gebhart/patrepeval huggingface dataset:
BRCA1 mRNA expression levels as an indicator of chemoresistance in lung cancer (2004)

Lung cancer is the most common cancer, with dismal outcome. Treatment approaches, including cisplatin-based chemotherapy and surgery, are currently based on the clinical classification of the tumor, without genetic assessment for predicting differential chemosensitivity. BRCA1 plays a central role in DNA repair, and decreased BRCA1 mRNA expression in the human breast cancer HCC1937 cell line caused cisplatin hypersensitivity, but the relation between BRCA1 and survival in lung cancer patients has never been examined. We used real-time quantitative polymerase chain reaction to determine BRCA1 mRNA levels in 55 surgically resected tumors of non-small-cell lung cancer patients who had received neoadjuvant gemcitabine/cisplatin chemotherapy, and divided the gene expression values into quartiles. When results were correlated with outcome, two cut-offs were observed; patients with levels <0.61 had better outcome, and those >2.45 had poorer outcome. Median survival was not reached for the 15 patients in the bottom quartile, whereas for the 28 in the two middle quartiles, it was 37.8 months (95% CI, 10.6-65), and for the 12 patients in the top quartile, it was 12.7 months (95% CI, 0.28-28.8) (P=0.01). Moreover, when patients were stratified by pathologic stage, those in the bottom quartile had a decreased risk of death (HR=0.206; 95% CI, 0.05-0.83; P=0.026) compared with those in the top quartile, and those in the two middle quartiles also had a decreased risk of death (HR=0.294; 95% CI, 0.10-0.83; P=0.020) compared with those in the top quartile. BRCA1 expression is potentially an important tool for use in cancer management and should be assessed for predicting differential chemosensitivity and tailoring chemotherapy in lung cancer.
Disruption of SEMA4D Ameliorates Platelet Hypersensitivity in Dyslipidemia and Confers Protection Against the Development of Atherosclerosis (2009)

These results show that loss of sema4D expression reduces the platelet hyperactivity otherwise found in dyslipidemia, and confers protection against the development of atherosclerosis.
Selective Inactivation of the Exonuclease Activity of Bacteriophage T7 DNA Polymerase by in Vitro Mutagenesis (1989)

The 3' to 5' exonuclease activity of bacteriophage T7 DNA polymerase (gene 5 protein) can be inactivated selectively by reactive oxygen species. Differences in the enzymatic properties between the two forms are exploited to show by a chemical screen that modification of a histidine residue reduces selectively the exonuclease activity. In vitro mutagenesis of the histidine at residue 123, and of the neighboring residues, results in varying reduction of the exonuclease activity, including mutant enzymes that have no detectable exonuclease activity; as a consequence their polymerase activity is increased up to 9-fold. T7 phage containing the mutant genes have a greatly reduced burst size and demonstrate up to a 14-fold increase in the spontaneous mutation rate.
Probing Single DNA Molecule Transport Using Fabricated Nanopores (2004)

Nanopores can serve as high throughput, single molecule sensing devices that provide insight into the distribution of static and dynamic molecular activities, properties, or interactions. We have studied double stranded DNA electrophoretic transport dynamics through fabricated nanopores in silicon nitride. A fabricated pore enables us to interrogate a broader range of molecules with a wider range of conditions than can be investigated in a self-assembled protein pore in a lipid membrane.
Kicking off adaptive immunity: the discovery of dendritic cells (2006)

In 1973, Ralph Steinman and Zanvil Cohn discovered an unusual looking population of cells with an unprecedented ability to activate naive T cells. Dubbed "dendritic cells," these cells are now known as the primary instigators of adaptive immunity.
The RNA2–PNA2hybrid i-motif—a novel RNA-based building block (2007)

We report the formation of a hybrid RNA2-PNA2 i-motif comprised of two RNA and two PNA strands based on the sequence specific self assembly of RNA, with potential as a building block for structural RNA nanotechnology.
Self-Renewal and Cancer of the Gut: Two Sides of a Coin (2005)

The intestinal epithelium follows the paradigms of stem cell biology established for other self-renewing tissues. With a unique topology, it constitutes a two-dimensional structure folded into valleys and hills: the proliferative crypts and the differentiated villi. Its unprecedented self-renewal rate appears reflected in a high susceptibility to malignant transformation. The molecular mechanisms that control homeostatic self-renewal and those that underlie colorectal cancer are remarkably symmetrical. Here, we discuss the biology of the intestinal epithelium, emphasizing the roles played by Wnt, bone morphogenic protein, and Notch signaling cascades in epithelial self-renewal and cancer.
LCN2 and TIMP1 as Potential Serum Markers for the Early Detection of Familial Pancreatic Cancer (2013)

High-risk individuals of familial pancreatic cancer (FPC) families are considered to be good candidates for screening programs to detect early PC or its high-grade precursor lesions, especially pancreatic intraepithelial neoplasia (PanIN) 2/3 lesions. There is a definite need for diagnostic markers as neither reliable imaging methods nor biomarkers are available to detect these lesions. On the basis of a literature search, the potential serum markers neutrophil gelatinase-associated lipocalin (LCN2), metallopeptidase inhibitor 1 (TIMP1), chemokine (C-X-C motif) ligand 16 (CXCL16), IGFBP4, and iC3a, which were first tested in transgenic KrasLSL.(G12D/+);p53(R172H/+);Pdx1-Cre mice, were identified. ELISA analyses of LCN2, TIMP1, and CXCL16 revealed significantly higher levels in mice with PanIN2/3 lesions or PC compared to mice with normal pancreata or PanIN1 lesions. Analysis of preoperative human serum samples from patients with sporadic PC (n = 61), hereditary PC (n = 24), chronic pancreatitis (n = 28), pancreatic neuroendocrine tumors (n = 11), and FPC patients with histologically proven multifocal PanIN2/3 lesions (n = 3), as well as healthy control subjects (n = 20), confirmed significantly higher serum levels of LCN2 and TIMP1 in patients with PC and multifocal PanIN2/3 lesions. The combination of LCN2 and TIMP1 as a diagnostic test for the detection of PC had a sensitivity, specificity, and positive predictive value of 100% each. Although this preliminary finding needs to be validated in a large series of individuals at high risk for FPC, serum measurement of LCN2 and TIMP1 might be a promising screening tool.
Ensemble deep learning for speech recognition (2014)

Deep learning systems have dramatically improved the accuracy of speech recognition, and various deep architectures and learning methods have been developed with distinct strengths and weaknesses in recent years. How can ensemble learning be applied to these varying deep learning systems to achieve greater recognition accuracy is the focus of this paper. We develop and report linear and log-linear stacking methods for ensemble learning with applications specifically to speechclass posterior probabilities as computed by the convolutional, recurrent, and fully-connected deep neural networks. Convex optimization problems are formulated and solved, with analytical formulas derived for training the ensemble-learning parameters. Experimental results demonstrate a significant increase in phone recognition accuracy after stacking the deep learning subsystems that use different mechanisms for computing high-level, hierarchical features from the raw acoustic signals in speech.
Cross‐reactions of anti‐DNA autoantibodies with cell surface proteins (1993)

Anti-DNA autoantibodies are thought to play a major role in the pathogenesis of systemic lupus erythematosus. However, the mechanism(s) by which they participate in tissue and organ damage is not well understood. It has been suggested that these antibodies combine with DNA or DNA-histone complexes to produce circulating immune complexes which may deposit in various tissues. Alternatively, anti-DNA autoantibodies could interact directly with tissue components by way of immunological cross-reaction. In this study we have used a panel of mouse monoclonal autoantibodies with anti-nuclear specificity and measured their binding to membrane proteins of several tissues and cell lines. We show that the anti-DNA antibodies, but not anti-RNA or anti-histone antibodies bind to membrane proteins of molecular weights 102, 80, 42, 35 and 31 kDa, which are expressed in different combinations on several cell types. The binding of anti-DNA antibodies to these cell surface proteins was not affected by DNase treatment of the target cells, was increased by DNase treatment of the antibody preparations and was completely inhibited by DNA, indicating a true cross-reaction and not an indirect interaction of antibody and membrane proteins through a DNA bridge. Our results suggest that direct binding of anti-DNA autoantibodies to cell surface membrane proteins may play an important role in the induction of the pleomorphic tissue damage in systemic lupus erythematosus.
The GLI gene encodes a nuclear protein which binds specific sequences in the human genome. (1990)

The GLI gene is amplified in a subset of human tumors and encodes a protein product with five zinc finger DNA-binding motifs. In this study, we show that the GLI gene product has a predominantly nuclear localization and binds DNA in a sequence-specific fashion. Three GLI binding sites were identified by using a novel procedure in which total human DNA was bound to a GLI recombinant fusion protein, and the polymerase chain reaction was used to amplify and recover the bound sequences. The GLI protein protected a 23- to 24-base region within all three binding sites, and the protected region in each case included the 9-base-pair sequence 5'-GACCACCCA-3'. One of the binding sites was contained within a 63-base-pair repeat of the variable number of tandem repeat type, whereas the other two sites were represented once in the genome. The approach used here to identify GLI binding sites should be applicable to the characterization of other zinc finger proteins.
The Bohr Effect and the Haldane Effect (1973)

(1973). The Bohr Effect and the Haldane Effect. Scandinavian Journal of Clinical and Laboratory Investigation: Vol. 31, No. 1, pp. 1-8.
Wave-Direction and Conduction-Velocity Analysis From Intracardiac Electrograms–A Single-Shot Technique (2010)

Atrial arrhythmias, such as atrial flutter or fibrillation, are frequent indications for catheter ablation. Recorded intracardiac electrograms (EGMs) are, however, mostly evaluated subjectively by the physicians. In this paper, we present a method to quantitatively extract the wave direction and the local conduction velocity from one single beat in a circular mapping catheter signal. We simulated typical clinical EGMs to validate the method. We then showed that even with noise, the average directional error was below 10(°) and the average velocity error was below 5.4 cm/s. In a realistic atrial simulation, the method could clearly distinguish between stimuli from different pulmonary veins. We further analyzed eight clinical data segments from three patients in normal sinus rhythm and with stimulation. We obtained stable wave directions for each segment and conduction velocities between 70 and 115 cm/s. We conclude that the method allows for easy quantitative analysis of single macroscopic wavefronts in intracardiac EGMs, such as during atrial flutter or in typical clinical stimulation procedures after termination of atrial fibrillation. With corresponding simulated data, it can provide an interface to personalize electrophysiological (EP) models. Furthermore, it could be integrated into EP navigation systems to provide quantitative data of high diagnostic value to the physician.
Prolonged administration of weekly paclitaxel and trastuzumab in patients with advanced breast cancer. (2003)

Prolonged administration of weekly paclitaxel and trastuzumab is effective and well-tolerated in women with HER2-positive metastatic breast cancer.
Leaf Rust‐Resistance Genes Lr41, Lr42, and Lr43 Transferred from Triticum tauschii to Common Wheat (1994)

In order to diversify the genetic base of resistance in hard red winter wheat ( Triticum aestivum L.) to leaf rust (caused by Puccinia recondita Rob. ex Desm.), five genes for resistance were transferred from the diploid goatgrass T. tauschii (Coss.) Schmal. to hexaploid wheat lines. One of the derived lines, KS90WGRC10, had a very low infection type when inoculated with 23 cultures of P. recondita . The others, KS91WGRC11, KS92WGRC16, U1865, and U1866, had low to intermediate infection types with three cultures. Their infection types varied similarly to those of lines carrying previously transferred alleles of Lr21 . WGRC10 carries a completely dominant gene, Lr41 , on chromosome 1D that segregates independently of any other T. tauschii ‐derived leaf rust‐resistance genes. WGRC11 carries the partially dominant gene, Lr42 , also on 1D, that is linked to Lr21 with a recombination value of 0.286 ± 0.023. WGRC16 carries a partially dominant gene, Lr43 , that segregates independently of all known genes for seedling resistance from T. tauschii ; its chromosome location is not known. The genes carried by U1865 and U1866 are allelic to Lr21 . WGRC10, WGRC11, and WGRC16 have been released as germplasms by the Wheat Genetics Resource Center.
Non-catalytic - and -Subunit Isoforms of the 5′-AMP-activated Protein Kinase (1996)

The mammalian 5'-AMP-activated protein kinase (AMPK) is a heterotrimeric protein consisting of alpha-, beta-, and gamma-subunits. The alpha-subunit is the catalytic subunit and is related to the yeast Snf1p kinase. In this study, we report the cloning of full-length cDNAs for the non-catalytic beta- and gamma-subunits. The rat liver AMPK beta-subunit clone predicts a protein of 30,464 Da, which is related to the Sip1p, Sip2p, and Gal83p subfamily of yeast proteins that interact with Snf1p and are involved in glucose regulation of gene expression. The AMPK beta-subunit, when expressed in bacteria and in mammalian cells, migrates anomalously on SDS gels at an apparent molecular mass of 40 kDa. Rat and human liver AMPK gamma-subunit clones predict a protein of 37,577 Da (AMPK-gamma1), which is related to the yeast Snf4p protein that copurifies with Snf1p and to a larger family of other human AMPK gamma-isoforms. The mRNAs for both AMPK- beta and AMPK-gamma1 are widely expressed in rat tissues, consistent with a broad role for AMPK in cellular regulation. These data reveal a mammalian multisubunit protein kinase strikingly similar to the multisubunit glucose-sensing Snf1 kinase complex. The identification of isoform families for the AMPK subunits indicates the potential diversity of the roles of this highly conserved signaling system in nutrient regulation and utilization in mammalian cells.
Control of Citrus Canker and Citrus Bacterial Spot with Bacteriophages (2008)

Bacteriophages, alone or in combination with copper bactericides, were evaluated for managing Asiatic citrus canker and citrus bacterial spot incited by Xanthomonas axonopodis pathovars citri and citrumelo, respectively. In a set of five greenhouse experiments, phage treatment provided consistent control of citrus canker, causing an average of 59% reduction in disease severity. However, treatment with phage was ineffective if applied with skim milk, a protective formulation, which increases phage residual activity. In nursery settings, phage treatment also reduced disease but was less effective than copper-mancozeb, a chemical bactericide. The integration of phage and copper-mancozeb resulted in equal or less control than copper-mancozeb application alone. Phage treatments were evaluated in a commercial citrus nursery for reducing citrus bacterial spot caused by natural inoculum. Phage treatment provided significant disease reduction on moderately sensitive Valencia oranges in two trials (48 and 35%); however, on the highly susceptible grapefruit host it was ineffective. In an experimental citrus nursery, phage treatment provided significant control of citrus bacterial spot caused by a phage-sensitive strain, but was equally or less effective than copper-mancozeb. The combination of phage and copper-mancozeb did not increase control compared with copper-mancozeb alone.
Cloning and over‐expression in Escherichia coli of the gene encoding NADPH group III alcohol dehydrogenase from Thermococcus hydrothermalis (1999)

A NADP-dependent group III alcohol dehydrogenase (ADH) was purified from the hyperthermophilic strictly anaerobic archaeon Thermococcus hydrothermalis, which grows at an optimum temperature of 85 degrees C and an optimum pH of 6. The gene encoding this enzyme was cloned, sequenced, and over-expressed in Escherichia coli. The recombinant enzyme was purified, characterized and compared with the native form of the enzyme. The enzyme structure is pH-dependent, being a 197-kDa tetramer (subunit of 45 kDa) at pH 10.5, the pH optimum for alcohol oxidation, and a 80.5-kDa dimer at pH 7.5, the pH optimum for aldehyde reduction. The kinetic parameters of the enzyme show that the affinity of the enzyme is greater for the aldehyde substrate and NADPH cofactor, suggesting that the dimeric form of the enzyme is probably the active form in vivo. The ADH of T. hydrothermalis oxidizes a series of primary aliphatic and aromatic alcohols preferentially from C2 to C8 but is also active towards methanol and glycerol and stereospecific for monoterpenes. T. hydrothermalis ADH is the first Thermococcale ADH to be cloned and overproduced in a mesophilic heterologous expression system, and the recombinant and the native forms have identical main characteristics.
Monolithic high-performance three-dimensional coil inductors for wireless communication applications (2002)

An on-chip three-dimensional RF coil inductor is proposed as a key component to implement monolithic wireless transceivers. The device achieves a substantially superior performance compared to conventional spiral inductors, and is amenable to monolithic integration in a standard IC process due to its low thermal budget. Experimental devices fabricated on a standard silicon substrate (10 /spl Omega/-cm) achieve a 2.6 nH inductance with a peak quality-factor (Q) of 13 at 900 MHz. The Q-factor is limited by a lossy adhesive used in the fabrication. In a modified process without adhesive in the coil area, a 4.8 nH inductor achieves a peak Q-value of 30 at 1 GHz. High-Q 8 nH and 13.8 nH inductors have also been fabricated.
Brain Natriuretic Peptide Concentration in Dogs with Heart Disease and Congestive Heart Failure (2003)

Plasma brain natriuretic peptide concentration ([BNP]) is high in humans with cardiac disease and is further increased with congestive heart failure (CHF). The hypotheses of this study were that dogs with moderate to severe mitral regurgitation due to myxomatous mitral valve disease (MVD) would have increased plasma [BNP] compared to normal dogs, that plasma [BNP] would be higher in dogs with CHP, and that plasma [BNP] would predict premature death from cardiovascular disease. The study population consisted of 34 dogs: 9 normal dogs and 25 dogs with MVD. Patients were divided into 4 groups: group 1-10 dogs with moderate to severe MVD and no radiographic evidence of CHF; group II--6 dogs with severe MVD and mild CHF; group III--7 dogs with severe MVD and moderate CHF; and group IV--2 dogs with severe MVD and severe CHF. Diagnostic tests included thoracic radiographs, an echocardiogram, a serum chemistry profile, and the measurement of plasma [BNP] by a canine-specific radioimmunoassay. There was a significant positive correlation between the plasma [BNP] and heart disease/failure groups (P = .0036). Plasma [BNP] increased with progressively increasing severity of MVD and CHE Group I dogs had higher plasma [BNP] than did control dogs (P < .0001), and plasma [BNP] was higher in dogs with CHF (groups II-IV versus group I; P = .012). Plasma [BNP] was also weakly positively correlated with left atrial size (r = 0.43, P = .04). For every 10-pg/mL increase in plasma [BNP], the mortality rate over 4 months' time increased approximately 44%.
Exploring the Correlates of Suicide Attempts Among Individuals With Major Depressive Disorder (2008)

This study contributes to the existing literature on risk factors for suicide attempts in depressed individuals. Identifying specific depressive symptoms and comorbid mental illnesses may improve the clinical assessment of suicide risk in people with major depressive disorder.
Unmodified self antigen triggers human CD8 T cells with stronger tumor reactivity than altered antigen (2008)

Human cancer vaccines are often prepared with altered "analog" or "heteroclitic" antigens that have been optimized for HLA class I binding, resulting in enhanced immunogenicity. Here, we take advantage of CpG oligodeoxynucleotides as powerful vaccine adjuvants and demonstrate the induction of high T cell frequencies in melanoma patients, despite the use of natural (unmodified) tumor antigenic peptide. Compared with vaccination with analog peptide, natural peptide induced T cell frequencies that were approximately twofold lower. However, T cells showed superior tumor reactivity because of (i) increased functional avidity for natural antigen and (ii) enhancement of T cell activation and effector function. Thus, novel vaccine formulations comprising potent immune stimulators may allow to circumvent the need for modified antigens and can induce highly functional T cells with precise antigen specificity.
Bortezomib Provides Effective Therapy for Antibody- and Cell-Mediated Acute Rejection (2008)

Bortezomib therapy: (1) provides effective treatment of AMR and ACR with minimal toxicity and (2) provides sustained reduction in iDSA and non-iDSA levels. Bortezomib represents the first effective antihumoral therapy with activity in humans that targets plasma cells.
Introductory Techniques for 3-D Computer Vision (1998)

From the Publisher:
FEATURES:


Provides a guide to well-tested theory and algorithms including solutions of problems encountered in modern computer vision.
Contains many practical hints highlighted in the book.
Develops two parallel tracks in the presentation, showing how fundamental problems are solved using both intensity and range images, the most popular types of images used today.
Each chapter contains notes on the literature, review questions, numerical exercises, and projects.
Provides an Internet list for accessing links to test images, demos, archives and additional learning material.
Cyclopamine decreased the expression of Sonic Hedgehog and its downstream genes in colon cancer stem cells. (2014)

Overall, these findings show that cyclopamine treatment could down-regulate the expression of stemness markers, shh downstream genes and EMT markers on HCT-116 spheres.