gebhart/patrepeval huggingface dataset:
Detection of ammonium-oxidizing bacteria of the beta-subclass of the class Proteobacteria in aquatic samples with the PCR (1995)

The PCR was used as the basis for the development of a sensitive and specific assay for the detection of ammonium-oxidizing bacteria belonging to the beta-subclass of the class Proteobacteria. PCR primers were selected on the basis of nucleic acid sequence data available for seven species of nitrifiers in this subclass. The specificity of the ammonium oxidizer primers was evaluated by testing known strains of nitrifiers, several serotyped environmental nitrifier isolates, and other members of the Proteobacteria, including four very closely related, nonnitrifying species (as determined by rRNA sequence analysis). DNA extracts from 19 bacterio-plankton samples collected from Lake Bonney, Antarctica, and the Southern California Bight were assayed for the presence of ammonium oxidizers. By using a two-stage amplification procedure, ammonium oxidizers were detected in samples collected from both sites. Chemical data collected simultaneously support the occurrence of nitrification and the presence of nitrifiers. This is the first report describing PCR primers specific for ammonium-oxidizing bacteria and the successful amplification of nitrifier genes coding for rRNA from DNA extracts from natural samples. This application of PCR is of particular importance for the detection and study of microbes, such as autotrophic nitrifiers, which are difficult or impossible to isolate from indigenous microbial communities.
Influence of carbon dioxide on the activity of chicken egg white lysozyme (2011)

Rapid cooling of shell eggs by using liquid CO(2) has shown increased bactericidal effects along with saturation of the egg albumen with CO(2). Lysozyme is a bactericidal enzyme present in chicken eggs, and it lyses gram-positive bacteria. Newly laid chicken eggs have an initial pH of 7.6 to 8.5 and are saturated with CO(2). During storage, the pH gradually increases to 9.7, accompanied by a loss of CO(2). It is hypothesized that the lysozyme activity is influenced by either CO(2) concentration or pH changes resulting from CO(2) loss. The objective of this study was to determine the lytic activity of purified lysozyme and chicken egg white (unpurified lysozyme) under varying conditions of temperature, pH, and CO(2) gas concentration. Lytic activity was determined by a standard microbial assay using lyophilized Micrococcus lysodeikticus. A 2 × 4 × 2 × 2 × 3 factorial design consisting of 2 temperatures (5 and 22°C), 4 pH (4.5, 6.5, 8.0, and 9.5), 2 treatments (with and without CO(2)), 2 types of lysozyme (purified and unpurified egg white), and 3 replicates was used. The highest lytic activity was found at pH 6.5 and 22°C. At pH 4.5 and 8.0, the addition of CO(2) increased lytic activity by more than 50% at both temperatures. At pH 6.5, lytic activity was maintained with CO(2) addition at both temperatures. At pH 9.5, lytic activity without CO(2) addition was high; however, adding CO(2) reduced lytic activity to zero. In conclusion, both pH and CO(2) treatment influence lysozyme activity.
Contrast-enhanced 3D MR breathhold imaging of porcine coronary arteries using fluoroscopic localization and bolus triggering (1999)

The purpose of this study was to develop cardiac-gated contrast-enhanced 3D MRA for imaging the coronary arteries of pigs. Each major coronary artery was imaged individually in a single 3D slab in one breathhold. To permit acquisition within a breathhold, a limited number of partitions (12-16) were collected in a single, oblique, thin 3D slab. Typical resolution of the acquisition was 0.8 (X) x 1.6 (Y) x 1.6 (Z) mm. MR fluoroscopic localization was used to establish the 3D double-oblique orientation. Real-time MR fluoroscopy was also used to instantaneously trigger the 3D scan after detection in the aortic root of the intravenously administered contrast bolus. Six pigs were used in the study. Each pig was scanned on two separate days. Images routinely show the majority of the length of the three principal coronary arteries. Magn Reson Med 42:1159-1165, 1999.
Low Temperature Thin Layer Drying Model of Rough Rice (2004)

This study was performed to develop thin layer drying equations for low temperature. Thin layer drying tests of short grain rough rice were conducted at three low temperature levels of 15, 25, <TEX>$35^{\circ}C$</TEX> and two relative humidity levels of 30, <TEX>$50\%$</TEX>, respectively. The measured moisture ratios were fitted to the selected four drying models (Page, Thompson, Simplified diffusion and Lewis model) using stepwise multiple regression analysis. The overall drying rate increased as the drying air temperature was increased and as relative humidity was decreased, but the effect of temperature increase was dominant. Half response time (Moisture ratio=0.5) of drying was affected by both drying temperature and relative humidity at drying temperature of below <TEX>$25^{\circ}C$</TEX>, but at <TEX>$35^{\circ}C$</TEX> was mainly affected by drying temperature. The results of comparing coefficients of determination and root mean square error of moisture ratio for low drying models showed that Page model was found to fit adequately to all drying test data.
Recent applications of IBM's query by image content (QBIC) (1996)

The QBIC project at IBM's Almaden Research Center is studying methods to query large on-line image databases using the images' content as the basis of the queries. Examples of the content include color, color layout, texture, shape, size, orientation, and position of image objects and regions. We have developed an AIX prototype, WWW QBIC server with WWW demo, and a product called Ultimedia Manager (OS/2 and Windows). The key applications of this technology are in the areas where image patterns are the basis of the queries, and where keywords are not precise enough for satisfactory retrieval, such as in on-line stock photo, retail, art etc. In this paper we briefly outline several recent applications of QBIC. SEDONA Systems Corporation, PIP Printing and IBM announced an application where QBIC is used to help the user find images to be included in documents remotely printed in high resolution and quality; IBM in the UK is developing an "advisor" to textile designers; Prof. B. Holt (UC Davis) researches use of QBIC for retrieving art images based on examples of a motifs used across geography and time without having to use standard authority lists of text reference terms, especially when searching for visual elements that are difficult to describe in words; and Prof. J. Hethorn (UC Davis) uses Ultimedia Manager to study colors, styles and trends in fashion. In this paper we
Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota (2012)

Inflammation alters host physiology to promote cancer, as seen in colitis-associated colorectal cancer (CRC). Here, we identify the intestinal microbiota as a target of inflammation that affects the progression of CRC. High-throughput sequencing revealed that inflammation modifies gut microbial composition in colitis-susceptible interleukin-10-deficient (Il10(-/-)) mice. Monocolonization with the commensal Escherichia coli NC101 promoted invasive carcinoma in azoxymethane (AOM)-treated Il10(-/-) mice. Deletion of the polyketide synthase (pks) genotoxic island from E. coli NC101 decreased tumor multiplicity and invasion in AOM/Il10(-/-) mice, without altering intestinal inflammation. Mucosa-associated pks(+) E. coli were found in a significantly high percentage of inflammatory bowel disease and CRC patients. This suggests that in mice, colitis can promote tumorigenesis by altering microbial composition and inducing the expansion of microorganisms with genotoxic capabilities.
Tumor-specific genetically engineered murine/human chimeric monoclonal antibody. (1987)

Murine variable and human constant region exons were fused to produce "chimeric" immunoglobulin gamma and kappa genes. These constructs were cotransfected into murine myeloma cells which then produced and secreted intact, functional antibody. Cells secreting the chimeric antibody were introduced into mice. The engineered immunoglobulin was subsequently harvested from ascites fluid and was purified by affinity chromatography. Its immunological properties were compared to those of the parental murine monoclonal (B6.2), which exhibits specificity for human breast, lung, and colon carcinoma cells. Competitive binding, immunofluorescent cell staining, and analysis of immunoprecipitated antigen gave similar results for the chimeric and murine B6.2. The biodistribution of chimeric and murine B6.2 after injection into mice bearing human tumors was found to be identical. These results suggest that murine/human chimeric antibodies may be viable clinical replacements for murine monoclonals with the potential for better immunological tolerance and pharmacological efficacy.
Binary Bacterial Toxins: Biochemistry, Biology, and Applications of CommonClostridiumandBacillusProteins (2004)

Certain pathogenic species of Bacillus and Clostridium have developed unique methods for intoxicating cells that employ the classic enzymatic "A-B" paradigm for protein toxins. The binary toxins produced by B. anthracis, B. cereus, C. botulinum, C. difficile, C. perfringens, and C. spiroforme consist of components not physically associated in solution that are linked to various diseases in humans, animals, or insects. The "B" components are synthesized as precursors that are subsequently activated by serine-type proteases on the targeted cell surface and/or in solution. Following release of a 20-kDa N-terminal peptide, the activated "B" components form homoheptameric rings that subsequently dock with an "A" component(s) on the cell surface. By following an acidified endosomal route and translocation into the cytosol, "A" molecules disable a cell (and host organism) via disruption of the actin cytoskeleton, increasing intracellular levels of cyclic AMP, or inactivation of signaling pathways linked to mitogen-activated protein kinase kinases. Recently, B. anthracis has gleaned much notoriety as a biowarfare/bioterrorism agent, and of primary interest has been the edema and lethal toxins, their role in anthrax, as well as the development of efficacious vaccines and therapeutics targeting these virulence factors and ultimately B. anthracis. This review comprehensively surveys the literature and discusses the similarities, as well as distinct differences, between each Clostridium and Bacillus binary toxin in terms of their biochemistry, biology, genetics, structure, and applications in science and medicine. The information may foster future studies that aid novel vaccine and drug development, as well as a better understanding of a conserved intoxication process utilized by various gram-positive, spore-forming bacteria.
White cell reduction in platelet concentrates and packed red cells by filtration: a multicenter clinical trial. The Trap Study Group (1995)

There were significant losses of platelets during filtration, which could add to the costs of WBC reduction and lead to possible increases in donor exposures. Filtration failures still occurred, despite careful observation of the standard filtration procedures. The number of total WBCs in pooled platelets before filtration has been identified as an important factor in determining the success of WBC reduction.
Rose Bengal Staining of Epibulbar Squamous Neoplasms (1976)

SUMMARY Topically applied rose bengal, because of its ability to stain abnormal epithelial cells, has been found to be a useful adjunct to careful clinical examination in determining the extent of epibulbar squamous neoplasms, thus facilitating their complete excision.
QA forum (1987)

1Senior Consultant—Nursing Standards and Quality Assurance, Resource Applications, Inc. Baltimore, Maryland 2Director Of Nursing, Quality Assurance, Good Samaritan Medical, Center, phoenix, Arizona
Generalized Additive Models for Location Scale and Shape (GAMLSS) inR (2007)

GAMLSS is a general framework for fitting regression type models where the distribution of the response variable does not have to belong to the exponential family and includes highly skew and kurtotic continuous and discrete distribution. GAMLSS allows all the parameters of the distribution of the response variable to be modelled as linear/non-linear or smooth functions of the explanatory variables. This paper starts by defining the statistical framework of GAMLSS, then describes the current implementation of GAMLSS in R and finally gives four different data examples to demonstrate how GAMLSS can be used for statistical modelling.
A Comparison of Long-Term Postconcussive Symptoms between University Students with and without a History of Mild Traumatic Brain Injury or Orthopedic Injury (2012)

Mild traumatic brain injury (mild TBI) is often associated with postconcussive symptoms such as headache, memory problems, and irritability. However, high rates of similar symptoms in groups without a history of TBI raise questions about the clinical validity of the postconcussive syndrome. This study was conducted to address these issues through systematic examination of symptoms reported by those with and without a history of mild TBI or orthopedic injury. Responses to the Postconcussion Syndrome Checklist (PCSC), demographic information, and medical history were collected via online questionnaire from 3027 non-referred university students (2280 without a history of mild TBI or orthopedic injury, 491 with a history of orthopedic injury, and 256 with post-acute mild TBI). Although the mild TBI group reported higher mean levels of symptoms, confirmatory factor analyses demonstrated that symptoms clustered into parallel cognitive, somatic, affective, and sensory factors in all three groups. Despite modestly higher mean symptoms among those with a history of mild TBI, symptom clusters did not differ from non-TBI groups. These findings cast doubts about the clinical validity of the "postconcussive syndrome" and raise questions about pathways by which mild TBI and other factors may influence the expression of chronic symptoms.
The crystal structure of a mutant protein with altered but improved hydrophobic core packing. (1994)

The dense packing observed in protein interiors appears to be crucial for stabilizing the native structure--even subtle internal substitutions are usually destabilizing. Thus, steric complementarity of core residues is thought to be an important criterion for "inverse folding" predictive methods, which judge whether a newly determined sequence is consistent with any known folds. A major problem in the development of useful core packing evaluation algorithms, however, is that there are occasional mutations that are predicted to disrupt native packing but that yield an equally or more stable protein. We have solved the crystal structure of such a variant of lambda repressor, which, despite having three larger core substitutions, is more stable than the wild type. The structure reveals that the protein accommodates the potentially disruptive residues with shifts in its alpha-helical arrangement. The variant is apparently more stable because its packing is improved--the core has a higher packing density and little geometric strain. These rearrangements, however, cause repositioning of functional residues, which result in reduced DNA binding activity. By comparing these results with the predictions of two core packing algorithms, it is clear that the protein possesses a relatively high degree of main-chain flexibility that must be accounted for in order to predict the full spectrum of compatible core sequences. This study also shows how, in protein evolution, a particular set of core residue identities might be selected not because they provide optimal stability but because they provide sufficient stability in addition to the precise structure required for optimal activity.
Phosphorylation of the PTEN Tail Acts as an Inhibitory Switch by Preventing Its Recruitment into a Protein Complex (2001)

PTEN is a tumor suppressor protein that functions, in large part, by dephosphorylating the lipid second messenger phosphatidylinositol 3,4,5-trisphosphate and by doing so antagonizing the action of phosphoinositide 3-kinase. PTEN structural domains include an N-terminal phosphatase domain, a lipid-binding C2 domain, and a 50-amino acid C-terminal tail that contains a PDZ binding sequence. We showed previously that phosphorylation of the PTEN tail negatively regulates PTEN activity. We now show that phosphorylated PTEN exists in a monomeric "closed" conformation and has low affinity for PDZ domain-containing proteins. Conversely, when unphosphorylated, PTEN is in an "open" conformation, is recruited into a high molecular weight complex (PTEN-associated complex), and strongly interacts with PDZ-containing proteins such as MAGI-2. As a consequence, when compared with wild-type PTEN, the phosphorylation-deficient mutant form of PTEN strongly cooperates with MAGI-2 to block Akt activation. These results indicate that phosphorylation of the PTEN tail causes a conformational change that results in the masking of the PDZ binding domain. Consequently, the ability of PTEN to bind to PDZ domain-containing proteins is reduced dramatically. These data suggest that phosphorylation of the PTEN tail suppresses the activity of PTEN by controlling the recruitment of PTEN into the PTEN-associated complex.
GAZ—盘式分选机——难筛分作业的解决方法 (1999)

作为经过检验的多用途分选机,盘式分选机用于15-300mm物料,包括难筛分物料的分选。近来,由于装配了附加的匹配零部件,它的应用范围已经扩大。另外,已经获得一个改进的维护—友好型机型。列举了土壤复整领域作为盘式分选机用于难筛分作业的实例。
Asiaticoside‐induced elevation of antioxidant levels in healing wounds (1999)

Asiaticoside derived from the plant Centella asiatica is known to possess good wound healing activity. Enhanced healing activity has been attributed to increased collagen formation and angiogenesis. Since antioxidants have been reported to play a significant role in the wound healing process we studied the effect of asiaticoside on the levels of certain antioxidants in the wound so as to explore the possible involvement of such a mechanism in the asiaticoside induced wound healing. Asiaticoside application (0.2%, topical) twice daily for 7 days to excision-type cutaneous wounds in rats led to increased enzymatic and non-enzymatic antioxidants, namely superoxide dismutase (35%), catalase (67%), glutathione peroxidase (49%), vitamin E (77%) and ascorbic acid (36%) in newly formed tissues. It also resulted in a several fold decrease in lipid peroxide levels (69%) as measured in terms of thiobarbituric acid reactive substance. However, continued application for 14 days showed no significant difference in these antioxidants compared with their values in vehicle treated wound tissue. It appears from the present study that asiaticosides enhanced induction of antioxidant levels at an initial stage of healing which may be an important contributory factor in the healing properties of this substance. Copyright © 1999 John Wiley & Sons, Ltd.
Synthesis and Biological Evaluation of α-Halogenated Bisphosphonate and Phosphonocarboxylate Analogues of Risedronate (2007)

Alpha-halogenated analogues of the anti-resorptive bisphosphonate risedronate (5, Ris) and its phosphonocarboxylate cognate (7, 3-PEHPC) were synthesized and compared with 5, 7, and the corresponding desoxy analogues in bone mineral affinity and mevalonate pathway inhibition assays. The Ris (5e-h) and 3-PEHPC (7e-h) analogues had decreased bone mineral affinity, confirming that the alpha-OH group in 5 and 7 enhances bone affinity. The 5 alpha-halo-analogues potently inhibited farnesyl pyrophosphate synthase (FPPS) with IC50 values from 16 (alpha-F) to 340 (alpha-Br) nM (5, 6 nM). In contrast, 7 alpha-halo-analogues were ineffective versus FPPS (IC50 > 600 microM), but inhibited Rab geranylgeranyl transferase (RGGT) (IC50 = 16-35 microM) similarly to 7 itself (IC50 = 24 microM). The alpha-F analogue 7e was 1-2 times as active as 7 in J774 cell viability and Rab11 prenylation inhibition assays.
Novel Rabies Virus-Neutralizing Epitope Recognized by Human Monoclonal Antibody: Fine Mapping and Escape Mutant Analysis (2005)

Anti-rabies virus immunoglobulin combined with rabies vaccine protects humans from lethal rabies infections. For cost and safety reasons, replacement of the human or equine polyclonal immunoglobulin is advocated, and the use of rabies virus-specific monoclonal antibodies (MAbs) is recommended. We produced two previously described potent rabies virus-neutralizing human MAbs, CR57 and CRJB, in human PER.C6 cells. The two MAbs competed for binding to rabies virus glycoprotein. Using CR57 and a set of 15-mer overlapping peptides covering the glycoprotein ectodomain, a neutralization domain was identified between amino acids (aa) 218 and 240. The minimal binding region was identified as KLCGVL (aa 226 to 231), with key residues K-CGV- identified by alanine replacement scanning. The critical binding region of this novel nonconformational rabies virus epitope is highly conserved within rabies viruses of genotype 1. Subsequently, we generated six rabies virus variants escaping neutralization by CR57 and six variants escaping CRJB. The CR57 escape mutants were only partially covered by CRJB, and all CRJB-resistant variants completely escaped neutralization by CR57. Without exception, the CR57-resistant variants showed a mutation at key residues within the defined minimal binding region, while the CRJB escape viruses showed a single mutation distant from the CR57 epitope (N182D) combined with mutations in the CR57 epitope. The competition between CR57 and CRJB, the in vitro escape profile, and the apparent overlap between the recognized epitopes argues against including both CR57 and CRJB in a MAb cocktail aimed at replacing classical immunoglobulin preparations.
Kinetic Analysis of the Interleukin-13 Receptor Complex (2002)

Interleukin (IL)-13 is a key cytokine associated with the asthmatic phenotype. It signals via its cognate receptor, a complex of IL-13 receptor alpha1 chain (IL-13Ralpha1) with IL-4Ralpha; however, a second protein, IL-13Ralpha2, also binds IL-13. To determine the binding contributions of the individual components of the IL-13 receptor to IL-13, we have employed surface plasmon resonance and equilibrium binding assays to investigate the ligand binding characteristics of shIL-13Ralpha1, shIL-13Ralpha2, and IL-4Ralpha. shIL-13Ralpha1 bound IL-13 with moderate affinity (K(D) = 37.8 +/- 1.8 nm, n = 10), whereas no binding was observed for hIL-4Ralpha. In contrast, shIL-13Ralpha2 produced a high affinity interaction with IL-13 (K(D) = 2.49 +/- 0.94 nm n = 10). IL-13Ralpha2 exhibited the binding characteristics of a negative regulator with a fast association rate and an exceptional slow dissociation rate. Although IL-13 interacted weakly with IL-4Ralpha on its own (K(D) > 50 microm), the presence of hIL-4Ralpha significantly increased the affinity of shIL-13Ralpha1 for IL-13 but had no effect on the binding affinity of IL-13Ralpha2. Detailed kinetic analyses of the binding properties of the heteromeric complexes suggested a sequential mechanism for the binding of IL-13 to its signaling receptor, in which IL-13 first binds to IL-13Ralpha1 and this then recruits IL-4Ralpha to stabilize a high affinity interaction.