gebhart/patrepeval huggingface dataset:
Integrated Analysis Reveals hsa-miR-142 as a Representative of a Lymphocyte-Specific Gene Expression and Methylation Signature (2012)

Gene expression profiling has provided insights into different cancer types and revealed tissue-specific expression signatures. Alterations in microRNA expression contribute to the pathogenesis of many types of human diseases. Few studies have integrated all levels of gene expression, miRNA and methylation to uncover correlations between these data types. We performed an integrated profiling to discover instances of miRNAs associated with a gene expression and DNA methylation signature across multiple cancer types. Using data from The Cancer Genome Atlas (TCGA), we revealed a concordant gene expression and methylation signature associated with the microRNA hsa-miR-142 across the same samples. In all cancer types examined, we found a signature of co-expression of a gene set R and methylated sites M, which correlate positively (M+) or negatively (M–) with the expression of hsa-miR-142. The set R consistently contains many genes, such as TRAF3IP3, NCKAP1L, CD53, LAPTM5, PTPRC, EVI2B, DOCK2, LCP2, CYBB and FYB. The signature is preserved across glioblastoma, ovarian, breast, colon, kidney, lung, uterine and rectum cancer. There is 28% overlap of methylation sites in M between glioblastoma (GBM) and ovarian cancer. There is 60% overlap of genes in R between GBM and ovarian ( P = 1.3e −-11 ). Most of the genes in R are known to be expressed in lymphocytes and haematopoietic stem cells, while M reflects membrane proteins involved in cell-cell adhesion functions. We speculate that the hsa-miR-142 associated signature may signal haematopoietic-specific processes and an accumulation of methylation events triggering a progressive loss of cell-cell adhesion. We also observed that GBM samples belonging to the proneural subtype tend to have underexpressed hsa-miR-142 and R genes, hypomethylated M+ and hypermethylated M–, while the mesenchymal samples have the opposite profile.
Use of X-Ray Diffraction in Study of Human Diabetic and Aging Collagen (1991)

Extensive investigations of the solubility and fluorescence of collagen fibers in diabetes have revealed that there are significant changes in their physical properties. These changes are associated with increased cross-link formation. We used X-ray diffraction to study these changes in human extensor tendons at a molecular level in relation to both aging and diabetes. Our results indicate that diabetes induces significant alterations in the ultrastructure of collagen in the lateral packing of the molecules and the axial structure of the specimen. These changes can be induced in normal tendon by incubation in ribose and glucose-6-phosphate but are different from those associated with the normal process of aging.
Structure-guided pharmacophore based virtual screening, docking, and molecular dynamics to discover repurposed drugs as novel inhibitors against endoribonuclease Nsp15 of SARS-CoV-2 (2022)

COVID-19 (Corona Virus Disease of 2019) caused by the novel 'Severe Acute Respiratory Syndrome Coronavirus-2' (SARS-CoV-2) has wreaked havoc on human health and the global economy. As a result, for new medication development, it's critical to investigate possible therapeutic targets against the novel virus. 'Non-structural protein 15' (Nsp15) endonuclease is one of the crucial targets which helps in the replication of virus and virulence in the host immune system. Here, in the current study, we developed the structure-based pharmacophore model based on Nsp15-UMP interactions and virtually screened several databases against the selected model. To validate the screening process, we docked the top hits obtained after secondary filtering (Lipinski's rule of five, ADMET & Topkat) followed by 100 ns molecular dynamics (MD) simulations. Next, to revalidate the MD simulation studies, we have calculated the binding free energy of each complex using the MM-PBSA procedure. The discovered repurposed drugs can aid the rational design of novel inhibitors for Nsp15 of the SARS-CoV-2 enzyme and may be considered for immediate drug development.
[Novel high-throughput sequencing strategies in genetic diagnostics]. (2013)

Novel high-throughput sequencing strategies in genetic diagnostics Capabilities of novel high-throughput DNA sequencing systems have revolutionized genetic research and made it possible to analyze complex eukaryotic genomes. Despite the radical improvements, sequencing of the entire human genome still remains too complicated and expensive for clinical diagnostic applications. Recently developed targeted sequencing strategies provide an immediate technological solution to analyze all clinically significant genomic regions and radically reduce sequencing costs, increase variant detection quality and limit ethical issues. In the near future, these advanced approaches can be applied for diagnostics of several diseases that have known genetic backgrounds and optimization of treatments based on individual genetic traits.
Neurophysiology of Performance Monitoring and Adaptive Behavior (2014)

Successful goal-directed behavior requires not only correct action selection, planning, and execution but also the ability to flexibly adapt behavior when performance problems occur or the environment changes. A prerequisite for determining the necessity, type, and magnitude of adjustments is to continuously monitor the course and outcome of one's actions. Feedback-control loops correcting deviations from intended states constitute a basic functional principle of adaptation at all levels of the nervous system. Here, we review the neurophysiology of evaluating action course and outcome with respect to their valence, i.e., reward and punishment, and initiating short- and long-term adaptations, learning, and decisions. Based on studies in humans and other mammals, we outline the physiological principles of performance monitoring and subsequent cognitive, motivational, autonomic, and behavioral adaptation and link them to the underlying neuroanatomy, neurochemistry, psychological theories, and computational models. We provide an overview of invasive and noninvasive systemic measures, such as electrophysiological, neuroimaging, and lesion data. We describe how a wide network of brain areas encompassing frontal cortices, basal ganglia, thalamus, and monoaminergic brain stem nuclei detects and evaluates deviations of actual from predicted states indicating changed action costs or outcomes. This information is used to learn and update stimulus and action values, guide action selection, and recruit adaptive mechanisms that compensate errors and optimize goal achievement.
Building blocks for mobile free-space-optical networks (2005)

Existence of line of sight (LOS) and alignment between the communicating antennas are one of the key requirements for free-space-optical (FSO) communication. To ensure uninterrupted data flow, auto-aligning transmitter and receiver modules are necessary. We propose a new optical antenna design that employs spherical antennas covered with transmitter and receiver modules for maintaining optical links even when antennas are in relative motion. In this paper, for proof-of-concept, we design and test an auto-configurable circuit integrated with light sources and detectors placed on spherical surfaces. We also perform simulation-based analysis of these multi-element FSO modules that can enable mobility and high bandwidth in wireless, particularly indoor, networks. Broader impact of our work is to make FSO communication technology widely applicable in mobile, ad-hoc, and multi-hop wireless networks.
A Cellular Automata approach for superpixel segmentation (2011)

This paper presents a novel Cellular Automata (CA) approach for image segmentation. We treat the image segmentation problem as cell merging in a cellular space constructed in the image plane. A cell is defined to be a pixel or a group of pixels with close RGB values. In each iteration, a cell checks the similarities between itself and its neighboring cells. Cells with similar properties are merged into large cells, which will eventually lead to high quality superpixels. The segmentation process is a trade-off between accuracy and computation cost. We have proved that the proposed approach is able to obtain satisfactory results efficiently while keeping image details.
Sweet and sour: an update on classic galactosemia (2017)

Classic galactosemia is a rare inherited disorder of galactose metabolism caused by deficient activity of galactose-1-phosphate uridylyltransferase (GALT), the second enzyme of the Leloir pathway. It presents in the newborn period as a life-threatening disease, whose clinical picture can be resolved by a galactose-restricted diet. The dietary treatment proves, however, insufficient in preventing severe long-term complications, such as cognitive, social and reproductive impairments. Classic galactosemia represents a heavy burden on patients' and their families' lives. After its first description in 1908 and despite intense research in the past century, the exact pathogenic mechanisms underlying galactosemia are still not fully understood. Recently, new important insights on molecular and cellular aspects of galactosemia have been gained, and should open new avenues for the development of novel therapeutic strategies. Moreover, an international galactosemia network has been established, which shall act as a platform for expertise and research in galactosemia. Herein are reviewed some of the latest developments in clinical practice and research findings on classic galactosemia, an enigmatic disorder with many unanswered questions warranting dedicated research.
Experimental and theoretical study on device-processing-incorporated fluorine in AlGaN/GaN heterostructures (2020)

This paper reports on an in-depth research on the etching-process induced current degradation in AlGaN/GaN heterostructures by experimental research and theoretical calculations. The channel current degrades by 60% after the etching process and recovers to 90% after thermal annealing at 400 °C. It is found that fluorine is incorporated into the heterostructures of both AlGaN and GaN layers during the etching process. The degradation and recovery of the current is accompanied by the change in the concentration of fluorine in both AlGaN and GaN layers during the experiment. First-principles defect calculations of fluorine in GaN indicate that the dominant defect configuration of F is negatively charged interstitial (Fi−) with the lowest formation energy. The accompanied technology computer-aided design simulation of the energy bands reveals that Fi− raises the conduction band minimum of GaN and, thus, decreases the density of the two-dimensional electron gas, causing degradation of the channel current. This result leads to the post-etching recovery treatment without a high temperature process and ohmic contact degradation.
On consensus biomarker selection (2007)

The proposed methodology can improve the classification results and at the same time provide a unified biomarker list for further biological examinations and interpretation.
Regulation of poly(ADP-ribose) polymerase 1 activity by the phosphorylation state of the nuclear NAD biosynthetic enzyme NMN adenylyl transferase 1 (2007)

Nuclear NAD(+) metabolism constitutes a major component of signaling pathways. It includes NAD(+)-dependent protein deacetylation by members of the Sir2 family and protein modification by poly(ADP-ribose) polymerase 1 (PARP-1). PARP-1 has emerged as an important mediator of processes involving DNA rearrangements. High-affinity binding to breaks in DNA activates PARP-1, which attaches poly(ADP-ribose) (PAR) to target proteins. NMN adenylyl transferases (NMNATs) catalyze the final step of NAD(+) biosynthesis. We report here that the nuclear isoform NMNAT-1 stimulates PARP-1 activity and binds to PAR. Its overexpression in HeLa cells promotes the relocation of apoptosis-inducing factor from the mitochondria to the nucleus, a process known to depend on poly(ADP-ribosyl)ation. Moreover, NMNAT-1 is subject to phosphorylation by protein kinase C, resulting in reduced binding to PAR. Mimicking phosphorylation, substitution of the target serine residue by aspartate precludes PAR binding and stimulation of PARP-1. We conclude that, depending on its state of phosphorylation, NMNAT-1 binds to activated, automodifying PARP-1 and thereby amplifies poly(ADP-ribosyl)ation.
Detection of aneuploidy and chromosomal mosaicism in human embryos during preimplantation sex determination by fluorescent <i>in situ</i> hybridisation, (FISH) (1993)

Five couples at risk of producing offspring with X-linked recessive disease underwent in vitro fertilisation with a view to preimplantation determination of embryo sex and selective transfer of females. On day three postinsemination, one or two blastomeres were removed by embryo biopsy, and used for dual fluorescent in situ hybridisation with X and Y chromosome-specific DNA probes. In two cases, two female embryos were transferred and one pregnancy, (sex confirmed), is ongoing at 19 weeks. All eight embryos from one couple were of such poor quality that diagnosis was possible in one only. In the remaining two cases no embryos were transferred due to the detection of an abnormal number of X chromosome signals. Investigation of the biopsied embryos that were not transferred revealed evidence of mitotic non-disjunction in one and of complete X monosomy in a second. A surviving fetus with this latter constitution would have developed Turner syndrome and would also have been at high risk of X-linked disease. The use of fluorescent in situ hybridisation rather than the polymerase chain reaction allowed the detection of abnormal copy numbers of X chromosomes thus preventing the transfer of potentially abnormal zygotes.
European Coatings Handbook (2019)

The eBook edition covers the entire spectrum of coatings formulation in a single volume and acts as a vehicle for acquiring and deepening a sound knowledge of all the important principles of coatings production. The handbook's topicality in all aspects of coatings composition, application methodology, quality assurance, environment and industrial health, and safety is highly useful -not only to those in training but also to established professionals who wish to update their knowledge thoroughly. With this eBook you acquire a nonexclusive, nontransferable, spatially and temporally unrestricted right to download the purchased content on a device of your choice as well as to download and transfer it up to five additional devices in your possession.You can save the downloaded content on each of the individual devices once to view it unlimited times
Gripping Without Slipping — The Safe Handling and Running of Chrome Pipe with Hard Surfaces (2002)

Abstract In a corrosive downhole environment, the service life of a completion can be severely reduced if suitable precautions are not taken. Pipe made of corrosion resistant alloys (C.R.A.) is used to minimize corrosion. Recently, steel manufactures have developed modified corrosion resistant alloys (C.R.A.), specifically derivatives of Cr13, that are characterized by a black smooth scale surface on the outside of the pipe. When these so called "Super" or "Hyper" alloys were first used, occasional slipping was reported by field personnel. Fortunately no string was lost and no injuries occurred, however, precious rig time was lost in resuming safe operations. These slippages occurred with various inserts and with all types of slip-type elevators or spiders. An investigation carried out by the University of Hannover revealed that the surface scale on the pipe had a hardness of over 60 Rc. Even inserts specifically designed for C.R.A. pipe that use special gripping elements, such as the Micro-Grip™ system have a hardness that is only slightly higher than this surface scale. Using conventional wedge type spider and elevator systems can lead to slippage under certain load conditions, if no special precautions are taken. Based on these results and on the operating principles of wedge type spiders and elevators, a new Compact Spider/Elevator was designed. This device can be either air or hydraulically operated and puts an additional downward force onto the slip, as much as 40 tons for the hydraulic version, so that a firm grip is assured. In addition to conventional steel inserts, the device can be equipped with so called MicroGrip ™ inserts, a gripping system that distributes the required load equally onto a large number of small peaks. This minimizes the indentation of each single peak and thus, as previous research and field experience has shown, preserves the surface integrity of the pipe with regard to corrosion [2, 3, 4]. The device can be run flush-mounted, further enhancing safety on the rig-floor.
Constrained minimum-time path planning for robot manipulators via virtual knots of the cubic B-spline functions (1990)

The B-spline functions are used to generate the constrained minimum-time path for a robot manipulator. The interpolated path via B-spline functions is determined via a unique set of virtual knots so that the robot path can pass every intermediate knot and satisfy the boundary conditions. The local control property of the B-spline functions can also be utilized to simplify the involved computational complexities. The flexible polyhedron search algorithm is used to generate the near minimum-time path with velocity, acceleration, and jerk constraints on every intermediate point. This approach can simplify the formulation and procedures for generating the near minimum-time cubic B-spline path. The use of this method to generate the constrained minimum-time joint trajectories for a PUMA 560 robot is discussed as an example.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Power spectra of geomagnetic fluctuations between 0.1 and 10.0 Hz (1978)

An optically pumped Cesium vapor magnetometer was used to measure the temporal fluctuations of the total geomagnetic field at Monterey, California. Power spectra were obtained from these recordings for the frequency range 0.1-10 Hz. Measurements were made during the month of April 1978 with the Kp index varying from 0+-8+. The power spectra obtained displayed a characteristic -20 dB/decade slope from 0.1-2.0 Hz and were essentially flat between 2.0-10 Hz. Measurement times were: Local night (0000-0200), local morning (0800-1000) and local afternoon (1600-1800). Local morning exhibited the highest power density levels, exceeding the lowest power density levels (recorded during local night) by 10dB at .1 Hz and 3dB at 10 Hz. A comparison of a magnetically disturbed day (Fredricksburg a index of 7) with a magnetically quiet day (Fredricksburg a index of 3) showed that at the low frequency end of the spectrum (.1-.6 Hz) there was 10dB more power on the disturbed day. (Author)
Proteomics in pathology research (2004)

Proteomics is a multifaceted approach to study various aspects of protein expression, post-translational modification, interactions, organization and function at a global level. While DNA constitutes the 'information archive of the genome', it is the proteins that actually serve as the functional effectors of cellular processes. Thus, analysis of protein derangements on a proteome-wide scale will reveal insights into deregulated pathways and networks involved in the pathogenesis of disease. Although the field of proteomics has advanced tremendously in recent years, there are significant technical challenges that pose limitations to the routine application of mass spectrometry to clinical research. Despite these challenges, proteomic studies have yielded unparalleled information and understanding of the cellular biology of diseased states. The application of mass spectrometry to the study of diseases will ultimately lead to identification of biomarkers that are critical for the detection, diagnosis, prognosis and treatment of specific disease entities.
DNp73 improves generation efficiency of human induced pluripotent stem cells (2012)

This study found DNp73, a family member of p53, is also involved in the human iPS cell generation. Specifically, that the involvement of DNp73 generates iPS cells that are more resistant to in vitro and in vivo differentiation. Therefore, this data may prove to be useful in future developmental studies and cancer researches.
Dynamic argument embedding: preserving state on the World Wide Web (1997)

At the IBM T.J. Watson Research Center we implemented a way of preserving state during HTTP sessions by modifying hypertext links to encode state information. We call the method dynamic argument embedding, and it was developed in response to problems we encountered implementing the Coyote Virtual Store, a transaction-processing system prototype. Virtual store applications, such as IBM's NetCommerce and Netscape's Merchant System, typically need to maintain information such as the contents of shopping baskets while customers are shopping. We wanted our application to be flexible enough to maintain such state information without restricting the sorts of HTML pages a customer might view. We also wanted a system that did not require extensions to the hypertext transfer protocol (HTTP) and so could be implemented on any standard Web server and client browser. Finally, we wanted to permit customers to access several accounts at once by using the browser's cache to concurrently store pages corresponding to multiple invocations of the virtual store application.
An efficient feature selection using multi-criteria in text categorization for naïve Bayes classifier (2005)

Feature selection is one of the most interesting problems in machine learning in general and text categorization in particular. Previous researches in feature selection often focus on choosing appropriate measument to evaluate features. This seems to be good for structured data but rather difficult to text, a nonstructured data. Our main contribution in this paper is to propose a new approach of feature selection based on multi-criteria ranking of features. A new model for feature selection is propose; based on a threshold value for each criterion, a new procedure for feature selection is proposed and applied to a text categorization. Experiments show that the proposed model outperforms performances in compare to conventional feature selection methods.
New isotonic drinks with antioxidant and biological capacities from berries (maqui, açaí and blackthorn) and lemon juice (2013)

The aim of the study was to design new isotonic drinks with lemon juice and berries: maqui [Aristotelia chilensis (Molina) Stuntz], açaí (Euterpe oleracea Mart.) and blackthorn (Prunus spinosa L.), following on from previous research. Quality parameters - including colour (CIELab parameters), minerals, phytochemical identification and quantification by high-performance liquid chromatography with diode array detector, total phenolic content by the Folin-Ciocalteu reagent, the antioxidant capacity (ABTS(+), DPPH• and [Formula: see text] assays) and biological activities (in vitro alpha-glucosidase and lipase inhibitory effects) - were tested in the samples and compared to commercially available isotonic drinks. The new isotonic blends with lemon and anthocyanins-rich berries showed an attractive colour, especially in maqui samples, which is essential for consumer acceptance. Significantly higher antioxidant and biological effects were determined in the new blends, in comparison with the commercial isotonic beverages.