gebhart/patrepeval huggingface dataset:
On Combinatorial Optimization Problems with Mobile Sites and Resources (2006)

This paper develops a framework to solve combinatorial resource allocation problems in a setting where the sites and resources are allowed to have dynamics. The formulation draws analogy from statistical physics to define the Free Energy function which is used as a measure of coverage function. A class of dynamics for the sites and resources is prescribed which guarantees coverage. This is done by casting the problem as a control problem in which we design the resource velocities to ensure that the time derivative of the Free Energy function is non positive.
Table S2 from Matched Targeted Therapy for Pediatric Patients with Relapsed, Refractory, or High-Risk Leukemias: A Report from the LEAP Consortium (2023)

&lt;p&gt;Inhibitor Recommendation Usage Summary.&lt;/p&gt;
Transfer of sperm into a chemically defined environment by centrifugation through 12% (wt/vol) Accudenz (1998)

Centrifugation is commonly used to wash sperm; however, most washing techniques do not put sperm in a chemically defined environment. Rather, washing by centrifugation, in effect, dilutes seminal plasma components. A 0.5-mL volume of 30% (wt/vol) Accudenz was layered beneath 5 mL of 12% (wt/vol) Accudenz in a 15-mL polypropylene centrifuge tube. Diluted semen from individual males (n = 10) was overlaid upon the 12% (wt/vol) Accudenz. After centrifugation at 1,250 x g at 4 C for 25 min, washed sperm were present at the interface of the Accudenz layers. Based upon hemacytometer counts, sperm recovery was 83% (CV = 12%). Neither sperm viability nor morphology was affected by washing. Efficacy of the washing procedure was evaluated by using extracellular glucose, glutamic acid, Ca+2, and protein as markers. Washing eliminated 99% of the glutamic acid and glucose associated with sperm. Likewise, washing removed 98.5% of the extracellular Ca+2 associated with sperm. As evidenced by total protein analysis and SDS-PAGE, washing removed 98% of soluble seminal plasma proteins from sperm. In addition, washing did not affect sperm mobility or fertilizing ability. This procedure returns extended sperm to a physiological concentration in a chemically defined environment. By suspending washed sperm in distinct media, we induced differential sperm mobility. Therefore, this procedure is suitable for the study of the effect of specific substances upon sperm cell function.
A Speculative Technique for Auto-Memoization Processor with Multithreading (2009)

We have proposed an auto-memoization processor. This processor automatically and dynamically memoizes both functions and loop iterations, and skips their execution by reusing their results. On the other hand, multi/many-core processors have come into wide use. The number of cores is expected to increase to a hundred or more. However, many programs do not have so much parallelism in them. Therefore it becomes very important to consider how to utilize many cores effectively. This paper describes a speedup technique for auto-memoization processor using speculative multi-threading. Two speculative threads will be forked on reuse test. The one assumes that the reuse test will succeed, and executes the following codes of the reuse target block speculatively. The other assumes that the reuse test will fail, and executes the reuse target block. These two threads conceal the overhead of auto-memoization processor. The result of the experiment with SPEC CPU95 suite benchmarks shows that proposing method improves the maximum speedup from 13.9% to 36.0%.
Acoustic daylight: Imaging the ocean with ambient noise. (1992)

For many years the principal means of probing the ocean using sound has been through the use of either ‘‘active’’ or ‘‘passive’’ techniques. With an active system, an object is illuminated by a pulse of sound and its presence inferred from the echo it produces, whereas the passive approach involves simply listening for the sound that the object itself emits. Here a new method of employing sound in the ocean is reported, which is neither passive nor active. It relies on the naturally occurring, incoherent ambient noise field in the ocean as the sole source of acoustic illumination. By analogy with daylight in the atmosphere, ambient noise scattered from an object in the ocean can be focused onto an image plane, and from this acoustic image, with appropriate signal processing, a visual image can be produced on a television-type monitor of the object space in the ocean. To test this concept, several simple experiments have been conducted in the ocean off Scripps pier, with a single parabolic reflector acting as an acoustic lens, which confirm that objects illuminated only by ambient noise can indeed be ‘‘seen’’ over a frequency band between 5 and 50 kHz. [Work supported by ONR.]
A dual fluorescent multiprobe assay for prion protein genotyping in sheep (2005)

We report the development and validation of a robust, reliable and reproducible method for PRNP genotyping of a few to many sheep samples in a fast, simple and cost-effective way, applicable in standard equipped molecular genetic laboratories. The described primer/probe design strategy can also be applied for the detection of other polymorphisms or disease causing mutations.
Robust ground surface map generation using vehicle-mounted stereo camera (2014)

We propose a robust method for incrementally estimating a regular-grid ground surface map from stereo image sequences captured by nearly front-looking vehicle-mounted stereo cameras. The method simultaneously estimates a camera ego-motion and vertex heights of a regular mesh, which is composed of piecewise triangular patches drawn on a level plane in the ground coordinate system, by minimizing pixel value differences over the ground surface. The method combinationally uses feature-based approach and pixel-based approach for robustly estimating ego-motion parameters. We also show that this combination is beneficial for removing outlier pixels, which mainly represent the edge of the self-shadow area on the ground surface. The validity of the proposed method is demonstrated through experiments using real images.
Cyclic AMP, the microtubule-microfilament system, and cancer. (1977)

Additional evidence is presented for the previously proposed existence in normal fibroblasts of a cyclic AMP-dependent network of microtubules and microfilaments, which is connected with cell membrane elements on one end and with nuclear structures on the other and whose disorganization leads to malignant transformation. In the presence of cyclic AMP derivatives sufficient to promote integrity of this network, cell growth limitation in suspension, increased transport of alpha-[14C]aminobutyrate, and the relatively tranquilized membrane of the normal fibroblast are also achieved. A pattern of distribution of actin and tubulin has been demonstrated showing aggregated actin deposits which are presumably responsible for the oscillatory knob activity of cells with the transformed habitus. Specific orientations of microtubular and filamentous elements with respect to the nucleus can be demonstrated. The hypothesis that the microtubular-microfilamentous structure conveys growth-regulatory information from the cell membrane to the nucleus and that its disorganization can lead to malignancy has been extended to explain various cellular manifestations.
EFFECTS OF TEXTURAL CHANGES IN COOKED APPLES ON THE HUMAN BITE, AND INSTRUMENTAL TESTS (2003)

A multiple‐point sheet sensor was used to measure the bite force applied to raw and cooked apple specimens during the first bite with incisors. Wedge penetration tests were compared with human bite measurements on the same samples. The shape of the force‐time curves during biting of cooked apples clearly differed from that for raw apples. The first curve of cooked apple biting became jagged, and the maximum force was reduced. The second curve emerged following the first curve in most subjects as a characteristic feature of cooked apple biting, whereas it was not seen in the bite curve of a raw specimen or the wedge penetration curve of a cooked specimen. The maximum force for tissue fracture decreased for cooked apples, but the duration of biting increased. No adequate counterparts for the impulse of biting could be obtained from the load‐displacement curves of the wedge penetration tests. The existence of parameters only measurable by bite tests and not by mechanical tests suggests the necessity of directly measuring the human bite.
Survey of the response of 82 domestic landraces of Zea mays to cucumber mosaic virus ( CMV ) reveals geographical region‐related resistance to CMV in Japan (2018)

Zea mays has been historically imported to Japan via two independent geographical routes: into southern Japan by trading with Europe in the 16th century and into northern Japan by import from North America in the 19th century. Breeding to genetically improve on quality traits and high yields has led to the current domestic landraces in each region. In a survey of 82 domestic landraces, nine out of 38 landraces originating from southern Japan showed complete immunity to cucumber mosaic virus yellow strain (CMV(Y)) without the formation of necrotic local lesions (NLLs). In contrast, three out of 44 landraces originating from northern Japan developed NLLs, but revealed no systemic spread of the virus. Due to the absence of good documentation on NLL formation in Z. mays , the response of domestic landraces Aso‐1 and Aso‐3, originating from Ibaraki in northern Japan, to a challenge with CMV(Y) and CMV(Ma‐1) was further analysed. Aso‐3 only formed NLL in response to CMV(Y) but not to CMV(Ma‐1). Moreover, in CMV(Y)‐inoculated Aso‐3, virus spread was restricted to the primary infection site and the expression of defence‐related genes was up‐regulated, whereas Aso‐1 became systemically infected with either CMV(Y) or CMV(Ma‐1). The response of Aso‐3 to CMV(Y) was inherited as a single dominant trait. Together, these results pointed towards the induction of hypersensitive response (HR)‐mediated resistance to CMV(Y) in Aso‐3. Although HR‐mediated resistance to viruses has been studied mainly in dicots, the pathosystem CMV– Z. mays may provide a model to investigate HR‐mediated resistance to viruses in monocot plants.
Defective Intracellular Trafficking of Uromodulin Mutant Isoforms (2006)

Medullary cystic kidney disease/familial juvenile hyperuricemic nephropathy (MCKD/FJHN) are autosomal dominant renal disorders characterized by tubulo-interstitial fibrosis, hyperuricemia and medullary cysts. They are caused by mutations in the gene encoding uromodulin, the most abundant protein in urine. Uromodulin (or Tamm-Horsfall protein) is a glycoprotein that is exclusively expressed by epithelial tubular cells of the thick ascending limb of Henle's loop and distal convoluted tubule. To date, 37 different uromodulin mutations have been described in patients with MCKD/FJHN. Interestingly, 60% of them involve one of the 48 conserved cysteine residues. We have previously shown that cysteine-affecting mutations could lead to partial endoplasmic reticulum (ER) retention. In this study, as a further step in understanding uromodulin biology in health and disease, we provide the first extensive study of intracellular trafficking and subcellular localization of wild-type and mutant uromodulin isoforms. We analyzed a set of 12 different uromodulin mutations that were representative of the different kind of mutations identified so far by different experimental approaches (immunofluorescence, electron microscopy, biochemistry and in vivo imaging) in transiently transfected HEK293 and Madin-Darby canine kidney cells. We assessed protein processing in the secretory pathway and could demonstrate that although to different extent, all uromodulin mutations lead to defective ER to Golgi protein transport, suggesting a common pathogenetic mechanism in MCKD/FJHN.
Low Moments for Small Samples: A Comparative Study of Order Statistics (1947)

The means, variances, and covariances for samples of size $\leq 10$ from the normal distribution, a selected long-tailed distribution, and the uniform distribution are tabled and compared with the usual asymptotic approximations. The methods of computation used and the accuracy expected are discussed. Use is made of the representation of an arbitrarily distributed variate as a monotone function of a uniformly (rectangularly) distributed variate. It is hoped that these tables will encourage experimentation with new statistical procedures.
Conformational studies of dithiastannolanes by dynamic nuclear magnetic resonance spectroscopy (1982)

The barriers to conformational interconversion of the five-membered rings of the title compounds of general type SnRR′(SCH2CHR″S)(R, R′= Me or Ph; R″= H or Me) have been measured for the first time by low-temperature n.m.r. studies. Room-temperature measurements indicate that the chelate rings exist as half-chair conformations with the –CH2CHR″– moiety in a fully staggered configuration, as in the solid state. These findings are at variance with a previous n.m.r. study of this type of system. The ΔG‡ values for the interconversion of the two half-chair conformations lie in the range 30–32 kJ mol–1 and are essentially independent of the substituents on the SnIV atom and on the five-membered ring.
New Editorial Team of Circulation Journal (2010)

On behalf of the Circulation Journal, I would like to announce that I have been re-appointed as the Editor-in-Chief of the Circulation Journal for another 2 years, from July 2010 to June 2012, by Prof. Matsuzaki, the new president of the Japanese Circulation Society. Over the past 2 years, our editorial team has made every effort to improve the Journal’s scientific impact and level of internationalization. To further facilitate our endeavors in these areas, I have expanded our Editorial team through the addition of new Associate Editors from both Japan and overseas, and new Japanese Editorial board members. I am also pleased to announce a new series, ‘Controversies in Cardiovascular Medicine’, and the publication of English versions of Guidelines developed by the Japanese Circulation Society, starting from next month’s issue.
Hevige pijn in de pols bij een 26-jarige man, als gevolg van een hyperextensietrauma tijdens een volleybalwedstrijd (2010)

Tijdens een wedstrijd werd een smash door een 26-jarige volleyballer zodanig geblokkeerd dat de rechterpols een hyperextensietrauma onderging. Op dat moment hoorde hij een krak en er ontstond hevige pijn en vrijwel direct een forse zwelling. Verder spelen was onmogelijk en de man bezocht de eerstehulpafdeling van ons ziekenhuis. Conventioneel röntgenonderzoek toonde op dat moment geen bijzonderheden. Patiënt kreeg een drukverband en pijnmedicatie en er werd een afspraak gemaakt voor een consult de volgende dag bij onze dienst.
Data analysis methods for solid-state nanopores (2015)

We describe a number of techniques for the analysis of solid-state nanopore ionic current traces and introduce a new package of Matlab analysis scripts with GUI front ends. We discuss methods for the detection of the local baseline and propose a new detection algorithm that bypasses some of the classical weaknesses of moving-average detection. Our new approach removes detected events and re-creates an ideal event-free baseline subsequently used to recalculate the local baseline. Iterative operation of this algorithm causes both the moving average of the baseline current and its standard deviation to converge to their correct values. We explain different approaches to selecting events and building event populations, and we show the value of keeping track of the changes in parameters, such as the event rate and the pore resistance, throughout the course of the experiment. Finally, we introduce a new technique for separating unfolded events and detecting current spikes present within translocation events. This open source software package is available online at: http://ceesdekkerlab.tudelft.nl/downloads/
Physicochemical and rheological properties of a novel monoolein-based vesicle gel (2012)

The present paper deals with the preparation and characterization of an innovative vesicle-based gel composed of monoolein and lauroylcholine chloride. A number of vesicular formulations were prepared, in the range of 4–14 wt% of the dispersed phase, to investigate the system evolution from a dilute uni-lamellar vesicle dispersion to a vesicle lipid gel. Morphology, thermal stability up to 55 °C, and viscoelastic properties, along with the effect of acid diclofenac inclusion within the formulation, were evaluated by cryo-TEM, SAXS, and rheological measurements. Moreover, the nanostructure of the vesicle dispersion obtained upon gel dilution in water was assessed by cryo-TEM and SAXS, while DLS was used to monitor the formulation stability (size and ζ-potential). All the collected results lead to the conclusion that this new vesicle-based gel displays all the requirements needed for application in the pharmaceutical and cosmetic fields.
AutoSpill: A method for calculating spillover coefficients to compensate or unmix high-parameter flow cytometry data (2020)

Abstract Compensating in classical flow cytometry or unmixing in spectral systems is an unavoidable challenge in the data analysis of fluorescence-based flow cytometry. In both cases, spillover coefficients are estimated for each fluorophore using single-color controls. This approach has remained essentially unchanged since its inception, and is increasingly limited in its ability to deal with high-parameter flow cytometry. Here, we present AutoSpill, a novel approach for calculating spillover coefficients or spectral signatures of fluorophores. The approach combines automated gating of cells, calculation of an initial spillover matrix based on robust linear regression, and iterative refinement to reduce error. Moreover, autofluorescence can be compensated out, by processing it as an endogenous dye in an unstained control. AutoSpill uses single-color controls and is compatible with common flow cytometry software, but it differs in two key aspects from current methods: (1) it is much less demanding in the preparation of controls, as it does not require the presence of well-defined positive and negative populations, and (2) it does not require manual tuning of the spillover matrix, as the algorithm iteratively computes the tuning, producing an optimal compensation matrix. Another algorithm, AutoSpread, complements this approach, providing a robust estimate of the Spillover Spreading Matrix (SSM), while avoiding the need for well-defined positive and negative populations. Together, AutoSpill and AutoSpread provide a superior solution to the problem of fluorophore spillover, allowing simpler and more robust workflows in high-parameter flow cytometry.
Molecular Organization of Glutamate Receptors in the Postsynaptic Density (2005)

Abstract A significant advance in the field of excitatory amino acid (EAA) transmission has been the great progress made toward elucidation of the molecular composition and function of the postsynaptic density (PSD) complex, one of the defining structural features of excitatory synapses. The PSD complex is a marked thickening localized to the postsynaptic side of asymmetric, excitatory synapses and consists of a network of scaffolding, cytoskeletal, and regulatory proteins in association with ionotropic glutamate receptors (iGluRs) and some of the metabotropic glutamate receptors (mGluRs). Biochemical and immunocytochemical characterization showed that, among its constituent proteins, N-methyl-D-aspartate (NMDA) receptors are highly represented compared with the other EAA receptors, reflecting the fact that they are the most tightly integrated receptors within the complex. This chapter looks at the molecular organization of glutamate receptors in the PSD complex, NMDA receptors within the PSD complex, AMPA receptors within the PSD complex, kainate receptors within the PSD complex, and mGluRs within the PSD complex.
Leveraging Blowing as a Directly Controlled Interface (2019)

Breathing is a natural and directly controllable human interaction method. Currently, only a few works have considered breath as a direct input controlling mechanism. The equipment relied upon in these works is generally complicated, expensive, inconvenient to wear, and sometimes insufficiently controllable. This paper proposes a simple method to implement a natural and directly controllable interaction based on blowing air. The method can provide interaction operations to applications by transferring blowing of air into sound using headset microphones and classifying them into different categories of blowing air in conjunction with support vector machines and particle swarm optimization. During tests, it's proved that this interface not only increases the type of blowing used for interaction, but also eliminates interference from speaking in a normal volume effectively. This user interface can be conveniently used in special environments (e.g., noise, unavailability of hands) or for special groups (e.g., deaf-mutes).
The crystal structure of trypanothione reductase from the human pathogen Trypanosoma cruzi at 2.3 Å resolution (1996)

Trypanothione reductase (TR) is an NADPH-dependent flavoprotein unique to protozoan parasites from the genera Trypanosoma and Leishmania and is an important target for the design of improved trypanocidal drugs. We present details of the structure of TR from the human pathogen Trypanosoma cruzi, the agent responsible for Chagas' disease or South American trypanosomiasis. The structure has been solved by molecular replacement, using as the starting model the structure of the enzyme from the nonpathogenic Crithidia fasciculata, and refined to an R-factor of 18.9% for 53,868 reflections with F > or = sigma F between 8.0 and 2.3 A resolution. The model comprises two subunits (968 residues), two FAD prosthetic groups, two maleate ions, and 419 water molecules. The accuracy and geometry of the enzyme model is improved with respect to the C. fasciculata enzyme model. The new structure is described and specific features of the enzyme involved in substrate interactions are compared with previous models of TR and related glutathione reductases from human and Escherichia coli. Structural differences at the edge of the active sites suggest an explanation for the differing specificities toward glutathionylspermidine disulfide.
A novel heavily doped drift - auxiliary cathode lateral insulated gate transistor structure (2005)

A novel CMOS-compatible, heavily doped drift auxiliary cathode lateral insulated gate transistor (HDD-ACLIGT) structure is analyzed using two-dimensional device simulation techniques. Simulation results indicate that low on-resistance and a fast turn-off time of less than 50 ns can be achieved by incorporating an additional n+ region which is self-aligned to the gate between the p+ auxiliary cathode and the p well, together with an extended p buried layer in an anode-shorted modified lateral insulated gate transistor (MLIGT) structure. The on-state and its transient performance are analyzed in detail. The on-state performances of the HDD-ACLIGT and the MLIGT are compared and discussed. The results indicate that the HDD-ACLIGT structure is well suited for HVICs. The device is also well suited for integration with self-aligned digital CMOS.