gebhart/patrepeval huggingface dataset:
Mapping of a visceral leishmaniasis-specific immunodominant B-cell epitope of Leishmania donovani Hsp70 (1992)

We have shown that a member of the 70-kDa heat shock protein (Hsp70) family is a major target of the humoral immune response during Leishmania donovani infection. A recombinant fusion protein was recognized by sera from 92% (35 of 38) of patients with visceral leishmaniasis, including representatives from each of the major regions where it is endemic. Serological analysis of recombinant Hsp70, expressed by a series of deletion constructs, identified the carboxy-terminal region as the immunodominant site. This region, which is the most evolutionarily divergent part of the molecule, was recognized by all sera from patients with visceral leishmaniasis which exhibited an anti-Hsp70 response. Purified recombinant L. donovani Hsp70 was not recognized by sera from patients with cutaneous leishmaniasis, Chagas' disease, leprosy, malaria, or schistosomiasis. To determine the regions involved in antibody recognition, a series of overlapping peptides were synthesized on polyethylene pins by the Pepscan method, and a hexamer, EADDRA, was identified by the visceral leishmaniasis serum samples as an immunodominant B-cell epitope.
Fabrication of 64 M DRAM with i-line phase-shift lithography (2002)

New phase-shift lithography applicable to all device patterns has been developed which combines pattern formation with the shifter alone and edge contrast enhancement with the shifter. Using it one can make 0.3 mu m patterns with i-line photolithography. A 64 M DRAM having memory cells unrestricted by angular considerations was designed for use with this lithography, and experimental 64 M DRAM chips were fabricated. The technique eliminates the need for special pattern design such as assistant patterns. Since it requires only the original design pattern, it is easy to apply to fabrication.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Data Mining: Practical Machine Learning Tools and Techniques (2011)

As with any burgeoning technology that enjoys commercial attention, the use of data mining is surrounded by a great deal of hype. Exaggerated reports tell of secrets that can be uncovered by setting algorithms loose on oceans of data. But there is no magic in machine learning, no hidden power, no alchemy. Instead there is an identifiable body of practical techniques that can extract useful information from raw data. This book describes these techniques and shows how they work. The book is a major revision of the first edition that appeared in 1999. While the basic core remains the same, it has been updated to reflect the changes that have taken place over five years, and now has nearly double the references. The highlights for the new edition include thirty new technique sections; an enhanced Weka machine learning workbench, which now features an interactive interface; comprehensive information on neural networks; a new section on Bayesian networks; plus much more.
Enhanced radiosensitization with gemcitabine in mismatch repair-deficient HCT116 cells. (2003)

Gemcitabine [2',2'-difluoro-2'-deoxycytidine (dFdCyd)] is a potent ionizing radiation sensitizer in solid tumor cells in vitro and in vivo. Previously, we have demonstrated (Shewach et al., Cancer Res., 54: 3218-3223, 1994) a strong correlation between depletion of dATP (caused by dFdCyd diphosphate-mediated inhibition of ribonucleotide reductase) and radiosensitization. In addition, we and others (Latz et al., Int. J. Radiat. Oncol. Biol. Phys., 41: 875-882, 1998; Ostruszka and Shewach, Cancer Res., 60: 6080-6088, 2000) have shown that the accumulation of cells in S phase prior to irradiation is also important for radiosensitization with dFdCyd. This led us to hypothesize that the incorporation of incorrect nucleotides because of the dATP pool imbalance was important for radiosensitization with dFdCyd, and, therefore, cells deficient in mismatch repair (MMR) would exhibit greater radiosensitization. We tested this hypothesis by evaluating the ability of HCT116 colon carcinoma cell lines, which differ in MMR proficiency, to be radiosensitized by dFdCyd. The MMR-proficient cell line (HCT116 + ch3) was more sensitive to dFdCyd alone than were the MMR-deficient cell lines (HCT116, HCT116 + ch2, and HCT116 p53(-/-)). Interestingly, the MMR-proficient cells could not be radiosensitized at concentrations of dFdCyd <or=IC(90), although extremely high concentrations of dFdCyd (>IC(96)) enhanced cell killing with radiation. In contrast, the MMR-deficient cells were radiosensitized at concentrations of dFdCyd <or=IC(50), with radiation enhancement ratios of approximately 1.5. Cell cycle analysis, using dual parameter flow cytometry, demonstrated that all of the cell lines accumulated in S phase after dFdCyd treatment, and, shortly after irradiation, a prominent but transient G(2)-M block was observed. In the MMR-deficient cells, the IC(50) for dFdCyd produced a >or=80% decrease in dATP within 4 h after drug addition, and this low dATP level was maintained for another 12-20 h. Although the IC(50) of dFdCyd was unable to sustain a >80% decrease in the dATP level in the MMR-proficient cells, the IC(90) did achieve this level of dATP depletion; however, it was unable to radiosensitize the MMR-proficient cells. Similar results were obtained with HCT116 cells, in which the MMR deficiency was corrected by transfection with a vector containing the hMLH1 cDNA. In addition, the deletion of p53 did not increase radiation enhancement ratios. These results demonstrate that MMR deficiency promotes radiosensitization with dFdCyd. We suggest that dATP depletion produces errors of replication in MMR-deficient cells, which, if left unrepaired, enhances cell death by ionizing radiation.
Expression, function and clinical relevance of MIA (melanoma inhibitory activity). (2002)

Despite its ambiguous name the protein melanoma-inhibitory-activity (MIA) was identified as a key molecule involved in progression and metastasis of malignant melanomas. Therefore, in this review we intend to update the current knowledge on expression patterns, transcriptional regulation, function and clinical relevance of MIA. Furthermore, we will cover the recently discovered MIA homologous proteins OTOR/MIAL, MIA 2 and TANGO. In order to identify autocrine growth-regulatory factors secreted by melanoma cells, MIA was purified and cloned. Subsequent analyses of non-neoplastic tissues revealed specific MIA expression patterns in cartilage. In neoplastic tissues MIA expression was detected in malignant melanomas, in chondrosarcomas and less frequently in a variety of different adenocarcinomas including breast and colon cancers. For melanoma cells and chondrocytes it was shown that regulation of expression pattern was controlled on the level of mRNA transcription by defined transcription factors. Evidence obtained from in vitro and in vivo experiments indicated that MIA plays an important functional role in melanoma metastasis and invasion. A number of studies from different laboratories evaluated MIA as a highly specific and sensitive marker, clinically useful for follow-up and therapy-monitoring of patients with malignant melanomas. In addition, preliminary data suggests a further potential application as a surrogate marker for measuring cartilage damage in rheumatoid arthritis. Recently, it has become evident that MIA belongs to a gene family of four homologous proteins, MIA, OTOR (FDP, MIAL), MIA 2 and TANGO. Determination of the three-dimensional structure in solution identified MIA as the first member of this novel family of secreted, extracellular proteins adopting an SH3 domain-like fold. The data suggest specific protein-protein interactions with components of the extracellular matrix and possibly epitopes on cellular surfaces and will certainly attract further interest and investigations.
Chemotherapy of Filariasis -On the Search of New Agents Effective on the Reproductive System of Female Adult Worms (1990)

The design and synthesis of a series of alkyl 5(6)-substituted benzimidazole-2-carbamates (1-13), 7-chloro-4-(4-substituted phenyl)aminoquinolines (14-16), 1,2-dimethyl-3-methoxy-carbonyl-4,5-disubstituted pyrroles (17-19) and some compounds belonging to the class pimelonitrile (20), dihydroquinoline (21), pyridine (22), pyridoquinoline (23) and tetrahydro-pyrimidine (24) have been carried out as possible antifilarial agents. All these compounds have been evaluated for their activity against male and female adult worms of Litomosoides carinii in cotton rats. The effect of these compounds was also observed on the reproductive system (condition of developing microfilariae and their release from uterus) of adult female worms. In this study, three types of compounds were discovered: (a) those which showed activity on both the male and female adult worms and also had sterilizing effects on surviving adult females (1-3, 6-9, 13, 19), (b) those which only sterilized the adult females (14-16, 21, 24), and (c) those which had no effect on female reproduction but killed only adult worms (4, 5, 11, 12, 17, 18, 20, 22, 23). This tends to open up a new avenue in the chemotherapy of filariasis and the future scope of work on chemosterilization of adult females has been discussed.
Erbium Fiber Laser Accelerometer (2007)

A new form of fiber accelerometer based on an erbium fiber laser sensor is presented. The transducer is a unique shape derived by an automated finite element analysis design optimization program and is constructed using stereolithography
Prognostic and predictive factors in breast cancer by immunohistochemical analysis. (1998)

Most recent decisions for breast cancer patients are made on the basis of prognostic and predictive factors. In addition to the traditional tumor/nodal/metastasis staging variables, estrogen and progesterone receptor status as assessed by biochemical ligand-binding assays are the only other factors that have been adequately validated and recommended for routine clinical use. Pathologists today, however, are evaluating estrogen and progesterone receptors almost exclusively by immunohistochemical means. Although many studies suggest that these tests might have equivalent or even superior abilities to predict patient outcome, there are important methodologic shortcomings to resolve before this technology achieves the clinical and technical validation necessary to justify its routine use. Many laboratories are also evaluating other factors for clinical use by immunohistochemical techniques, including, in particular, c-erbB-2, p53, and Ki-67 proliferation indices. Although available studies suggest that these factors might indeed be helpful in making treatment decisions, their clinical usefulness is still controversial, and, like the assessment of hormone receptors, there are important unresolved technical issues, such as how to prepare the tissue, which reagents to use and, most importantly, how to interpret the results. A few laboratories have gone to considerable effort to develop reproducible methods for evaluating these factors, and they have performed comprehensive studies demonstrating the prognostic and predictive significance of their results. Nonetheless, most laboratories offering these tests have not adequately validated them and might not even be aware of the issues needing attention. Unless laboratories validate their tests or follow the procedures of others who have, they run the risk of reporting meaningless and potentially harmful results. In the future, these and other factors will be incorporated into a prognostic index that will better reflect the biologic diversity of breast cancer and that will more accurately predict clinical outcome.
Triacylglycerol profiling by using chromatographic techniques (2004)

Abstract Triacylglycerols (TGs) make up the major part of naturally occurring fats and oils. The composition and fine structure of TGs determine to a large extent the functionality of fats and oils as food ingredients and the physiological effects of fats and oils as component of the human diet. Analysis of intact TGs is usually performed by chromatographic methods. In this article the application of gas‐liquid chromatography, high‐performance chromatography in normal and reversed phase mode, thin‐layer chromatography and supercritical fluid chromatography for the qualitative and quantitative determination of TGs is reviewed. Emphasis is put on those factors that are decisive for obtaining reliable quantitative data. Furthermore, techniques for the stereospecific analysis of the fatty acid distribution along the glycerol backbone of TGs are presented briefly.
Interleukin-15 is associated with disease severity in viral bronchiolitis (2015)

Disease severity in viral bronchiolitis in infancy is difficult to predict and has been linked to host innate immunity. The study aimed to investigate the innate cytokine interleukin-15 (IL-15) as a marker of disease severity.A prospective single-centre observational study was conducted in a university-affiliated paediatric teaching hospital, comparing children (0-18 months) hospitalised for viral bronchiolitis, those admitted to the paediatric intensive care unit with severe disease and healthy age-matched controls. IL-15-related parameters were compared between groups. PCR and microRNA (miRNA) sequencing was undertaken on natural killer (NK) cells collected from study participants.Samples from 88 children with viral bronchiolitis and 43 controls enrolled between 2009 and 2012 were analysed. Peripheral blood mononuclear cell (PBMC) IL-15 mRNA expression was significantly higher in those with moderate severity bronchiolitis compared with controls and those with severe disease. Serum IL-15 levels correlated with disease severity. The relative frequency of NK cells in peripheral blood was significantly reduced in participants with bronchiolitis. The NK cell miRNA transcriptome in bronchiolitis was distinct. Targets of de-regulated miRNA were differentially expressed in bronchiolitis, including JAK3, STAT5A and NFKB1 on the IL-15 signalling pathway.IL-15 is associated with disease severity in children hospitalised with viral bronchiolitis.
Low Reflectivity and High Flexibility of Tin-Doped Indium Oxide Nanofiber Transparent Electrodes (2010)

Tin-doped indium oxide (ITO) has found widespread use in solar cells, displays, and touch screens as a transparent electrode; however, two major problems with ITO remain: high reflectivity (up to 10%) and insufficient flexibility. Together, these problems severely limit the applications of ITO films for future optoelectronic devices. In this communication, we report the fabrication of ITO nanofiber network transparent electrodes. The nanofiber networks show optical reflectivity as low as 5% and high flexibility; the nanofiber networks can be bent to a radius of 2 mm with negligible changes in the sheet resistance.
BAFF, APRIL, TWEAK, BCMA, TACI and Fn14 Proteins Are Related to Human Glioma Tumor Grade: Immunohistochemistry and Public Microarray Data Meta-Analysis (2013)

Gliomas are common and lethal tumors of the central nervous system (CNS). Genetic alterations, inflammatory and angiogenic processes have been identified throughout tumor progression; however, treatment still remains palliative for most cases. Biological research on parameters influencing cell survival, invasion and tumor heterogeneity identified several cytokines interfering in CNS inflammation, oxidative stress and malignant transformation, including TNF-superfamily (TNFSF) members. In this report we performed a meta-analysis of public gene-array data on the expression of a group of TNFSF ligands (BAFF, APRIL, TWEAK) and their receptors (BAFF-R, TACI, BCMA, Fn14) in gliomas. In addition, we investigated by immunohistochemistry (IHC) the tumor cells' expression of these ligands and receptors in a series of 56 gliomas of different grade. We show that in IHC, BAFF and APRIL as well as their cognate receptors (BCMA, TACI) and Fn14 expression correlate with tumor grade. This result was not evidenced in micro-arrays meta-analysis. Finally, we detected for the first time Fn14, BAFF, BCMA and TACI in glioma-related vascular endothelium. Our data, combined with our previous report in glioma cell lines, suggest a role for these receptors and ligands in glioma biology and advance these molecules as potential markers for the classification of these tumors to the proliferative, angiogenic or stem-like molecular subtype.
Optimization principles and application performance evaluation of a multithreaded GPU using CUDA (2008)

GPUs have recently attracted the attention of many application developers as commodity data-parallel coprocessors. The newest generations of GPU architecture provide easier programmability and increased generality while maintaining the tremendous memory bandwidth and computational power of traditional GPUs. This opportunity should redirect efforts in GPGPU research from ad hoc porting of applications to establishing principles and strategies that allow efficient mapping of computation to graphics hardware. In this work we discuss the GeForce 8800 GTX processor's organization, features, and generalized optimization strategies. Key to performance on this platform is using massive multithreading to utilize the large number of cores and hide global memory latency. To achieve this, developers face the challenge of striking the right balance between each thread's resource usage and the number of simultaneously active threads. The resources to manage include the number of registers and the amount of on-chip memory used per thread, number of threads per multiprocessor, and global memory bandwidth. We also obtain increased performance by reordering accesses to off-chip memory to combine requests to the same or contiguous memory locations and apply classical optimizations to reduce the number of executed operations. We apply these strategies across a variety of applications and domains and achieve between a 10.5X to 457X speedup in kernel codes and between 1.16X to 431X total application speedup.
The Effects of Nordihydroguaiaretic Acid, Salt and Temperature of Storage on the Stability of Fat and Fat-Soluble Vitamins in Cream and Butter (1949)

In a recent paper (2) evidence was presented to show that the oxidized flavors in fresh milk are not associated with deterioration of fat but with the unstable lipids which are mostly a part of the stabilizing fat globule membrane. It has been pointed out, however, that the fat itself also may undergo deterioration in the presence of ascorbic acid, resulting in the development of metallic to fishy flavors and losses in vitamins A and E and carotenoids. The susceptibility of fat to this type of deterioration, as determined by the re-emulsification test (2), depends on the type of product, the temperature of pasteurization and the conditions of storage. Thus, from the biochemica ! point of view, at least two reactions which produce the oxidized flavors may be stimulated by the addition of ascorbic acid to milk products containing unstable fat.
5-year incidence of atherosclerotic vascular disease in relation to general risk factors, insulin level, and abnormalities in lipoprotein composition in non-insulin-dependent diabetic and nondiabetic subjects. (1990)

The 5-year incidence of myocardial infarction and claudication was examined in a group of middle-aged patients (n = 133, 70 men and 63 women) with newly diagnosed non-insulin-dependent diabetes and nondiabetic control subjects (n = 144, 62 men and 82 women). The effects of general risk factors, plasma insulin level, and lipoprotein abnormalities on the incidence of myocardial infarction and claudication were also evaluated by univariate analyses in both diabetic patients and nondiabetic subjects and by multivariate analyses combining both groups. The age-adjusted incidence of myocardial infarction was higher both in diabetic men (19.4%) and diabetic women (11.0%) than in nondiabetic men (3.2%, p = 0.009) and nondiabetic women (3.0%, p = 0.047). Similarly, the age-adjusted incidence of claudication was higher among the diabetic patients (20.3% vs. 8.0% for men, p = 0.06; 21.8% vs. 4.2% for women, p = 0.003). None of the general risk factors (i.e., low density lipoprotein [LDL] cholesterol, blood pressure, smoking, and high density lipoprotein [HDL] cholesterol) showed an association with the risk of myocardial infarction either in the diabetic or nondiabetic groups of subjects, but an ischemic electrocardiographic abnormality at the baseline examination predicted myocardial infarction in diabetic men. In univariate analyses in diabetic subjects, high serum total cholesterol, low HDL cholesterol, high very low density lipoprotein (VLDL) cholesterol, and high total, LDL and VLDL triglycerides, and in nondiabetic subjects, high VLDL cholesterol and LDL triglycerides were associated with the appearance of claudication. In multivariate analyses including both diabetic and control subjects, only diabetes had an independent association with myocardial infarction, whereas smoking, high LDL triglycerides or VLDL cholesterol, and high fasting plasma insulin showed independent relations to claudication. The present results indicate that changes in lipoprotein composition characteristic of non-insulin-dependent diabetes are atherogenic and increase the risk of atherosclerotic vascular disease. Furthermore, high plasma insulin might also be involved in atherogenesis, independent of lipoprotein abnormalities.
De novo sequencing of peptides by MS/MS (2009)

The current status of de novo sequencing of peptides by MS/MS is reviewed with focus on collision cell MS/MS spectra. The relation between peptide structure and observed fragment ion series is discussed and the exhaustive extraction of sequence information from CID spectra of protonated peptide ions is described. The partial redundancy of the extracted sequence information and a high mass accuracy are recognized as key parameters for dependable de novo sequencing by MS. In addition, the benefits of special techniques enhancing the generation of long uninterrupted fragment ion series for de novo peptide sequencing are highlighted. Among these are terminal (18)O labeling, MS(n) of sodiated peptide ions, N-terminal derivatization, the use of special proteases, and time-delayed fragmentation. The emerging electron transfer dissociation technique and the recent progress of MALDI techniques for intact protein sequencing are covered. Finally, the integration of bioinformatic tools into peptide de novo sequencing is demonstrated.
Neutrophil Mac-1 and MEL-14 Adhesion Proteins Inversely Regulated by Chemotactic Factors (1989)

The neutrophil Mac-1 and gp100MEL-14 adhesion proteins are involved in neutrophil extravasation during inflammation. Both the expression and activity of Mac-1 are greatly increased after neutrophil activation. In contrast, neutrophils shed gp100MEL-14 from the cell surface within 4 minutes after activation with chemotactic factors or phorbol esters, releasing a 96-kilodalton fragment of the antigen into the supernatant. Immunohistology showed that gp100MEL-14 was downregulated on neutrophils that had extravasated into inflamed tissue. The gp100MEL-14 adhesion protein may participate in the binding of unactivated neutrophils to the endothelium; rapid shedding of gp100MEL-14 may prevent extravasation into and damage of normal tissues by activated neutrophils.
LSD: a Line Segment Detector (2012)

LSD is a linear-time Line Segment Detector giving subpixel accurate results. It is designed to work on any digital image without parameter tuning. It controls its own number of false detections: On average, one false alarm is allowed per image. The method is based on Burns, Hanson, and Riseman's method, and uses an a-contrario validation approach according to Desolneux, Moisan, and Morel's theory. The version described here includes some further improvement over the one described in the original article.