gebhart/patrepeval huggingface dataset:
Polyp segmentation method for CT colonography computer-aided detection (2003)

We have developed a new method employing the Canny edge detector and Radon transformation to segment images of polyp candidates for CT colonography (CTC) computer aided polyp detection and obtain features useful for distinguishing true polyps from false positive detections. The technique is applied to two-dimensional subimages of polyp candidates selected using various 3-D shape and curvature characteristics. We detect boundaries using the Canny operator. The baseline of the colon wall is detected by applying the Radon transform to the edge image and locating the strongest peak in the resulting transform matrix. The following features are calculated and used to classify detections as true positives (TP) and false positives (FP): polyp boundary length, polyp base length, polyp internal area, average intensity, polyp height, and inscribed circle radius. The segmentation technique was applied to a data set of 15 polyps larger than 3 mm and 617 false positives taken from 80 CTC studies (supine and prone screening of 40 patients). The sensitivity was 100% (15 of 15). 58% of the FP's were eliminated leaving an average of 3 false positives per study. Our method is able to segment polyps and quantitatively measure polyp features independently of orientation and shape.
Photodynamic Therapy in Oncology (2006)

Photodynamic therapy (PDT) is increasingly being recognized as an attractive, alternative treatment modality for superficial cancer. Treatment consists of two relatively simple procedures: the administration of a photosensitive drug and illumination of the tumor to activate the drug. Efficacy is high for small superficial tumors and, except for temporary skin photosensitization, there are no long-term side effects if appropriate protocols are followed. Healing occurs with little or no scarring and the procedure can be repeated without cumulative toxicity. Considering the efficacy and lack of long-term toxicity of PDT, and the fact that the first treatment of cancer with PDT was done more than 100 years ago, one might expect that this treatment had already become an established therapy. However, PDT is currently offered in only a few selected centers, although it is slowly gaining acceptance as an alternative to conventional cancer therapies. Here, we show the developmental steps PDT underwent and summarize the current clinical applications. The data show that, when properly used, PDT is an effective alternative treatment option in oncology.
Sensitivity of the Swedish statutory surveillance system for communicable diseases 1998–2002, assessed by the capture–recapture method (2005)

To assess the sensitivity of the Swedish surveillance system, four notifiable communicable diseases in Sweden were examined during 1998-2002 with the two-sources capture-recapture method, based on parallel clinical and laboratory notifications. The sensitivity (proportion of diagnosed diseases actually being notified) was highest for salmonellosis (99.9%), followed by meningococcal infection (98.7%), and tularaemia (98.5%). For penicillin-resistant pneumococci, introduced as a notifiable disease in 1996, the overall sensitivity was 93.4%--increasing from 86.5% in 1998 to 98.5% in 2002. The system benefited from parallel reporting, with a sensitivity of clinical and laboratory notifications alone (all diseases combined) of 91.6% and 95.9% respectively. The sensitivity of both clinical and laboratory notifications was markedly higher in counties using the national electronic reporting system, SmiNet. Thus, sensitivity was higher for diseases with a long tradition of reporting, and there is a run-in period after a new disease becomes notifiable.
Experimental Models to Study Development and Function of the Human Immune System In Vivo (2006)

The study of development and function of the immune system in vivo has made intensive use of animal models, but performing such work in humans is difficult for experimental, practical, and ethical reasons. Confronted with this scientific challenge, several pioneering groups have developed in the late 1980s mouse models of human immune system development. Although these experimental approaches were proven successful and useful, they were suffering from limitations due to xenograft transplantation barriers. By reviewing the characteristics of the successive models over the last 20 years, it becomes apparent that screening of potentially interesting mouse strains and usage of combinations of genetic deficiencies has led to major advances. This is particularly true for human T cell development in the murine thymus. This review will focus on these advances and the potential future improvements that remain to be accomplished.
Contribution of Are1p and Are2p to steryl ester synthesis in the yeast Saccharomyces cerevisiae (2000)

In the yeast Saccharomyces cerevisiae, two acyl-CoA:sterol acyltransferases (ASATs) that catalyze the synthesis of steryl esters have been identified, namely Are2p (Sat1p) and Are1p (Sat2p). Deletion of either ARE1 or ARE2 has no effect on cell viability, and are1are2 double mutants grow in a similar manner to wild-type despite the complete lack of cellular ASAT activity and steryl ester formation [Yang, H., Bard, M., Bruner, D. A., Gleeson, A., Deckelbaum, R. J., Aljinovic, G., Pohl, T. M., Rothstein, R. & Sturley, S. L. (1996) Science 272, 1353-1356; Yu, C., Kennedy, J., Chang, C. C. Y. & Rothblatt, J. A. (1996) J. Biol. Chem. 271, 24157-24163]. Here we show that both Are2p and Are1p reside in the endoplasmic reticulum as demonstrated by measuring ASAT activity in subcellular fractions of are1 and are2 deletion strains. This localization was confirmed by fluorescence microscopy using hybrid proteins of Are2p and Are1p fused to green fluorescent protein (GFP). Lipid analysis of are1 and are2 deletion strains revealed that Are2p and Are1p utilize sterol substrates in vivo with different efficiency; Are2p has a significant preference for ergosterol as a substrate, whereas Are1p esterifies sterol precursors, mainly lanosterol, as well as ergosterol. The specificity towards fatty acids is similar for both isoenzymes. The lack of steryl esters in are1are2 mutant cells is largely compensated by an increased level of free sterols. Nevertheless, terbinafine, an inhibitor of ergosterol biosynthesis, inhibits growth of are1are2 cells more efficiently than growth of wild-type. In a growth competition experiment are1are2 cells grow more slowly than wild-type after several rounds of cultivation, suggesting that Are1p and Are2p or steryl esters, the product formed by these two enzymes, are more important in the natural environment than under laboratory conditions.
β-Secondary Kinetic Isotope Effects in the Clavaminate Synthase-Catalyzed Oxidative Cyclization of Proclavaminic Acid and in Related Azetidinone Model Reactions (1999)

Clavaminate synthase is an Fe(II)/α-ketoglutarate-dependent oxygenase that catalyzes three mechanistically distinct reactions in the course of clavulanic acid biosynthesis. Clavulanic acid is of significant chemical importance as a potent inhibitor/inactivator of β-lactamase enzymes, a prominent means of bacterial resistance to, for example, penicillin. Primary and α-secondary T(V/K) kinetic isotope effects have been determined in earlier work for the clavaminate synthase-catalyzed oxidative cyclization of proclavaminic acid, one of the three reactions mediated by this enzyme. In this paper the β-secondary deuterium kinetic isotope effect for this reaction has been determined using remote 3H and 14C labels in an attempt to distinguish between radical or cationic intermediates in the reaction as suggested by the magnitudes of the primary and secondary α-effects. The presence of the adjacent azetidinone nitrogen and the intervention of an azetinone intermediate, formally antiaromatic in the resonance form of the amide, make interpretation of the low β-secondary effect (1.056 ± 0.002 for dideuteriation at C-3‘) problematic. To assist interpretation of this result, a 4-chloroazetidinone model system has been constructed dideuteriated at C-3 identically to proclavaminic acid and bearing remote radiolabels. Reaction of this substrate at 25 °C under both radical and solvolysis conditions afforded β-secondary kinetic isotope effect data for direct comparison to the enzymic reaction. The measured effects are similarly small but strongly dependent on the polarity/acidity of the reaction medium. These results are discussed in terms of the commitment to catalysis and the extent to which amide resonance may be favored in the transition state of the oxidative cyclization.
Isolation of Highly Infectious and Pure Adeno-Associated Virus Type 2 Vectors with a Single-Step Gravity-Flow Column (2001)

One of the most promising gene transfer vectors in human clinical trials is AAV2. The quality of the vector preparations is a key element in obtaining reliable and reproducible data in preclinical studies. However, established protocols either result in impure, low infectious virus (CsCl2 gradient centrifugation) or demand a high level of manual and technical skills (CsCl2 gradient centrifugation, iodixanol/heparin or HPLC purification). In this study, we present an easy-to-do single-step column purification (SSCP) of AAV2 by gravity flow based on its affinity to heparin, without ultracentrifugation. Various vector preparations generated by our method reproducibly showed high titers, infectivity, and purity. In vivo, our single-step column-purified AAV2 vectors mediate significantly higher transduction efficiency compared with conventional protocols. Investigators still unsatisfied with previously published techniques or new to the field of AAV production may find in our method an interesting alternative.
Random Search and Reproducibility for Neural Architecture Search (2019)

Neural architecture search (NAS) is a promising research direction that has the potential to replace expert-designed networks with learned, task-specific architectures. In this work, in order to help ground the empirical results in this field, we propose new NAS baselines that build off the following observations: (i) NAS is a specialized hyperparameter optimization problem; and (ii) random search is a competitive baseline for hyperparameter optimization. Leveraging these observations, we evaluate both random search with early-stopping and a novel random search with weight-sharing algorithm on two standard NAS benchmarks---PTB and CIFAR-10. Our results show that random search with early-stopping is a competitive NAS baseline, e.g., it performs at least as well as ENAS, a leading NAS method, on both benchmarks. Additionally, random search with weight-sharing outperforms random search with early-stopping, achieving a state-of-the-art NAS result on PTB and a highly competitive result on CIFAR-10. Finally, we explore the existing reproducibility issues of published NAS results. We note the lack of source material needed to exactly reproduce these results, and further discuss the robustness of published results given the various sources of variability in NAS experimental setups. Relatedly, we provide all information (code, random seeds, documentation) needed to exactly reproduce our results, and report our random search with weight-sharing results for each benchmark on multiple runs.
Non–ECG‐gated myocardial perfusion MRI using continuous magnetization‐driven radial sampling (2014)

Non-ECG-gated FPP imaging using optimized continuous golden-angle radial acquisition achieves desirable image quality (i.e., adequate myocardial contrast, high spatial resolution, and minimal artifacts) in the setting of ischemia.
Rapid PCR-Based Identification of Methicillin-Resistant Staphylococcus aureus from Screening Swabs (2002)

A PCR identification of methicillin-resistant Staphylococcus aureus (MRSA), obviating the need for subculture on agar media, was investigated. The combination of MRSA detection by mecA femB PCR with prior enrichment in selective broth was tested for 439 swabs. PCR identified 36 MRSA-positive samples, in concordance with conventional methods.
Target Site Selection by Tn 7 : att Tn 7 Transcription and Target Activity (2000)

The bacterial transposon Tn7 inserts at high frequency into a specific site called attTn7, which is present in the chromosomes of many bacteria. We show here that transcription of a nearby gene, glmS, decreases the frequency of Tn7 insertion into attTn7, thus providing a link between Tn7 transposition and host cell metabolism.
End-of-life care: What do the American courts say? (2001)

End-of-life care of critically ill patients generally consists of two closely related practices: the withholding and withdrawal of life support, and the administration of palliative care. In the United States, the withholding or withdrawal of life support is legally justified by the principles of informed consent and informed refusal. The U.S. Supreme Court has held that competent patients may refuse any and all treatments, including those that sustain life. All states sanction such refusal by competent patients, and most states allow surrogates to refuse treatment on behalf of incompetent patients. Although some physicians use the concept of futility to unilaterally withhold or withdraw life support, the Supreme Court has not heard a futility case, and the only clear legal rule on futile treatment is the traditional malpractice test, which measures physician actions against standards of medical care. However, the Supreme Court has furnished guidelines on the administration of palliative care. By using the principle of double effect, these guidelines allow physicians to give sedative and analgesic agents to dying patients if they intend to relieve pain and suffering but not to hasten death.
Analysis of the rat liver gap junction protein : clarification of anomalies in its molecular size (1988)

Abstract The major gap junction polypeptide in most tissues has an apparent molecular mass of 27 kDa with a 47 kDa dimer present in junction-enriched fractions. However, a 54 kDa protein recognized by gap junction-specific antibodies has been reported and a complementary DNA (cDNA) sequence for both human and rat liver gap junctions codes for a 32 kDa protein. In this paper we show that these are all forms of the same gap junction protein that can be observed on SDS–polyacrylamide gels simply by varying the concentration of acrylamide in the gels. A 64 kDa dimer is also obtainable. Antibodies to the gap junction protein or to a synthetic peptide constructed to match the rat liver gap junction amino-terminal sequence recognize all of these forms. Under some conditions a 54 kDa dimer is ‘preferred’, explaining the presence of this species in whole tissue homogenate Western blots. These results clarify several controversies and indicate that the protein forming the gap junction channel probably undergoes no major post-translational modification as the cDNA sequence codes for a protein of molecular mass 32 kDa and this protein species and its 64 kDa dimer are demonstrable on SDS–polyacrylamide gels under appropriate conditions.
El trabajo social comunitario: apoyo social, producción de saber y posibilidad de construcción reconstrucción del tejido social (2000)

Una perspectiva del desarrollo que trascienda lo economico, que asuma las dimensiones materiales y postmateriales del sistema de necesidades de los individuos y de los grupos humanos, y que propugne por la autonomia y la participacion (la descosificacion del ser humano) se configura como una opcion realizativa de los intereses individuales y colectivos y como posible idea rectora del quehacer del trabajo social comunitario.
En esta direccion esbozamos algunas consideraciones respecto a lo que podria ser, mas que un perfil ocupacional o profesional, una perspectiva del oficio, asumiendo el trabajo social comunitario como saber orientado a la accion, saber social aplicado, en la cual confluyen varias disciplinas que entran a contribuir en la comprension de realidades concretas en aras a plantear y realizar acciones colectivas transformadoras � potenciadoras de los sujetos y de los grupos humanos.
Adding Chloroquine to Conventional Treatment for Glioblastoma Multiforme (2006)

Chloroquine may improve mid-term survival when given in addition to conventional therapy for glioblastoma multiforme. These results suggest that larger, more definitive studies of chloroquine as adjuvant therapy for glioblastoma are warranted.
Filter disc supported oligonucleotide synthesis by the phosphite method (1984)

The phosphite approach to oligodeoxynucleotide synthesis has been applied to the filter disc support. The method is exemplified here by the preparation of eight decadeoxynucleotides.
Cleavage specificity of the restriction endonuclease isolated from Haemophilus gallinarum (Hga I). (1977)

The nucleotide sequences in the replicative form (duplex) of phiX174 DNA around six sites cut by Hga I, a restriction endonuclease from Haemophilus gallinarum, have been compared. The enzyme produces a staggered cleavage resulting in a pentanucleotide 5'-terminal extension. The sequences within and immediately surrounding the pentanucleotide cleavage site have no obvious relationship. However, the sequence 5'-G-A-C-G-C-3' 3'-C-T-G-C-G-5' occurs five nucleotide pairs to the left of the cut in the upper strand and 10 nucleotide pairs to the left of the cut in the lower strand and, therefore, is believed to constitute the recognition site. This is a member of the class of restriction endonucleases in which recognition and cleavage sites lack 2-fold rotational symmetry. The method used to define the cleavage site is of general applicability.
Carbohydrate Oxidation From A Carbohydrate Gel Compared To A Drink During Exercise (2009)

Studies investigating exogenous carbohydrate (CHO) oxidation from CHO drinks during exercise have revealed that ingestion of a mixture of glucose (GLU) and fructose (FRU) leads to 20-50% higher CHO oxidation rates as compared to GLU alone. However, athletes often ingest CHO in the form of gels (semi-solid form). It is currently not known if CHO ingested in the form of a gel is oxidised as effectively as a drink. PURPOSE: To investigate exogenous CHO oxidation from CHO provided in either semi-solid (GEL) or solution (DRINK) form, when delivered at relatively high rates during cycling exercise. METHODS: Eight well trained cyclists (34±3yrs; 76±3kg; 1.78±0.02m; VO2max: 61±3ml/kg/min) performed three exercise trials in random order. The trials consisted of cycling at 59±1% VO2max for 180min while receiving one of the following three treatments: GEL plus plain water, DRINK, or plain water. Both CHO treatments delivered GLU plus FRU in a ratio of 2:1 at a rate of 1.8g/min. Fluid intake was matched between treatments. RESULTS: Exogenous CHO oxidation from both treatments showed a similar time course with peak exogenous CHO oxidation rates being reached at the end of 180min exercise. Peak exogenous CHO oxidation rates were not different between GEL and DRINK (1.44±0.1g/min vs. 1.42±0.08g/min, respectively, p=0.40). Oxidation efficiency was also similar between the GEL and DRINK trial (71±5%vs. 69±5%, respectively, p=0.36). CONCLUSIONS: This study demonstrated that a GLU+FRC mixture is oxidised to the same degree when administered as a semi-solid GEL or liquid DRINK. Both forms of CHO administration led to similarly high peak oxidation rates and showed similar oxidation efficiencies. This study was Supported by a Research Grant from Nestec Ltd., Nestlé Nutrition, Vevey, Switzerland.
Roles of IFN-γ and IFN-α in IL-12-induced T helper cell-1 development (1996)

IL-12 and IL-4 direct T cell development toward Th1 and Th2 phenotypes, respectively. While IFN-gamma and IFN-alpha have been reported to regulate Th1 development as well, the mechanism and cellular locus of their effects are unclear. In this study, we use a TCR-transgenic system to examine the actions of these cytokines on CD4+ T cell phenotype development. We find that neither IFN-gamma nor IFN-alpha can induce Th1 development alone. However, IFN-gamma can significantly augment IL-12 priming for subsequent IFN-gamma production by T cells. Interestingly, lymphocyte endothelial cell adhesion molecule-1bright (naive) T cells require IFN-gamma during primary activation for maximal IL-12-induced Th1 development, whereas lymphocyte endothelial cell adhesion molecule-1dull (memory) T cells do not. IFN-alpha only partially substitutes for IFN-gamma in promoting IL-12-induced Th1 development. When the endogenous IFN-gamma present in primary T cell cultures is neutralized, IFN-alpha treatment augments IL-12-induced effects on inhibition of subsequent IL-4 production, but fails to significantly enhance IL-12 priming for subsequent IFN-gamma production. Thus, our data suggest that IFN-gamma provides a direct costimulatory signal to T cells to up-regulate IL-12-induced Th1 development and may operate by inducing IL-12 responsiveness in naive T cells.
Carcinogenicity of Epoxides, Lactones, and Peroxy Compounds. V. Subcutaneous Injection in Rats<xref ref-type="fn" rid="FN1">2</xref> (1967)

Twelve epoxides, lactones, and peroxy compounds were tested for carcinogenic activity by subcutaneous injection in rats. Three of these compounds induced sarcomas at the injection site. They are, in order of decreasing activity, glycidaldehyde, β-butyrolactone, and 2,2,4-trimethyl-3-hydroxy-3-pentenoic acid-β-lactone.
Templating of Silsesquioxane Cross‐Linking Using Unimolecular Self‐Organizing Polymers (2003)

Nanopores created by micellar star polymers in amorphous organic silsequioxane thermosets produce morphologically controlled porous materials for semiconductor chip applications (see picture). Pore size is independent of concentration and processing conditions, but depends solely on the size of the polymer molecule.
Will schizophrenia become a graveyard for molecular geneticists? (1992)

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1,25-Dihydroxycalciferol and calcium therapy in osteoporosis with calcium malabsorption. Dose response relationship of calcium absorption and indices of bone turnover. (1985)

We have studied some effects of small doses of 1,25-dihydroxycalciferol (calcitriol) and calcium, either combined or separately, in 45 patients with osteoporosis and malabsorption of calcium. In 24 patients on 0.25 micrograms/d of calcitriol the hourly fractional rate of radiocalcium absorption rose from 0.37 +/- 0.02 to 0.55 +/- 0.04 (p less than 0.001) and in 21 patients on 0.50 micrograms/d it rose from 0.36 +/- 0.02 to 0.69 +/- 0.05 (p less than 0.001). These responses were seen within 5 days and were not increased further at 6 weeks to 3 months. The combined therapy significantly reduced the fasting urinary hydroxyproline/creatine ratio (OHPr/Cr) and plasma alkaline phosphatase activity (ALP) in 6-12 weeks, the smaller dose of calcitriol (0.25 micrograms/d) being as effective as the larger one (0.50 micrograms/d) in this respect. Calcium alone (1 g/d) had no effect and calcitriol alone (0.25 mcg/d) had a lesser effect on both OHPr/Cr and ALP than the combined therapy. The falls in OHPr/Cr and ALP tended to be greatest in the cases with the highest initial levels but constituted only partial suppression of these variables towards the theoretical non-bone components. These results suggest that treatment with calcitriol and calcium suppresses bone resorption in osteoporosis associated with malabsorption of calcium and is more effective than calcium or calcitriol given alone.