gebhart/patrepeval huggingface dataset:
Branching and Circular Features in High Dimensional Data (2011)

Large observations and simulations in scientific research give rise to high-dimensional data sets that present many challenges and opportunities in data analysis and visualization. Researchers in application domains such as engineering, computational biology, climate study, imaging and motion capture are faced with the problem of how to discover compact representations of high-dimensional data while preserving their intrinsic structure. In many applications, the original data is projected onto low-dimensional space via dimensionality reduction techniques prior to modeling. One problem with this approach is that the projection step in the process can fail to preserve structure in the data that is only apparent in high dimensions. Conversely, such techniques may create structural illusions in the projection, implying structure not present in the original high-dimensional data. Our solution is to utilize topological techniques to recover important structures in high-dimensional data that contains non-trivial topology. Specifically, we are interested in high-dimensional branching structures. We construct local circle-valued coordinate functions to represent such features. Subsequently, we perform dimensionality reduction on the data while ensuring such structures are visually preserved. Additionally, we study the effects of global circular structures on visualizations. Our results reveal never-before-seen structures on real-world data sets from a variety of applications.
DNA position-specific repression of transcription by a Drosophila zinc finger protein. (1992)

Expression of the yellow (y) gene of Drosophila melanogaster is controlled by a series of tissue-specific transcriptional enhancers located in the 5' region and intron of the gene. Insertion of the gypsy retrotransposon in the y2 allele at -700 bp from the start of transcription results in a spatially restricted phenotype: Mutant tissues are those in which yellow expression is controlled by enhancers located upstream from the insertion site, but all other structures whose enhancers are downstream of the insertion site are normally pigmented. This observation can be reproduced by inserting just a 430-bp fragment containing the suppressor of Hairy-wing [su(Hw)]-binding region of gypsy into the same position where this element is inserted in y2, suggesting that the su(Hw)-binding region is sufficient to confer the mutant phenotype. Insertion of this sequence into various positions in the y gene gives rise to phenotypes that can be rationalized assuming that the presence of the su(Hw) protein inhibits the action of those tissue-specific enhancers that are located more distally from the su(Hw)-binding region with respect to the promoter. These results are discussed in light of current models that explain long-range effects of enhancers on gene expression.
Preparation of 2,5-Diamino-3,6-Dinitropyrazine (ANPZ-i): A Novel Candidate High Energy Insensitive Explosive (2000)

2,5-Diamino-3,6-dinitropyrazine (ANPZ-i) has been prepared via the electrophilic nitration of 2,5-diethoxypyrazine using nitronium tetrafluoroborate in sulpholane and subsequent amination under autoclave conditions. Molecular modelling studies have been carried out which indicate that ANPZ-i should have a similar performance to RDX but with an expected higher insensitivity. ANPZ-i (1) is therefore a novel candidate high energy insensitive explosive. Darstellung von 2,5-Diamino-3,6-Dinitropyrazin (ANPZ-i): Ein neuer Kandidat für einen unempfindlichen Hochenergie-Sprengstoff. 2,5-Diamino-3,6-Dinitropyrazin (ANPZ-i) wurde durch elektrophile Nitrierung von 2,5-Diethoxypyrazin unter Verwendung von Nitroniumtetrafluoroborat in Sulfolan und sukzessiver Aminolyse im Autoklaven dargestellt. Die Ergebnisse rechnergestützter Untersuchungen deuten darauf hin, daß ANPZ-i eine ähnliche Leistung wie Hexogen bei einer zu erwartenden höheren Unempfindlichkeit aufweisen sollte. ANPZ-i (1) ist deshalb ein neuer Kandidat für einen unempfindlichen Hochenergie-Sprengstoff. Préparation de la 2,5-diamino-3,6-dinitropyrazine (ANPZ-i): Unnouveau candidat pour un explosif énergétique insensible La 2,5-diamino-3,6-dinitropyrazine (ANPZ-i) a été préparée par nitration électrophile de 2,5-diéthoxypyrazine en utilisant du tétrafluoroborate de nitronium dans du sulfolane, suivie d'une aminolyse dans l'autoclave. Les résultats des simulations numériques indiquent que l'ANPZ-i devrait donner des performances semblables à celles de l'hexogène pour une insensibilité escomptée plus élevée. l'ANPZ-i (1) est donc un nouveau candidat pour un explosif énergétique insensible.
Ectopic ventricular tachycardia in association with a concealed accessory pathway. (1979)

Ventricular tachycardia may result in retrograde atrial depolarization. In all previous examples studied by intracardiac recording techniques retrograde conduction to the atria has been thought to occur via the normal conduction system. In the patient reported here, 1 : 1 retrograde conduction with atrial preexcitation during ventricular tachycardia indicated the presence of a concealed accessory pathway. This was confirmed by the phenomenon of exact atrial capture. The achievement of atrioventricular dissociation during tachycardia by atrial overdrive pacing excluded a reentrant tachycardia involving such a pathway. The widely variable H--V interval in the presence of a constant V--A interval during tachycardia suggested anterograde His bundle depolarization following atrial activation over the accessory pathway. This hypothesis was supported by the long V--H interval during tachycardia and the relationship of the ventricular, atrial and His bundle electrograms of the first and least beat of the tachycardia. This report illustrates the value of careful electrophysiological investigation in evaluating the relationship of an accessory pathway to the tachycardia mechanism.
A process-insensitive current-controlled delay generator with threshold voltage compensation (2010)

A process-insensitive current-controlled delay generator is presented with a large tunable range of the time delay. By adopting process variation compensation techniques in the generation of time delay, the delay generator is able to provide process-insensitive clock pulses. The circuit has been fabricated in 90 nm CMOS technology, consumes 310 μW from a 1.1V supply. Using, in a typical case, 20μA of reference current, it can generate a delay of 2.36 ns. The delay variation observed in 14 measured chips has shown a standard deviation of 1.24%.
Photodetector sensitivity control for weight setting in optoelectronic neural networks (1991)

In optoelectronic neural processors weights are set optically and neural states electrically. Reversing this arrangement allows weights to be set by adjusting photodetector sensitivity.
Douglas v. Faith Baptist Church under Constitutional Scrutiny (1982)

MR images can show long-lasting abnormal nerve enhancement, especially in the distal intrameatal nerve segment, related to the long-lasting breakdown of the blood/peripheral nerve barrier associated with nerve degeneration and regeneration after traumatic stretching of the greater superficial petrosal nerve. Additionally, intraoperatively observed perineural and intraneural scar formation leads to thickening and intense enhancement of the affected nerve segments on MR images. A hematoma in the region of the geniculate ganglion can be seen in some but not all patients. Associated damage of the inner ear structures in patients with transverse fractures is also visible on MR images.
Global flow optimization in automatic logic design (1991)

A method for optimizing digital logic networks is described. This approach uses the techniques of global flow analysis to efficiently gather information about the relationship between different wires in a circuit and uses methods from network flow to use this information to optimize the circuit. It differs from earlier methods for optimization of multilevel logic networks in that valid rearrangements of signal connections depend on the maintenance of global circuit invariants. An algorithm which reduces the problem of finding small circuits in this equivalence class to the problem of finding a min-cut in an associated graph is described. This algorithm has been implemented and forms part of an automatic design system in use within IBM. The authors describe the results of experiments undertaken to evaluate the effect of the techniques.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Passband Equalization of Differentially Phase-Modulated Data Signals (1973)

A new approach to the automatic equalization of differentially phase-modulated data signals passing through a linear distorting medium is presented. The equalizer, which is of the transversal filter type, operates in the frequency passband and contains two sets of taps — in-phase and quadrature. A tap-rotation property of the equalizer is used to establish an absolute phase reference at the equalizer output, and once this crucial step is taken, the passband equalizer output can be used to automatically (as well as adaptively) adjust the tap weights so as to minimize a mean-square distortion function. The resulting algorithm requires correlating an error signal with the tap voltages, and thus it is possible to use a structure similar to that employed when equalizing baseband PAM. The generality of the approach makes it applicable to the equalization of any double-sideband data signal.
Spatial and Temporal Correlation of Water Quality Parameters of Produced Waters from Devonian-Age Shale following Hydraulic Fracturing (2013)

The exponential increase in fossil energy production from Devonian-age shale in the Northeastern United States has highlighted the management challenges for produced waters from hydraulically fractured wells. Confounding these challenges is a scant availability of critical water quality parameters for this wastewater. Chemical analyses of 160 flowback and produced water samples collected from hydraulically fractured Marcellus Shale gas wells in Pennsylvania were correlated with spatial and temporal information to reveal underlying trends. Chloride was used as a reference for the comparison as its concentration varies with time of contact with the shale. Most major cations (i.e., Ca, Mg, Sr) were well-correlated with chloride concentration while barium exhibited strong influence of geographic location (i.e., higher levels in the northeast than in southwest). Comparisons against brines from adjacent formations provide insight into the origin of salinity in produced waters from Marcellus Shale. Major cations exhibited variations that cannot be explained by simple dilution of existing formation brine with the fracturing fluid, especially during the early flowback water production when the composition of the fracturing fluid and solid-liquid interactions influence the quality of the produced water. Water quality analysis in this study may help guide water management strategies for development of unconventional gas resources.
Heavy particle collisions. (1969)

Diatomic heavy particle collisions and elastic scattering and inelastic processes involving electronic excitation, ionization, and charge transfer or electronic energy
Induction of B7-1 in podocytes is associated with nephrotic syndrome (2004)

Kidney podocytes and their slit diaphragms form the final barrier to urinary protein loss. This explains why podocyte injury is typically associated with nephrotic syndrome. The present study uncovered an unanticipated novel role for costimulatory molecule B7-1 in podocytes as an inducible modifier of glomerular permselectivity. B7-1 in podocytes was found in genetic, drug-induced, immune-mediated, and bacterial toxin-induced experimental kidney diseases with nephrotic syndrome. The clinical significance of our results is underscored by the observation that podocyte expression of B7-1 correlated with the severity of human lupus nephritis. In vivo, exposure to low-dose LPS rapidly upregulates B7-1 in podocytes of WT and SCID mice, leading to nephrotic-range proteinuria. Mice lacking B7-1 are protected from LPS-induced nephrotic syndrome, suggesting a link between podocyte B7-1 expression and proteinuria. LPS signaling through toll-like receptor-4 reorganized the podocyte actin cytoskeleton in vitro, and activation of B7-1 in cultured podocytes led to reorganization of vital slit diaphragm proteins. In summary, upregulation of B7-1 in podocytes may contribute to the pathogenesis of proteinuria by disrupting the glomerular filter and provides a novel molecular target to tackle proteinuric kidney diseases. Our findings suggest a novel function for B7-1 in danger signaling by nonimmune cells.
Compensating fibre splice technique (1977)

A low-loss, rugged splicing technique has been demonstrated. The technique compensates for fibre core eccentricity, cladding-diameter variations and cladding noncircularity. No precision connectors or housings are left on the fibres.
Redescription mining: structure theory and algorithms (2005)

We introduce a new data mining problem—redescription mining—that unifies considerations of conceptual clustering, constructive induction, and logical formula discovery. Re-description mining begins with a collection of sets, views it as a propositional vocabulary, and identifies clusters of data that can be defined in at least two ways using this vocabulary. The primary contributions of this paper are conceptual and theoretical: (i) we formally study the space of redescriptions underlying a dataset and characterize their intrinsic structure, (ii) we identify impossibility as well as strong possibility re-sults about when mining redescriptions is feasible, (iii) we present several scenarios of how we can custom-build re-description mining solutions for various biases, and (iv) we outline how many problems studied in the larger machine learning community are really special cases of redescription mining. By highlighting its broad scope and relevance, we aim to establish the importance of redescription mining and make the case for a thrust in this new line of research.
Transduction of the Central Nervous System After Intracerebroventricular Injection of Adeno-Associated Viral Vectors in Neonatal and Juvenile Mice (2013)

Several neurodevelopmental and neurodegenerative disorders affecting the central nervous system are potentially treatable via viral vector-mediated gene transfer. Adeno-associated viral (AAV) vectors have been used in clinical trials because of their desirable properties including a high degree of safety, efficacy, and stability. Major factors affecting tropism, expression level, and cell type specificity of AAV-mediated transgenes include encapsidation of different AAV serotypes, promoter selection, and the timing of vector administration. In this study, we evaluated the ability of single-stranded AAV2 vectors pseudotyped with viral capsids from serotype 9 (AAV2/9) to transduce the brain and target gene expression to specific cell types after intracerebroventricular injection into mice. Titer-matched AAV2/9 vectors encoding the enhanced green fluorescent protein (eGFP) reporter, driven by the cytomegalovirus (CMV) promoter, or the neuron-specific synapsin-1 promoter, were injected bilaterally into the lateral ventricles of C57/BL6 mice on postnatal day 5 (neonatal) or 21 (juvenile). Brain sections were analyzed 25 days after injection, using immunocytochemistry and confocal microscopy. eGFP immunohistochemistry after neonatal and juvenile administration of viral vectors revealed transduction throughout the brain including the striatum, hippocampus, cerebral cortex, and cerebellum, but with different patterns of cell-specific gene expression. eGFP expression was seen in astrocytes after treatment on postnatal day 5 with vectors carrying the CMV promoter, expanding the usefulness of AAVs for modeling and treating diseases involving glial cell pathology. In contrast, injection of AAV2/9-CMV-eGFP on postnatal day 21 resulted in preferential transduction of neurons. Administration of AAV2/9-eGFP with the synapsin-1 promoter on either postnatal day 5 or 21 resulted in widespread neuronal transduction. These results outline efficient methods and tools for gene delivery to the nervous system by direct, early postnatal administration of AAV vectors. Our findings highlight the importance of promoter selection and age of administration on the intensity, distribution, and cell type specificity of AAV transduction in the brain.
Progress towards a new government standard 2400 bps voice coder (2002)

In order to support the need for higher quality low rate voice communications for government, industry, and military customers, the United States Government is conducting a search for a new voice compression algorithm at 2400 bits per second (bps). The United States Department of Defense Digital Voice Processing Consortium (DDVPC), consisting of members from civilian and military branches of the US Government, is directing the testing and evaluation of several candidate 2400 bps algorithms. The goal of the DDVPC is to select a new algorithm which meets or exceeds the published requirements by mid 1996. The selected algorithm, to become the new standard, should be implementable in a small, low powered device by 1997. This paper describes the status of the testing and evaluation process from its beginning in early 1993 through the end of 1994.
Screening for colorectal cancer using the hemoccult II stool guaiac slide test (1984)

Following a series of educational spots on colorectal cancer shown on a local television news program, stool guaiac slide kits (Hemoccult II; Smith Kline Diagnostics) were distributed in shopping malls in Erie County, New York during a 3-day period in February 1982. The tests kits were sold for $1.00 a piece. A total of 8711 persons purchased test kits and 3822 persons (44%) returned slides for testing. One or more slides were positive in 107 persons (2.8%). Ninety of the 107 positive screenees (84%) saw a physician for further evaluation after screening. Eighteen positive screenees had no evidence of pathology which could cause blood in their stool when evaluated by a physician, yielding an overall false-positive rate of less than 0.5%. Seven new cases of colorectal cancer were found through screening. Five of the seven cancers (71%) detected were localized disease (Dukes' Stage A, B1 or B2), and four cases had no symptoms of disease prior to diagnosis. The findings from this study suggest that screening for fecal occult blood using the stool guaiac slide test is effective in detecting some colorectal cancers at an early stage of disease, often before symptoms appear.
Effects of the presence/absence of HCl during gate oxidation on the electrical and structural properties of polycrystalline silicon thin-film transistors (1989)

The influence of the presence or absence of HCl during gate oxidation at 1100 and 1150 °C on the electrical and structural properties of polycrystalline silicon thin-film transistors was investigated. Devices processed without HCl exhibited a lower leakage current, a larger current switching ratio, a 25%–55% increase in carrier mobility, and a 21%–30% lower grain-boundary trap density. Materials investigation showed that the improvement was not primarily due to an increase in grain size, which was about 1000 Å irrespective of processing conditions, but to a change in crystallite orientation. X-ray diffraction measurements showed an increased {110} texture in devices processed without HCl. In addition, in the latter devices, dopant diffusion under the gate from the source and drain contacts was reduced by 7.6% to 12%. A linear relationship was observed between the average grain-boundary trap density and the average lateral dopant diffusion length. These findings are explained by considering the point defect chemistry and its relationship to grain-boundary mobility. Removal of HCl from the oxidation ambient increases the concentration of silicon self-interstitials. The increased migration of these point defects to grain boundaries enhances their nonconservative motion and therefore increases grain-boundary mobility. This in turn, allows the boundary to more completely acquire a lower-energy configuration. This lower-energy configuration of the boundary contains a minimum of broken bonds and therefore minimizes both the grain-boundary electrical activity and the diffusion along grain boundaries.
Flexible Optical Transmission close to the Shannon Limit by Probabilistically Shaped QAM (2017)

We are reviewing the application of probabilistic shaping in long haul optical transmission systems and investigate the linear, nonlinear and implementation limits for this format in comparison to pragmatic QAM formats.
Web site auditing (2002)

There is a growing demand for redesigning the existing Web sites. Many organisations want their sites evaluated, or audited, with recommendations to improve them. Historically, auditing has related to financial matters. It is now applied to other disciplines such as quality, environment, safety, information systems and security. Correspondingly, there are many national and international standards for such audits. Operationally, a financial audit is an independent and expert opinion on how an organisation handles its resources and may recommend, if necessary, changes in the organisational practices to meet the established standards and obligations. In contrast, a Quality audit is meant to aid continuous improvement strategies. The definition and role of a Web site audit are not so clear. This paper addresses these two problems. First, it establishes a general context for Web site auditing in terms of the types of Web-based systems, the stages of Web development and the need for frequent re-engineering of the existing sites. The paper then argues that Web site auditing, as currently understood, is qualitatively different from normal auditing and recommends that it be an integral part of the re-engineering strategy and not be seen as mainly a reassurance exercise.
Heterogeneity in the developmental potential of motor neuron progenitors revealed by clonal analysis of single cells in vitro (2009)

These findings support a model whereby continuous Shh signaling is required to maintain the identity of ventral progenitors isolated from the spinal cord, including motor neuron progenitors, after in vitro expansion. They also demonstrate that pre-patterned neural progenitors isolated from the central nervous system can change their regional identity in vitro to acquire a broader developmental potential.