gebhart/patrepeval huggingface dataset:
Development and evaluation of a microdevice for amino acid biomarker detection and analysis on Mars (2005)

The Mars Organic Analyzer (MOA), a microfabricated capillary electrophoresis (CE) instrument for sensitive amino acid biomarker analysis, has been developed and evaluated. The microdevice consists of a four-wafer sandwich combining glass CE separation channels, microfabricated pneumatic membrane valves and pumps, and a nanoliter fluidic network. The portable MOA instrument integrates high voltage CE power supplies, pneumatic controls, and fluorescence detection optics necessary for field operation. The amino acid concentration sensitivities range from micromolar to 0.1 nM, corresponding to part-per-trillion sensitivity. The MOA was first used in the lab to analyze soil extracts from the Atacama Desert, Chile, detecting amino acids ranging from 10-600 parts per billion. Field tests of the MOA in the Panoche Valley, CA, successfully detected amino acids at 70 parts per trillion to 100 parts per billion in jarosite, a sulfate-rich mineral associated with liquid water that was recently detected on Mars. These results demonstrate the feasibility of using the MOA to perform sensitive in situ amino acid biomarker analysis on soil samples representative of a Mars-like environment.
Hoxb13 knockout adult skin exhibits high levels of hyaluronan and enhanced wound healing (2003)

In contrast to adult cutaneous wound repair, early gestational fetal cutaneous wounds heal by a process of regeneration, resulting in little or no scarring. Previous studies indicate that down-regulation of HoxB13, a member of the highly conserved family of Hox transcription factors, occurs during fetal scarless wound healing. No down-regulation was noted in adult wounds. Here, we evaluate healing of adult cutaneous wounds in Hoxb13 knockout (KO) mice, hypothesizing that loss of Hoxb13 in adult skin should result in enhanced wound healing. Tensiometry was used to measure the tensile strength of incisional wounds over a 60-day time course; overall, Hoxb13 KO wounds are significantly stronger than wild-type (WT). Histological evaluation of incisional wounds shows that 7-day-old Hoxb13 KO wounds are significantly smaller and that 60-day-old Hoxb13 KO wounds exhibit a more normal collagen architecture compared with WT wounds. We also find that excisional wounds close at a faster rate in Hoxb13 KO mice. Biochemical and histochemical analyses show that Hoxb13 KO skin contains significantly elevated levels of hyaluronan. Because higher levels of hyaluronan and enhanced wound healing are characteristics of fetal skin, we conclude that loss of Hoxb13 produces a more "fetal-like" state in adult skin.
EXPRESSION OF SECRETOGLOBIN3A2 (SCGB3A2) IN PRIMARY PULMONARY CARCINOMAS (2008)

Secretoglobin (SCGB) 3A2 is a downstream target gene for the thyroid transcription factor-1 (TITF1). SCGB3A2 plays a role as an anti-inflammatory agent, however, its role in primary pulmonary carcinomas has not been examined. We assessed immunohistochemical expression of SCGB3A2 in primary pulmonary carcinomas and evaluated the correlation between the expression and histopathological phenotypes and prognosis. One hundred and fifty-six primary lung cancers undergone for surgical resection were examined. The percentages of SCGB3A2 positive cells were scored and tumors had immunoreactivity in more than 10% of tumor cells were considered positive for SCGB3A2. Overall reactivity for SCGB3A2 was observed in 116 (74.4%) of 156 primary lung cancers. SCGB3A2 was predominantly expressed in adenocarcinomas (86.5%), compared with squamous cell carcinomas (50.0%) and small cell carcinomas (42.9%). The expression in papillary adenocarcinomas was seen at higher frequency than that in tubular adenocarcinomas. There was no significant relationship between SCGB3A2 expression and tumor differentiation, and pathological stage. Positive expression of SCGB3A2 was not associated with better survival rate. SCGB3A2 expression in primary pulmonary carcinomas is high, especially in adenocarcinomas. Our results indicate that SCGB3A2 has a potential to be a specific and useful marker for primary pulmonary adenocarcinomas.
Principles of antibody therapy. (1992)

The success of monoclonal antibodies in clinical practice is dependent on good design. Finding a suitable target is the most important part as other properties of the antibody can be altered by genetic engineering. Antibodies that target lymphocyte antigens offer less toxic immunosuppressive treatment than currently available drugs and the first monoclonal antibody approved for human use is an immunosuppressive agent for treating rejection of renal transplants. Human trails of monoclonal antibodies to treat septic shock have been done and antibodies are also being developed to target common pathogens such as herpes simplex virus. Although monoclonal antibodies against cancer have been much heralded, their success has been limited by the poor access to the inside of tumours. Treatment of blood cancers has been more successful and a human antibody against B cell malignancies is being clinically tested. As knowledge about natural immune responses and antibody engineering increases many more monoclonals are likely to feature in clinical practice.
A Longitudinal Study of Abnormalities on MRI and Disability from Multiple Sclerosis (2002)

In patients who first present with isolated syndromes suggestive of multiple sclerosis, the increases in the volume of the lesions seen on magnetic resonance imaging of the brain in the first five years correlate with the degree of long-term disability from multiple sclerosis. This relation is only moderate, so the volume of the lesions alone may not be an adequate basis for decisions about the use of disease-modifying treatment.
Depression, anxiety, and the gastrointestinal system. Discussion (2001)

Functional disorders of the digestive system, such as irritable bowel syndrome, are often associated with affective disorders, such as depression, anxiety, panic, and posttraumatic stress disorder (PTSD). Some of these associations are observed not only in clinical populations, but also in population-based samples, suggesting a relationship with pathophysiologic mechanisms underlying both gastrointestinal (GI) dysfunction and certain affective disorders. Sustained and acute life-threatening stressors play an important role in the onset and modulation of GI symptoms as well as in the development of affective disorders and PTSD. A neurobiological model is proposed that attempts to explain the development of visceral hypersensitivity, the neuroendocrine and autonomic dysfunction characteristic of functional GI disorders, as well as the overlap with affective disorders.
A Survey of Collaborative Filtering Techniques (2009)

As one of the most successful approaches to building recommender systems, collaborative filtering ( CF ) uses the known preferences of a group of users to make recommendations or predictions of the unknown preferences for other users. In this paper, we first introduce CF tasks and their main challenges, such as data sparsity, scalability, synonymy, gray sheep, shilling attacks, privacy protection, etc., and their possible solutions. We then present three main categories of CF techniques: memory-based, model-based, and hybrid CF algorithms (that combine CF with other recommendation techniques), with examples for representative algorithms of each category, and analysis of their predictive performance and their ability to address the challenges. From basic techniques to the state-of-the-art, we attempt to present a comprehensive survey for CF techniques, which can be served as a roadmap for research and practice in this area.
Thermal Effects on Reverse Transcription: Improvement of Accuracy and Processivity in cDNA Synthesis (2001)

Reverse transcription, coupled with DNA amplification, has been widely used for molecular analysis of RNAs. Reverse transcriptases are retroviral DNA polymerases that can synthesize DNA from both RNA and DNA. In general, because of the lack of 3'-->5' exonuclease activity in retroviral reverse transcriptases, the reverse transcription step is error prone. Mutations created during the reverse transcription step of cDNA synthesis or RT-PCR are delivered to the final products to be analyzed, interfering with accurate analysis of the RNAs. In addition, because reverse transcription uses RNA as a template, processive DNA synthesis by reverse transcriptase is frequently interrupted by secondary structures of the RNA templates, causing difficulties in full-length cDNA synthesis. Here, we report that an increase in reaction temperature greatly enhances both the accuracy and the processivity of reverse transcription catalyzed by murine leukemia virus (MuLV) and human immunodeficiency virus type 1 (HIV-1) reverse transcriptases.
A Facile Synthesis of Cyanohydrin Trimethylsilyl Ethers by the Addition Reaction of Trimethylsilyl Cyanide with Aldehydes under Basic Condition (1991)

Abstract In the presence of a catalytic amount of Lewis base such as amine, phosphine, arsine or antimony, trimethylsilyl cyanide (TMS-CN) smoothly reacts with aldehydes to afford the corresponding cyanohydrin trimethylsilyl ethers in excellent yields.
PilC of Neisseria meningitidis is involved in class II pilus formation and restores pilus assembly, natural transformation competence and adherence to epithelial cells in PilC‐deficient gonococci (1997)

Type 4 pili produced by the pathogenic Neisseria species constitute primary determinants for the adherence to host tissues. In addition to the major pilin subunit (PilE), neisserial pili contain the variable PilC proteins represented by two variant gene copies in most pathogenic Neisseria isolates. Based upon structural differences in the conserved regions of PilE, two pilus classes can be distinguished in Neisseria meningitidis. For class I pili found in both Neisseria gonorrhoeae and N. meningitidis, PilC proteins have been implicated in pilus assembly, natural transformation competence and adherence to epithelial cells. In this study, we used primers specific for the pilC2 gene of N.gonorrhoeae strain MS11 to amplify, by the polymerase chain reaction, and clone a homologous pilC gene from N. meningitidis strain A1493 which produces class II pili. This gene was sequenced and the deduced amino acid sequence showed 75.4% and 73.8% identity with the gonococcal PilC1 and PilC2, respectively. These values match the identity value of 74.1% calculated for the two N. gonorrhoeae MS11 PilC proteins, indicating a horizontal relationship between the N. gonorrhoeae and N. meningitidis pilC genes. We provide evidence that PilC functions in meningococcal class II pilus assembly and adherence. Furthermore, expression of the cloned N. meningitidis pilC gene in a gonococcal pilC1,2 mutant restores pilus assembly, adherence to ME-180 epithelial cells, and transformation competence to the wild-type level. Thus, PilC proteins exhibit indistinguishable functions in the context of class I and class II pili.
Translation as negotiation : a musical perspective (2010)

Discource on translation studies is situated in this article outside studies. Contextualising and problematising issues when music from African choir culture is translated for non-Africans (Westerners) to perform, the main problem - translation as negotiation - is explored together with notions of hybridity, the 'third space' boundaries, identity, authencity and cultural compatibility within performance contexts.&#13;\n&#13;\nCultural studies bring to linguistics a wider perspective of translation; how translation studies relate to other disciplines and expressive forms, like music. The researchers argue that translation of African choir music for perfomance by non-Africans can only be achieved in cultural dialogue.
Determination of the Relative Orientation of the Two Halves of the Domain-Swapped Dimer of Cyanovirin-N in Solution Using Dipolar Couplings and Rigid Body Minimization (2000)

The HIV-inactivating protein cyanovirin-N (CVN) exists in two forms that are pH- and solvent-dependent: a monomer which predominates at neutral pH (≥90%) and a symmetric domain-swapped dimer. We have investigated the orientation of the two halves of the domain-swapped dimer of CVN at neutral pH in solution using dipolar couplings measured in a neutral liquid crystalline bicelle medium. 1DNH dipolar couplings for the dimer were readily measured for 18 out of 101 residues, and are shown to be inconsistent with the orientation of the two halves of the dimer observed in the X-ray structure obtained from crystals grown at low pH in the presence of organic solvent. The orientation of the two halves of the domain-swapped dimer was determined by rigid body minimization, subject to the requirements of C2 symmetry. The starting coordinates for the calculations consisted of the X-ray coordinates for the two halves (with the linker residues deleted), separated by ∼45 Å and placed in three different relative orientations. One-half of the dimer is held fixed, the other half is free to rotate and translate (6 degrees of freedom), and the alignment tensor for the dipolar couplings is free to rotate (3 degrees of freedom). The target function comprised only four terms: dipolar coupling restraints (18 × 2), distance restraints (12) to link the two halves and to prevent steric clash, a radius of gyration restraint to achieve appropriate compaction, and a quartic van der Waals repulsion term. Structures were calculated for different target values of the radius of gyration, and back-calculation of the alignment tensor and dipolar couplings on the basis of molecular shape was used to filter the resulting structures. Prediction of dipolar couplings in this manner is predicated on the assumption that orientational order is dictated by steric interactions between the liquid crystalline medium and the protein. The validity of this assumption in this particular case is evidenced by the excellent agreement between predicted and observed dipolar couplings for the monomer. We show that the data is only consistent with a very small range of orientations of the two halves of the dimer in which the angle between the long axes of the two halves is ∼110°. The relative orientation of the two halves of the dimer at neutral pH in solution is quite different from that observed in the crystals obtained at low pH in organic solvent. The factors stabilizing the relative orientation of the two halves of the dimer under different conditions are discussed. The methodology presented in this paper should find a wide range of applicability to numerous other structural problems involving multimeric proteins and protein−protein complexes.
Control methods and thresholds of acceptability for antibrucella vaccines. (1992)

Protection against brucellosis involves both cellular and humoral effectors not yet fully appreciated. Living or killed vaccines can protect against the infection itself or only against abortion. For official controls, vaccines (or new procedures of vaccination) must first be characterized pharmacologically and tested for innocuity. Protection must be tested on natural hosts with a reference vaccine (S19 or Rev. 1) by the agreed method which reproduces the natural infection and measures immunity in toto. Control and vaccinated females are challenged by the conjunctival route at mid-pregnancy under standard conditions (strain, dose) to measure the resulting infection by bacteriological analysis of excretion at parturition and of infection in target organs at slaughter. Results are principally expressed by the infection rate which should be +/- 95% in the control group. In the new vaccine group the rate should be equivalent to, or lower than, the reference vaccine group. To be statistically valid, at least 30 animals per group are required. For routine controls, laboratory models using guinea pigs, not well standardized, inaccurate and expensive, have long been proposed. The mouse model, extensively studied and standardized, should now be preferred to the guinea pig model. In the mouse model, residual virulence of a living vaccine is estimated by the time required by 50% of the mice to eradicate the strain from their spleen (Recovery Time 50%). Immunogenicity is measured by the ability of mice to restrict their splenic infection after a virulent i.p. challenge at a dose (B. abortus 544; 2 x 10(5) cfu) chosen in order that all mice were still infected 15 days post challenge.(ABSTRACT TRUNCATED AT 250 WORDS)
Adipose Tissue Is a Major Source of Interleukin-1 Receptor Antagonist (2003)

The secreted form of the interleukin-1 receptor antagonist (IL-1Ra) is an acute-phase protein intervening in the counterregulation of inflammatory processes. We previously showed that this cytokine antagonist is upregulated in the serum of obese patients, correlating with BMI and insulin resistance. In this study, we examined the expression pattern of IL-1Ra and showed that it is highly expressed not only in liver and spleen, but also in white adipose tissue (WAT), where it is upregulated in obesity. In WAT of obese humans, IL-1Ra was also markedly increased. Moreover, human WAT explants secreted IL-1Ra into the medium, a process that could be stimulated fivefold by interferon-beta. Finally, lipopolysaccharide administration induced a long-lasting expression of IL-1Ra in mouse WAT, suggesting that adipose tissue is an important source of IL-1Ra in both obesity and inflammation. In summary, we demonstrated that WAT is one of the most important sources of IL-1Ra quantitatively, suggesting that this tissue could represent a novel target for anti-inflammatory treatment. Moreover, it can be speculated that IL-1Ra, whose production is markedly increased in WAT in obese individuals, contributes further to weight gain because of its endocrine and paracrine effects on the hypothalamus and adipocytes, respectively.
Regulation of adiponectin receptor gene expression in diabetic mice (2004)

Adiponectin is an adipocyte-derived factor that plays pivotal roles in lipid and glucose metabolism in muscle and liver. The following two adiponectin receptor types were recently identified: AdipoR1 is abundantly expressed in muscle, whereas AdipoR2 is predominantly expressed in the liver. To clarify the regulation of adiponectin receptor gene expression in diabetic states, we examined mRNA levels of AdipoR1 in the muscles of diabetic animals by Northern blotting. The level of AdipoR1 mRNA was increased ∼2.5-fold in muscle of streptozotocin (STZ) diabetic mice, but the normal level was restored by insulin administration, indicating that insulin has an inhibitory effect on AdipoR1 expression. To confirm this inhibitory effect of insulin, we performed in vitro experiments using C 2 C 12 skeletal muscle cells. Insulin treatment for 24 h decreased AdipoR1 expression by ∼60% in C 2 C 12 cells. In addition, this effect was mediated by the phosphatidylinositol 3-kinase-dependent pathway rather than the mitogen-activated protein kinase pathway. AdipoR1 expression in insulin-resistant diabetic mice was also investigated. AdipoR1 expression was decreased by 36% in type 2 diabetic obese db/db mice compared with lean mice. In contrast, hepatic AdipoR2 expression was not significantly changed in either STZ mice or genetically obese mice. Our results indicate that regulation of AdipoR1, but not that of AdipoR2, may be involved in glucose and lipid metabolism in diabetic states.
Synthesis and biological activity of α-galactosyl ceramide KRN7000 and galactosyl (α1→2) galactosyl ceramide (2009)

We herein report a faster and less cumbersome synthesis of the biologically attractive, alpha-galactosyl ceramide (alpha-GalCer), known as KRN7000, and its analogues. More importantly, the use of a silicon tethered intramolecular glycosylation reaction gave easy access to the diglycosyl ceramide Gal(alpha1-->2)GalCer, which has been shown to require uptake and processing to the biologically active alpha-GalCer derivative.
Theoretical Property Predictions (2003)

Methods for the prediction of octanol / water partition coefficient, aqueous solubility and acid / base dissociation constants are described and discussed. The advantages and limitations of the different approaches are described and an indication of problem areas discussed. Available prediction software is described and listed and attempts are made to assess the likely reliability of the predictions. The concept of “drug-likeness” is introduced and put into context and models for the prediction of ADME properties and toxicity are briefly described and assessed. Software for ADME / toxicity prediction is listed and the impact of these techniques on current drug design efforts is described. Web references are given for both commercial and public domain software which is available for property prediction from chemical structure.
Tumor necrosis factor a microsatellite polymorphism is associated with rheumatoid arthritis severity through an interaction with the HLA-DRB1 shared epitope (1999)

The data suggest that TNFa is associated with RA severity through an interaction with the HLA-DRB1 SE.
A Short Review on Cardiotonic Steroids and Their Aminoguanidine Analogues (2000)

A short review on cardiotonic steroids and their analogues is presented. The natural, semisynthetic and synthetic derivatives, as well as their mechanism of action and structure-activity relationships are shown, with a special reference to aminoguanidine derivatives.
Technology enhancements for high performance BAW duplexer (2013)

In this article we will present the recent improvements in the performance of Solidly Mounted Resonator (SMR) high performance duplexer using Band2 duplexer for illustration purpose. Over the past 4 years insertion loss and rejection steepness were improved dramatically. Optimization of resonator intrinsic performance has played obviously a critical role but less expectedly the introduction of new building block (MIM capacitor) capitalizing on SMR technology has proven key for both performance improvement and size reduction. A new design approach based on the selective reduction of the effective coupling coefficient of certain resonators will be presented. We will discuss its impact on slope steepness improvement. The additional flexibility provided by this method enables as well to reduce further the impedance variation presented on the transmit path. This feature is critical to maintain high efficiency and linearity of any Power Amplifier upfront in the chain.
Determination of Interferon-α-Producing Capacity in Whole Blood Cultures from Patients with Various Diseases and from Healthy Persons (1996)

To assess the clinical value of determination of the interferon (IFN)-producing capacity of patients, IFN production induced by Sendai virus (HVJ) in vitro was measured in cell cultures of whole blood from patients with various diseases. IFN production in patients with lung cancer, myelodysplastic syndromes, noninsulin-dependent diabetes mellitus, pulmonary tuberculosis, and asymptomatic HIV-1 infection was lower than that in healthy persons. Furthermore, periodic measurements of IFN production revealed decreasing IFN producing capacities in patients with lung cancer with progression of the tumor stage. However, increased IFN-producing capacities were observed in patients with tuberculosis after standard therapy. Further experiments showed that the main type of IFN induced in whole blood cultures was IFN-alpha, and decreased IFN production in patients did not result from a decreased number of leukocytes but rather from an impairment of cellular IFN production. The evaluation of IFN production in whole blood cell cultures may be a feasible method of assessing the impaired immune status.