gebhart/patrepeval huggingface dataset:
A new framework for the definition and recognition of free form features (2007)

Feature recognition techniques have been developed in the past that dealt with parameterizing regular features. In response to the availability of free form shape, researchers have turned to free form features. Some of the methods developed for features can be re-used in the free form domain, but many methods have to be developed anew. In this paper it is argued that there is a need for a general framework to provide a common point of reference for new methods and to increase the cohesion between such methods. An initial framework is proposed for the definition of features and for one of the possible applications of features, feature recognition. Two existing free form feature recognition methods are analysed with regard to the framework, in order to critically review the proposed framework as well as the two methods.
Semantic Image Segmentation with Deep Convolutional Nets and Fully Connected CRFs (2014)

Deep Convolutional Neural Networks (DCNNs) have recently shown state of the art performance in high level vision tasks, such as image classification and object detection. This work brings together methods from DCNNs and probabilistic graphical models for addressing the task of pixel-level classification (also called "semantic image segmentation"). We show that responses at the final layer of DCNNs are not sufficiently localized for accurate object segmentation. This is due to the very invariance properties that make DCNNs good for high level tasks. We overcome this poor localization property of deep networks by combining the responses at the final DCNN layer with a fully connected Conditional Random Field (CRF). Qualitatively, our "DeepLab" system is able to localize segment boundaries at a level of accuracy which is beyond previous methods. Quantitatively, our method sets the new state-of-art at the PASCAL VOC-2012 semantic image segmentation task, reaching 71.6% IOU accuracy in the test set. We show how these results can be obtained efficiently: Careful network re-purposing and a novel application of the 'hole' algorithm from the wavelet community allow dense computation of neural net responses at 8 frames per second on a modern GPU.
Functional Importance of the Coiled-Coil of the Ebola Virus Glycoprotein (2000)

Ebola virus contains a single glycoprotein (GP) that is responsible for receptor binding and membrane fusion and is proteolytically cleaved into disulfide-linked GP1 and GP2 subunits. The GP2 subunit possesses a coiled-coil motif, which plays an important role in the oligomerization and fusion activity of other viral GPs. To determine the functional significance of the coiled-coil motif of GP2, we examined the effects of peptides corresponding to the coiled-coil motif of GP2 on the infectivity of a mutant vesicular stomatitis virus (lacking the receptor-binding/fusion protein) pseudotyped with the Ebola virus GP. A peptide corresponding to the C-terminal helix reduced the infectivity of the pseudotyped virus. We next introduced alanine substitutions into hydrophobic residues in the coiled-coil motif to identify residues important for GP function. None of the substitutions affected GP oligomerization, but some mutations, two in the N-terminal helix and all in the C-terminal helix, reduced the ability of GP to confer infectivity to the mutant vesicular stomatitis virus without affecting the transport of GP to the cell surface, its incorporation into virions, and the production of virus particles. These results indicate that the coiled-coil motif of GP2 plays an important role in facilitating the entry of Ebola virus into host cells and that peptides corresponding to this region could act as efficient antiviral agents.
Residents’ Satisfaction of Indoor Environmental Quality in Their Old Apartment Homes (2010)

The purpose of this study is to determine the characteristics of indoor environmental quality (IEQ) of old apartment homes and the residents’ satisfaction with living in these properties. About 168 households were surveyed in this study. The survey was based on the evaluation of deterioration using housing performance indicators and the questionnaire study. First, this study compared and analysed the results of both technical evaluation and residents’ satisfaction on the IEQ of old apartments based on case studies. Second, the study validated the IEQ evaluation of the home environments using multiple regression analyses based on residents’ satisfaction and their perception about the indoor environment. Third, the importance of the indoor environment composition factors contributing to the home environmental quality was assessed based on the survey of residents’ perception and experts’ opinions. Analytic hierarchy process was used to evaluate the housing experts’ opinions. The objective evaluation by technical criteria was also carried out to determine the conditions of the apartment homes. This study should contribute to elaborate evaluation models for the development of guidelines for the home environmental quality of high-rise and high-density old apartment buildings in Korea.
Oncogenic NRAS, KRAS, and HRAS Exhibit Different Leukemogenic Potentials in Mice (2007)

RAS proteins are small GTPases that play a central role in transducing signals that regulate cell proliferation, survival, and differentiation. The RAS proteins interact with a common set of activators and effectors; however, they associate with different microdomains of the plasma membrane as well as other endomembranes and are capable of generating distinct signal outputs. Mutations that result in constitutive activation of RAS proteins are associated with approximately 30% of all human cancers; however, different RAS oncogenes are preferentially associated with different types of human cancer. In myeloid malignancies, NRAS mutations are more frequent than KRAS mutations, whereas HRAS mutations are rare. The mechanism underlying the different frequencies of RAS isoforms mutated in myeloid leukemia is not known. In this study, we compared the leukemogenic potential of activated NRAS, KRAS, and HRAS in the same bone marrow transduction/transplantation model system. We found that all three RAS oncogenes have the ability to induce myeloid leukemias, yet have distinct leukemogenic strengths and phenotypes. The models established here provide a system for further studying the molecular mechanisms in the pathogenesis of myeloid malignancies and for testing targeted therapies.
Bench-Scale Demonstration of Molten Alkali Metal Borates for High-Temperature CO2 Capture (2020)

The molten alkali metal borates represent an opportunity for carbon dioxide capture and the on-going challenge of adapting to a carbon-constrained world with the immediacy of climate change. We demonstrate the performance of this new class of materials at the bench scale, highlighting the ability to operate isothermally at high temperatures through the use of steam as a sweep gas. Breakthrough curves for a wide set of conditions are presented and linked to the sorbents' underlying thermodynamic and kinetic properties. We demonstrate the ability to capture over 99.9% of incoming CO2 even at low concentrations or to capture ∼90% CO2 under high flow rates and utilize a greater portion of the sorbent capacity. The advantages of the molten alkali metal borates scale well, and their unique position as high-temperature liquid phase sorbents may enable new process designs for efficient low-cost CO2 capture facilities.
Indicadores del bienestar y sentimiento del consumidor español (1984)

The present study was performed in two phases. In phase I, 112 patients were randomized to either 2 g cefotetan as a single prophylactic dose or 2 g cefoxitin every 6 hours for a maximum of 4 doses; phase II included 148 patients who were randomized to either 1 g cefotetan as a single dose or cefoxitin dosed as in phase I. The randomization was 2:1 cefotetan to cefoxitin in both phases. Nonevaluability rates were 10 percent for the cefotetan patients and 22 percent for the cefoxitin patients, the majority being due to dosing errors. Demographic characteristics demonstrated 88 percent to be female, 81 percent to be less than 65 years of age, and the average weight to be 165 lb. There were no differences in these characteristics among the groups. Common duct exploration was performed in 6 percent of the 2 g cefotetan patients, 9 percent in the 1 g cefotetan patients, and 13 percent in the 2 g cefoxitin patients. There were five clinical failures of prophylaxis: one wound infection in the 2 g cefotetan patients, one wound infection and one drain tract infection in the 1 g cefotetan patients, and one wound infection and one case of cholangitis in the 2 g cefoxitin patients. The clinical success rates were 98 percent in the 2 g cefotetan patients, 98 percent in the 1 g cefotetan patients, and 97 percent in the 2 g cefoxitin patients.
Heparin kinetics in venous thrombosis and pulmonary embolism. (1976)

The response to a standard dose of heparin was studied in 20 patients with venous thromboembolism. The heparin regimen consisted of intravenous injection of 70 units per kg, followed after 90 minutes by a maintenance dose of 400 units per kg per 24 hours given by continuous infusion. Plasma heparin activity and the activated partial thromboplastin time (APTT) were measured at intervals to determine clearance of the initial injection and the response to maintenance dose. Large inter-individual variations were found in the anticoagulant effect and these were due in part to differences in heparin clearance and in part to differences in the APTT response to given amounts of heparin (heparin effect index). The heparin half-life was 63 +/- 15 minutes when plasma heparin activities were used for this calculation and 84 +/- 71.5 minutes when the APTT was used. These results are similar to values previously reported in normal volunteers. Four of the 20 patients had pulmonary embolism and in these heparin half-life was significantly shortened (P less than 0.005).
Purification and Properties of Codeinone Reductase (NADPH) from Papaver somniferum Cell Cultures and Differentiated Plants (1995)

Codeinone reductase (NADPH), which catalyzes the stereospecific reduction of (-)codeinone to (-)codeine, was detected and purified to electrophoretic homogeneity from a cytosolic fraction of Papaver somniferum L. cell cultures. The purification involved ammonium sulfate precipitation (40-80%), affinity chromatography (matrex red A), gel filtration (fractogel TSK HW 55S), affinity chromatography (fractogel TSK AF Blue), ion-exchange chromatography (DEAE-Sephacel) and native PAGE. The purified codeinone reductase was found to be a monomeric protein of 35 +/- 1 kDa that is highly substrate-specific, reducing only the C6 oxo group of codeinone and morphinone as well as a few analogues. The physiological forward reaction has a pH optimum at 7.0, the reverse reaction at 9.1. The temperature optimum is at 40 degrees C and the isoelectric point (p1) at 4.4. The apparent Km values (forward reaction) for codeinone and NADPH are 23 microM and 168 microM, respectively. Using capsule tissue of differentiated P. somniferum plants as an enzyme source, two codeinone reductase (NADPH) isoenzymes were detected and purified to homogeneity. These isoenzymes could not be separated for characterization and showed slightly different kinetic features (Km values: codeinone 9 microM; NADPH 81 microM) compared with the cell culture enzyme.
Multiple mutations in the T region of the Agrobacterium tumefaciens tumor-inducing plasmid. (1983)

Three genetic loci affecting tumor morphology lie within pTiA6NC T-DNA: tms, tmr, and tml. Using deletions and multiple transposon insertions, we constructed tumor-inducing (Ti) plasmids representing every possible double and triple mutant combination. tms tmr and tms tmr tml mutants did not incite tumors on most plants and produced a very weak response on a few other hosts but tms tml and tmr tml mutants were virulent. Thus, either tms+ or tmr+ alone can promote significant tumor growth but tml+ by itself is not sufficient. On hosts where tms mutants induce tumors accompanied by shoot proliferation, addition of a tml mutation reduces or eliminates shoot proliferation, suggesting that tml+ promotes shoot development. The small calli incited by tms tmr and tms tmr tml mutants contain agropine, an indication that these plant cells incorporate T-DNA in the absence of substantial tumor growth.
Analysis of the production of soluble ICAM-1 molecules by human cells. (1996)

The adhesion molecule intercellular adhesion molecule-1 (ICAM-1), in addition to its membrane-associated form (mICAM-1), also exists as a soluble form (sICAM-1). sICAM-1 is capable of binding to lymphocyte function associated antigen-1 (LFA-1) molecules, and production of sICAM-1 is therefore thought to have immunomodulatory consequences. The present study, which employed normal human keratinocytes as a model for sICAM-1-producing cells, was conducted to determine the mechanism responsible for the production of sICAM-1 and to develop a strategy for specific inhibition of sICAM-1 production. Stimulation of keratinocytes with recombinant human gamma-interferon (rhIFN-gamma) induced both expression of mICAM-1 and production of sICAM-1. Western blot analysis revealed that keratinocyte-derived sICAM-1, compared to mICAM-1, had a smaller molecular size, approximately a 7-kD difference. Neither by Northern blot analysis nor by reverse-transcriptase polymerase chain reaction (RT-PCR) was any evidence for alternatively spliced ICAM-1 mRNA obtained. Addition of the protease inhibitors iodoacetamide and E-64, however, inhibited the production of sICAM-1 in a dose-dependent manner. The involvement of proteolytic cleavage in the production of sICAM-1 was corroborated in minimal peptide protection assays, in which minimal peptides covering the potential cleavage site of ICAM-1 were added to sICAM-1-producing keratinocytes. One of these peptides, ICAM cleavage inhibitory peptide (ICAM-CIP), inhibited the production of sICAM-1 without affecting mICAM-1 expression. These studies demonstrate that sICAM-1 production in human keratinocytes is due to proteolytic cleavage, and that the oligopeptide ICAM-CIP may specifically inhibit this mechanism. The capacity of ICAM-CIP to selectively prevent production of sICAM-1 may be useful for the development of novel therapeutic approaches relevant for the management of inflammation and cancer.
Interleukin-8 induces rapid mobilization of hematopoietic stem cells with radioprotective capacity and long-term myelolymphoid repopulating ability (1995)

Interleukin-8 (IL-8) belongs to a family of chemoattractant cytokines involved in chemotaxis and activation of neutrophils. As in vivo administration of IL-8 induces granulocytosis and the release of immature white blood cells into the circulation, we assessed a possible mobilizing effect of IL-8 on myeloid progenitor cells. IL-8 was administered at intraperitoneal doses ranging from 0.1 to 100 micrograms per mouse to female Balb/C mice (aged 8 to 12 weeks; weight, 20 to 25 g). Animals were killed at time intervals ranging from 1 to 240 minutes after IL-8 administration, and blood, bone marrow, and spleen cells were harvested. Injection of 30 micrograms IL-8 resulted in an increment from 25 +/- 9 to 418 +/- 299 granulocyte-macrophage colony-forming units (CFU-GM) per milliliter blood at 15 minutes after a single intraperitoneal injection. Sixty minutes after the injection of IL-8, the numbers of circulating CFU-GM per milliliter blood had almost returned to pretreatment values (82 +/- 39 CFU-GM per milliliter). A dose of 100 micrograms IL-8 per animal did not result in a further increment in the number of circulating CFU-GM. Transplantation of 5 x 10(5) blood-derived mononuclear cells (MNC) obtained at 30 minutes after IL-8 injection (30 micrograms) resulted in 69% survival of lethally irradiated (8.5 Gy) recipients at 60 days versus 22% for animals transplanted with an equal number of nonprimed blood-derived MNC. Transplantation of 1.5 x 10(6) MNC obtained from IL-8-treated donors resulted in 100% survival. Six months after transplantation, female recipients of MNC derived from IL-8-treated male donors were killed, and chimerism was determined in bone marrow, spleen, and thymus using a Y chromosome-specific probe and fluorescent in situ hybridization (FISH). The majority of bone marrow, spleen, and thymus cells (83% +/- 25%, 89% +/- 5%, and 64 +/- 28%, respectively) consisted of Y chromosome-positive cells, showing that the IL-8-mobilized cells had myelolymphoid repopulating ability. We conclude that IL-8 is a cytokine that induces rapid mobilization of progenitor cells and pluripotent stem cells that are able to rescue lethally irradiated mice and that are able to completely and permanently repopulate host hematopoietic tissues.
Statistical Methods for Identifying Differentially Expressed Genes in DNA Microarrays (2003)

In this chapter we discuss the problem of identifying differentially expressed genes from a set of microarray experiments. Statistically speaking, this task falls under the heading of “multiple hypothesis testing.” In other words, we must perform hypothesis tests on all genes simultaneously to determine whether each one is differentially expressed. Recall that in statistical hypothesis testing, we test a null hypothesis vs an alternative hypothesis. In this example, the null hypothesis is that there is no change in expression levels between experimental conditions. The alternative hypothesis is that there is some change. We reject the null hypothesis if there is enough evidence in favor of the alternative. This amounts to rejecting the null hypothesis if its corresponding statistic falls into some predetermined rejection region. Hypothesis testing is also concerned with measuring the probability of rejecting the null hypothesis when it is really true (called a false positive), and the probability of rejecting the null hypothesis when the alternative hypothesis is really true (called power).
Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis (2012)

Freezing stool samples prior to DNA extraction and downstream analysis is widely used in metagenomic studies of the human microbiota but may affect the inferred community composition. In this study, DNA was extracted either directly or following freeze storage of three homogenized human fecal samples using three different extraction methods. No consistent differences were observed in DNA yields between extractions on fresh and frozen samples; however, differences were observed between extraction methods. Quantitative PCR analysis was subsequently performed on all DNA samples using six different primer pairs targeting 16S rRNA genes of significant bacterial groups, and the community composition was evaluated by comparing specific ratios of the calculated abundances. In seven of nine cases, the Firmicutes to Bacteroidetes 16S rRNA gene ratio was significantly higher in fecal samples that had been frozen compared to identical samples that had not. This effect was further supported by qPCR analysis of bacterial groups within these two phyla. The results demonstrate that storage conditions of fecal samples may adversely affect the determined Firmicutes to Bacteroidetes ratio, which is a frequently used biomarker in gut microbiology.
Pacemaker prevention therapies for the control of drug-refractory paroxysmal atrial fibrillation (2003)

Atrial septal pacing resulted in a marked improvement in AF burden and symptoms. Activation of specific prevention pacing algorithms provided more continuous atrial pacing but had limited and heterogeneous effects on AF burden.
Comparison of Insulin Autoantibodies in Diabetes-Related and Healthy Populations by Precise Displacement ELISA (1989)

The second international workshop on insulin autoantibodies (IAAs) demonstrated improved concordance among laboratories with both radioimmunoassay (RIA) and enzyme-linked immunosorbent assay (ELISA) when measurements were based on signals displaceable by preincubation with excess insulin. This feature has been incorporated into our original ELISA for IAAs, and the assay was used to compare IAAs in diabetes-related and healthy populations. The serum from a healthy islet cell antibody (ICA)+ and IAA+ subject was used to construct standard curves with and without preincubation with 1 U/ml human insulin. Reporting results in arbitrary displacement (delta +/- IAA) units derived from the standard curve improved precision and increased the specificity of the assay. Frequency analysis of the results from 200 control adults did not show a normal distribution, and cumulative frequency analysis demonstrated two populations: 10 of 200 (5%) control adults, 8 of 241 (3.3%) healthy schoolchildren, and 18 of 229 (7.9%) non-insulin-dependent diabetes mellitus (NIDDM) patients had IAAs greater than 12 delta +/- IAA units. On the same basis, we tested samples from 89 individuals in the prospective Bart's Windsor Family Study for insulin-dependent diabetes mellitus (IDDM), 31 of whom had ICAs greater than 5 Juvenile Diabetes Foundation (JDF) units. Of those with ICAs greater than 5 JDF units, 12 developed IDDM and 1 developed NIDDM in 10 yr of study. IAAs greater than 12 delta +/- IAA units were found in 6 of 12 (50%) who became diabetic and in 4 of 18 (22%) who remain healthy.(ABSTRACT TRUNCATED AT 250 WORDS)
Elution of “blocking factors” from human tumors, capable of abrogating tumor‐cell destruction by specifically immune lymphocytes (1972)

Abstract Sera from patients with growing neoplasms have been previously shown capable of specifically blocking the cytotoxic effect of lymphocytes immune to tumor‐associated antigens (TAA) of the respective patients' neoplasms. The present investigation demonstrates that a similar blocking activity can be eluted at pH 3.1 from human tumor tissues, obtained at surgery (seminomas and osteogenic sarcomas) and from tumor cells growing in ascites and pleural effusions (carcinomas of endometrium, breast and ovary). A high (MW above 100,000) and a low (MW below 100,000) molecular weight fraction can be separated from the eluates by ultrafiltration. Neither of these fractions could block lymphocyte‐mediated cytotoxicity in vitro when tested by itself, while a 1:1 mixture of them could. Blocking was also obtained when the tumor cells were first exposed to the high and then to the low molecular weight fractions, but not when the sequence was reversed. The observations obtained are analogous to previous findings in animal tumor systems and provide evidence that tumors growing in human patients are coated by “blocking factors”.
Morphology and Properties of Soy Protein Isolate Thermoplastics Reinforced with Chitin Whiskers (2004)

Environmentally friendly thermoplastic nanocomposites were successfully developed using a colloidal suspension of chitin whiskers as a filler to reinforce soy protein isolate (SPI) plastics. The chitin whiskers, having lengths of 500 +/- 50 nm and diameters of 50 +/- 10 nm on average, were prepared from commercial chitin by acid hydrolysis. The dependence of morphology and properties on the chitin whiskers content in the range from 0 to 30 wt % for the glycerol plasticized SPI nanocomposites was investigated by dynamic mechanical thermal analysis, scanning electron microscopy, swelling experiment, and tensile testing. The results indicate that the strong interactions between fillers and between the filler and SPI matrix play an important role in reinforcing the composites without interfering with their biodegradability. The SPI/chitin whisker nanocomposites at 43% relative humidity increased in both tensile strength and Young's modulus from 3.3 MPa for the SPI sheet to 8.4 MPa and from 26 MPa for the SPI sheet to 158 MPa, respectively. Further, incorporating chitin whisker into the SPI matrix leads to an improvement in water resistance for the SPI based nanocomposites.