gebhart/patrepeval huggingface dataset:
Going the Distance for Protein Function Prediction: A New Distance Metric for Protein Interaction Networks (2013)

In protein-protein interaction (PPI) networks, functional similarity is often inferred based on the function of directly interacting proteins, or more generally, some notion of interaction network proximity among proteins in a local neighborhood. Prior methods typically measure proximity as the shortest-path distance in the network, but this has only a limited ability to capture fine-grained neighborhood distinctions, because most proteins are close to each other, and there are many ties in proximity. We introduce diffusion state distance (DSD), a new metric based on a graph diffusion property, designed to capture finer-grained distinctions in proximity for transfer of functional annotation in PPI networks. We present a tool that, when input a PPI network, will output the DSD distances between every pair of proteins. We show that replacing the shortest-path metric by DSD improves the performance of classical function prediction methods across the board.
Computing reserve prices and identifying the value distribution in real-world auctions with market disruptions (2008)

Single-good ascending auctions, including the English Auction and its close variants (e.g. eBay), are the most widely used type of auction. Effective strategies for buyers and sellers in these auctions can have an enormous economic impact. We present a system that, relying on minimal assumptions, computes reserve prices for real-world ascending auctions by inferring the value distribution from past auction data. Our contributions include improvements on previous methods for estimating the bidder value distribution, and novel Bayesian methods for adapting to disruptions in market conditions. We demonstrate the effectiveness of our system in both simulated auctions and in real Internet auctions that we conducted in the domain of selling off returned merchandise.
Latent Link Analysis for Expert Finding in User-Interactive Question Answering Services (2009)

In this paper, we propose a latent link analysis approach for improving the accuracy of expert finding in user-interactive question answering (UIQA) services. Both direct and latent relationship links are considered in the link analysis of the user relation graph model. In the graph model, the direct links can be acquired directly from question-answer relationship between users. While the latent links, which reveal the latent question-answer relation between users, can be obtained indirectly by measuring the similarity between users' asked and answered question profiles. Finally, a propagation-based approach is employed to calculate the expert score for evaluating users' expertise levels. Experimental results show that our approach can perform better than the method without considering latent relationship links in terms of expert finding and ranking.
Expression of Asialoglycoprotein Receptor 1 in Human Hepatocellular Carcinoma (2013)

Human hepatocellular carcinoma (HCC) is the fifth most common cancer in the world. Currently, surgical resection is the only effective treatment for HCC if the tumor is resectable. Small molecule, biologics and siRNA anti-cancer drugs have been explored for the treatment of HCC. Selective targeting to tumor tissue rather than normal liver in HCC patients is still a challenge. Galactosamine-mediated targeting delivery of anti-cancer drugs in the liver has been tested because its receptor, asialoglycoprotein receptor 1 (ASGPR1), is expressed in the liver and not in other human tissues. We examined ASGPR1 expression levels by immunohistochemistry in HCC with different grades. Guidance for a targeting delivery strategy for anti-cancer drugs to HCC is suggested in this report.
Modulatory Effects of Melatonin and Vitamin E on Doxorubicin-Induced Cardiotoxicity in Ehrlich Ascites Carcinoma-Bearing Mice (2000)

Doxorubicin (Dox), an anthracycline antibiotic, has a wide spectrum of antitumor activity with dose-limiting cardiotoxicity. The drug's toxicity is known to be closely related to the generation of active oxygen free radicals. In our study the normal cardiac tissue contents of total protein, glutathione (GSH) and malondialdehyde (MDA) were significantly decreased, by 25%, 33% and 92%, respectively, in the group of mice bearing Ehrlich ascites carcinoma (EAC) and treated with Dox (4 mg/kg/week x 2, ip). Administration of melatonin (5 mg/kg/day x 15, po) starting 24 hours prior to Dox treatment significantly increased the cardiac contents of total protein and GSH as well as the superoxide dismutase (SOD) activity, by 31%, 36% and 39%, respectively, compared to treatment with Dox only, while the content of MDA was decreased by 26%. Similarly, administration of vitamin E (250 mg/kg/day x 15, po) starting 24 hours prior to Dox treatment significantly increased the cardiac contents of total protein, GSH and SOD, by 23%, 26% and 42%, respectively, while the cardiac content of MDA was decreased by 35% compared with the Dox-only-treated group. As to the oncolytic activity of Dox, pretreatment of EAC-bearing mice with melatonin (5 mg/kg/day x 30, po) or vitamin E (250 mg/kg/day x 30, po) 24 hours prior to Dox administration (4 mg/kg/week x 4, ip) improved the antitumor activity of Dox as indicated by the increase in the average life span of the animals and the number of long-term survivors as well as the decrease in body weight loss induced by Dox treatment. It is clear from these results that administration of melatonin not only protects against the cardiotoxicity induced by Dox treatment but also enhances its antitumor activity to a more significant extent than does vitamin E.
Microrna-Dependent Regulation of Dna Methyltransferase-1 and Tumor Suppressor Gene Expression by Interleukin-6 in Human Malignant Cholangiocytes (2009)

These data indicate that IL-6 can regulate the activity of DNMT-1 and expression of methylation-dependent tumor suppressor genes by modulation of miR-148a and miR-152, and provide a link between this inflammation-associated cytokine and oncogenesis in cholangiocarcinoma.
FULMINANT EOSINOPHILIC MYOCARDITIS LEADING TO SUDDEN DEATH IN A YOUNG ACROMEGALIC WOMAN (2005)

Click to increase image sizeClick to decrease image sizeKeywords: acromegaliaeosinophilic myocarditis
A probabilistic roadmap planner for flexible objects with a workspace medial-axis-based sampling approach (2003)

Probabilistic roadmap planners have been used with success to plan paths for flexible objects such as metallic plates or plastic flexible pipes. This paper improves the performance of these planners by using the medial axis of the workspace to guide the random sampling. At a preprocessing stage, the medial axis of the workspace is computed using a recent efficient algorithm. Then the flexible object is fitted at random points along the medial axis. The energy of all generated configurations is minimized and the planner proceeds to connect them with low-energy quasi-static paths in a roadmap that captures the connectivity of the free space. Given an initial and a final configuration, the planner connects these to the roadmap and searches the roadmap for a path. Our experimental results show that the new sampling scheme is successful in identifying critical deformations of the object along solution paths which results in a significant reduction of the computation time. Our work on planning for flexible objects has applications in industrial settings, virtual reality environments, and medicine.
A system for automatic software evaluation (1976)

The production of consistently executable and dependable software demands a thoughtful systematic implementation—with clear documentation at each production stage. Recognizing this, the Data Systems Laboratory, at Marshall Space Flight Center, NASA, began a research effort to help discover and institute sound engineering principles into a methodology for the production of software. The design of this methodology is based upon five principal stages of software development:1. Feasibility: Can software be written to solve the initial problem?2. Requirements/Design: Are software requirements and design clear, complete, traceable, and testable?3. Coding: Is use being made of reliable high level coding practices?4. Testing: Is testing sufficiently thorough to instill initial user confidence?5. Maintenance: has the software and its design been explicitly documented?
The DSI technique used on DDD paced patients (2002)

Digital subtraction imaging (DSI) can be used instead of standard chest X-ray radiographs for the radiological assessment after implantation of a duel chamber (DDD) pacemaker. The DSI system description, its processing functions, and use during pacemaker follow-up are outlined. By using edge-enhancement techniques and background subtraction, this method provides sharper visual information on the location of the pacemaker, the status of the lead-connection, and on the position and the functional integrity of the pacemaker leads which all can be examined in more detail using different zoom-functions. Pacemaker- and lead-related problems can therefore be more easily detected using DSI techniques.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Molecular Determinants of Human T-lymphotropic Virus Type 1 Transmission and Spread (2011)

Human T-lymphotrophic virus type-1 (HTLV-1) infects approximately 15 to 20 million people worldwide, with endemic areas in Japan, the Caribbean, and Africa. The virus is spread through contact with bodily fluids containing infected cells, most often from mother to child through breast milk or via blood transfusion. After prolonged latency periods, approximately 3 to 5% of HTLV-1 infected individuals will develop either adult T-cell leukemia/lymphoma (ATL), or other lymphocyte-mediated disorders such as HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). The genome of this complex retrovirus contains typical gag, pol, and env genes, but also unique nonstructural proteins encoded from the pX region. These nonstructural genes encode the Tax and Rex regulatory proteins, as well as novel proteins essential for viral spread in vivo such as, p30, p12, p13 and the antisense encoded HBZ. While progress has been made in the understanding of viral determinants of cell transformation and host immune responses, host and viral determinants of HTLV-1 transmission and spread during the early phases of infection are unclear. Improvements in the molecular tools to test these viral determinants in cellular and animal models have provided new insights into the early events of HTLV-1 infection. This review will focus on studies that test HTLV-1 determinants in context to full length infectious clones of the virus providing insights into the mechanisms of transmission and spread of HTLV-1.
A Smorgasbord of Features for Statistical Machine Translation (2004)

We conducted a case-control study to investigate whether vascular endothelial growth factor (VEGF -2578, -1154, -634, and 936) and kinase insert domain containing receptor (KDR -604, 1192, and 1719) polymorphisms are associated with moyamoya disease. Korean patients with moyamoya disease (n = 107, mean age, 20.9±15.9 years; 66.4% female) and 243 healthy control subjects (mean age, 23.0±16.1 years; 56.8% female) were included. The subjects were divided into pediatric and adult groups. Among the 64 surgical patients, we evaluated collateral vessel formation after 2 years and divided patients into good (collateral grade A) or poor (collateral grade B and C) groups. The frequencies and distributions of four VEGF (-2578, -1154, -634, and 936) and KDR (-604, 1192, and 1719) polymorphisms were assessed from patients with moyamoya disease and compared to the control group. No differences were observed in VEGF -2578, -1154, -634, and 936 or KDR -604, 1192, and 1719 polymorphisms between the control group and moyamoya disease group. However, we found the -634CC genotype occurred less frequently in the pediatric moyamoya group (p = 0.040) whereas the KDR -604C/1192A/1719T haplotype increased the risk of pediatric moyamoya (p = 0.024). Patients with the CC genotype of VEGF -634 had better collateral vessel formation after surgery. Our results suggest that the VEGF -634G allele is associated with pediatric moyamoya disease and poor collateral vessel formation.
The electronics system for the LBNL positron emission mammography (PEM) camera (2001)

Describes the electronics for a high-performance positron emission mammography (PEM) camera. It is based on the electronics for a human brain positron emission tomography (PET) camera (the Siemens/CTI HRRT), modified to use a detector module that incorporates a photodiode (PD) array. An application-specified integrated circuit (ASIC) services the photodetector (PD) array, amplifying its signal and identifying the crystal of interaction. Another ASIC services the photomultiplier tube (PMT), measuring its output and providing a timing signal. Field-programmable gate arrays (FPGAs) and lookup RAMs are used to apply crystal-by-crystal correction factors and measure the energy deposit and the interaction depth (based on the PD/PMT ratio). Additional FPGAs provide event multiplexing, derandomization, coincidence detection, and real-time rebinning. Embedded PC/104 microprocessors provide communication, real-time control, and configure the system. Extensive use of FPGAs make the overall design extremely flexible, allowing many different functions (or design modifications) to be realized without hardware changes. Incorporation of extensive onboard diagnostics, implemented in the FPGAs, is required by the very high level of integration and density achieved by this system.
Efficient Boolean function matching (1992)

Efficient algorithms for performing the matching step in technology mapping are proposed. The main result is an algorithm for matching under input negations that takes time polynomial in the size of the BDDs representing the functions to be matched. This algorithm is the basis for efficient methods for matching under permutations, bridging and constant inputs. A simple mapper based on the algorithms was implemented and tested on a suite of combinational circuits. Using the Actel type 1 mother cell, the mapper required an average of 8.5% fewer cells than mispga. When integrated into a more sophisticated technology mapper, the matching algorithms could provide even better performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Structure-activity relationship studies at benzodiazepine receptor (BZR): a comparison of the substituent effects of pyrazoloquinolinone analogs (1993)

The synthesis of a series of 2-phenylpyrazolo[4,3-c]quinolin-3-one derivatives and their in vitro biological evaluation as ligands for the benzodiazepine receptor are described. The in vitro activities, as determined by an analysis of GABA shift ratios, and binding affinities of these compounds to BZR are compared in terms of the electronic, lipophilic, and steric effect changes of their substituents.
Perigranuloma Localization and Abnormal Maturation of B Cells (2012)

The large B-cell infiltrates in granulomatous tissue and increased molecular signs of antibody maturation are indicative of direct involvement of B cells in local inflammatory processes in patients with sarcoidosis. Moreover, CD27(-)IgA(+) B cells could be a marker for treatment with TNF-α blockers. These findings of B cells as emerging key players provide a rationale for a systematic study on B-cell ablative therapy in patients with sarcoidosis.
Analysis of the static and dynamic characteristics of push-pull parallel resonant converters (1986)

The basic circuit of a push-pull parallel resonant converter with an input inductor is analyzed for the continuous conduction mode and the discontinuous conduction mode concerning the output-inductor current. It is found that the output voltage of this resonant converter is controlled by varying the switching frequency in the discontinuous conduction mode, while another power controller is required in the continuous conduction mode. The static and dynamic characteristics are examined analytically and experimenta1ly.
Blind source separation for groundwater pressure analysis based on nonnegative matrix factorization (2014)

Abstract The identification of the physical sources causing spatial and temporal fluctuations of aquifer water levels is a challenging, yet a very important hydrogeological task. The fluctuations can be caused by variations in natural and anthropogenic sources such as pumping, recharge, barometric pressures, etc. The source identification can be crucial for conceptualization of the hydrogeological conditions and characterization of aquifer properties. We propose a new computational framework for model‐free inverse analysis of pressure transients based on Nonnegative Matrix Factorization (NMF) method for Blind Source Separation (BSS) coupled with k ‐means clustering algorithm, which we call NMF k . NMF k is capable of identifying a set of unique sources from a set of experimentally measured mixed signals, without any information about the sources, their transients, and the physical mechanisms and properties controlling the signal propagation through the subsurface flow medium. Our analysis only requires information about pressure transients at a number of observation points, m , where , and r is the number of unknown unique sources causing the observed fluctuations. We apply this new analysis on a data set from the Los Alamos National Laboratory site. We demonstrate that the sources identified by NMF k have real physical origins: barometric pressure and water‐supply pumping effects. We also estimate the barometric pressure efficiency of the monitoring wells. The possible applications of the NMF k algorithm are not limited to hydrogeology problems; NMF k can be applied to any problem where temporal system behavior is observed at multiple locations and an unknown number of physical sources are causing these fluctuations.
Use of a 1-Piece Chlorhexidine Gluconate Transparent Dressing on Critically Ill Patients (2012)

A low rate of catheter-related bloodstream infections can be maintained, nurses' satisfaction achieved, and cost savings realized with the new dressing.
Thick film conductors for 175°C operation in automotive electronics (1997)

Relentless pursuit of higher reliability and lower cost has been the hallmark of the automotive industry. Performance expectations have further risen due to the changing nature of electro-mechanical systems in automobiles. An increasing number of functions are controlled by solid state modules. The need to mount such modules on or closer to the engine block requires circuit reliability after numerous excursions to higher temperatures than ever. Most recently, the target temperature has risen to 175°C. To realize both the high temperature performance and the desired cost effectiveness, palladium-silver compositions with Ag/Pd ratio of 3/1 to 100% Ag were developed. A barrier to full commercialization of the newly developed materials has been the performance of high melting solders needed for continuous operation to 175°C. Most solders undergo fatigue during thermal cycling, with different type and severity of manifestations. This fatigue phenomenon is individually investigated for a number of solder compositions. Fast curing conductive polymer is also evaluated as a solder replacement, under 175°C storage and -35°C to 175°C cycling.
Receptor tyrosine kinases and downstream pathways as druggable targets for cancer treatment: the current arsenal of inhibitors (2018)

Searching for targets that allow pharmacological inhibition of cell proliferation in over-proliferative states, such as cancer, leads us to finely understand the complex mechanisms orchestrating the perfect control of mitosis number, frequency and pace as well as the molecular arrangements that induce cells to enter functional quiescence and brings them back to cycling in specific conditions. Although the mechanisms regulating cell proliferation have been described several years ago, never before has so much light been shed over this machinery as during the last decade when therapy targets have been explored and molecules, either synthetic or in the form of antibodies with the potential of becoming cancer drugs were produced and adjusted for specific binding and function. Proteins containing tyrosine kinase domains, either membrane receptors or cytoplasmic molecules, plus the ones activated by those in downstream pathways, having tyrosine kinase domains or not, such as RAS which is a GTPase and serine/threonine kinases such as RAF, play crucial role in conducting proliferation information from cell surroundings to the nucleus where gene expression takes place. Tyrosine kinases phosphorylate tyrosine residues in an activating mode and are found in important growth factor receptors, such as for ligands from families collectively known as VEGF, PDGF and EGF, to name a few and in intracellular downstream molecules. They all play important roles in normal physiology and are commonly found mutated or overexpressed in neoplastic states. Our objective here is to present such kinases as druggable targets for cancer therapy, highlighting the ones for which the pharmacological arsenal is available, discussing specificity, resistance mechanisms and treatment alternatives in cases of resistance, plus listing potential targets that have not been successfully worked yet.
Analysis of noisy dynamic light scattering data using constrained regularization techniques (2012)

Dynamic light scattering (DLS) from colloidal particles often contains noise, which makes inversion of the correlation function to obtain the particle size distribution (PSD) unreliable. In this work, poor-quality correlation function data with baseline error were analyzed using constrained regularization techniques. The effect of baseline error was investigated, and two strategies were proposed to compensate for baseline error. One strategy is based on edge proportion detection of spurious peaks at large size in the PSD, and the other is based on the solution norm. Results from simulated and experimental data demonstrate the effectiveness of our proposed strategies. The L-curve rules for standard Tikhonov and for constrained regularization, the generalized cross-validation (GCV) rule, and the robust GCV rule were investigated for determination of the regularization parameter. A comparison of these rules was done using both simulated and experimental data. It is shown that correction of baseline error with baseline compensation as well as a reasonable regularization parameter choice improves the accuracy of PSD recovery in poor-quality DLS data analysis.