gebhart/patrepeval huggingface dataset:
SIMD Ray Stream Tracing - SIMD Ray Traversal with Generalized Ray Packets and On-the-fly Re-Ordering - (2007)

Achieving high performance on modern CPUs requires efficient utilization of SIMD units. Doing so requires that algorithms are able to take full advantage of the SIMD width offered and to not waste SIMD instructions on low utilization cases. Ray tracers exploit SIMD extensions through packet tracing. This re-casts the ray tracing algorithm into a SIMD framework, but high SIMD efficiency is only achieved for moderately complex scenes, and highly coherent packets. In this paper, we present a stream programming oriented traversal algorithm that processes streams of rays in SIMD fashion; the algorithm is motivated by breadth-first ray traversal and implicitly re-orders streams of rays on the fly by removing deactivated rays after each traversal step using a stream compaction step. This improves SIMD efficiency in the presence of complex scenes and diverging packets, and is, in particular, designed for potential wider-than-four SIMD architectures with scatter/gather support.
Vagal stimulation for heart failure (2010)

The initial observations with chronic vagal stimulation in man, though limited by very small numbers, are very encouraging and seem to open new paths, or perhaps avenues, for the management of symptomatic heart failure. This transition between experimental and clinical approaches represents an exciting example of translational research.
Smolin and Thoft's the cornea : scientific foundations and clinical practice (2005)

Fundamentals Basic Science Anatomy Conjunctiva and Lids Cornea Limbus Sclera Physiology Cornea Conjunctiva Limbus Sclera Biochemistry and Cell Biology Cornea Conjunctiva Limbus Sclera Immunology: Basic and tissue specific Cornea Conjunctiva Limbus Sclera Pathologic responses Cornea Conjunctiva Limbus Sclera Corneal Neovascularization Examination and Evaluation Techniques Slit lamp biomicroscopy & Photography Pachymetry Keratometry Topography Specular microscopy Confocal microscopy Epidemiology of Cornea and External Diseases Clinical Topics Infectious Diseases Bacterial keratitis and conjunctivitis Bacteriology Clinical entities Viral keratitis and conjunctivitis Virology Clinical entities Fungal keratitis, conjunctivitis and canaliculitis Mycology Clinical entities Parasitic keratitis and conjunctivitis Parasitology Clinical entities Chlamydial keratitis and conjunctivitis Chlymidiology Clinical aspects Suspected Immunologic Disease Conjunctivitis Atopy Chronic cicatrizing conjunctivitis Drug hypersensitivity Phlyctenular Keratitis Rheumatologic disorders Mooren's ulcer Scleritis Ocular Surface Disease Keratoconjunctivitis Sicca - Intro Physiology and biochemistry of the tear film Clinical aspects Keratitis sicca Sjogren's syndrome Meibomian Gland Dysfunction and Blepharitis Recurrent Erosion Syndrome and Other Superior limbic keratoconjunctivitis Ligneous conjunctivitis Rosacea Thygeson's disease Filamentary Keratitis Climactic Keratitis Dacryoadenitis Metabolic and Congenital Disease
Prenatal programming of postnatal endocrine responses by glucocorticoids (2002)

Epidemiological studies have led to the hypothesis that a major component of the risk of diseases such as hypertension, coronary heart disease and non-insulin-dependent diabetes (the 'metabolic syndrome') is established before birth. Although the underlying mechanisms of this 'programming' of disease have not yet been conclusively determined, a reduced fetal nutrient supply as a consequence of poor placental function or unbalanced maternal nutrition is strongly implicated. It has been proposed that one outcome of suboptimal nutrition is exposure of the fetus to excess glucocorticoids, which restrict fetal growth and programme permanent alterations in its cardiovascular, endocrine and metabolic systems. This review focuses on the effects of endogenous and exogenous glucocorticoid exposure in utero on postnatal hypothalamo-pituitary-adrenal (HPA) axis activity, both in humans and experimental animals. The physiological consequences and proposed underlying molecular and cellular mechanisms are discussed. Current data indicate that key targets for programming may include not only the HPA axis but also glucocorticoid receptor gene and 11beta-hydroxysteroid dehydrogenase type 2 (11betaHSD2) gene expression in a range of tissues.
NON-DESTRUCTIVE DETERMINATION OF THE ENRICHMENT OF U-235 IN A FUEL PLATE BY GAMMA-RAY SPECTRA (1963)

Under the optimal conditions, the practical activity ratio is 34.8%. The determination coefficient (R2) is 0.9442, ensuring adequate credibility of the model. LLAE3, extracted from Folium nelumbinis in our laboratory, has prominently activated effects on PGK.
Correction for geometric distortion in echo planar images from B0 field variations (1995)

A method is described for the correction of geometric distortions occurring in echo planar images. The geometric distortions are caused in large part by static magnetic field inhomogeneities, leading to pixel shifts, particularly in the phase encode direction. By characterizing the field inhomogeneities from a field map, the image can be unwarped so that accurate alignment to conventionally collected images can be made. The algorithm to perform the unwarping is described, and results from echo planar images collected at 1.5 and 4 Tesla are shown.
Less harm, less worry or how to improve network security by bounding system offensiveness (2002)

We describe a new class of tools for protecting computer systems from security attacks. Their distinguished feature is the principle they are based on. Host or network protection is not achieved by strengthening their defenses but by weakening the enemy's offensive capabilities. A prototype tool has been implemented that demonstrates that such an approach is feasible and effective. We show that some of the most popular DoS attacks are effectively blocked with limited impact on the sender's performance. Measurements of the implemented prototype show that controlling the outgoing traffic does not affect performance at the sender machine, when traffic is not hostile. If traffic is hostile, the limited slow down experienced at the source is the price to pay to make the Internet a safer place for all its users. The limited performance impact and the efficacy in attack prevention make tools like the one presented a new component of security architectures. Furthermore, such a type of tools represents an effective way to address security problems that are still unsolved or for which only partial solutions are available, such as the liability problem, intranet security, security tools performance and the use of distributed tools for intrusion.
Artificial intelligence in radiology: decision support systems. (1994)

Computer-based systems that incorporate artificial intelligence techniques can help physicians make decisions about their patients' care. In radiology, systems have been developed to help physicians choose appropriate radiologic procedures and to formulate accurate diagnoses. These decision support systems use techniques such as rule-based reasoning, artificial neural networks, hypertext, Bayesian networks, and case-based reasoning. This article reviews these artificial intelligence techniques, describes their application in radiology, and discusses the role that decision support systems may play in radiology's future.
Site directed mutagenesis of subunit 8 of yeast mitochondrial ATP synthase (1990)

The function of the positively charged C-terminal region of mitochondrially encoded subunit 8 of yeast mitochondrial ATP synthase was investigated using derivatives truncated at each of the 3 positively charged residues (Arg37, Arg42 and Lys47). Each construct, allotopically expressed in the nucleus, was tested for its ability to import and assemble functionally into ATP synthase in yeast cells unable to synthesize mitochondrial subunit 8. The efficiency of import of each construct into isolated wild-type yeast mitochondria was also determined. One construct truncated at the penultimate residue of subunit 8 (Lys47) functions in vivo and shows efficient import in vitro. Thus subunit 8 can function with only two positively charged residues. The remainder of the subunit 8 variants failed to rescue in vivo. Since they all show greatly reduced or undetectable import in vitro, presumably because of the increased hydrophobic character of the subunit 8 moiety in the chimaeric precursors, the status of these variants as regards assembly and function is not clear.
MATERNAL-ZYGOTIC GENE INTERACTIONS DURING FORMATION OF THE DORSOVENTRAL PATTERN IN DROSOPHILA EMBRYOS (1983)

Maternal-zygotic interactions involving the three genes dorsal (dl), twist (twi) and snail (sna) are described. The results suggest that all three are involved in the process by which the dorsoventral pattern of the Drosophila embryo is established. First, the lethal embryonic mutant phenotypes are rather similar. In homozygous twi or sna embryos invagination of the ventral presumptive mesodermal cells fails to occur, and the resulting embryos are devoid of internal organs. This is very similar to the dominant phenotype described for dl; in the case of dl, however, the effect is a maternal one dependent on the mutant genotype of the female. Second, a synergistic interaction has been found whereby dominant lethality of twi- or sna-bearing zygotes is observed in embryos derived from heterozygous dl females at high temperature. The temperature sensitivity of this interaction permitted definition of a temperature-sensitive period which is probably that of dl. This was found to extend from approximately 12 hr prior to oviposition to 2-3 hr of embryogenesis. A zygotic action for the dl gene in addition to the maternal effect was revealed by the finding that extra doses of dl(+) in the zygotes can partially rescue the dominant lethality of heterozygous twi embryos derived from heterozygous dl females. Two possible interpretations of the synergism are considered: (1) twi and sna are activated in the embryos as a result of positional signals placed in the egg as a consequence of the functioning of the dl gene during oogenesis and, thus, play a role in embryonic determination. (2) The gene products of dl(+) and twi (+) (or sna(+)) combine to produce a functional molecule that is involved in the specification of dorsoventral pattern in the early embryo.
Transcription factor T-bet regulates inflammatory arthritis through its function in dendritic cells (2006)

The transcription factor T-bet (Tbx21) plays a major role in adaptive immunity and is required for optimal IFN-gamma production by DCs. Here we demonstrate an essential function for T-bet in DCs in controlling inflammatory arthritis. We show that collagen antibody-induced arthritis (CAIA), a model of human RA, is a bipartite disease characterized by an early innate immune system component intact in RAG2 mice and a later adaptive immune system phase. Mice lacking T-bet had markedly reduced joint inflammation at both early and late time points and RAG2T-bet double-deficient mice were essentially resistant to disease. Remarkably, adoptive transfer of T-bet-expressing DCs reconstituted inflammation in a T-bet deficient and T-bet/RAG2-deficient milieu. T-bet regulates the production of proinflammatory cytokine IL-1alpha and chemokines macrophage inflammatory protein-1alpha (MIP-1alpha) and thymus- and activation-related chemokine (TARC) by DCs. Further, T-bet expression in DCs is required for T helper cell activation. We conclude that T-bet plays a vital function in DCs that links innate and adaptive immunity to regulate inflammatory responses. T-bet provides an attractive new target for the development of novel therapeutics for inflammatory arthritis.
The Dance of Wellbeing: Defining the Musical Therapeutic Effect (2000)

Abstract Music making is a human activity that communicates motives – the underlying impulses for action, by which experience is gained, and which are accompanied by feelings. Music evokes narratives of experience, based on our innate ability to share the passing of expressive ‘mind time’, an ability that may be called ‘musicality’. which is inseparable from the impulse to move with anticipation of rhythmic sensory consequences and varied emotional evaluations. Communicative musicality is the source of the music therapeutic experience and its effects. An inborn musicality is clearly uncovered in acoustic analyses of parent/infant vocal interactions, where, independent of verbal communication, a shared sense of time and the shaping of jointly-created pitch contours describe phrases and narrative cycles of feeling. There is new evidence that the communication of motives and experience is supported by systems of ‘sympathy neurones’ in the regulatory core of the brain, and by the ‘vitality affects’ they generate. The music therapy relationship seeks a dance of human passion and well-being by fundamentally intuitive means. Its verbal/cognitive regulation is necessary for the cultivation and recording of its technique, but not the origin of its immediate power 1. Keywords: musicality - therapy - infants - movement - emotion - timing - communication
Wobble decoding by the Escherichia coli selenocysteine insertion machinery (2013)

Selenoprotein expression in Escherichia coli redefines specific single UGA codons from translational termination to selenocysteine (Sec) insertion. This process requires the presence of a Sec Insertion Sequence (SECIS) in the mRNA, which forms a secondary structure that binds a unique Sec-specific elongation factor that catalyzes Sec insertion at the predefined UGA instead of release factor 2-mediated termination. During overproduction of recombinant selenoproteins, this process nonetheless typically results in expression of UGA-truncated products together with the production of recombinant selenoproteins. Here, we found that premature termination can be fully avoided through a SECIS-dependent Sec-mediated suppression of UGG, thereby yielding either tryptophan or Sec insertion without detectable premature truncation. The yield of recombinant selenoprotein produced with this method approached that obtained with a classical UGA codon for Sec insertion. Sec-mediated suppression of UGG thus provides a novel method for selenoprotein production, as here demonstrated with rat thioredoxin reductase. The results also reveal that the E. coli selenoprotein synthesis machinery has the inherent capability to promote wobble decoding.
Formation of Disulfide Bonds in Synthetic Peptides and Proteins (2003)

Disulfide bridges play a crucial role in the folding and structural stabilization of many important extracellular peptide and protein molecules, including hormones, enzymes, growth factors, toxins, and immunoglo-bulins (1–10). In addition, the artificial introduction of extra disulfide bridges into peptides or proteins allows the creation of conformational constraints that can improve biological activity (11–15) or confer ther-mostability (5, 16–19). Given this intrinsic biological interest, disulfide-con-taining peptides have long been attractive targets for chemical synthesis. Starting with the pioneering work of du Vigneaud on oxytocin (20), the challenge to reproduce and engineer increasingly complex arrays of disulfide bridges as are found in natural peptides and proteins (7, 10, 21– 23) has stimulated the efforts and ingenuities of many peptide chemists. Table 1 provides a representative, but by no means exhaustive, listing of noteworthy syntheses of peptides or small proteins with one or more disulfides. The methods can be readily generalized to analogs in which cysteine residues are replaced by homologs, such as homocysteine, or by sterically restricted derivatives, such as penicillamine (β,β-dimethylcysteine).
The Blood-Brain Barrier and Cancer: Transporters, Treatment, and Trojan Horses (2007)

Despite scientific advances in understanding the causes and treatment of human malignancy, a persistent challenge facing basic and clinical investigators is how to adequately treat primary and metastatic brain tumors. The blood-brain barrier is a physiologic obstruction to the delivery of systemic chemotherapy to the brain parenchyma and central nervous system (CNS). A number of physiologic properties make the endothelium in the CNS distinct from the vasculature found in the periphery. Recent evidence has shown that a critical aspect of this barrier is composed of xenobiotic transporters which extrude substrates from the brain into the cerebrospinal fluid and systemic circulation. These transporters also extrude drugs and toxins if they gain entry into the cytoplasm of brain endothelial cells before they enter the brain. This review highlights the properties of the blood-brain barrier, including the location, function, and relative importance of the drug transporters that maintain this barrier. Primary and metastatic brain malignancy can compromise this barrier, allowing some access of chemotherapy treatment to reach the tumor. The responsiveness of brain tumors to systemic treatment found in past clinical research is discussed, as are possible explanations as to why CNS tumors are nonetheless able to evade therapy. Finally, strategies to overcome this barrier and better deliver chemotherapy into CNS tumors are presented.
Analysis of Acidic Oligosaccharides and Glycopeptides by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (1996)

2,5-Dihydroxybenzoic acid (DHB) is the most commonly used matrix for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI/TOF) of oligosaccharides. Because acidic, sialylated oligosaccharides are detected at only the low picomole level with DHB, alternative matrices were screened to identify a matrix with a lower limit of detection. Negative-ion spectra of pure mono-, di-, and trisialylated oligosaccharides were acquired with either 6-aza-2-thiothymine or 2',4',6'-trihydroxyacetophenone (THAP) in the linear mode. Detection limits of less than 50 fmol with signal-to-noise ratios of better than 5:1 were achieved with both matrices. THAP was the preferred matrix because it provided a lower limit of detection and gave less prompt fragmentation. Incorporation of ammonium citrate into the matrix, along with vacuum drying of the sample, was required in order to obtain maximum sensitivity with THAP. No evidence of competition for ionization was found when a mixture of mono-, di-, and trisialylated oligosaccharides was analyzed with THAP. These findings suggest that MALDI/TOF analysis may provide a rapid means to identify changes in carbohydrate composition in glycoproteins. In addition, THAP offered improved sensitivity for detection of acidic glycopeptides over alpha-cyano-4-hydroxycinnamic acid.
Combined Effect of Cyclosporine and Sirolimus on Improving the Longevity of Recombinant Adenovirus–Mediated Transgene Expression in the Retina (2001)

The intraocular safety of rAd should be carefully considered before clinical trials are performed.
Biology Today (2003)

Biology Today is a truly innovative introductory biology text. Designed to combine the teaching of biological concepts within the context of current societal issues, Biology Today encourages introductory biology students to think critically about the role that science plays in their world. The Third Edition has been revised and updated, and contains three new chapters: Genetic Engineering and Genomics, New Infectious Threats, and Protecting the Biosphere.
Terminology finite-state preprocessing for computational LFG (1998)

This paper presents a technique to deal with multiword nominal terminology in a computational Lexical Functional Grammar. This method treats multiword terms as single tokens by modifying the preprocessing stage of the grammar (tokenization and morphological analysis), which consists of a cascade of two-level finite-state automata (transducers). We present here how we build the transducers to take terminology into account. We tested the method by parsing a small corpus with the without this treatment of multiword terms. The number of parses and parsing time decrease without affecting the relevance of the results. Moreover, the method improves the perspicuity of the analyses.
A case of advanced infantile myofibromatosis harboring a novel MYH10-RET fusion (2016)

Supplemental File S1. Methods Comprehensive genomic profiling Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Denosumab, a Fully Human Monoclonal Antibody to RANKL, Inhibits Bone Resorption and Increases BMD in Knock-In Mice That Express Chimeric (Murine/Human) RANKL (2008)

RANKL is a TNF family member that mediates osteoclast formation, activation, and survival by activating RANK. The proresorptive effects of RANKL are prevented by binding to its soluble inhibitor osteoprotegerin (OPG). Recombinant human OPG-Fc recognizes RANKL from multiple species and reduced bone resorption and increased bone volume, density, and strength in a number of rodent models of bone disease. The clinical development of OPG-Fc was discontinued in favor of denosumab, a fully human monoclonal antibody that specifically inhibits primate RANKL. Direct binding assays showed that denosumab bound to human RANKL but not to murine RANKL, human TRAIL, or other human TNF family members. Denosumab did not suppress bone resorption in normal mice or rats but did prevent the resorptive response in mice challenged with a human RANKL fragment encoded primarily by the fifth exon of the RANKL gene. To create mice that were responsive to denosumab, knock-in technology was used to replace exon 5 from murine RANKL with its human ortholog. The resulting "huRANKL" mice exclusively express chimeric (human/murine) RANKL that was measurable with a human RANKL assay and that maintained bone resorption at slightly reduced levels versus wildtype controls. In young huRANKL mice, denosumab and OPG-Fc each reduced trabecular osteoclast surfaces by 95% and increased bone density and volume. In adult huRANKL mice, denosumab reduced bone resorption, increased cortical and cancellous bone mass, and improved trabecular microarchitecture. These huRANKL mice have potential utility for characterizing the activity of denosumab in a variety of murine bone disease models.
Optical Phase Conjugation (1999)

Optical Phase Conjugation provides an introduction to the subject as well as an up-to-date account of the latest developments and applications. The nonlinear optical methods and materials used to obtain phase-conjugate reflectors are discussed in detail by several authors. In particular the processes of degenerate four-wave mixing, stimulated Brillouin scattering and Brillouin-enhanced four-wave mixing are discussed in depth. The properties and theoretical modelling of photorefractive materials, the most important class of materials used to produce conjugate reflectors, are described at length.
Determination of Carbohydrates by Anion Exchange Chromatography with Pulsed Amperometric Detection (1983)

Abstract Carbohydrates such as sugar alcohols, monosaccharides, disaccharides, and other oligosaccharides are separated as anions by ion exchange chromatography with a sodium hydroxide eluent. Retention time and selectivity are controlled by varying eluent strength and column temperature. The carbohydrates are detected by oxidation at a gold electrode. A repeating sequence of three potentials electrochemically cleans the electrode surface of oxidation products and other interfering species. Detection limits are as low as 30 ppb for sugar alcohols and monosaccharides, and about 100 ppb for oligosaccharides. Other species containing CHOH groups can also be detected, such as alcohols and glycols.
The Impact of Overnight Wear on the Risk of Contact Lens—Associated Ulcerative Keratitis (1994)

Overnight wear of contact lenses is the overwhelming risk factor for ulcerative keratitis among contact lens users. We estimate that 49% to 74% of cases of contact lens-associated ulcerative keratitis could be prevented by eliminating overnight wear.