gebhart/patrepeval huggingface dataset:
BitWeaving (2013)

This paper focuses on running scans in a main memory data processing system at "bare metal" speed. Essentially, this means that the system must aim to process data at or near the speed of the processor (the fastest component in most system configurations). Scans are common in main memory data processing environments, and with the state-of-the-art techniques it still takes many cycles per input tuple to apply simple predicates on a single column of a table. In this paper, we propose a technique called BitWeaving that exploits the parallelism available at the bit level in modern processors. BitWeaving operates on multiple bits of data in a single cycle, processing bits from different columns in each cycle. Thus, bits from a batch of tuples are processed in each cycle, allowing BitWeaving to drop the cycles per column to below one in some case. BitWeaving comes in two flavors: BitWeaving/V which looks like a columnar organization but at the bit level, and BitWeaving/H which packs bits horizontally. In this paper we also develop the arithmetic framework that is needed to evaluate predicates using these BitWeaving organizations. Our experimental results show that both these methods produce significant performance benefits over the existing state-of-the-art methods, and in some cases produce over an order of magnitude in performance improvement.
Plasma analysis of di- and trihydroxycholestanoic acid diastereoisomers in peroxisomal α-methylacyl-CoA racemase deficiency (2001)

We identified a new peroxisomal disorder caused by a deficiency of the enzyme alpha-methylacyl-coenzyme A (CoA) racemase. Patients with this disorder show elevated plasma levels of pristanic acid and the bile acid intermediates di- and trihydroxycholestanoic acid (DHCA and THCA), which are all substrates for the peroxisomal beta-oxidation system. alpha-Methylacyl-CoA racemase plays an important role in the beta-oxidation of branched-chain fatty acids and fatty acid derivatives because it catalyzes the conversion of several (2R)-methyl-branched-chain fatty acyl-CoAs to their (2S)-isomers. Only stereoisomers with the 2-methyl group in the (S)-configuration can be degraded via beta-oxidation. In this study we used liquid chromatography/tandem mass spectrometry (LC-MS/MS) to analyze the bile acid intermediates that accumulate in plasma from patients with a deficiency of alpha-methylacyl-CoA racemase and, for comparison, in plasma from patients with Zellweger syndrome and patients with cholestatic liver disease.We found that racemase-deficient patients accumulate exclusively the (R)-isomer of free and taurine-conjugated DHCA and THCA, whereas in plasma of patients with Zellweger syndrome and patients with cholestatic liver disease both isomers were present. On the basis of these results we describe an easy and reliable method for the diagnosis of alpha-methylacyl-CoA racemase-deficient patients by plasma analysis. Our results also show that alpha-methylacyl-CoA racemase plays a unique role in bile acid formation. - Ferdinandusse, S., H. Overmars, S. Denis, H. R. Waterham, R. J. A. Wanders, and P. Vreken. Plasma analysis of di- and trihydroxycholestanoic acid diastereoisomers in peroxisomal alpha-methylacyl-CoA racemase deficiency. J. Lipid Res. 2001. 42: 137;-141.
Tracking pitches for broadcast television (2002)

During a baseball game, dramatic changes in lighting conditions and the movement of objects and players can result in a shifting pattern of light and color that makes it especially difficult to track a pitched ball. Further, several ballparks have a net in place behind home plate, which contributes further to the visual clutter that the image processing system must filter out when tracking the baseball. Meeting these challenges required developing a complex system that fuses high-end computer graphics with a sophisticated algorithm for calculating flight trajectories. The paper considers the ESPN K Zone system which uses computer-generated graphics to create a shaded, translucent box that outlines the strike zone boundaries for viewers. Behind the flashy graphics, K Zone-named after a synonym for the strike zone is a sophisticated computing system that monitors each pitch's trajectory.
The Hedgehog Pathway Promotes Blood-Brain Barrier Integrity and CNS Immune Quiescence (2011)

The blood-brain barrier (BBB) is composed of tightly bound endothelial cells (ECs) and perivascular astrocytes that regulate central nervous system (CNS) homeostasis. We showed that astrocytes secrete Sonic hedgehog and that BBB ECs express Hedgehog (Hh) receptors, which together promote BBB formation and integrity during embryonic development and adulthood. Using pharmacological inhibition and genetic inactivation of the Hh signaling pathway in ECs, we also demonstrated a critical role of the Hh pathway in promoting the immune quiescence of BBB ECs by decreasing the expression of proinflammatory mediators and the adhesion and migration of leukocytes, in vivo and in vitro. Overall, the Hh pathway provides a barrier-promoting effect and an endogenous anti-inflammatory balance to CNS-directed immune attacks, as occurs in multiple sclerosis.
Pathogenesis of human immunodeficiency virus infection (1993)

The lentivirus human immunodeficiency virus (HIV) causes AIDS by interacting with a large number of different cells in the body and escaping the host immune response against it. HIV is transmitted primarily through blood and genital fluids and to newborn infants from infected mothers. The steps occurring in infection involve an interaction of HIV not only with the CD4 molecule on cells but also with other cellular receptors recently identified. Virus-cell fusion and HIV entry subsequently take place. Following virus infection, a variety of intracellular mechanisms determine the relative expression of viral regulatory and accessory genes leading to productive or latent infection. With CD4+ lymphocytes, HIV replication can cause syncytium formation and cell death; with other cells, such as macrophages, persistent infection can occur, creating reservoirs for the virus in many cells and tissues. HIV strains are highly heterogeneous, and certain biologic and serologic properties determined by specific genetic sequences can be linked to pathogenic pathways and resistance to the immune response. The host reaction against HIV, through neutralizing antibodies and particularly through strong cellular immune responses, can keep the virus suppressed for many years. Long-term survival appears to involve infection with a relatively low-virulence strain that remains sensitive to the immune response, particularly to control by CD8+ cell antiviral activity. Several therapeutic approaches have been attempted, and others are under investigation. Vaccine development has provided some encouraging results, but the observations indicate the major challenge of preventing infection by HIV. Ongoing research is necessary to find a solution to this devastating worldwide epidemic.
3D reconstruction of coronary arteries from rotational X-ray angiography (2012)

This paper presents a 3D reconstruction method of coronary arteries from multiple projections, that works efficiently in two steps: first, a 2D processing is performed to obtain and classify the vessels branches on the projections, estimating also the radii. Then, a novel 3D reconstruction step is performed from pair of projections, finding the best intersections between ray bundles corresponding to the same branches to extract the 3D vessel trajectories, that is robust to motion. Topological constraints are included implicitly imposing vessel connectivity and tubular construction. The preliminary results presented here from a digital phantom and from real data, show good accuracy and performance of the method.
Mammalian Urea Transporters (2003)

Urea plays a key role in the urine-concentrating mechanism. Physiologic and molecular data demonstrate that urea transport in kidney and red blood cells occurs by specific urea transporter proteins. Two gene families for facilitated urea transporters, UT-A and UT-B, and several urea transporter cDNA isoforms have been cloned from human, rat, mouse, and several non-mammalian species. Polyclonal antibodies have been generated to many of the urea transporter proteins, and several novel findings have resulted from their use in integrative animal studies. For example, (a) vasopressin increases the phosphorylation of UT-A1 in rat inner medullary collecting duct; (b) UT-A1 protein abundance is increased in the rat inner medulla during conditions in which urine-concentrating ability is reduced; and (c) urea transporters are expressed in non-renal tissues, and UT-A protein abundance is up-regulated in uremia in both liver and heart. In addition to the facilitated urea transporters, functional evidence exists for active urea transport in the kidney collecting duct. This review summarizes the physiologic evidence for the existence of facilitated and active urea transporters, the molecular biology of the facilitated urea transporter gene families and cDNAs, and integrative studies into urea transporter protein regulation, both in the kidney and in other organs.
Noninvasive gene transfer to the lung for systemic delivery of therapeutic proteins (2002)

This study evaluates the use of vectors based on adeno-associated viruses (AAVs) to noninvasively deliver genes to airway epithelial cells as a means for achieving systemic administration of therapeutic proteins. We intranasally delivered AAV vectors to mice in which the same AAV2 genome encoding a cellular marker was packaged in capsids from AAV1, 2, or 5 (AAV2/1, AAV2/2, or AAV2/5, respectively). Gene expression levels achieved in both airways and alveoli were higher with AAV2/5 than with AAV2/1 and were undetectable with AAV2/2. The same set of vectors encoding a secreted therapeutic protein, erythropoietin (Epo), under the control of a lung-specific promoter (CC10) was intranasally delivered to mice, resulting in polycythemia with the highest levels of serum Epo obtained with AAV2/5 vectors. After a single intranasal administration of this vector, secretion of Epo was documented for 150 days. Similarly, intranasal administration of an AAV2/5–CC10–factor IX vector resulted in secretion of functional recombinant protein in the bloodstream of hemophiliac, factor IX-deficient mice. In addition, we demonstrate successful readministration of AAV2/5 to the lung 5 months after the first delivery of the same vector. In conclusion, we show that intranasal administration of AAV vectors results in efficient gene transfer to the lung only when the vector contains the AAV5 capsid and that this noninvasive route of administration results in sustained secretion of therapeutic proteins in the bloodstream.
LYSERGIC ACID DIETHYLAMIDE (LSD-25) (1952)

Lysergic acid diethylamide (LSD-25 Sandoz) given orally in single doses as low as 20 micrograms produces depersonalization, derealization, and increased imagery in "normal" individuals. Larger doses are required to produce the same effect in psychotic patients. Of 15 patients with depressive reactions, 3 recovered and 4 improved after one month's treatment with daily oral doses of 20-100 micrograms of LSD. Four patients showed no improvement. In 4 cases, treatment was discontinued before proper evaluation could be made. Anxiety was a prominent reaction while less frequently euphoria was observed. In 3 patients who developed euphoria it served as an aid to psychotherapy by encouraging expression of feeling. In the others the heightened anxiety encouraged reticence rather than confidence. Improvement obtained during the course of LSD therapy was not greater than that obtained without its use in comparable cases. However, LSD affords therapeutically valuable insights into unconscious processes by the medium of the hallucinations it produces.
Pathophysiology and clinical implications of pulmonary arterial enlargement in COPD (2013)

Chronic obstructive pulmonary disease (COPD) is a complex condition defined by progressive airflow limitation in response to noxious stimuli, inflammation, and vascular changes. COPD exacerbations are critical events in the natural history of the disease, accounting for the majority of disease burden, cost, and mortality. Pulmonary vascular disease is an important risk factor for disease progression and exacerbation risk. Relative pulmonary artery enlargement on computed tomography scan, defined by a pulmonary artery to aortic (PA:A) ratio >1, has been evaluated as a marker of pulmonary vascular disease. The PA:A ratio can be measured reliably independent of electrocardiographic gating or the use of contrast, and in healthy patients a PA:A ratio >0.9 is considered to be abnormal. The PA:A ratio has been compared with invasive hemodynamic parameters, primarily mean pulmonary artery pressure in various disease conditions and is more strongly correlated with mean pulmonary artery pressure in obstructive as compared with interstitial lung disease. In patients without known cardiac or pulmonary disease, the PA:A ratio is predictive of mortality, while in COPD, an elevated PA:A ratio is correlated with increased exacerbation risk, outperforming other well established predictors of these events. Future studies should be aimed at determining the stability of the metric over time and evaluating the utility of the PA:A ratio in guiding specific therapies.
Mass spectrometry in coupling with affinity capture–release and isotope‐coded affinity tags for quantitative protein analysis (2001)

Affinity capture-release electrospray ionization mass spectrometry (ACESIMS) and isotope-coded affinity tags (ICAT) are two recently introduced techniques for the quantitation of protein activity and content with applications to clinical enzymology and functional proteomics, respectively. One common feature of these methods is that they use biotinylated tags that function as molecular handles for highly selective and reversible affinity capture of conjugates from complex biological mixtures such as cell homogenates and sub-cellular organelles. ACESIMS uses synthetic substrate conjugates specifically to target cellular enzymes that, when deficient, are the cause of genetic diseases. Multiplex determination of enzyme activities is used for the diagnosis of lysosomal storage diseases. The ICAT method relies on selective conjugation of cysteine thiol groups in proteins, followed by enzymatic digestion and quantitative analysis of peptide conjugates by mass spectrometry. Another common feature of the ACESIMS and ICAT approaches is that both use conjugates labeled with stable heavy isotopes as internal standards for quantitation. Selected applications of the ACESIMS and ICAT techniques are presented that include molecular-level diagnosis of genetic diseases in children and quantitative determination of protein expression in cells.
Fatigue and Anaemia in Patients with Chronic Heart Failure (2006)

Our findings suggest that the subjective experience of fatigue in patients with CHF is associated with low haemoglobin concentration and reduced functional status after controlling for age and sex.
Differential Uptake of Functionalized Polystyrene Nanoparticles by Human Macrophages and a Monocytic Cell Line (2011)

Tumor cell lines are often used as models for the study of nanoparticle-cell interactions. Here we demonstrate that carboxy (PS-COOH) and amino functionalized (PS-NH2) polystyrene nanoparticles of ∼100 nm in diameter are internalized by human macrophages, by undifferentiated and by PMA-differentiated monocytic THP-1 cells via diverse mechanisms. The uptake mechanisms also differed for all cell types and particles when analyzed either in buffer or in medium containing human serum. Macrophages internalized ∼4 times more PS-COOH than THP-1 cells, when analyzed in serum-containing medium. By contrast, in either medium, THP-1 cells internalized PS-NH2 more rapidly than macrophages. Using pharmacological and antisense in vitro knockdown approaches, we showed that, in the presence of serum, the specific interaction between the CD64 receptor and the particles determines the macrophage uptake of particles by phagocytosis, whereas particle internalization in THP-1 cells occurred via dynamin II-dependent endocytosis. PMA-differentiated THP-1 cells differed in their uptake mechanism from macrophages and undifferentiated THP-1 cells by internalizing the particles via macropinocytosis. In line with our in vitro data, more intravenously applied PS-COOH particles accumulated in the liver, where macrophages of the reticuloendothelial system reside. By contrast, PS-NH2 particles were preferentially targeted to tumor xenografts grown on the chorioallantoic membrane of fertilized chicken eggs. Our data show that the amount of internalized nanoparticles, the uptake kinetics, and its mechanism may differ considerably between primary cells and a related tumor cell line, whether differentiated or not, and that particle uptake by these cells is critically dependent on particle opsonization by serum proteins.
Antagonism of Glyphosate Toxicity to Johnsongrass (<i>Sorghum halepense</i>) by 2,4-D and Dicamba (1989)

Greenhouse studies were conducted to determine the basis for reduced johnsongrass control when glyphosate was applied in mixtures with 2,4-D or dicamba. Glyphosate was applied to johnsongrass at 0.28, 0.56, 0.84, and 1.12 kg/ha alone and in combination with 2,4-D or dicamba at 0.14, 0.28, 0.14, or 0.56 kg/ha. Johnsongrass shoot and root fresh weights measured 4 weeks after treatment were higher when glyphosate was applied with 2,4-D (0.28 kg/ha glyphosate) or dicamba (0.28 kg/ha or 0.56 kg/ha glyphosate) compared to glyphosate applied alone at these rates. The antagonism of johnsongrass control was not observed with combinations of some of the higher glyphosate rates with 2,4-D (0.56 or 0.84 kg/ha glyphosate) or dicamba (0.84 or 1.12 kg/ha glyphosate). The reduction of glyphosate activity on johnsongrass occurred when any of four forms of 2,4-D or two forms of dicamba were added to the glyphosate spray mixture. Glyphosate uptake into johnsongrass leaves and subsequent translocation to the roots was reduced by the presence of 2,4-D or dicamba. The reduced glyphosate uptake and translocation could account for the decreased toxicity of glyphosate to johnsongrass when applied with 2,4-D or dicamba.
A Photocleavable and Mass Spectrometry Identifiable Cross-Linker for Protein Interaction Studies (2010)

In this paper, we present the results of proof-of-concept experiments using a novel photocleavable and mass spectrometry identifiable cross-linker pcPIR (photocleavable protein interaction reporter). pcPIR can be dissociated under UV irradiation either off- or online before the introduction to the mass spectrometers. Photo dissociation of cross-linkers is different from either the gas phase or the chemical cleavage of cross-linkers. Different types of cross-links can be identified using the pcPIR mass relationships, where the mass of cross-linked precursor equals the sum of the masses of the released products and reporter. Since pcPIR is cleaved prior to the entrance to the mass spectrometer, the released peptides are available to be sequenced with routine collision-induced dissociation (CID) MS/MS experiments and database search algorithms. In this report, the pcPIR strategy of identifying the cross-linked peptides with on- and off-line photocleavage coupled with novel targeted data dependent LC-MS/MS is demonstrated with the use of standard peptides, bovine serum albumin (BSA), and human hemoglobin tetramer protein complex.
JAK mutations in high-risk childhood acute lymphoblastic leukemia (2009)

Pediatric acute lymphoblastic leukemia (ALL) is a heterogeneous disease consisting of distinct clinical and biological subtypes that are characterized by specific chromosomal abnormalities or gene mutations. Mutation of genes encoding tyrosine kinases is uncommon in ALL, with the exception of Philadelphia chromosome-positive ALL, where the t(9,22)(q34;q11) translocation encodes the constitutively active BCR-ABL1 tyrosine kinase. We recently identified a poor prognostic subgroup of pediatric BCR-ABL1-negative ALL patients characterized by deletion of IKZF1 (encoding the lymphoid transcription factor IKAROS) and a gene expression signature similar to BCR-ABL1-positive ALL, raising the possibility of activated tyrosine kinase signaling within this leukemia subtype. Here, we report activating mutations in the Janus kinases JAK1 (n = 3), JAK2 (n = 16), and JAK3 (n = 1) in 20 (10.7%) of 187 BCR-ABL1-negative, high-risk pediatric ALL cases. The JAK1 and JAK2 mutations involved highly conserved residues in the kinase and pseudokinase domains and resulted in constitutive JAK-STAT activation and growth factor independence of Ba/F3-EpoR cells. The presence of JAK mutations was significantly associated with alteration of IKZF1 (70% of all JAK-mutated cases and 87.5% of cases with JAK2 mutations; P = 0.001) and deletion of CDKN2A/B (70% of all JAK-mutated cases and 68.9% of JAK2-mutated cases). The JAK-mutated cases had a gene expression signature similar to BCR-ABL1 pediatric ALL, and they had a poor outcome. These results suggest that inhibition of JAK signaling is a logical target for therapeutic intervention in JAK mutated ALL.
An antitoxidant formulation that induces differentiation of neuroblastoma in culture (2003)

Abstract Neuroblastoma, the most common of all cancers found in children, may arise from a block of differentiation and a resultant continuation of the proliferative state. Neuroblastoma often spontaneously revert by undergoing partial differentiation and ultimate degeneration. A useful therapeutic approach for clinical neuroblastoma may encompass strategies to force neuroblastoma to differentiate. In ongoing studies on neuronal health, we have developed an anti‐oxidant synergy formulation (“ASF”), comprised of α‐tocopherol (vitamin E), sodium pyruvate and phosphatidyl choline, which lessens neurotoxicity and promotes axonal elaboration in cultured neurons. We demonstrate herein that ASF prevents proliferation and promotes differentiation of neuroblastoma in culture, even in the presence of serum, which normally induces rapid neuroblastoma proliferation in culture. These data leave open the possibility that ASF, with proper administration, may foster differentiation, and therefore ultimate degeneration, of neuroblastoma in situ , and may therefore represent a novel approach towards suppression of clinical neuroblastoma.
A highly photoconductive polyimide film. (1990)

We developed a new type of polymer having a high photoconductivity in the visible light region. The polymer is composed of a series of thiophenylene moieties, -C6H4S-, and an imide group. The polymer with this type of chemical structure is called polyimide [PI].The casted films of polyamic acid precursors were imidized to PI films and crystallized by annealing at suitable temperatures near the melting points. The thickness of crystallites in the PI film is estimated to be about 100ÅÅ, which corresponds to the 20 polymer chains stacked perpendicular to the axis. In the crystallizing process, both the absorption and the photoconductivity of this film in the visible light region increase extremely. From the UV-visible absorption spectra, we evaluated the optical energy gap, Eg. In the most sensitive polymer, BPDA-Ph3, Eg changed from about 2.5eV in the amorphous phase to about 1.85eV in the crystalline phase. Aromatic rings of thiophenylene moieties and imide rings of the PI films are so stacked that the π-orbitals of both rings are more overlapped, which increases absorption in the visible region. Our highly crystallized PI films with extensively overlapped π-orbitals between the adjacent chains show high photoconductivities. In the crystallizing process the photoconductive property, ημτ, increases in magnitude three orders or more. The most sensitive polymers, BPDA-Ph3 and -Ph5, have ημτ values more than 10-8cm2/v in the visible region 350-550nm.