gebhart/patrepeval huggingface dataset:
<scp>PTEN</scp> expression is consistent in colorectal cancer primaries and metastases and associates with patient survival (2013)

Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) negatively regulates the phosphoinositide-3-kinase (PI3K) signaling pathway. In colorectal cancer (CRC), observed frequencies of loss of PTEN expression, concordant expression in primary tumors and metastases, and the association of PTEN status with outcome vary markedly by detection method. We determined the degree to which PTEN expression is consistent in 70 matched human CRC primaries and liver metastases using a validated immunohistochemistry assay. We found loss of PTEN expression in 12.3% of assessable CRC primaries and 10.3% of assessable liver metastases. PTEN expression (positive or negative) was concordant in 98% of matched colorectal primaries and liver metastases. Next we related PTEN status to mutations in RAS and PI3K pathway genes (KRAS, NRAS, BRAF , and PIK3CA) and to overall survival (OS). PTEN expression was not significantly associated with the presence or absence of mutations in RAS or PI3K pathway genes. The median OS of patients whose tumors did not express PTEN was 9 months, compared to 49 months for patients whose tumors did express PTEN (HR = 6.25, 95% confidence intervals (CI) (1.98, 15.42), P = 0.0017). The association of absent PTEN expression with increased risk of death remained significant in multivariate analysis (HR = 6.31, 95% CI (2.03, 17.93), P = 0.0023). In summary, PTEN expression was consistent in matched CRC primaries and in liver metastases. Therefore, future investigations of PTEN in metastatic CRC can use primary tumor tissue. In patients with liver-only metastases, loss of PTEN expression predicted poor OS.
Computational methods for the detection of cis-regulatory modules (2009)

Metazoan transcription regulation occurs through the concerted action of multiple transcription factors that bind co-operatively to cis-regulatory modules (CRMs). The annotation of these key regulators of transcription is lagging far behind the annotation of the transcriptome itself. Here, we give an overview of existing computational methods to detect these CRMs in metazoan genomes. We subdivide these methods into three classes: CRM scanners screen sequences for CRMs based on predefined models that often consist of multiple position weight matrices (PWMs). CRM builders construct models of similar CRMs controlling a set of co-regulated or co-expressed genes. CRM genome screeners screen sequences or complete genomes for CRMs as homotypic or heterotypic clusters of binding sites for any combination of transcription factors. We believe that CRM scanners are currently the most advanced methods, although their applicability is limited. Finally, we argue that CRM builders that make use of PWM libraries will benefit greatly from future advances and will prove to be most instrumental for the annotation of regulatory regions in metazoan genomes.
Dynamic Representation of Multivariate Time Series Data (1984)

Abstract In this article we describe a procedure for representing multivariate time series data by means of interactive, computer-generated dynamic imagery with computer-music accompaniment. This innovation conveys the novel insights that dynamic imagery can provide; yet, the imagery is developed from principles that make the representation useful when examined either statically or dynamically. This is because the development of the dynamic representation is guided by the same perceptual and technical principles used in making a motion picture. The particular implementation we describe is evaluated by a formal psychophysics experiment in which we measure the threshold correlation that can be perceived in our dynamic representation, and in each of three different types of graphical portrayals.
A high performance bus and cache controller for PowerPC multiprocessing systems (2002)

The PowerPC 620 microprocessor introduces a new integrated secondary cache controller and system bus interface. The secondary cache interface is 128 bits wide, supports L2 sizes from 1 MB to 128 MB, is ECC protected, can transfer 2.0 GB/sec at 133 MHz and supports an optional co-processor mode. The 620 bus is optimized for server-class systems requiring significant multiprocessing capability and supports the 64-bit PowerPC architecture with a 40-bit physical address bus and a separate 128-bit data bus. Address transfer rates of up to 33 M Addresses/sec at 66 MHz are achieved by pipelining the address snoop response with the address bus. The address and data buses are explicitly tagged allowing data transfers to be reordered with respect to the addresses. The data bus can transfer up to 1.0 GB/sec at 66 MHz. The bus protocol and the integrated L2 controller presented support the snoop-based MESI cache coherency protocol and direct cache-to-cache data transfers.
Patients Diagnosed With Diabetes Are at Increased Risk for Asthma, Chronic Obstructive Pulmonary Disease, Pulmonary Fibrosis, and Pneumonia but Not Lung Cancer (2009)

Individuals with diabetes are at increased risk of several pulmonary conditions (asthma, COPD, fibrosis, and pneumonia) but not lung cancer. This increased risk may be a consequence of declining lung function in patients with diabetes.
A spectroscopic survey of naturally-occurring vacancy-related colour centres in diamond (1982)

A spectroscopic survey of a large number of natural brown and yellow diamonds shows that the H3 centre (a vacancy plus an A-aggregate of nitrogen) is observed in absorption quite frequently in brown diamonds and occasionally in yellow samples. The H4 centre (a vacancy plus a B-aggregate of nitrogen) occurs much less frequently, even in diamonds containing predominantly B-nitrogen, and the relationship between the H3:H4 ratio and the A:B ratio observed for diamonds irradiated and annealed at approximately 800 degrees C in the laboratory generally does not apply to naturally coloured crystals. However, annealing a laboratory-irradiated diamond at 1500 degrees C resulted in an H3:H4 ratio more nearly like that observed in natural specimens, and produced an absorption line seen previously only in natural diamonds. It is believed that this is due to partial fragmentation of the H4 centre, and that the process goes to completion at the more modest temperatures experienced over a much longer time period by natural diamonds. Those natural processes which might be responsible for the production of vacancy-related colour centres are considered, and it is concluded that plastic deformation, or gamma -ray irradiation from a localised concentration of uranium, are possible candidates.
Canonical prayer (<i>ṣalāt</i>) and supplication (<i>duʿāʾ</i>) (2013)

What did the word ṣalāt mean in Arabic before the revelation of the Qurʾān, and was it in origin Arabic at all? Was the ritual (or its components) already familiar in pre-Islamic Arabia? What might it have meant to contemporary observers? As noted by Gerhard Böwering, the Qurʾān appears to assume that the word requires no explanation. The Qurʾān also gives ṣalāt an ancient pedigree, using the word to refer to the forms of prayer that were performed and commanded by previous prophets. Prayer – including physical prostration – is represented as a prophetic heritage going back to the beginnings of the human race. Verses 19:58–9 associate prostration and ṣalāt with the descendants of Adam, Noah, and Abraham. In some passages it is particularly associated with the line of Abraham, who beseeches in verse 14:40, "O Lord! Make me one who establishes regular prayer (yuqīm al-ṣalāt), and also [raise such] among my offspring." Ishmael is described (verse 19:55) as one "who used to enjoin on his people prayer and charity," and Isaac and Jacob were inspired by God "to do good deeds, to establish regular prayers, and to practice regular charity" (21:73). Ritual prayer is also associated with the Jewish and Christian communities; verse 98:5 affirms of the People of the Book, "They have been commanded no more than this: To worship God, offering Him sincere devotion, being true [in faith]; to establish regular prayer, and to practice regular charity." Despite the strong thematic connection between ṣalāt and Abrahamic monotheism, however, in the Qurʾān ritual prayer is not associated exclusively with Abrahamic figures; in verse 31:17 the Arabian sage Luqmān counsels his son to "establish regular prayer, enjoin what is just, and forbid what is wrong."
MICRONEEDLE-ASSISTED TRANSDERMAL DELIVERY OF NALTREXONE SPECIES: IN VITRO PERMEATION AND IN VIVO PHARMACOKINETIC STUDIES (2011)

Complete hemispherotomy leads to a lateralized whole-brain organization, with the remaining hemisphere claiming most of the brain's energetic reserves supported by subcortical structures. Our results further underline the contribution of nonneuronal vascular signals on contralateral connectivity, shedding light on the nature of network organization in the isolated tissue. The disconnected hemisphere is characterized by a level of consciousness which is necessary but insufficient for conscious processing, paving the way for more specific inquiries about its role in awareness in the absence of behavioral output.
Understanding How People use Search to Support their Everyday Creative Tasks (2019)

Creativity is an essential part of people's daily life and work across a range of everyday tasks. However, little prior work has explored how people use search engines and information resources as part of their creative processes, and how systems might better support users working on creative tasks. In this paper, we conducted an online survey with 175 participants to explore how people use search engines and online resources (e.g., images, videos, and social media) to support their creative tasks. Our participants reported information seeking to support a broad range of everyday creativity including tasks in arts, writing, crafts, and technical projects. Our findings show that participants' tasks included multiple stages of creative processes (e.g., creating ideas, combining ideas, executing plans) and that participants reported using search engines along with other tools (such as images and videos) to facilitate their creative process. By using Bayesian random effects regression models, we found that different stages of the creative process influence participants' use of tools. For example, for tasks that involved creating ideas, participants were more likely to use images and social sites, and when needing to put ideas into practice they were more likely to use videos. We also found differences in users' satisfaction with using the tools for different creative stages. Based on our findings, we provide recommendations for supporting users' information seeking needs during creative tasks.
Smart management system for digital photographs using temporal and spatial features with EXIF metadata (2007)

Due to the popular use of digital cameras and the growing capacity of storage, managing a large collection of digital photos is a burdensome job for the average customers. One distinct feature of current digital photos is that image contents are embedded with metadata EXIF, which varies among digital camera manufactures. Since these metadata have abundant information about the photographing environment, it can provide useful hints for managing photos. Most previous digital photo clustering methods were mainly dependent on the timestamp of the photo taken, so users can not always find the intended photos especially if adjacent pictures have very small time gap. The timing gap of digital photos is not a sufficient and reliable clustering condition to satisfy the average customer. In this paper, we propose a novel parameterized clustering system for digital photos by exploiting temporal (time gap between adjacent photos) and spatial features (content similarity on color pixel domain), so each user can adjust his or her own clustering parameters according to the preference between event (temporal condition) and people (spatial content condition). In order to compute the spatial similarity, we applied the adapted color weight function depending on the distribution of a quantified color set. This enabled us not to use the dominant background color in image similarity matching. We also propose a new content matching algorithm called the block matching-expansion procedure. In this experiment, we compared the result with Cooper's most recent work. Using a set of testing 54 photos, we obtained 4 different clusterings from 4 average photographers' manual work. For each manual clustering, we could find a near optimal parameter (balancing temporal and spatial clustering), which were all superior to Cooper's clustering using temporal condition only.
Double-stranded RNA induces mRNA degradation in<i>Trypanosoma</i><i>brucei</i> (1998)

Double-stranded RNA (dsRNA) recently has been shown to give rise to genetic interference in Caenorhabditis elegans and also is likely to be the basis for phenotypic cosuppression in plants in certain instances. While constructing a plasmid vector for transfection of trypanosome cells, we serendipitously discovered that in vivo expression of dsRNA of the alpha-tubulin mRNA 5' untranslated region (5' UTR) led to multinucleated cells with striking morphological alterations and a specific block of cytokinesis. Transfection of synthetic alpha-tubulin 5' UTR dsRNA, but not of either strand individually, caused the same phenotype. On dsRNA transfection, tubulin mRNA, but not the corresponding pre-mRNA, was rapidly and specifically degraded, leading to a deficit of alpha-tubulin synthesis. The transfected cells were no longer capable of carrying out cytokinesis and eventually died. Analysis of cytoskeletal structures from these trypanosomes revealed defects in the microtubules of the flagellar axoneme and of the flagellar attachment zone, a complex cortical structure that we propose is essential for establishing the path of the cleavage furrow at cytokinesis. Last, dsRNA-mediated mRNA degradation is not restricted to alpha-tubulin mRNA but can be applied to other cellular mRNAs, thus establishing a powerful tool to genetically manipulate these important protozoan parasites.
Biohydrogen Production from Sugar Manufacturing Wastewater and Analysis of Microbial Diversity (2012)

Biohydrogen production and analysis of microbial community were attempted from the sugar manufacturing wastewater with anaerobic fermentation process. Addtion of nutrients () into sugar manufacturing wastewater stimulates hydrogen production from 9.53 to COD. Butyric acid, acetic acid, lactic acid, and propionic acid were detected in the sample of the anaerobic fermentation process. Butyric acid/Acetic acid(B/A) ratio was increased 0.50 to 0.92 according to the nutrients addtion into the wastewater. Microbial community was analyzed as Clostridium sp. in the phylum of Firmicutes and Klebsiella sp., Erwinia sp., and enterobacter sp. of the class of -Proteobacteria. As the improvement of hydrogen production, Erwinia sp. was decreased and Klebsiella sp. was increased.
Application of AFLP technique in genetics and breeding of animal (2004)

The principle, technological process, technologic key and optimized measure of AFLP technique are briefly described in this paper. Its feature, research and perspective of AFLP technique in genetics and breeding of animal are also introduced.
Using a new GA-based multiobjective optimization technique for the design of robot arms (1998)

This paper presents a hybrid approach to optimize the counterweight balancing of a robot arm. A new technique that combines an artificial intelligence technique called the genetic algorithm (GA) and the weighted min-max multiobjective optimization method is proposed. These techniques are included in a system developed by the authors, called MOSES, which is intended to be used as a tool for engineering design optimization. The results presented here show how the new proposed technique can get better trade-off solutions and a more accurate Pareto front for this highly non-convex problem using an ad-hoc floating point representation and traditional genetic operators. Finally, a methodology to compute the ideal vector using a genetic algorithm is presented. It is shown how with a very simple dynamic approach to adjust the parameters of the GA, it is possible to obtain better results than those previously reported in the literature for this problem.
The 'miss rate' for the analysis of gene expression data (2004)

Multiple testing issues are important in gene expression studies, where typically thousands of genes are compared over two or more experimental conditions. The false discovery rate has become a popular measure in this setting. Here we discuss a complementary measure, the 'miss rate', and show how to estimate it in practice.
Two mask step polysilicon TFT technology for flat panel displays (1988)

Polysilicon thin film transistors (TFTs) have been fabricated on borosilicate glass with a new, short process. In this process, indium tin oxide (ITO) is used to form the source and drain of the TFTs. The electrical characteristics of these TFTs make them suitable for the realisation of liquid crystal flat panel displays.
<title>DOD and Navy applications for laser power beaming</title> (1995)

Satellites are of vital importance to the Department of Defense and the Navy as well as to the civilian economy. For example, about 90% of the communications to the fleet are by satellite. Economical means for putting satellites into orbit and maintaining and extending their lifetimes in orbit are just as important for the military as for civilian industries. There is also a significant economic impact to the ability to repair rather than replace satellites that are malfunctioning or have been inserted into the wrong orbits. Laser power beaming can not only accomplish these tasks but also promises to move satellites in orbit quickly and inexpensively, provide boost power for degraded satellites or those which suffer intentional jamming from adversaries, remove space junk even in geosynchronous orbit and provide very high resolution pictures of objects in space by eliminating atmospheric disturbances.
An investigation of filter choice for filtered back-projection reconstruction in PET (1998)

A key parameter in the practical application of filtered back-projection (FBP), the standard clinical image reconstruction algorithm for positron emission tomography (PET), is the choice of a low-pass filter window function and its cut-off frequency. However, the filter windows and cut-off frequencies for clinical reconstruction are usually chosen empirically, based on a small sample of images and filters. By considering the features of the signal and noise spectra in a sinogram, the desired image resolution, and the signal-to-noise ratio (SNR) of the filtered sinogram, a methodology for informed selection of a filter function and cut-off frequency for FBP was investigated. Simulations of sinogram data similar to whole body or cardiac studies provided information on the signal and noise frequency-domain spectra of noisy projection data. The improvements in SNR with different filter windows and cut-off frequencies were evaluated and compared. The projection spectrum SNR measure did not prove to be an accurate indicator of subjective image quality or lesion detectability with variations in Poisson noise and image resolution.
Painful Stimuli Evoke Potentials Recorded Over the Human Anterior Cingulate Gyrus (1998)

Clinical studies of cingulotomy patients and imaging studies predict that the human cingulate gyrus might display pain-related activity. We now report potentials evoked by painful cutaneous stimulation with a CO2 laser (LEP) and recorded from subdural electrodes over the medial wall of the hemisphere. In response to facial laser stimulation on both sides, a negative (latency 211-242 ms) and then a positive wave (325-352 ms) were recorded from the cortex of right medial wall and from the falcine dura overlying the left medial wall. Medial wall LEPs were similar to scalp LEPs and were largest over the anterior cingulate and superior frontal gyri just anterior to motor cortex contralateral to the side of stimulation. These results demonstrate that there is significant direct nociceptive input to the human anterior cingulate gyrus (Brodmann's area 24).
Comparative sequence analyses of the 16S rRNA genes of<i>Lactobacillus minutus, Lactobacillus rimae</i>and<i>Streptococcus parvulus</i>: Proposal for the creation of a new genus<i>Atopobium</i> (1992)

16S rRNA gene sequencing was performed on the species Lactobacillus minutus, Lactobacillus rimae and Streptococcus parvulus in order to clarify their taxonomic position. Based on comparative sequence analyses these organisms represent a hitherto unknown line of descent within the lactic acid group of bacteria for which a new genus, Atopobium gen. nov., is proposed.
Development of Hanford Site Lysimeter Facilities (1991)

Lysimeters have been constructed at the Hanford Site near Richland, Washington, to quantify mechanisms that affect migration of radioactive and hazardous waste in geologic media. The history of design and construction of specific lysimeter facilities is summarized. Design criteria and construction specifications are also provided for comparison of facilities. 8 refs., 2 figs.
Preparation, Crystal and Properties of Nitrogen-Rich Energetic Salt of Bis(semicarbazide) 5,5′-Bitetrazole-1,1′-diolate (2016)

A novel energetic salt of Bis(semicarbazide) 5,5′-bitetrazole-1,1′-diolate [2(SCZ)·BTO] was synthesized by using semicarbazide hydrochloride and 1H,1’H-5,5’-bitetrazole-1,1’-diol (BTO) as raw materials, and its structure was characterized by elemental analysis, Fourier Transform infrared spectroscopy (FT-IR) spectroscopy, 13C NMR spectrum and mass spectrum. The single crystal of the title salt was obtained and its structure was determined by an X-ray single-crystal diffractometer. Results show that 2(SCZ)·BTO belongs to the monoclinic space group P21/c with a density of 1.685 g·cm−3. The thermal decomposition behavior was investigated by differential scanning calorimetry (DSC) and thermogravimetry-derivative thermogravimetry (TG-DTG) analyses, and non-isothermal kinetic parameters were also calculated. The results indicated that it has a good thermal stability with a decomposition temperature above 200 °C. The apparent activation energies were 231.2 kJ·mol−1 (Kissinger's method) and 228.1 kJ·mol−1 (Ozawa-Doyle's method), respectively, and the critical temperature of thermal explosion is 240.6 °C. The enthalpy of formation for the salt was calculated as 158.1 kJ·mol−1. The detonation pressure (P) and detonation velocities (D) of the salt were determined by using the Kamlet-Jacobs equation. The results indicated that the title salt has potential applications in the field of energetic materials.
Integration of a multi-wavelength compressive-strained multi-quantum-well distributed-feedback laser array with a star coupler and optical amplifiers (2005)

We report the integration of a multi-wavelength multi-quantum-well distributed-feedback (DFB) laser array with a star coupler and optical booster amplifiers on the same chip for future wavelength-division multiplexed lightwave communication systems and multi-wavelength optical networks.
A Highly Facile and Efficient One-Step Synthesis of <i>N</i><sup>6</sup>-Adenosine and <i>N</i><sup>6</sup>-2‘-Deoxyadenosine Derivatives (2005)

[reaction: see text] A highly facile and efficient one-step synthesis of N6-adenosine and N6-2'-deoxyadenosine derivatives has been developed. Treatment of inosine or 2'-deoxyinosine, without protection of sugar hydroxyl groups, with alkyl or arylamines, in the presence of BOP and DIPEA in DMF, led to the formation of N6-adenosine and N6-2'-deoxyadenosine derivatives in good to excellent yields. Carcinogenic polyaromatic hydrocarbon (PAH) N6-2'-deoxyadenosine adduct 10 and a rare DNA constituent 11 were thus synthesized directly from 2'-deoxyinosine both in 98% yield.