gebhart/patrepeval huggingface dataset:
PepCVAE: Semi-Supervised Targeted Design of Antimicrobial Peptide Sequences (2018)

Given the emerging global threat of antimicrobial resistance, new methods for next-generation antimicrobial design are urgently needed. We report a peptide generation framework PepCVAE, based on a semi-supervised variational autoencoder (VAE) model, for designing novel antimicrobial peptide (AMP) sequences. Our model learns a rich latent space of the biological peptide context by taking advantage of abundant, unlabeled peptide sequences. The model further learns a disentangled antimicrobial attribute space by using the feedback from a jointly trained AMP classifier that uses limited labeled instances. The disentangled representation allows for controllable generation of AMPs. Extensive analysis of the PepCVAE-generated sequences reveals superior performance of our model in comparison to a plain VAE, as PepCVAE generates novel AMP sequences with higher long-range diversity, while being closer to the training distribution of biological peptides. These features are highly desired in next-generation antimicrobial design.
ICONE11-36550 Advances in Cylindrical IEC Neutron Source Design for Driven Sub-Critical Operation (2003)

Prior work has studied the potential use of cy]indrical IEC neutron sources fbr driven sub-critical operation This approach has the advantage that the small IEC neutron sources can be inserted in fuel element positions, providing a distributed neutron source.
reanalysis techniques for robust topology optimization (2012)

The article focuses on the reduction of the computational eort involved in robust topology optimization procedures. The performance of structures designed by means of topology optimization may be seriously degraded due to fabrication errors. Robust formulations of the optimization problem were shown to yield optimized designs that are tolerant with respect to such manufacturing uncertainties. The main drawback of such procedures is the added compu- tational cost associated with the need to evaluate a set of designs by performing multiple finite element analyses. In this article, we propose ecient robust topology optimization procedures based on reanalysis techniques. The approach is demonstrated on two compliant mechanism design problems where robust design is achieved by employing either a worst case formulation or a stochastic formulation. It is shown that the time spent on finite element analysis within robust topology optimization can be reduced significantly, without aecting the outcome of the optimization process.
STREAMLInED Challenges: Aligning Research Interests with Shared Tasks (2017)

Gina-Anne Levow, Emily M. Bender, Patrick Littell, Kristen Howell, Shobhana Chelliah, Joshua Crowgey, Dan Garrette, Jeff Good, Sharon Hargus, David Inman, Michael Maxwell, Michael Tjalve, Fei Xia. Proceedings of the 2nd Workshop on the Use of Computational Methods in the Study of Endangered Languages. 2017.
Chronoamperometric study of membrane electrode assembly operation in continuous flow photoelectrochemical water splitting (2013)

Water splitting was performed in a photoelectrochemical cell (PEC) with water oxidation and hydrogen formation reactions in two separate compartments. A photoanode consisting of carbon paper loaded with TiO2 and a cathode made of Pt dispersed on carbon black spread also on carbon paper were fixed on both sides of a Nafion® membrane and electrically coupled via an external circuit. Anode and cathode compartments with serpentine flow field were operated either in the liquid or vapour phase. Electrical current was monitored with chronoamperometry and D2 formation from deuterated water using mass spectrometry. Mapping the photocurrent under a variety of reaction conditions enabled identification of the limiting factors related to proton and photocarrier transport and reaction product evacuation. This comprehensive research approach to the operation of a PEC will assist future optimisation of cell design and development of membrane electrode assemblies.
Room-temperature laser action at 4.3--4.4 {micro}m in CaGa{sub 2}S{sub 4}:Dy{sup 3+} (1999)

The authors report room-temperature mid-IR laser operation in a new low-phonon-frequency, non-hygroscopic host crystal CaGa{sub 2}S{sub 4} (calcium thiogallate). Laser action at 4.31 {micro}m on the {sup 6}H{sub 11/2} {r_arrow}{sup 6}H{sub 13/2} transition of trivalent dysprosium was achieved with a slope efficiency of 1.6%.
Optimization of electrical performance of Cu(In,Ga)Se<inf>2</inf> thin film solar cells sputtered from quaternary targets (2014)

Utilizing a quaternary target to sputter Cu(In,Ga)Se <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> (CIGS) yields films which are dense, polycrystalline and highly oriented. Devices fabricated from these films exhibited efficiencies >10%. In this paper, we study the electrical characteristics of these devices, including current-voltage (I-V), external quantum efficiency (EQE) and sheet and contact resistances measured by the transfer length method, to improve their overall performance. The effect of edge termination by different techniques is reviewed to investigate perimeter effects and edge defects. It was found in these particular devices that mechanical scribing of device areas contributed to both edge and bulk shunt effects. We discuss the extent of these effects in the context of increasing device efficiency through the optimization of edge termination.
Heterogeneous Massive MIMO with Small Cells (2016)

A heterogeneous system of a Massive multiple- input-multiple-output (MIMO) macro cell with low power ancillary small cells can achieve higher spectral and energy efficiency than a Massive MIMO macro cell alone. The performance of such heterogeneous system is examined in this paper. A few small cells are used to enhance the spectral and energy efficiency of the overall system. Macro Massive MIMO base station uses a large number of antennas, which enables accurate nulling of small cell users to suppress the interference between macro cell and small cells. We derive analytical expressions for the capacity and signal-to- interference-plus-noise-ratio (SINR) lower bounds for both the downlink (DL) and uplink (UL) of the heterogeneous Massive MIMO system. Our simulation results show that nulling from macro cell Massive MIMO is essential for small cells' good and stable performance.
Deconstructing concurrency heisenbugs (2009)

Concurrency is pervasive in large systems. Unexpected interference among threads often results in ldquoHeisenbugsldquo that are extremely difficult to reproduce and eliminate. We have implemented a tool called CHESS for finding and reproducing such bugs. When attached to a program, CHESS takes control of thread scheduling and uses efficient search techniques to drive the program through possible thread interleavings. This systematic exploration of program behavior enables CHESS to quickly uncover bugs that might otherwise have remained hidden for a long time. For each bug, CHESS consistently reproduces an erroneous execution manifesting the bug, thereby making it significantly easier to debug the problem. CHESS scales to large concurrent programs and has found numerous bugs in existing systems that had been tested extensively prior to being tested by CHESS. CHESS has been integrated into the test frameworks of many code bases inside Microsoft and is used by testers on a daily basis.
‘Nano on micro’ hierarchical porous all carbon structures: an insight into interfacial interactions with bacteria (2018)

Micron long carbon nanofibers (CNFs) were grown on porous carbon beads to give an active surface for rapid immobilization of guest molecules. The fabrication of nanostructures using a catalytic route involving chemical vapour deposition on a porous substrate was accomplished by the controlled synthesis of iron nanoclusters on the surface of porous carbon beads. The challenge of catalyst nanoparticle diffusion into the porous substrate was addressed by using iron coordinated ligand complexes and optimizing the loading percentage of metal salts onto beads. The effect of using tethered bottom up surface processed CNFs on the porous beads' morphologies was established using structural characterization. The protruding architecture of CNFs on the porous carbon surface was subjected to bacterial colonisation in order to determine the efficiency of cell conjugation onto hairy structures, particularly at a low concentration. The interfaces of immobilized bacteria on the textured surface were studied by varying the pH and external physical stimuli to check the biofilm formation. The strategy of fabricating all carbon porous beads, which had topologically controlled 'nano on micro' geometries, to give fast immobilization of guest molecules could be useful in the future for developing an active disinfectant surface.
Mechanical Analysis of Stretchable AlGaN/GaN High Electron Mobility Transistors (2016)

Adding waves or kinks to a conductor is a well-known method for relieving strain in stretchable systems. Although transistors and other devices made of brittle semiconductors have also been demonstrated, the effects of the crystalline anisotropy on the mechanical behavior has not been previously investigated. In this work, a numerical solver is used to simulate the peak stresses in silicon and gallium nitride embedded within soft silicone in common stretchable geometries. As expected from other work, adding waves reduces peak stress by more than a factor of ten. The effects of in-plane rotations were then investigated. In the typical [0001] growth direction for gallium nitride, the matrix is rotationally invariant, with no variation in peak stress upon rotation about the [0001] direction. For silicon, however, peak stress was found to vary by as much as 17 percent for rotation about the [001] direction.
Structure-Based Understanding of ABCA3 Variants (2021)

ABCA3 is a crucial protein of pulmonary surfactant biosynthesis, associated with recessive pulmonary disorders such as neonatal respiratory distress and interstitial lung disease. Mutations are mostly private, and accurate interpretation of variants is mandatory for genetic counseling and patient care. We used 3D structure information to complete the set of available bioinformatics tools dedicated to medical decision. Using the experimental structure of human ABCA4, we modeled at atomic resolution the human ABCA3 3D structure including transmembrane domains (TMDs), nucleotide-binding domains (NBDs), and regulatory domains (RDs) in an ATP-bound conformation. We focused and mapped known pathogenic missense variants on this model. We pinpointed amino-acids within the NBDs, the RDs and within the interfaces between the NBDs and TMDs intracellular helices (IHs), which are predicted to play key roles in the structure and/or the function of the ABCA3 transporter. This theoretical study also highlighted the possible impact of ABCA3 variants in the cytosolic part of the protein, such as the well-known p.Glu292Val and p.Arg288Lys variants.
Characterization of the surface structural, mechanical, and thermal properties of benzocyclobutene dielectric polymers using scanned probe microscopy (2001)

Scanning probe microscopy (SPM) techniques are used to characterize surfaces related to the processing of benzocyclobutene (BCB) dielectric thin films. Thermally cured resins and photodefineable resins are sold under the trade name CYLCOTENETM1) for electronic applications. TappingMode AFM (TMAFM) imaging is used to follow changes in adhesion promoter morphology upon baking to help explain adhesion performance. Power spectral density (PSD) analysis of TMAFM images of plasma treated BCB surfaces are unique and can be used to ‘fingerprint’ processes. Selective oxidation of the BCB surface can be used to fabricate a phase imaging standard for TMAFM. Near surface modulus of the BCB materials is 3.6 ± 0.2 GPa and the hardness is 0.38 ± 0.2 GPa measured by depth-sensing nanoindentation. Creep recovery of indents can be used to qualitatively distinguish between thermal and photocureable materials. A heated tip in a scanning thermal microscope can induce the thermal curing of BCB over micron sized areas. Local thermal analysis with the same probe allows the measurement of the changes in the glass transition, Tg, at the surface with cure temperature.
Interleukin-4 (IL-4) inhibits secretion of IL-1 beta, tumor necrosis factor alpha, and IL-6 by human monocytes (1990)

Monocytes activated by lipopolysaccharide (LPS) and interferon gamma (IFN gamma) rapidly secrete a number of monokines with different functional properties. Interleukin–4 (IL–4), a T-cell derived cytokine, has been shown to reduce the production of monokines with cytostatic activity for tumor cells, chemotactic activity for monocytes, and factors that stimulate thymocyte proliferation. This latter activity is mediated by a number of monokines like IL–1, tumor necrosis factor alpha (TNF alpha), and IL–6. To elucidate which cytokines produced by monocytes are controlled by IL–4, we tested the effect of IL–4 on the secretion of IL–1 alpha, IL–1 beta, TNF alpha, and IL–6 induced by LPS or IFN gamma. IL–4 was found to inhibit the secretion of IL–1 beta and TNF alpha by activated monocytes almost 100%. The secretion of IL–6 was found to be reduced 70% to 85% in the presence of IL–4, whereas there was no effect on the secretion of IL–1 alpha (IL–1 alpha is mainly cell- associated). Time-course experiments demonstrate that IL–4 reduces the secretion of monokines for a prolonged period of time (greater than 40 hours). The reduced secretion of IL–1 beta and TNF alpha was specifically induced by IL–4 because anti-IL–4 antiserum completely restored normal monokine production. These data suggest that IL–4 plays a role in the regulation of immune responses by reducing the production of functionally important monokines.
41.4: AMOLED based on Silicon‐On‐Glass (SiOG) Technology (2007)

Abstract We have demonstrated that the single crystalline silicon films on the glass substrates can be utilized in the conventional mass production lines. The single crystalline Si layers were transferred to the 370 mm × 470 mm glass substrates using Silicon‐On‐Glass (SiOG) technology. Using the thin film transistor backplanes made by conventional CMOS technology, 2.4″ qVGA AMOLED with integrated circuits were successfully fabricated. A completed 2.4″ qVGA AMOLED module shows wide viewing angle (&gt; 170°) and 73% color gamut. The advantages of SiOG technology and its significances will be presented.
Diameter Enlargement of HiPco Single-Wall Carbon Nanotubes by Heat Treatment (2001)

The diameters of HiPco single-wall carbon nanotubes were increased by heat treatments. The original diameters estimated from Raman spectra were in the range of 0.79 to 1.2 nm; they increased with the heat-treatment temperature, reaching about 1.47 nm after 1800 °C heat treatment. Thermogravimetric analyses showed that the burning temperature of the HiPco tubes rose by about 350 °C after 1800 °C heat treatment, and the metal content, which was about 30% in the original HiPco, decreased to about 2% after heat treatment at 1800 °C.
RapidQ: A reader-free microfluidic platform for the quantitation of antibodies against the SARS-CoV-2 spike protein (2022)

We describe RapidQ, a fast, disposable, easy-to-use microfluidic assay for the quantitation of the anti-SARS-CoV-2 spike (S) protein IgG in plasma samples. The assay utilizes antigen-coated paramagnetic microbeads, which are induced to aggregate inside the RapidQ microfluidic device in the presence of the target antibody. Aggregation occurs via interaction between the biotinylated detection antibody and polymeric streptavidin. The mobility of the beads inside the two microchannels of the device depends on their aggregation state, with larger clusters moving at higher velocities under a given liquid flow rate. One of the microchannels incorporates a permanent magnet that captures arriving beads and forms a localized constriction that retards liquid flow. Since the constriction grows faster when the beads are more aggregated, the length of the liquid column accumulated downstream from the constriction relative to that of the unconstricted control channel is proportional to the sample antibody concentration. The assay demonstrates a detection limit of 4 <i>μ</i>g/ml of monoclonal anti-S protein antibody diluted in plasma with CV ≤ 13%, as well as negative and positive percent agreements of 100% (95% CI: 92.75%-100%) and 100% (95% CI: 80.5%-100%), respectively, when compared to a nucleic acid amplification test used to identify COVID-19 positive individuals, whose samples were collected ≥17 d from a positive PCR test. Finally, the RapidQ assay was used to monitor the kinetics of antibody responses to COVID-19 vaccination in a small study cohort.
Functionality of Chimeric E2 Glycoproteins of BVDV and CSFV in Virus Replication (2008)

An intriguing difference between the E2 glycoprotein of CSFV and the other groups of pestiviruses (nonCSFV) is a lack of two cysteine residues on positions cysteine 751 and 798. Other groups of pestivirus are not restricted to one species as swine, whereas CSFV is restricted to swine and wild boar. We constructed chimeric CSFV/BVDV E2 genes based on a 2D model of E2 proposed by van Rijn et al. (van Rijn et al. 1994, J Virol 68, 3934–42) and confirmed their expression by immunostaining of plasmid-transfected SK6 cells. No equivalents for the antigenic units B/C and A were found on E2 of BVDVII. This indicates major structural differences in E2. However, the immunodominant BVDVII domain A, containing epitopes with essential amino acids between position 760–764, showed to be dependent on the presence of the region defined by amino acids 684 to 796. As for the A domain of CSFV, the BVDVII A-like domain seemed to function as a separate unit. These combined domains in E2 proved to be the only combination which was functional in viral background of CSFV C-strain. The fitness of this virus (vflc36 BVDVII 684–796 ) seemed to be reduced compared to vflc9 (with the complete antigenic region of BVDVII).
The MPEG-4 standard and its applications in virtual 3D environments (2002)

The Moving Pictures Experts Group (SC11/WG29 of ISO/IEC) is currently developing the MPEG-4 standard aiming at interactive multimedia applications. Its first version was released in early 1999, a second one will follow early 2000. In addition to an increased compression efficiency for storage and transmission applications at a wide range of bit-rates, MPEG-4 will offer advanced content-based functionalities for interactive services, such as the possibility of accessing and manipulating natural or synthetic audiovisual objects in 2D or 3D scene representations. Against this background the paper first outlines the current status of MPEG-4 standardization and then concentrates on an example application if MPEG-4 to interactive services using virtual 3D environments in combination with streaming of real-time data.
Dinuclear Nickel–Ruthenium Complexes as Functional Bio‐Inspired Models of [NiFe] Hydrogenases (2007)

Abstract The front cover picture shows a bioinspired model for the active site of [NiFe] hydrogenases. Interactions between the metal centers in combination with the structural features at the active site allow these complexes to serve as suitable catalysts for H 2 electroproduction. Details are discussed in the article by V. Artero, M. Foutecave et al. on p. 2613 ff.
Modeling of magnetic vibrational energy harvesters using equivalent circuit representations (2007)

This paper develops and analyzes an equivalent circuit model of magnetic energy harvesters using reduced-order lumped element modeling (LEM) methods. This model is intended to enhance the design and analysis of a magnetic energy harvesting system by enabling direct physical insight into the system dynamics and simple circuit analysis techniques to extract all relevant performance parameters. Moreover, the model provides the ability to use circuit simulation software (e.g. PSPICE) to model the entire system in conjunction with nonlinear and/or active power electronic circuits. The circuit model is experimentally validated through electrical and mechanical measurements on a prototypical electromagnetic energy harvester.
A Dose-Ranging Study of a Prototype Synthetic HIV-1MN V3 Branched Peptide Vaccine (1996)

A phase I double-blind trial was done to examine the safety and immunogenicity of a prototype synthetic human immunodeficiency virus type 1 MN strain (HIV-1MN) third variable region domain (V3) branched peptide vaccine in HIV-1-uninfected healthy adult volunteers. Subjects were randomly assigned to receive 20, 100, or 500 micrograms of vaccine or alum adjuvant control on days 0, 28, and 168. The vaccine was well-tolerated and appeared safe. Induction of binding antibody to V3 MN branched peptide was vaccine dose-related and was detectable in 9 of 10 subjects in the highest-vaccine-dose group. HIV-1MN-neutralizing antibody was detected after the third 500-micrograms dose in 8 of 10 subjects at the 90% neutralization end point. V3 MN peptide stimulated lymphocyte proliferation in 15 (75%) of 20 subjects after vaccination. In conclusion, this prototype vaccine was safe and it induced humoral and cell-mediated immune responses.
Spectral modulation of two coherently separated femtosecond laser pulses (1992)

A train of 150-fs 76-MHz pulses is directed into a Michelson interferometer with a path difference larger than the pulse spatial length. A modulated spectrum with a modulation frequency that increases with the path difference is observed. The consequence is discussed.
SECEC Research Grant 2008 II: Use of platelet- and leucocyte-rich fibrin (L-PRF) does not affect late rotator cuff tendon healing: a prospective randomized controlled study (2015)

Arthroscopic rotator cuff repair with application of L-PRF yields no beneficial effect in clinical outcome, anatomic healing rate, mean postoperative defect size, and tendon quality at 12 months of follow-up.
Immunological studies of young adults with severe periodontitis (1981)

The objective of this study was to determine whether young adults (19–30 yrs.) with severe, generalized periodontal destruction differed from an age matched population with a healthy periodontium when compared by a thorough medical evaluation and/or an evaluation of humoral immunoglobulins and complement levels. The medical laboratory testing included BP, EKG, chest film, VDRL, urinalysis, hematology, blood chemistry, GTT, and a physical examination. The evaluations of immunoglobulins and complement included levels of serum and salivary IgG, IgA, IgM and 8 proteins of the classical and alternative complement pathway and levels of serum antibody to a panel of bacteria. The two groups were very similar in results of medical evaluations, antibody, complement, properdin, and immunoglobulin levels in most comparisons. The periodontally diseased group did have higher IgG levels and a tendency for higher IgA in saliva, probably due to gingival fluid contributing to saliva, including production of IgG locally in the gingiva. There was also a tendency for higher IgG in serum of the diseased group, resulting from more individuals in that group having elevated levels than in the healthy group. The mean levels of both