gebhart/patrepeval huggingface dataset:
Multi-view Synchronization of Human Actions and Dynamic Scenes (2009)

This paper deals with the temporal synchronization of image sequences. Two instances of this problem are considered: (a) synchronization of human actions and (b) synchronization of dynamic scenes with view changes. To address both tasks and to reliably handle large view variations, we use self-similarity matrices which remain stable across views. We propose time-adaptive descriptors that capture the structure of these matrices while being invariant to the impact of time warps between views. Synchronizing two sequences is then performed by aligning their temporal descriptors using the Dynamic Time Warping algorithm. We present quantitative comparison results between time-fixed and time-adaptive descriptors for image sequences with different frame rates. We also illustrate the performance of the approach on several challenging videos with large view variations, drastic independent camera motions and within-class variability of human actions.
Three Pregnancy Proteins (PP12, PP14, AND PAPP-A): Their Biological and Clinical Relevance (1989)

The three pregnancy proteins, PP12, PP14, and PAPP-A, reviewed here are all produced by the endometrium under the influence of progesterone. Their production is low during the secretory phase and increases dramatically after decidualization and pregnancy. PP12 and PP14 are synthesized by the epithelial cells and PAPP-A is synthesized by the stromal cells. Reflecting perhaps the relative abundance of stromal cells, PAPP-A concentrations increase progressively to term, whereas the levels of PP12 and PP14 level off and even decline after the 20th week of gestation. These proteins are also found in nonpregnant subjects in extrauterine sites: follicles, follicular fluid, luteal cells, and fallopian tubes, and in males, in seminal vesicles and seminal fluid. PP12 has been found in several forms of cancer, although not with sufficient frequency to make it a useful tumor marker. The biologic function of these proteins is still subject to speculation, but they do reflect the biosynthetic capacity of decidualized endometrium, and especially PP14 may find clinical application in the management of infertility patients.
KcsA Crystal Structure as Framework for a Molecular Model of the Na+ Channel Pore (2000)

The crystal structure of the pore-forming part of the KcsA bacterial K(+)-selective channel suggests a possible motif for related voltage-gated channels. We examined the hypothesis that the spacial orientation of the KcsA M1 and M2 alpha-helices also predicts the backbone location of S5 and S6 helices of the voltage-gated Na(+) channel. That channel's P region structure is expected to be different because selectivity is determined by side-chain interactions rather than by main-chain carbonyls, and its outer vestibule accommodates relatively large toxin molecules, tetrodotoxin (TTX) and saxitoxin (STX), which interact with selectivity ring residues. The Na(+) channel P loop was well-modeled by the alpha-helix-turn-beta-strand motif, which preserves the relationships for toxin interaction with the Na(+) channel found experimentally. This outer vestibule was docked into the extracellular part of the inverted teepee structure formed by the S5 and S6 helices that were spacially located by coordinates of the KcsA M1 and M2 helix main chains [Doyle et al. (1998) Science 280, 69-74], but populated with side chains of the respective S5 and S6 structures. van der Waals contacts were optimized with minimal adjustment of the S5, S6, and P loop structures, forming a densely packed pore structure. Nonregular external S5-P and P-S6 segments were not modeled here, except the P-S6 segment of domain II. The resulting selectivity region structure is consistent with Na(+) channel permeation properties, offering suggestions for the molecular processes involved in selectivity. The ability to construct a Na(+) channel pore model consistent with most of the available biophysical and mutational information suggests that the KcsA structural framework may be conserved in voltage-gated channels.
Where Are We Now? Real-Time Estimates of the Macroeconomy (2005)

This paper describes a method for calculating daily realtime estimates of the current state of the U.S. economy. The estimates are computed from data on scheduled U.S. macroeconomic announcements using an econometric model that allows for variable reporting lags, temporal aggregation, and other complications in the data. The model can be applied to find real-time estimates of GDP, inflation, unemployment, or any other macroeconomic variable of interest. In this paper, I focus on the problem of estimating the current level of and growth rate in GDP. I construct daily real-time estimates of GDP that incorporate public information known on the day in question. The real-time estimates produced by the model are uniquely suited to studying how perceived developments in the macroeconomy are linked to asset prices over a wide range of frequencies. The estimates also provide, for the first time, daily time series that can be used in practical policy decisions. JEL Codes: E37, C32. Information about the current state of real economic activity is widely dispersed across consumers, firms, and policymakers. While individual consumers and firms know the recent history of their own decisions, they are unaware of the contemporaneous consumption,
Microbial producers of plant growth stimulators and their practical use: A review (2006)

The ability of pro- and eukaryotic microorganisms to synthesize growth-stimulating phytohormones is reviewed, with emphasis on pathways of biosynthesis of these compounds and their effects on physiological and biochemical properties of the producers. Phytohormones are viewed as specific mediators in interactions between various organisms inhabiting the same ecological niche, the biological role of which is not limited to processes taking place in plants. In addition to setting forth theoretical aspects of this problem, the review underscores the need to utilize such producer microorganisms in plant cultivation and biotechnology.
Structural and phylogenetic analysis of the MHC class I-like Fc receptor gene. (1995)

The intestinal epithelium of neonatal mice and rats expresses an Fc receptor that mediates selective uptake of IgG in mothers' milk. This receptor (FcRn), which helps newborn animals to acquire passive immunity, is an MHC class I-like heterodimer made up of a heavy chain and beta 2-microglobulin. In the present study, we determined the genomic structure of a mouse gene (Fcrn) encoding the heavy chain of FcRn. The overall exon-intron organization of the Fcrn gene was similar to that of the MHC class I gene, thus providing structural evidence that Fcrn is a bona fide class I gene. The 5'-flanking region of the Fcrn gene contained the binding motifs for two cytokine-inducible transcription factors, NF-IL6 and NF1. However, regulatory elements found in MHC class I genes (enhancer A, enhancer B, and the IFN response element) were absent. Phylogenetic tree analysis suggested that, like the MICA, AZGP1, and CD1 genes, the Fcrn gene diverged from MHC class I genes after the emergence of amphibians but before the split of placental and marsupial mammals. Consistent with this result, Southern blot analysis with a mouse Fcrn cDNA probe detected cross-hybridizing bands in various mammalian species and chickens. Sequence analysis of the Fcrn gene isolated from eight mouse strains showed that the membrane-distal domain of FcRn has at least three amino acid variants. The fact that Fcrn is a single copy gene indicates that it is expressed in both the neonatal intestine and the fetal yolk sac.
The role of cytokines as biomarkers in systemic lupus erythematosus and lupus nephritis (2011)

Cytokines play an important role in the pathogenesis of systemic lupus erythematosus (SLE) and lupus nephritis. This is currently a very active area of research. Of particular interest is the use of cytokines as biomarkers of disease activity in SLE and lupus nephritis. Can cytokine measurements assist in early detection of renal flare in known lupus nephritis? Can such measurements be used to distinguish between flare and chronic damage? Or help to confirm renal remission? Could they be used to help assess the required duration of immunosuppression and reduce the need for invasive renal biopsy? This review discusses limitations of current laboratory methods in monitoring SLE, how measurements of cytokines may contribute in relation to following disease activity and summarizes what is known about cytokines as biomarkers in SLE and lupus nephritis.
The sen1+ Gene of Schizosaccharomyces pombe, a Homologue of Budding Yeast SEN1, Encodes an RNA and DNA Helicase (1999)

Two polynucleotide-dependent ATPases, 95 and 181 kDa in size, have been purified to near homogeneity from cell-free extracts of Schizosaccharomyces pombe. Despite their size differences, their biochemical properties were strikingly similar. Both enzymes were capable of unwinding RNA and DNA duplexes in keeping with their ability to hydrolyze ATP in the presence of either ribo- or deoxyribopolynucleotide. In addition, they were capable of unwinding DNA/RNA or RNA/DNA hybrid duplexes and translocated in the 5' to 3' direction. These results strongly indicate that they are closely related to each other. Determination of the partial amino acid sequence of the 95-kDa enzyme revealed that it is encoded by the sen1(+)() gene, an S. pombe homologue of yeast SEN1, a protein essential for the processing of small nucleolar RNA, transfer RNA, and ribosomal RNA. The molecular weight of the S. pombe Sen1 protein (SpSen1p) predicted from the sen1(+)() open reading frame was 192.5 kDa, suggesting that the 181-kDa enzyme is likely to be a full-length protein, whereas the 95-kDa polypeptide has arisen by proteolysis. In accord with this possibility, polyclonal antibodies specific to the C-terminal region of sen1(+)() cross-reacted with both 95- and 181-kDa polypeptides. We discuss the biochemical activities associated with SpSen1p and their relevance to the apparently divergent functions ascribed to the yeast Sen1 protein in RNA metabolism.
Spherical microphone arrays (2015)

AccessScience is an authoritative and dynamic online resource that contains incisively written, high-quality educational material covering all major scientific disciplines. An acclaimed gateway to scientific knowledge, AccessScience is continually expanding the ways it can demonstrate and explain core, trustworthy scientific information that inspires and guides users to deeper knowledge.
Client-server performance on flow-controlled ATM networks: a Web database of simulation results (2002)

Extensive simulation has demonstrated the effectiveness of credit-based ATM flow control in supporting client-server applications. In particular, request/response protocols used in these applications allow efficient sharing of switch buffer, for the case when all the VCs sharing the same buffer are subject to the same degree of downstream congestion. The required buffer size can be as small as the minimum of bandwidth/sup */RTT for the link and Clients/sup */Reply-Size. Request/response protocols generally tolerate congestion better than greedy loads. Being able to avoid synchronization, FIFO scheduling is sometimes more efficient than VC round-robin scheduling. These findings are derived from an online Web database of simulation results covering more than 10,000 network and load configurations. The Web database approach has proven to be effective in managing and navigating a large set of simulation results.
Immune reactivity towards insulin, its amyloid and protein S100B in blood sera of Parkinson's disease patients (2007)

Peripheral immune responses can be sensitive indicators of disease pathology. We evaluated the autoimmune reactions to endocrine (insulin) and astrocytical (S100B) biomarkers in the blood sera of 26 Parkinson's disease (PD) patients compared with controls by using ELISA. We found a statistically significant increase of the autoimmune responses to both antigens in PD patients compared with controls with a mean increase of 70% and 50% in the autoimmune reactions towards insulin and S100B, respectively. Heterogeneity of the immune responses observed in patients may reflect the modulating effect of multiple variables associated with neurodegeneration and also changes in the basic mechanisms of individual autoimmune reactivity. We did not detect any pronounced immune reactions towards insulin amyloid fibrils and oligomers in PD patients, indicating that an amyloid-specific conformational epitope is not involved in immune recognition of this amyloid type, while sequential epitope of native insulin is hidden within the amyloid structures. Immune reactions towards S100B and insulin may reflect the neurodegenerative brain damaging processes and impaired insulin homeostasis occurring in PD.
A Mouse IgG 1 Monoclonal Antibody Specific for N -Glycolyl GM3 Ganglioside Recognized Breast and Melanoma Tumors (2000)

14F7 murine monoclonal antibody (MAb) is an IgG1 immunoglobulin that is generated by immunizing Balb/c mice with GM3(NeuGc) ganglioside hydrophobically conjugated with human very-low-density lipoproteins and in the presence of Freund's adjuvants. 14F7 MAb binds specifically to GM3(NeuGc), whereas neither N-glycolyl or N-acetyl gangliosides, nor a sulfated glycolipid, are recognized as assessed by enzyme-linked immunosorbent assay or immunostaining on thin layer chromatograms. Immunohistochemical studies in fresh tumor tissues showed that 14F7 MAb strongly recognized in antigen expressed in human breast and melanoma tumors.
Neuro-psychopharmacogenetics and Neurological Antecedents of Posttraumatic Stress Disorder: Unlocking the Mysteries of Resilience and Vulnerability (2010)

We propose that successful treatment of PTSD will involve preliminary genetic testing for specific polymorphisms. Early detection is especially important, because early treatment can improve outcome. When genetic testing reveals deficiencies, vulnerable individuals can be recommended for treatment with "body friendly" pharmacologic substances and/or nutrients. Results of our research suggest the following genes should be tested: serotoninergic, dopaminergic (DRD2, DAT, DBH), glucocorticoid, GABAergic (GABRB), apolipoprotein systems (APOE2), brain-derived neurotrophic factor, Monamine B, CNR1, Myo6, CRF-1 and CRF-2 receptors, and neuropeptide Y (NPY). Treatment in part should be developed that would up-regulate the expression of these genes to bring about a feeling of well being as well as a reduction in the frequency and intensity of the symptoms of PTSD.
Surgical Treatment of Renal Cancer with Vena Cava Extension (1987)

Fifty-four patients with renal cancer and vena cava tumour thrombus underwent radical nephrectomy and removal of the thrombus; the operative mortality rate was 9.3% (5 patients). The extent of the vena cava thrombus did not affect survival. Of 36 patients with no known pre-operative metastases and complete (29 patients) and incomplete (7 patients) removal of the vena cava tumour thrombus, the 5-year survival rate was 68 and 17%, respectively (P = 0.01). Thirteen patients (45%) who underwent complete removal of the vena cava tumour thrombus are alive and free of disease, with a mean follow-up of 51.2 months (range 4-144); three died without disease 110, 31 and 23 months after operation. The 2-year and 5-year survival rates of 18 patients with known pre-operative metastases was 37.5 and 12.5% respectively; 14 died between 1 and 27 months post-operatively (mean 11.6) of metastatic disease. Two of these 18 patients experienced long-term remission: one died of unrelated causes 151 months after operation; the other was lost to follow-up 219 months after operation, with no evidence of disease. Of 14 patients with positive regional nodes, the mean survival in those with metastases compared with those without metastases was 7.5 versus 15 months, respectively; only one patient survived at 14 months. Operative intervention in patients without metastatic disease (systemic or regional) and complete removal of the vena cava thrombus achieved a 5-year survival rate of 68%. Variables which significantly decreased survival and may be considered contraindications for operation were systemic metastasis, regional lymph node involvement and incomplete removal of the vena cava thrombus.
Reaction mechanism and structure of the active site of proline racemase (1975)

Proline racemase catalyzes the interconversion of D- and L-proline. Previous studies in this laboratory have established that the reaction proceeds by means of a two-base mechanism in which one base on the enzyme removes the substrate alpha-hydrogen as a proton and the conjugate acid of another base donates a proton to the opposite side of the alpha-carbon (Cardinale, G.J., and Abeles, R.H., (1968), Biochemistry 7, 3970. An assumption of the proposed mechanism was that no proton exchange occurs from the enzyme-substrate complex. In the present study, we have shown that the rate of 3H release from DL-[alpha-3H]proline, in the presence of proline racemase, decreases with increasing proline concentrations. These results establish that release of the substrate derived proton from the enzyme occurs largely, possibly exclusively, after release of the product. Under initial velocity conditions, the rate of 3H release from L-[alpha-3H]proline is not reduced with increasing L-proline concentrations. Thus, the enzyme-bound proton derived from one isomer can only be "captured" by the other isomer. We conclude that there are two forms of the enzyme; one binds L-proline and the other D-proline. Release of the substrate derived proton from enzyme is more rapid than the interconversion of these two forms. These results are consistent with the previously proposed mechanism. Proline racemase is composed of similar subunits of mol wt 38,000 as determined by gel electrophoresis in the presence of sodium dodecyl sulfate. Equilibrium dialysis experiments detect only one substrate binding site for every two subunits. When the oxidized form of the enzyme, which is inactive and cannot bind substrate, is reduced by thiol to yield active enzyme, two cysteine sulfhydryl groups per dimer become available to react with iodoacetate. Inactivation of the enzyme occurs upon modification of one of these cysteines. All iodoacetate incorporation occurs at the same point in the primary sequence of the enzyme, and can be prevented by the presence of proline or pyrrole-2-carboxylate, a substrate analog. A model is proposed in which a single active site is formed by elements of two identical subunits. Although the data are consistent with this model, another interpretation, in which half of the subunits are nonfunctional, cannot be ruled out.
The structure of granulocyte-colony-stimulating factor and its relationship to other growth factors. (1993)

We have determined the three-dimensional structure of recombinant human granulocyte-colony-stimulating factor by x-ray crystallography. Phases were initially obtained at 3.0-A resolution by multiple isomorphous replacement and were refined by solvent flattening and by averaging of the electron density of the three molecules in the asymmetric unit. The current R factor is 21.5% for all data between 6.0- and 2.2-A resolution. The structure is predominantly helical, with 104 of the 175 residues forming a four-alpha-helix bundle. The only other secondary structure is also helical. In the loop between the first two long helices a four-residue 3(10)-helix is immediately followed by a 6-residue alpha-helix. Three residues in the short connection between the second and third bundle helices form almost one turn of left-handed helix. The up-up-down-down connectivity with two long crossover connections has been reported previously for five other proteins, which like granulocyte-colony-stimulating factor are all signaling ligands: growth hormone, granulocyte/macrophage-colony-stimulating factor, interferon beta, interleukin 2, and interleukin 4. Structural similarity among these growth factors occurs despite the absence of similarity in their amino acid sequences. Conservation of this tertiary structure suggests that these different growth factors might all bind to their respective sequence-related receptors in an equivalent manner.
Prasugrel in Clinical Practice (2009)

On July 10, 2009, after an 18-month review, the Food and Drug Administration (FDA) approved the thienopyridine prasugrel for use in patients with unstable angina or myocardial infarction who undergo percutaneous coronary intervention (PCI). The new drug is the latest addition to a class of agents that inhibit the platelet adenosine diphosphate (ADP) receptor, preventing initial platelet activation and consequent platelet aggregation — a mechanism that has represented a major advance in the treatment of atherothrombotic diseases.1 Indeed, the use of the thienopyridine ticlopidine in combination with aspirin to inhibit platelet aggregation facilitated the widespread use of coronary-artery stenting. Because . . .
Cauliflower Mosaic Viral Promoter - A Recipe for Disaster? (1999)

AbstractConcerns have been raised over the spread of transgenic DNA by horizontal gene transfer. One main factor determining the success of horizontal gene transfer is its tendency to recombine. This paper examines the safety implication of recent revelations on the recombination hotspot of the cauliflower mosaic viral (CaMV) promoter, which is in practically all current transgenic crops released commercially or undergoing field trials. As a precautionary measure, we strongly recommend that all transgenic crops containing CaMV 35S or similar promoters which are recombinogenic should be immediately withdrawn from commercial production or open field trials. All products derived from such crops containing transgenic DNA should also be immediately withdrawn from sale and from use for human consumption or animal feed.
Platelets Take Up the Monoclonal Antibody Bevacizumab (2007)

These studies show that bevacizumab is taken up by platelets and may explain its clinical effect on wound healing and tumor growth.
Bivalve filter feeding revisited (1996)

Recent developments concerning the nature of bivalve filter feeding are reviewed and interpretations of data are examined. No convincing evidence was found for: (1) a function of mucus in the normal feeding mechanism;
Human Papillomavirus Type 16/18 Up-Regulates the Expression of Interleukin-6 and Antiapoptotic Mcl-1 in Non–Small Cell Lung Cancer (2008)

The up-regulating effects of HPV 16/18 E6 and E7 to IL-6 and Mcl-1 expressions were observed in E6- and E7-transfected A549 cells and in HPV16-infected TL-1 cells, mainly through the phosphatidylinositol-3-OH kinase pathway. The involvement of HPV infection in lung tumorigenesis may be partly through a concomitant increased expression of autocrine and/or paracrine IL-6 and the downstream Mcl-1.
Nonlinear Blind Source Separation by Self-Organizing Maps (1996)

In neural blind source separation most approaches have considered the linear source separation problem where the input data consist of unknown linear mixtures of unknown independent source signals. The solution is a linear transformation which makes the output vector components statistically independent. More generally we can consider nonlinear mixtures of sources. Then we can try to separate the sources by constructing mappings that make the components of the output vectors independent. We show that such a mapping can be approximately realized using self-organizing maps with rectangular map topology. We apply these mappings to the separation of nonlinear mixtures of sub-Gaussian sources.