gebhart/patrepeval huggingface dataset:
Resveratrol inhibition of Propionibacterium acnes (2007)

Resveratrol, an anti-inflammatory hydroxystilbene, is capable of inhibiting P. acnes growth.
Toward a Model for the Interaction Between Elongation Factor Tu and the Ribosome (1993)

In the elongation cycle of bacterial protein synthesis the interaction between elongation factor-Tu (EF-Tu).guanosine triphosphate (GTP), aminoacyl-transfer RNA (aa-tRNA), and messenger RNA-programmed ribosomes is associated with the hydrolysis of GTP. This interaction determines the selection of the proper aa-tRNA for incorporation into the polypeptide. In the canonical scheme, one molecule of GTP is hydrolyzed in the EF-Tu-dependent binding of aa-tRNA to the ribosome, and a second molecule is hydrolyzed in the elongation factor-G (EF-G)-mediated translocation of the polypeptide from the ribosomal A site to the P site. Substitution of Asp138 with Asn in EF-Tu changed the substrate specificity from GTP to xanthosine triphosphate and demonstrated that the EF-Tu-mediated reactions involved the hydrolysis of two nucleotide triphosphates for each Phe incorporated. This stoichiometry of two is associated with the binding of the correct aa-tRNA to the ribosome.
The human cytomegalovirus genome revisited: comparison with the chimpanzee cytomegalovirus genome FN1 (2003)

The gene complement of wild-type human cytomegalovirus (HCMV) is incompletely understood, on account of the size and complexity of the viral genome and because laboratory strains have undergone deletions and rearrangements during adaptation to growth in culture. We have determined the sequence (241 087 bp) of chimpanzee cytomegalovirus (CCMV) and have compared it with published HCMV sequences from the laboratory strains AD169 and Toledo, with the aim of clarifying the gene content of wild-type HCMV. The HCMV and CCMV genomes are moderately diverged and essentially collinear. On the basis of conservation of potential protein-coding regions and other sequence features, we have discounted 51 previously proposed HCMV ORFs, modified the interpretations for 24 (including assignments of multiple exons) and proposed ten novel genes. Several errors were detected in the published HCMV sequences. We presently recognize 165 genes in CCMV and 145 in AD169; this compares with an estimate of 189 unique genes for AD169 made in 1990. Our best estimate for the complement of wild-type HCMV is 164 to 167 genes.
Achieving High Reliability on Linux for K2 System (2012)

Driver faults are the main reasons of causing failure in operating system. In order to address this issue and improve the kernel reliability, this paper presents an intelligent kernel-mode driver enhancement mechanism - Style Box which can limit the driver's rights to access kernel by a private page table and a call control list. This method captures a variety of type errors, synchronization errors and behavior errors of the driver, and intelligently predicts and rapidly recovers driver errors. Experimental results show that Style Box can effectively detect and deal with driver errors, and obviously improve the reliability of the operating system.
Molecular Cloning and Expression of Glucuronyltransferase I Involved in the Biosynthesis of the Glycosaminoglycan-Protein Linkage Region of Proteoglycans (1998)

We isolated a cDNA encoding a novel glucuronyltransferase from human placenta cDNA with the use of the degenerate reverse transcriptase-polymerase chain reaction method. Degenerate primers were designed based upon the amino acid sequence alignment of rat glucuronyltransferase (GlcAT-P) involved in the biosynthesis of the carbohydrate epitope HNK-1 with putative proteins in Caenorhabditis elegans and Schistosoma mansoni. The new cDNA sequence revealed an open reading frame coding for a protein of 335 amino acids with a type II transmembrane protein topology. The amino acid sequence displayed 43% identity to the rat GlcAT-P, and the highest sequence identity was found in the COOH-terminal catalytic domain. The expression of a soluble recombinant form of the protein in COS-1 cells produced an active glucuronyltransferase with marked specificity for a glycoserine Galbeta1-3Galbeta1-4Xylbeta1-O-Ser. In contrast, asialoorosomucoid, which contains the Galbeta1-4GlcNAc sequence and is a good acceptor substrate for the GlcAT-P, did not serve as an acceptor. The reaction product was sensitive to beta-glucuronidase digestion and co-chromatographed with authentic GlcAbeta1-3Galbeta1-3Galbeta1-4Xylbeta1-O-Ser in high-performance liquid chromatography, suggesting that the enzyme is a beta1, 3-glucuronyltransferase. These results indicate that this new member of the glucuronyltransferase gene family is the enzyme previously described as glucuronyltransferase I that forms the glycosaminoglycan-protein linkage region, GlcAbeta1-3Galbeta1-3Galbeta1-4Xylbeta1-O-Ser, of proteoglycans.
HDZip class I genes in Arabidopsis: expression profiles and phylogenetic relationships (2004)

Homeodomain leucine zipper (HDZip) proteins constitute a large family of transcription factors characterised by the presence of a DNA-binding homeodomain and an adjacent leucine zipper motif, which mediates protein-dimer formation. The HDZip genes of Arabidopsis have been divided into four classes, HDZip I-IV. This thesis describes the characterisation and phylogeny of the class I HDZip genes and focuses on the expression and function of four HDZip I genes, ATHB5, -6, -7 and -16. The phylogenetic analyses of the 17 HDZip I sequences defined six subclasses, supported by the intron patterning and the traced duplication history of the genes. The members within each subclass showed diversification in expression, suggesting that the cis regulatory regions of the closely related genes have undergone evolutionary changes. However, similarities in the gene expression patterns between genes also exist and external factors like the availability of water and quality of light directs the expression of a subset of HDZip I genes. Expression analyses revealed that the plant hormone abscisic acid (ABA) is involved as a systemic signal for the salt or osmoticum induced ATHB7 expression, whereas light signals mediated through the blue light photoreceptors was found to direct the expression of ATHB6. Phenotypic analyses of plants with altered levels of ATHB6 or ATHB16 suggested that these paralogous genes encode proteins with very similar functions. ATHB16 was shown to act as a negative regulator of leaf cell expansion, as a suppressor of the flowering time sensitivity to photoperiod and as a positive regulator of blue light dependent inhibition of hypocotyl growth. A similar role for ATHB6 in the regulation of hypocotyl elongation was recorded. Further, analyses of multiple loss-of-function plants demonstrated that ATHB5, -6 and -16 function at least in part redundantly in mediating light effects on hypocotyl elongation.
Next-generation Web searches for visual content (2000)

Major search engines such as Hotbot (http://www.hotbot.com) help us find text on the Web, but typically have few or no capabilities for finding visual media. Yet many Web users, such as magazine editors or professional Web site designers, need to find images using just a few global features. My colleagues and I developed a prototype system called ImageScape (http://skynet.liacs.nl) to find visual media over intranets and the Web. The system integrates technologies such as vector quantization-based compression of the image database and k-d trees for fast searching over high-dimensional spaces.
Indium tin oxide template development for step and flash imprint lithography (2005)

Step and Flash Imprint Lithography (S-FIL) is an attractive method for printing sub-100 nm geometries. Relative to other imprinting processes S-FIL has the advantage that the template is transparent, thereby facilitating conventional overlay techniques. Previous work on S-FIL templates has focused on a chromium and quartz pattern transfer process that is compatible with processes that are currently used in mask shops. It is likely that 1X templates will require electron beam inspection, however, and templates that include buried charge conduction layers may be required. The purpose of this work was to investigate the issues associated with fabricating and inspecting these types of templates. The patterning stack examined included a layer of ZEP520A positive electron beam resist, followed by thin layers of chromium, silicon oxynitride, and indium tin oxide. The chromium layer was needed to avoid laser height sensor problems encountered prior to electron beam exposure. The pattern transfer process was characterized, and CD uniformity was characterized in four quadrants of the photoplate. A prototype electron beam inspection system was then used to inspect an array of programmed defect patterns. Two methods for fabricating templates were considered.
Increased expression of senescence markers in cystic fibrosis airways (2013)

Cystic Fibrosis (CF) is a chronic lung disease characterized by chronic neutrophilic airway inflammation and increased levels of neutrophil elastase (NE) in the airways. We have previously reported that NE treatment triggers cell cycle arrest. Cell cycle arrest can lead to senescence, a complete loss of replicative capacity. Importantly, senescent cells can be proinflammatory and would perpetuate CF chronic inflammation. By immunohistochemistry, we evaluated whether airway sections from CF and control subjects expressed markers of senescence, including p16(INK4a) (p16), a cyclin-dependent kinase inhibitor, phospho-Histone H2A.X (γH2A.X), and phospho-checkpoint 2 kinase (phospho-Chk2), which are also DNA damage response markers. Compared with airway epithelium from control subjects, CF airway epithelium had increased levels of expression of all three senescence markers. We hypothesized that the high load of NE in the CF airway triggers epithelial senescence by upregulating expression of p16, which inhibits cyclin-dependent kinase 4 (CDK4). Normal human bronchial epithelial (NHBE) cells, cultured in air-liquid interface were treated with NE (0, 200, and 500 nM) to induce visible injury. Total cell lysates were collected and evaluated by Western analysis for p16 protein expression and CDK4 kinase activity. NE significantly increased p16 expression and decreased CDK4 kinase activity in NHBE cells. These results support the concept that NE triggers expression of senescence markers in CF airway epithelial cells.
Detection of Low-Level K65R Variants in Nucleoside Reverse Transcriptase Inhibitor–Naive Chronic and Acute HIV-1 Subtype C Infections (2011)

To substantiate reports of greater emergence of the K65R nucleoside reverse transcriptase inhibitor (NRTI) mutation in human immunodeficiency virus type 1 (HIV-1) subtype C, we examined natural low-level K65R expression in subtype C relative to subtypes B and AE. We used allele-specific polymerase chain reaction to screen HIV-1 amplified by reverse-transcription high-fidelity polymerase chain reaction from subtype C-infected South African women and infants and CRF01(subtype AE) from Thailand; all subjects were NRTI naive. We found low-level K65R of unknown clinical significance in NRTI-naive subtype C-infected women and infants at frequencies above the natural occurrence in subtypes B and AE. The frequent appearance of subtype C frameshift deletions at codon 65 supports a propensity for transcription error in this region.
Interleukin-6--a key mediator of systemic and local symptoms in rheumatoid arthritis. (2007)

Interleukin-6 (IL-6) is a pleiotropic cytokine, present at elevated levels in patients with rheumatoid arthritis (RA). Il-6 signaling involves both a specific IL-6 receptor (IL-6R) and a ubiquitous signal-transducing protein, gp130 that is also utilized by other members of the IL-6 family. Il-6 signaling occurs by two mechanisms. Conventional signaling involves the binding of IL-6 to transmembrane IL-6R on cells expressing this receptor. In contrast, trans-signaling involves binding between the complex of soluble IL-6R/IL-6 and membrane-bound gp130. Trans-signaling allows IL-6 to affect cells that do not express IL-6R, including many synovial cells. The biological activities of IL-6 contribute to both systemic and local RA symptoms. Il-6 is a strong inducer of the acute-phase response, which can result in fever, secondary amyloidosis, anemia, and elevations in acute-phase proteins, such as C-reactive protein (CRP). The ability of IL-6 to induce B-cell differentiation may lead to the formation of rheumatoid factor and other autoantibodies. In joints, IL-6 promotes osteoclast activation and induces the release of matrix metalloproteinases, thus contributing to joint damage. In patients with RA, IL-6 levels correlate with markers of disease activity and clinical symptoms, and animal studies support the concept that this cytokine plays a role in the development of inflammatory arthritis. Clinical trials with tocilizumab, a humanized monoclonal antibody to soluble IL-6R, have shown that blocking IL-6 signaling reduces RA symptoms and markers of disease activity. Current evidence thus strongly supports the association between IL-6 and RA symptoms and suggests that IL-6 blockade will be a useful therapeutic strategy for patients with this disease.
GMM-1: A 50 degree and order gravitational field model for Mars (1993)

Knowledge of the gravitational field, in combination with surface topography, provides one of the principal means of inferring the internal structure of a planetary body. The highest resolution gravitational field for Mars published thus far was derived from Doppler tracking data from the Mariner 9 and Viking 1 and 2 spacecraft and is complete to degree and order 18 corresponding to a half wavelength resolution of approximately 600 km. This field, which is characterized by a spatial resolution that is slightly better than that of the highest resolution (16x16) topographic model, has been utilized extensively in analyses of the state of stress and isostatic compensation of the Martian lithosphere. However, the resolution and quality of current gravity and topographic fields are such that the origin and evolution of even the major physiographic features on Mars, such as the hemispheric dichotomy and Tharsis rise, are not well understood. We have re-analyzed the Viking and Mariner data sets and have derived a new gravitational field, which we designated GMM-1 (Goddard Mars Model-1). This model is complete to spherical harmonic degree and order 50 with a corresponding (half wavelength) spatial resolution of 200-300 km where the data permit. In contrast to previous models, GMM-1 was solved to as high degree and order as necessary to nearly exhaust the attenuated gravitational signal contained in the tracking data.
Dysbiosis in the Pathogenesis of Pediatric Inflammatory Bowel Diseases (2012)

Inflammatory bowel diseases (IBDs) are chronic inflammatory conditions of the gastrointestinal tract that occur in genetically susceptible individuals. Crohn's disease (CD) and ulcerative colitis (UC) are two major types of IBD. In about 20-25% of patients, disease onset is during childhood and pediatric IBD can be considered the best model for studying immunopathogentic mechanisms. The fundamentals of IBD pathogenesis are considered a defective innate immunity and bacterial killing with overaggressive adaptive immune response. A condition of "dysbiosis", with alterations of the gut microbial composition, is regarded as the basis of IBD pathogenesis. The human gastrointestinal (GI) microbial population is a complex, dynamic ecosystem and consists of up to one thousand different bacterial species. In healthy individuals, intestinal microbiota have a symbiotic relationship with the host organism and carry out important metabolic, "barrier," and immune functions. Microbial dysbiosis in IBD with lack of beneficial bacteria, together with genetic predisposition, is the most relevant conditions in the pathogenesis of the pediatric IBD.
Gas-Phase Databases for Quantitative Infrared Spectroscopy (2004)

The National Institute of Standards and Technology (NIST) and the Pacific Northwest National Laboratory (PNNL) are each creating quantitative databases containing the vapor-phase infrared spectra of pure chemicals. The digital databases have been created with both laboratory and remote-sensing applications in mind. A spectral resolution of approximate, equals 0.1 cm(-1) was selected to avoid degrading sharp spectral features, while also realizing that atmospheric broadening typically limits line widths to 0.1 cm(-1). Calculated positional (wave- number, cm(-1)) uncertainty is </=0.005 cm(-1), while the 1sigma statistical uncertainty in absorbance values is <2% for most compounds. The latter was achieved by measuring multiple (typically >/=9) path length-concentration burdens and fitting a weighted Beer's law plot to each wavenumber channel. The two databases include different classes of compounds and were compared using 12 samples. Though these 12 samples span a range of polarities, absorption strengths, and vapor pressures, the data agree to within experimental uncertainties with only one exception.
Life Review and Heroic Narrative: Embracing Pathology and Attention to Context (1999)

Holding the Man (Conigrave, 1995), chronicles a fifteen‐year relationship between Timothy Conigrave and his partner, John, and the process of their coping with John's impending death from AIDS related illness. In this article I discuss the autobiography as a naturalistic example of the therapeutic method of life review. What result would have emerged if a narrative therapist had assisted in the writing of the book? Based on my friendship with the protagonists, I would have argued for a less negative picture of the author, but Tim's aim seems to have been to represent the relationship in a dramatic form, with the author embracing his own pathology, and the imbalances and unfairness in their relationship. I suggest that employing methods which externalise pathology to elicit ‘the heroic 2 narrative’ may have disregarded these goals. I highlight the need to recognise and understand individual pattern and context, and raise alternative, less interventionist positions as appropriate for clients involved in such reviews of their lives.
Metabolism of Organically Bound Tritium in Man (1984)

The classic methodology for estimating dose to man from environmental tritium assumes that all tritium, whether organically bound or free, enters directly into man's free body water compartment and is uniformly distributed as tritiated water. This methodology ignores the fact that organically bound tritium in foodstuffs may be directly assimilated in the bound compartment of tissues without previous oxidation. A four-compartment model consisting of a free body water compartment, two organic compartments, and a small, rapidly metabolizing compartment is proposed. The utility of this model lies in the ability to input organically bound tritium directly into organic compartments representing tissue solids. The model will be used to illustrate the potential importance of organically bound tritium to cumulative dose estimates. It is found that organically bound tritium in foodstuffs can increase cumulative total body dose by a factor of 1.7-4.5 times the free body water dose alone, depending on the bound-to-loose ratio of tritium in the diet.
A Biodegradable Patch used as a Pericardial Substitute after Cardiac Surgery: 6- and 24-Month Evaluation with CT (1995)

Biodegradable patches made of polyhydroxybutyrate (PHB) were recently shown to limit postoperative pericardial adhesions when inserted into the pericardium in sheep. The present study was carried out to evaluate the presence of post-operative retrosternal adhesions after cardiac surgery in patients operated on with the PHB patch compared with those operated on without the insertion of such a patch. 50 patients admitted for CABG and/or valvular replacement were randomised to treatment either with pericardial closure with a patch or with the pericardium left open. In 39 of these (19 with and 20 without a PHB patch) computerised tomography was carried out six and twenty-four months postoperatively. Computerised tomography indicated a lower incidence (p < 0.05) of postoperative adhesions between the patch and the cardiac surface in the patch group, compared with the corresponding area in the non-patch group. A reduction of patch size in 27% (p = 0.003) was also seen.
MEMS flow sensors for nano-fluidic applications (2002)

This paper presents micromachined thermal sensors for measuring liquid flow rates in the nanoliter-per-minute range. The sensors use a boron-doped polysilicon thin-film heater that is embedded in the silicon nitride wall of a microchannel. The boron doping is chosen to increase the heater's temperature coefficient of resistance within tolerable noise limits. And the microchannel is suspended from the substrate to improve thermal isolation. The sensors have demonstrated a flow rate resolution below 10 nL/min, as well as the capability for detecting micro bubbles in the liquid. Heat transfer simulation has also been performed to explain the sensor operation and yielded good agreement with experimental data.
Error-Resilience Transcoding of H.264/AVC Compressed Videos (2007)

We propose an error resilience transcoder based on the intra refresh technique for H.264/AVC videos. Our algorithm focuses on making decisions on the number of inserted intra MBs, allocations of proper MBs for intra refresh, and the quantization parameter for each P-frame, according to varying channel condition and frame contents. We build source distortion, channel distortion, and bit-rate models for prediction and adopt the Lagrangian multiplier approach for constrained optimization. Existing algorithms are compared in experiments. The results show that our algorithm improves PSNR by 0.28~2.76 dB, compared to the "equal intra refresh" approach. Our algorithm also outperforms CBERC (Chen and Wang, 2001) by 0.1~1.13 dB, with the same number of inserted intra MBs, but different MB priorities in allocation
[Properties of alpha-chymotrypsin and cis-cinnamoylchymotrypsin in free, covalently bound to a carrier and microcapsulated states]. (1977)

alpha-Chymotrypsin and its light-sensitive derivative, cis-cinnamoylchymotrypsin, free and immobilysed (by means of microcapsulation, covalent binding with sepharose 4B and p-aminobenzyl cellulose) are studied. Effect of pH on the hydrolysis rate of N-alpha-acetyl-L-tyrosine ethyl ester by different immobilized enzyme preparations, their acylation with isomeric mixture of cis- and trans-cinnamoylimidazole, reactivation of stable cis-derivatives of different enzyme samples and thermal stability of native and microcapsulated enzyme preparations are investigated.
Protection from oxidation enhances the survival of cultured mesencephalic neurons (1995)

Oxidative stress has been linked to the destruction of dopaminergic neurons in the substantia nigra and may be a significant factor in both Parkinson's disease and MPTP toxicity. Using primary cultures of embryonic rat mesencephalon and standard immunocytochemical techniques, we have examined the survival of tyrosine hydroxylase-containing (TH+) neurons cultured in the presence of antioxidants and/or in an environment of low oxygen partial pressure. The number of TH+ neurons increased approximately twofold if superoxide dismutase, glutathione peroxidase (GP), or N-acetyl cysteine (NAC) were added to the culture media. Exposure of the neurons to a 5% oxygen environment (38 torr, i.e., 38 mm Hg) also increased the survival of TH+ neurons by about twofold. A dramatic enhancement of survival, however, was seen when NAC was used in combination with the 5% oxygen environment. In this case, the number of TH+ neurons increased fourfold from nontreated controls. Morphological changes were also noted. GP increased the average neurite length while NAC increased the average area of the cell body in the TH+ neuron. These results suggest that manipulation of oxidative conditions by changing the ambient O2 tension or the level of antioxidants promotes survival of TH+ neurons in culture and may have implications for transplantation therapies in Parkinson's disease.