as indicated by its ability to block colon tumor initiation by azoxymethane and skin tumor promotion induced by phorbol ester TPA. Curcumin possesses anti-inflammatory activity and is a potent inhibitor of reactive oxygen-generating enzymes such as lipoxygenase/cyclooxygenase, xanthine dehydrogenase/oxidase and inducible nitric oxide synthase. Curcumin is also a potent inhibitor of protein kinase C, EGF-receptor tyrosine kinase and IkappaB kinase. Subsequently, curcumin inhibits the activation of NFkappaB and the expressions of c-jun, c-fos, c-myc and iNOS. It is proposed that curcumin may suppress tumor promotion through blocking signal transduction pathways in the target cells. Curcumin was first biotransformed to dihydrocurcumin and tetrahydrocurcumin and that these compounds subsequently were converted to monoglucuronide conjugates. These results suggest that curcumin-glucuronide, dihydro-curcumin-glucuronide, tetrahydrocurcumin-glucuronide and tetrahydrocurcumin are major metabolites of curcumin in mice.
Identity and ranking of colonic mesenchymal stromal cells (2011)

Although ongoing clinical trials utilize systemic administration of bone-marrow mesenchymal stromal cells (BM-MSCs) in Crohn's disease (CD), nothing is known about the presence and the function of mesenchymal stromal cells (MSCs) in the normal human bowel. MSCs are bone marrow (BM) multipotent cells supporting hematopoiesis with the potential to differentiate into multiple skeletal phenotypes. A recently identified new marker, CD146, allowing to prospectively isolate MSCs from BM, renders also possible their identification in different tissues. In order to elucidate the presence and functional role of MSCs in human bowel we analyzed normal adult colon sections and isolated MSCs from them. In colon (C) sections, resident MSCs form a net enveloping crypts in lamina propria, coinciding with structural myofibroblasts or interstitial stromal cells. Nine sub-clonal CD146(+) MSC lines were derived and characterized from colon biopsies, in addition to MSC lines from five other human tissues. In spite of a phenotype qualitative identity between the BM- and C-MSC populations, they were discriminated and categorized. Similarities between C-MSC and BM-MSCs are represented by: Osteogenic differentiation, hematopoietic supporting activity, immune-modulation, and surface-antigen qualitative expression. The differences between these populations are: C-MSCs mean intensity expression is lower for CD13, CD29, and CD49c surface-antigens, proliferative rate faster, life-span shorter, chondrogenic differentiation rare, and adipogenic differentiation completely blocked. Briefly, BM-MSCs, deserve the rank of progenitors, whereas C-MSCs belong to the restricted precursor hierarchy. The presence and functional role of MSCs in human colon provide a rationale for BM-MSC replacement therapy in CD, where resident bowel MSCs might be exhausted or diverted from their physiological functions.
Characterization And Setup Techniques For A 5X Stepper (1986)

A direct means of measuring the aerial image profile of a microlithographic stepper system is described. The position of the peak gives the relative overlay error and the shape of the curve relates to the resolution. Reduction and focus shifts due to barometric pressure change are reported. Vibration between the aerial image and the wafer was measured, as well as the effects of vibration on resist imagery. We also describe applications of such techniques for fast and accurate setup of stepper overlay offset and focus.
Multivariate Analysis of Prognostic Factors Among 2,313 Patients With Stage III Melanoma: Comparison of Nodal Micrometastases Versus Macrometastases (2010)

In this multi-institutional analysis, we demonstrated remarkable heterogeneity of prognosis among patients with stage III melanoma, especially among those with nodal micrometastases. These results should be incorporated into the design and interpretation of future clinical trials involving patients with stage III melanoma.
A Wide Range Charge-Balancing Circuit using Floating-Gate Transistors (2007)

A CMOS circuit has been designed to produce charge-balanced biphasic current pulses for electrical stimulation of neurons. The circuit uses synaptic current source to generate discharging current pulses for stimulating current with amplitude ranging from 100pA to 110nA and period ranging from 0.2s to 1s. The amplitude and duration of the discharging current is controlled using programmable floating-gate transistors. The circuit has high stimulation efficiency and can be used in various neural microstimulators.
Adoptive Cell Therapy for Lymphoma with CD4 T Cells Depleted of CD137-Expressing Regulatory T Cells (2012)

Adoptive immunotherapy with antitumor T cells is a promising novel approach for the treatment of cancer. However, T-cell therapy may be limited by the cotransfer of regulatory T cells (T(reg)). Here, we explored this hypothesis by using 2 cell surface markers, CD44 and CD137, to isolate antitumor CD4 T cells while excluding T(regs). In a murine model of B-cell lymphoma, only CD137(neg)CD44(hi) CD4 T cells infiltrated tumor sites and provided protection. Conversely, the population of CD137(pos)CD44hi CD4 T cells consisted primarily of activated T(regs). Notably, this CD137(pos) T(reg) population persisted following adoptive transfer and maintained expression of FoxP3 as well as CD137. Moreover, in vitro these CD137(pos) cells suppressed the proliferation of effector cells in a contact-dependent manner, and in vivo adding the CD137(pos)CD44(hi) CD4 cells to CD137(neg)CD44(hi) CD4 cells suppressed the antitumor immune response. Thus, CD137 expression on CD4 T cells defined a population of activated T(regs) that greatly limited antitumor immune responses. Consistent with observations in the murine model, human lymphoma biopsies also contained a population of CD137(pos) CD4 T cells that were predominantly CD25(pos)FoxP3(pos) T(regs). In conclusion, our findings identify 2 surface markers that can be used to facilitate the enrichment of antitumor CD4 T cells while depleting an inhibitory T(reg) population.
Cytochrome c oxidase rapidly metabolises nitric oxide to nitrite (2000)

Previous studies have shown that the addition of nitric oxide to cytochrome c oxidase rapidly generates spectral changes compatible with the formation of nitrite at the binuclear haem:copper centre. Here we directly demonstrate nitrite release following nitric oxide addition to the enzyme. The nitrite complex is kinetically inactive and the off rate for nitrite was found to be slow (0.024 min(-1)). However, the presence of reductants enhances the off rate and enables cytochrome oxidase to catalyse the rapid oxidation of nitric oxide to nitrite free in solution. This may play a major role in the mitochondrial metabolism of nitric oxide.
Thawing Frozen Robust Multi-array Analysis (fRMA) (2011)

By allowing the user to easily create his or her own fRMA implementation, the frmaTools package greatly increases the applicability of the fRMA algorithm. The frmaTools package is freely available as part of the Bioconductor project.
Execution replay of multiprocessor virtual machines (2008)

Execution replay of virtual machines is a technique which has many important applications, including debugging, fault-tolerance, and security. Execution replay for single processor virtual machines is well-understood, and available commercially. With the advancement of multi-core architectures, however, multiprocessor virtual machines are becoming more important. Our system, SMP-ReVirt, is the first system to log and replay a multiprocessor virtual machine on commodity hardware. We use hardware page protection to detect and accurately replay sharing between virtual cpus of a multi-cpu virtual machine, allowing us to replay the entire operating system and all applications. We have tested our system on a variety of workloads, and find that although sharing under SMP-ReVirt is expensive, for many workloads and applications, including debugging, the overhead is acceptable.
Farnesyl transferase expression determines clinical response to the docetaxel‐lonafarnib combination in patients with advanced malignancies (2011)

Despite the small number of patients, these findings support our preclinical mechanistic studies and warrant further clinical investigations using FTase-beta mRNA expression as a potential predictive biomarker to select for an enriched patient population to study the effects of taxane and FTase inhibitor combination therapies.
Expression of gastric cancer-associated MG7 antigen in gastric cancer, precancerous lesions andH. pylori-associated gastric diseases (2002)

MG7 antigen expression is highly specific in gastric cancer and can be used as a good marker for screening of gastric cancer; type III intestinal metaplasia, atrophic gastritis and dysplasia should be followed up and MG7 antigen expression has high clinical value in the dynamic follow-up study; although the positive -MG7 in positive -H. pylori superficial gastritis show benign morphology in features, there is still the potential risk of developing into gastric cancer, hence special attention should be paid to those showing increasing MG7 antigen expression.
Bactericidal Activity of Colicin V Is Mediated by an Inner Membrane Protein, SdaC, of Escherichia coli (2005)

ABSTRACT Colicin V (ColV) is a peptide antibiotic that kills sensitive cells by disrupting their membrane potential once it gains access to the inner membrane from the periplasmic face. Recently, we constructed a translocation suicide probe, RR-ColV, that is translocated into the periplasm via the TAT pathway and thus kills the host cells. In this study, we obtained an RR-ColV-resistant mutant by using random Tn 10 transposition mutagenesis. Sequencing analysis revealed that the mutant carried a Tn 10 insertion in the sdaC (also called dcrA ) gene, which is involved in serine uptake and is required for C1 phage adsorption. ColV activity was detected both in the cytoplasm and in the periplasm of this mutant, indicating that RR-ColV was translocated into the periplasm but failed to interact with the inner membrane. The sdaC ::Tn 10 mutant was resistant only to ColV and remained sensitive to colicins Ia, E3, and A. Most importantly, the sdaC ::Tn 10 mutant was killed when ColV was anchored to the periplasmic face of the inner membrane by fusion to EtpM, a type II integral membrane protein. Taken together, these results suggest that the SdaC/DcrA protein serves as a specific inner membrane receptor for ColV.
Regulation of the Replication of the Murine Immunoglobulin Heavy Chain Gene Locus: Evaluation of the Role of the 3′ Regulatory Region (1997)

DNA replication in mammalian cells is a precisely controlled physical and temporal process, likely involving cis-acting elements that control the region(s) from which replication initiates. In B cells, previous studies showed replication timing to be early throughout the immunoglobulin heavy chain (Igh) locus. The implication from replication timing studies in the B-cell line MPC11 was that early replication of the Igh locus was regulated by sequences downstream of the C alpha gene. A potential candidate for these replication control sequences was the 3' regulatory region of the Igh locus. Our results demonstrate, however, that the Igh locus maintains early replication in a B-cell line in which the 3' regulatory region has been deleted from one allele, thus indicating that replication timing of the locus is independent of this region. In non-B cells (murine erythroleukemia cells [MEL]), previous studies of segments within the mouse Igh locus demonstrated that DNA replication likely initiated downstream of the Igh gene cluster. Here we use recently cloned DNA to demonstrate that segments located sequentially downstream of the Igh 3' regulatory region continue to replicate progressively earlier in S phase in MEL. Furthermore, analysis by two-dimensional gel electrophoresis indicates that replication forks proceed exclusively in the 3'-to-5' direction through the region 3' of the Igh locus. Extrapolation from these data predicts that initiation of DNA replication occurs in MEL at one or more sites within a 90-kb interval located between 40 and 130 kb downstream of the 3' regulatory region.
Huntingtin Aggregate-Associated Axonal Degeneration is an Early Pathological Event in Huntington's Disease Mice (2001)

Huntington's disease (HD) is characterized by the selective loss of striatal projection neurons. In early stages of HD, neurodegeneration preferentially occurs in the lateral globus pallidus (LGP) and substantia nigra (SN), two regions in which the axons of striatal neurons terminate. Here we report that in mice expressing full-length mutant huntingtin and modeling early stages of HD, neuropil aggregates form preferentially in the LGP and SN. The progressive formation of these neuropil aggregates follows intranuclear accumulation of mutant huntingtin and becomes prominent from 11 to 27 months after birth. Neuropil aggregates, but no intranuclear inclusions, were observed in the LGP and SN, suggesting that huntingtin aggregates are formed in the axons of striatal projection neurons. In the LGP and SN, we observed degenerated axons in which huntingtin aggregates were associated with dark, swollen organelles that resemble degenerated mitochondria. Neuritic aggregates also form in cultured striatal neurons expressing mutant huntingtin, block protein transport in neurites, and cause neuritic degeneration before nuclear DNA fragmentation occurs. These findings suggest that the early neuropathology of HD originates from axonal dysfunction and degeneration associated with huntingtin aggregates.
A NEW LOCATION CODING SCHEME FOR INTELLIGENT TRANSPORTATION SYSTEMS (1996)

Abstract Many Intelligent Transportation Systems (ITS) applications require some form of location information. For example, traveler information services and traffic management are both critically dependent on the specification of location(s). Some ITS applications may need this information in finer resolution than others as demonstrated by the navigation and route guidance systems vs. severe weather warnings for a local area. A location can be a street address, a highway segment, an intersection, a stretch of roadway or a small geographical area. These types of locations can be coded in various ways. In this paper, we first examine several coding schemes reported in the literature and/or used in real applications. Then, we propose a new location coding scheme based on the first three digits of the Zipcode plus local information. This scheme uniquely represents all useful types of locations and is versatile and efficient. Moreover, it fits well the location reference message protocol (LRMP) described in [Goodwin et al., 1995; Goodwin and Xiong, 1994]. To demonstrate its utility and power, we compare the proposed scheme with the Road Name ID scheme [Ramakrishnan et al., 1994]. Key words: Intelligent Transportation Systems (ITS)Advanced Traveler Information System (ATIS)location codinglocation namingZipcode-based codingZip+Local
PROTEOLYTIC PROCESSING OF PICORNAVIRAL POLYPROTEIN (1990)

Human coronavirus (HCoV) infection causes respiratory diseases with mild to severe outcomes. In the last 15 years, we have witnessed the emergence of two zoonotic, highly pathogenic HCoVs: severe acute respiratory syndrome coronavirus (SARS-CoV) and ...Read More
Low Stress Program and Single Wordline Erase Schemes for NAND Flash Memory (2007)

Voltage stress during programming is a major factor limiting reliability in NAND Flash memory. To control programming stress several desirable features such as random page program, partial page program, and low Vcc operation are eliminated or restricted. Program stress becomes more significant as process technology is scaled down and as single-level cell (SLC) gives way to multi-level cell (MLC) devices. To increase device reliability a low stress program scheme for random page program in SLC devices and a sequential program scheme for MLC devices is introduced. Separately, system-level performance degrades as a function of the NAND block size due to the additional operations necessitated by wear-leveling algorithms. Techniques for single wordline erase in SLC and partial block erase in MLC are introduced to minimize system overhead due to larger block size and to extend the system lifetime.
Characterization of In Vivo Reporter Systems for Gene Expression and Biosensor Applications Based on luxAB Luciferase Genes (1996)

Advances in genetic engineering methods have allowed the development of an increasing number of practical and scientific applications for bioluminescence with lux genes cloned from a variety of organisms. Bioluminescence derived from the shortened lux operon (luxAB genes) is a complex process, and applications seem to be proliferating in advance of an understanding of the underlying biochemical processes. In this report, we describe a two-phase kinetic behavior of the light emission which must be properly taken into account in any quantitative measurements of the bioluminescence signal. By using strains of Escherichia coli and Caulobacter crescentus, this behavior was characterized and interpreted in terms of the biochemistry underlying the bacterial luciferase mechanism. We show that the intensity profile of each of the two phases of the luminescence signal is responsive (and exhibits different sensitivities) to the concentration of added decanal and other components of the assay mix, as well as to the order of mixing and incubation times. This study illustrates the importance of appropriate protocol design, and specific recommendations for using the luxAB system as a molecular reporter are presented, along with versatile assay protocols that yield meaningful and reproducible signals.
Sodium phenylbutyrate in Huntington's disease: A dose‐finding study (2007)

Transcriptional dysregulation in Huntington's disease (HD) is mediated in part by aberrant patterns of histone acetylation. We performed a dose-finding study in human HD of sodium phenylbutyrate (SPB), a histone deacetylase inhibitor that ameliorates the HD phenotype in animal models. We used a dose-escalation/de-escalation design, using prespecified toxicity criteria and standard clinical and laboratory safety measures. The maximum tolerated dose was 15 g/day. At higher doses, toxicity included vomiting, lightheadedness, confusion, and gait instability. We saw no significant laboratory or electrocardiographic abnormalities. Gene expression changes in blood suggested an inverse dose-response. In conclusion, SPB at 12 to 15 g/day appears to be safe and well-tolerated in human HD.