gebhart/patrepeval huggingface dataset:
Dopamine-Assisted Deposition of Dextran for Nonfouling Applications (2014)

Nonfouling surfaces are essential for many biomedical applications, such as diagnostic biosensors and blood- or tissue-contacting implants. In this study, we demonstrate a simple one-step method to introduce dextran onto various substrates based on dopamine polymerization. It has been shown for the first time that dextran molecules could be incorporated into a dopamine polymerization product via mixing dextran with dopamine in a slightly alkaline solution. The codeposited film was characterized by X-ray photoelectron spectroscopy (XPS), the water contact angle, ellipsometry, and atomic force microscopy (AFM). Results reveal that it is possible to control the thickness and surface roughness via the deposition time and deposition repeat cycles. Furthermore, quartz crystal microbalance (QCM) measurements show that the dextran-modified surface inhibits protein adhesion. In addition, cell attachment has been significantly inhibited on dextran-modified surfaces even after exposure to water for as long as 2 months. The described dopamine-assisted dextran modification represents a simple and universal method for nonfouling surface preparation and can be potentially applied to improve the performance of various medical devices and materials.
Plasmonic nanohole array sensors fabricated by template transfer with improved optical performance (2013)

Surface plasmon resonance sensors of the nanohole array type provide a promising platform for label-free biosensing on surfaces. For their extensive use, an efficient fabrication procedure to make nanoscale features on metallic films is required. We develop a simple and robust template-transfer approach to structure periodic nanohole arrays in optically thick Au films on poly(dimethylsiloxane) substrates. This technique significantly simplifies the process of sensor fabrication and reduces the cost of the device. A spectral analysis approach is also developed for improving the sensor performance. The sensitivity of the resulting sensor to refractive index change is 522 nm/RIU (refractive index unit) and the resolution is improved to 2 × 10(-5) RIU, which are among the best reported values for localized surface plasmon resonance sensors. We also demonstrate the limit of detection of this sensor for cardiac troponin-I.
Domain Generalization with Adversarial Feature Learning (2018)

In this paper, we tackle the problem of domain generalization: how to learn a generalized feature representation for an "unseen" target domain by taking the advantage of multiple seen source-domain data. We present a novel framework based on adversarial autoencoders to learn a generalized latent feature representation across domains for domain generalization. To be specific, we extend adversarial autoencoders by imposing the Maximum Mean Discrepancy (MMD) measure to align the distributions among different domains, and matching the aligned distribution to an arbitrary prior distribution via adversarial feature learning. In this way, the learned feature representation is supposed to be universal to the seen source domains because of the MMD regularization, and is expected to generalize well on the target domain because of the introduction of the prior distribution. We proposed an algorithm to jointly train different components of our proposed framework. Extensive experiments on various vision tasks demonstrate that our proposed framework can learn better generalized features for the unseen target domain compared with state-of-the-art domain generalization methods.
Accelerating recurrent neural networks in analytics servers: Comparison of FPGA, CPU, GPU, and ASIC (2016)

Recurrent neural networks (RNNs) provide state-of-the-art accuracy for performing analytics on datasets with sequence (e.g., language model). This paper studied a state-of-the-art RNN variant, Gated Recurrent Unit (GRU). We first proposed memoization optimization to avoid 3 out of the 6 dense matrix vector multiplications (SGEMVs) that are the majority of the computation in GRU. Then, we study the opportunities to accelerate the remaining SGEMVs using FPGAs, in comparison to 14-nm ASIC, GPU, and multi-core CPU. Results show that FPGA provides superior performance/Watt over CPU and GPU because FPGA's on-chip BRAMs, hard DSPs, and reconfigurable fabric allow for efficiently extracting fine-grained parallelisms from small/medium size matrices used by GRU. Moreover, newer FPGAs with more DSPs, on-chip BRAMs, and higher frequency have the potential to narrow the FPGA-ASIC efficiency gap.
Ca<sup>2+</sup> signaling in the regulation of dendritic cell functions (2011)

Dendritic cells (DCs) are highly versatile antigen-presenting cells critically involved in both innate and adaptive immunity as well as maintenance of self-tolerance. DC function is governed by Ca(2+) signaling, which directs the DC responses to diverse antigens, including Toll-like receptor ligands, intact bacteria, and microbial toxins. Ca(2+)-sensitive DC functions include DC activation, maturation, migration, and formation of immunological synapses with T cells. Moreover, alterations of cytosolic Ca(2+) trigger immune suppression or switch off DC activity. Ca(2+) signals are generated by the orchestration of Ca(2+) transport processes across plasma, endoplasmic reticulum, and inner mitochondrial membrane. These processes include active pumping of Ca(2+), Ca(2+)/Na(+) antiport, and electrodiffusion through Ca(2+)-permeable channels or uniporters. Ca(2+) channels in the plasma membrane such as Ca(2+) release-activated Ca(2+) or L-type Ca(2+) channels are tightly regulated by the membrane potential which in turn depends on the activity of voltage-gated K(+) or Ca(2+)-activated nonselective cation channels. The rapidly growing knowledge on the function and regulation of these membrane transport proteins provides novel insight into pathophysiological mechanisms underlying dysfunction of the immune system and opens novel therapeutic opportunity to favorably influence the function of the immune system.
Quantitative analysis of the effect of Acanthamoeba profilin on actin filament nucleation and elongation (1984)

The current view of the mechanism of action of Acanthamoeba profilin is that it binds to actin monomers, forming a complex that cannot polymerize [Tobacman, L. S., & Korn, E. D. (1982) J. Biol. Chem. 257, 4166-4170; Tseng, P., & Pollard, T. D. (1982) J. Cell Biol. 94, 213-218; Tobacman, L. S., Brenner, S. L., & Korn, E. D. (1983) J. Biol. Chem. 258, 8806-8812]. This simple model fails to predict two new experimental observations made with Acanthamoeba actin in 50 mM KC1, 1 mM MgCl2, and 1 mM EGTA. First, Acanthamoeba profilin inhibits elongation of actin filaments far more at the pointed end than at the barbed end. According, to the simple model, the Kd for the profilin-actin complex is less than 5 microM on the basis of observations at the pointed end and greater than 50 microM for the barbed end. Second, profilin inhibits nucleation more strongly than elongation. According to the simple model, the Kd for the profilin-actin complex is 60-140 microM on the basis of two assays of elongation but 2-10 microM on the basis of polymerization kinetics that reflect nucleation. These new findings can be explained by a new and more complex model for the mechanism of action that is related to a proposal of Tilney and co-workers [Tilney, L. G., Bonder, E. M., Coluccio, L. M., & Mooseker, M. S. (1983) J. Cell Biol. 97, 113-124]. In this model, profilin can bind both to actin monomers with a Kd of about 5 microM and to the barbed end of actin filaments with a Kd of about 50-100 microM. An actin monomer bound to profilin cannot participate in nucleation or add to the pointed end of an actin filament. It can add to the barbed end of a filament. When profilin is bound to the barbed end of a filament, actin monomers cannot bind to that end, but the terminal actin protomer can dissociate at the usual rate. This model includes two different Kd's--one for profilin bound to actin monomers and one for profilin bound to an actin molecule at the barbed end of a filament. The affinity for the end of the filament is lower by a factor of 10 than the affinity for the monomer, presumably due to the difference in the conformation of the two forms of actin or to steric constraints at the end of the filament.
El antidiabético “perfecto” para cada persona (2019)

Mujer 66 anos, acude para control de DM2. 
- Antecedentes personales: DM2 desde hace 9 anos.HTA con cardiopatia hipertensiva.DL. AIT hace 2 meses. 
- Tratamiento actual: Olmesartan40/hidroclotiazida12.5 mg,Amlodipino10mg,Rosuvastatina20mg,Clopidogrel 75,Metformina 850. 
- Anamnesis: ultimo ingreso hospitalario hace 2 meses,tratada con insulina,sufrio 3 hipoglucemias, le preocupada la posibilidad de que repitan.Sintomatologia cardinal ocasional,sin hipoglucemias ni otra sintomatologia de interes.No practica ejercicio fisico,seguimiento de la dieta irregular. Desea evitar cualquier medida que induzca ganancia de peso.
Comprehensive Analysis of the Naturally Processed Peptide Repertoire: Differences between HLA-A and B in the Immunopeptidome (2015)

The cytotoxic T cell (CTL) response is determined by the peptide repertoire presented by the HLA class I molecules of an individual. We performed an in-depth analysis of the peptide repertoire presented by a broad panel of common HLA class I molecules on four B lymphoblastoid cell-lines (BLCL). Peptide elution and mass spectrometry analysis were utilised to investigate the number and abundance of self-peptides. Altogether, 7897 unique self-peptides, derived of 4344 proteins, were eluted. After viral infection, the number of unique self-peptides eluted significantly decreased compared to uninfected cells, paralleled by a decrease in the number of source proteins. In the overall dataset, the total number of unique self-peptides eluted from HLA-B molecules was larger than from HLA-A molecules, and they were derived from a larger number of source proteins. These results in B cells suggest that HLA-B molecules possibly present a more diverse repertoire compared to their HLA-A counterparts, which may contribute to their immunodominance. This study provides a unique data set giving new insights into the complex system of antigen presentation for a broad panel of HLA molecules, many of which were never studied this extensively before.
Electroless plating of Pd-P alloys from ethylenediamine complex solutions. (1989)

Electroless plating of Pd-P alloys from palladium-ethylenediamine complex solutions containing sodium hypophosphite as a reducing agent, was investigated. The deposition rate of Pd-P alloys was markedly influenced by the concentration of palladium chloride and bath temperature. The phosphorus content of deposits was proportional to the 0.2 power of sodium hypophosphite concentration. In Pd-P alloys, the amorphous solid was converted with heat treatment at 250-300°C into either stable crystal phase Pd plus Pd8P or Pd plus Pd6P, according to phosphorus content. It was found that hardness increased when heat treatment of the alloy resulted in the formation of PdxP crystals.
Brominated Tyrosine and Polyelectrolyte Multilayer Analysis by Laser Desorption Vacuum Ultraviolet Postionization and Secondary Ion Mass Spectrometry (2011)

The small molecular analyte 3,5-dibromotyrosine (Br(2)Y) and chitosan-alginate polyelectrolyte multilayers (PEM) with and without adsorbed Br(2)Y were analyzed by laser desorption postionization-mass spectrometry (LDPI-MS). LDPI-MS using a 7.87 eV laser and tunable 8-12.5 eV synchrotron vacuum ultraviolet (VUV) radiation found that desorption of clusters from Br(2)Y films allowed detection by ≤8 eV single photon ionization. Thermal desorption and electronic structure calculations determined the ionization energy of Br(2)Y to be ~8.3 ± 0.1 eV and further indicated that the lower ionization energies of clusters permitted their detection at ≤8 eV photon energies. However, single photon ionization could only detect Br(2)Y adsorbed within PEMs when using either higher photon energies or matrix addition to the sample. All samples were also analyzed by 25 keV Bi(3)(+) secondary ion mass spectrometry (SIMS), with the negative ion spectra showing strong parent ion signal which complemented that observed by LDPI-MS. However, the negative ion SIMS appeared strongly dependent on the high electron affinity of this specific analyte and the analyte's condensed phase environment.
Accessing Protein Methyltransferase and Demethylase Enzymology Using Microfluidic Capillary Electrophoresis (2020)

The discovery of small molecules targeting the > 80 enzymes that add (methyltransferases) or remove (demethylases) methyl marks from lysine and arginine residues, most notably present in histone tails, may yield unprecedented chemotherapeutic agents and facilitate regenerative medicine. To better enable chemical exploration of these proteins, we have developed a novel and highly quantitative microfluidic capillary electrophoresis assay to enable full mechanistic studies of these enzymes and the kinetics of their inhibition. This technology separates small biomolecules, i.e., peptides, based on their charge-to-mass ratio. Methylation, however, does not alter the charge of peptide substrates. To overcome this limitation, we have employed a methylation-sensitive endoproteinase strategy to separate methylated from unmethylated peptides. The assay was validated on a lysine methyltransferase (G9a) and a lysine demethylase (LSD1) and was employed to investigate the inhibition of G9a by small molecules.
A cytoadhesion assay for the binding of cloned hemopoietic progenitor cells to stroma. (1993)

Cell adhesion molecules responsible for the specific recognition and adhesion that necessarily occur between hemopoietic progenitor cells (HPC) and stromal cells within the bone marrow are likely of multiple nature in the cell membrane. Systems less complex than intact bone marrow, in which the interactions between adhesion molecules and their ligands may be studied, is greatly needed. Using 4 cloned murine IL-3-dependent HPC lines, B6Sut, FDCP-1, FDCP-2 and FDCP-Mix, a system of co-culture has been established and standardized with 2 murine stromal cell lines, GB1/6 and 3T3. HPC were radiolabeled with 51Cr, and an optimal set of conditions was established for the adherence of HPC to stromal cells. It was found that a source of IL-3, whether supplied as recombinant murine IL-3 or WEHI-conditioned medium, was a necessary component of the labeling and assay medium to achieve maximal adherence to stroma. Likewise, the presence of serum also resulted in overall better cytoadhesion than did serum-free conditions. All 4 cell lines bound GB1/6 in a reproducible manner from approximately 63% for FDCP-1 to 20% for FDCP-Mix; binding to 3T3 was higher than to GB1/6 for all HPC. Approximately 25 to 30% of the cell populations were not able to adhere to stroma, indicating a fairly constant degree of heterogeneity with respect to expression of adhesion molecules. Cytoadhesion was found to have at least one component that was temperature-sensitive, as adhesion of FDCP-1 to GB1/6 was 41.5 +/- 1.3% at 4 degrees C compared with 63.2 +/- 1.1% at 37 degrees C. The adhesion reaction itself occurred independently of metabolic energy production and relied on the presence of receptor-ligand molecules. This very standard and reproducible system should allow closer examination of the individual cytoadhesive events that occur between HPC and marrow stromal cells using cloned cell lines.
Short Text Clustering via Convolutional Neural Networks (2015)

Short text clustering has become an increasing important task with the popularity of social media, and it is a challenging problem due to its sparseness of text representation. In this paper, we propose a Short Text Clustering via Convolutional neural networks (abbr. to STCC), which is more beneficial for clustering by considering one constraint on learned features through a self-taught learning framework without using any external tags/labels. First, we embed the original keyword features into compact binary codes with a localitypreserving constraint. Then, word embeddings are explored and fed into convolutional neural networks to learn deep feature representations, with the output units fitting the pre-trained binary code in the training process. After obtaining the learned representations, we use K-means to cluster them. Our extensive experimental study on two public short text datasets shows that the deep feature representation learned by our approach can achieve a significantly better performance than some other existing features, such as term frequency-inverse document frequency, Laplacian eigenvectors and average embedding, for clustering.
Mechanistic Switch in Dual Gold Catalysis of Diynes: C(sp<sup>3</sup>)–H Activation through Bifurcation—Vinylidene versus Carbene Pathways (2013)

The other side of the mountain: Changing the framework of diyne systems opens up new cyclization modes for dual gold catalysis. Instead of a 5-endo cyclization and gold vinylidenes a 6-endo cyclization gives rise to gold-stabilized carbenes as key intermediates for selective C-H insertions.
Biochemical Synthesis and Manipulation of a 70 nm DNA Linker for the Assembly of DNA‐Functionalized Gold Nanoparticles (2007)

Abstract DNA oligonucleotides are extraordinarily well suited as linkers for the programmable assembly of nanoparticles. To extend the scope of DNA‐directed particle assembly, a 70 nm DNA linker molecule for the DNA‐directed assembly of gold nanoparticles is synthesized by biochemical reactions. In particular, polymerase chain reaction (PCR) and subsequent restriction and ligation reactions are employed to synthesize the DNA linker, comprising a 178 base pair (bp) double helical core region supplemented with two sticky‐end binding sites of 12 nucleotides in length, attached to one of the core‐forming strands. The linker is used for the assembly of DNA‐functionalized gold nanoparticles employing yet another biochemical reaction, namely covalent linkage through the enzyme DNA ligase. The resulting nanoparticle assemblies are characterized by using atomic force microscopy. The methodology described here represents a general way of synthesizing programmable DNA linker molecules with dimensions that exceed those presently available by using chemical synthetic methods, and thus, supplements the synthetic toolbox of nanobiotechnology to asses complex and functional nanoparticle/linker architectures for potential applications in sensing and materials science.
Experiments on turbidity currents over an erodible bed (1987)

Experiments were conducted to determine the behaviour of turbidity currents laden with non-cohesive silt (silica flour) moving down a slope the bed of which is covered with similar silt. Each current was sustained with constant inlet conditions for six to eight minutes. The motion of the head was not studied; measurements were concentrated on the continuous part of the current that was essentially constant in time but developing in space. Only supercritical currents were studied. The currents were free to erode sediment from, and deposit sediment on, the bed. Measurements of vertical profiles of downstream velocity and sediment concentration allowed for the development of approximate similarity relations. These relations can be used to estimate most of the shape factors that occur in the vertically-integrated equations of motion. The values do not deviate grossly from those found by using a "top-hat" function, i.e. a step function, such that velocity or concentration equals its average value in the layer and vanishes outside the layer. Coefficients of water entrainment from above, sediment entrainment from the bed, and bed resistance were determined. Where possible, the data were compared with other data and relations in the literature. Several modified relations were developed. Several researchers have suggested that a continuous supercritical turbidity current would ultimately either "ignite" (self-accelerate and entrain sediment in the net) or subside (decelerate and deposit sediment in the net) in the downstream direction. This ignition hypothesis has been offered as an explanation for the formation of submarine canyons. The experimental facility was too short to allow for a test of ignition. If the data obtained are used in conjunction with the equations of motion to extrapolate the experimentally measured currents farther downstream, however, ignition is predicted in several cases.
Sympathetic nervous system and serum leptin level in obese patients with and without obstructive sleep apnea (2006)

The aim of the present study was to investigate sympathetic nervous system activity and serum leptin level in obese patients with and without obstructive sleep apnea (OSA). We examined 75 OSA patients and 40 age, weight, BMI and blood pressure levels matched obese patients without OSA. As a result, patients with OSA had higher sympathetic activity associated not only with repetitive episodes of hypoxia/hypercapnia during sleep, but also with more marked central obesity and higher serum leptin level.
Impaired Organic Anion Transport in Kidney and Choroid Plexus of Organic Anion Transporter 3 (Oat3 (Slc22a8)) Knockout Mice (2002)

To begin to develop in vivo model systems for the assessment of the contributions of specific organic anion transporter (OAT) family members to detoxification, development, and disease, we carried out a targeted disruption of the murine organic anion transporter 3 (Oat3) gene. Surviving Oat3(-/-) animals appear healthy, are fertile, and do not exhibit any gross morphological tissue abnormalities. No Oat3 mRNA expression was detected in kidney, liver, or choroid plexus (CP) of Oat3(-/-) mice. A distinct phenotype manifested by a substantial loss of organic anion transport capacity in kidney and CP was identified. Uptake sensitive to inhibition by bromosulfophthalein or probenecid was observed for taurocholate, estrone sulfate, and para-aminohippurate in renal slices from wild-type mice, whereas in Oat3(-/-) animals transport of these substances was greatly reduced. No discernable differences in uptake were observed between hepatic slices from wild-type and Oat3(-/-) littermates, suggesting Oat3 does not play a major role in hepatic organic anion uptake. Cellular accumulation of fluorescein was reduced by approximately 75% in CP from Oat3(-/-) mice. However, capillary accumulation of fluorescein-methotrexate was unchanged, indicating the effects of Oat3 loss are restricted to the entry step and that Oat3 is localized to the apical membrane of CP. These data indicate a key role for Oat3 in systemic detoxification and in control of the organic anion distribution in cerebrospinal fluid.