gebhart/patrepeval huggingface dataset:
Identification of Human Anti-HIV gp160 Monoclonal Antibodies That Make Effective Immunotoxins (2016)

There is increased interest in using antibodies to treat and cure HIV infection. Antibodies can neutralize free virus and kill cells already carrying the virus. The virus envelope (Env) is the only HIV protein expressed on the surfaces of virions and infected cells. In this study, we examined a panel of human anti-Env antibodies for their ability to deliver cell-killing toxins to HIV-infected cells and to perform other antiviral functions. The ability of an antibody to make an effective immunotoxin could not be predicted from its other functional characteristics, such as its neutralizing activity. Anti-HIV immunotoxins could be used to eliminate virus reservoirs that persist despite effective antiretroviral therapy.
Solid State Polycondensation in Dispersed Medium of 11-Aminoundecanoic Acid (2001)

The polycondensation of 11-aminoundecanoic acid was carried out in the solid state in dispersed medium: Decalin which is an inert saturated cyclic hydrocarbon and does not react whith the monomer and the condensation by product, water, was added to the monomer. In order to avoid a coagulation of the reaction mixture, an original strategy was developed using a liquid-solid dispersion instead of a liquid-liquid dispersion as described in the few studies reported in the literature for the polycondenstation of this monomer. A liquid-liquid suspension step was used at the early beginning of the reaction in order to melt, disperse and break the crystallinity of the monomer, then, the liquid droplets were solidified by cooling. During the polycondensation, the temperature was raised in successive steps in order to maintain the particles in the solid state. With a convenient treatment, it was possible to obtain a polymer powder with a defined particle size distribution and to reach fairly high molecular weights.
Statistical Frameworks for Detecting Tunnelling in Cyber Defence Using Big Data (2014)

How can we effectively use costly statistical models in the defence of large computer networks? Statistical modelling and machine learning are potentially powerful ways to detect threats as they do not require a human level understanding of the attack. However, they are rarely applied in practice as the computational cost of deploying all but the most simple algorithms can become implausibly large. Here we describe a multilevel approach to statistical modelling in which descriptions of the normal running of the network are built up from the lower netflow level to higher-level sessions and graph-level descriptions. Statistical models at low levels are most capable of detecting the unusual activity that might be a result of malicious software or hackers, but are too costly to run over the whole network. We develop a fast algorithm to identify tunnelling behaviour at the session level using 'telescoping' of sessions containing other sessions, and demonstrate that this allows a statistical model to be run at scale on netflow timings. The method is applied to a toy dataset using an artificial 'attack'.
Dry etching of single-point cutting tool made of nano-polycrystalline diamond using oxygen plasma (Shapeable cutting edge radius) (2022)

Dry etching using oxygen plasma was conducted on a single-point cutting tool made of nano-polycrystalline diamond to clarify the shapeable cutting edge radius (CER). The CER of the tool was measured by atomic force microscopy (AFM). The cantilever employed was made of single crystal silicon and had a tetrahedral shape with a probe tip radius of 4 to 10 nm. The CER can be identified by subtracting the probe tip radius from a measured CER when the probe tip radius is fixed at a certain value. Dry etching tests revealed that the measured CER decreased and converged to a constant value equivalent to the probe tip radius with increasing etching time. Utilizing this phenomenon, a standard tool suitable for calibrating the probe tip radius was fabricated. The CER and the variation in the CER of the standard tool were less than 0.1 nm. This calibration using the standard tool made it possible to identify the CER from the measured CER. It became clear that the CER converged to less than 0.1 nm, and the variation in converged CER was less than 0.5 nm. Hence, it can be concluded that the shapeable CER that can be formed by dry etching using oxygen plasma is less than 0.5 nm.
Phase-Shift-Based Antenna Selection for MIMO Channels (2004)

This paper addresses the antenna subset selection in multiple antenna systems with full diversity transmission, for both correlated and uncorrelated channels. To reduce the severe performance degradation of traditional selection/combining schemes, we propose to embed phase-shift-only operations in the RF chains before selection. The resulting system shows a significant advantage in utilizing the multiple antenna diversity under almost any channel condition while incurring only a small hardware overhead. With the optimum phase shifter design given in analytical form, our analysis shows that with more than two branches allowed for selection, the new scheme can achieve the same SNR gain as the full-complexity MRC (maximum-ratio-combining). Even when only one branch is allowed, the performance is still well above the conventional selection scheme and near optimum.
The synthesis of 1,3‐dihydro‐1‐[1‐[(4‐methyl‐4H‐6H‐pyrrolo[1,2‐a][4,1]benzoxazepin‐4‐yl)methyl]‐4‐piperidinyl]‐2H‐benzimidazol‐2‐one (1:1) maleate (CGS 9343 B, potent calmodulin inhibitor) (1988)

Abstract A practical synthesis of the title compound 7b is described in seven steps in approximately 10% overall yield. The key step in the synthesis is the formation of the unusual tricyclic ring system 4 via acid catalyzed cyclization.
Immediate observation of embedded structure after top-down delayering by using “Dig and See” technology for GFIS-SIM based accurate overlay metrology (Conference Presentation) (2020)

When manufacturing a semiconductor device having a three-dimensional structure, grasping the positional relationship between the upper and lower structures is important. Our “Dig & See” technology using GFIS-SIM enables such a device to be processed and its lower layers observed by quickly switching ion beams. With this technology, the digging of only the narrow areas of interest expedites delayering. Moreover, the structure of the lower layer can be exposed by top-down delayering and observed without using another tool. Unlike with other methods, the position of the lower layer can be determined with reference to the upper layer position.
A Controlled Investigation of Optimal Internal Medicine Ward Team Structure at a Teaching Hospital (2012)

Altering internal medicine ward team structure to reduce the ratio of housestaff to attending physicians improved the perceived educational experience without altering objective healthcare outcomes.
Konditionale Kontrolle der CRISPR/Cas9‐Funktion (2016)

Abstract Das CRISPR/Cas9‐Endonukleasesystem, das aus einer Guide‐RNA zur Erkennung einer Zielsequenz der DNA und dem Cas9‐Nukleaseprotein zur Bindung und Prozessierung der Ziel‐DNA besteht, wurde intensiv erforscht und findet bereits breite Anwendung im Gen‐Editing, der Synthesebiologie und der transkriptionellen Modulation in Zellen und Tieren. Mit dem Ziel einer präziseren Genmodifizierung und der Weiterentwicklung des CRISPR/Cas9‐Systems zu einem räumlich‐zeitlich kontrollierbaren Genregulationssystem wurden kürzlich mehrere Ansätze zur konditionalen Aktivierung der Cas9‐Funktion durch niedermolekulare Verbindungen (“kleine Moleküle”) oder Licht entwickelt. Diese Methoden führten zu einer verbesserten Spezifität des CRISPR/Cas9‐Systems im Gen‐Editing und ermöglichten dessen Aktivierung mit zeitlicher und räumlicher Präzision.
The GOL-NB program: further steps in multiple-mirror confinement research (2016)

Physical and technical details of the GOL-NB project are presented. GOL-NB is a medium-scale multiple-mirror trap that is under development in the Budker Institute, Novosibirsk, Russia. This device will be created in several years as a deep conversion of the existing GOL-3 facility. It will consist of a central trap with two 0.75 MW neutral beams, two multiple-mirror solenoids, two expander tanks and a plasma gun that creates the start plasma. The central trap with the neutral beam injection-heated plasma is a compact gas-dynamic system. The multiple-mirror sections should decrease the power and particle losses along the magnetic field. The confinement improvement factor depends on plasma parameters and on the magnetic configuration in the multiple mirrors. The main physical task of GOL-NB is direct demonstration of the performance of multiple-mirror sections that will change equilibrium plasma parameters in the central trap. In this paper we discuss results of the scenario modeling and progress in the hardware.
Effect of receptor binding domain mutations on receptor binding and transmissibility of avian influenza H5N1 virusesâ (2011)

Although H5N1 influenza viruses have been responsible for hundreds of human infections, these avian influenza viruses have not fully adapted to the human host. The lack of sustained transmission in humans may be due, in part, to their avian-like receptor preference. Here, we have introduced receptor binding domain mutations within the hemagglutinin (HA) gene of two H5N1 viruses and evaluated changes in receptor binding specificity by glycan microarray analysis. The impact of these mutations on replication efficiency was assessed in vitro and in vivo. Although certain mutations switched the receptor binding preference of the H5 HA, the rescued mutant viruses displayed reduced replication in vitro and delayed peak virus shedding in ferrets. An improvement in transmission efficiency was not observed with any of the mutants compared to the parental viruses, indicating that alternative molecular changes are required for H5N1 viruses to fully adapt to humans and to acquire pandemic capability.
An In Situ Multiscale Study of Ion and Electron Motion in a Lithium‐Ion Battery Composite Electrode (2014)

This work reveals the great potential of in situ dielectric spectroscopy for deciphering the motion of ions and electrons on different scales in lithium‐ion battery electrodes. One of the main bottlenecks limiting composite electrode kinetics and energy density, is a critical lack of fundamental understanding with respect to the electronic and the ionic transport within the electrode architecture. The latter is a granular material made up of clusters of particles, in which the particles are separated by boundaries that limit the electronic transport. The ionic transport is also severely restricted due to its tortuous porosity. Here, in situ dielectric spectroscopy is used to study the lithium‐ion battery LiNi 1/3 Co 1/3 Mn 1/3 O 2 composite electrodes. Short‐ and long‐range motions of ions are evident in the low‐frequency region. At higher frequencies, the influence of the adsorbed electrolyte ions on the electronic transfer at the micrometer scale is shown.
Complimentary mechanisms of dual checkpoint blockade expand unique T-cell repertoires and activate adaptive anti-tumor immunity in triple-negative breast tumors (2017)

Triple-negative breast cancer (TNBC) is an aggressive and molecularly diverse breast cancer subtype typified by the presence of p53 mutations (∼80%), elevated immune gene signatures and neoantigen expression, as well as the presence of tumor infiltrating lymphocytes (TILs). As these factors are hypothesized to be strong immunologic prerequisites for the use of immune checkpoint blockade (ICB) antibodies, multiple clinical trials testing single ICBs have advanced to Phase III, with early indications of heterogeneous response rates of <20% to anti-PD1 and anti-PDL1 ICB. While promising, these modest response rates highlight the need for mechanistic studies to understand how different ICBs function, how their combination impacts functionality and efficacy, as well as what immunologic parameters predict efficacy to different ICBs regimens in TNBC. To address these issues, we tested anti-PD1 and anti-CTLA4 in multiple models of TNBC and found that their combination profoundly enhanced the efficacy of either treatment alone. We demonstrate that this efficacy is due to anti-CTLA4-driven expansion of an individually unique T-cell receptor (TCR) repertoire whose functionality is enhanced by both intratumoral Treg suppression and anti-PD1 blockade of tumor expressed PDL1. Notably, the individuality of the TCR repertoire was observed regardless of whether the tumor cells expressed a nonself antigen (ovalbumin) or if tumor-specific transgenic T-cells were transferred prior to sequencing. However, responsiveness was strongly correlated with systemic measures of tumor-specific T-cell and B-cell responses, which along with systemic assessment of TCR expansion, may serve as the most useful predictors for clinical responsiveness in future clinical trials of TNBC utilizing anti-PD1/anti-CTLA4 ICB.
Soft Robotics for Chemists (2011)

„Weiche“ Roboter: Eine Methode auf der Grundlage pneumatischer Netzwerke (PneuNets) ermöglicht ausgeprägte Aktuationen in weichen Elastomeren durch Druckaufbau in den eingelassenen Kanälen der Netzwerke. Beispiele umfassen eine Struktur, die ihre Krümmung von konvex zu konkav ändern kann, sowie Greifer für zerbrechliche Gegenstände (z. B. ein rohes Hühnerei).
A robust parallel implementation of 2D model-based recognition (2003)

An approach to 2D model-based object recognition is developed, suitable for implementation on a highly parallel SIMD (single-instruction, multiple data stream) computer. Object models and image data are represented as contour features. Transformation sampling is used to determine the optimal model-feature-to-image-feature transformation by sampling the space of possible transformations. Only a small part of this space need actually be sampled due to the constraints placed on transformations by individual matches of image features to model features. The procedure requires O(Kmn) processors and O(log/sup 2/ (Kmn)) time, where m is the number of model features, n is the number of image features, and K depends on the size of the image. The procedure works well and is extremely robust in the presence of occlusion. An implementation of the procedure on the Connection Machine is described, and some experimental results given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
REGULATION OF GENE EXPRESSION IN LECTIN-STIMULATED OR LYMPHOKINE-STIMULATED T LYMPHOCYTES1 (1988)

The effects of cyclosporine were examined on gene expression induced in T lymphocytes by mitogenic lectins and interleukin 2 (IL-2). Used at concentrations that inhibited proliferation of human peripheral blood lymphocytes by approximately 90%, CsA suppressed, to different extents, the phytohemagglutinin-stimulated expression of various genes, with levels of mRNAs for IL-2 being inhibited by approximately 100%, c-myc and N-ras by approximately 80%, and c-fos and IL-2 receptors by approximately 50%. Comparisons of the actions of CsA on gene expression in a cloned murine T cell (L2), stimulated with concanavalin A or IL-2, demonstrated that CsA specifically blocked the accumulation of mRNAs for the c-myc and p53 protooncogenes when induced by Con A, but not when induced by IL-2. Taken together, these findings indicate that several pathways can control the expression of a particular gene, and suggest that CsA interferes with only some of these regulatory pathways of gene expression in T lymphocytes.
Physical Modelling and Simulation of Advanced Si-devices - An Industrial Approach (1993)

A review is given of our recently improved physical models for device simulators. They have been implemented in MEDICI and MINIMOS. Examples of actual MOS and Bipolar transistors as well as more exploratory transistor structures will be presented. The physical insight obtained from these device simulations is used in our compact transistor models. Their strength and large validity range will be illustrated.
A High-Efficiency Driver Circuit for a Gas-Sensor Microheater Based on a Switch-Mode DC-to-DC Converter (2020)

Low power consumption is one of the critical factors for successful Internet of Things (IoT) applications. In such applications, gas sensors have become a main source of power consumption because energy conversion efficiency of the microheater is relative over a wide range of operating temperatures. To improve the energy-conversion efficiency of gas-sensor microheaters, this paper proposes integrated switch-mode DC-to-DC power converter technology which we compare with traditional driving methods such as pulse-width modulation and the linear mode. The results indicate that energy conversion efficiency with this proposed method remains over 90% from 150 °C to 400 °C when using a 3.0, 4.2 and 5.0 V power supply. Energy-conversion efficiency increases by 1-74% compared with results obtained using the traditional driving methods, and the sensing film still detects alcohol and toluene at 200 °C and 280 °C, respectively, with high energy conversion efficiency. These results show that the proposed method is useful and should be further developed to drive gas-sensor microheaters, and then integrated into the circuits of the complementary metal-oxide-semiconductor micro electro mechanical systems (CMOS-MEMS).
Theoretical Study of the Inverting Mechanism in a Processive Cellobiohydrolase with Quantum Mechanical Calculations (2012)

The Hypocrea jecorina Family 6 cellobiohydrolase (Cel6A) is one of most efficient enzymes for cellulose deconstruction to soluble sugars and is thus of significant current interest for the growing biofuels industry. Cel6A is known to hydrolyze b(1,4)-glycosidic linkages in cellulose via an inverting mechanism, but there are still questions that remain regarding the role of water and the catalytic base. Here we study the inverting, single displacement, hydrolytic reaction mechanism in Cel6A using density functional theory (DFT) calculations. The computational model used to follow the reaction is a truncated active site model with several explicit waters based on structural studies of H. jecorina Cel6A. Proposed mechanisms are evaluated with several density functionals. From our calculations, the role of the water in nucleophilic attack on the anomeric carbon, and the roles of several residues in the active site loops are elucidated explicitly for the first time. We also apply quantum mechanical calculations to understand the proton transfer reaction which completes the catalytic cycle.
Overexpression of wbkF gene in Brucella abortus RB51WboA leads to increased O-polysaccharide expression and enhanced vaccine efficacy against B. abortus 2308, B. melitensis 16M, and B. suis 1330 in a murine brucellosis model (2019)

Brucella abortus RB51 is an attenuated, stable, spontaneous rough mutant derived in the laboratory from the virulent strain B. abortus 2308. Previous studies discovered that the wboA gene, which encodes a glycosyltransferase required for synthesis of the O-polysaccharide, is disrupted in strain RB51 by an IS711 element. However, complementation of strain RB51 with a functional wboA gene (strain RB51WboA) does not confer it a smooth phenotype but results in low levels of cytoplasmic O-polysaccharide synthesis. In this study, we asked if increasing the potential availability of bactoprenol priming precursors in strain RB51WboA would increase the levels of O-polysaccharide synthesis and enhance the protective efficacy against virulent Brucella challenge. To achieve this, we overexpressed the wbkF gene, which encodes a putative undecaprenyl-glycosyltransferase involved in bactoprenol priming for O-polysaccharide polymerization, in strain RB51WboA to generate strain RB51WboAKF. In comparison to strain RB51WboA, strain RB51WboAKF expressed higher levels of O-polysaccharide, but was still attenuated and remained phenotypically rough. Mice immunized with strain RB51WboAKF developed increased levels of smooth LPS-specific serum antibodies, primarily of IgG2a and IgG3 isotype. Splenocytes from mice vaccinated with strain RB51WboAKF secreted higher levels of antigen-specific IFN-γ and TNF-α and contained more numbers of antigen-specific IFN-γ secreting CD4+ and CD8+ T lymphocytes when compared to those of the RB51 or RB51WboA vaccinated groups. Immunization with strain RB51WboAKF conferred enhanced protection against virulent B. abortus 2308, B. melitensis 16M and B. suis 1330 challenge when compared to the currently used vaccine strains. Our results suggest that strain RB51WboAKF has the potential to be a more efficacious vaccine than its parent strain in natural hosts.
Design and recognition properties of a hydropathically complementary peptide to human interleukin 1 β (1992)

A computer-designed hydropathically complementary peptide to human interleukin 1 beta (IL1 beta) precursor sequence 204-215 recognized the 204-215 peptide as well the entire IL1 beta protein with binding affinities in the micromolar range. Interaction between the complementary pair was characterized by analytical high-performance liquid affinity chromatography on columns derivatized with the computer-generated peptide. Recognition selectivity was clearly shown by the ability of the computer-generated complementary peptide columns to purify the IL1 beta-(204-215)-peptide from complex synthetic mixtures with high yields, independently of the type of solid support used. Recognition specificity was demonstrated by the inability of the IL1 beta-(204-215)-peptide and IL1 beta molecules to interact with blank columns or columns derivatized with other non-related peptides. Furthermore, scrambling the sequence of the computer-generated peptide or the IL1 beta-(204-215)-peptide in such a way as to alter their hydropathic profiles had the effect of abolishing binding. The complementary pair failed to interact in the presence of competing peptide, thus providing further evidence of specificity. Computer-generated complementary peptide affinity columns also proved useful for purification of recombinant human IL1 beta protein directly from crude Escherichia coli lysates.
ChemInform Abstract: Inhibitors of Tyrosine Kinases Involved in Inflammation and Autoimmune Disease (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
The Bolocam Lockman Hole Millimeter‐Wave Galaxy Survey: Galaxy Candidates and Number Counts (2005)

We present results of a new deep 1.1 mm survey using Bolocam, a millimeter-wavelength bolometer array camera designed for mapping large fields at fast scan rates, without chopping. A map, galaxy candidate list, and derived number counts are presented. This survey encompasses 324 arcmin^2 to an rms noise level (filtered for point sources) of 1.4 mJy/beam and includes the entire regions surveyed by the published 8 mJy 850 micron JCMT SCUBA and 1.2 mm IRAM MAMBO surveys. We reduced the data using a custom software pipeline to remove correlated sky and instrument noise via a principal component analysis. Extensive simulations and jackknife tests were performed to confirm the robustness of our source candidates and estimate the effects of false detections, bias, and completeness. In total, 17 source candidates were detected at a significance > 3.0 sigma, with six expected false detections. Nine candidates are new detections, while eight candidates have coincident SCUBA 850 micron and/or MAMBO 1.2 mm detections. From our observed number counts, we estimate the underlying differential number count distribution of submillimeter galaxies and find it to be in general agreement with previous surveys. Modeling the spectral energy distributions of these submillimeter galaxies after observations of dusty nearby galaxies suggests extreme luminosities of L = 1.0-1.6 x 10^13 L_solar and, if powered by star formation, star formation rates of 500-800 M_solar/yr.