gebhart/patrepeval huggingface dataset:
Network Analyses of Integrated Differentially Expressed Genes in Papillary Thyroid Carcinoma to Identify Characteristic Genes (2019)

Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. Identifying characteristic genes of PTC are of great importance to reveal its potential genetic mechanisms. In this paper, we proposed a framework, as well as a measure named Normalized Centrality Measure (NCM), to identify characteristic genes of PTC. The framework consisted of four steps. First, both up-regulated genes and down-regulated genes, collectively called differentially expressed genes (DEGs), were screened and integrated together from four datasets, that is, GSE3467, GSE3678, GSE33630, and GSE58545; second, an interaction network of DEGs was constructed, where each node represented a gene and each edge represented an interaction between linking nodes; third, both traditional measures and the NCM measure were used to analyze the topological properties of each node in the network. Compared with traditional measures, more genes related to PTC were identified by the NCM measure; fourth, by mining the high-density subgraphs of this network and performing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, several meaningful results were captured, most of which were demonstrated to be associated with PTC. The experimental results proved that this network framework and the NCM measure are useful for identifying more characteristic genes of PTC.
Dynamic retraction of the psoas muscle to expose the lumbar spine using the retroperitoneal approach (2006)

The retroperitoneal surgical approach has gained acceptance as a way to access the ventral aspect of the lumbar spine. Visualization is often limited, however, by the psoas muscle, which lies along the posterolateral aspect of the spine. Improved visualization is often attempted by retracting the muscle from the wound, which generally pulls the muscle laterally from the spine but not posteriorly, which is desirable for a better exposure of the spine, particularly the neural elements. In this paper, the authors describe a simple, atraumatic technique for retraction of the psoas muscle that allows excellent visualization of the spine.
Flavonoid Dimers as Bivalent Modulators for P-Glycoprotein-Based Multidrug Resistance:  Synthetic Apigenin Homodimers Linked with Defined-Length Poly(ethylene glycol) Spacers Increase Drug Retention and Enhance Chemosensitivity in Resistant Cancer Cells (2006)

Much effort has been spent on searching for better P-glycoprotein- (P-gp-) based multidrug resistance (MDR) modulators. Our approach was to target the binding sites of P-gp using dimers of dietary flavonoids. A series of apigenin-based flavonoid dimers, linked by poly(ethylene glycol) chains of various lengths, have been synthesized. These flavonoid dimers modulate drug chemosensitivity and retention in breast and leukemic MDR cells with the optimal number of ethylene glycol units equal to 2-4. Compound 9d bearing four ethylene glycol units increased drug accumulation in drug-resistant cells and enhanced cytotoxicity of paclitaxel, doxorubicin, daunomycin, vincristine, and vinblastine in drug-resistant breast cancer and leukemia cells in vitro, resulting in reduction of IC50 by 5-50 times. This compound also stimulated P-gp's ATPase activity by 3.3-fold. Its modulating activity was presumably by binding to the substrate binding sites of P-gp and disrupting drug efflux.
Architecture and CAD for FPGAs (2004)

Long past are the days when programmable logic (FPGAs and CPLDs) were used only for prototyping and interface logic. Today's modern devices have complicated architectures with close to 200,000 logic elements and flip-flops, dedicated blocks for DSP processing, embedded memories and processors, and support many I/O standards including high-speed serial and now embedded tranceivers. The CAD software to support FPGAs has grown in sophistication and scope to support these larger, more complicated, devices and the size of software groups at FPGA vendors is now larger than all but the biggest EDA companies. Most user designs are now complete systems and go to production as an FPGA.In this tutorial we will talk about recent FPGA and CPLD device architectures and CAD tools, with an emphasis on the interaction between the software and the architecture, and how this has driven recent evolutions and revolutions in PLD architecture. We will discuss the software behind the FPGA - the synthesis, place and route algorithms and CAD flow used to convert a high-level design into a bitstream to program the device. Finally, we will discuss issues in designing hardware for FPGAs, including coding styles to achieve better performance and area, and effective use of dedicated resources on FPGAs.
A new turbo coded QAM scheme with very low decoding complexity for ADSL system (2002)

For ADSL applications, very large constellation sizes are used, which can be as large as 32768QAM. It is a big challenge to design turbo TCM for such a large constellation size while still maintaining low decoding complexity. We propose a new turbo coded QAM scheme with a unique "concatenated Gray mapping" for an ADSL system. This new mapping can not only provide good performance for turbo coded bits but can also efficiently maximize the minimum Euclidean distance of uncoded bits. This new turbo coded QAM scheme not only has as good error correcting performance as the conventional bit-interleaved turbo coded QAM and symbol-interleaved turbo TCM schemes, but also has very low decoding complexity which is only about 17% of the conventional bit-interleaved turbo coded QAM.
Effect of Increased Yeast Alcohol Acetyltransferase Activity on Flavor Profiles of Wine and Distillates (2000)

The distinctive flavor of wine, brandy, and other grape-derived alcoholic beverages is affected by many compounds, including esters produced during alcoholic fermentation. The characteristic fruity odors of the fermentation bouquet are primarily due to a mixture of hexyl acetate, ethyl caproate (apple-like aroma), iso-amyl acetate (banana-like aroma), ethyl caprylate (apple-like aroma), and 2-phenylethyl acetate (fruity, flowery flavor with a honey note). The objective of this study was to investigate the feasibility of improving the aroma of wine and distillates by overexpressing one of the endogenous yeast genes that controls acetate ester production during fermentation. The synthesis of acetate esters by the wine yeast Saccharomyces cerevisiae during fermentation is ascribed to at least three acetyltransferase activities, namely, alcohol acetyltransferase (AAT), ethanol acetyltransferase, and iso-amyl AAT. To investigate the effect of increased AAT activity on the sensory quality of Chenin blanc wines and distillates from Colombar base wines, we have overexpressed the alcohol acetyltransferase gene (ATF1) of S. cerevisiae. The ATF1 gene, located on chromosome XV, was cloned from a widely used commercial wine yeast strain of S. cerevisiae, VIN13, and placed under the control of the constitutive yeast phosphoglycerate kinase gene (PGK1) promoter and terminator. Chromoblot analysis confirmed the integration of the modified copy of ATF1 into the genome of three commercial wine yeast strains (VIN7, VIN13, and WE228). Northern blot analysis indicated constitutive expression of ATF1 at high levels in these yeast transformants. The levels of ethyl acetate, iso-amyl acetate, and 2-phenylethyl acetate increased 3- to 10-fold, 3.8- to 12-fold, and 2- to 10-fold, respectively, depending on the fermentation temperature, cultivar, and yeast strain used. The concentrations of ethyl caprate, ethyl caprylate, and hexyl acetate only showed minor changes, whereas the acetic acid concentration decreased by more than half. These changes in the wine and distillate composition had a pronounced effect on the solvent or chemical aroma (associated with ethyl acetate and iso-amyl acetate) and the herbaceous and heads-associated aromas of the final distillate and the solvent or chemical and fruity or flowery characters of the Chenin blanc wines. This study establishes the concept that the overexpression of acetyltransferase genes such as ATF1 could profoundly affect the flavor profiles of wines and distillates deficient in aroma, thereby paving the way for the production of products maintaining a fruitier character for longer periods after bottling.
Laboratory Evaluation of a Commercial Dielectric Soil Water Sensor (2003)

Development of management strategies for efficient water utilization of crop production requires measurements of changes in soil water content on a dynamic basis. Many of the methods currently used for measuring these changes are destructive, slow, or relatively expensive for large-scale investigations. A commercially available, low-cost, nondestructive soil moisture sensor for measuring changes in soil volumetric water content (VWC) on the basis of changes in the dielectric constant of the soil water was evaluated under laboratory conditions for two soil series (Amarillo fine sandy loam [fine-loamy, mixed, superactive, thermic Aridic Paleustalfs] and Pullman clay loam [fine, mixed, thermic Torretic Paleustolls]) and a potting material across a wide range of water contents. Probes were placed in containers filled with deionized water and soil. Containers with Amarillo fine sandy loam were placed in a programmable temperature chamber and subjected to a series of changes in both temperature and VWC. Containers with Pullman soil and potting material were only subjected to changes in VWC at a constant temperature. Probe output at a constant temperature between air dry and a VWC of 0.25 m3 m−3 was linear for the Pullman soil and potting material and nonlinear for the Amarillo soil. When the Amarillo soil temperature varied between 15.9 and 39.1°C−1 at a constant VWC, probe output changed the equivalent of 0.10 m3 m−3 The temperature sensitivity was 0.5 mV °C−1 for air-dry and about 5 mV °C−1 for wet Amarillo soil. We conclude that probe output is soil specific and, given the nonlinear response to increasing water content on some soils and sensitivity to temperature, will require soil-specific calibration equations.
Pharmacological Treatment of a Diffuse Arteriovenous Malformation of the Upper Extremity in a Child (2009)

A young girl with an arteriovenous malformation involving the right upper extremity developed rapidly progressive bony destruction that did not respond to embolization. Treatment with marimastat, starting at 3 years of age, resulted in rapid resolution of pain and gradual healing of bony destruction, associated with regression of the intraosseous arteriovenous shunts. New arteriovenous shunts with bony destruction developed over the years and responded to an increase in the dose of marimastat. Interruption of therapy resulted in recurrence of pain and formation of new lesions. The patient has been treated in this way for 12 years with no adverse effects from the drug.
Mechanisms of platelet-stimulated colon cancer invasion: role of clusterin and thrombospondin 1 in regulation of the P38MAPK-MMP-9 pathway (2013)

Platelets have been implicated in colon cancer metastasis and prognosis but the underlying molecular mechanisms remain unclear. We evaluated the role of the different mitogen-activated protein kinase (MAPK) pathways in platelet-stimulated matrix metalloproteinase-9 (MMP-9) generation and colon cancer invasion. In addition, proteins released during platelet-tumour cell interactions were studied. For this purpose, interactions of Caco-2 and HT29 cells with platelets were studied using scanning electron microscopy, aggregometry, flow cytometry and cell invasion chambers. Quantitative PCR and zymography were used to study MMP-9 gene expression and activity, respectively, whereas western blot was used to study p38MAPK. Finally, the origin of proteins during platelet-cancer cell interactions was investigated using stable isotope labelling by amino acids in cell culture (SILAC)-based proteomics. We found that platelets promoted p38MAPK phosphorylation and MMP-9 up-regulation in both cell lines, with the subsequent cell-invasion-promoting effects. Pharmacological inhibition of p38MAPK led to a significant down-regulation of MMP-9 and colon cancer cell invasiveness. Also, p38MAPK-small interfering RNA abolished the induction of platelet-stimulated MMP-9. SILAC experiments demonstrated that thrombospondin 1 (TSP1) was released mainly from platelets and clusterin by both platelets and cancer cells. Finally, inhibition of TSP1 and clusterin abolished p38MAPK phosphorylation, MMP-9 activity and platelet-stimulated colon cancer invasion. Our results indicate that platelet-secreted TSP1 and clusterin promote the signal regulation of MMP-9 in platelet-induced colonic cancer invasion via a P38MAPK-regulated pathway. These findings are relevant to the development of therapeutic approaches to preventing and reducing tumour cell metastasis induced by colon adenocarcinoma.
A new insight into the suggestion of a possible antigenic role of a member of the 70 kD heat shock proteins. (1993)

In the present study the cellular distribution of the inducible (hsp72) and constitutive (hsc73) forms of human 70 kD heat shock protein was evaluated. A weak reactivity of the anti-hsp72/hsc73 MoAb was found in the cytoplasm of the unstressed human epidermal cells, while stressed cells showed an enhanced reactivity at the cytoplasmic level and the expression of the molecules on the cell surface. Moreover, the antigenic properties of the two proteins were investigated by sequence analysis. Our findings provided evidence for at least three regions in the hsp72 which can be considered good candidates to represent T-immunogenic antigens. This data as well as the cell surface localization of the hsp72, could suggest an antigenic role of the hsp72.
Joint Launch + One Year Science Review of USML-1 and USMP-1 with the Microgravity Measurement Group (1994)

On September 22-24, 1993, investigators from the First United States Microgravity Laboratory (USML-1) and the First United States Microgravity Payload (USMP-1) Missions met with the Microgravity Measurement Group (MGMG) in Huntsville, Alabama, to discuss science results and the microgravity environments from the respective missions. USML-1 was launched June 1992, and USMP-1 was launched October 1992. This document summarizes from the various investigations, the comprehensive results and highlights, and also serves as a combined mission report for the two missions. USML-1 was the first totally U.S.-sponsored mission dedicated to microgravity research and included 31 investigations in fluid dynamics, crystal growth, combustion, biotechnology, and technology demonstrations supported by 11 facilities. The papers in these proceedings attest to the wealth of information gleaned from the highly successful mission. On the USMP-1 mission, both the MEPHISTO and the Lambda Point experiments exceeded by over 100% their planned science objectives. The mission also marked the first time that acceleration data were down-linked and analyzed in real-time. The meeting, which concentrated on flight results, brought low-gravity investigators, accelerometer designers, and acceleration data analysis experts together. This format facilitated a tremendous amount of information exchange between these varied groups. Several of the experimenters showed results, sane for the very first time, of the effects of residual accelerations on their experiment. The proceedings which are published in two volumes also contain transcriptions of the discussion periods following talks and also submittals from a simultaneous poster session.
Projection Regression Models for Multivariate Imaging Phenotype (2012)

This paper presents a projection regression model (PRM) to assess the relationship between a multivariate phenotype and a set of covariates, such as a genetic marker, age, and gender. In the existing literature, a standard statistical approach to this problem is to fit a multivariate linear model to the multivariate phenotype and then use Hotelling's T(2) to test hypotheses of interest. An alternative approach is to fit a simple linear model and test hypotheses for each individual phenotype and then correct for multiplicity. However, even when the dimension of the multivariate phenotype is relatively small, say 5, such standard approaches can suffer from the issue of low statistical power in detecting the association between the multivariate phenotype and the covariates. The PRM generalizes a statistical method based on the principal component of heritability for association analysis in genetic studies of complex multivariate phenotypes. The key components of the PRM include an estimation procedure for extracting several principal directions of multivariate phenotypes relating to covariates and a test procedure based on wild-bootstrap method for testing the association between the weighted multivariate phenotype and explanatory variables. Simulation studies and an imaging genetic dataset are used to examine the finite sample performance of the PRM.
The intelligent enterprise a new paradigm (2005)

Executive Overview The development and use of technology for services—whether in the “service industries” or in manufacturing—may be the key to future wealth and productivity in advanced industrial countries. Quinn believes that the organization of enterprises and effective strategies will depend more on the development and deployment of intellectual resources than on the management of physical assets. In this article he discusses the concept of disaggregating corporate activities into manageable intellectual clusters—called service activities.
A Quantum-Enhanced Radar Prototype (2019)

We have built and evaluated a prototype quantum radar in the laboratory which operates at microwave frequencies. Because the signal generation process relies on quantum mechanical principles, the system is considered to contain a quantum-enhanced radar transmitter. This transmitter generates a pair of entangled microwave signals and transmits one of them through free space, where the one-way signal is measured using a simple and rudimentary receiver. The type of entanglement used is called two-mode squeezed vacuum (TMSV), so we may call our radar a quantum two-mode squeezing radar (QTMS radar). At the heart of the transmitter is a device called a Josephson parametric amplifier (JPA), which generates the entangled microwave beams; these are then sent through a chain of amplifiers. One beam passes through 0.5 m of free space; the other is measured directly. The two measurement results are correlated in order to distinguish noise from signal. We compare this quantum-enhanced transmitter to a similar one using only conventional components, and find that there is a significant gain when the two systems broadcast signals at approximately the same power.
AZAINDOLES: I. PREPARATION OF 7-AZAINDOLES BY THERMAL INDOLIZATION OF 2-PYRIDYLHYDRAZONES (1966)

The preparation of 2-pyridylhydrazones and their thermal indolization to 2- and 3-monosubstituted and 2,3-disubstituted 7-azaindoles, and to 3,3-disubstituted and 2,3,3-trisubstituted 7-azaindolenhies are described. Attempts to cause thermal indolization of two 2-(5-nitropyridyI)hydrazones were unsuccessful.
Germline Mutations Affecting Gα11 in Hypoparathyroidism (2013)

In a study reported here, genomewide linkage analysis and whole-exome sequencing were used to identify two different heterozygous Gα11 mutations in autosomal-dominant, isolated hypoparathyroidism.
Model-based quantification of the natural diabetes disease progression and lifestyle intervention effects on weight, beta cell function and insulin sensitivity for subjects with impaired glucose tolerance (2017)

Model-based quantification of the natural diabetes disease progression and lifestyle intervention effects on weight, beta cell function and insulin sensitivity for subjects with impaired glucose tolerance
Effects of acid, sodium and its salt counterions on the atomic emission of copper and zinc in plasma pencil (2019)

Copper, zinc and sodium atomic line emissions in the pencil plasma under the influence of easily ionizable elements (EIE), counterions and nitric acid were studied.
Electrofuel Production Using Genetically Engineered Acidithiobacillus Ferrooxidans (2014)

We have been developing an electrofuels platform for the production of fuels and chemicals from dilute CO 2 using electricity. The electricity can come from diverse sources which enables this technology to serve as an alternative means for storing and utilizing renewable energy. The process uses Acidothiobacillus ferrooxidans which are chemolithoautotrophic bacteria that can oxidize iron at low pH. The oxidized iron can be reduced electrochemically and recycled to the bioreactor. We have extensively characterized the growth of the wild type Acidothiobacillus ferrooxidans cells in continuous cultures and we have found that the use of chelators such as citric acid can enable growth at higher pH ranges which can improve growth efficiency, maximum cell yields, and steady state cell densities. We have also developed a platform for genetically modifying the Acidothiobacillus ferrooxidans cells and we have now expressed 4 different exogenous genes in this host organism. This is enabling us to explore new promoters and regulatory sequences to direct carbon flux through new synthetic metabolic pathways. For example, we have introduced a pathway for isobutyric acid production and the results of the characterization of these new cell lines will be presented. We have developed an optimized media formulation for combining the biochemical and electrochemical reactors together, and we have performed extended experiments of the integrated system using wild type cells, allowing us to calculate biomass produced per kWhr of electricity under different operating conditions. We have also build a prototype system with some process control to enable longer term evaluation of the electrofuels platform, and the latest results of this technology will be presented.
Correction: A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato (2015)

There is an error in the second sentence of the sub-
Growth and physiology of loblolly pine in response to long-term resource management: defining growth potential in the southern United States (2008)

Leaf physiology and stem growth were assessed in loblolly pine ( Pinus taeda L.) in response to 10 to 11 years of treatment with weed control (W), weed control plus irrigation (WI), weed control plus irrigation and fertigation (WIF), or weed control plus irrigation, fertigation, and pest control (WIFP) to determine whether increased resource availability can push productivity of loblolly pine closer to its biological growth potential expressed in favorable, exotic environments. Maximum basal area and stem biomass were 41 m 2 ·ha –1 and 172 Mg·ha –1 , respectively, in response to fertigation. Stemwood biomass production was positively and linearly related to basal area. Belowground woody biomass was highest in the WIF and WIFP treatments and averaged 50 Mg·ha –1 , but the W and WI treatments exploited a greater area of soil with low-density coarse roots. Fertigation increased foliar nitrogen concentration and foliage biomass, but treatment had no effect on leaf physiological parameters or growth efficiency. Comparison with growth rates reported for loblolly pine in Hawaii revealed that loblolly pine grown in its native range can produce the high yields observed in exotic environments when stands are below maximum carrying capacity.