gebhart/patrepeval huggingface dataset:
Application of Pearson correlation coefficient (PCC) and Kolmogorov-Smirnov distance (KSD) metrics to identify disease-specific biomarker genes (2010)

Background DNA microarrays have been widely applied in cancer research for better diagnosis and prediction of the disease states. Traditionally, most microarray studies aim to identify differentially expressed genes (DEGs) by comparing the average gene expression levels between two groups (e.g., the treated vs. control or disease vs. non-disease) based on statistical analysis such as t-test and Significance Analysis of Microarrays (SAM) [1,2]. Materials and methods In this study, we defined the gene expression profile (GEP) of a gene as the distribution of the log2 values of its normalized expression signal intensities across the samples in the similarly studied microarrays. We hypothesized that the biomarker genes that distinguish disease samples from normal samples might form distinct GEPs between comparison groups. We applied Pearson Correlation Coefficient (PCC) and Kolmogorov-Smirnov Distance (KSD) metrics to identify disease-specific biomarkers by comparing GEPs between normal and disease states and then applied this technology to disease (e.g., cancer) related studies in order to discover some disease genes as biomarker candidates. These biomarkers’ gene profiles in normal and disease samples might be used to diagnose or monitor patient’s disease state via regular gene expression analysis.
Contents of methyl‐, ethyl‐, propyl‐, butyl‐ and benzylparaben in cosmetic products (1995)

The contents of methyl-, ethyl-, propyl-, butyl- and benzylparaben in 215 cosmetic products have been determined to elucidate the concentration and frequency of use of these parabens in cosmetic products, and to monitor whether the products complied with the Danish and EEC regulations. The results showed that 77% of the products investigated contained 0.01%-0.87% parabens. Nearly all (99%) of the leave-on cosmetics and 77% of rinse-off cosmetics were found to contain parabens. A maximum of 0.32% methyl- and propylparaben, 0.19% ethylparaben, and 0.07% butyl- and benzylparaben were present in paraben-positive cosmetics. A preferential use of methyl-/ethyl-/propyl-/butyl-/benzylparaben in various groups of cosmetic products was revealed.
High-speed ECL-compatible serial I/O in 0.35 μm CMOS (2002)

This paper presents high-speed input and output interface circuits for serial data communication at 622 Mb/s (OC-12) standard. The circuits are designed in a 0.35 /spl mu/m triple-metal CMOS process. Signal levels are compatible with industry standards for low-voltage positive ECL. Combining circuit design techniques with the features of a submicron technology, the presented I/O blocks enable a full-CMOS chip to communicate directly with high-speed ECL-compatible devices at rates up to 1 Gb/s.
Inhibition of Fatty-acid Synthase Induces Caspase-8-mediated Tumor Cell Apoptosis by Up-regulating DDIT4 (2008)

Fatty-acid synthase (FAS) is up-regulated in a broad range of cancers, including those of the breast, prostate, and ovaries. In tumor cells, the inhibition of FAS elicits cell cycle arrest and apoptosis, so it is considered a potential drug target for oncology. Results from this study show that inhibition of FAS, by either knockdown with small interfering RNA or inhibition with the small molecule drug orlistat, leads to activation of the receptor-mediated apoptotic cascade (caspase-8-mediated) and ultimately to cell death. However, knockdown of two enzymes upstream of FAS, acetyl-CoA carboxylase-alpha and ATP-citrate lyase, fails to activate caspase-8 or to elicit apoptosis in tumor cells, even though palmitate synthesis was suppressed. Using differential gene analysis, we traced the unique apoptotic effect of FAS inhibition to up-regulation of DDIT4 (DNA damage-inducible transcript 4), a stress-response gene that negatively regulates the mTOR pathway. These findings indicate that suppression of palmitate synthesis is not sufficient for eliciting tumor cell death and suggest that the unique effect of inhibition of FAS results from negative regulation of the mTOR pathway via DDIT4.
Involvement of MicroRNA in T-Cell Differentiation and Malignancy. (2015)

MicroRNAs are 19-22 nucleotide RNAs involved in such important processes as development, proliferation, differentiation and apoptosis. Different miRNAs are uniquely expressed in lymphoid T cells, and play a role indevelopment and differentiation of various subtypes by targeting their target genes. Recent studies have shown that aberrant miRNA expression may be involved in T cell leukemogenesis and lymphogenesis, and may function as tumor suppressor (such as miR-451, miR-31, miR-150, and miR-29a) or oncogene (e.g. miR-222, miR-223, miR-17-92, miR-155). MiRNAs can be used as new biomarkers for prognosis and diagnosis or as an index of disease severity in T-cell leukemia and lymphoma. This article presents a review of studies in recent years on the role of miRNAs in T-cell development and their aberrant expression in pathogenesis of T-cell leukemia and lymphoma. Characterizing miRNAs can help recognize their role as new important molecules with prognostic and therapeutic applications.
The problems and promise of DNA barcodes for species diagnosis of primate biomaterials (2005)

The Integrated Primate Biomaterials and Information Resource (www.IPBIR.org) provides essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing DNA and RNA derived from primate cell cultures. The IPBIR uses mitochondrial cytochrome c oxidase subunit I sequences to verify the identity of samples for quality control purposes in the accession, cell culture, DNA extraction processes and prior to shipping to end users. As a result, IPBIR is accumulating a database of 'DNA barcodes' for many species of primates. However, this quality control process is complicated by taxon specific patterns of 'universal primer' failure, as well as the amplification or co-amplification of nuclear pseudogenes of mitochondrial origins. To overcome these difficulties, taxon specific primers have been developed, and reverse transcriptase PCR is utilized to exclude these extraneous sequences from amplification. DNA barcoding of primates has applications to conservation and law enforcement. Depositing barcode sequences in a public database, along with primer sequences, trace files and associated quality scores, makes this species identification technique widely accessible. Reference DNA barcode sequences should be derived from, and linked to, specimens of known provenance in web-accessible collections in order to validate this system of molecular diagnostics.
Cyclic prefix reduction for 20.48 Gb/s direct‐detection optical OFDM transmission over 2560 km of SSMF (2011)

Abstract Optical Orthogonal Frequency Division Multiplexing (O‐OFDM) provides major advantages in mitigating Group‐Velocity Dispersion (GVD) in Single Mode Fiber (SMF). Unfortunately, when the uncompensated long‐haul transmission ranges become very large, substantial dispersion is accumulated. Owing to the large accumulated dispersion, the Cyclic Prefix (CP) duration will occupy a substantial fraction of the OFDM frame. This effect sets some limitations on the overall throughput and the spectral efficiency. Moreover, the transmission is inefficient because of the energy wastage contained within the CP. In the case where the CP length is shorter than the Channel Impulse Response (CIR), energy wastage is reduced but the system performance is limited by the Inter Symbol Interference (ISI) and Inter Carrier Interference (ICI). To overcome this problem, a Time Domain Equalizer (TEQ) immediately after the channel is proposed. It can cancel the residual ISI and ICI caused by both the GVD and the CP length being shorter than the CIR. The simulation results show that, using BER of 10 −3 as a reference, the system performance improves by 2.69thinspacedB while considering 6‐feedforward/5‐feedback‐weight Decision Feedback TEQ (DF‐TEQ) and 2.03 dB while considering 10‐tap Least Mean Square TEQ (LMS‐TEQ) even though the CP length is shorter than the CIR. This method reduces size of the CP, and consequently the performance of the system will be improved. Copyright © 2011 John Wiley & Sons, Ltd.
Observation of a giant two-dimensional band-piezoelectric effect on biaxial-strained graphene (2015)

Piezoelectric materials used in the development of nanoscale mechanical sensors, actuators and energy harvesters have received much attention. More recently, devices made of graphene are of particular interest because of graphene's intriguing electronic and mechanical properties. Intrinsic graphene has long been considered devoid of the piezoelectric effect, although flexoelectricity has been exploited to demonstrate piezoelectricity in functionalized graphene and graphene nanoribbons. The perceived lack of this property has restricted graphene's use in nanoelectromechanical systems (NEMS) for electromechanical coupling purposes. Here an unprecedented two-dimensional (2D) piezoelectric effect on a strained/unstrained graphene junction is reported. In stark contrast to the bulk piezoelectric effect that results from the occurrence of electric dipole moments in solids, the 2D piezoelectric effect arises from the charge transfer along a work function gradient introduced by the biaxial-strainengineered band structure. The observed effect, termed the band-piezoelectric effect, exhibits an enormous magnitude due to the ultrathin structure of graphene. On the basis of the band-piezoelectric effect, a graphene nanogenerator and a pressure gauge were fabricated. The results not only provide a versatile NEMS platform for sensing, actuating and energy harvesting, but also pave the way for efficiently modulating graphene via strain engineering.
Development of Tight-fitting Upper Clothing for Measuring ECG -A Focus on Weft Reduction Rate and Subjective Assessment- (2012)

This study develops tight-fitting upper clothing to measure electrocardiography (ECG) data. Taking into consideration the elasticity of the clothing, we made 4 experimental clothes by applying to each a weft reduction rate of 40%, 50%, 60%, and 70%. The 4 experimental clothes were used to measure resting ECG, exercise ECG, and post-exercise ECG for 4 men in their 20s. We compared clothing pressures using sensors on the human body and on a dressform. Subjective wear sensations of the 4 experimental clothes were evaluated using a subjective 7-point scale (with 7 being most excellent). We measured clothing pressures by using the air type pressure (AMI 3037-2) for upper and lower chest sensors in the developed tight-fitting upper clothing. The lower chest sensor showed that the clothing pressure on a human body and dressform changed consistently as the weft reduction rate decreased. The upper chest sensor showed inconsistent changes in clothing pressure as the weft reduction rate decreased. The wearing-test result for preliminary subjects showed that the lower chest sensor was more stable than the upper chest sensor; therefore, we inserted the sensor at the lower chest position before performing ECG. Except for Subject 4, the resting ECGs were stably measured for 3 subjects (Subject 1, Subject 2, and Subject 3) in all the developed clothes (A clothing, B clothing, C clothing, and D clothing). However, D clothing showed stable ECG values after exercise. The results of the experiment showed that we could measure ECG without difficulty using clothes with a weft reduction rate of 40% when the movement was not intense; however, tight-fitting upper clothing with a weft reduction rate of 70% was necessary to measure exercise ECG and post-exercise ECG values.
Syntheses of three metabolites of icosapentaenoic and docosahexaenoic acids (2000)

Starting from the n − 3 polyunsaturated fatty acids icosapentaenoic acid (1, EPA) and docosahexaenoic acid (2, DHA), the syntheses of methyl 2E,4Z,8Z,11Z,14Z,17Z-icosa-2,4,8,11,14,17-hexaenoate (6), 2E,8Z,11Z,14Z,17Z-icosa-2,8,11,14,17-pentaenoate (7) and 2E,4Z,7Z,10Z,13Z,16Z,19Z-docosa-2,4,7,10,13,16,19-heptaenoate (8), in high stereochemical purity, have been accomplished. The corresponding carboxylic acids have been reported as metabolites in the bioconversion of EPA and DHA.
Terpolymers of ethylene and propylene with <i>d</i>‐limonene and β‐pinene (1965)

Abstract An experimental program was undertaken to produce a series of ethylene–propylene terpolymers containing either limonene (dipentene) or β‐pinene from a variety of Ziegler‐Natta type catalysts. All attempts to obtain a satisfactory vulcanizate from the limonene EPT and β‐pinene EPT rubbers were unsuccessful.
Noninvasive Quantification of Solid Tumor Microstructure Using VERDICT MRI (2014)

There is a need for biomarkers that are useful for noninvasive imaging of tumor pathophysiology and drug efficacy. Through its use of endogenous water, diffusion-weighted MRI (DW-MRI) can be used to probe local tissue architecture and structure. However, most DW-MRI studies of cancer tissues have relied on simplistic mathematical models, such as apparent diffusion coefficient (ADC) or intravoxel incoherent motion (IVIM) models, which produce equivocal results on the relation of the model parameter estimate with the underlying tissue microstructure. Here, we present a novel technique called VERDICT (Vascular, Extracellular and Restricted Diffusion for Cytometry in Tumors) to quantify and map histologic features of tumors in vivo. VERDICT couples DW-MRI to a mathematical model of tumor tissue to access features such as cell size, vascular volume fraction, intra- and extracellular volume fractions, and pseudo-diffusivity associated with blood flow. To illustrate VERDICT, we used two tumor xenograft models of colorectal cancer with different cellular and vascular phenotypes. Our experiments visualized known differences in the tissue microstructure of each model and the significant decrease in cell volume resulting from administration of the cytotoxic drug gemcitabine, reflecting the apoptotic volume decrease. In contrast, the standard ADC and IVIM models failed to detect either of these differences. Our results illustrate the superior features of VERDICT for cancer imaging, establishing it as a noninvasive method to monitor and stratify treatment responses.
Modified Stoichiometry in Homogeneous Indium–Zinc Oxide System as Vertically Graded Oxygen Deficiencies by Controlling Redox Reactions (2015)

The present study suggests a way to improve electrical characteristics and stabilities by forming a different stoichiometry in a homogeneous system without using a multiple deposition process. Post treatment by sequential pressure annealing (SPA) of a homogeneous indium–zinc oxide system is carried out to fabricate vertically graded oxygen deficiencies via redox reactions. The SPA treatment consists of several steps. First, hydrogen pressure annealing is performed to chemically expedite the reduction reaction of weak chemical bonds in the overall channel region and thereby make the material highly conducting. Second, oxygen pressure annealing is performed to render the channel a poor conductor by gradually oxidizing the channel from the back to the front. Such SPA‐treated devices have significantly more oxygen deficiencies in the front‐channel region than in the back‐channel region. The stoichiometry of the channel region modified in this manner provided enhanced mobility, a higher on/off ratio, and a decreased threshold voltage shift (under positive and negative bias stresses).
Isolation of normal nonane from a midcontinent petroleum (1931)

An account is given of the separation of n-nonane in a high state of purity from a midcontinent petroleum by alternating fractional distillation and fractional crystallization.
The effect of triiodothyronine-prednisolone treatment on the development of digestive enzymes in the suckling pig (1982)

Thirty suckling pigs of 4 litters were divided into an experimental and a control group. The experimental piglets were treated perorally from 14 to 20 days of age with rising doses of triiodothyronine, which were combined with prednisolone for the last 3 days. On the day following the conclusion of the treatment (at 3 weeks of age) the piglets were killed by bleeding for the determination of digestive enzymes. The experimental piglets showed a significant increase of intestinal trypsin (p less than 0.01) and pancreatic amylase (P less than 0.05) activities over the control; a significant decrease of gastric chymosin activity (P less than 0.05) was caused by the great inter-group differences within one litter. Ten of the 11 parameters tested indicated precocious maturation of the digestive enzymes of the experimental piglets, however, most of these differences were not significant. Further studies are required for the possible utilization of this finding in the early weaning practice.
Microvascular perfusion experimental spinal cord injury. (1978)

Microperfusion of the spinal cords in cats was studied using a colloidal carbon perfusion technique following compression injury at 1/2 hour, 2 hours, 4 hours, 8 hours, 24 hours, and 51 days. Quantitative estimates of vascular filling were determined at these post-compression intervals. Microperfusion diminished in both the gray and white matter at 1/2 hour following injury and severe lack of perfusion was evident at 8 and 24 hours. Diminished filling of the vessels of gray and white matter seemed to parallel the degree of hemorrhagic necrosis of the gray matter. An increased number of vessels were evident in the spinal cords of long term survivals. The observation that microperfusion in the white matter of the spinal cord was diminished at 24 hours is at variance with some previous investigations. The hypoperfusion of the white matter found in this study suggests that ischemia plays a role in paraplegia resulting from experimental compression injury of the spinal cord.
Mucosal region detection and 3D reconstruction in wireless capsule endoscopy videos using active contours (2012)

Wireless capsule endoscopy (WCE) provides an inner view of the human digestive system. The inner tubular like structure of the intestinal tract consists of two major regions: lumen - intermediate region where the capsule moves, mucosa - membrane lining the lumen cavities. We study the use of the Split Bregman version of the extended active contour model of Chan and Vese for segmenting mucosal regions in WCE videos. Utilizing this segmentation we obtain a 3D reconstruction of the mucosal tissues using a near source perspective shape-from-shading (SfS) technique. Numerical results indicate that the active contour based segmentation provides better segmentations compared to previous methods and in turn gives better 3D reconstructions of mucosal regions.
Mammalian Housekeeping Genes Evolve More Slowly than Tissue-Specific Genes (2004)

Do housekeeping genes, which are turned on most of the time in almost every tissue, evolve more slowly than genes that are turned on only at specific developmental times or tissues? Recent large-scale gene expression studies enable us to have a better definition of housekeeping genes and to address the above question in detail. In this study, we examined 1581 human-mouse orthologous gene pairs for their patterns of sequence evolution, contrasting housekeeping genes with tissue-specific genes. Our results show that, in comparison to tissue-specific genes, housekeeping genes on average evolve more slowly and are under stronger selective constraints as reflected by significantly smaller values of Ka/Ks. Besides stronger purifying selection, we explored several other factors that can possibly slow down nonsynonymous rates in housekeeping genes. Although mutational bias might slightly slow the nonsynonymous rates in housekeeping genes, it is unlikely to be the major cause of the rate difference between the two types of genes. The codon usage pattern of housekeeping genes does not seem to differ from that of tissue-specific genes. Moreover, contrary to the old textbook concept, we found that approximately 74% of the housekeeping genes in our study belong to multigene families, not significantly different from that of the tissue-specific genes ( approximately 70%). Therefore, the stronger selective constraints on housekeeping genes are not due to a lower degree of genetic redundancy.
Cell-to-cell movement of potato virus X involves distinct functions of the coat protein (2001)

Complementation of movement-deficient potato virus X (PVX) coat protein (CP) mutants, namely PVX.CP-Xho lacking the 18 C-terminal amino acid residues and PVX.DeltaCP lacking the entire CP gene, was studied by transient co-expression with heterologous proteins. These data demonstrated that the potyvirus CPs and both the major and minor CPs of beet yellows closterovirus could complement cell-to-cell movement of PVX.CP-Xho but not PVX.DeltaCP. These data also indicated that the C-terminally truncated PVX CP lacked a movement function which could be provided in trans by the CPs of other filamentous viruses, whereas another movement determinant specified by some region outside the most C-terminal part of the PVX CP could not be complemented either by potyvirus or closterovirus CPs. Surprisingly, the CP of spherical cocksfoot mottle sobemovirus rescued all of the PVX CP movement functions, complementing the spread of PVX.CP-Xho and, to a lesser extent, PVX.DeltaCP. Both these mutants were also rescued by the tobacco mosaic virus (TMV) movement protein (MP). To shed light on the movement function of PVX CP, attempts were made to complement PVX.CP-Xho by a series of TMV MP mutants. An internal deletion abolished complementation, suggesting that the internal region of TMV MP, which includes a number of overlapping functional domains important for cell-to-cell transport, provides an activity complementing movement determinant(s) specified by the C-terminal region of PVX CP.
Counting People Based on Linear, Weighted, and Local Random Forests (2017)

Recently, many works have been published for counting people. However, when being applied to real-world train station videos, they have exposed many limitations due to problems such as low resolution, heavy occlusion, various density levels and perspective distortions. In this paper, following the recent trend of regression-based density estimation, we present a linear regression approach based on local Random Forests for counting either standing or moving people on station platforms. By dividing each frame into sub-windows and extracting features with ground truth densities as well as learned weights, we perform a linear transformation for counting people to overcome the perspective problems of the existing patch-based approaches. We present improvements against several recent baselines on the UCSD dataset and a dataset of CCTV videos taken from a train station. We also show improvements in speed compared with the state-of-the-art models based on detection and Deep Learning.