gebhart/patrepeval huggingface dataset:
In vitro selection of zinc fingers with altered DNA-binding specificity (1994)

We have used random mutagenesis and phage display to alter the DNA-binding specificity of Zif268, a transcription factor that contains three zinc finger domains. Four residues in the helix of finger 1 of Zif268 that potentially mediate DNA binding were identified from an X-ray structure of the Zif268-DNA complex. A library was constructed in which these residues were randomly mutated and the Zif268 variants were fused to a truncated version of the gene III coat protein on the surface of M13 filamentous phage particles. The phage displayed the mutant proteins in a monovalent fashion and were sorted by repeated binding and elution from affinity matrices containing different DNA sequences. When the matrix contained the natural nine base pair operator sequence 5'-GCG-TGG-GCG-3', native-like zinc fingers were isolated. New finger 1 variants were found by sorting with two different operators in which the singly modified triplets, GTG and TCG, replaced the native finger 1 triplet, GCG. Overall, the selected finger 1 variants contained a preponderance of polar residues at the four sites. Interestingly, the net charge of the four residues in any selected finger never derived more that one unit from neutrality despite the fact that about half the variants contained three or four charged residues over the four sites. Measurements of the dissociation constants for two of these purified finger 1 variants by gel-shift assay showed their specificities to vary over a 10-fold range, with the greatest affinity being for the DNA binding site for which they were sorted.(ABSTRACT TRUNCATED AT 250 WORDS)
Clinicopathological significance of epigenetic inactivation of RASSF1A at 3p21.3 in stage I lung adenocarcinoma. (2002)

These results indicated that epigenetic inactivation of RASSF1A plays an important role in the progression of lung adenocarcinoma, and that RASSF1A hypermethylation appears to be a useful molecular marker for the prognosis of patients with stage I lung adenocarcinoma.
Specific protein phosphorylation in human promyelocytic HL-60 leukemia cells susceptible or resistant to induction of cell differentiation by phorbol-12-myristate-13-acetate. (1985)

The pattern of protein phosphorylation induced by phorbol-12-myristate-13-acetate (PMA) was analyzed by two-dimensional gel electrophoresis in human HL-60 leukemia cells, which are susceptible to induction of cell differentiation by PMA, and in cells from an HL-60 cell variant designated R-94 that are resistant to such an induction. Protein phosphorylation was detected by observing either a rapid acid-directed charge shift of [35S]methionine-labeled protein or an increase in the amount of phosphate label in a 32P-labeled protein. The results indicated that PMA at 10(-7) M causes within 30 min after treatment the phosphorylation of at least ten different proteins in both the HL-60 and R-94 cells. Among these ten phosphorylated proteins, we identified a major cytoplasmic polypeptide (Mr approximately 64,000), a cytoskeletal protein (Mr approximately 56,000), a nonmuscle myosin light chain, and two proteins (Mr approximately 60,000 and 64,000) localized in or around the cell nucleus. Phosphoamino acid analysis of six of the ten phosphoproteins showed that they contain phosphoserine. None of these proteins contained phosphotyrosine or phosphothreonine. The R-94 cell variant was found to be capable of increased protein phosphorylation after PMA treatment; however, the level of phosphate incorporation reached only the level of the untreated HL-60 cells and thus fell far short of the level observed in the HL-60 cells after PMA treatment. It is suggested that the basis for the acquired resistance in R-94 cells towards induction of cell differentiation by PMA is a block in signal transmission involving phosphorylation of nuclear protein(s) following the binding of the inducer PMA to its receptor (protein kinase C).
Tree-dependent component analysis (2002)

We present a generalization of independent component analysis (ICA), where instead of looking for a linear transform that makes the data components independent, we look for a transform that makes the data components well fit by a tree-structured graphical model. Treating the problem as a semiparametric statistical problem, we show that the optimal transform is found by minimizing a contrast function based on mutual information, a function that directly extends the contrast function used for classical ICA. We provide two approximations of this contrast function, one using kernel density estimation, and another using kernel generalized variance. This tree-dependent component analysis framework leads naturally to an efficient general multivariate density estimation technique where only bivariate density estimation needs to be performed. 1
Gefitinib for the treatment of non-small-cell lung cancer (2010)

Gefitinib is expected to have an important impact on management of pretreated and selected chemotherapy-naive patients with advanced NSCLC. In addition, activating EGFR mutations are proven to be of value for prediction of those who will derive most benefit.
Fluorescence In situ hybridization to Y chromosomes in decondensed human sperm nuclei (1990)

Human sperm nuclei were isolated with mixed alkyltrimethylammonium bromide and dithiothreitol (MATAB/DTT) and decondensed by treatments with lithium diiodosalicylate (LIS), sodium chloride, or Tris salts. Concentrations as low as 1 mM LIS induced measurable nuclear swelling compared to 600 mM required for the other two salts. As measured by image analyses, the projected nuclear area increased linearly up to approximately fivefold with LIS concentrations up to 10 mM. Swollen nuclei also maintained the elliptical shapes characteristic of the human sperm head. Expanded sperm nuclei of three men were hybridized with a fluorescently labeled 3.4 kb Y chromosome-specific repetitive DNA probe; 50.1% of the nuclei of each semen sample showed fluorescent labeling over a part of the nucleus indicating presence of the Y chromosome. In comparison, unswollen sperm did not yield reliable hybridization signals. This procedure is suitable for determining the proportion of human sperm with Y chromosomes and can be used to evaluate sperm separation techniques. The availability of probes specific for most human chromosomes suggests that this procedure may find general application in studies of sperm chromosomal constitution.
SPICE Modeling of Self Sustained Operation (SSO) to Program Sub-90nm Floating Body Cells (2009)

A SPICE model that predicts the self sustained operation (SSO) used in programming of a floating body cell (FBC) is presented. This model, which is calibrated to the contributions of the MOS, BJT and impact ionization (II) currents, is demonstrated to accurately predict the static and switching characteristics of the cell. Accurate modeling of device capacitances and leakages allow for quantitative estimation of static and dynamic retention of cells in an array, greatly enhancing the ability to model floating body memories.
Synthesis of Tetrahexahedral Platinum Nanocrystals with High-Index Facets and High Electro-Oxidation Activity (2007)

The shapes of noble metal nanocrystals (NCs) are usually defined by polyhedra that are enclosed by {111} and {100} facets, such as cubes, tetrahedra, and octahedra. Platinum NCs of unusual tetrahexahedral (THH) shape were prepared at high yield by an electrochemical treatment of Pt nanospheres supported on glassy carbon by a square-wave potential. The single-crystal THH NC is enclosed by 24 high-index facets such as {730}, {210}, and/or {520} surfaces that have a large density of atomic steps and dangling bonds. These high-energy surfaces are stable thermally (to 800 degrees C) and chemically and exhibit much enhanced (up to 400%) catalytic activity for equivalent Pt surface areas for electro-oxidation of small organic fuels such as formic acid and ethanol.
Simultaneous transmission of speech and data using an adaptive cancelling technique (1985)

A new scheme to transmit data and analogue speech simultaneously over an analogue transmission line is presented. The transmitter simply combines speech and modulated voice-band data signals together while the receiver uses an adaptive cancelling technique to recover these signals from the received composite. The scheme works for phase-dispersive channels and without bandwidth expansion.
Crystal structures of human antibodies: a detailed and unfinished tapestry of immunoglobulin gene products (2002)

Sequencing of all human immunoglobulin (Ig) germline gene segments has recently been completed. However, our first glimpses of the recombined products of this combinatorial gene system were in the 1970s, in landmark publications, reporting the crystal structures of two human myeloma proteins, the Mcg lambda light chain dimer and the New IgG1(lambda) Fab. Although numerous crystal structures of murine and human antibodies have now been determined, only a relatively small proportion of the human germline genes have had their corresponding protein three-dimensional structures resolved. Therefore, further structural investigations are required before the inherent diversity of the antibody repertoire can be fully appreciated. We discuss the detailed structural information available for human antibodies with regard to their immune functions. Also discussed, is how the structural information is finding application in the 'humanization' of murine antibodies as part of their development as 'biopharmaceuticals' for the treatment of human disease.
StealthDB: a Scalable Encrypted Database with Full SQL Query Support (2017)

Encrypted database systems provide a great method for protecting sensitive data in untrusted infrastructures. These systems are built using either special-purpose cryptographic algorithms that support operations over encrypted data, or by leveraging trusted computing co-processors. Strong cryptographic algorithms (e.g., public-key encryptions, garbled circuits) usually result in high performance overheads, while weaker algorithms (e.g., order-preserving encryption) result in large leakage profiles. On the other hand, some encrypted database systems (e.g., Cipherbase, TrustedDB) leverage non-standard trusted computing devices, and are designed to work around the architectural limitations of the specific devices used. In this work we build StealthDB - an encrypted database system from Intel SGX. Our system can run on any newer generation Intel CPU. StealthDB has a very small trusted computing base, scales to large transactional workloads, requires minor DBMS changes, and provides a relatively strong security guarantees at steady state and during query execution. Our prototype on top of Postgres supports the full TPC-C benchmark with a 30% decrease in the average throughput over an unmodified version of Postgres operating on a 2GB unencrypted dataset.
Lossless embedded compression using multi-mode DPCM & averaging prediction for HEVC-like video codec (2013)

Video encoders and decoders for HEVC-like compression standards require huge external memory bandwidth, which composes a significant portion of the codec power consumption. To reduce the memory bandwidth, this paper presents a new lossless embedded compression algorithm and a high-throughput hardware architecture. Firstly, hybrid spatial-domain prediction is proposed to combine the merits of DPCM scanning and averaging. The prediction is then enhanced with multiple modes to accommodate various image characteristics. Finally, efficient residual regrouping is used to improve the compression performance based on semi-fixed length (SFL) coding. Experimental results show the proposed scheme can reduce data traffic by an average of 57.6%. The average compression ratio is 2.49, improved by at least 13.2% relative to the state-of-the-art algorithms. Although the complexity is increased, by applying several optimizations the hardware cost of designed architecture increases slightly. This work can be implemented with 54.2k gates cost for compressor and 46k gates for decompressor, which can support 4k×2k@120fps decoder.
Up-regulation of small intestinal interleukin-17 immunity in untreated coeliac disease but not in potential coeliac disease or in type 1 diabetes (2011)

Up-regulation of interleukin (IL)-17 in small intestinal mucosa has been reported in coeliac disease (CD) and in peripheral blood in type 1 diabetes (T1D). We explored mucosal IL-17 immunity in different stages of CD, including transglutaminase antibody (TGA)-positive children with potential CD, children with untreated and gluten-free diet-treated CD and in children with T1D. Immunohistochemistry was used for identification of IL-17 and forkhead box protein 3 (FoxP3)-positive cells and quantitative polymerase chain reaction (qPCR) for IL-17, FoxP3, retinoic acid-related orphan receptor (ROR)c and interferon (IFN)-γ transcripts. IL-1β, IL-6 and IL-17 were studied in supernatants from biopsy cultures. Expression of the apoptotic markers BAX and bcl-2 was evaluated in IL-17-stimulated CaCo-2 cells. The mucosal expression of IL-17 and FoxP3 transcripts were elevated in individuals with untreated CD when compared with the TGA-negative reference children, children with potential CD or gluten-free diet-treated children with CD (P < 0·005 for all IL-17 comparisons and P < 0·01 for all FoxP3 comparisons). The numbers of IL-17-positive cells were higher in lamina propria in children with CD than in children with T1D (P < 0·05). In biopsy specimens from patients with untreated CD, enhanced spontaneous secretion of IL-1β, IL-6 and IL-17 was seen. Activation of anti-apoptotic bcl-2 in IL-17-treated CaCo-2 epithelial cells suggests that IL-17 might be involved in mucosal protection. Up-regulation of IL-17 could, however, serve as a biomarker for the development of villous atrophy and active CD.
Evidence for heterogeneous nuclear ribonucleoprotein K overexpression in oral squamous cell carcinoma (2007)

Evidence for heterogeneous nuclear ribonucleoprotein K overexpression in oral squamous cell carcinoma
Instrumented Posterolateral Lumbar Fusion (1998)

Study Design. Prospective case series. Objectives. To assess the results of instrumented posterolateral lumbar fusion, using recognized outcome assessment techniques, to evaluate the correlation between technical and clinical results and the effects of assessment techniques, and to compare the outcome with that of anterior lumbar fusion. Summary of Background Data. Assessments of lumbar spinal fusion results have frequently been published in forms that render direct comparison difficult and thus have not provided optimal assistance in the selection of a preferred method of treatment. Methods. One hundred and thirty-five patients with intractable back pain underwent instrumented posterolateral lumbar spinal fusion performed by a single surgeon. Review of results was undertaken by independent observers, using a recognized outcome assessment measure. Results. A solid bony fusion was obtained in 82% of patients. The method of outcome assessment profoundly affected the results; whereas 65% of patients rated themselves significantly improved by the procedure, only 19% achieved a good or excellent result on the Low Back Outcome Score. Patients undergoing a second procedure did not do well, and "salvage" surgery is not recommended. Compensation status was a significant prognostic factor. Psychological distress at review had a profound effect on the disability score and on patient satisfaction ratings. Overall, the results were inferior to those in a similar series treated by anterior lumbar fusion. Conclusion. It is recommended that in future studies a recognized outcome score be used and that the analysis specifically include compensation status and psychological distress.
The Saccharomyces cerevisiae Hap5p Homolog from Fission Yeast Reveals Two Conserved Domains That Are Essential for Assembly of Heterotetrameric CCAAT-Binding Factor (1997)

The CCAAT-binding factor is an evolutionarily conserved heteromeric transcription factor that binds to CCAAT box-containing upstream activation sites within the promoters of numerous eukaryotic genes. The CCAAT-binding factor from Saccharomyces cerevisiae is a heterotetramer that contains the subunits Hap2p, Hap3p, Hap4p, and Hap5p and that functions in the activation of genes involved in respiratory metabolism. Here we describe the isolation of the cDNA encoding the Schizosaccharomyces pombe homolog of Hap5p, designated php5+. We have shown that Php5p is a subunit of the CCAAT-binding factor in fission yeast and is required for transcription of the S. pombe cyc1+ gene. Analysis of the evolutionarily conserved regions of Hap5p, Php5p, and the mammalian homolog CBF-C revealed two essential domains within Hap5p that are required for DNA binding and transcriptional activation. One is an 87-amino-acid core domain that is conserved among Hap5p, Php5p, and CBF-C and that is required for the assembly of the Hap2p-Hap3p-Hap5p heterotrimer both in vitro and in vivo. A second domain that is essential for the recruitment of Hap4p into the CCAAT-binding complex was identified in Hap5p and Php5p.
Stability of Predictor-Based Dynamic Bandwidth Allocation over EPONs (2007)

We establish a system model to analyze the stability of the predictor-based dynamic bandwidth allocation (PDBA) scheme over Ethernet passive optical networks (EPONs). We prove that an EPON system with PDBA is stable by proper pole placement as the traffic changes dynamically. Our analysis suggests a straightforward framework for designing the DBA algorithm that enables EPONs with stability.
Pointer networks (2015)

We introduce a new neural architecture to learn the conditional probability of an output sequence with elements that are discrete tokens corresponding to positions in an input sequence. Such problems cannot be trivially addressed by existent approaches such as sequence-to-sequence [1] and Neural Turing Machines [2], because the number of target classes in each step of the output depends on the length of the input, which is variable. Problems such as sorting variable sized sequences, and various combinatorial optimization problems belong to this class. Our model solves the problem of variable size output dictionaries using a recently proposed mechanism of neural attention. It differs from the previous attention attempts in that, instead of using attention to blend hidden units of an encoder to a context vector at each decoder step, it uses attention as a pointer to select a member of the input sequence as the output. We call this architecture a Pointer Net (Ptr-Net). We show Ptr-Nets can be used to learn approximate solutions to three challenging geometric problems - finding planar convex hulls, computing Delaunay triangulations, and the planar Travelling Salesman Problem - using training examples alone. Ptr-Nets not only improve over sequence-to-sequence with input attention, but also allow us to generalize to variable size output dictionaries. We show that the learnt models generalize beyond the maximum lengths they were trained on. We hope our results on these tasks will encourage a broader exploration of neural learning for discrete problems.
Electrothermal isotope dilution inductively coupled plasma mass spectrometry method for the determination of sub-ng ml–1levels of lead in human plasma (1994)

An isotope dilution technique coupled with electrothermal volatilization and inductively coupled plasma mass spectrometric detection is reported for the quantitative determination of Pb in human blood plasma with a calculated limit of detection of 16 × 10–15 g. Sample preparation is simple, requiring only addition of concentrated nitric acid and a measured amount of 204Pb spike in solution. Analysis time is typically 2.5 min, the relative standard deviation is <2%(n= 5), calculations require only simple numeric manipulations and the isotopic ratio of the Pb isotopes can be monitored. The Pb concentration of a commercially available dehydrated human plasma was found to be 1.27 ± 0.02 ng ml–1.
Positive regulatory interactions of the HIS4 gene of Saccharomyces cerevisiae. (1984)

The role of cis- and trans-acting elements in the expression of HIS4 has been examined by using HIS4-lacZ fusions in which lacZ expression is dependent upon the HIS4 5' noncoding region. The cis-acting sequences involved in regulation were defined by studying the effects of the wild-type and various deletions and their revertants on regulation via the general control of amino acid biosynthesis. The role of trans-acting genes was analyzed by studying the regulation of the HIS4-lacZ fusions in strains carrying mutations in the GCN (AAS) or GCD (TRA) genes and in strains carrying the GCN genes on high-copy-number plasmids. These studies have led to the following conclusions. (i) HIS4 is positively regulated by the general control. (ii) At least one copy of the 5'TGACTC3' repeat at -136 is required in cis for this regulation. (iii) Both the GCN4 gene and at least one copy of the repeated sequence are required for expression at the repressed level. (iv) The open reading frames in the 5' noncoding region are not required in either cis or trans for the regulation of HIS4.
Implementation of E.U. Water Framework Directive: source assessment of metallic substances at catchment levels (2009)

The E.U. Water Framework Directive (WFD) aims to prevent deterioration of water quality and to phase out or reduce the concentrations of priority substances at catchment levels. It requires changes in water management from a local scale to a river basin scale, and establishes Environmental Quality Standards (EQS) as a guideline for the chemical status of receiving waters. According to the Directive, the standard and the scope of the investigation for water management are more stringent and expanded than in the past, and this change also needs to be applied to restoring the level of metals in water bodies. The aim of this study was to identify anthropogenic emission sources of metallic substances at catchment levels. Potential sources providing substantial amounts of such substances in receiving waters included stormwater, industrial effluents, treated effluents, agricultural drainage, sediments, mining drainage and landfill leachates. Metallic substances have more emission sources than other dangerous substances at catchment levels. Therefore, source assessment for these substances is required to be considered more significantly to restore their chemical status in the context of the WFD. To improve source assessment quality, research on the role of societal and environmental parameters and contribution of each source to the chemical distribution in receiving waters need to be carried out.