gebhart/patrepeval huggingface dataset:
Heuristic search approach to shape matching in image sequences (1991)

The problem of detecting correspondences between object contours belonging to successive image frames of a dynamic scene is addressed. The object contours are represented using concave, convex and straight line segments which are extracted after smoothing the contour with a Gaussian kernel. The matching problem is tackled using heuristic search with a state space formulation. An admissible heuristic function is designed for guiding the search. Experimental results are presented to demonstrate the capabilities of the method.
Clicking polymers: a straightforward approach to novel macromolecular architectures (2007)

Living/controlled polymerization techniques have enabled the synthesis of a large variety of different well-defined (co)polymer structures. In addition, the use of click chemistry in polymer science is a quickly emerging field of research since it allows the fast and simple creation of well-defined and complex polymeric structures in yields that were previously unattainable. In this critical review, the application of the azide-alkyne 1,3-dipolar cycloaddition for the construction of well-defined polymer architectures will be discussed in detail, providing a comprehensive overview for all disciplines related to polymeric materials.
Random sampling with a reservoir (1985)

We introduce fast algorithms for selecting a random sample of n records without replacement from a pool of N records, where the value of N is unknown beforehand. The main result of the paper is the design and analysis of Algorithm Z; it does the sampling in one pass using constant space and in O ( n (1 + log( N/n ))) expected time, which is optimum, up to a constant factor. Several optimizations are studied that collectively improve the speed of the naive version of the algorithm by an order of magnitude. We give an efficient Pascal-like implementation that incorporates these modifications and that is suitable for general use. Theoretical and empirical results indicate that Algorithm Z outperforms current methods by a significant margin.
Cerebral Intravascular Oxygenation Correlates With Mean Arterial Pressure in Critically Ill Premature Infants (2000)

We conclude that NIRS can be used in a noninvasive manner at the bedside to identify premature infants with impaired cerebrovascular autoregulation, that this impairment is relatively common in such infants, and that the presence of this impairment is associated with a high likelihood of occurrence of severe GMH-IVH/PVL.
Breeding Alfalfa Which Regenerates from Callus Tissue in Culture1 (1975)

Tetraplold alfalfa ( Medicago sativa L.) germplasm, in which two‐thirds of the plants are capable of regeneration from callus tissue in culture, has been developed by recurrent selection. It descends from one ‘DuPuits’ and four ‘Saranac’ clones which regenerated in the cycle 0 population. Frequency of regeneration was 12% in cycle 0, about 50% in cycle 1, and 67% in cycle 2. Seed produced by hand‐intercrossing 75 plants regenerated from cycle 2 has been termed ‘Regen‐S’ (Regen for regeneration; S for Saranac). It is purple‐flowered and phenotypically similar to Saranac. One‐gram lots of Regen‐S seed are presently available for distribution, and larger amounts are expected to be available in late 1975. A yellow‐flowered regenerator ‘Regen‐Y,’ is now being bred from selections out of ‘Rhizoma,’ ‘Rambler,’ and ‘Drylander.’ Small amounts of Regen‐Y seed are also presently available, thus providing a contrasting qualitative genetic marker stock.
Continuous positive airways pressure for obstructive sleep apnoea in adults (2006)

Obstructive sleep apnoea is the periodic reduction (hypopnoea) or cessation (apnoea) of breathing due to narrowing or occlusion of the upper airway during sleep. The main symptom is daytime sleepiness and it has been suggested it is linked to premature death, hypertension, ischaemic heart disease, stroke and road traffic accidents.The main treatment for sleep apnoea is with the use of continuous positive airways pressure (CPAP), which requires a flow generator and mask. These are used at night to prevent apnoea, hypoxia and sleep disturbance. The objective was to assess the effects of CPAP in the treatment of obstructive sleep apnoea in adults.We searched the Cochrane Airways Group Trials Register and reference lists of articles. We consulted experts in the field. Searches were current to July 2005.We included randomised trials comparing nocturnal CPAP with an inactive control or oral appliances in adults with obstructive sleep apnoea (an apnoea and hypopnoea index greater than five per hour). Trials had a minimum intervention period of two weeks.Trial quality was assessed and two review authors extracted data independently. Study authors were contacted for missing information. Parallel and crossover group trials were analysed separately.Thirty-six trials involving 1718 people met the inclusion criteria. Study quality was mixed. Compared with control, CPAP showed significant improvements in certain objective and subjective sleepiness, measures of quality of life and cognitive function (parallel-group studies: Epworth sleepiness scale (ESS) -3.83 units, 95% CI -4.57 to -3.09; crossover studies: ESS -1.84 units, 95% CI -2.57 to -1.11). Twenty-four hour systolic and diastolic blood pressures were lower with CPAP compared with control (parallel-group trials). Compared with oral appliances, CPAP significantly reduced the apnoea and hypopnoea index (crossover studies: -7.97 events/hr, 95% CI -9.56 to -6.38) and improved sleep efficiency (crossover studies: 2.31%, 95% CI 0.02 to 4.6) and minimum oxygen saturation (4.14%, 95% CI 3.25 to 5.03). Responders to both treatments expressed a strong preference for the oral appliance. However, participants were more likely to withdraw on OA than on CPAP therapy.CPAP is effective in reducing symptoms of sleepiness and improving quality of life measures in people with moderate and severe obstructive sleep apnoea (OSA). It is more effective than oral appliances in reducing respiratory disturbances in these people but subjective outcomes are more equivocal. Certain people tend to prefer oral appliances to CPAP where both are effective. This could be because they offer a more convenient way of controlling OSA. Short-term data indicate that CPAP leads to lower blood pressure than control. Long-term data are required for all outcomes in order to determine whether the initial benefits seen in short-term clinical trials persist.
Mechanistic Investigations of Unsaturated Glucuronyl Hydrolase from Clostridium perfringens (2014)

Experiments were carried out to probe the details of the hydration-initiated hydrolysis catalyzed by the Clostridium perfringens unsaturated glucuronyl hydrolase of glycoside hydrolase family 88 in the CAZy classification system. Direct (1)H NMR monitoring of the enzymatic reaction detected no accumulated reaction intermediates in solution, suggesting that rearrangement of the initial hydration product occurs on-enzyme. An attempt at mechanism-based trapping of on-enzyme intermediates using a 1,1-difluoro-substrate was unsuccessful because the probe was too deactivated to be turned over by the enzyme. Kinetic isotope effects arising from deuterium-for-hydrogen substitution at carbons 1 and 4 provide evidence for separate first-irreversible and overall rate-determining steps in the hydration reaction, with two potential mechanisms proposed to explain these results. Based on the positioning of catalytic residues in the enzyme active site, the lack of efficient turnover of a 2-deoxy-2-fluoro-substrate, and several unsuccessful attempts at confirmation of a simpler mechanism involving a covalent glycosyl-enzyme intermediate, the most plausible mechanism is one involving an intermediate bearing an epoxide on carbons 1 and 2.
A Partial E3 Deletion in Replication-Defective Adenoviral Vectors Allows for Stable Expression of Potentially Toxic Transgene Products (2016)

Adenovirus (Ad) is used extensively for construction of viral vectors, most commonly with deletion in its E1 and/or E3 genomic regions. Previously, our attempts to insert envelope proteins (Env) of HIV-1 into such vectors based on chimpanzee-derived Ad (AdC) viruses were thwarted. Here, we describe that genetic instability of an E1- and E3-deleted AdC vector of serotype C6 expressing Env of HIV-1 can be overcome by reinsertion of E3 sequences with anti-apoptotic activities. This partial E3 deletion presumably delays premature death of HEK-293 packaging cell lines due to Env-induced cell apoptosis. The same partial E3 deletion also allows for the generation of stable glycoprotein 140 (gp140)- and gp160-expressing Ad vectors based on AdC7, a distinct AdC serotype. Env-expressing AdC vectors containing the partial E3 deletion are genetically stable upon serial cell culture passaging, produce yields comparable to those of other AdC vectors, and induce transgene product-specific antibody responses in mice. A partial E3 deletion thereby allows expansion of the repertoire of transgenes that can be expressed by Ad vectors.
Stereocomplementary Bioreduction of α,β-Unsaturated Dicarboxylic Acids and Dimethyl Esters using Enoate Reductases:  Enzyme- and Substrate-Based Stereocontrol (2007)

Asymmetric bioreduction of alpha,beta-unsaturated dicarboxylic acids, such as 2-methylmaleic/fumaric and 2-methylenesuccinic acid, as well as the corresponding dimethyl esters, using three cloned enoate reductases furnished 2-methylsuccinic acid or dimethyl 2-methylsuccinate, respectively. Opposite stereoisomeric products were obtained in up to >99% ee either by choice of the enzyme or by using E/Z-configurated substrates. Cofactor-recycling systems (NADH/FDH/formate, NADH/GDH/glucose or NADPH/G6PDH/glucose-6-phosphate) only worked in presence of a divalent metal ion, such as Ca2+, Mg2+, or Zn2+.
A pattern-recognition-based, fault-tolerant monitoring and diagnostic technique (1995)

A properly designed monitoring and diagnostic system must be capable of detecting and distinguishing sensor and process malfunctions in the presence of signal noise, varying process states and multiple faults. The technique presented in this paper addresses these objectives through the implementation of a multivariate state estimation algorithm based upon pattern recognition methodology coupled with a statistically-based hypothesis test. Utilizing a residual signal vector generated from the difference between the estimated and measured current states of a process, disturbances are detected and identified with statistical hypothesis testing. Since the hypothesis testing utilizes the inherent noise on the signals to obtain a conclusion and the state estimation algorithm requires only a majority of the sensors to be functioning to ascertain the current state, this technique has proven to be quite robust and fault-tolerant. Several examples of its application are presented.
Epitope mapping of ADAMTS13 autoantibodies in acquired thrombotic thrombocytopenic purpura (2004)

Severe deficiency of the von Willebrand factor (VWF)-cleaving protease ADAMTS13 can lead to thrombotic thrombocytopenic purpura (TTP), a disease associated with the widespread formation of platelet-rich thrombi in many organs. Autoantibodies that inactivate ADAMTS13 are the most frequent cause of acquired TTP. Little is known about epitope specificity and reactivity of anti-ADAMTS13 antibodies. In this study, a series of ADAMTS13 domains were expressed in Escherichia coli, and the reactivity of purified recombinant fragments with anti-ADAMTS13 auto-antibodies from 25 patients with severe ADAMTS13 deficiency was evaluated in vitro. All TTP plasmas contained antibodies directed against the cysteine-rich spacer (cys-rich/spacer) domain of ADAMTS13. In the plasma of 3 patients, antibodies were detected that reacted exclusively with the cys-rich/spacer domain, underscoring the importance of this region for functional activity of ADAMTS13. In 64% of the plasmas, antibodies reacted with the 2 CUB domains, and in 56% they reacted with the isolated first thrombospondin type 1 (TSP-1) repeat and with the compound fragment consisting of the catalytic, the disintegrin-like, and the TSP1-1 domain. Less frequently, in 28% of the plasmas, antibodies reacted with the TSP1 repeats 2 to 8. Unexpectedly, antibodies reacted with the propeptide region in 20% of the plasmas. In conclusion, this study shows that even though anti-ADAMTS13 autoantibodies react with multiple domains of the protease, the cys-rich/spacer domain is consistently involved in antibody reactivity.
Stereochemical requirements for cannabinoid activity (1980)

Several pairs of cannabinoid isomers were synthesized and tested for psychotropic activity in rhesus monkeys. Two regularities were observed: (a) In the absence of the other substituents, the equatorial stereochemistry of the substituent at C-1 determines activity. (b) Two groups of THC-type cannabinoids which differ only in that the chemical groupings in one of them at C-1, C-2 are situated at C-1, C-6 in the other (but retain their stereochemistry) have almost equivalent psychotropic activity.
Skeletal Overexpression of Gremlin Impairs Bone Formation and Causes Osteopenia (2004)

Skeletal cells synthesize bone morphogenetic proteins (BMPs) and BMP antagonists. Gremlin, a BMP antagonist, is expressed in osteoblasts and opposes BMP effects on osteoblastic differentiation and function in vitro. However, its effects in vivo are not known. To investigate the actions of gremlin on bone remodeling in vivo, we generated transgenic mice overexpressing gremlin under the control of the osteocalcin promoter. Gremlin transgenics exhibited bone fractures and reduced bone mineral density by 20-30%, compared with controls. Static and dynamic histomorphometry of femurs revealed that gremlin overexpression caused reduced trabecular bone volume and the appearance of woven bone. Polarized light microscopy revealed disorganized collagen bundles at the endosteal cortical surface. Gremlin transgenic mice displayed a 70% decrease in the number of osteoblasts/trabecular area and reduced mineral apposition and bone formation rates. In vivo bromodeoxyuridine labeling and marrow stromal cell cultures demonstrated an inhibitory effect of gremlin on osteoblastic cell replication, but no change on apoptosis was detected. Marrow stromal cells from gremlin transgenics displayed a reduced response to BMP on phosphorylated mothers against decapentaplegic 1/5/8 phosphorylation and reduced free cytosolic beta-catenin levels. In conclusion, transgenic mice overexpressing gremlin in the bone microenvironment have decreased osteoblast number and function leading to osteopenia and spontaneous fractures.
Hippo Signaling Mediates Proliferation, Invasiveness, and Metastatic Potential of Clear Cell Renal Cell Carcinoma (2014)

Recent work has identified dysfunctional Hippo signaling to be involved in maintenance and progression of various human cancers, although data on clear cell renal cell carcinoma (ccRCC) have been limited. Here, we provide evidence implicating aberrant Hippo signaling in ccRCC proliferation, invasiveness, and metastatic potential. Nuclear overexpression of the Hippo target Yes-associated protein (YAP) was found in a subset of patients with ccRCC. Immunostaining was particularly prominent at the tumor margins and highlighted neoplastic cells invading the tumor-adjacent stroma. Short hairpin RNA-mediated knockdown of YAP significantly inhibited proliferation, migration, and anchorage-independent growth of ccRCC cells in soft agar and led to significantly reduced murine xenograft growth. Microarray analysis of YAP knockdown versus mock-transduced ccRCC cells revealed down-regulation of endothelin 1, endothelin 2, cysteine-rich, angiogenic inducer, 61 (CYR61), and c-Myc in ccRCC cells as well as up-regulation of the cell adhesion molecule cadherin 6. Signaling pathway impact analysis revealed activation of the p53 signaling and cell cycle pathways as well as inhibition of mitogen-activated protein kinase signaling on YAP down-regulation. Our data suggest CYR61 and c-Myc as well as signaling through the endothelin axis as bona fide downstream effectors of YAP and establish aberrant Hippo signaling as a potential therapeutic target in ccRCC.
Synthesis of Oligoribonucleotides Bearing Morpholino-Nucleosides with Carbamate Internucleoside Linkages at the 3′-Terminus (1993)

Abstract Oligoribonucleotides containing morpholino-nucleosides with carbamate internucleoside linkages at the 3′-terminus were synthesized by the solid phase method. These analogues were examined for stability in a prokaryotic cell-free system.
Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse (2009)

We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.
Flagellin stimulation of intestinal epithelial cells triggers CCL20-mediated migration of dendritic cells (2001)

Enteropathogenic bacteria elicit mucosal innate and adaptive immune responses. We investigated whether gut epithelial cells played a role in triggering an adaptive immune response by recruiting dendritic cells (DCs). Immature DCs are selectively attracted by the CCL20 chemokine. The expression of the CCL20 gene in human intestinal epithelial cell lines was up-regulated by pathogenic bacteria, including Salmonella species, but not by indigenous bacteria of the intestinal flora. The Salmonella machinery for epithelial cell invasion was not required for CCL20 gene activation. Flagellin but not the lipopolysaccharide was found to be the Salmonella factor responsible for stimulation of epithelial CCL20 production. CCL20 in turn triggered a specific migration of immature DCs. Our data show that crosstalk between bacterial flagellin and epithelial cells is essential for the recruitment of DCs, a mechanism that could be instrumental to initiate adaptive immune responses in the gut.
Simple quantum error-correcting codes (1996)

Methods of finding good quantum error-correcting codes are discussed, and many example codes are presented. The recipe ${\mathit{C}}_{2}^{\mathrm{\ensuremath{\perp}}}$\ensuremath{\subset}${\mathit{C}}_{1}$, where ${\mathit{C}}_{1}$ and ${\mathit{C}}_{2}$ are classical codes, is used to obtain codes for up to 16 information quantum bits (qubits) with correction of small numbers of errors. The results are tabulated. More efficient codes are obtained by allowing ${\mathit{C}}_{1}$ to have reduced distance, and introducing sign changes among the code words in a systematic manner. This systematic approach leads to single-error-correcting codes for 3, 4, and 5 information qubits with block lengths of 8, 10, and 11 qubits, respectively. \textcopyright{} 1996 The American Physical Society.
Analytic displacement mapping using hardware tessellation (2013)

Displacement mapping is ideal for modern GPUs since it enables high-frequency geometric surface detail on models with low memory I/O. However, problems such as texture seams, normal recomputation, and undersampling artifacts have limited its adoption. We provide a comprehensive solution to these problems by introducing a smooth analytic displacement function. Coefficients are stored in a GPU-friendly tile-based texture format, and a multiresolution mip hierarchy of this function is formed. We propose a novel level-of-detail scheme by computing per-vertex adaptive tessellation factors and select the appropriate prefiltered mip levels of the displacement function. Our method obviates the need for a precomputed normal map since normals are directly derived from the displacements. Thus, we are able to perform authoring and rendering simultaneously without typical displacement map extraction from a dense triangle mesh. This not only is more flexible than the traditional combination of discrete displacements and normal maps, but also provides faster runtime due to reduced memory I/O.
Determination of herpes simplex virus type-specific antibodies by enzyme-linked immunosorbent assay (1983)

We determined type-specific antibodies to herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) by an indirect enzyme-linked immunosorbent assay, using as antigens HSV-1 glycoprotein gC-1 and a HSV-2-specific polypeptide purified on affinity columns of monoclonal antibodies. All sera were initially screened for HSV antibodies by the enzyme-linked immunosorbent assay with a pool of Triton X-100-extracted antigens of HSV-1- and HSV-2-infected HEp-2 cells. The titer of HSV antibodies was predicted from a linear regression curve based on the absorbance of the initial 1:50 serum dilution. The sensitivity and specificity of the screening assay and of the assay for type-specific antibodies were established.
Synthese von basisch substituierten Chromonen (1953)

Abstract Es wird gezeigt, dass man durch Kondensation von basisch substituierten Estern mit o‐Oxy‐acylphenonen und Ringschluss der entstandenen 1,3‐Diketone zu Chromonen gelangt, die in 2‐Stellung basisch substituiert sind. Die Synthese liess sich auch mit N‐acetylierten Estern durchführen.
Genetically Associated CD16+56− Natural Killer Cell Interferon (IFN)–αR Expression Regulates Signaling and Is Implicated in IFN-α–Induced Hepatitis C Virus Decline (2012)

IFN-αR expression on CD16(+)56(-) NK cells during chronic HCV infection may in part be genetically determined, and level of expression regulates IFN-α signaling, which in turn may contribute to control of HCV infection.
Requirement of p27 Kip1 for Restriction Point Control of the Fibroblast Cell Cycle (1996)

Cells deprived of serum mitogens will either undergo immediate cell cycle arrest or complete mitosis and arrest in the next cell cycle. The transition from mitogen dependence to mitogen independence occurs in the mid-to late G1 phase of the cell cycle and is called the restriction point. Murine Balb/c-3T3 fibroblasts deprived of serum mitogens accumulated the cyclin-dependent kinase (CDK) inhibitor p27Kip1. This was correlated with inactivation of essential G1 cyclin-CDK complexes and with cell cycle arrest in G1. The ability of specific mitogens to allow transit through the restriction point paralleled their ability to down-regulate p27, and antisense inhibition of p27 expression prevented cell cycle arrest in response to mitogen depletion. Therefore, p27 is an essential component of the pathway that connects mitogenic signals to the cell cycle at the restriction point.
Association between muscular strength and mortality in men: prospective cohort study (2008)

Muscular strength is inversely and independently associated with death from all causes and cancer in men, even after adjusting for cardiorespiratory fitness and other potential confounders.