gebhart/patrepeval huggingface dataset:
Recommending Concepts to Experts: An Exploration of Recommender Techniques for Collaborative Ontology Engineering Platforms in the Biomedical Domain (2012)

Biomedical ontologies such as the 11 th revision of the International Classification of Diseases and others are increasingly produced with the help of collaborative ontology engineering platforms that facilitate cooperation and coordination among a large number of users and contributors. While collaborative approaches to engineering biomedical ontologies can be expected to yield a number of advantages, such as increased participation and coverage, they come with a number of novel challenges and risks. For example, they might suffer from low participation, lack of coordination, lack of control or other related problems that are neither well understood nor addressed by the current state of research. In this paper, we aim to tackle some of these problems by exploring techniques for recommending concepts to experts on collaborative ontology engineering platforms. In detail, this paper will (i) discuss different recommendation techniques from the literature (ii) map and apply these categories to the domain of collaboratively engineered biomedical ontologies and (iii) present prototypical implementations of selected recommendation techniques as a proof-of-concept. 1
Observation of two-step excitation of photoluminescence in silicon nanostructures (1998)

Efficient visible-range photoluminescence with photon energy higher than the photon energy of the exciting radiation is observed in nanostructures of porous silicon subjected to heat treatment in vacuum. The photoluminescence intensity is found to be virtually identical for cw and femtosecond excitation by Ti:sapphire laser radiation with the same average power. The results can be explained by a two-step cascade photoluminescence excitation process in which optical passivation of defects of the dangling silicon bond type occurs.
Dengue: the risk to developed and developing countries. (1994)

Dengue viruses are members of the Flaviviridae, transmitted principally in a cycle involving humans and mosquito vectors. In the last 20 years the incidence of dengue fever epidemics has increased and hyperendemic transmission has been established over a geographically expanding area. A severe form, dengue hemorrhagic fever (DHF), is an immunopathologic disease occurring in persons who experience sequential dengue infections. The risk of sequential infections, and consequently the incidence of DHF, has risen dramatically, first in Asia and now in the Americas. At the root of the emergence of dengue as a major health problem are changes in human demography and behavior, leading to unchecked populations of and increased exposure to the principal domestic mosquito vector, Aedes aegypti. Virus-specified factors also influence the epidemiology of dengue. Speculations on future events in the epidemiology, evolution, and biological expression of dengue are presented.
The Putative Tumor Suppressors EXT1 and EXT2 Are Glycosyltransferases Required for the Biosynthesis of Heparan Sulfate (1998)

Hereditary multiple exostoses, characterized by multiple cartilaginous tumors, is ascribed to mutations at three distinct loci, denoted EXT1-3. Here, we report the purification of a protein from bovine serum that harbored the D-glucuronyl (GlcA) and N-acetyl-D-glucosaminyl (GlcNAc) transferase activities required for biosynthesis of the glycosaminoglycan, heparan sulfate (HS). This protein was identified as EXT2. Expression of EXT2 yielded a protein with both glycosyltransferase activities. Moreover, EXT1, previously found to rescue defective HS biosynthesis (McCormick, C., Leduc, Y., Martindale, D., Mattison, K., Esford, L. E., Dyer, A. P., and Tufaro, F. (1998) Nat. Genet. 19, 158-161), was shown to elevate the low GlcA and GlcNAc transferase levels of mutant cells. Thus at least two members of the EXT family of tumor suppressors encode glycosyltransferases involved in the chain elongation step of HS biosynthesis.
Automated directory listing retrieval system based on isolated word recognition (1980)

Automated directory listing retrieval has been a goal of the Bell System and others for a long time. Recent attempts at implementing such a system relied on button pushing on the part of the user. Since the Touch-Tone <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> keyboard does not contain a unique key corresponding to each letter of the alphabet, the button pushing system had some drawbacks. In an attempt to alleviate these problems and to provide a more natural form of communication for the user, the use of spoken spelled names was proposed in place of pushing buttons. An early form of this directory listing retrieval system was a speaker trained system (i.e., it had to be trained to each user individually) and it used a simplified directory search algorithm. Subsequent improvements and modifications to both the recognition algorithm and the directory search procedure have led to the current implementation in which the overall system is speaker independent and can automatically find the name (or names) in the directory which provides the best acoustic match to the spoken name. The new system can automatically detect and correct simple (i.e., single letter) anomalies in the spelling of the name, including letter substitutions, inversions, deletions, and insertions. If a conflict in the detected name occurs (e.g., 2 or more names with the same or close acoustic distance scores), the system automatically requests additional information to help resolve the ambiguity. In evaluational tests on an 18 000 name Bell Laboratories directory, the directory listing retrieval system found the unique correct name in 98.3 percent of the trials, on average, even though the acoustic recognizer provided the correct letters only about 70 percent of the time.
The relationship between synovitis and erosions in rheumatoid arthritis (1997)

If clinically evident synovitis causes erosions, then the two should be highly correlated within individual joints. Separate hand joints (total 2064) were examined for the presence of synovitis (the simultaneous presence of soft-tissue swelling and tenderness) on nine occasions over 2 yr. The cumulative synovitis score was compared to the change in the Larsen score over the same period. The mean correlation between synovitis and erosion progression was r = 0.248 (explained variance = 6%). Of the 216 joints which showed progressive X-ray damage, 44% had a cumulative synovitis score of < 3. When all the joints of one hand were taken together, the correlation was increased to r = 0.418 and for all the joints of both hands taken together it was further increased to r = 0.424. These results argue against there being a direct causal relationship between clinically inflamed synovitis and erosions in rheumatoid arthritis, and question the assumption that erosions and the signs of synovitis represent the same pathological process.
Third International Conference on Cancer Vaccines/Adjuvants/Delivery for the Next Decade (CVADD 2009) (2010)

The Third International Conference on Cancer Vaccines/Adjuvants/Delivery for the Next Decade (CVADD), chaired by Malcolm S Mitchell, was hosted in Dublin, Ireland, on 11-13 November 2009. The conference was intended to aid the translation of basic research into clinical progress and to bridge the gap between academia and industrial innovation. In total, 44 speakers gave presentations on preclinical and clinical vaccine development, mostly focusing on cancer vaccination. The present report does not represent a comprehensive review of all topics covered, but highlights selected points of particular novelty and interest. Within the field of cancer vaccines, the considerable discrepancy between high immune response rates and limited clinical effects has led to increased focus on how vaccines may best be applied to maximize their clinical impact. This challenge emerged at the forefront of the conference, reflected by fruitful discussions on adjuvants, delivery systems, strategies for countering tumor tolerance and on combination with conventional therapy. The studies presented at CVADD 2009 support the argument for combining active immunization with agents countering tumor tolerance and with conventional cancer treatment, while also pointing to a need for improved knowledge on how to develop these multimodal regimes.
Helicobacter pyloriInfection and Gastric Carcinoma among Japanese Americans in Hawaii (1991)

Infection with H. pylori is strongly associated with an increased risk of gastric carcinoma. However, most persons infected with H. pylori will never have gastric carcinoma. Therefore, other factors that increase the risk of gastric carcinoma among persons infected with H. pylori need to be identified.
Millimeter-Wave Self-Healing Power Amplifier With Adaptive Amplitude and Phase Linearization in 65-nm CMOS (2012)

A self-healing two-stage millimeter-wave broadband power amplifier (PA) with on-chip amplitude/phase compensation is realized in 65-nm CMOS. The amplitude and phase compensations are accomplished by using feedback bias/capacitive schemes to extend the linear operation region and optimize the PA efficiency. Tunable control knobs are inserted in the linearization block to enhance the PA performance yield against process/temperature variations and device ageing effects. This prototype shows a 5.5-dB improvement of the output 1-dB compression point ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">P</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1dB</sub> ) and a less than 2% chip-to-chip gain variation. At a 1-V supply, the differential PA achieves a saturation output power ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">P</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sat</sub> ) of 14.85 dBm with a peak power-added-efficiency (PAE) of 16.2%. With the amplitude compensation, <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">P</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1dB</sub> is increased to 13.7 dBm. With the phase compensation, the output phase variation is decreased to less than 0.5°. To the best of our knowledge, this prototype provides the highest <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">P</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sat</sub> and <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">P</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1dB</sub> with simultaneously high PAE from a single PA reported to date. The PA delivers a linear gain of 9.7 dB and has a 7-GHz 3-dB bandwidth from 55.5 to 62.5 GHz with a compact total area of 0.042 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Triggering receptor expressed on myeloid cell-like transcript 2 (TLT-2) is a counter-receptor for B7-H3 and enhances T cell responses (2008)

The B7 family member B7-H3 (CD276) plays important roles in immune responses. However, the function of B7-H3 remains controversial. We found that murine B7-H3 specifically bound to Triggering receptor expressed on myeloid cells (TREM)-like transcript 2 (TLT-2, TREML2). TLT-2 was expressed on CD8(+) T cells constitutively and on activated CD4(+) T cells. Stimulation with B7-H3 transfectants preferentially up-regulated the proliferation and IFN-gamma production of CD8(+) T cells. Transduction of TLT-2 into T cells resulted in enhanced IL-2 and IFN-gamma production via interactions with B7-H3. Blockade of the B7-H3:TLT-2 pathway with a mAb against B7-H3 or TLT-2 efficiently inhibited contact hypersensitivity responses. Our results demonstrate a direct interaction between B7-H3 and TLT-2 that preferentially enhances CD8(+) T cell activation.
A Single-Clock Asynchronous Input COSL Set-Reset Flip-Flop and SFQ to Voltage State Interface (2005)

Although published research in COSL has stagnated, it remains a useful logic family for interfacing the much faster RSFQ family to hot-logic circuits. COSL has always been plagued by the absence of latches, and previous attempts at implementing such latches were clumsy. A new COSL Set-Reset flip-flop is discussed here, and results shown. This asynchronous input latch, which can also be configured as a T flip-flop, can function on a single-phase clock. It was also adapted to convert SFQ output pulses from RSFQ logic circuits to voltage state levels that can be viewed on standard laboratory oscilloscopes. Due to the asynchronous nature of the inputs, the RSFQ-COSL converter is also more reliable than earlier DRO-to-COSL elements.
Two-Dimensional Electronic Correlation and Relaxation Spectra:  Theory and Model Calculations (1999)

Hybl et al. demonstrated a technique for recording two-dimensional Fourier transform electronic correlation and relaxation spectra based on detecting phase modulation of the signal electric field in a noncollinear femtosecond four-wave mixing experiment. A theoretical analysis of 2D correlation and relaxation experiments is presented for a system consisting of two electronic states each having two or more sublevels. The separation between absorption and dispersion mode 2D spectra in these experiments is investigated in detail for nonzero pulse duration and compared to related 2D NMR experiments based on a nonlinear optical definition of coherence order. Phase-twisted peaks, which mix absorption and dispersion line shapes, can occur under some circumstances. A 1D projection of the complex 2D spectrum is shown to equal the transient grating signal field, and the real part of this projection is related to the spectrally resolved pump−probe signal. Calculated 2D spectra for a two-level Bloch model, an underdamped Brownian oscillator, and a few models of polar solvent dynamics based on the correlation function approach to the nonlinear response developed by Mukamel and co-workers are presented. The real parts of the 2D spectra are primarily positive (indicative of ground state bleaching and excited state emission) but contain negative regions arising from excitation of coherent superposition states (e.g. vibrational wavepackets) in both the ground and excited electronic states. Assignment of the 2D spectra displaying wavepacket motion at the vibronic level is discussed, and the manifestations of wavepacket motion and vibrational relaxation in the 2D spectra are explored. As suggested by Hybl et al., an increase in pulse duration is found to affect a 2D spectrum primarily as a spectral filter that limits the range of the spectrum. The Gaussian correlation function characteristic of inertial solvent motion is found to be faithfully reflected in a homogeneous 2D cross width which is nearly independent of pulse duration. An alternative experimental method for obtaining only the real part of 2D spectra is proposed.
Fader Networks: Manipulating Images by Sliding Attributes (2017)

This paper introduces a new encoder-decoder architecture that is trained to reconstruct images by disentangling the salient information of the image and the values of attributes directly in the latent space. As a result, after training, our model can generate different realistic versions of an input image by varying the attribute values. By using continuous attribute values, we can choose how much a specific attribute is perceivable in the generated image. This property could allow for applications where users can modify an image using sliding knobs, like faders on a mixing console, to change the facial expression of a portrait, or to update the color of some objects. Compared to the state-of-the-art which mostly relies on training adversarial networks in pixel space by altering attribute values at train time, our approach results in much simpler training schemes and nicely scales to multiple attributes. We present evidence that our model can significantly change the perceived value of the attributes while preserving the naturalness of images.
Review of FINFET technology (2009)

In view of the difficulties in planar CMOS transistor scaling to preserve an acceptable gate to channel control FINFET based multi-gate (MuGFET) devices have been proposed as a technology option for replacing the existing technology. The attractiveness of FINFET consists in the realization of self-aligned double-gate devices with a conventional CMOS process. This allows extending the gate scaling beyond the planar transitor limits, maintaining a steep subthreshold slope, better performance with bias voltage scaling and good matching due to low doping concentration in the channel. There are, however, several challenges and roadblocks that FINFET technology has to face to be competitive with other technology options: high access resistance related to the extremely thin body, V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">tau</sub> setting, implementation of strain boosters and manufacturability related to the non planar process and very tight process control.
Lipid Solubility and Drug Penetration of the Blood Brain Barrier (1974)

SummaryLipid/water partition coefficients of 19 radiolabeled drugs were correlated with uptake by brain during a single microcirculatory passage following carotid arterial injection. Uptake was measured relative to a simultaneously injected diffusible reference. When the lipid/ water partition coefficient was greater than about 0.03 a substantial fraction of the drug penetrated the blood-brain barrier and for most drugs above this range, uptake was essentially complete. These data suggest there is probably little reason to greatly exceed this degree of lipid solubility when designing drugs for blood-brain barrier penetration and central nervous system effects.Valuable discussions with Dr. Arthur K. Cho and Dr. Jared M. Diamond are acknowledged. Helpful suggestions from Mrs. Stella Z. Oldendorf were received, and technical assistance was provided by Mrs. Shigeyo Hyman and Mr. Leon Braun. Support is also acknowledged from the NIH-NINDS Project Grant No. NS 8711 and the Veterans Administration.
A Novel Set of DNA Methylation Markers in Urine Sediments for Sensitive/Specific Detection of Bladder Cancer (2007)

Methylation profiling of an 11-gene set in urine sediments provides a sensitive and specific detection of bladder cancer.
Transcriptional and Translational Control in the Mammalian Unfolded Protein Response (2002)

Cells monitor the physiological load placed on their endoplasmic reticulum (ER) and respond to perturbations in ER function by a process known as the unfolded protein response (UPR). In metazoans the UPR has a transcriptional component that up-regulates expression of genes that enhance the capacity of the organelle to deal with the load of client proteins and a translational component that insures tight coupling between protein biosynthesis on the cytoplasmic side and folding in the ER lumen. Together, these two components adapt the secretory apparatus to physiological load and protect cells from the consequences of protein malfolding.
Probability Distribution of Majorana End-State Energies in Disordered Wires (2011)

One-dimensional topological superconductors harbor Majorana bound states at their ends. For superconducting wires of finite length L, these Majorana states combine into fermionic excitations with an energy ε(0) that is exponentially small in L. Weak disorder leaves the energy splitting exponentially small, but affects its typical value and causes large sample-to-sample fluctuations. We show that the probability distribution of ε(0) is log normal in the limit of large L, whereas the distribution of the lowest-lying bulk energy level ε(1) has an algebraic tail at small ε(1). Our findings have implications for the speed at which a topological quantum computer can be operated.
Cellular network design and smart antenna systems (2002)

Using switched narrow-beam antenna systems allows a frequency planner greater flexibility in designing a cellular system. In addition to flexible sector sizes, more precise traffic data is available. By studying the amount of time particular beams or antennas are being used, the probability of having an unacceptable interference condition can be determined. As a result of having improved interference reduction and more detailed system information, aggressive frequency reuse is possible. Field results confirm theoretical calculations and show that it is possible to increase the system capacity by having aggressive frequency reuse without degrading network switch statistics.
Biomimetic technique for adhesion-based collection and separation of cells in a microfluidic channel (2004)

A basic step in many biological assays is separating and isolating different types of cells from raw samples. To better meet these requirements in microfluidic devices for miniature biomedical analytical systems, an alternative method for separating cells has been devised by mimicking the physiological process of leukocyte recruitment to blood vessel walls: adhesive cell rolling and transient tethering. Reproducing these interactions for cells on surfaces of microstructured fluidic channels can serve to capture and concentrate cells and even to fractionate different cell types from a continuously flowing sample. To demonstrate this principle, two designs for microstructured fluidic channels were fabricated: an array of Square pillars and another with slender, Offset pillars. These structures were coated with E-selectin IgG chimera and the interactions of HL-60 and U-937 cells with these structures were characterized. With inflow of fluidic cell suspensions, the structures were able to efficiently capture and arrest cells directly from the rapid free stream flow. After capture, cells transit through the channel in three phases: cell rolling, cell tethering, and transient re-suspension in free stream flow before re-capture. Under these interactions, captured cells were enriched several hundred-fold from the original concentration. Additionally, among collected cells, the difference in flow-driven, adhesion-mediated cell transit in the Square design suggested that the two cell types could at least be partially fractionated.