gebhart/patrepeval huggingface dataset:
A comparison of five methods for selecting tagging single-nucleotide polymorphisms (2005)

Our goal was to compare methods for tagging single-nucleotide polymorphisms (tagSNPs) with respect to the power to detect disease association under differing haplotype-disease association models. We were also interested in the effect that SNP selection samples, consisting of either cases, controls, or a mixture, would have on power. We investigated five previously described algorithms for choosing tagSNPS: two that picked SNPs based on haplotype structure (Chapman-haplotypic and Stram), two that picked SNPs based on pair-wise allelic association (Chapman-allelic and Cousin), and one control method that chose equally spaced SNPs (Zhai). In two disease-associated regions from the Genetic Analysis Workshop 14 simulated data, we tested the association between tagSNP genotype and disease over the tagSNP sets chosen by each method for each sampling scheme. This was repeated for 100 replicates to estimate power. The two allelic methods chose essentially all SNPs in the region and had nearly optimal power. The two haplotypic methods chose about half as many SNPs. The haplotypic methods had poor performance compared to the allelic methods in both regions. We expected an improvement in power when the selection sample contained cases; however, there was only moderate variation in power between the sampling approaches for each method. Finally, when compared to the haplotypic methods, the reference method performed as well or worse in the region with ancestral disease haplotype structure.
Drug Trafficking: Recent Advances in Therapeutics and Disease (2012)

Drug transporter proteins are of ever-increasing interest because of their role both in processes regulating pharmacokinetic properties of drugs (absorption, distribution, and elimination) and in the development of cellular drug resistance through decreased uptake or increased efflux of drugs in the target organ or tumor. Further understanding of the role of transporters in drug-drug interactions and identification of these proteins as possible therapeutic targets could contribute to improved treatment of a wide variety of diseases.
A Computational Model of Spatial Memory Anticipation during Visual Search (2006)

Some visual search tasks require to memorize the location of stimuli that have been previously scanned. Considerations about the eye movements raise the question of how we are able to maintain a coherent memory, despite the frequent drastically changes in the perception. In this article, we present a computational model that is able to anticipate the consequences of the eye movements on the visual perception in order to update a spatial memory
Abstract 10673: Early Diastolic Strain Rate Predicts Response to Heart Failure Therapy in Patients With Dilated Cardiomyopathy (2012)

Objective: The aim of this prospective study was to assess the value of speckle tracking echocardiographic (2D-STE) parameters to predict response to heart failure therapy in patients with dilated ...
H3-receptor antagonists: conformational analysis of thioperamide and x-ray crystal structure of the analog N-cyclohexyl-4-methylpiperidine-1-carbothioamide. (1998)

Thioperamide (N-cyclohexyl-4-[4(5)-imidazolyl]piperidine-1-carbothioamide) is a potent H3-receptor antagonist, the low conformational flexibility of which could be a favourable feature in the design of new H3-receptor antagonists using its structure as a template. Minimum-energy conformations of thioperamide were studied with the molecular mechanics approach, integrated by X-ray crystallography on an analogue, N-cyclohexyl-4-methylpiperidine-1-carbothioamide (1). Compound 1 was synthesized, and its structure has been solved by X-ray diffraction in order to verify the conformation of the piperidine-1-carbothioamide fragment, and to compare the crystallographic results with those of molecular mechanics. Conformational analysis on the free-rotating bonds of thioperamide was performed with different search methods in order to find the minimum-energy conformations and to estimate rotational barriers. For steric reasons, the rotation around the bond connecting the cyclohexane ring with the carbothioamide nitrogen is more hampered than that around the bond connecting imidazole with piperidine. The rotation around the first bond presents two symmetrical energy minima separated from a third minimum by an energy barrier of 40 KJ/mol. The spatial disposition of compound 1 in the crystal and the common part of thioperamide in one of its minimum-energy conformations are very similar. The minimum-energy conformations of thioperamide calculated by molecular mechanics are therefore reliable and they can be used for structural comparisons with other H3-receptor antagonists.
Functional brain imaging of peripheral and central vestibular disorders (2008)

This review summarizes our current knowledge of multisensory vestibular structures and their functions in humans. Most of it derives from brain activation studies with PET and fMRI conducted over the last decade. The patterns of activations and deactivations during caloric and galvanic vestibular stimulations in healthy subjects have been compared with those in patients with acute and chronic peripheral and central vestibular disorders. Major findings are the following: (1) In patients with vestibular neuritis the central vestibular system exhibits a spontaneous visual-vestibular activation-deactivation pattern similar to that described in healthy volunteers during unilateral vestibular stimulation. In the acute stage of the disease regional cerebral glucose metabolism (rCGM) increases in the multisensory vestibular cortical and subcortical areas, but simultaneously it significantly decreases in the visual and somatosensory cortex areas. (2) In patients with bilateral vestibular failure the activation-deactivation pattern during vestibular caloric stimulation shows a decrease of activations and deactivations. (3) Patients with lesions of the vestibular nuclei due to Wallenberg's syndrome show no activation or significantly reduced activation in the contralateral hemisphere during caloric irrigation of the ear ipsilateral to the lesioned side, but the activation pattern in the ipsilateral hemisphere appears 'normal'. These findings indicate that there are bilateral ascending vestibular pathways from the vestibular nuclei to the vestibular cortex areas, and the contralateral tract crossing them is predominantly affected. (4) Patients with posterolateral thalamic infarctions exhibit significantly reduced activation of the multisensory vestibular cortex in the ipsilateral hemisphere, if the ear ipsilateral to the thalamic lesion is stimulated. Activation of similar areas in the contralateral hemisphere is also diminished but to a lesser extent. These data demonstrate the functional importance of the posterolateral thalamus as a vestibular gatekeeper. (5) In patients with vestibulocerebellar lesions due to a bilateral floccular deficiency, which causes downbeat nystagmus (DBN), PET scans reveal that rCGM is reduced in the region of the cerebellar tonsil and flocculus/paraflocculus bilaterally. Treatment with 4-aminopyridine lessens this hypometabolism and significantly improves DBN. These findings support the hypothesis that the (para-) flocculus and tonsil play a crucial role in DBN. Although we can now for the first time attribute particular activations and deactivations to functional deficits in distinct vestibular disorders, the complex puzzle of the various multisensory and sensorimotor functions of the phylogenetically ancient vestibular system is only slowly being unraveled.
THE IMMUNOSUPPRESSIVE ACTIVITY OF ARA-CYTIDINE (CYTARABINE) (1969)

SUMMARY The effect of cytarabine (ara-cytidine, cytosine arabinoside), a potent antitumor and immunosuppressive agent, on canine renal transplantation has been studied. Cytarabine did not prolong the survival of the renal allografts although a modification of the histological pattern of rejection was observed. In contrast, the antibody (hemagglutinin) response induced by injections of sheep red blood cells was significantly suppressed by cytarabine. In addition, the appearance of both total and mercaptoethanol-resistant antibody titers were delayed. Cytarabine injections in normal and kidney transplant dogs resulted in a general leukopenia. No selectivity for leukocyte type was observed.
Length heteroplasmy of sturgeon mitochondrial DNA: an illegitimate elongation model. (1990)

Extensive length polymorphism and heteroplasmy (multiple forms within an individual) of the D-loop region are observed in mitochondrial DNA of the white sturgeon (Acipenser transmontanus). The nucleotide sequence of this region, for both a short and a long form, shows that the differences are due to variable numbers of a perfect 82-bp direct repeat. We propose a model for the replicative origin of length differences, involving a competitive equilibrium between the heavy strand and the D-loop strand. This model suggests that frequent misalignment in the repeat region prior to elongation, facilitated by a stable secondary structure in the displaced strand, can explain both the polymorphism and heteroplasmy in this species.
Particle control challenges in process chemicals and ultra-pure water for sub-10nm technology nodes (2014)

Particle contamination in ultra-pure water (UPW) and chemicals will eventually end up on the surface of a wafer and may result in killer defects. To improve the semiconductor processing yield in sub-10 nm half pitch nodes, it is necessary to control particle defectivity. In a systematic study of all major techniques for particle detection, counting, and sizing in solutions, we have shown that there is a gap in the required particle metrology which needs to be addressed by the industry. To reduce particles in solutions and improve filter retention for sub-10 nm particles with very low densities (&lt;10 particles/mL), liquid particle counters that are able to detect small particles at low densities are required. Non-volatile residues in chemicals and UPW can result in nanoparticles. Measuring absolute non-volatile residues in UPW with concentrations in the ppb range is a challenge. However, by using energy-dispersive spectroscopy (EDS) analysis through transmission electron microscopy (TEM) of non-volatile residues we found silica both in dissolved and colloidal particle form which is present in one of the cleanest UPW that we tested. A particle capture/release technique was developed at SEMATECH which is able to collect particles from UPW and release them in a controlled manner. Using this system we showed sub-10 nm particles are present in UPW. In addition to colloidal silica, agglomerated carbon containing particles were also found in UPW.
ChemInform Abstract: Recent Synthetic Approaches to 6,15‐Iminoisoquino[3,2‐b]3‐benzazocine Compounds (2010)

Abstract Review: 71 refs.
Obfuscated Memory Malware Detection in Resource-Constrained IoT Devices for Smart City Applications (2023)

Obfuscated Memory Malware (OMM) presents significant threats to interconnected systems, including smart city applications, for its ability to evade detection through concealment tactics. Existing OMM detection methods primarily focus on binary detection. Their multiclass versions consider a few families only and, thereby, fail to detect much existing and emerging malware. Moreover, their large memory size makes them unsuitable to be executed in resource-constrained embedded/IoT devices. To address this problem, in this paper, we propose a multiclass but lightweight malware detection method capable of identifying recent malware and is suitable to execute in embedded devices. For this, the method considers a hybrid model by combining the feature-learning capabilities of convolutional neural networks with the temporal modeling advantage of bidirectional long short-term memory. The proposed architecture exhibits compact size and fast processing speed, making it suitable for deployment in IoT devices that constitute the major components of smart city systems. Extensive experiments with the recent CIC-Malmem-2022 OMM dataset demonstrate that our method outperforms other machine learning-based models proposed in the literature in both detecting OMM and identifying specific attack types. Our proposed method thus offers a robust yet compact model executable in IoT devices for defending against obfuscated malware.
ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models (2022)

ABSTRACT ModelCIF ( github.com/ihmwg/ModelCIF ) is a data information framework developed for and by computational structural biologists to enable delivery of Findable, Accessible, Interoperable , and Reusable ( FAIR ) data to users worldwide. It is an extension of the Protein Data Bank Exchange / macromolecular Crystallographic Information Framework (PDBx/mmCIF), which is the global data standard for representing experimentally-determined, three-dimensional (3D) structures of macromolecules and associated metadata. ModelCIF provides an extensible data representation for deposition, archiving, and public dissemination of predicted 3D models of proteins. The PDBx/mmCIF framework and its extensions ( e.g ., ModelCIF) are managed by the Worldwide Protein Data Bank partnership (wwPDB, wwpdb.org ) in collaboration with relevant community stakeholders such as the wwPDB ModelCIF Working Group ( wwpdb.org/task/modelcif ). This semantically rich and extensible data framework for representing computed structure models (CSMs) accelerates the pace of scientific discovery. Herein, we describe the architecture, contents, and governance of ModelCIF, and tools and processes for maintaining and extending the data standard. Community tools and software libraries that support ModelCIF are also described.
WarpCore: A Library for fast Hash Tables on GPUs (2020)

Hash tables are ubiquitous. Properties such as an amortized constant time complexity for insertion and querying as well as a compact memory layout make them versatile associative data structures with manifold applications. The rapidly growing amount of data emerging in many fields motivated the need for accelerated hash tables designed for modern parallel architectures. In this work, we exploit the fast memory interface of modern GPUs together with a parallel hashing scheme tailored to improve global memory access patterns, to design WarpCore - a versatile library of hash table data structures. Unique device-sided operations allow for building high performance data processing pipelines entirely on the GPU. Our implementation achieves up to 1.6 billion inserts and up to 4.3 billion retrievals per second on a single GV100 GPU thereby outperforming the state-of-the-art solutions cuDPP, SlabHash, and NVIDIA RAPIDS cuDF. This performance advantage becomes even more pronounced for high load factors of over 90%. To overcome the memory limitation of a single GPU, we scale our approach over a dense NVLink topology which gives us close-to-optimal weak scaling on DGX servers. We further show how WarpCore can be used for accelerating a real world bioinformatics application (metagenomic classification) with speedups of over two orders-of-magnitude against state-of-the-art CPU-based solutions. WarpCore is open source software written in C++/CUDA-C and can be downloaded at https://github.com/sleeepyjack/warpcore.
High activity of hot electrons from bulk 3D graphene materials for efficient photocatalytic hydrogen production (2017)

Design and synthesis of efficient photocatalysts for hydrogen production via water splitting are of great importance from both theoretical and practical viewpoints. Many metal-based semiconductors have been explored for this purpose in recent decades. Here, for the first time, an entirely carbon-based material, bulk three-dimensionally cross-linked graphene (3DG), has been developed as a photocatalyst for hydrogen production. It exhibits a remarkable hydrogen production rate of 270 μmol·h−1·g cat −1 under full-spectrum light via a hot/free electron emission mechanism. Furthermore, when combined with the widely used semiconductor TiO2 to form a TiO2/3DG composite, it appears to become a more efficient hydrogen production photocatalyst. The composite achieves a production rate of 1,205 μmol·h−1·g cat −1 under ultraviolet–visible (UV–vis) light and a 7.2% apparent quantum efficiency at 350 nm due to the strong synergetic effects between TiO2 and 3DG.
Polarization insensitive, low-loss, low-crosstalk wavelength multiplexer modules (1999)

A method for compensating polarization sensitivity of arrayed waveguide gratings (AWG's) based on silica-on-Si waveguide technology using stress release grooves and its realization are described. These stress release grooves compensate fabrication-induced waveguide birefringence without performance degradation. An advanced design for low-loss, low-channel imbalance, and low-crosstalk multiplexer is given and results of the realized modules are presented. The TE/TM passband shift could be reduced from 0.7 nm to below 0.05 nm. Insertion loss of the fully packaged wavelength multiplexer modules is <5 dB and adjacent channel crosstalk is as low as <-40 dB.
Study and Characterization of Sisal Fiber/Zein Resin Interface (2018)

The interfacial shear strength (IFSS) between natural sisal fiber and zein protein resin was explored using the microbond test. Commercially available zein protein was processed into resins and their IFSS with sisal fiber was measured. Effects of sorbitol plasticizer content and microfibrillated cellulose (MFC) reinforcement loading on the IFSS with the resin were studied. Scanning electron microscopy (SEM) was used to characterize the fracture surfaces before and after the microbond test. Energy dispersive X-ray spectroscopy (EDX) was utilized to map the residual resin on the sisal fiber surface after the microbond test. The results showed that sisal fiber/ zein IFSS decreased with sorbitol content. At 20 wt% sorbitol content 53% decrease in IFSS was observed. IFSS increased with MFC loading from 1.32 MPa (control) to 2.40 MPa for resin containing 15 wt% MFC. Physical entanglements between sisal fibers and MFC are believed to be responsible for this enhancement in the IFSS.
Picosecond carrier lifetime and large optical nonlinearities in InGaAsP grown by He-plasma-assisted molecular beam epitaxy (1997)

We report the measurement of a fast carrier lifetime and large band-gap-resonant optical nonlinearities in an InGaAsP sample grown by He-plasma-assisted molecular beam epitaxy. Using a 2-microm-thick sample grown on an InP substrate, we observed a carrier lifetime of 15 ps and an index change as large as 0.077 induced by an intense 1-ps pulse at a wavelength of 1.57 microm. Good crystalline structure is maintained in the material during growth, and the absorption spectrum shows a sharp band edge. These properties indicate that materials produced by He-plasma-assisted growth have potential applications in compact ultrafast photonic devices.
Role of the 5' upstream sequence and tandem promoters in regulation of the rpsU-dnaG-rpoD macromolecular synthesis operon (1988)

Bal31 exonuclease deletion analysis and transposon Tn5 mutagenesis of the 5' regulatory region of the rpsU-dnaG-rpoD macromolecular synthesis operon fused to the chloramphenicol acetyltransferase gene (pGLR301) demonstrated that sequences 5' to the operon promoters were not involved in operon transcriptional regulation and that the three tandem promoters P1, P2, and P3 were functionally independent. P2 was the strongest promoter, and P3 was the weakest. P1, P2, and P3 acting in combination appeared to be stronger than the individual promoters.
Origin of Nonmetallic Inclusions in Ladle Transition part of Continuously Cast Slabs (2007)

In the continuous casting process, it is important to reduce the off-quality portion due to ladle exchange or variation in process parameters. In the present study, experimental investigation and thermodynamic calculation has been carried out for analysis origin of non-metallic inclusions in ladle transition part of continuously cast slabs.The following results are obtained.(1) In the present study, entrapped nonmetallic inclusions in the transition part of ladle exchange slabs are mainly spherical inclusions (CaO-Al2O3).(2) According to thermodynamic calculation, origin of spherical inclusions are mainly ladle slag and tundish slag.(3) Applying thermodynamic calculation for the equilibrium between slag and molten steel is useful for analysis origin of nonmetallic inclusions in the continuously cast slabs.
Single event effects induced by heavy ions in SONOS charge trapping memory arrays. (2021)

Abstract not provided.
Measurement of the Branching Fraction ofΥ(4S)→B0B¯0 (2005)

We report the first measurement of the branching fraction f(00) for Gamma(4S) --> B(0)B(0). The data sample consists of 81.7 fb(-1) collected at the Gamma(4S) resonance with the BABAR detector at the SLAC PEP-II asymmetric-energy e(+)e(-) storage ring. Using partial reconstruction of the decay B(0) --> D(*+) l(-)nu(l) in which only the charged lepton and the soft pion from the decay D(*+) --> D(0)pi(+) are reconstructed, we obtain f(00) = 0.487 +/- 0.010(stat) +/- 0.008(syst). Our result does not depend on the branching fractions of B(0) --> D(*+)l(-)nu(l) and D(*+) --> D(0)pi(+) decays, on the ratio of the charged and neutral B meson lifetimes, nor on the assumption of isospin symmetry.
Crystallization and Dissolution of Flow-Induced Precursors (2008)

We make use of a specially synthesized linear high density polyethylene with a bimodal molecular weight distribution (MWD) to demonstrate that it is possible to produce a suspension of extended-chain (shish) crystals only. Such a suspension can be generated at high temperatures, above but close to the equilibrium melting temperature of the unconstrained extended-chain crystals (T(m)(0)=141.2 degrees C) and requires stretch of the longest chains of the MWD. After the application of a shear flow of 120 s(-1) for 1 s at 142 degrees C, x-ray scattering suggests the presence of a large number of metastable needlelike precursors with limited or no crystallinity. Precursors that are too small dissolve on a timescale that correlates perfectly with the reptation time of the longest polymer molecules. Whereas, precursors that exceed a critical size crystallize forming extended-chain shishes.
Effects of Zinc Deficiency and Pneumococcal Surface Protein A Immunization on Zinc Status and the Risk of Severe Infection in Mice (2003)

Streptococcus pneumoniae is a major cause of illness and death in children in developing countries. In these children, zinc deficiency is associated with an increased risk of acute respiratory tract infections, which can be reduced by daily zinc administration. Severe infections decrease zinc levels in plasma and may thereby move individuals with preexisting low zinc stores into a vicious cycle of infection and unavailable zinc. Pneumococcal surface protein A (PspA) has emerged as a promising vaccine candidate, and immunization with this antigen protects animals from pneumococcal infection. In an animal experiment, we measured the effect of zinc depletion on the immune response to parenterally administrated PspA and assessed the effect of this PspA vaccination and zinc depletion on the severity of pneumococcal infection and on zinc status. Mice were kept on different diets for 5 weeks, immunized twice 14 days apart, and challenged intranasally with S. pneumoniae. Mice on the zinc-deficient diet showed substantially reduced immune responses to PspA, more extensive pneumococcal colonization in the nasal mucosa, more severe infections, and an increased risk of death. PspA immunization reduced the risk of severe disease, and the reduction in severity was reflected in substantially reduced zinc depletion from bones.