gebhart/patrepeval huggingface dataset:
Machine Learning-Assisted Network Inference Approach to Identify a New Class of Genes that Coordinate the Functionality of Cancer Networks (2017)

Emerging evidence indicates the existence of a new class of cancer genes that act as "signal linkers" coordinating oncogenic signals between mutated and differentially expressed genes. While frequently mutated oncogenes and differentially expressed genes, which we term Class I cancer genes, are readily detected by most analytical tools, the new class of cancer-related genes, i.e., Class II, escape detection because they are neither mutated nor differentially expressed. Given this hypothesis, we developed a Machine Learning-Assisted Network Inference (MALANI) algorithm, which assesses all genes regardless of expression or mutational status in the context of cancer etiology. We used 8807 expression arrays, corresponding to 9 cancer types, to build more than 2 × 10<sup>8</sup> Support Vector Machine (SVM) models for reconstructing a cancer network. We found that ~3% of ~19,000 not differentially expressed genes are Class II cancer gene candidates. Some Class II genes that we found, such as SLC19A1 and ATAD3B, have been recently reported to associate with cancer outcomes. To our knowledge, this is the first study that utilizes both machine learning and network biology approaches to uncover Class II cancer genes in coordinating functionality in cancer networks and will illuminate our understanding of how genes are modulated in a tissue-specific network contribute to tumorigenesis and therapy development.
Homocoupling of Aryl Halides Using Nickel(II) Complex and Zinc in the Presence of Et4NI. An Efficient Method for the Synthesis of Biaryls and Bipyridines (1990)

Abstract Reduction of NiX2(PPh3)2 with zinc in the presence of Et4NI gives a nickel catalyst which has been proven to be useful for the coupling of aryl halides. This nickel catalyst can be prepared in THF without an additional triphenylphosphine and is effective for the homocoupling of aryl chlorides, bromides, and iodides to produce biaryls and bipyridines in good yields. The reported new approach provides a simple access to novel derivatives of biaryls and bipyridines.
Design of thiol–ene photoclick hydrogels using facile techniques for cell culture applications (2014)

Thiol-ene 'click' chemistries have been widely used in biomaterials applications, including drug delivery, tissue engineering, and controlled cell culture, owing to their rapid, cytocompatible, and often orthogonal reactivity. In particular, hydrogel-based biomaterials formed by photoinitiated thiol-ene reactions afford spatiotemporal control over the biochemical and biomechanical properties of the network for creating synthetic materials that mimic the extracellular matrix or enable controlled drug release. However, the use of charged peptides functionalized with cysteines, which can form disulfides prior to reaction, and vinyl monomers that require multistep syntheses and contain ester bonds, may lead to undesired inhomogeneity or degradation under cell culture conditions. Here, we designed a thiol-ene hydrogel formed by the reaction of allyloxycarbonyl-functionalized peptides and thiol-functionalized poly(ethylene glycol). Hydrogels were polymerized by free radical initiation under cytocompatible doses of long wavelength ultraviolet light in the presence of water-soluble photoinitiators (lithium acylphosphinate, LAP, and 2-hydroxy-1-[4-(2-hydroxyethoxy)phenyl]-2-methyl-1-propanone, Irgacure 2959). Mechanical properties of these hydrogels were controlled by varying the monomer concentration to mimic a range of soft tissue environments, and hydrogel stability in cell culture medium was observed over weeks. Patterns of biochemical cues were created within the hydrogels post-formation and confirmed through the incorporation of fluorescently-labeled peptides and Ellman's assay to detect free thiols. Human mesenchymal stem cells remained viable after encapsulation and subsequent photopatterning, demonstrating the utility of the monomers and hydrogels for three-dimensional cell culture. This facile approach enables the formation and characterization of hydrogels with well-defined, spatially-specific properties and expands the suite of monomers available for three-dimensional cell culture and other biological applications.
Application of the Two-Dimensional Frequency Domain Least Squares Algorithm to Airborne Surveillance Radar Detection (2000)

The application of the two-dimensional frequency domain least squares (2D-FD-LS) algorithm to parametric-based airborne radar detection is discussed herein. Several issues such as model order selection and model stabilization are considered. The frequency-domain version of the test statistic is also derived here. Simulation-based results demonstrate that good performance can be obtained.
Sensitivity to binaural timing in bilateral cochlear implant users (2007)

Various measures of binaural timing sensitivity were made in three bilateral cochlear implant users, who had demonstrated moderate-to-good interaural time delay (ITD) sensitivity at 100 pulses-per-second (pps). Overall, ITD thresholds increased at higher pulse rates, lower levels, and shorter durations, although intersubject differences were evident. Monaural rate-discrimination thresholds, using the same stimulation parameters, showed more substantial elevation than ITDs with increased rate. ITD sensitivity with 6000 pps stimuli, amplitude-modulated at 100 Hz, was similar to that with unmodulated pulse trains at 100 pps, but at 200 and 300 Hz performance was poorer than with unmodulated signals. Measures of sensitivity to binaural beats with unmodulated pulse-trains showed that all three subjects could use time-varying ITD cues at 100 pps, but not 300 pps, even though static ITD sensitivity was relatively unaffected over that range. The difference between static and dynamic ITD thresholds is discussed in terms of relative contributions from initial and later arriving cues, which was further examined in an experiment using two-pulse stimuli as a function of interpulse separation. In agreement with the binaural-beat data, findings from that experiment showed poor discrimination of ITDs on the second pulse when the interval between pulses was reduced to a few milliseconds.
Neuritic Plaque Amyloid in Alzheimer's Disease Is Highly Racemized (1988)

Neuritic plaque core amyloid protein in Alzheimer's disease brain tissue was investigated for the extent of amino acid racemization. Long-lived human proteins exhibit racemization of certain amino acids over the course of a human lifetime. Purified core amyloid was found to contain relatively large proportions of D-aspartate and D-serine, suggesting that neuritic plaque amyloid is derived from a long-lived precursor protein. Alternatively, racemization of protein amino acids may be abnormally accelerated in Alzheimer's disease.
Stretchable Displays: Stretchable Active Matrix Inorganic Light‐Emitting Diode Display Enabled by Overlay‐Aligned Roll‐Transfer Printing (Adv. Funct. Mater. 11/2017) (2017)

An all-inorganic-material-based stretchable display, which is composed of single-crystal Si transistor and inorganic light-emitting diode, synthesized via the overlay-aligned roll transfer printing method, is demonstrated by Jae-Hyun Kim, Jong-Hyun Ahn, and co-workers in article number 1606005. The display, which presents excellent, reliable electrical and mechanical properties, suggests the feasibility of an emerging stretchable and wearable display.
Design of Compact RFQs (1996)

New features have been put into the design of RFQ accelerators, which result in small emittance growth, reduce the length of the RFQ structure and can be used to improve the matching to the following linac, buncher, chopper or funneling line. Design examples are presented for the new high current linac at GSI, for the ESS study, and for the HIIF injectors.
A clinicopathologic and immunohistochemical analysis of 53 cases of medulloblastoma with emphasis on synaptophysin expression. (1990)

Synaptophysin (SYN) has been identified as an integral membrane glycoprotein of presynaptic vesicles in neurons and neuroendocrine cells, and as a marker for medulloblastoma and other neuronal tumors. SYN expression was studied with a monoclonal antibody (MAb) by the immunoperoxidase technique in 53 medulloblastomas. The expression of neuron-specific enolase (NSE), Leu-7 (LEU), S-100 protein (S100), glial fibrillary acidic protein (GFAP), neurofilament protein (NF), vimentin (VIM), cytokeratin (CKER), and desmin (DES) was also assessed with antisera and MAbs. SYN reactivity was present in 94% of tumors, whereas reactivity with other markers of neuronal differentiation was also observed: NSE (100%) and LEU (83%). Regarding the intermediate filament proteins, 38% of the cases were reactive for VIM, 21% for GFAP, and 9% for DES; none expressed NF or CKER. Eight percent were reactive for S100. Among the 53 cases, the male-female ratio was 1:3; 80% of DES-positive tumors occurred in females. The mean age was 10.5 yr, (60% diagnosed in the first decade; peak age incidence between 5 and 10 yr). Five tumors were discovered in patients older than 20 yr of age. Follow-up showed that 40% of patients developed a recurrence and 47% of patients died of tumor. No statistically significant relationship was demonstrated between patterns of immunoreactivity and prognosis. We conclude that SYN is a useful marker for medulloblastomas, indicating that this tumor is a primitive neuronal-neuroblastic neoplasm. However, it is but one of several immunophenotypic markers expressed by the medulloblastoma.
Efficient Mapping and Cloning of Mutations in Zebrafish by Low-Coverage Whole-Genome Sequencing (2011)

The generation and analysis of mutants in zebrafish has been instrumental in defining the genetic regulation of vertebrate development, physiology, and disease. However, identifying the genetic changes that underlie mutant phenotypes remains a significant bottleneck in the analysis of mutants. Whole-genome sequencing has recently emerged as a fast and efficient approach for identifying mutations in nonvertebrate model organisms. However, this approach has not been applied to zebrafish due to the complicating factors of having a large genome and lack of fully inbred lines. Here we provide a method for efficiently mapping and detecting mutations in zebrafish using these new parallel sequencing technologies. This method utilizes an extensive reference SNP database to define regions of homozygosity-by-descent by low coverage, whole-genome sequencing of pooled DNA from only a limited number of mutant F(2) fish. With this approach we mapped each of the five different zebrafish mutants we sequenced and identified likely causative nonsense mutations in two and candidate mutations in the remainder. Furthermore, we provide evidence that one of the identified mutations, a nonsense mutation in bmp1a, underlies the welded mutant phenotype.
<i>p</i> -type SiGe channel modulation doped field-effect transistors with post-evaporation patterned submicrometre Schottky gates (1993)

Schottky gate biased p-type MODFETs with an Si0.03Ge0.35 channel are presented. A wet-chemical post-evaporation procedure of the Schottky gates allows the reduction of the gate length LG to submicrometre dimensions (0.5 μm). The gate length dependence of the transconductance gme and gmi is reported. Maximum values are 37 or 103mS/mm at 300 or 77 K. The devices work in the enhancement mode.
Evolutionary privacy-preserving data mining (2010)

Data mining technology can help extract useful knowledge from large data sets. The process of data collection and data dissemination may, however, result in an inherent risk of privacy threats. Some sensitive or private information about individuals, businesses and organizations has to be suppressed before it is shared or published. The privacy-preserving data mining (PPDM) has thus become an important issue in recent years. In this paper, we propose an evolutionary privacy-preserving data mining method to find appropriate transactions to be hidden from a database. The proposed approach designs a flexible evaluation function with three factors, and different weights may be assigned to them depending on users' preference. Besides, the concept of prelarge itemsets is used to reduce the cost of rescanning a database and speed up the evaluation process of chromosomes. The proposed approach can thus easily make a good trade-off between privacy preserving and execution time.
Islet Inflammation Impairs the Pancreatic β-Cell in Type 2 Diabetes (2009)

Onset of Type 2 diabetes occurs when the pancreatic beta-cell fails to adapt to the increased insulin demand caused by insulin resistance. Morphological and therapeutic intervention studies have uncovered an inflammatory process in islets of patients with Type 2 diabetes characterized by the presence of cytokines, immune cells, beta-cell apoptosis, amyloid deposits, and fibrosis. This insulitis is due to a pathological activation of the innate immune system by metabolic stress and governed by IL-1 signaling. We propose that this insulitis contributes to the decrease in beta-cell mass and the impaired insulin secretion observed in patients with Type 2 diabetes.
Melatonin and breast cancer: cellular mechanisms, clinical studies and future perspectives (2009)

Recent studies have suggested that the pineal hormone melatonin may protect against breast cancer, and the mechanisms underlying its actions are becoming clearer. Melatonin works through receptors and distinct second messenger pathways to reduce cellular proliferation and to induce cellular differentiation. In addition, independently of receptors melatonin can modulate oestrogen-dependent pathways and reduce free-radical formation, thus preventing mutation and cellular toxicity. The fact that melatonin works through a myriad of signalling cascades that are protective to cells makes this hormone a good candidate for use in the clinic for the prevention and/or treatment of cancer. This review summarises cellular mechanisms governing the action of melatonin and then considers the potential use of melatonin in breast cancer prevention and treatment, with an emphasis on improving clinical outcomes.
Shiryayev sequential probability ratio test for redundancy management (1984)

An essential aspect in the design of fault-tolerant digital flight control systems is the design of failure detection and redundancy management systems. A decision rule, the Shiryayev sequential probability ratio test (SPRT), is derived from a dynamic programming approach and is used to detect failures between similar instruments, as well as between dissimilar instruments through analytic redundancy. Unlike the Wald SPRT, which tests for the presence of failure or no failure in all of the data sequence, the Shiryayev SPRT detects the occurrence of a fault in the data sequence in minimum time if certain conditions are met. The performance of the Shiryayev SPRT in detecting a failure between two rate gyros as compared to standard fixed interval schemes is presented, as well as the performance of a single accelerometer failure using translational kinematic equations to form a parity relation for analytic redundancy.
A robust video watermarking method (2002)

We propose a new watermarking method to embed a label in a video which is robust against the change of the group of picture. The proposed method embeds labels in the pixel domain, but detects them in the DCT frequency domain. A lookup table of the unique relationship between the pixel patterns and their sign sequences of eight low DCT coefficients is employed. To keep a quality of videos after embedding a label, the size of watermark is determined based on the human visual system. We analyze bit error rates of labels embedded in MPEG2 compressed video using the central limit theorem and compare the simulation results with previous methods.
Drugs of natural origin : a textbook of pharmacognosy (1999)

1. Crude Drugs 2. Plant Tissue and Cell Culture (Plant Biotechnology) 3. Formation of Pharmacologically Active Compounds in Plants - Biosynthesis 4. Carbohydrates 5. Natural Products Derived Biosynthetically from Shikimic Acid 6. Natural Products Derived Biosynthetically From Acetate 7. Amino Acids 8. Natural Products Derived Biosynthetically From Amino Acids 9. Alkaloids 10. Purines 11. Vitamin B Complex 12. Allergy and Allergens.
Connection mechanism of physical-contact optical fiber connectors with spherical convex polished ends (1991)

We present an experimental and analytical investigation of the connection mechanism of physical-contact optical-fiber connectors with spherical convex polished ends and confirm that reducing the curvature radius of the spherical convex ferrule end face is effective for establishing a stable connection with slight axial compressive force on the ferrules.
1 000 000 °C/s thin film electrical heater: <i>In</i> <i>situ</i> resistivity measurements of Al and Ti/Si thin films during ultra rapid thermal annealing (1994)

We introduce a new technique for rapidly heating (106 °C/s) thin films using an electrical thermal annealing (ETA) pulse technique. By applying a high-current dc electrical pulse to a conductive substrate-heater material (Si), joule heating occurs thus heating the thin film. This method was demonstrated by heating thin films of aluminum at rates ranging from 103 to 106 °C/s. The temperature of the system is measured by using the substrate heater as a thermistor and is found to be within ≊±10 °C during anneals at ≊105 °C/s. Phase transformations in the Ti-Si system were also observed using in situ resistivity measurements during ETA at ≊104 °C.
Combined Fish Oil and High Oleic Sunflower Oil Supplements Neutralize their Individual Effects on the Lipid Profile of Healthy Men (2013)

Both n-3 and n-9 fatty acids share a common metabolic pathway and can potentially and individually improve cardiovascular disease risk factors. Dietary n-6 is known to weaken the efficacy of n-3 fatty acids due to competition for the same enzymes. Still unclear is whether a similar competition exists between n-3 and n-9 fatty acids. Thus, a 12-week intervention study was conducted to investigate the effect of different combinations of fish oil and high-oleic sunflower oil (OSO) on healthy subjects. Included were five groups (98 subjects): three groups received a fixed amount of n-9 (8 g/day) with varying amounts of n-3 (1, 2 or 4 g/day), one group was given n-3 fatty acids only (2 g/day) and another was given n-9 only (8 g/day). We found that fish oil supplement (2 g/day) was able to decrease TAG by about 13 %, this effect was diminished with the co-ingestion of n-9 (OSO). Intake of OSO (8 g/day) reduced both total and LDL cholesterol by about 10 %, this effect was reduced by the addition of fish oil. Both fish oil and OSO failed to have any significant effect on both glycemic and blood pressure parameters. In conclusion; the impact of oleic acid (n-9) on total and LDL cholesterol was altered by the addition fish oil (n-3). These effects may have been the result of enzymatic competition between the two types of fatty acids.
Visual Interface for Online Watching of Frequent Itemset Generation in Apriori and Eclat (2006)

This paper describes an interactive graphical user interface tool called Visual Apriori that can be used to study two famous frequent itemset generation algorithms, namely, Apriori and Eclat. Understanding the functional behavior of these two algorithms is critical for students taking a data mining course; and Visual Apriori provides a hands-on environment for doing so. Visual Apriori relies on active participation from the user, where one inputs a transactional database and the tool produces a tree-based frequent itemset generation animation for the algorithm chosen. Visual Apriori provides an effortless learning experience by featuring user-friendly and easy to understand controls.
Role of Trauma in Isomorphic Response in Psoriasis (1965)

The induced isomorphic response was used as a model in the study of the pathogenesis of psoriasis. Scraping to minute bleeding and freezing with Frigiderm induced a positive isomorphic response in 22 out of 49 patients, and in 48 out of 94 patients, respectively. These differences are not statistically significant. Pretreatment with lidocaine (Xylocaine), however, reduced significantly the number of positive responses. This effect is ascribed to the vasoconstrictor action of this substance. Dermal knife injury did not result in psoriatic lesions in the epidermis overlying the dermal cut. The intradermal placement of catgut produced a minimal inflammatory response in the dermis with no demonstrable change in the overlying epidermis. Hyaluronidase injected intradermally provoked moderate inflammatory reaction in the upper dermis with no elicitation of the isomorphic response. Chymotrypsin injected intradermally produced a severe inflammatory reaction in the mid- and upper dermis with no elicitation of the Koebner response. The dermal injury alone as employed in this study, therefore, was not sufficient to evoke an isomorphic response. There seems to be a relationship between the amount of trauma and appearance of the isomorphic response. This reaction is more likely to occur in patients with active psoriasis.
Changes in maternal ratings of children's overt and covert antisocial behavior (2005)

Maternal ratings of overt and covert forms of aggression were collected for two samples of children ranging in age from 2 through 12 years. It was hypothesized that longitudinal analyses would show the slope scores for these two forms of aggression to be quite different from each other. The data were consistent with this hypothesis. An effort was made to find alternative explanations for the negative slope for overt antisocial behavior. Alternatively, it was hypothesized that the more extreme cases would not show this negative slope. It was also hypothesized that careful examination of intraindividual curves would identify a significant number of individuals growing from normal to clinical levels of overt antisocial behavior. The findings led to the rejection of both alternative hypotheses. It was hypothesized that overt and covert scores would correlate significantly for first grade boys. It was also assumed that both covert and overt scores would show moderate stability over the 5-year interval. The findings were consistent with both of these hypotheses. Aggr. Behav. 00:1–12, 2005. © 2005 Wiley-Liss, Inc.
HVAC System Cloud Based Diagnostics Model (2014)

We present a new monitoring and diagnostics model for residential Heating, Ventilation, and Air Conditioning (HVAC) systems. This model will provide a new diagnostics technology system that leverages the latest technology advancements. The model benefits from the cloud computing advantages and offers continuous diagnostic capabilities. Using embedded sensors and monitoring modules for the indoor and outdoor HVAC units, various measurements are transmitted to a cloud sever utilizing the homeowner pre-existing Wi-Fi network. On the cloud side, algorithms process the data and generate triggers that a problem may exist. Relevant information is then shared with home owners and contractors via e-mail & portals. In this paper we explain the system in more detail by providing actual case studies which demonstrate the value in a proactive maintenance and repair model as supported by time-series data. This contrasts the reactive model that exists today.
Interaction Between the Serotonin Transporter Gene (5-HTTLPR), Stressful Life Events, and Risk of Depression (2009)

This meta-analysis yielded no evidence that the serotonin transporter genotype alone or in interaction with stressful life events is associated with an elevated risk of depression in men alone, women alone, or in both sexes combined.