gebhart/patrepeval huggingface dataset:
Protein identification with deep learning: from abc to xyz (2017)

Proteins are the main workhorses of biological functions in a cell, a tissue, or an organism. Identification and quantification of proteins in a given sample, e.g. a cell type under normal/disease conditions, are fundamental tasks for the understanding of human health and disease. In this paper, we present DeepNovo, a deep learning-based tool to address the problem of protein identification from tandem mass spectrometry data. The idea was first proposed in the context of de novo peptide sequencing [1] in which convolutional neural networks and recurrent neural networks were applied to predict the amino acid sequence of a peptide from its spectrum, a similar task to generating a caption from an image. We further develop DeepNovo to perform sequence database search, the main technique for peptide identification that greatly benefits from numerous existing protein databases. We combine two modules de novo sequencing and database search into a single deep learning framework for peptide identification, and integrate de Bruijn graph assembly technique to offer a complete solution to reconstruct protein sequences from tandem mass spectrometry data. This paper describes a comprehensive protocol of DeepNovo for protein identification, including training neural network models, dynamic programming search, database querying, estimation of false discovery rate, and de Bruijn graph assembly. Training and testing data, model implementations, and comprehensive tutorials in form of IPython notebooks are available in our GitHub repository (https://github.com/nh2tran/DeepNovo).
Design of potent and highly selective inhibitors for human β-secretase 2 (memapsin 1), a target for type 2 diabetes (2016)

Design, synthesis and evaluation of very potent and selective β-Secretase 2 (memapsin 1, BACE 2) inhibitors are described. The inhibitors were designed specifically to interact with the S2'-site of β-secretase 2 to provide >170,000-fold selectivity over β-secretase (BACE 1) and >15,000-fold selectivity over cathepsin D. BACE 2 is implicated in Type 2 diabetes. The studies serve as an important guide to selective BACE 2 inhibitors.
Robust Adaptive Control for Hydraulic Servosystems (1996)

The application of an indirect (self-tuning) adaptive controller to an electro-hydraulic positioning system is described. The underlying control method is pole placement, with the addition of a demand filter to allow noise effects to be reduced without degrading closed-loop performance. Recursive least squares is used to estimate the plant parameters, but the data is pre-filtered to reduce bias. A novel covariance trace limiting algorithm provides estimator reliability despite periods of insufficient excitation. Off-line system identification is employed to help controller design for the electro-hydraulic servosystem. The resulting controller performs well, and adapts rapidly to changes in load stiffness and supply pressure.
ChemInform Abstract: Silicon Nanowires as Efficient Thermoelectric Materials. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Reducing the Effects of Plasma Proximity in Plasma Immersion Ion Implantation (1997)

Plasma Immersion Ion Implantation is shown to be a promising candidate for low-energy, high-dose ultra large-scale integration (ULSI) applications like ultra-shallow junction processing. Junctions shallower than 65 nm at a background concentration of 10 18 cm -3 have been made with BF 3 PIII (p-type) and PH 3 /H 2 PIII (n-type). Remaining concerns about PIII processing include impurity contamination, surface erosion, charging of thin oxide devices, and interaction with photoresist. Contamination can be reduced through proper machine design and cleaning. Surface erosion is minimized by using higher frequency implantation: although the erosion rate rises, the dose rate increases faster. Charging becomes severe at higher frequencies, so a moderate frequency (around 10–20 kHz) is recommended to minimize both effects. The effect of PIII-photoresist interaction on devices is comparable to that seen with conventional implantation.
Responses to the Selective Bruton’s Tyrosine Kinase (BTK) Inhibitor Tirabrutinib (ONO/GS-4059) in Diffuse Large B-cell Lymphoma Cell Lines (2018)

Bruton's tyrosine kinase (BTK) is a key regulator of the B-cell receptor signaling pathway, and aberrant B-cell receptor (BCR) signaling has been implicated in the survival of malignant B-cells. However, responses of the diffuse large B-cell lymphoma (DLBCL) to inhibitors of BTK (BTKi) are infrequent, highlighting the need to identify mechanisms of resistance to BTKi as well as predictive biomarkers. We investigated the response to the selective BTKi, tirabrutinib, in a panel of 64 hematopoietic cell lines. Notably, only six cell lines were found to be sensitive. Although activated B-cell type DLBCL cells were most sensitive amongst all cell types studied, sensitivity to BTKi did not correlate with the presence of activating mutations in the BCR pathway. To improve efficacy of tirabrutinib, we investigated combination strategies with 43 drugs inhibiting 34 targets in six DLBCL cell lines. Based on the results, an activated B-cell-like (ABC)-DLBCL cell line, TMD8, was the most sensitive cell line to those combinations, as well as tirabrutinib monotherapy. Furthermore, tirabrutinib in combination with idelalisib, palbociclib, or trametinib was more effective in TMD8 with acquired resistance to tirabrutinib than in the parental cells. These targeted agents might be usefully combined with tirabrutinib in the treatment of ABC-DLBCL.
Ag/(SnO (2012)

According to the principle that the fibre-like arrangement of reinforcing SnO
 2
 particles paralleling to the direction of current is propitious to the electrical and mechanical performance of the electrical contact materials (ECM), we proposed and reported the novel precursor route used to prepare Ag/(SnO
 2
)
 12
 ECM with fibre-like arrangement of reinforcing nanoparticles. The as-prepared samples were characterized by means of X-ray diffraction (XRD), scanning electron microscopy (SEM), optical metallurgical (OM), energy-dispersive X-ray spectroscopy (EDX), MHV2000 microhardness test, and double bridge tester. The mechanism for the formation of fibre-like arrangement of reinforcing nanoparticles in Ag/(SnO
 2
)
 12
 ECM was also discussed. The analysis results show that Ag/(SnO
 2
)
 60
 sphere with mosaic structure of SnO
 2
 nanoparticles embedded in Ag matrix is believed to play a pivotal role in formation of fibre-like structure. The fibre-like structured Ag/(SnO
 2
)
 12
 ECM exhibits a high elongation of 24%, a particularly low electrical resistivity of 2.08 μΩ·cm, low arcing energy and low contact resistivity, and thus has considerable technical, economical and environmental benefits.
GPLOM: The Generalized Plot Matrix for Visualizing Multidimensional Multivariate Data (2013)

Scatterplot matrices (SPLOMs), parallel coordinates, and glyphs can all be used to visualize the multiple continuous variables (i.e., dependent variables or measures) in multidimensional multivariate data. However, these techniques are not well suited to visualizing many categorical variables (i.e., independent variables or dimensions). To visualize multiple categorical variables, 'hierarchical axes' that 'stack dimensions' have been used in systems like Polaris and Tableau. However, this approach does not scale well beyond a small number of categorical variables. Emerson et al. [8] extend the matrix paradigm of the SPLOM to simultaneously visualize several categorical and continuous variables, displaying many kinds of charts in the matrix depending on the kinds of variables involved. We propose a variant of their technique, called the Generalized Plot Matrix (GPLOM). The GPLOM restricts Emerson et al.'s technique to only three kinds of charts (scatterplots for pairs of continuous variables, heatmaps for pairs of categorical variables, and barcharts for pairings of categorical and continuous variable), in an effort to make it easier to understand. At the same time, the GPLOM extends Emerson et al.'s work by demonstrating interactive techniques suited to the matrix of charts. We discuss the visual design and interactive features of our GPLOM prototype, including a textual search feature allowing users to quickly locate values or variables by name. We also present a user study that compared performance with Tableau and our GPLOM prototype, that found that GPLOM is significantly faster in certain cases, and not significantly slower in other cases.
Synthetic Archaeosome Vaccines Containing Triglycosylarchaeols Can Provide Additive and Long-Lasting Immune Responses That Are Enhanced by Archaetidylserine (2012)

The relation between archaeal lipid structures and their activity as adjuvants may be defined and explored by synthesizing novel head groups covalently linked to archaeol (2,3-diphytanyl-sn-glycerol). Saturated archaeol, that is suitably stable as a precursor for chemical synthesis, was obtained in high yield from Halobacterium salinarum. Archaeosomes consisting of the various combinations of synthesized lipids, with antigen entrapped, were used to immunize mice and subsequently determine CD8(+) and CD4(+)-T cell immune responses. Addition of 45 mol% of the glycolipids gentiotriosylarchaeol, mannotriosylarchaeol or maltotriosylarchaeol to an archaetidylglycerophosphate-O-methyl archaeosome, significantly enhanced the CD8(+) T cell response to antigen, but diminished the antibody titres in peripheral blood. Archaeosomes consisting of all three triglycosyl archaeols combined with archaetidylglycerophosphate-O-methyl (15/15/15/55 mol%) resulted in approximately additive CD8(+) T cell responses and also an antibody response not significantly different from the archaetidylglycerophosphate-O-methyl alone. Synthetic archaetidylserine played a role to further enhance the CD8(+) T cell response where the optimum content was 20-30 mol%. Vaccines giving best protection against solid tumor growth corresponded to the archaeosome adjuvant composition that gave highest immune activity in immunized mice.
Cathode Dependence of Liquid-Alloy Na–K Anodes (2018)

Alkali ions can be plated dendrite-free into a liquid alkali-metal anode. Commercialized Na-S battery technology operates above 300 °C. A low-cost Na-K alloy is liquid at 25 °C from 9.2 to 58.2 wt% of sodium; sodium and/or potassium can be plated dendrite-free in the liquid range at room temperature. The co-existence of two alkali metals in an anode raises a question: whether the liquid Na-K alloy acts as a Na or a K anode. Here we show the alkali-metal that is stripped from the liquid Na-K anode is dependent on the preference of the cathode host. It acts as the anode of a sodium rechargeable cell if the cathode host structure selectively accepts only Na<sup>+</sup> ions; as the anode of a potassium rechargeable cell if the cathode accepts K<sup>+</sup> ions in preference to Na<sup>+</sup> ions. This dual-anode behavior means the liquid Na-K alkali-alloy can be applied as a dendrite-free anode in Na-metal batteries as well as K-metal batteries.
Exploiting error-control coding and cyclic-prefix in channel estimation for coded OFDM systems (2003)

OFDM systems typically use coding and interleaving across subchannels to exploit frequency diversity on frequency-selective channels. This letter presents a low-complexity iterative algorithm for blind and semi-blind joint channel estimation and soft decoding in coded OFDM systems. The proposed algorithm takes advantage of the channel finite delay-spread constraint and the extra observation offered by the cyclic-prefix. It converges within a single OFDM symbol and, therefore, has a minimum latency.
Embedded media marker (2010)

An Embedded Media Marker (EMM) is a transparent mark printed on a paper document that signifies the availability of additional media associated with that part of the document. Users take a picture of the EMM using a camera phone, and the media associated with that part of the document is displayed on the phone. Unlike bar codes, EMMs are nearly transparent and thus do not interfere with the document appearance. Retrieval of media associated with an EMM is based on image features of the document within the EMM boundary. Unlike other feature-based retrieval methods, the EMM clearly indicates to the user the existence and type of media associated with the document location. A semi-automatic authoring tool is used to place an EMM at a location in a document, in such a way that it encompasses sufficient identification features with minimal disturbance to the original document. We will demonstrate how to create an EMM-enhanced document, and how the EMM enables access to the associated media on a cell phone.
Maskless photoencoded selective etching for glass-based microtechnology applications (1996)

Two-photon excitation of carriers in boron E'-center-containing borosilicate glasses results in a photoencoding of selectively etchable regions. Using a turbulent etching process followed by polishing, we have demonstrated a number of patterning capabilities for microtechnology applications such as ultrafast capillary electrophoresis chips and rapid prototyping of diffractive optical elements.
Compositions and methods for generation of gases containing hydrogen or hydrogen isotopes. [decomposition of hydride mixtures] (1982)

A composition which upon heating generates hydrogen or hydrogen isotopes comprises an intimate mixture of a hydride component selected from the group consisting of calcium hydride, magnesium hydride, sodium hydride, lithium hydride and mixtures thereof, and a salt component selected from the group consisting of ammonium salts, hydrazinium salts and mixtures thereof, said hydride component being present in at least a stoichiometric amount.
k‐Space weighted least‐squares algorithm for accurate and fast motion extraction from magnetic resonance navigator echoes (2001)

Navigator echoes provide an effective method to monitor physiological motion, allowing motion artifacts to be suppressed by modifying the data acquisition accordingly. The displacement can be measured directly from the navigator phase using an algorithm suggested by Ahn and Cho (IEEE Trans Med Imaging 1987;MI-6:32–36). Although computationally efficient, it is susceptible to noise, particularly contributions from points at the edges of k-space. A k-space weighted least-squares (kLS) algorithm is proposed which fits a straight line to the motion-induced phase shift. The linear fit is weighted strongly to high SNR points near the k-space center and only weakly to the poor SNR points at the edges of k-space. This algorithm was found to be as efficient as Ahn's algorithm but more robust against noise. Magn Reson Med 46:1037–1040, 2001. © 2001 Wiley-Liss, Inc.
Design of a controlled-brake orthosis for regulating FES-aided gait (1992)

A hybrid FES/orthosis system is being developed which includes a long-legged brace with controllable friction brakes at the knee and hip joints. The intent of this system is to achieve acceptable lower limb trajectories by utilizing the stimulated muscles as a source of unregulated power and to regulate this power at each joint through control of the brakes. The design of a laboratory version of the orthosis to test this concept is described.
Glucose Sensing Using Near-Infrared Surface-Enhanced Raman Spectroscopy:  Gold Surfaces, 10-Day Stability, and Improved Accuracy (2005)

This research presents the achievement of significant milestones toward the development of a minimally invasive, continuously monitoring, glucose-sensing platform based on the optical quantitation of glucose in interstitial fluid. We expand our initial successes in the measurement of glucose by surface-enhanced Raman scattering (SERS), demonstrating substantial improvements not only in the quality and optical properties of the substrate system itself but also in the robustness of the measurement methodology and the amenability of the technique to compact, diode laser-based instrumentation. Herein, we compare the long-term stability of gold to silver film over nanosphere (AuFON, AgFON) substrates functionalized with a partitioning self-assembled monolayer (SAM) using both electrochemical and SERS measurements. AuFONs were found to be stable for a period of at least 11 days. The switch to AuFONs not only provides a more stable surface for SAM formation but also yields better chemometric results, with improved calibration and validation over a range of 0.5-44 mM (10-800 mg/dL). Measured values for glucose concentrations in phosphate-buffered saline (pH approximately 7.4) based on 160 independent SERS measurements on AuFONs have a root-mean-square error of prediction of 2.7 mM (49.5 mg/dL), with 91% of the values falling within an extended A-B range on an expanded Clarke error grid. Furthermore, AuFONs exhibit surface plasmon resonances at longer wavelengths than similar AgFONs, which make them more efficient for SERS at near-infrared wavelengths, enabling the use of low-power diode lasers in future devices.
Arsenic-Implanted HfON Charge-Trapping Flash Memory With Large Memory Window and Good Retention (2011)

We have fabricated the TaN-[SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> -LaAlO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> ]-HfON-[LaAlO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> -SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ]-Si charge-trapping Flash device. A large 6.4-V initial memory window, a 4.3-V 10-year extrapolated reten tion window at 125°C, and a 5.5-V endurance window at 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> cycles were measured under very fast 100-μs and low ±16-V program/erase. These excellent results were achieved using an As <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> implant into the HfON trapping layer, which were sig nificantly better than those of the control device without ion implantation.
Generation of monoclonal pan-hemagglutinin antibodies for the quantification of multiple strains of influenza (2017)

Vaccination is the most effective course of action to prevent influenza. About 150 million doses of influenza vaccines were distributed for the 2015-2016 season in the USA alone according to the Centers for Disease Control and Prevention. Vaccine dosage is calculated based on the concentration of hemagglutinin (HA), the main surface glycoprotein expressed by influenza which varies from strain to strain. Therefore yearly-updated strain-specific antibodies and calibrating antigens are required. Preparing these quantification reagents can take up to three months and significantly slows down the release of new vaccine lots. Therefore, to circumvent the need for strain-specific sera, two anti-HA monoclonal antibodies (mAbs) against a highly conserved sequence have been produced by immunizing mice with a novel peptide-conjugate. Immunoblots demonstrate that 40 strains of influenza encompassing HA subtypes H1 to H13, as well as B strains from the Yamagata and Victoria lineage were detected when the two mAbs are combined to from a pan-HA mAb cocktail. Quantification using this pan-HA mAbs cocktail was achieved in a dot blot assay and results correlated with concentrations measured in a hemagglutination assay with a coefficient of correlation of 0.80. A competitive ELISA was also optimised with purified viral-like particles. Regardless of the quantification method used, pan-HA antibodies can be employed to accelerate process development when strain-specific antibodies are not available, and represent a valuable tool in case of pandemics. These antibodies were also expressed in CHO cells to facilitate large-scale production using bioreactor technologies which might be required to meet industrial needs for quantification reagents. Finally, a simulation model was created to predict the binding affinity of the two anti-HA antibodies to the amino acids composing the highly conserved epitope; different probabilities of interaction between a given amino acid and the antibodies might explain the affinity of each antibody against different influenza strains.
Microstructural Stability and Oxidation Resistance of 9-12 Chromium Steels at Elevated Temperatures (2006)

Various martensitic 9-12 Cr steels are utilized currently in fossil fuel powered energy plants for their good elevated temperature properties such as creep strength, steam side oxidation resistance, fire side corrosion resistance, and thermal fatigue resistance. Need for further improvements on the properties of 9-12 Cr steels for higher temperature (>600oC) use is driven by the environmental concerns (i.e., improve efficiency to reduce emissions and fossil fuel consumption). In this paper, we will discuss the results of the research done to explore new subsitutional solute solution and precipitate hardening mechanisms for improved strength of 9-12 Cr martensitic steels. Stability of the phases present in the steels will be evaluated for various temperature and time exposures. A comparison of microstructural properties of the experimental steels and commercial steels will also be presented. <br><br> The influence of a Ce surface treatment on oxidation behavior of a commercial (P91) and several experimental steels containing 9 to 12 weight percent Cr was examined at 650ºC in flowing dry and moist air. The oxidation behavior of all the alloys without the Ce modification was significantly degraded by the presence of moisture in the air during testing. For instance the weight gain for P91 was two orders of magnitude greater in moist air than in dry air. This was accompanied by a change in oxide scale from the formation of Cr-based scales in dry air to the formation of Fe-based scales in moist air. The Ce surface treatment was very effective in improving the oxidation resistance of the experimental steels in both moist and dry air. For instance, after exposure to moist air at 650ºC for 2000 hours, an experimental alloy with the cerium surface modification had a weight gain three orders of magnitude lower than the alloy without the Ce modification and two orders of magnitude lower than P91. The Ce surface treatment suppressed the formation of Fe-based scales and promoted the formation of more protective Cr-based scales. However, the Ce surface treatment was not effective in improving the resistance of P91. The results are discussed in terms of synergistic effects of constituent alloying elements.
Technique for the reduction of fading in interferometers (1985)

Abstract : This patent application discloses a passive device for reducing polarization fading in interferometers without significantly degrading the signal-to-noise ratio. In one embodiment, light form an interferometer output is passed through a lens to a polarization mask. The polarization mask comprises at least three independent polarizers which pass independent states of polarizers each independently polarized signal is detected, demodulated and passed to a means for signal extraction.
Serological diagnosis and prognosis of severe acute pancreatitis by analysis of serum glycoprotein 2 (2016)

Serum GP2a is a specific marker of acute pancreatitis and analysis of GP2a can aid in the differential diagnosis of acute upper abdominal pain and prognosis of severe acute pancreatitis.