gebhart/patrepeval huggingface dataset:
ColoType: a forty gene signature for consensus molecular subtyping of colorectal cancer tumors using whole-genome assay or targeted RNA-sequencing (2020)

Colorectal cancer (CRC) tumors can be partitioned into four biologically distinct consensus molecular subtypes (CMS1-4) using gene expression. Evidence is accumulating that tumors in different subtypes are likely to respond differently to treatments. However, to date, there is no clinical diagnostic test for CMS subtyping. In this study, we used novel methodology in a multi-cohort training domain (n = 1,214) to develop the ColoType scores and classifier to predict CMS1-4 based on expression of 40 genes. In three validation cohorts (n = 1,744, in total) representing three distinct gene-expression measurement technologies, ColoType predicted gold-standard CMS subtypes with accuracies 0.90, 0.91, 0.88, respectively. To accommodate for potential intratumoral heterogeneity and tumors of mixed subtypes, ColoType was designed to report continuous scores measuring the prevalence of each of CMS1–4 in a tumor, in addition to specifying the most prevalent subtype. For analysis of clinical specimens, ColoType was also implemented with targeted RNA-sequencing (Illumina AmpliSeq). In a series of formalin-fixed, paraffin-embedded CRC samples (n = 49), ColoType by targeted RNA-sequencing agreed with subtypes predicted by two independent methods with accuracies 0.92, 0.82, respectively. With further validation, ColoType by targeted RNA-sequencing, may enable clinical application of CMS subtyping with widely-available and cost-effective technology.
Generalized electrolyte‐NRTL model for mixed‐solvent electrolyte systems (2004)

Abstract A generalized electrolyte Non‐Random Two‐Liquid (eNRTL) model proposed by Chen and coworkers is presented as a comprehensive excess Gibbs energy expression to represent the liquid‐phase nonideality for aqueous and mixed‐solvent electrolyte systems over the entire concentration range from pure solvents to saturated solutions or fused salts. The eNRTL model is used to correlate mean ionic activity coefficients of mixed‐solvent electrolyte systems. The segment interaction concept provides the framework necessary to represent the attractive interaction of ions with the hydrophilic segments of organic solvents and the repulsive interaction of ions with the hydrophobic segments of organic solvents. The ability to explicitly account for such distinctly different ion–segment interactions is shown to be the key for quantitative correlation of mean ionic activity coefficients in mixed‐solvent electrolyte systems. © 2004 American Institute of Chemical Engineers AIChE J, 50: 1928–1941, 2004
A novel device for elimination of cancer cells from blood specimens (2020)

Circulating tumor cells (CTCs) are derivatives of solid cancerous lesions that detach from the tumor mass and enter the blood circulation. CTCs are considered to be the precursors of metastasis in several cancer types. They are present in the blood of cancer patients as single cells or clusters, with the latter being associated with a higher metastatic potential. Methods to eliminate CTCs from the bloodstream are currently lacking. Here, we took advantage of the lower shear stress-resistance of cancer cells compared to blood cells, and developed a device that can eliminate cancer cells without blood damage. The device consists of an axial pump and a coupled rotating throttle, controllable to prevent local blood flow impairment, yet maintaining a constant shear performance. When processing cancer cells through our device, we observe cancer cell-cluster disruption and viability reduction of single cancer cells, without noticeable effects on human blood cells. When injecting cancer cell-containing samples into tumor-free recipient mice, processed samples fail to generate metastasis. Together, our data show that a selective disruption of cancer cells is possible while preserving blood cells, paving the way towards the development of novel, implantable tools for CTC disruption and metastasis prevention.
Evidence for self-organized criticality in human epileptic hippocampus (2002)

Self-organized criticality (SOC) is a property of complex dynamic systems that evolve to a critical state, capable of producing scale-free energy fluctuations. A characteristic feature of dynamical systems exhibiting SOC is the power-law probability distributions that describe the dynamics of energy release. We show experimental evidence for SOC in the epileptic focus of seven patients with medication-resistant temporal lobe epilepsy. In the epileptic focus the probability density of pathological energy fluctuations and the time between these energy fluctuations scale as (energy) and (time), respectively. The power-laws characterizing the probability distributions from these patients are consistent with computer simulations of integrate-and-fire oscillator networks that have been reported recently. These findings provide insight into the neuronal dynamics of epileptic hippocampus and suggest a mechanism for interictal epileptiform fluctuations. The presence of SOC in human epileptic hippocampus may provide a method for identifying the network involved in seizure generation.
Predicting the Empirical Distribution of Video Quality Scores Using Recurrent Neural Networks (2020)

Video quality assessment is a crucial routine in the broadcasting industry. Due to the duration and the excessive number of video files, a computer-based video quality assessment mechanism is the only solution. While it is common to measure the quality of a video file at the compression stage by comparing it against the raw data, at later stages, no reference video is available for comparison. Therefore, a no-reference (Blind) video quality assessment (NR-VQA) technique is essential. The current NR-VQA methods predict only the mean opinion score (MOS) and do not provide further information about the distribution of people score. However, this distribution is informative for the evaluation of QoE. In this paper, we propose a method for predicting the empirical distribution of human opinion scores in the assessment of video quality. To this end, we extract some frame-level features, and next, we feed these features to a recurrent neural network. Finally, the distribution of opinion score is predicted in the last layer of the RNN. The experiments show that averages of predicted distributions have comparable or better results with previous methods on the KonVid-1k dataset.
Characterization of an Equine Infectious Anemia Antigen Extracted from Infected Horse Spleen Tissue (1971)

The spleens of horses infected with equine infectious anemia contain an antigen that is useful for a diagnostic immunodiffusion test. This antigen was extracted from the spleen by homogenization of the tissue, centrifugation, and precipitation from the supernatant fluid at 50% saturation with (NH(4))(2)SO(4). The antigen was purified by subjecting it to two cycles of electrophoresis in a continuous free-flow electrophoresis cell and finally filtering through a column of Sephadex G-200 gel. The antigen was found to be a small protein with a molecular weight of 27,500 and sedimentation coefficient of 2.1S. Its density was about 1.18 and its isoelectric point 5.8. At 45 to 50 C, it coagulated, losing its antigenicity. The antigen was useful for assaying antibody in the serum from infected horses by using the complement fixation test or the immunodiffusion test. Complement-fixing antibodies were found to be more transient than the precipitating antibodies.
Theoretical analysis of gate level information flow tracking (2010)

Understanding the flow of information is an important aspect in computer security. There has been a recent move towards tracking information in hardware and understanding the flow of individual bits through Boolean functions. Such gate level information flow tracking (GLIFT) provides a precise understanding of all flows of information. This paper presents a theoretical analysis of GLIFT. It formalizes the problem, provides fundamental definitions and properties, introduces precise symbolic representations of the GLIFT logic for basic Boolean functions, and gives analytic and quantitative analysis of the GLIFT logic.
Temporofunctional crosstalk noise analysis (2003)

Noise affects circuit operation by increasing gate delays and causing latches to capture incorrect values. This paper proposes a method of characterizing correlation of signal transitions in multiple nets by considering both timing and functionality of the signals, and uses it in an analysis procedure to eliminate noise faults that cannot actually happen when such correlations are considered. It uses four-variable Boolean logic to characterize signal transitions in a time interval, and formulates Boolean satisfiability between aggressors and a victim under the min-max delay model for gates. The technique has been successfully applied to commercial ASIC designs and has eliminated up to 35% of delay noise faults reported by a state-of-the-art noise analysis tool.
The MEK-inhibitor CI-1040 displays a broad anti-influenza virus activity in vitro and provides a prolonged treatment window compared to standard of care in vivo (2017)

Influenza viruses (IV) continue to pose an imminent threat to human welfare. Yearly re-occurring seasonal epidemic outbreaks and pandemics with high mortality can occur. Besides vaccination against a limited number of viral strains only a few antiviral drugs are available, which are losing their effectiveness as more and more IV strains become resistant. Thus, new antiviral approaches that omit IV resistance are urgently needed. Here, the dependency on the cellular Raf/MEK/ERK signaling pathway for IV replication opens a new perspective. In consequence, we studied the antiviral potential of the MEK inhibitor Cl-1040 (PD184352). We show that Cl-1040 significantly reduces virus titers in vitro via retention of viral RNP complexes in the cell nucleus. Furthermore, Cl-1040 is effective against a broad range of IV strains, including highly pathogenic avian IV, as well as against a Tamiflu<sup>®</sup>-resistant IV strain. Using a mouse model, we demonstrate that Cl-1040 can reduce IV lung titers in vivo. Importantly, the treatment window for Cl-1040 expands up to 48 h post infection when Tamiflu<sup>®</sup> treatment has no effect. In conclusion, Cl-1040 offers an interesting perspective for anti-IV approaches.
Preparation and Evaluation of ZnSe and ZnS sub X Se sub 1-X Epitaxial Layers on Ge Substrates for Applications in Surface Passivation and Heterojunction Devices. (1984)

This report summarizes a detailed study of ZnSe and ZnSxSe1-x epitaxial growth on germanium and gallium arsenide substrates, for application in surface passivation and heterojunction devices. These layers were prepared by a novel low pressure, low temperature organometallic chemical vapor deposition (OM-CVD) process. Both nominally undoped, intrinsic ZnSe and Al-doped, highly conductive n-type ZnSe were prepared by this method. Excellent epitaxial growth was achieved as indicated by the large intensity in the near bandgap photoluminescence and the rather weak intensity in the self-activated luminescence spectra. This indicates a low concentration of intrinsic and extrinsic defects and a low compensation ratio. An important relationship was observed between reproducibility of layer characteristics and substrate and reactor preparation. Also, deep center luminescence revealed that ZnSe layers deposited on both GaAs and Ge (100) surfaces have luminescence properties superior to those deposited on other substrate orientations. This study revealed a large disparity in the electrical conductivity depending on substrate orientation, of Al-doped, n-type ZnSe layers deposited both on GaAs and Ge Substrates. The defect structure of ZnSe layers grown on (100), (110), and (111)b GaAs, and on (100) and (111) Ge substrates were imaged for the first time by high resolution transmission electron microscopy. ZeSe-Ge heterojunctions were successfully fabricated and reflect the orientation dependent of interface properties and layer resistivity in their current - voltage characteristics.
Totally relaxed Ge<i>x</i>Si1−<i>x</i> layers with low threading dislocation densities grown on Si substrates (1991)

We have grown compositionally graded GexSi1−x layers on Si at 900 °C with both molecular beam epitaxy and rapid thermal chemical vapor deposition techniques. Triple-crystal x-ray diffraction reveals that for 0.10&lt;x&lt;0.53, the layers are totally relaxed. GexSi1−x cap layers grown on these graded layers are threading-dislocation-free when examined with conventional plan-view and cross-sectional transmission electron microscopy. Electron beam induced current images were used to count the low threading dislocation densities, which were 4×105±5×104 cm−2 and 3×106±2×106 cm−2 Eq. 2×106 cm−2 for x=0.23 and x=0.50, respectively. Photoluminescence spectra from the cap layers are identical to photoluminescence from bulk GexSi1−x.
Ca<sup>2+</sup>‐dependent activity of human DNase I and its hyperactive variants (1999)

We have recently constructed hyperactive human deoxyribonuclease I (DNase I) variants that digest double-stranded DNA more efficiently under physiological saline conditions by introducing positively charged amino acids at eight positions that can interact favorably with the negatively charged DNA phosphates. In this study, we present data from supercoiled DNA nicking, linear DNA digestion, and hyperchromicity assays that distinguish two classes of DNase I hyperactive variants based upon their activity dependence on Ca2+. Class A variants are highly dependent upon Ca2+, having up to 300-fold lower activity in the presence of Mg2+ alone compared to that in the presence of Mg2+ and Ca2+, and include Q9R, H44K, and T205K, in addition to wild-type DNase I. In contrast, the catalytic activity of Class B variants, which comprise the E13R, T14K, N74K, S75K, and N110R hyperactive variants, is relatively Ca2+ independent. A significant proportion of this difference in Ca2+-dependent activity can be attributed to one of the two structural calcium binding sites in DNase I. Compared to wild-type, the removal of Ca2+ binding site 2 by alanine replacements at Asp99, Asp107, and Glu112 decreased activity up to 26-fold in the presence of Mg2+ and Ca2+, but had no effect in the presence of Mg2+ alone. We propose that the rate-enhancing effect of Ca2+ binding at site 2 can be replaced by favorable electrostatic interactions created by proximal positively charged amino acid substitutions such as those found in the Class B variants, thus reducing the dependence on Ca2+.
Prevention of a plant disease by specific inhibition of fungal polyamine biosynthesis. (1985)

DL-alpha-Difluoromethylornithine (DFMO), an inhibitor of the polyamine biosynthetic enzyme ornithine decarboxylase (EC 4.1.1.17), strongly retards the growth of several species of phytopathogenic fungi in vitro. Such inhibition can be completely reversed by putrescine or spermidine, confirming the essentiality of polyamines for growth of fungal hyphae. We now show that DFMO can protect bean plants (Phaseolus vulgaris Linnaeus cv. Pinto) against infection by uredospores of the bean rust fungus, Uromyces phaseoli Linnaeus, race O. Unifoliolate leaves of 10-day-old greenhouse-grown seedlings were sprayed with 400 microliter per leaf of DFMO at various concentrations in 0.01% Tween 20 at pH 7.0 before or after inoculation with uredospores of Uromyces. After 16 hr in darkness in dew chambers to facilitate spore germination, plants were transferred to the greenhouse, arranged randomly, and examined for local lesions 7 days later. All concentrations of DFMO 0.50 mM or higher gave complete protection against the pathogen; at lower concentrations, postinoculation treatments with DFMO were generally more effective than preinoculation. The appearance of lesions on plants treated with lower concentrations of DFMO was retarded 2-6 days. DFMO also confers protection on unsprayed parts of treated plants, indicating the translocation of some protective effect from sprayed areas. DL-alpha-Difluoromethylarginine, an analogous inhibitor of arginine decarboxylase (EC 4.1.1.19), which is the rate-limiting enzyme in an alternative pathway for polyamine biosynthesis in higher plants, confers no protection even at 5 mM. This emphasizes ornithine decarboxylase as the biochemical locus of choice for the prevention of plant diseases by inhibiting polyamine metabolism.
The Effect of pH on Metal Accumulation in Two <i>Alyssum</i> Species (2004)

Nickel phytoextraction using hyperaccumulator plants offers a potential for profit while decontaminating soils. Although soil pH is considered a key factor in metal uptake by crops, little is known about soil pH effects on metal uptake by hyperaccumulator plants. Two Ni and Co hyperaccumulators, Alyssum murale and A. corsicum, were grown in Quarry muck (Terric Haplohemist) and Welland (Typic Epiaquoll) soils contaminated by a Ni refinery in Port Colborne, Ontario, Canada, and in the serpentine Brockman soil (Typic Xerochrepts) from Oregon, USA. Soils were acidified and limed to cover pH from strongly acidic to mildly alkaline. Alyssum grown in both industrially contaminated soils exhibited increased Ni concentration in shoots as soil pH increased despite a decrease in water-soluble soil Ni, opposite to that seen with agricultural crop plants. A small decrease in Alyssum shoot Ni concentration as soil pH increased was observed in the serpentine soil. The highest fraction of total soil Ni was phytoextracted from Quarry muck (6.3%), followed by Welland (4.7%), and Brockman (0.84%). Maximum Ni phytoextraction was achieved at pH 7.3, 7.7, and 6.4 in the Quarry, Welland, and Brockman soils, respectively. Cobalt concentrations in shoots increased with soil pH increase in the Quarry muck, but decreased in the Welland soil. Plants extracted 1.71, 0.83, and 0.05% of the total soil Co from Welland, Quarry, and Brockman, respectively. The differences in uptake pattern of Ni and Co by Alyssum from different soils and pH were probably related to the differences in organic matter and iron contents of the soils.
CXCL12–CXCR4 signalling axis confers gemcitabine resistance to pancreatic cancer cells: a novel target for therapy (2010)

Our findings demonstrate, for the first time, a role of CXCL12-CXCR4 signalling axis in conferring drug resistance to pancreatic cancer cells and suggest that it could serve as a novel therapeutic target for pancreatic cancer therapy, alone and in combination with the cytotoxic drug.
Interval Extensions of Signed Distance Functions: iSDF-reps and Reliable Membership Classification (2010)

This paper considers the problem of inferring the geometry of an object from values of the signed distance sampled on a uniform grid. The problem is motivated by the desire to effectively and efficiently model objects obtained by 3D imaging technology such as magnetic resonance, computed tomography, and positron emission tomography. Techniques recently developed for automated segmentation convert intensity to signed distance, and the voxel structure imposes the uniform sampling grid. The specification of the signed distance function (SDF) throughout the ambient space would provide an implicit and function-based representation (f-rep) model that uniquely specifies the object, and we refer to this particular f-rep as the signed distance function representation (SDF-rep). However, a set of uniformly sampled signed distance values may uniquely determine neither the distance function nor the shape of the object. Here, we employ essential properties of the signed distance to construct the upper and lower bounds on the allowed variation in signed distance, which combine to produce interval-valued extensions of the signed distance function. We employ an interval extension of the signed distance function as an interval SDF-rep that defines the range of object geometries that are consistent with the sampled SDF data. The particular interval extensions considered include a tight global extension and more computationally efficient local extensions that provide useful criteria for root exclusion/isolation. To illustrate a useful application of the interval bounds, we present a reliable approach to top-down octree membership classification for uniform samplings of signed distance functions.
Simultaneous mobility: analytical framework, theorems and solutions (2006)

Abstract The original Mobile IP (MIP) protocol does not perform Route Optimisation but uses Home Agents to forward traffic. Thus, it does not have problems with simultaneous mobility, that is, the special case when both end hosts are mobile and move at about the same time. However, MIP for IPv6 (MIPv6) uses binding updates that are sent directly to a correspondent node. Session Initiation Protocol based mobility management (SIPMM) and MIP with location registers (MIP‐LR) also use direct binding updates between a mobile host and a correspondent node. Thus, MIPv6, MIP‐LR and SIPMM are vulnerable to the simultaneous mobility problem. In this paper, we analyse the simultaneous mobility problem and solution mechanisms, and propose new ways for MIPv6, MIP‐LR and SIPMM to handle simultaneous mobility. Copyright © 2006 John Wiley & Sons, Ltd.
<title>Progress toward combined phase and amplitude demodulation fluorescence lifetime measurements by flow cytometry</title> (1998)

A phase-sensitive flow cytometer has been developed to quantify fluorescence lifetimes directly as a parameter in real time on particles and cells labeled with fluorophores. This instrument combines flow cytometry and frequency-domain fluorescence lifetime spectroscopy measurement principles to provide unique features for making excited-state lifetime measurements. Cells are analyzed as they intersect a high- frequency, intensity-modulated (sine wave) laser excitation beam. Fluorescence signals are processed by analog phase comparator measurement electronics to provide output signals proportional to the sine and cosine of the phase difference between the modulated signal input and a steady state reference signal. The ratios, which are proportional to the lifetimes, are displayed as frequency distributions histograms. In this study we present the underlying theory to measure fluorescence lifetimes by both phase shift and amplitude demodulation. Prototype analog amplitude demodulation electronics have been constructed and are being tested using simulated signals, fluorescent microspheres, and cells labeled with fluorescent probes.