gebhart/patrepeval huggingface dataset:
Alterations of expression of Rb, p16INK4A and cyclin D1 in non-small cell lung carcinoma and their clinical significance (1999)

Inactivation of the Rb pathway in non-small cell lung carcinoma (NSCLC) occurs mostly through inactivation of the cyclin-dependent kinase inhibitor p16(INK4A) and/or up-regulation of cyclin D1. In order to assess the frequency and the prognostic value of these abnormalities in NSCLC, immunohistochemical analysis of Rb, p16(INK4), and cyclin D1 has been performed on 168 cases of NSCLC including 77 squamous cell carcinomas, 43 adenocarcinomas, and 48 basaloid carcinomas. The reduced survival rate of basaloid carcinoma (stage I-II) compared with other histological types of NSCLC was confirmed (p = 0.008). Loss of protein expression of Rb and p16(INK4A) was observed in 12 per cent and 58 per cent of NSCLC cases respectively and cyclin D1 overexpression in 43 per cent. There was an inverse correlation between Rb and p16 expression ( p < 0.0001) and a direct correlation between Rb and cyclin D1 expression ( p = 0.0007). In univariate analysis, Rb-negative adenocarcinomas at stages I-II had a significantly shorter survival than Rb-positive cases ( p = 0.04) and stages I-II p16-positive cases had a shorter survival than p16-negative cases ( p = 0.02), which was more significant in basaloid carcinoma ( p = 0.003). p16 status retained its influence on survival in multivariate analysis at stage I-II for all cases ( p = 0.01) and for basaloid carcinoma ( p = 0.005). Cyclin D1 overexpression did not influence survival. Combined Rb/p16/cyclin D1 phenotypes in univariate analysis showed a shorter survival for Rb-negative/p16-positive/cyclin D1-negative tumours ( p = 0.002). These results, linked to previous data, indicate that the Rb pathway of G1 arrest is initially disrupted in the vast majority of NSCLCs (83 per cent), but could not confirm an unfavourable role for each individual event (p16(INK4A) loss or cyclin D1 up-regulation) in prognosis.
Transcriptional Activation of Inflammatory Genes: Mechanistic Insight into Selectivity and Diversity (2015)

Acute inflammation, an integral part of host defence and immunity, is a highly conserved cellular response to pathogens and other harmful stimuli. An inflammatory stimulation triggers transcriptional activation of selective pro-inflammatory genes that carry out specific functions such as anti-microbial activity or tissue healing. Based on the nature of inflammatory stimuli, an extensive exploitation of selective transcriptional activations of pro-inflammatory genes is performed by the host to ensure a defined inflammatory response. Inflammatory signal transductions are initiated by the recognition of inflammatory stimuli by transmembrane receptors, followed by the transmission of the signals to the nucleus for differential gene activations. The differential transcriptional activation of pro-inflammatory genes is precisely controlled by the selective binding of transcription factors to the promoters of these genes. Among a number of transcription factors identified to date, NF-κB still remains the most prominent and studied factor for its diverse range of selective transcriptional activities. Differential transcriptional activities of NF-κB are dictated by post-translational modifications, specificities in dimer formation, and variability in activation kinetics. Apart from the differential functions of transcription factors, the transcriptional activation of selective pro-inflammatory genes is also governed by chromatin structures, epigenetic markers, and other regulators as the field is continuously expanding.
Stochastic database cracking (2012)

Modern business applications and scientific databases call for inherently dynamic data storage environments. Such environments are characterized by two challenging features: (a) they have little idle system time to devote on physical design; and (b) there is little, if any, a priori workload knowledge, while the query and data workload keeps changing dynamically. In such environments, traditional approaches to index building and maintenance cannot apply. Database cracking has been proposed as a solution that allows on-the-fly physical data reorganization, as a collateral effect of query processing. Cracking aims to continuously and automatically adapt indexes to the workload at hand, without human intervention. Indexes are built incrementally, adaptively, and on demand. Nevertheless, as we show, existing adaptive indexing methods fail to deliver workload-robustness ; they perform much better with random workloads than with others. This frailty derives from the inelasticity with which these approaches interpret each query as a hint on how data should be stored. Current cracking schemes blindly reorganize the data within each query's range, even if that results into successive expensive operations with minimal indexing benefit. In this paper, we introduce stochastic cracking , a significantly more resilient approach to adaptive indexing. Stochastic cracking also uses each query as a hint on how to reorganize data, but not blindly so; it gains resilience and avoids performance bottlenecks by deliberately applying certain arbitrary choices in its decision-making. Thereby, we bring adaptive indexing forward to a mature formulation that confers the workload-robustness previous approaches lacked. Our extensive experimental study verifies that stochastic cracking maintains the desired properties of original database cracking while at the same time it performs well with diverse realistic workloads.
DNAzyme-mediated recovery of small recombinant RNAs from a 5S rRNA-derived chimera expressed in Escherichia coli (2010)

The feasibility of a fermentation-based approach for manufacturing large quantities of small RNAs in vivo using a "5S rRNA scaffold" strategy is demonstrated. The approach provides a route towards an economical method for the large-scale production of small RNAs including shRNAs, siRNAs and aptamers for use in clinical and biomedical research.
Sequence of the intron/exon junctions of the coding region of the human androgen receptor gene and identification of a point mutation in a family with complete androgen insensitivity. (1989)

Androgens act through a receptor protein (AR) to mediate sex differentiation and development of the male phenotype. We have isolated the eight exons in the amino acid coding region of the AR gene from a human X chromosome library. Nucleotide sequences of the AR gene intron/exon boundaries were determined for use in designing synthetic oligonucleotide primers to bracket coding exons for amplification by the polymerase chain reaction. Genomic DNA was amplified from 46,XY phenotypic female siblings with complete androgen insensitivity syndrome. AR binding affinity for dihydrotestosterone in the affected siblings was lower than in normal males, but the binding capacity was normal. Sequence analysis of amplified exons demonstrated within the AR steroid-binding domain (exon G) a single guanine to adenine mutation, resulting in replacement of valine with methionine at amino acid residue 866. As expected, the carrier mother had both normal and mutant AR genes. Thus, a single point mutation in the steroid-binding domain of the AR gene correlated with the expression of an AR protein ineffective in stimulating male sexual development.
Glycosylation site prediction using ensembles of Support Vector Machine classifiers (2007)

Ensembles of Support Vector Machine classifiers offer an accurate and reliable approach to automated identification of putative glycosylation sites in glycoprotein sequences.
Multichannel structures made from micrometre-thick plastic foils (1999)

A method to fabricate multichannel structures based on micrometre-thick plastic foil is described. In a reel-to-reel process, metallized plastic foil is patterned by laser ablation and stacked. Foil-to-foil joints are established by heating the foil stack under pressure. Expansion of the foil stack perpendicular to the plane of the foils yields a multichannel structure. We have realized structures with many thousands of channels with a diameter of a few hundred micrometres. The multichannel structures can serve for mechanical, optical, electrical as well as chemical functions.
Two-Dimensional Random Arrays for Real Time Volumetric Imaging (1994)

Two-dimensional arrays are necessary for a variety of ultrasonic imaging techniques, including elevation focusing, 2-D phase aberration correction, and real time volumetric imaging. In order to reduce system cost and complexity, sparse 2-D arrays have been considered with element geometries selected ad hoc, by algorithm, or by random process. Two random sparse array geometries and a sparse array with a Mills cross receive pattern were simulated and compared to a fully sampled aperture with the same overall dimensions. The sparse arrays were designed to the constraints of the Duke University real time volumetric imaging system, which employs a wide transmit beam and receive mode parallel processing to increase image frame rate. Depth-of-field comparisons were made from simulated on-axis and off-axis beamplots at ranges from 30 to 160 mm for both coaxial and offset transmit and receive beams. A random array with Gaussian distribution of transmitters and uniform distribution of receivers was found to have better resolution and depth-of-field than both a Mills cross array and a random array with uniform distribution of both transmit and receive elements. The Gaussian random array was constructed and experimental system response measurements were made at several ranges. Comparisons of B-scan images of a tissue mimicking phantom show improvement in resolution and depth-of-field consistent with simulation results.
Growth stimulus-mediated differential translocation of casein kinase 2 to the nuclear matrix. Evidence based on androgen action in the prostate. (1994)

Recently, we documented that a significant amount of nuclear casein kinase 2 (CK2) (a ubiquitous multipotential messenger-independent serinekhreonine protein kinase) is associated with the nuclear matrix (NM), where it may be involved in the phosphorylation of several intrinsic proteins (Tawfic, S., and Ahmed, K. (1994) J.
Drugs Five Years Later (1974)

Dextran 40 has been approved for use as a volume expander for shock of any cause and as a pump primer for extracorporeal circulation. Since its approval, no critical studies that clearly show its superiority over other solutions have been published. It is being used increasingly for prophylactic antithrombotic therapy in surgical patients who are at high risk of thromboembolic complications, and comparative studies show it to be as effective as warfarin for this purpose. But its dangerous and potentially fatal side effects should be known to the potential user. These include anaphylaxis and other allergic reactions, hypervolemia, renal failure, and a bleeding diathesis. These side effects may be overlooked because they can be easily ascribed to the condition for which the drug is being given. Because other equally effective drugs are available for all the approved uses of dextran 40, we cannot recommend this drug until we have comparative data that establish it as being at least as safe and effective as the alternatives.
The solubilization and biological activities of<i>Aspergillus</i>Î²-(1â3)-d-glucan (2004)

We have recently demonstrated that the cell wall beta-glucan of Candida albicans could be solubilized by sodium hypochlorite, followed by dimethylsulfoxide-extraction (NaClO-DMSO method). In this study, applying this method to Aspergillus spp., we prepared mycelial cell wall beta-glucan and examined its physical properties and immunotoxicological activity. The acetone-dried mycelia of Aspergillus spp. were oxidized by the NaClO-DMSO method. An analysis of (13)C NMR spectra revealed the preparations to be composed of alpha-(1 --> 3) and beta-(1 --> 3)-D-glucan. Also, the proportion of alpha-(1 --> 3) and beta-(1 --> 3)-D-glucan varied. Furthermore, a solubilized Aspergillus beta-glucan (ASBG) was prepared from OX-Asp by urea-autoclave treatment. ASBG showed limulus activity similar to Candida solubilized beta-glucan (CSBG), and there was little difference in the activity of ASBG between various Aspergillus spp. ASBG affected the production of IL-8 by human peripheral blood mononuclear cells (PBMC). ASBG should be useful for analyzing the clinical role of beta-glucan.
Analysis of the coupling characteristics of a tapered three-guide coupled system (1990)

Optical coupling characteristics of a three-guide coupled system are discussed. Application of a taper-formed waveguide in the system is proposed. A theoretical analysis of the tapered waveguide system is presented by applying a modified coupled-mode theory, with the tapered guide being approximated by successive stepped small guide segments. Based on numerical examinations, particular coupling characteristics of the tapered guide system are demonstrated. An application of the tapered three-guide coupled system in a type of optical isolator is proposed. The main working principles of the isolator are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
GSK-3.BETA., a Therapeutic Target for Cardiomyocyte Protection (2009)

Glycogen synthase kinase-3beta (GSK-3beta) is a multifunctional Ser/Thr kinase that plays important roles in necrosis and apoptosis of cardiomyocytes. A major mechanism of cell necrosis is the opening of the mitochondrial permeability transition pore (mPTP), which consists of multiple protein subunits, including adenine nucleotide translocase (ANT). The threshold for mPTP opening is elevated by phosphorylation of GSK-3beta at Ser9, which reduces activity of this kinase. How inactivation of GSK-3beta suppresses mPTP opening has not been fully understood, but evidence to date suggests that preservation of hexokinase-II in the mPTP complex, inhibition of cyclophilin-D-ANT binding, inhibition of p53 and inhibition of ANT into the mitochondria are contributory. GSK-3beta phosphorylation is a step to which multiple protective signaling pathways converge, and thus GSK-3beta phosphorylation is crucial in cardioprotection of a variety of interventions against ischemia/reperfusion injury. Apoptosis of cardiomyocytes by pressure overload or ischemia/reperfusion is also suppressed by inactivation of GSK-3beta, in which reduced phosphorylation of p53, heat shock factor-1 and myeloid cell leukemia sequence-1 and inhibition of Bax translocation might be involved. Considering predominant roles of GSK-3beta in cardiomyocyte death, manipulation of this protein kinase is a promising strategy for myocardial protection in coronary artery disease and heart failure.
Beyond Intraocular Pressure: Neuroprotective Strategies for Future Glaucoma Therapy (2001)

Glaucoma is a complex disease with a number of risk factors and mechanisms leading to ganglion cell death. Future glaucoma therapy will likely include neuroprotectants that could be used as an adjunct therapy with other medications designed to lessen the initial insult (i.e., intraocular pressure-lowering compounds). As the word neuroprotection becomes more popular, care must be taken in evaluating the research literature for clinically effective therapies.
Genetic control of the frequency of hematopoietic stem cells in mice: mapping of a candidate locus to chromosome 1. (1996)

The genetic elements that govern the differentiation and proliferation of hematopoietic stem cells remain to be defined. We describe here marked strain-specific differences in the frequency of long-term culture-initiating cells (LTC-IC) in the bone marrow of different strains of mice. Mice of C57Bl/6 background showed the lowest levels of stem cells in marrow, averaging 2.4 +/- .06 LTC-IC/10(5) cells, BALB/c is intermediate (9.1 +/- 4.2/10(5) cells), and DBA/2 mice contained a 11-fold higher frequency of LTC-IC (28.1 +/- 16.5/10(5) cells) than C57Bl/6 mice. The genetic factors affecting the size of the stem cell pool were analyzed in the C57Bl/6 X DBA/2 recombinant inbred strains; LTC-IC frequencies ranged widely, indicating that stem cell frequencies are controlled by multiple genes. Quantitative trait linkage analysis suggested that two loci that have major quantitative effects are located on chromosome 1 near Adprp and Acrg, respectively. The mapping of the locus near Adprp was confirmed by finding an elevated stem cell frequency in B6.C-H25, a C57Bl/6 congenic strain that carries a portion of chromosome 1 derived from BALB/c mice. We have named this gene Scfr1 (stem cell frequency regulator 1). The allelic forms of this gene may be an important predictor of stem cell number and thus would be useful for evaluating cell sources in clinical stem cell transplantation.
Clinicopathologic Significance and Prognostic Value of Chromosomal Imbalances in Diffuse Large B-Cell Lymphomas (2004)

These results suggest that DLBCLs have a characteristic pattern of genomic alterations; 18q gains or amplifications and 17p losses are associated with particular clinicopathological features and aggressive clinical behavior. Additional studies are needed to confirm these observations in larger series of patients.
Motility and Chemotaxis in <i>Agrobacterium tumefaciens</i> Surface Attachment and Biofilm Formation (2007)

Bacterial motility mechanisms, including swimming, swarming, and twitching, are known to have important roles in biofilm formation, including colonization and the subsequent expansion into mature structured surface communities. Directed motility requires chemotaxis functions that are conserved among many bacterial species. The biofilm-forming plant pathogen Agrobacterium tumefaciens drives swimming motility by utilizing a small group of flagella localized to a single pole or the subpolar region of the cell. There is no evidence for twitching or swarming motility in A. tumefaciens. Site-specific deletion mutations that resulted in either aflagellate, flagellated but nonmotile, or flagellated but nonchemotactic A. tumefaciens derivatives were examined for biofilm formation under static and flowing conditions. Nonmotile mutants were significantly deficient in biofilm formation under static conditions. Under flowing conditions, however, the aflagellate mutant rapidly formed aberrantly dense, tall biofilms. In contrast, a nonmotile mutant with unpowered flagella was clearly debilitated for biofilm formation relative to the wild type. A nontumbling chemotaxis mutant was only weakly affected with regard to biofilm formation under nonflowing conditions but was notably compromised in flow, generating less adherent biomass than the wild type, with a more dispersed cellular arrangement. Extragenic suppressor mutants of the chemotaxis-impaired, straight-swimming phenotype were readily isolated from motility agar plates. These mutants regained tumbling at a frequency similar to that of the wild type. Despite this phenotype, biofilm formation by the suppressor mutants in static cultures was significantly deficient. Under flowing conditions, a representative suppressor mutant manifested a phenotype similar to yet distinct from that of its nonchemotactic parent.
Learning task structure from video examples for workflow tracking and authoring (2012)

We present a robust real-time capable and simple framework for segmenting video sequences and live-streams of manual workflows into the comprising single tasks. Using classifiers trained on these segments we can follow a user that is performing the workflow in real-time as well as learn task variants from additional video examples. Our proposed method neither requires object detection nor high-level features. Instead we propose a novel measure derived from image distance that evaluates image properties jointly without prior segmentation. Our method can cope with repetitive and free-hand activities and the results are in many cases comparable or equal to manual task segmentation. One important application of our method is the automatic creation of a step-by-step task documentation from a video demonstration. The entire process to automatically create a fully functional augmented reality manual will be explained in detail and results are shown.
A new human B-lymphocyte surface antigen (BL 2) detectable by a hybridoma monoclonal antibody: distribution on benign and malignant lymphoid cells. (1983)

A hybridoma-derived monoclonal antibody, produced by immunization with the Burkitt's tumor-derived B-lymphoblastoid cell line, B35M, was previously shown to detect a 68,000 dalton surface membrane protein, BL2, on the surface of peripheral blood B cells, which is absent from thymocytes, T cells, and granulocytes. In this study, we investigated the expression and distribution of BL2 on benign and malignant human lymphoid cells. Indirect immunofluorescent assay with this monoclonal antibody demonstrated that BL2 is expressed by cells within the fetal liver and by a variable proportion of lymph node, tonsil, and spleen B cells, but not by T cells. The neoplastic cells isolated from 18 T-cell malignancies were BL2- . BL2 was was heterogeneously expressed by a variable proportion of the malignant cells in 29/32 cases of B-chronic lymphocytic leukemia and 33/38 cases of B-cell lymphomas, but appeared to be lost in the terminal stages of B-cell differentiation, as myeloma plasma cells were BL2- . BL2 expression was not limited to B cells of a particular surface immunoglobulin isotype. Immunofluorescent staining for BL2 in cryostat tissue sections demonstrated that the majority, but not all, germinal center and interfollicular Ia+ (non-T) cells are BL2+. These findings suggest that BL2 is a B-cell lineage-specific differentiation marker that may be useful in the study of B-cell ontogeny and in defining subgroups of the B-cell malignancies.
Clock skew optimization for ground bounce control (1996)

High speed synchronous digital systems require large switching currents to facilitate rapid signal transitions. These large currents create voltage drops on the power distribution network and necessitate expensive chip packaging with a large number of supply pins. In this paper we propose a novel technique to reduce the dynamic transient current drawn from the supply pins. Our approach is based on sub-dividing the synchronous clocking into multiple sub-clocks with relative skew. This spreads the computation across the entire clock cycle instead of largely occurring at the beginning. Timing constraints must also be obeyed, so that no races or timing errors are introduced. We propose an exact algorithm based on integer linear programming to solve this problem. We have used our method in the design of a 5 GHz ECL encoder chip to achieve a factor of two reduction in ground bounce, as shown by HSPICE simulations. We also obtained order-of-magnitude improvements in ground bounce on benchmarks laid our in submicron CMOS technology. The approach potentially leads to significant reductions in packaging costs.