gebhart/patrepeval huggingface dataset:
Limits of Neurogenesis in Primates (1985)

Systematic analysis of autoradiograms prepared from postpubertal rhesus monkeys given single and multiple injections of tritium-labeled thymidine and killed 3 days to 6 years later displayed a slow turnover of glial cells but failed to reveal any radiolabeled neurons. Therefore, unlike neurons of some nonprimate species, all neurons of the rhesus monkey brain are generated during prenatal and early postnatal life. A stable population of neurons in primates, including humans, may be important for the continuity of learning and memory over a lifetime.
A Knowledge-Based System for the Detection and Diagnosis of Out-of-Control Events in Manufacturing Processes (1989)

In this paper, we discuss a system which combines statistical process control principles and knowledge of the process to automatically arrive at a comprehensive detection and diagnosis of out-of-control conditions in a manufacturing process. This approach consists of capturing data from the process and passing selected signals from it through a two level decision-making system. The first level of this system employs nonlinear filtering techniques to detect three features (peaks, steps, and ramps) of the input signals. These features are examined to produce a set of out-of-control events. The second level of the process applies a ruleset to each event using a backward chaining algorithm to attempt to diagnose a process cause that led to the event. Status reports of diagnosed and undiagnosed events are generated by the system. A detailed description of the entire system and some discussion of its use in an actual aluminum rolling mill will be presented.
Hot Electron Reduction at n‐Si/Au Thin Film Electrodes (1992)

Schottky barrier electrodes were prepared by deposition of thin films of Au on device quality n‐Si. Barrier heights for fourteen day old films, determined by high frequency capacitance measurements at open circuit in the presence of , were found to be 0.60 eV in the thickness range of 200 to 1000 Å. The exchange current densities were determined as a function of film thickness and aging time up to about one month after deposition. Ideal solid‐state‐controlled Tafel slopes of 60 mV/decade were observed for overpotentials up to 120 mV. Mott‐Schottky plots confirmed the symmetry factor was unity. The ratio of the exchange current was about 100 for measurements made within 1 h after deposition. A similar increase in with decreasing thickness was observed at five and fourteen days, but the magnitude of the currents were lower by one to two orders of magnitude, with larger changes for thinner films. The lower currents after aging, were attributed to larger barrier heights, perhaps caused by changes in the interfacial layer such as oxidation. The observed dependence of exchange current on thickness after each aging period, was successfully modeled by assuming ballistic transport of hot electrons across the metal film. The ballistic mean‐free path of electrons in our Au films, determined by application of the theory developed in Paper I , was .
A Rh-Catalyzed C−H Insertion Reaction for the Oxidative Conversion of Carbamates to Oxazolidinones (2001)

Selective intramolecular alkane oxidations: an Rh<sup>II</sup> carboxylate catalyzed C-H amination reaction facilitates the preparation of 1,2-amino alcohols from primary carbamates. The reaction is stereospecific, providing access to chiral α-branched amines from optically pure starting materials with no loss in enantiomeric excess.
Effects of Complementarity Determining Region Mutations on the Affinity of an α/β T Cell Receptor: Measuring the Energy Associated with CD4/CD8 Repertoire Skewing (1999)

It has been proposed that the generally low affinities of T cell receptors (TCRs) for their peptide-major histocompatibility complex (pMHC) ligands (Kd approximately 10(-4) to 10(-7) M) are the result of biological selection rather than an intrinsic affinity limitation imposed by the TCR framework. Using a soluble version of the 2C TCR, we have used complementarity determining region (CDR)-directed mutagenesis to investigate whether the affinity of this receptor for its allogeneic pMHC ligand can be improved upon. We report that several mutants at positions lying within CDR3alpha and CDR2beta showed increased affinities for pMHC compared with the wild-type receptor. Additionally, we have investigated whether Valpha mutations that have been implicated in the phenomenon of CD8(+) repertoire skewing achieve this skewing by means of generalized increases in affinity for MHC-I molecules. Two mutants (S27F and S51P), which each promote skewing toward a CD8(+) phenotype, exhibited significantly reduced affinity for pMHC-I, consistent with a quantitative-instructional model of CD4/CD8 lineage commitment. This model predicts that CD8 is downregulated on thymocytes that have TCR-ligand interactions above a minimal energy threshold. Together, the results (a) demonstrate that engineering higher affinity TCRs is feasible, and (b) provide TCR-pMHC energy values associated with CD4/CD8 repertoire skewing.
Structural Basis for Selective Vascular Endothelial Growth Factor-A (VEGF-A) Binding to Neuropilin-1 (2012)

Neuropilin-1 (Nrp1) is an essential receptor for angiogenesis that binds to VEGF-A. Nrp1 binds directly to VEGF-A with high affinity, but the nature of their selective binding has remained unclear. Nrp1 was initially reported to bind to the exon 7-encoded region of VEGF-A and function as an isoform-specific receptor for VEGF-A(164/165). Recent data have implicated exon 8-encoded residues, which are found in all proangiogenic VEGF-A isoforms, in Nrp binding. We have determined the crystal structure of the exon 7/8-encoded VEGF-A heparin binding domain in complex with the Nrp1-b1 domain. This structure clearly demonstrates that residues from both exons 7 and 8 physically contribute to Nrp1 binding. Using an in vitro binding assay, we have determined the relative contributions of exon 7- and 8-encoded residues. We demonstrate that the exon 8-encoded C-terminal arginine is essential for the interaction of VEGF-A with Nrp1 and mediates high affinity Nrp binding. Exon 7-encoded electronegative residues make additional interactions with the L1 loop of Nrp1. Although otherwise conserved, the primary sequences of Nrp1 and Nrp2 differ significantly in this region. We further show that VEGF-A(164) binds 50-fold more strongly to Nrp1 than Nrp2. Direct repulsion between the electronegative exon 7-encoded residues of the heparin binding domain and the electronegative L1 loop found only in Nrp2 is found to significantly contribute to the observed selectivity. The results reveal the basis for the potent and selective binding of VEGF-A(164) to Nrp1.
Electron Transfer and Catalytic Activity of Nitric Oxide Synthases (1998)

The nitric oxide synthases (NOS) are single polypeptides that encode a heme domain, a calmodulin binding motif, and a flavoprotein domain with sequence similarity to P450 reductase. Despite this basic structural similarity, the three major NOS isoforms differ significantly in their rates of .NO synthesis, cytochrome c reduction, and NADPH utilization and in the Ca2+ dependence of these rates. To assign the origin of these differences to specific protein domains, we constructed chimeras in which the reductase domains of endothelial and inducible NOS, respectively, were replaced by the reductase domain of neuronal NOS. The results with the chimeric proteins confirm the modular organization of the NOS polypeptide chain and demonstrate that (a) similar residues establish the necessary contacts between the reductase and heme domains in the three NOS isoforms, (b) the maximal rate of .NO synthesis is determined by the maximum intrinsic ability of the reductase domain to deliver electrons to the heme domain, (c) the Ca2+ independence of inducible NOS requires interactions of calmodulin with both the calmodulin binding motif and the flavoprotein domain, and (d) the effects of tetrahydrobiopterin and L-arginine on electron transfer rates are mediated exclusively by heme domain interactions.
Clinical and laboratorial features of visceral toxocariasis in infancy (1994)

Forty children with a diagnosis of Visceral Toxocariasis were evaluated prospectively from February 1982 to June 1989. Diagnosis was established by clinical, laboratory and serological (ELISA - ES Toxocara canis antigen) evaluations. A great clinical polymorphism was found in our patients, ranging from unspecific or absent manifestations to an exuberant symptomatology. The laboratory findings were: leukocytosis, eosinophilia and elevation of serum gammaglobulin and isohemagglutinin levels. No significant relationship between clinical findings and laboratory parameters was found. Serology (ELISA) was a method of great diagnostic support but did not show a correlation with clinical and laboratory findings in this study. There was a significant relationship between pulmonary manifestations and the presence of signs and/or symptoms, when the patients were sent to us. Our findings, especially the high incidence of pulmonary manifestations, suggest that Visceral Toxocariasis has to be included in the differential diagnostic of children with pulmonary manifestations, characteristic epidemiological data and associated eosinophilia.
Deep Learning for Content-Based Image Retrieval (2014)

Learning effective feature representations and similarity measures are crucial to the retrieval performance of a content-based image retrieval (CBIR) system. Despite extensive research efforts for decades, it remains one of the most challenging open problems that considerably hinders the successes of real-world CBIR systems. The key challenge has been attributed to the well-known ``semantic gap'' issue that exists between low-level image pixels captured by machines and high-level semantic concepts perceived by human. Among various techniques, machine learning has been actively investigated as a possible direction to bridge the semantic gap in the long term. Inspired by recent successes of deep learning techniques for computer vision and other applications, in this paper, we attempt to address an open problem: if deep learning is a hope for bridging the semantic gap in CBIR and how much improvements in CBIR tasks can be achieved by exploring the state-of-the-art deep learning techniques for learning feature representations and similarity measures. Specifically, we investigate a framework of deep learning with application to CBIR tasks with an extensive set of empirical studies by examining a state-of-the-art deep learning method (Convolutional Neural Networks) for CBIR tasks under varied settings. From our empirical studies, we find some encouraging results and summarize some important insights for future research.
Urinary Metabolic Phenotyping Differentiates Children with Autism from Their Unaffected Siblings and Age-Matched Controls (2010)

Autism is an early onset developmental disorder with a severe life-long impact on behavior and social functioning that has associated metabolic abnormalities. The urinary metabolic phenotypes of individuals (age range=3-9 years old) diagnosed with autism using the DSM-IV-TR criteria (n = 39; male = 35; female = 4), together with their nonautistic siblings (n = 28; male = 14; female = 14) and age-matched healthy volunteers (n = 34, male = 17; female = 17) have been characterized for the first time using (1)H NMR spectroscopy and pattern recognition methods. Novel findings associated with alterations in nicotinic acid metabolism within autistic individuals showing increased urinary excretion of N-methyl-2-pyridone-5-carboxamide, N-methyl nicotinic acid, and N-methyl nicotinamide indicate a perturbation in the tryptophan-nicotinic acid metabolic pathway. Multivariate statistical analysis indicated urinary patterns of the free amino acids, glutamate and taurine were significantly different between groups with the autistic children showing higher levels of urinary taurine and a lower level of urinary glutamate, indicating perturbation in sulfur and amino acid metabolism in these children. Additionally, metabolic phenotype (metabotype) differences were observed between autistic and control children, which were associated with perturbations in the relative patterns of urinary mammalian-microbial cometabolites including dimethylamine, hippurate, and phenyacetylglutamine. These biochemical changes are consistent with some of the known abnormalities of gut microbiota found in autistic individuals and the associated gastrointestinal dysfunction and may be of value in monitoring the success of therapeutic interventions.
A Sequential Learning Scheme for Function Approximation Using Minimal Radial Basis Function Neural Networks (1997)

This article presents a sequential learning algorithm for function approximation and time-series prediction using a minimal radial basis function neural network (RBFNN). The algorithm combines the growth criterion of the resource-allocating network (RAN) of Platt (1991) with a pruning strategy based on the relative contribution of each hidden unit to the overall network output. The resulting network leads toward a minimal topology for the RBFNN. The performance of the algorithm is compared with RAN and the enhanced RAN algorithm of Kadirkamanathan and Niranjan (1993) for the following benchmark problems: (1) hearta from the benchmark problems database PROBEN1, (2) Hermite polynomial, and (3) Mackey-Glass chaotic time series. For these problems, the proposed algorithm is shown to realize RBFNNs with far fewer hidden neurons with better or same accuracy.
Nitro-Substituted Hoveyda−Grubbs Ruthenium Carbenes:  Enhancement of Catalyst Activity through Electronic Activation (2004)

The design, synthesis, stability, and catalytic activity of nitro-substituted Hoveyda-Grubbs metathesis catalysts are described. The highly active and stable meta- and para-substituted complexes are attractive from a practical point of view. These catalysts operate in very mild conditions and can be successfully applied in various types of metathesis [ring-closing metathesis, cross-metathesis (CM), and enyne metathesis]. Although the presence of a NO(2) group leads to catalysts that are dramatically more active than both the second-generation Grubbs's catalyst and the phosphine-free Hoveyda's carbene, enhancement of reactivity is somewhat lower than that observed for a sterically activated Hoveyda-Grubbs catalyst. Attempts to combine two modes of activation, steric and electronic, result in severely decreasing a catalyst's stability. The present findings illustrate that different Ru catalysts turned out to be optimal for different applications. Whereas phosphine-free carbenes are catalysts of choice for CM of various electron-deficient substrates, they exhibit lower reactivity in the formation of tetrasubstituted double bonds. This demonstrates that no single catalyst outperforms all others in all possible applications.
Gepard: a rapid and sensitive tool for creating dotplots on genome scale (2007)

Both source codes and executable binaries are available at http://mips.gsf.de/services/analysis/gepard
The Preparation and Properties of Adenovirus Cores (1971)

Summary Purified preparations of adenovirus were readily disrupted by heating them for a short time in the presence of sodium deoxycholate. The inner complex of proteins and virus DNA (cores) was partially purified by velocity gradient centrifugation in sucrose or glycerol. Further purification was achieved by equilibrium centrifugation on a preformed gradient of ‘Urografin’. Acrylamide gel electrophoresis showed that the cores contained principally two protein components one of which could be removed at the last stage of purification. The core preparations were infective at an extremely low efficiency, the infectivity being sensitive to DNase, trypsin and to various antivirus sera.
Expression of dihydrodiol dehydrogenase in the resected stage I non-small cell lung cancer (2002)

Recently, by using differential display on specimens of non-small cell lung cancer (NSCLC), we detected overexpression of dihydrodiol dehydrogenase (DDH) that was rarely expressed in the corresponding normal lung tissue. DDH overexpression was correlated with poor prognosis of patients with advanced NSCLC. Because DDH could metabolize polycyclic aromatic hydrocarbons (PAH) in the liver, DDH overexpression in NSCLC would suggest an association with carcinogenesis and disease progression. In this study, we investigated DDH expression in 103 patients with resected stage I NSCLC. Expression of DDH was detected by using immunohistochemistry. Relation between DDH expression and clinicopathological parameter (age, gender, smoking habit, tumor status, histological type, cell differentiation, local recurrence, distant metastasis or survival) was analyzed by statistical analysis. DDH overexpression was detected in 39 (37.9%) of 103 pathological sections. Frequency of DDH overexpression was significantly higher in male patients (p=0.043) and patients with squamous cell carcinoma (p<0.005). Among 103 patients, 14 patients had local recurrence and 28 patients had distant metastasis during follow-up examination. The 5-year survival rate of these patients was poorer than those who did not have local recurrence or distant metastasis (both were p<0.005, respectively). Although patients with low DDH expression had more favorable outcome than those with DDH overexpression, in terms of survival rate no statistical significance was detected (p=0.889). The results suggest that DDH expression may serve as an early but not prognostic biomarker for patients with resectable stage I NSCLC.
Intestinal peptide transport: ex vivo uptake studies and localization of peptide carrier PEPT1 (2001)

The nature of protein breakdown products and peptidomimetic drugs such as beta-lactams is crucial for their transmembrane transport across apical enterocyte membranes, which is accomplished by the pH-dependent high-capacity oligopeptide transporter PEPT1. To visualize oligopeptide transporter-mediated uptake of oligopeptides, an ex vivo assay using the fluorophore-conjugated dipeptide derivative D-Ala-Lys-N(epsilon)-7-amino-4-methylcoumarin-3-acetic acid (D-Ala-Lys-AMCA) was established in the murine small intestine and compared with immunohistochemistry for PEPT1 in murine and human small intestine. D-Ala-Lys-AMCA was accumulated by enterocytes throughout all segments of the murine small intestine, with decreasing intensity from the top to the base of the villi. Goblet cells did not show specific uptake. Inhibition studies revealed competitive inhibition by the beta-lactam cefadroxil, the angiotensin-converting enzyme inhibitor captopril, and the dipeptide glycyl-glutamine. Controls were performed using either the inhibitor diethylpyrocarbonate or an incubation temperature of 4 degrees C to exclude unspecific uptake. Immunohistochemistry for PEPT1 localized immunoreactivity to the enterocytes, with the highest intensity at the apical membrane. This is the first study that visualizes dipeptide transport across the mammalian intestine and indicates that uptake assays using D-Ala-Lys-AMCA might be useful for characterizing PEPT1-specific substrates or inhibitors.
Transbronchial laser ablation of benign and malignant tumors (2006)

An overview is given over different methods for thermal ablation in central airways. The most widely used method, endoscopic laser photocoagulation (Nd:YAG laser) is described in some detail. Other methods are electrocautery, argon plasma coagulation, photodynamic treatment and cryotherapy. Thermal ablation is usually a palliative treatment, but is sometimes performed with a curative intent. Such treatment should be performed in specialized centres for interventional bronchoscopy, with a broad range of methods available.
A schema based approach to dialog control (1998)

Frame-based approaches to spoken language interaction work well for limited tasks such as information access, given that the goal of the interaction is to construct a correct query then execute it. More complex tasks, however, can benefit from more active system participation. We describe two mechanisms that provide this, a modified stack that allows the system to track multiple topics, and form-specific schema that allow the system to deal with tasks that involve completion of multiple forms. Domain-dependent schema specify system behavior and are executed by a domain-independent engine. We describe implementations for a personal calendar system and for an air travel planning system.
Motility and Fertility of Bull Sperm Frozen-Thawed Differently in Egg Yolk and Milk Extenders Containing Detergent (1987)

The purpose of this study was to examine survival and fertility of frozen bull sperm processed in several extenders containing a detergent mixture, sodium, and triethanolamine lauryl sulfate. Addition of .5% (vol/vol) detergent to whole milk was completely spermicidal. When 10% egg yolk (vol/vol) was included in the glycerol or nonglycerol fractions or both fractions of milk, sperm were equally well preserved in the presence of .5% detergent, and sperm survival following thawing at 4 degrees C was dramatically improved by the detergent. This improved result with the 4 degrees C thaw temperature also was obtained by adding .5% detergent to an egg yolk-Tris extender. Thawing temperatures of 30 and 50 degrees C (later for 15 s) were generally superior to 4 degrees C. A fertility trial with whole milk, whole milk-10% yolk, whole milk-10% yolk-.5% detergent, egg yolk-Tris, and egg yolk-Tris-.5% detergent was conducted. The 59-d percent nonreturns, respectively, were 73.4, 65.8, 65.6, 69.5, and 73.4. Whole milk or egg yolk-Tris plus detergent were equally superior to the other extenders for bull semen.
The period clock gene is expressed in central nervous system neurons which also produce a neuropeptide that reveals the projections of circadian pacemaker cells within the brain of Drosophila melanogaster. (1995)

The period protein (PER) is a essential component of the circadian clock in Drosophila melanogaster. Although PER-containing pacemaker cells have been previously identified in the brain, the neuronal network that comprises the circadian clock remained unknown. Here it is shown that some PER neurons are also immunostained with an antiserum against the crustacean pigment-dispersing hormone (PDH). This antiserum reveals the entire arborization pattern of these pacemaker cells. The arborizations of these neurons are appropriate for modulation of the activity of many neurons and they might interact with PER-containing glial cells. A putative physiological role of PDH in the circadian system is discussed.