gebhart/patrepeval huggingface dataset:
Iterative Computing over a Unified Relationship Matrix for Information Integration (2006)

In this dissertation I use a Unified Relationship Matrix (URM) to represent a set of heterogeneous data objects and their inter-relationships. I argue that integrated and iterative computations over the Unified Relationship Matrix can help overcome the data sparseness problem (a common situation in various information application scenarios), and detect latent relationships (such as latent term associations discovered by LSI) among heterogeneous data objects. Thus, this kind of computation can be used to improve the quality of various information applications that require combining information from heterogeneous data sources. To support the argument, I further develop a unified link analysis algorithm, the Link Fusion algorithm, and a unified similarity-calculating algorithm, the SimFusion algorithm. Both algorithms attempt to better integrate information from heterogeneous sources by iteratively computing over the Unified Relationship Matrix in order to calculate some specific property of data object(s); such as the importance of a data object (as in the Link Fusion algorithm) and the similarity between a pair of data objects (as in the SimFusion algorithm). Then, I develop two set of experiments on real-world datasets to investigate whether the algorithms proposed in this dissertation can better integrate information from multiple sources. The performance of the algorithms is compared to that of traditional link analysis and similarity-calculating algorithms. Experimental results show that the algorithms developed can significantly outperform the traditional link analysis and similarity-calculating algorithms. I further investigate various pruning technologies aiming at improving efficiency and investigating the scalability of the algorithms designed. Experimental results showed that pruning technology can effectively be used to improve the efficiency of the algorithms.
Effect of Cytochrome P450 polymorphism on the action and metabolism of selective serotonin reuptake inhibitors (2015)

Genetic polymorphisms in CYP2D6 and CYP2C19 exert large influences on the individual exposure to SSRIs, leading to the aim to achieve similar concentration time courses in different metabolizer phenotypes. The implementation of a stratified approach to medication with SSRIs in different metabolic phenotypes on a rational basis will require new studies assessing the association between clinical outcomes (such as adverse reactions) and genetically determined elevated plasma concentrations.
Endocrine milieu of perioestrus in the giant panda (Ailuropoda melanoleuca), as determined by non-invasive hormone measures (2010)

The aim of the present study was to determine the efficacy of faecal hormonal measures for evaluating ovarian activity in a significant sized cohort of giant pandas during the perioestrual period. Faecal excretion of oestrogen and progestagen metabolites corresponded with urinary patterns and receptive behaviours. Longitudinal assessment of 10 females revealed that, on average, faecal oestrogen concentrations started to rise (P < 0.05) above baseline (baseline mean +/- s.e.m.; 64.7 +/- 6.6 ng g(-1)) 5 days before the preovulatory oestrogen peak (484.6 +/- 126.8 ng g(-1)), which was followed by a gradual descent over 4 days to nadir. Mean faecal progestagen metabolite concentrations increased approximately twofold above baseline (from 186.2 +/- 37.7 to 347.2 +/- 75.7 ng g(-1); P < 0.05) during the 20-day interval after the preovulatory oestrogen surge. Variability within and among females precluded the use of a threshold of oestrogen or progestagen metabolites to predict reproductive status, yet faeces collected 2-3 days per week provided sufficient data to recognise that an individual was in the perioestrual period. Finally, in females that were examined for at least 3 consecutive years, there was an 18-53 day variation in the onset and an 8-13 day variation in the duration of perioestrual behaviour from year to year. In summary, these findings indicate that gonadal hormone profiles associated with the period immediately before, during and after oestrus are accurately revealed by analysis of the fibrous faeces of the giant panda. This approach has potential value for providing point-in-time information on the reproductive status of free-living individuals.
Pseudo random forests for tube identification (2015)

Random forests are widely used in machine learning as they can potentially offer higher accuracy than individual decision trees by the averaging of multiple independent models.We propose a modification called "Pseudo-random forests" that combines stochastic feature selection with dynamic problem-specific feature generation.As proof of concept, we apply the method to the problem of edge detection and classification in radiographic images.In particular, we use the method to detect feeding tubes in pediatric patients, which are inserted to deliver food and medicine.Since multiple layers of tissues and medical objects are overlaid in a single image, these can be difficult to read on x-rays, even for trained radiologists.The placement of these tubes is critical to the well-being and care of the patient.Automating the recognition of these tubes can help confirm the correct placement of these tubes, as an improperly placed tube could delay treatment or jeopardize the health of the patient.It can also save time by enhancing the visibility of tubes for interpretation by
PCR Protocol for Phusion® High-Fidelity DNA Polymerase (M0530) v2 (2017)

This is the PCR protocol for Phusion® High-Fidelity DNA Polymerase (M0530)
Scheduling Methods to Reduce Response Latency of Function as a Service (2020)

Function as a Service (FaaS) permits cloud customers to deploy to cloud individual functions, in contrast to complete virtual machines or Linux containers. All major cloud providers offer FaaS products (Amazon Lambda, Google Cloud Functions, Azure Serverless); there are also popular open-source implementations (Apache OpenWhisk) with commercial offerings (Adobe I/O Runtime, IBM Cloud Functions). A new feature of FaaS is function composition: a function may (sequentially) call another function, which, in turn, may call yet another function - forming a chain of invocations. From the perspective of the infrastructure, a composed FaaS is less opaque than a virtual machine or a container. We show that this additional information enables the infrastructure to reduce the response latency. In particular, knowing the sequence of future invocations, the infrastructure can schedule these invocations along with environment preparation. We model resource management in FaaS as a scheduling problem combining (1) sequencing of invocations, (2) deploying execution environments on machines, and (3) allocating invocations to deployed environments. For each aspect, we propose heuristics. We explore their performance by simulation on a range of synthetic workloads. Our results show that if the setup times are long compared to invocation times, algorithms that use information about the composition of functions consistently outperform greedy, myopic algorithms, leading to significant decrease in response latency.
<title>Performance evaluation methods for multiple-target-tracking algorithms</title> (1991)

Scoring methods are described for evaluating the performance of a multiple target tracking (MTT) algorithm fairly, without undue bias towards any particular type. The methods were initially developed by individuals and further developed and adapted by the members of the SDI panels on tracking. Ambiguous track-to-target truth association is the fundamental difficulty in MTT performance evaluation. The methods use a global nearest neighbor assignment algorithm to uniquely associate tracks to targets. With the track- to-target associations, the methods employ measures of effectiveness for track purity, data association, state estimation accuracy, and credibility of filter calculated covariance.
Twelve months follow-up after retrograde recanalization of superficial femoral artery chronic total occlusion (2017)

The retrograde SFA puncture seems to be a safe and successful technique for CTO recanalization and is associated with a low rate of perioperative and long-term follow-up complications.
An update of the federal regs (1996)

Because of resource limitations and pending reauthorization of the Safe Drinking Water Act, the pace of regulatory activity has slowed considerably. This article reports the current developments related to rules promulgated or proposed under the Safe Drinking Water Act, such as the Lead and Copper Rule, Phase V Rule, the Disinfectants/Disinfection By‐products Rule (including the Enhanced Surface Water Treatment Rule and the Information Collection Rule), the Radionuclides Rule, and the Sulfate Rule. Anticipated new rules that will update analytical methods, reestablish regulatory priorities, and streamline revisions to current regulations are reviewed as well.
New building blocks for the assembly of sequence selective molecular zippers (2003)

Synthetic H-bonded molecular zippers contain no sequence information that can be used to engineer the selective binding interactions characteristic of biopolymers; reversing the sense of the amide bonds in the two binding partners generates a new orthogonal recognition motif and the mutually complementary binding partners form complexes an order of magnitude more stable than the corresponding mismatch complexes.
Loading characteristics and chemical stability of headgroup‐functionalized poly(ethylene glycol)‐lipid ligand tethers on polypropylene capillary‐channeled polymer fibers (2014)

Polypropylene capillary-channeled polymer fibers have been modified by adsorption of headgroup-functionalized poly(ethylene glycol)-lipids to generate a species-specific stationary phase. In order to study ligand binding characteristics, a fluorescein-labeled poly(ethylene glycol)-lipid was used as a model system. Breakthrough curves and frontal analysis were employed to characterize the surface loading characteristics across a range of lipid concentrations and mobile phase flow rates. Efficient mass transfer and fluid transport yield a linear adsorption isotherm up to the maximum loading concentration of 3 mg/mL, at a linear velocity of 57.1 mm/s. Under these conditions, the dynamic binding capacity was found to be 1.52 mg/g of fiber support. Variation of the linear velocity from 8.6 to 57.1 mm/s showed only small changes in breakthrough volume. The maximum capacity of 1.8 mg/g is found under conditions of a load velocity of 34.2 mm/s and a concentration of 3 mg/mL lipid. Exposure of the lipid modified fibers to several challenge solvents reveals a chemically robust system, with only 50% acetonitrile and hexanes able to disrupt the lipid adsorption. The straightforward capillary-channeled polymer fiber surface modification with headgroup-functionalized lipids provides both a diverse yet practically robust ligand tethering system.
Acid Catalysis in Basic Solution: A Supramolecular Host Promotes Orthoformate Hydrolysis (2007)

Although many enzymes can promote chemical reactions by tuning substrate properties purely through the electrostatic environment of a docking cavity, this strategy has proven challenging to mimic in synthetic host-guest systems. Here, we report a highly charged, water-soluble, metal-ligand assembly with a hydrophobic interior cavity that thermodynamically stabilizes protonated substrates and consequently catalyzes the normally acidic hydrolysis of orthoformates in basic solution, with rate accelerations of up to 890-fold. The catalysis reaction obeys Michaelis-Menten kinetics and exhibits competitive inhibition, and the substrate scope displays size selectivity, consistent with the constrained binding environment of the molecular host.
The Expressive Power of Neural Networks: A View from the Width (2017)

The expressive power of neural networks is important for understanding deep learning. Most existing works consider this problem from the view of the depth of a network. In this paper, we study how width affects the expressiveness of neural networks. Classical results state that depth-bounded (e.g. depth-$2$) networks with suitable activation functions are universal approximators. We show a universal approximation theorem for width-bounded ReLU networks: width-$(n+4)$ ReLU networks, where $n$ is the input dimension, are universal approximators. Moreover, except for a measure zero set, all functions cannot be approximated by width-$n$ ReLU networks, which exhibits a phase transition. Several recent works demonstrate the benefits of depth by proving the depth-efficiency of neural networks. That is, there are classes of deep networks which cannot be realized by any shallow network whose size is no more than an exponential bound. Here we pose the dual question on the width-efficiency of ReLU networks: Are there wide networks that cannot be realized by narrow networks whose size is not substantially larger? We show that there exist classes of wide networks which cannot be realized by any narrow network whose depth is no more than a polynomial bound. On the other hand, we demonstrate by extensive experiments that narrow networks whose size exceed the polynomial bound by a constant factor can approximate wide and shallow network with high accuracy. Our results provide more comprehensive evidence that depth is more effective than width for the expressiveness of ReLU networks.
Air Traffic Simulation: An Object Oriented, Discrete Event Simulation on the Intel iPSC/2 Parallel System (2005)

A discrete event simulation model of air traffic flow within the United States has been written and executed on the Intel iPSC8/2 parallel system. The simulation program was written in an object oriented manner using the Interwork IITM Concurrent Programming Toolkit. This simulation demonstrates how object oriented programming can simplify the design of complex simulations and can simplify the effort to distribute and balance the processing load on distributed memory, parallel architectures, such as the iPSC/2. It also demonstrates the capacity of these architectures to solve very large simulation problems.
Curvelet based image fusion (2012)

This paper presents an efficient image fusion algorithm which is based on curvelet transform. It makes use of different characteristics of the same geographical area obtained from more than one image, to obtain a more informative image. Experiments have been carried out to fuse monochromatic PAN (PANchromatic) satellite image with a multispectral LISS (Linear Imaging and Self Scanning) III image and it has been found that the fused image contains much richer information in both the spatial and spectral domain simultaneously.
Fabrication of Nonwoven Coaxial Fiber Meshes by Electrospinning (2009)

There is a great need for biodegradable polymer scaffolds that can regulate the delivery of bioactive factors such as drugs, plasmids, and proteins. Coaxial electrospinning is a novel technique that is currently being explored to create such polymer scaffolds by embedding within them aqueous-based biological molecules. In this study, we evaluated the influence of various processing parameters such as sheath polymer concentration, core polymer concentration and molecular weight, and salt ions within the core polymer on coaxial fiber morphology. The sheath polymer used in this study was poly(e-caprolactone) (PCL), and the core polymer was poly(ethylene glycol) (PEG). We examined the effects of the various processing parameters on core diameters, total fiber diameters, and sheath thicknesses of coaxial microfibers using a 2(4) full factorial statistical model. The maximum increase in total fiber diameter was observed with increase in sheath polymer (PCL) concentration from 9 to 11 wt% (0.49+/-0.03 microm) and salt concentration within the core from 0 to 500 mM (0.38+/-0.03 microm). The core fiber diameter was most influenced by the sheath and core polymer (PCL and PEG, respectively) concentrations, the latter of which increased from 200 to 400 mg/mL (0.40+/-0.01 microm and 0.36+/-0.01 microm, respectively). The core polymer (PEG) concentration had a maximal negative effect on sheath thickness (0.40+/-0.03 microm), while salt concentration had the maximal positive effect (0.28+/-0.03 microm). Molecular weight increases in core polymer (PEG) from 1.0 to 4.6 kDa caused moderate increases in total and sheath fiber diameters and sheath thicknesses. These experiments provide important information that lays the foundation required for the synthesis of coaxial fibers with tunable dimensions.
Corrosion-related failures in power plant condensers. Final report. [PWR] (1980)

A survey of the literature has been conducted for the Electric Power Research Institute on corrosion failures in surface condensers. The survey was directed toward condenser failures in pressurized water reactor (PWR) power plants but includes pertinent literature related to fossil and to other nuclear power plants. It includes literature on reported service failures and on experimental studies that impact on these failures.
Cross-linking hybridization assay for direct detection of factor V Leiden mutation (1997)

A nucleic acid photocross-linking technology was used in the development of a direct assay for factor V Leiden, a point mutation in the factor V gene (G1691A) that is the most common inherited risk factor for thrombosis. This cross-linking hybridization assay included two allele-specific capture probes and six signal-generating reporter probes; all were modified with a photoactivated cross-linking compound. By using two different capture probes complementary to a 16-base sequence at the factor V Leiden mutation site, but differing in the nucleotide opposite the mutation site (C vs T), wild-type and factor V Leiden alleles were differentiated in purified DNA specimens. The assay was also successfully applied to genomic DNA in leukocytes isolated from whole blood; the factor V status of 122 patients as determined by this method was in complete concordance with a standard PCR-based assay and clearly discriminated between healthy individuals and factor V Leiden heterozygotes.
Reactions of hydrous titanium oxide colloids with strong oxidizing agents (1992)

The absorption spectra of the transients formed in the reactions of titanium hydrous oxide with SO4•-, Tl2+, or OH* species in alkaline aqueous solution have been studied by using the pulse radiolysis technique. Direct hole capture via interfacial electron transfer from colloidal titanium hydrous oxide to SO4•- radicals leads to the formation of a product which has the broad absorption spectrum with an onset at about 480 nm rising steeply toward the UV region. A completely different absorption spectrum was found for the hydroxyl radical adduct formed by the reaction of OH* with titanium hydrous oxide that has a maximum at 620 nm. This maximum disappears in acidic solution at pH 3 with assistance of H+aq which transforms the OH adduct to the product the same as that formed in the reaction with SO4•-. The low-weight aggregates of titanium hydroxide also react with OH* radicals, and in the alkaline solution a similar transient spectrum with a maximum at 570 nm was obtained. In neutral and alkaline solutions the absorption spectra of transients formed in the reactions of OH*, Tl2+, or SO4•- with TiO2 do not appear to be dependent upon the mode of the colloid preparation. However, decay kinetics of these transients are very sensitive to surface chemistry.
A rapid biologic assay for the detection of interleukin 1. (1983)

The detection of human peripheral blood-derived IL 1 was accomplished by a modification of the monokine-dependent conversion assay of the cell line LBRM-33 from the IL 2 nonproducer to producer phenotype after incubation with the monokine and lectin. The conversion of the LBRM-33 subclone, 1A5B6, was modified by directly adding the IL 2-dependent cell line CTLL-2 to metabolically inactivated LBRM-33. This enabled the more rapid identification of macrophage-derived IL 1 and was approximately 1000 to 10,000 times more sensitive than the traditional thymocyte proliferation assay. It is hoped that with the assay described here, it will be feasible to more accurately screen for the presence of this important immunoregulatory molecule in an immune response.
Prevention of azoxymethane-induced intestinal tumors by a crude ethyl acetate-extract and tryptanthrin extracted from Polygonum tinctorium Lour. (2002)

The effect of a crude ethyl acetate (AcOEt)-extract and tryptanthrin extracted from the Indigo plant (Polygonum tinctorium Lour.) on azoxymethane (AOM)-induced intestinal tumors was examined in F344 rats. The rats were given subcutaneous (s.c.) injections of either AOM (15 mg/kg body weight (b.w.)) once a week for 3 weeks to induce atypical crypt foci (ACF) as a known cancer precursor, or AOM (7.5 mg/kg b.w.) once a week for 10 weeks to induce intestinal tumors. The rats were also administered the AcOEt-extract (500 mg/kg b.w.) or tryptanthrin (50 mg/kg b.w.) orally, 5 days a week, for 7 or 30 weeks, starting two days before the first administration of AOM. All rats were killed 4 or 20 weeks after the last treatment. In the short-term experiment, the incidence of ACE and atypical crypts (AC) in the groups receiving the AcOEt-extract and tryptanthrin was significantly lower than in the control group. In the tumor-inducing experiment, intestinal tumor incidence in the tryptanthrin group was lower than in the AOM-control group (5% versus 26%), and small intestine tumor incidence in the AcOEt-extract and tryptanthrin groups were lower than in the AOM-control group (0% and 0% versus 23%). These results show that the AcOEt-extract of Indigo and tryptanthrin have cancer chemopreventive activity.
Synchronous selection of homing peptides for multiple tissues by<i>in vivo</i>phage display (2006)

In vivo phage display is a technology used to reveal organ-specific vascular ligand-receptor systems in animal models and, recently, in patients, and to validate them as potential therapy targets. Here, we devised an efficient approach to simultaneously screen phage display libraries for peptides homing to any number of tissues without the need for an individual subject for each target tissue. We tested this approach in mice by selecting homing peptides for six different organs in a single screen and prioritizing them by using software compiled for statistical validation of peptide biodistribution specificity. We identified a number of motif-containing biological candidates for ligands binding to organ-selective receptors based on similarity of the selected peptide motifs to mouse proteins. To demonstrate that this methodology can lead to targetable ligand-receptor systems, we validated one of the pancreas-homing peptides as a mimic peptide of natural prolactin receptor ligands. This new comprehensive strategy for screening phage libraries in vivo provides an advantage over the conventional approach because multiple organs internally control for organ selectivity of each other in the successive rounds of selection. It may prove particularly relevant for patient studies, allowing efficient high-throughput selection of targeting ligands for multiple organs in a single screen.
Techniques for evaluating control of automated multi-determinant analytical instruments by computer (1986)

Analytical data collected from calibration standards and other quality control standards using an amino acid analyser (18 ninhydrin products) and a plasma emission spectrometer (20 elements) are logged regularly during analysis periods. Principal components are derived from the data using principal component analysis and those that contain the most variation (usually first three) are plotted on cumulative sum charts (Cusums). Changes in the physico-chemical control of instruments can be clearly demonstrated and out of control events identified. The computer program can be run on any computer with sufficient memory to handle large matrix transformations. The technique is applicable to any instrument measuring several or many variables.