gebhart/patrepeval huggingface dataset:
Detection of Phylogenetically Diverse Human Immunodeficiency Virus Type 1 Groups M and O from Plasma by Using Highly Sensitive and Specific Generic Primers (1999)

The high degree of genetic diversity within human immunodeficiency virus type 1 (HIV-1), which includes two major groups, M (major) and O (outlier), and various env subtypes within group M (subtypes A to J), has made designing assays that will detect all known HIV-1 strains difficult. We have developed a generic primer set based on the conserved immunodominant region of transmembrane protein gp41 that can reliably amplify as few as 10 copies/PCR of viral DNA from near-full-length clones representing group M subtypes A to H (subtypes I and J were not available). The assay is highly sensitive in detecting plasma viral RNA from HIV-1 strains of diverse geographic origins representing different subtypes of HIV-1 group M as well as HIV-1 group O. Of the 253 group M plasma specimens (subtypes A, 68 specimens; B, 71; C, 19; D, 27; E, 23; F, 33; and G, 12), 250 (98.8%) were amplified by using the gp41 M/O primer set. More importantly, all 32 (100%) group O plasma samples were also amplified with these primers. In vitro spiking experiments further revealed that the assay could reliably detect as few as 25 copies/ml of viral RNA and gave positive signals in HIV-1-seropositive specimens with plasma copy numbers below the limits of detection by all commercially available viral load assays. In addition, analysis of five seroconversion panels indicated that the assay is highly sensitive for early detection of plasma viremia during the "window period." Thus, the highly sensitive assay will be useful for early detection of HIV-1 in clinical specimens from all known HIV-1 infections, regardless of their genotypes and geographic origins.
Engineering oxygen nanobubbles for the effective reversal of hypoxia (2018)

Hypoxia, which results from an inadequate supply of oxygen, is a major cause of concern in cancer therapy as it is associated with a reduction in the effectiveness of chemotherapy and radiotherapy in cancer treatment. Overexpression and stabilization of hypoxia-inducible factor 1α (HIF-1α) protein in tumours, due to hypoxia, results in poor prognosis and increased patient mortality. To increase oxygen tension in hypoxic areas, micro- and nanobubbles have been investigated by various researchers. In the present research, lipid-shelled oxygen nanobubbles (ONBs) were synthesized through a sonication method to reverse hypoxic conditions created in a custom-made hypoxic chamber. Release of oxygen gas from ONBs in deoxygenated water was evaluated by measuring dissolved oxygen. Hypoxic conditions were evaluated by performing in vitro experiments on MDA-MB231 breast cancer cells through the expression of HIF-1α and the fluorescence of image-iT™ hypoxia reagent. The results indicated the degradation of HIF-1α after the introduction of ONBs. We propose that ONBs are successful in reversing hypoxia, downregulating HIF-1α, and improving cellular conditions, leading to further medical applications.
Silicon photodetector structure for direct coupling of optical fibers to integrated circuits (1987)

A novel detector structure exhibiting real-estate efficient coupling of optical fibers to semiconductor devices is described. The integrated fiber-optic coupler employs vertical insertion of a tapered single-mode fiber into a laser-etched cylindrical hole in the substrate. It features a small surface footprint, mechanical stability, and accurate alignment. Fabricated in silicon, the p-n junction detectors have typically shown responsivities of 0.23 A/W at 0.63 µm, corresponding to a quantum efficiency of 45 percent, and dark currents below 1 nA.
Structural, optical, and electronic studies of wide-bandgap lead halide perovskites (2015)

Color tunability in mixed Br/Cl lead-based perovskite thin films.
Label‐Free Polypeptide‐Based Enzyme Detection Using a Graphene‐Nanoparticle Hybrid Sensor (2012)

A graphene-nanoparticle (NP) hybrid biosensor that utilizes an electrical hysteresis change to detect the enzymatic activity and concentration of Carboxypeptidase B was developed. The results indicate that the novel graphene-NP hybrid biosensor, utilizing electrical hysteresis, has the ability to detect concentrations of targeted enzyme on the micromolar scale. Furthermore, to the knowledge of the authors, this is the first demonstration of a graphene-based biosensor that utilizes a hysteresis change resulting from metallic NPs assembled on a graphene surface.
20Gb/s 1/4-rate and 40Gb/s 1/8-rate burst-mode CDR circuits in 0.13 &#x03BC;m CMOS (2008)

In this paper, 20Gb/s 1/4-rate and 40Gb/s 1/8-rate burst-mode clock and data recovery (BMCDR) circuits are presented. The proposed inductorless gated digitally-controlled oscillator using a digitally frequency calibration loop is presented. These two BMCDR circuits have been fabricated in 0.13..m CMOS technology. For a PRBS of 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7</sup> -1, the measured peak-to-peak jitter of the recovered clock for the 20Gb/s 1/4-rate and 40Gb/s 1/8-rate BMCDR circuits is 23.8ps and 51ps, respectively.
A highly selective fluorescent chemosensor for guanosine-5′-triphosphate via excimer formation in aqueous solution of physiological pH (2011)

A new water-soluble and fluorescent imidazolium-anthracene cyclophane 1 effectively recognizes and differentiates the biologically important GTP and ATP in 100% aqueous solution of physiological pH 7.4. Fluorescence, (1)H-NMR spectra and ab initio calculations demonstrate that excimer formation and fluorescence enhancement occur upon GTP and ATP binding, respectively, through (C-H)(+)···A(-) hydrogen bond interactions.
Transient severe parkinsonism after acute organophosphate poisoning (1999)

Acute poisonings with organophosphate pesticides occur often. The acute phase is characterised by muscarinergic (miosis, bradycardia, hypotension, dyspnoea, cyanosis, salivation, vomiting, and diarrhoea) and nicotinergic symptoms (fasciculations, cramps, paralysis) as well as multiple central nervous manifestations (headache, anxiety, generalised weakness, confusion, convulsion, and coma) caused by an irreversible inhibition of acetylcholinesterase (AChE). In some patients the acute cholinergic crisis is followed by an intermediate syndrome characterised by weakness of proximal limb muscle, neck flexors, and respiratory muscles and paralysis of motor cranial nerves due to a neuromuscular junctional defect. A delayed polyneuropathy manifested as distal motor polyneuropathy may appear 2 to 3 weeks after poisoning.1 

In addition, a limited number of case studies are available describing extrapyramidal manifestations after acute organophosphate poisoning such as dystonia,1 2 rest tremor,2cog wheel rigidity,2 and choreoathetosis.2-4Only one study describes a case of possible organophosphate induced parkinsonism. However, there was no clear relation between poisoning and extrapyramidal symptoms due to chronic organophosphate exposure and, in addition, numerous episodes of acute intoxication.5 

To our knowledge, no patient has previously been documented presenting with the complete picture of transient severe parkinsonism including bradyphrenia, rigidity, rest tremor, akinesia, impairment of speech and swallowing, and salivation after acute organophosphate intoxication and, in …
Near-field edge fringes at sharp material boundaries (2017)

We have studied the formation of near-field fringes when sharp edges of materials are imaged using scattering-type scanning near-field optical microscope (s-SNOM). The materials we have investigated include dielectrics, metals, a near-perfect conductor, and those that possess anisotropic permittivity and hyperbolic dispersion. For our theoretical analysis, we use a technique that combines full-wave numerical simulations of tip-sample near-field interaction and signal demodulation at higher orders akin to what is done in typical s-SNOM experiments. Unlike previous tip-sample interaction near-field models, our advanced technique allows simulation of the realistic tip and sample structure. Our analysis clarifies edge imaging of recently emerged layered materials such as hexagonal boron nitride and transition metal dichalcogenides (in particular, molybdenum disulfide), as well as traditional plasmonic materials such as gold. Hexagonal boron nitride is studied at several wavelengths, including the wavelength where it possesses excitation of phonon-polaritons and hyperbolic dispersion. Based on our results of s-SNOM imaging in different demodulation orders, we specify resonant and non-resonant types of edges and describe the edge fringes for each case. We clarify near-field edge-fringe formation at material sharp boundaries, both outside bright fringes and the low-contrast region at the edge, and elaborate on the necessity of separating them from propagating waves on the surface of polaritonic materials.
[Study on application of SELDI protein chip technique in diagnosis of systemic lupus erythematosus of yin deficiency caused internal heat syndrome]. (2010)

Significant differences of PBMC protein expression patterns were found between SLE patients of YDHS and healthy persons at times of before, during and after treatment, suggesting that SELDI may be used as a new method to create the diagnosis model, and its application in effecter protein screening, activity scoring and Chinese medicine syndrome type researching are expectable and waiting for further study in depth.
Labscape: a smart environment for the cell biology laboratory (2002)

Labscape is a smart environment that we designed to improve the experience of people who work in a cell biology laboratory. Our goal in creating it was to simplify, laboratory work by making information available where it is needed and by collecting and organizing data where and when it is created into a formal representation that others can understand and process. By helping biologists produce a more complete record of their work with less effort, Labscape is designed to foster improved collaboration in conjunction with increased individual efficiency and satisfaction. A user-driven system, although technologically conservative, embraces a central goal of ubiquitous computing: to enhance the ability to perform domain tasks through fluid interaction with computational resources. Smart environments could soon replace the pen and paper commonly used in the laboratory setting.
PLC advanced technology demonstrator TestChipB (2002)

Rising complexity in ASIC Systems-On-Chip (SOC) has changed the nature of ASIC design and created a tremendous gap between the manufacturing capability and the engineering capability of ASIC designers and users. To solve this, LSI Logic has licensed the Programmable Logic Core (PLC) architecture developed by Adaptive Silicon Inc. This technology will allow ASIC designers to move some portions of the design later in the cycle, even as late as post tape-out. It will also allow for field reprogrammability. A simple test-chip TestChipA containing only the PLC was produced to verify the basic operation of the architecture. This device showed us that the architecture could be produced on an LSI process, but only exposed the physical design portions of the technology to testing. The next step is to develop a complete SOC device utilizing the PLC. This would enable us to rigorously test the methodologies, comb through the documentation and train our engineers to deliver a fully developed and well supported product. This paper describes the PLC architecture as well as the design methodologies needed to develop the test chip named TestChipB.
Improved Audio Embeddings by Adjacency-Based Clustering with Applications in Spoken Term Detection (2018)

Embedding audio signal segments into vectors with fixed dimensionality is attractive because all following processing will be easier and more efficient, for example modeling, classifying or indexing. Audio Word2Vec previously proposed was shown to be able to represent audio segments for spoken words as such vectors carrying information about the phonetic structures of the signal segments. However, each linguistic unit (word, syllable, phoneme in text form) corresponds to unlimited number of audio segments with vector representations inevitably spread over the embedding space, which causes some confusion. It is therefore desired to better cluster the audio embeddings such that those corresponding to the same linguistic unit can be more compactly distributed. In this paper, inspired by Siamese networks, we propose some approaches to achieve the above goal. This includes identifying positive and negative pairs from unlabeled data for Siamese style training, disentangling acoustic factors such as speaker characteristics from the audio embedding, handling unbalanced data distribution, and having the embedding processes learn from the adjacency relationships among data points. All these can be done in an unsupervised way. Improved performance was obtained in preliminary experiments on the LibriSpeech data set, including clustering characteristics analysis and applications of spoken term detection.
Cardiac dysfunction in mice lacking cytochrome-<i>c</i>oxidase subunit VIaH (2002)

Cytochrome-c oxidase subunit VIaH (COXVIaH) has been implicated in the modulation of COX activity. A gene-targeting strategy was undertaken to generate mice that lacked COXVIaH to determine its role in regulation of oxidative energy production and mechanical performance in cardiac muscle. Total COX activity was decreased in hearts from mutant mice, which appears to be a consequence of altered assembly of the holoenzyme COX. However, total myocardial ATP was not significantly different in wild-type and mutant mice. Myocardial performance was examined using the isolated working heart preparation. As left atrial filling pressure increased, hearts from mutant mice were unable to generate equivalent stroke work compared with hearts from wild-type mice. Direct measurement of left ventricular end-diastolic volume using magnetic resonance imaging revealed that cardiac dysfunction was a consequence of impaired ventricular filling or diastolic dysfunction. These findings suggest that a genetic deficiency of COXVIaH has a measurable impact on myocardial diastolic performance despite the presence of normal cellular ATP levels.
Synthesis and calcium antagonistic activity of a new class of 1,4-dihydropyridines having an alkoxyimino group in position 3. (1987)

The synthesis of new 1,4-dihydropyridines having an alkoxyimino group in position 3 is described. Pharmacological evaluation included calcium antagonistic activity in the guinea pig Taenia coli test, acute toxicity and oral antihypertensive activity in SHR. The compounds had a remarkable calcium antagonistic activity in vitro and low toxicity, but no antihypertensive activity in vivo, probably due to an unfavourable pharmacokinetic profile.
Circuit demonstration of radiation hardened chalcogenide non-volatile memory (2004)

BAE SYSTEMS in Manassas, Virginia, and Ovonyx, Inc., have previously reported electrical test results fiom stand-alone single-bit chalcogenide memories. In this paper we present a description of two test chips, one that has been used to integrate the chalcogenide memory element with BAE SYSTEMS' radiation hardened 0.5 pm CMOS technology, and another to develop 64 kbit arrays with full write-read circuitry suitable for environmental and radiation testing. Electrical test results fiom these test chips will be presented showing full functionality.
Modeling and simulating a path planning and obstacle avoidance algorithm for an autonomous robotic vehicle (2009)

Path planning in robotics deals with developing the logic for the navigation of a robot. The implementation details of most previous algorithms are proprietary to specific organizations. The requirement of a customized strategy for collision free and concerted navigation of an all-terrain vehicle (ATV) led to the activities of this research. As a part of this research an algorithm has been developed and visually simulated. The algorithm is evolutionary and capable of path planning for ATVs in the presence of completely known and newly-discovered obstacles. This algorithm helps the ATV model to maneuver in an open field in a specific pattern and avoid obstacles, if any, along its path. The algorithm is implemented and simulated using C and WINAPI. As a result, given the data of known obstacles and the field, the virtually-modeled ATV can maneuver in a systematic and optimum manner towards its goal by avoiding all the obstacles in its path.
Audience aware computational discourse generation for instruction and persuasion (2014)

If we are to take artificial intelligence to the next level, we must further our under-standing of human storytelling, arguably the most salient aspect of human intelli-gence. The idea that the study and understanding of human narrative capability can advance multiple fields, including artificial intelligence, isn&apos;t a new one. The follow-ing, however, is: I claim that the right way to study and understand storytelling is not through the traditional lens of human creativity, aesthetics or even as a plain planning problem, but through formulating storytelling as a question of goal driven social interaction. In particular, I claim that any theory of storytelling must account for the goals of the storyteller and the storyteller&apos;s audience. To take a step toward such an account, I offer a framework, which I call Audi-ence Aware Narrative Generation, drawing inspiration in particular from narratology, cognitive science, and of course, computer science. I propose questions that we need to work on answering, and suggest some rudimentary starter thoughts to serve as guidelines for continued research. I picked a small subset of the proposed questions
Modeling and Design of Cruise Control System with Feedforward for all Terrian Vehicles (2013)

This paper presents PID controller with feed-forward control. The cruise control system is one of the most enduringly popular and important models for control system engineering. The system is widely used because it is very simple to understand and yet the control techniques cover many important classical and modern design methods. In this paper, the mathematical modeling for PID with feed-forward controller is proposed for nonlinear model with disturbance effect. Feed-forward controller is proposed in this study in order to eliminate the gravitational and wind disturbance effect. Simulation will be carried out . Finally, a C++ program written and feed to the microcontroller type AMR on our robot
The consequences of genetic drift for bacterial genome complexity (2009)

Genetic drift, which is particularly effective within small populations, can shape the size and complexity of genomes by affecting the fixation of deleterious mutations. In Bacteria, assessing the contribution of genetic drift to genome evolution is problematic because the usual methods, based on intraspecific polymorphisms, can be thwarted by difficulties in delineating species' boundaries. The increased availability of sequenced bacterial genomes allows application of an alternative estimator of drift, the genome-wide ratio of replacement to silent substitutions in protein-coding sequences. This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria.
TOR and ageing: a complex pathway for a complex process (2010)

Studies in invertebrate model organisms have led to a wealth of knowledge concerning the ageing process. But which of these discoveries will apply to ageing in humans? Recently, an assessment of the degree of conservation of ageing pathways between two of the leading invertebrate model organisms, Saccharomyces cerevisiae and Caenorhabditis elegans, was completed. The results (i) quantitatively indicated that pathways were conserved between evolutionarily disparate invertebrate species and (ii) emphasized the importance of the TOR kinase pathway in ageing. With recent findings that deletion of the mTOR substrate S6K1 or exposure of mice to the mTOR inhibitor rapamycin result in lifespan extension, mTOR signalling has become a major focus of ageing research. Here, we address downstream targets of mTOR signalling and their possible links to ageing. We also briefly cover other ageing genes identified by comparing worms and yeast, addressing the likelihood that their mammalian counterparts will affect longevity.
A random forest method for real-time price forecasting in New York electricity market (2014)

This paper mainly focuses on the real-time price forecasting in New York electricity market through random forest. Accurate forecasting is regarded as the most practical way to win power bid in today's highly competitive electricity market. Comparing with existing price forecasting methods, random forest, as a newly introduced method, will provide a price probability distribution, which will allow the users to estimate the risks of their bidding strategy and also making the results helpful for later industrial using. Furthermore, the model can adjust to the latest forecasting condition, i.e. the latest climatic, seasonal and market condition, by updating the random forest parameters with new observations. This adaptability avoids the model failure in a climatic or economic condition different from the training set. A case study in New York HUD VL area is presented to evaluate the proposed model.
Studies Towards a Synthesis of AI‐77‐B. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Specificity of Binding of Single-Stranded DNA-Binding Protein to Its Target (2012)

Single-stranded DNA-binding proteins (SSBs) bind single-stranded DNA (ssDNA) and participate in all genetic processes involving ssDNA, such as replication, recombination, and repair. Here we applied atomic force microscopy to directly image SSB-DNA complexes under various conditions. We used the hybrid DNA construct methodology in which the ssDNA segment is conjugated to the DNA duplex. The duplex part of the construct plays the role of a marker, allowing unambiguous identification of specific and nonspecific SSB-DNA complexes. We designed hybrid DNA substrates with 5'- and 3'-ssDNA termini to clarify the role of ssDNA polarity on SSB loading. The hybrid substrates, in which two duplexes are connected with ssDNA, were the models for gapped DNA substrates. We demonstrated that Escherichia coli SSB binds to ssDNA ends and internal ssDNA regions with the same efficiency. However, the specific recognition by ssDNA requires the presence of Mg(2+) cations or a high ionic strength. In the absence of Mg(2+) cations and under low-salt conditions, the protein is capable of binding DNA duplexes. In addition, the number of interprotein interactions increases, resulting in the formation of clusters on double-stranded DNA. This finding suggests that the protein adopts different conformations depending on ionic strength, and specific recognition of ssDNA by SSB requires a high ionic strength or the presence of Mg(2+) cations.