gebhart/patrepeval huggingface dataset:
Single cell on-chip whole genome amplification via micropillar arrays for reduced amplification bias (2018)

Single cell whole genome amplification is susceptible to amplification biases that impact the accuracy of single cell sequencing data. To address this, we have developed a microfluidic device for the isolation and purification of genomic DNA from individual cells. The device uses a micropillar array to physically capture single cells and its chromosomal DNA upon extraction. The extracted DNA is immobilized within the micropillar array in a way that allows isothermal amplification. In this system, whole genome amplification of the single cell is carried out under a continual fluid flow within the microfluidic channel. We have demonstrated the process for amplification of individual human cancer cell genomes from the HeLa cell line. By sampling select gene loci along the human genome and performing whole exome sequencing, we demonstrate improved genome coverage and reduced amplification bias compared to amplification of single cells deposited in wells by fluorescence activated cell sorting.
Modal-insensitive biconical-taper couplers (1982)

A method for fabricating optical-fiber fused biconical-taper couplers that have coupling ratios insensitive to the modal distribution of light in the input fiber arms is demonstrated. Comparison measurements of the performance of these couplers and those made by the previous technique are presented and discussed.
Estimating Object Proper Motion Using Optical Flow, Kinematics, and Depth Information (2008)

For the interaction of a mobile robot with a dynamic environment, the estimation of object motion is desired while the robot is walking and/or turning its head. In this paper, we describe a system which manages this task by combining depth from a stereo camera and computation of the camera movement from robot kinematics in order to stabilize the camera images. Moving objects are detected by applying optical flow to the stabilized images followed by a filtering method, which incorporates both prior knowledge about the accuracy of the measurement and the uncertainties of the measurement process itself. The efficiency of this system is demonstrated in a dynamic real-world scenario with a walking humanoid robot.
Electronic dura mater for long-term multimodal neural interfaces (2015)

The mechanical mismatch between soft neural tissues and stiff neural implants hinders the long-term performance of implantable neuroprostheses. Here, we designed and fabricated soft neural implants with the shape and elasticity of dura mater, the protective membrane of the brain and spinal cord. The electronic dura mater, which we call e-dura, embeds interconnects, electrodes, and chemotrodes that sustain millions of mechanical stretch cycles, electrical stimulation pulses, and chemical injections. These integrated modalities enable multiple neuroprosthetic applications. The soft implants extracted cortical states in freely behaving animals for brain-machine interface and delivered electrochemical spinal neuromodulation that restored locomotion after paralyzing spinal cord injury.
Cerenkov Radiation in Photonic Crystals (2003)

In a conventional material, the coherent Cerenkov radiation due to a moving charged particle is associated with a velocity threshold, a forward-pointing radiation cone, and a forward direction of emission. We describe different behavior for the Cerenkov radiation in a photonic crystal. In particular, this radiation is intrinsically coupled with transition radiation and is observable without any threshold. Within one particle-velocity range, we found a radiation pattern with a backward-pointing radiation cone. In another velocity range, backward-propagating Cerenkov radiation can be expected. Potential applications include velocity-sensitive particle detection and radiation generation at selectable frequencies.
Remarkably similar antigen receptors among a subset of patients with chronic lymphocytic leukemia (2004)

Studies of B cell antigen receptors (BCRs) expressed by leukemic lymphocytes from patients with B cell chron- ic lymphocytic leukemia (B-CLL) suggest that B lymphocytes with some level of BCR structural restriction become transformed. While analyzing rearranged VHDJH and VLJL genes of 25 non–IgM-producing B-CLL cases, we found five IgG+ cases that display strikingly similar BCRs (use of the same H- and L-chain V gene segments with unique, shared heavy chain third complementarity-determining region [HCDR3] and light chain third complementarity-determining region [LCDR3] motifs). These H- and L-chain characteristics were not identified in other B-CLL cases or in normal B lymphocytes whose sequences are available in the public databases. Three-dimensional modeling studies suggest that these BCRs could bind the same antigenic epi- tope. The structural features of the B-CLL BCRs resemble those of mAb’s reactive with carbohydrate deter- minants of bacterial capsules or viral coats and with certain autoantigens. These findings suggest that the B lymphocytes that gave rise to these IgG+ B-CLL cells were selected for this unique BCR structure. This selec- tion could have occurred because the precursors of the B-CLL cells were chosen for their antigen-binding capabilities by antigen(s) of restricted nature and structure, or because the precursors derived from a B cell subpopulation with limited BCR heterogeneity, or both.
Structure and functional expression of the acid-labile subunit of the insulin-like growth factor-binding protein complex. (1992)

Nearly all of the insulin-like growth factor (IGF) in the circulation is bound in a heterotrimeric complex composed of IGF, IGF-binding protein-3, and the acid-labile subunit (ALS). Full-length clones encoding ALS have been isolated from human liver cDNA libraries by using probes based on amino acid sequence data from the purified protein. These clones encode a mature protein of 578 amino acids preceded by a 27-amino acid hydrophobic sequence indicative of a secretion signal. Expression of the cDNA clones in mammalian tissue culture cells results in the secretion into the culture medium of ALS activity that can form the expected complex with IGF-I and IGF-binding protein-3. The amino acid sequence of ALS is largely composed of 18-20 leucine-rich repeats of 24 amino acids. These repeats are found in a number of diverse proteins that, like ALS, participate in protein-protein interactions.
U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer’s disease (2013)

Deposition of insoluble protein aggregates is a hallmark of neurodegenerative diseases. The universal presence of β-amyloid and tau in Alzheimer's disease (AD) has facilitated advancement of the amyloid cascade and tau hypotheses that have dominated AD pathogenesis research and therapeutic development. However, the underlying etiology of the disease remains to be fully elucidated. Here we report a comprehensive study of the human brain-insoluble proteome in AD by mass spectrometry. We identify 4,216 proteins, among which 36 proteins accumulate in the disease, including U1-70K and other U1 small nuclear ribonucleoprotein (U1 snRNP) spliceosome components. Similar accumulations in mild cognitive impairment cases indicate that spliceosome changes occur in early stages of AD. Multiple U1 snRNP subunits form cytoplasmic tangle-like structures in AD but not in other examined neurodegenerative disorders, including Parkinson disease and frontotemporal lobar degeneration. Comparison of RNA from AD and control brains reveals dysregulated RNA processing with accumulation of unspliced RNA species in AD, including myc box-dependent-interacting protein 1, clusterin, and presenilin-1. U1-70K knockdown or antisense oligonucleotide inhibition of U1 snRNP increases the protein level of amyloid precursor protein. Thus, our results demonstrate unique U1 snRNP pathology and implicate abnormal RNA splicing in AD pathogenesis.
Pigments to Reflect the Infrared Radiation From Fire (1995)

Conventional paints transmit or absorb most of the intense infrared radiation emitted by fire, a fact that contributes to the spread of fire. Techniques used for design of coatings with high visible reflectivity are here adapted to the design of coatings that have high reflectivity in the 1 to 8 μm wavelength range important in fires. Promising materials for pigments include titanium dioxide, iron oxide, chromium oxide, and silicon, with particle diameters in the 1 to 2 μm range. Aluminum flake pigments are also effective. Pigment synthesis by the deposition of coatings on mica flakes is briefly discussed.
The Use of Primidone in Neonates With Theophylline-Resistant Apnea (1993)

Primidone represents a possible adjuvant therapy in theophylline-resistant apnea of prematurity. Caution is advised, because of primidone's complex pharmacologic characteristics, until there are further controlled prospective studies.
Influence of Phosphatidylethanolamine Concentration and Composition on the Detection of Antiphosphatidylethanolamine Antibodies by ELISA (2016)

These data raised the possibility of ultimately replacing natural PE antigens with a blend of defined synthetic lipid species, thus overcoming a known variable factor in aPE detection. The outcome of this study will help pave the way to developing a standardized aPE test.
A Cancer-Associated Galactosyltransferase Isoenzyme (1978)

In this note the H8 control problem with measurement feedback is investigated. It is well-known that for this problem, in general, we need controllers of the same dynamic order as the given system. However, in the case that some entries of the measurement vector are not noise-corrupted, we show that one can find dynamic compensators of a lower dynamical order. Note that this implies that the standard assumptions on the direct feedthrough matrices, as made in most papers on H8 control, are not satisfied. Our result can be derived by using reduced order observer based controllers.
Directed Placement for mVLSI Devices (2019)

Continuous-flow microfluidic devices based on integrated channel networks are becoming increasingly prevalent in research in the biological sciences. At present, these devices are physically laid out by hand by domain experts who understand both the underlying technology and the biological functions that will execute on fabricated devices. The lack of a design science that is specific to microfluidic technology creates a substantial barrier to entry. To address this concern, this article introduces Directed Placement, a physical design algorithm that leverages the natural “directedness” in most modern microfluidic designs: fluid enters at designated inputs, flows through a linear or tree-based network of channels and fluidic components, and exits the device at dedicated outputs. Directed placement creates physical layouts that share many principle similarities to those created by domain experts. Directed placement allows components to be placed closer to their neighbors compared to existing layout algorithms based on planar graph embedding or simulated annealing, leading to an average reduction in laid-out fluid channel length of 91% while improving area utilization by 8% on average. Directed placement is compatible with both passive and active microfluidic devices and is compatible with a variety of mainstream manufacturing technologies.
Method for varying the spring rigidity of an elastomer mount, and a corresponding mount (1993)

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Measurements of adhesive bondline effective thermal conductivity and thermal resistance using the laser flash method (2003)

Thermal modeling of device packages requires accurate thermophysical property data for package materials. Accurate data for the thermal resistance of the adhesive bondline used to attach a high power device to a substrate is critical because this thermal resistance can be a significant part of the total thermal resistance in the heat flow path from the device junction to the package case or ambient. The bondline thermal resistance can in principle be calculated by dividing the expected or measured bondline thickness by the adhesive thermal conductivity measured on a free-standing cured sample. However, at a typical bondline thickness of 15-75 /spl mu/m, the contact thermal resistance between the adhesive and its adherents can be significant compared to the intrinsic thermal resistance of the adhesive and thus cannot be ignored. Also, the thermal conductivity measured on a free-standing cured sample may not be equivalent to the thermal conductivity of the adhesive in the bonded assembly. This paper investigates some of the variables that determine adhesive bondline effective thermal conductivity and contact resistance. The results of multilayer laser flash diffusivity measurements are presented for a range of available adhesives in "sandwich" sample assemblies that simulate the package. Thermal conductivity measurements of the free-standing adhesives are also obtained by the laser flash method.
Price-based friendly jamming in a MISO interference wiretap channel (2016)

In this paper, we expand the scope of PHY-layer security by investigating TX-based friendly jamming (FJ) for the wiretap channel in multi-link settings. For the single-link scenario, creating a TX-based FJ is an effective and practical method in improving the secrecy rate. In a multi-link setting, several information signals must be transmitted simultaneously. Thus, the design must guarantee that the FJ signal of a given transmitter does not interfere with unintended but legitimate receivers. Under the assumption of exact knowledge of the eavesdropping channel, we first propose a distributed price-based approach to improve the secrecy sum-rate of a two-link network with one eavesdropper while satisfying an information-rate constraint for both link. Simulations show that price-based FJ control outperforms greedy FJ, and is close to the performance of a centralized approach. Next, we propose a method based on mixed strategic games that can offer robust solutions to the distributed secrecy sum-rate maximization problem under the assumption of an unknown eavesdropping channel. Lastly, we use simulations to show that in addition to outperforming the greedy approach, our robust optimization also satisfies practical network considerations. In particular, the transmission time for the robust optimization can be determined flexibly to match the channel's coherence time.
High Capacity Color Barcodes: Per Channel Data Encoding via Orientation Modulation in Elliptical Dot Arrays (2010)

We present a new high capacity color barcode. The barcode we propose uses the cyan, magenta, and yellow (C,M,Y) colorant separations available in color printers and enables high capacity by independently encoding data in each of these separations. In each colorant channel, payload data is conveyed by using a periodic array of elliptically shaped dots whose individual orientations are modulated to encode the data. The orientation based data encoding provides beneficial robustness against printer and scanner tone variations. The overall color barcode is obtained when these color separations are printed in overlay as is common in color printing. A reader recovers the barcode data from a conventional color scan of the barcode, using red, green, and blue (R,G,B) channels complementary, respectively, to the print C, M, and Y channels. For each channel, first the periodic arrangement of dots is exploited at the reader to enable synchronization by compensating for both global rotation/scaling in scanning and local distortion in printing. To overcome the color interference resulting from colorant absorptions in noncomplementary scanner channels, we propose a novel interference minimizing data encoding approach and a statistical channel model (at the reader) that captures the characteristics of the interference, enabling more accurate data recovery. We also employ an error correction methodology that effectively utilizes the channel model. The experimental results show that the proposed method works well, offering (error-free) operational rates that are comparable to or better than the highest capacity barcodes known in the literature.
GainNAs / InP Tensile-Strained Bulk Polarization-Insensitive SOA (2006)

A GaInNAs / InP tensile-strained bulk polarization-insensitive SOA was developed for the first time. It exhibited a red shift of gain peak, 50 nm, resulting in a low gain tilt of 1.5 dB in the wavelength of 1530-1570 nm.
Four chimpanzee monoclonal antibodies that neutralize hepatitis A virus (2003)

Chimpanzee immunoglobulins are virtually identical to human immunoglobulins and thus may have clinically useful applications. in a recent manuscript we described 4 chimpanzee monoclonal antibodies (MAbs) that neutralized hepatitis A virus (HAV) (1). The MAbs were isolated from a combinatorial cDNA library of chimpanzee gamma1/kappa antibody genes using bacteriophage displaying Fab fragments on their surfaces. Three of the MAbs recognized the same or overlapping epitopes on the HAV capsid, whereas the fourth recognized a different, nonoverlapping epitope on the capsid. All 4 MAbs neutralized the homologous HAV strain, HM-175, in a radioimmunofocus assay and 2 of the 4 MAbs. neutralized a heterologous simian HAV strain. AGM-27. From these data. we conclude that the MAbs must recognize at least 3 epitopes on the HAV capsid. Competition assays performed with neutralizing murine MAbs suggested that 3 of the chimpanzee MAbs recognized epitopes on the HAV capsid which have not been defined previously. it is hoped that these MAbs may be used directly in passive immunoprophylaxis to prevent hepatitis A in susceptible populations, e.g., travelers to legions where HAV is endemic or at risk individuals where epidemics are occurring.
Rate control and stream adaptation for scalable video streaming over multiple access networks (2010)

In a multihomed video streaming system, a video sequence is simultaneously transmitted over multiple access networks to a client. In this paper, we formulate the rate control and stream adaptation problems into a unified optimization problem, which determines the sending rates of individual networks, selects which video packets to transmit, and assigns each packet to an access network. We propose two heuristic algorithms with a trade-off between optimality and computational complexity. One of the proposed algorithms runs faster, while the other one results in better video quality. We propose a hybrid algorithm that demonstrates a good balance between optimality and computational complexity. We conduct extensive packet-level simulations to evaluate our algorithms using real network conditions and actual scalable video streams. We compare our algorithms against the rate control algorithms defined in the Datagram Congestion Control Protocol (DCCP) standard. The simulation results show that our algorithms significantly outperform current systems while being TCP-friendly. Our algorithms achieve at least 10 dB quality improvement over DCCP and result in up to 83% packet delivery delay reduction.
Sm-p80-based schistosomiasis vaccine mediated epistatic interactions identified potential immune signatures for vaccine efficacy in mice and baboons (2017)

Schistosomiasis is a neglected parasitic disease of major public health concern as it affects over 250 million people in developing countries. Currently there is no licensed vaccine available against schistosomiasis. The Schistosoma mansoni calpain protein, Sm-p80, is a leading vaccine candidate now ready to move to clinical trials. In order to better assess Sm-p80 vaccine immunogenicity; here we used a systems biology approach employing RNA-sequencing to identify gene signatures and epistatic interactions following Sm-p80 vaccination in mouse and baboon models that may predict vaccine efficacy. Recombinant Sm-p80 + CpG-oligodeoxynucleotide (ODN) vaccine formulation induced both cellular and humoral immunity genes with a predominant TH1 response as well as TH2 and TH17 gene signatures. Early gene responses and gene-network interactions in mice immunized with rSm-p80 + ODN appear to be initiated through TLR4 signaling. CSF genes, S100A alarmin genes and TNFRSF genes appear to be a signature of vaccine immunogenicity/efficacy as identified by their participation in gene network interactions in both mice and baboons. These gene families may provide a basis for predicting desirable outcomes for vaccines against schistosomiasis leading to a better understanding of the immune system response to vaccination.
Lymphoproliferative Disorders with Early Lethality in Mice Deficient in <i>Ctla-4</i> (1995)

The role of the cell-surface molecule CTLA-4 in the regulation of T cell activation has been controversial. Here, lymph nodes and spleens of CTLA-4-deficient mice accumulated T cell blasts with up-regulated activation markers. These blast cells also infiltrated liver, heart, lung, and pancreas tissue, and amounts of serum immunoglobulin were elevated. The mice invariably became moribund by 3 to 4 weeks of age. Although CTLA-4-deficient T cells proliferated spontaneously and strongly when stimulated through the T cell receptor, they were sensitive to cell death induced by cross-linking of the Fas receptor and by gamma irradiation. Thus, CTLA-4 acts as a negative regulator of T cell activation and is vital for the control of lymphocyte homeostasis.
From nucleation to nanowires: a single-step process in reactive plasmas (2010)

This feature article introduces a deterministic approach for the rapid, single-step, direct synthesis of metal oxide nanowires. This approach is based on the exposure of thin metal samples to reactive oxygen plasmas and does not require any intervening processing or external substrate heating. The critical roles of the reactive oxygen plasmas, surface processes, and plasma-surface interactions that enable this growth are critically examined by using a deterministic viewpoint. The essentials of the experimental procedures and reactor design are presented and related to the key process requirements. The nucleation and growth kinetics is discussed for typical solid-liquid-solid and vapor-solid-solid mechanisms related to the synthesis of the oxide nanowires of metals with low (Ga, Cd) and high (Fe) melting points, respectively. Numerical simulations are focused on the possibility to predict the nanowire nucleation points through the interaction of the plasma radicals and ions with the nanoscale morphological features on the surface, as well as to control the localized 'hot spots' that in turn determine the nanowire size and shape. This generic approach can be applied to virtually any oxide nanoscale system and further confirms the applicability of the plasma nanoscience approaches for deterministic nanoscale synthesis and processing.
Optical Fiber Thermometer For Medical Use (1984)

Optical fiber thermometers are of extreme interest for very localized and e.m. immune measurements in several medical procedures,such as cancer treatment by R.F. or microwave hyperthermia technique,or blood flow and cardiac output measurements by thermodilution techniques.Operational principle and technical data of an original sensor based on the light intensity modulation induced by a thermosensitive liquid cladding,applied on the distal end of a 200 μm core silica-plastic fiber,are reported.Performance characteristics of this ther-mometer are also reported.