gebhart/patrepeval huggingface dataset:
Molecular pathways in the formation of gliomas (1995)

The past few years have seen remarkable progress in understanding the molecular genetic basis of glioma formation. Affected oncogenes and tumor suppressor genes have been identified and putative tumor suppressor loci have been mapped. These studies have illustrated distinct molecular pathways for different glial neoplasms. We summarize the findings of an ongoing study initiated to characterize human gliomas on a molecular basis. The data are compiled from 150 astrocytic, oligodendroglial, and mixed gliomas that were assessed for genomic alterations characteristic of these neoplasms, i.e., loss of portions of chromosomes 1p, 9p, 10, 17p, 17q, and 19q, mutations of the p53 tumor suppressor gene, and amplification of the EGF receptor (EGFR) gene. Our findings support the hypothesis that distinct genetic pathways result in the formation of astrocytic and oligodendroglial neoplasms of different malignancy grades, and that glioblastoma multiforme may be subdivided into genetically distinct subsets. Such findings may not only lead to a better understanding of neoplastic transformation in glial cells, but may also have a major impact on clinical neuro-oncology.
Mobile robot navigation using artificial landmarks (1997)

This article describes a landmark-based navigation technique for a mobile robot. Robot position estimation is achieved by using a camera and a navigational landmark pattern, which consists of simple geometrical patterns. The Modified Elliptical Hough Transform (MEHT) is developed for detecting and measuring the projection of the landmark in the camera's image space. Robustness of this approach is demonstrated by studying the cases of noisy image data and partial occlusion of the landmark pattern. Error analysis of MEHT is performed to provide more understanding of the effects of applying elliptical approximation to the projection of a circular pattern. © 1997 John Wiley & Sons, Inc.
ZINC − A Free Database of Commercially Available Compounds for Virtual Screening (2004)

A critical barrier to entry into structure-based virtual screening is the lack of a suitable, easy to access database of purchasable compounds. We have therefore prepared a library of 727,842 molecules, each with 3D structure, using catalogs of compounds from vendors (the size of this library continues to grow). The molecules have been assigned biologically relevant protonation states and are annotated with properties such as molecular weight, calculated LogP, and number of rotatable bonds. Each molecule in the library contains vendor and purchasing information and is ready for docking using a number of popular docking programs. Within certain limits, the molecules are prepared in multiple protonation states and multiple tautomeric forms. In one format, multiple conformations are available for the molecules. This database is available for free download (http://zinc.docking.org) in several common file formats including SMILES, mol2, 3D SDF, and DOCK flexibase format. A Web-based query tool incorporating a molecular drawing interface enables the database to be searched and browsed and subsets to be created. Users can process their own molecules by uploading them to a server. Our hope is that this database will bring virtual screening libraries to a wide community of structural biologists and medicinal chemists.
Hydrogenation over supported gold catalysts (1973)

Gold on silica, or on γ-alumina, or on boehmite, prepared by thermal decomposition of impregnated chloroauric acid at 383–403 K, and by other methods, activates molecular hydrogen and catalyses the hydrogenation of mono-olefins, buta-1,3-diene, and but-2-yne.
Molecular Profiling of Breast Cancer Cell Lines Defines Relevant Tumor Models and Provides a Resource for Cancer Gene Discovery (2009)

Overall, breast cancer cell lines were genetically more complex than tumors, but retained expression patterns with relevance to the luminal-basal subtype distinction. The compendium of molecular profiles defines cell lines suitable for investigations of subtype-specific pathobiology, cancer stem cell biology, biomarkers and therapies, and provides a resource for discovery of new breast cancer genes.
Sacral neuromodulation effects on periurethral sensation and urethral sphincter activity (2012)

SNM does not alter urethral neuromuscular function 2 weeks post Stage 1 implantation.
Impact on survival of high-dose therapy with autologous stem cell support in patients younger than 60 years with newly diagnosed multiple myeloma: a population-based study. Nordic Myeloma Study Group. (2000)

High-dose therapy has become a common treatment for myeloma. The objectives of this study were to estimate in a prospective, population-based setting the impact on survival of high-dose therapy in newly diagnosed, symptomatic patients less than 60 years old and to compare the results with those of conventionally treated historic controls. The prospective population comprised 348 patients. Of these, 274 were treated according to a specified intensive-therapy protocol (Nordic Myeloma Study Group [NMSG] #5/94) and constituted the intensive-therapy group. The historic population consisted of 313 patients identified from 5 previous population-based Nordic studies. Of these, 274 fulfilled the eligibility criteria for high-dose therapy stated in NMSG #5/94 and constituted the control group. The expected numbers of patients in the prospective population and the historic population were 450 and 410, respectively, estimated from previously established data on the incidence in this population and the population base for each study. Survival was prolonged in the intensive-therapy group compared with the control group (risk ratio for the control group 1.62; 95% confidence interval 1.22-2.15; P =.001). These groups represented more than 60% of the expected number of patients. When survival for all the registered patients in the 2 populations was compared, representing more than 75% of the expected number of patients, the advantage for the prospective population persisted (risk ratio for the historic population 1.46; 95% confidence interval 1.14-1.86; P =. 002). These results indicate that the introduction of high-dose therapy for newly diagnosed myeloma has resulted in prolonged survival for the total patient population aged less than 60 years. (Blood. 2000; 95:7-11)
Dissolution Testing of Orally Disintegrating Tablets (2003)

Orally disintegrating tablets (ODT) are solid dosage forms that disintegrate in the oral cavity leaving an easy-to-swallow residue.The disintegration times are generally less than one minute.For orally disintegrating tablets,taste-masking of bitter or objectional-tasting drug substances is critical.The taste-masking aspect plays a significant role in dissolution method development,specifications,and testing.The USP 2 paddle apparatus is the most suitable and common choice for orally disintegrating tablets.Discriminating, robust dissolution methods are extremely useful for monitoring process optimization and changes during scale-up of taste-masked bulk drug and tablet manufacture.
Influence of some plasma proteins on in vitro bacterial adherence to PTFE and Dacron vascular prostheses (1993)

The in vitro adherence of Staphylococcus aureus, Staphylococcus epidermidis and Escherichia coli (one strain of each species) to commercially available, microporous polytetrafluoroethylene (PTFE) and woven Dacron vascular grafts before and after coating with human plasma was compared. Standard size segments of the materials were incubated with 35S-labeled bacteria for 0.5-18 h and, following washes, the radioactivity associated with the segment was measured. The binding of each of the tested species to native Dacron was higher than to PTFE. After coating with human plasma, however, the binding of all three species to PTFE was significantly enhanced, whereas the binding to Dacron was reduced. In addition, the influence of coating with serum albumin (HSA), immunoglobulin G (IgG), fibrinogen (Fg) or fibronectin (Fn) rather than whole plasma was tested. We found that coating with HSA reduced the binding of all three species to Dacron and of staphylococci to PTFE. IgG decreased the binding of S. epidermidis and E. coli to Dacron and of S. epidermidis to PTFE. In contrast, Fg enhanced the binding of S. aureus both to Dacron and PTFE, and that of E. coli to PTFE, but decreased the binding of S. epidermidis and E. coli to Dacron. Fn enhanced the binding of S. aureus to Dacron, and of E. coli to PTFE, but decreased the binding of S. aureus to PTFE and of S. epidermidis both to PTFE and Dacron. Thus, both whole plasma and some isolated plasma proteins were found to modulate bacterial adherence to two tested graft materials. From a clinical point of view, bacterial binding to plasma-coated rather than native materials may more adequately determine the likelihood of in vivo colonization of the various materials. Furthermore, precoating of materials with selected proteins may be of value in the prevention of graft colonization.
Supramolecular dendrimer capsules by cooperative binding (2010)

We exploit the unique features of dendrimers as molecular nanospheres with many peripheral binding sites to show that maximizing cooperative binding enables a novel modular self-assembly approach to construct supramolecular capsules.
Linezolid Therapy of Staphylococcus aureus Experimental Osteomyelitis (2000)

The in vivo activity of linezolid or cefazolin against a clinical isolate of methicillin-susceptible Staphylococcus aureus (linezolid MIC, 2 microg/ml) was studied in a rat model of experimental osteomyelitis. Sixty rats with experimental S. aureus osteomyelitis were treated for 21 days with no antimicrobial, with 25 microg of linezolid per kg of body weight administered intraperitoneally twice or three times a day, or with 50 microg of cefazolin per kg administered intramuscularly three times a day. After treatment, the animals were sacrificed and the infected tibiae were processed for quantitative bacterial cultures. The results of treatment were expressed as log(10) CFU/gram of bone and analyzed by rank sum analysis. The results of linezolid treatment were not significantly different from those of untreated controls, while cefazolin treatment was significantly more active than no treatment or linezolid treatment.
Synthesis and Characterization of New Ruthenium-Based Olefin Metathesis Catalysts Coordinated with Bidentate Schiff-Base Ligands (1998)

A novel series of Schiff-base-substituted ruthenium carbene complexes have been prepared by the treatment of RuCl2(CHPh)(PCy3)2 with a variety of Schiff-base ligands as the thallium salts. Modification of the Schiff-base electronic and/or structural substituents allowed for the tuning of the complexes activities in olefin metathesis reactions. The structures of the complexes were unambiguously characterized by NMR studies and X-ray analysis. These newly prepared complexes are highly stable to air, moisture, and temperature and even exhibit catalytic activity in polar protic solvents.
Plasminogen activators, activation inhibitors and alpha2‐macroglobulin produced by cultured normal and malignant human cells (1984)

In the present paper we have characterized the plasminogen activators (PA) synthesized by 25 different human cell lines. Technically easy methods were adopted for concentration and immunological characterization of the activators even in the presence of PA inhibitors. Most cell lines produced u-PA (mol. wt 55,000), melanoma and HeLa cells t-PA (mol. wt 66,000) and two carcinoma cell lines and normal skin fibroblasts produced no detectable PA. The classical 125I-fibrin method was compared to a caseinolytic assay and some of the discrepancies between results obtained with the two methods were shown to be due to cell-derived NaDodSO4-sensitive proteinase inhibitors in culture media. Additionally, synthesis and uptake by the cells of the wide-spectrum proteinase inhibitor alpha-2-macroglobulin ( alpha 2M ) were studied by radioimmunoassay and immunofluorescence. No production of alpha 2M could be measured in any of the malignant cell lines. In normal cells no correlation existed between the production of alpha 2M and the observed inhibition of PA activity, which indicates that other proteinase inhibitors are produced by the cells.
Combined vaccination with idiotype-pulsed allogeneic dendritic cells and soluble protein idiotype for multiple myeloma patients relapsing after reduced-intensity conditioning allogeneic stem cell transplantation (2005)

The results show for the first time that the use of Id-pulsed alloDC following RIC alloSCT is safe and feasible. However, crucial strategy improvements are warranted to possibly achieve clinical benefit.
Nested Duplex PCR To Detect Bordetella pertussis and Bordetella parapertussis and Its Application in Diagnosis of Pertussis in Nonmetropolitan Southeast Queensland, Australia (1999)

A duplex PCR to detect Bordetella pertussis and Bordetella parapertussis was developed with the insertion sequences IS481 (B. pertussis) and IS1001 (B. parapertussis) and evaluated with specimens from 520 consecutive patients presenting with possible pertussis. No culture-positive-PCR-negative results occurred, giving the method a sensitivity of 100%. For B. pertussis, 58 of 520 patients (11.2%) were positive by PCR compared to 17 of 520 patients positive (3.3%) by culture. For B. parapertussis, 7 of 520 patients (1.3%) were positive by PCR compared to 2 of 520 patients positive (0.4%) by culture. Two patients were positive for both B. pertussis and B. parapertussis. Patient records were reviewed to determine the validity of PCR-positive-culture-negative results. Forty-two of 49 patients who could be evaluated fulfilled the criteria for a case definition of pertussis, with 32 patients being <1 year of age and having classical pertussis symptoms. The seven patients who did not fulfil the criteria were aged 7 to 55 years and had a persistent cough for >2 weeks. The method was also used to investigate a classroom outbreak in which B. pertussis culture was positive for 5 of 28 patients. All five culture-positive specimens were confirmed by PCR, and an additional eight were positive by PCR. Of 25 patients from a suspected pertussis outbreak in a girls' dormitory, seven of seven specimens were negative for B. pertussis, although 13 of 25 patients were positive for B. pertussis immunoglobulin M (IgM) (2 of which produced equivocal IgA results, with 23 of 25 patients being negative). Five symptomatic patients were subsequently found to be positive (by IgM and particle agglutination assays) for Mycoplasma pneumoniae, demonstrating the value of PCR in rapidly excluding B. pertussis infection in an outbreak situation. Twenty-two of 71 (30. 1%) throat swabs were positive by PCR compared to 2 of 71 (2.8%) throat swabs positive by culture, indicating that a reassessment of the use of throat swabs should be considered, particularly for older patients, in contact tracing, and in situations in which specimen collection is difficult.
Tissue-specific Determinants of Human Atrial Natriuretic Factor Gene Expression in Cardiac Tissue (1989)

Elements controlling tissue-specific expression of the human atrial natriuretic factor gene have been examined in primary cultures of neonatal rat cardiocytes. When a 68-base pair fragment from human atrial natriuretic factor (hANF) 5'-flanking sequence (positions -400 to -333) was placed upstream from the herpes simplex thymidine kinase promoter linked to a bacterial reporter gene (chloramphenicol acetyltransferase), a tissue-specific positive regulatory effect was observed in atrial as well as ventricular cardiocytes but not in nonmyocardial cells. The cis-acting element in this fragment was orientation- and position-dependent. Examination of nuclear protein extracts for the presence of factors capable of interacting with the 5'-flanking sequence of the hANF gene revealed a cardiocyte-specific factor which bound to the 68-base pair fragment. This association was both tissue- and sequence-specific. These findings indicate that a cis-acting element present in the proximal 5'-flanking sequence confers tissue-specific expression upon the hANF gene, possibly through association with a cardiac-specific nuclear protein.
Dynamic piezoelectric translation devices (1987)

The principle of inertial sliding of a platform on a periodically accelerated support is exploited for the design of a piezoelectric fine-positioning device. The device provides step sizes of 0.04–0.2 μ, speeds of up to 0.2 mm/s, and practically unlimited translation range. It is powered by a sawtooth electric waveform of 60–300-V amplitude and useable for loads of up to 1 kg and probably even more. Mechanical parts and driver electronics are extremely simple, reliable, and easy to operate.
Effects of Mutations in DNA Repair Genes on Formation of Ribosomal DNA Circles and Life Span in Saccharomyces cerevisiae (1999)

A cause of aging in Saccharomyces cerevisiae is the accumulation of extrachromosomal ribosomal DNA circles (ERCs). Introduction of an ERC into young mother cells shortens life span and accelerates the onset of age-associated sterility. It is important to understand the process by which ERCs are generated. Here, we demonstrate that homologous recombination is necessary for ERC formation. rad52 mutant cells, defective in DNA repair through homologous recombination, do not accumulate ERCs with age, and mutations in other genes of the RAD52 class have varying effects on ERC formation. rad52 mutation leads to a progressive delocalization of Sir3p from telomeres to other nuclear sites with age and, surprisingly, shortens life span. We speculate that spontaneous DNA damage, perhaps double-strand breaks, causes lethality in mutants of the RAD52 class and may be an initial step of aging in wild-type cells.
Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders (2013)

Whole-exome sequencing identified the underlying genetic defect in 25% of consecutive patients referred for evaluation of a possible genetic condition. (Funded by the National Human Genome Research Institute.).
The Alpha-Adrenoceptor Blocking Properties of Cryptolepine on the Rat Isolated Vas Deferens (1980)

Cryptolepine, an alkaloid of Crypto-lepsis sanguinolenta (Lindl. Schlecter) is an antagonist of noradrenaline on the rat isolated vas deferens. It is of about the same potency as phentolamine (pA2 of phentolamine = 7.5 ± 0.40, pA2 of cryptolepine = 6.6 ± 0.35). We here report a potentiatory effect of small doses of cryptolepine (3.0 × 10-7-10-6M) on the effect of noradrenaline, an effect which has not been obtained with phentolamine, and methoxamine - induced contractions of the vas deferens. Cocaine antagonised the potentiatory effects of small doses of cryptolepine. Inhibition of neuronal uptake is suggested as the probable mechanism for the observed potentiation.
Roles played by a subset of integrin signaling molecules in cadherin-based cell–cell adhesion (2004)

Integrins can intercommunicate with cadherins. Here, we examined their possible relationship by use of small interfering RNA-mediated protein knockdown in HeLa cells. We found that a subset of integrin signaling molecules, namely Fak and paxillin, but not p130 Crk-associated substrate or proline-rich tyrosine kinase 2, participate in processes regulating N-cadherin-based cell-cell adhesion. Paxillin was found to be required primarily for the recruitment of Fak to robust focal adhesions. Our results suggest that at least some signals involving Fak are linked to a mechanism down-regulating Rac1 activity at the cell periphery, which appears to be important for the formation of N-cadherin-based adhesions in motile cells. Our analyses simultaneously exemplified the essential role of Fak in the maintenance of cell-cell adhesions in collective cell migration, a type of migration occurring in embryonic development and carcinoma invasion.
Natural and Therapy-Induced Anti-GM-CSF and Anti-G-CSF Antibodies in Human Serum (1997)

Serum samples were obtained from patients with lymphoid and plasma cell malignancies who received after chemotherapy human recombinant GM-CSF or G-CSF. Sera from some patients revealed the presence of anti-cytokine antibodies, particularly after repetitive cytokine injections. Antibody Fab binding in a saturable manner by ELISA and Western immuno-blotting confirmed antibody specificity. Anti-cytokine antibodies were detected before the exogenous cytokine injections in some patients, but increasing antibody levels were found after one or subsequent treatments. Low levels of anti-GM-CSF and anti-G-CSF antibodies were also detected in a relatively large proportion (about 10-30%) of normal sera from different adult healthy volunteers who had never been treated before with exologous cytokines as well as from cord blood. EBV-immortalized cord blood derived B-cell cultures were also found to produce anti GM-CSF and/or anti-G-CSF antibodies with high frequency.
Functional Interaction of an Axin Homolog, Conductin, with β-Catenin, APC, and GSK3β (1998)

Control of stability of beta-catenin is central in the wnt signaling pathway. Here, the protein conductin was found to form a complex with both beta-catenin and the tumor suppressor gene product adenomatous polyposis coli (APC). Conductin induced beta-catenin degradation, whereas mutants of conductin that were deficient in complex formation stabilized beta-catenin. Fragments of APC that contained a conductin-binding domain also blocked beta-catenin degradation. Thus, conductin is a component of the multiprotein complex that directs beta-catenin to degradation and is located downstream of APC. In Xenopus embryos, conductin interfered with wnt-induced axis formation.
Protection from Intestinal Inflammation by Bacterial Exopolysaccharides (2014)

Host inflammatory responses against pathogenic organisms can be abrogated by commensals; however, the molecular mechanisms by which pathogenesis is prevented are still poorly understood. Previous studies demonstrated that administration of a single dose of Bacillus subtilis prevented disease and inflammation by the enteric mouse pathogen Citrobacter rodentium, which causes disease similar to the human pathogen enteropathogenic Escherichia coli. No protection was observed when an exopolysaccharide (EPS)-deficient mutant of B. subtilis was used, suggesting that EPS are the protective factor. In this study, we isolated and characterized EPS and showed that they also prevent C. rodentium-associated intestinal disease after a single injection. Protection is TLR4 dependent because EPS-treated TLR4 knockout mice developed disease. Furthermore, protection could be conveyed to wild-type mice by adoptive transfer of macrophage-rich peritoneal cells from EPS-treated mice. We found that EPS specifically bind peritoneal macrophages, and because mice lacking MyD88 signaling in myeloid cells were not protected by EPS, we conclude that bacterial EPS prevent colitis in a TLR4-dependent manner that requires myeloid cells. These studies provide a simple means of preventing intestinal inflammation caused by enteric pathogens.
Analog Computing Using Reflective Plasmonic Metasurfaces (2014)

Motivated by the recent renewed interest in compact analog computing using light and metasurfaces ( Silva, A. et al. Science 2014 , 343, 160 - 163), we suggest a practical approach to its realization that involves reflective metasurfaces consisting of arrayed gold nanobricks atop a subwavelength-thin dielectric spacer and optically thick gold film, a configuration that supports gap-surface plasmon resonances. Using well-established numerical routines, we demonstrate that these metasurfaces enable independent control of the light phase and amplitude, and design differentiator and integrator metasurfaces featuring realistic system parameters. Proof-of-principle experiments are reported along with the successful realization of a high-quality poor-man's integrator metasurface operating at the wavelength of 800 nm.