gebhart/patrepeval huggingface dataset:
Author response: Soluble collectin-12 mediates C3-independent docking of properdin that activates the alternative pathway of complement (2020)

A systematic set of experiments reveals how properdin specifically directs AP activation independently of primary C3 deposition additionally as an alternative convertase stabilizer, thus revising immune machinery of complement activation.
Smart current collector—fibre optic hit detection system for improved security on railway tracks (2013)

In a deregulated EU railway market, monitoring the vehicle and infrastructure interfaces is mandatory for the enhanced availability of operation and for reducing costs. Therefore, infrastructure managers need monitoring tools on overhead contact lines (OCLs). We know from earlier investigations that a measurement of contact forces alone is not sufficient (Schröder et al 2013 Opt. Lasers Eng. 51 172–9). In this study, we introduce a system which is fast enough to detect short disturbances and which can be used with regular trains. It is based on fibre optic sensors integrated with conventional current collectors (CCs). The system is designed to monitor hard and soft hits on the CC in horizontal (driving) and vertical (contact) direction. It was systematically tested in the laboratory as well as in test runs on commercial railways in several countries. With its help, a variety of minor as well as serious defects have been discovered and repaired at the CC–OCL interface.
An efficient rapid system for profiling the cellular activities of molecular libraries (2006)

Rapid quantitative methods for characterizing small molecules, peptides, proteins, or RNAs in a broad array of cellular assays would allow one to discover new biological activities associated with these molecules and also provide a more comprehensive profile of drug candidates early in the drug development process. Here we describe a robotic system, termed the automated compound profiler, capable of both propagating a large number of cell lines in parallel and assaying large collections of molecules simultaneously against a matrix of cellular assays in a highly reproducible manner. To illustrate its utility, we have characterized a set of 1,400 kinase inhibitors in a panel of 35 activated tyrosine-kinase-dependent cellular assays in dose-response format in a single experiment. Analysis of the resulting multidimensional dataset revealed subclusters of both inhibitors and kinases with closely correlated activities. The approach also identified activities for the p38 inhibitor BIRB796 and the dual src/abl inhibitor BMS-354825 and exposed the expected side activities for Glivec/STI571, including cellular inhibition of c-kit and platelet-derived growth factor receptor. This methodology provides a powerful tool for unraveling the cellular biology and molecular pharmacology of both naturally occurring and synthetic chemical diversity.
A design space for three-dimensional curve edition (2014)

Designing and editing 3D curves is often involved in a wide array of applications such as CAD, multimedia content edition or landscape and road generation. This diversity resulted in a spread of 3D-related works across different communities such as SIGCHI or SIGGRAPH. In this article, we introduce a design space to gather existing techniques in the field of 3D curves creation and edition. This design space is built around two axes: system and language, in order to describe and compare existing techniques.
Whole-cell fungal-mediated structural transformation of anabolic drug metenolone acetate into potent anti-inflammatory metabolites (2020)

Seven new derivatives, 6<i>α</i>-hydroxy-1-methyl-3-oxo-5<i>α</i>-androst-1-en-17-yl acetate (<b>2</b>), 6<i>α</i>,17<i>β</i>-dihydroxy-1-methyl-3-oxo-5<i>α</i>-androst-1-en (<b>3</b>), 7<i>β</i>-hydroxy-1-methyl-3-oxo-5<i>α</i>-androst-1-en-17-yl acetate (<b>4</b>), 15<i>β</i>,20-dihydroxy-1-methyl-3-oxo-5<i>α</i>-androst-1-en-17-yl acetate (<b>5</b>), 15<i>β</i>-hydroxy-1-methyl-3-oxo-5<i>α</i>-androst-1-en-17-yl acetate (<b>6</b>), 12<i>β</i>,17<i>β</i>-dihydroxy-1-methyl-3-oxoandrosta-1,4-dien (<b>11</b>), and 7<i>β,</i>15<i>β,</i>17<i>β</i>-trihydroxy-1-methyl-3-oxo-5<i>α</i>-androst-1-en (<b>14</b>), along with six known metabolites, 17<i>β</i>-hydroxy-1-methyl-3-oxoandrosta-1,4-dien (<b>7</b>), 17<i>β</i>-hydroxy-1-methyl-3-oxo-5<i>α</i>-androst-1-en (<b>8</b>), 17<i>β</i>-hydroxy-1-methyl-3-oxo-5<i>β</i>-androst-1-en (<b>9</b>), 1-methyl-5<i>β</i>-androst-1-en-3,17-dione (10), 1-methyl-3-oxoandrosta-1,4-dien-3,17-dione (<b>12</b>), and 17<i>β</i>-hydroxy-1<i>α</i>-methyl-5<i>α</i>-androstan-3-one (<b>13</b>) of metenolone acetate (<b>1</b>), were synthesized through whole-cell biocatalysis with <i>Rhizopus stolonifer</i>, <i>Aspergillus alliaceous</i>, <i>Fusarium lini</i>, and <i>Cunninghamella elegans</i>. Atamestane (<b>12</b>), an aromatase inhibitor, was synthesized for the first time <i>via F. lini</i>-mediated transformation of <b>1</b> as the major product. Hydroxylation, dehydrogenation, and reduction were occurred during biocatalysis. Study indicated that <i>F. lini</i> was able to catalyze dehydrogenation reactions selectively. Structures of compounds <b>1</b>-<b>14</b> were determined through NMR, HRFAB-MS, and IR spectroscopic data. Compounds <b>1</b>-<b>14</b> were identified as non-cytotoxic against BJ human fibroblast cell line (ATCC CRL-2522). Metabolite <b>5</b> (81.0 ± 2.5%) showed a potent activity against TNF-<i>α</i> production, as compared to the substrate <b>1</b> (62.5 ± 4.4%). Metabolites <b>2</b> (73.4 ± 0.6%), <b>8</b> (69.7 ± 1.4%), <b>10</b> (73.2 ± 0.3%), <b>11</b> (60.1 ± 3.3%), and <b>12</b> (71.0 ± 7.2%), also showed a good inhibition of TNF-α production. Compounds <b>3</b> (IC<sub>50</sub> = 4.4 ± 0.01 µg/mL), and <b>5</b> (IC<sub>50</sub> = 10.2 ± 0.01 µg/mL) showed a significant activity against T-cell proliferation. Identification of selective inhibitors of TNF-α production, and T-cell proliferation is a step forward towards the development of anti-inflammatory drugs.
Acoustic characteristics of laboratory breaking waves (1992)

Results of a laboratory experiment to characterize the underwater sound field radiated from breaking waves are described. Waves are generated by a computer controlled plunging-type wave maker that propagate along a 40-ft-long channel and break at the surface of 12×12×8-ft anechoic water tank. The wave-maker parameters are controlled to produce spilling-type breakers with different breaker intensity (i.e., bubble cloud size). At smaller wave-maker amplitudes, a ‘‘gentle’’ spilling breaker can be produced to create a discrete number of bubbles. The number of bubbles and the sounds emitted by them can be measured and their type can be identified [H. Medwin and A. C. Daniel, J. Acoust. Soc. Am. 88, 408–412 (1990)]. Increasing the amplitude of the wave maker causes the breaker intensity to increase. The evolution of the bubble cloud size and its acoustic emissions are monitored by a high-speed video camera. The acoustic noise emitted at different breaker intensities by individual bubbles and by bubble clouds is presented and scaled to ocean breakers. Backscattering from bubble clouds was also observed using a parametric source. The scattered signal level was measured in the presence and absence of breaking waves as the insonifying frequency approached the collective oscillation frequencies of the bubble clouds. [Work supported by ONR.]
Search for excited leptons in proton-proton collisions ats=7  TeVwith the ATLAS detector (2012)

The ATLAS detector is used to search for excited leptons in the electromagnetic radiative decay channel ' ! '. Results are presented based on the analysis of pp collisions at a center-of-mass energy of 7 TeV corresponding to an integrated luminosity of 2:05 fb 1 . No evidence for excited leptons is found, and limits are set on the compositeness scale as a function of the excited lepton mass m ' . In the special case where m ' , excited electron and muon masses below 1.87 TeV and 1.75 TeV are excluded at 95% C.L., respectively.
Enhanced charge carrier mobility and lifetime suppress hysteresis and improve efficiency in planar perovskite solar cells (2017)

Turren-Cruz S-H, Saliba M, Mayer MT, et al. Enhanced charge carrier mobility and lifetime suppress hysteresis and improve efficiency in planar perovskite solar cells. &lt;em&gt;Energy &amp;amp; Environmental Science&lt;/em&gt;. 2018;11(1):78-86.
Deep interpretability for GWAS (2020)

Genome-Wide Association Studies are typically conducted using linear models to find genetic variants associated with common diseases. In these studies, association testing is done on a variant-by-variant basis, possibly missing out on non-linear interaction effects between variants. Deep networks can be used to model these interactions, but they are difficult to train and interpret on large genetic datasets. We propose a method that uses the gradient based deep interpretability technique named DeepLIFT to show that known diabetes genetic risk factors can be identified using deep models along with possibly novel associations.
Perfluorochemical liquids modulate cell-mediated inflammatory responses (2001)

At PFC concentrations comparable with those in blood during liquid ventilation, PFC liquids did not induce variables associated with inflammation. In the presence of high PFC concentrations, simulating the condition in which bronchoalveolar cells are exposed to PFC, monocytes may be induced by PFB to produce reactive oxygen species, and blood leukocytes induced by PFB to express CD11b and by PFD to secrete interleukin-8; the presence of either PFC attenuated tumor necrosis factor-alpha production after lipopolysaccharide stimulation.
How did the Decisions Come About? (2011)

During a long deliberative process, opinion stability is unlikely. This chapter documents the path taken by assembly members' views on electoral systems. It ascertains when preferences emerged, whether they moved afterwards, how volatile they were, and whether the movement was steered by comprehensible factors. The chapter shows that the opinions of ordinary citizens directly involved in an extensive exercise of public decision-making do not evolve chaotically over time. Assembly members' views and preferences about electoral systems developed gradually as they were acquiring information about the various options. These attitudes then remained quite stable over the subsequent months. Very little aggregate or individual volatility characterized the consultation and deliberation phases.
Instantly decodable network codes for real-time applications (2013)

We consider the scenario of broadcasting for realtime applications and loss recovery via instantly decodable network coding. Past work focused on minimizing the completion delay, which is not the right objective for real-time applications that have strict deadlines. In this work, we are interested in finding a code that is instantly decodable by the maximum number of users. First, we prove that this problem is NP-Hard in the general case. Then we consider the practical probabilistic scenario, where users have i.i.d. loss probability, and the number of packets is linear or polynomial in the number of users. In this case, we provide a polynomial-time (in the number of users) algorithm that finds the optimal coded packet. Simulation results show that the proposed coding scheme significantly outperforms an optimal repetition code and a COPE-like greedy scheme.
High Current Lanthanum Hexaboride Hollow Cathode for 20-200 kW Hall Thrusters (2017)

The demand for higher power Hall and ion thrusters continues for providing high thrust and long life for deep space mission. The X3 nested Hall thruster is capable of power levels in the 20 to 200-kW range, and is being developed by the University of Michigan and Aerojet for future cargo and manned-missions. The cathode for this thruster is required to produce discharge currents of 50 to 350 A with lifetimes in excess of 10 khrs. A high-current lanthanum hexaboride (LaB6) hollow cathode was previously developed at JPL for these applications, and was successfully operated at over 250 A of discharge current. An updated version of this cathode has been designed, built and tested at JPL, and then used to run the X3 nested Hall thruster at currents of up to 250 A. The new version is designed to reduced orifice plate overheating at high currents, and is capable of injecting auxiliary gas directly into the near-cathode plume from two locations to minimize energetic ion generation at high current. The cathode is predicted to be capable of producing over 350 A of discharge current, and has been tested to date at JPL at steady-state discharge currents from 25 A to 300 A.
Influence of the electronic state of the metals in Fe–Pt/SiO2 catalysts on the performance of hydrogenation of phenylacetylene (2019)

Iron-modified platinum bimetallic system, 1% Pt–1% Fe/SiO2, provides selective liquid-phase hydrogenation of phenylacetylene into styrene at 70 °C and 5 atm. This effect is attributed to the electron enrichment of the Pt surface atoms due to a charge transfer from Fe to Pt or contact interactions between these two metals, as indicated by XPS and DRIFTS-CO.
Classification and selection of biomarkers in genomic data using LASSO (2004)

High-throughput gene expression technologies such as microarrays have been utilized in a variety of scientific applications. Most of the work has been on assessing univariate associations between gene expression with clinical outcome (variable selection) or on developing classification procedures with gene expression data (supervised learning). We consider a hybrid variable selection/classification approach that is based on linear combinations of the gene expression profiles that maximize an accuracy measure summarized using the receiver operating characteristic curve. Under a specific probability model, this leads to consideration of linear discriminant functions. We incorporate an automated variable selection approach using LASSO. An equivalence between LASSO estimation with support vector machines allows for model fitting using standard software. We apply the proposed method to simulated data as well as data from a recently published prostate cancer study.
NT-04 * THE Jak2 SMALL MOLECULE INHIBITOR, G6, REDUCES THE TUMORIGENIC POTENTIAL OF T98G GLIOBLASTOMA CELLS IN VITRO AND IN VIVO (2014)

Glioblastoma multiforme (GBM) is the most common and the most aggressive form of primary brain tumor. Jak2 is a non-receptor tyrosine kinase that is involved in proliferative signaling through its association with various cell surface receptors. Hyperactive Jak2 signaling has been implicated in numerous hematological disorders as well as in various solid tumors including GBM. Our lab has developed a Jak2 small molecule inhibitor known as G6. It exhibits potent efficacy in vitro and in several in vivo models of Jak2-mediated hematological disease. Here, we hypothesized that G6 would inhibit the pathogenic growth of GBM cells expressing hyperactive Jak2. To test this, we screened several GBM cell lines and found that T98G cells express readily detectable levels of active Jak2. We found that G6 treatment of these cells reduced the phosphorylation of Jak2 and STAT3, in a dose-dependent manner. In addition, G6 treatment reduced the migratory potential, invasive potential, clonogenic growth potential, and overall viability of these cells. The effect of G6 was due to its direct suppression of Jak2 function and not via suppression of off-target kinases, as these effects were recapitulated in cells that received Jak2 specific shRNA. G6 also significantly increased the levels of caspase-dependent apoptosis in T98G cells, when compared to cells that were treated with vehicle control. Lastly, when T98G cells were injected into nude mice, G6 treatment significantly reduced tumor volume and this was concomitant with significantly decreased levels of phospho-Jak2 and phospho-STAT3 within the tumors themselves. Lastly, tumors harvested from mice that received G6 had significantly less vimentin protein levels and significantly increased fibrosis when compared to tumors from mice that received vehicle control solution. Overall, these combined in vitro and in vivo results indicate that G6 may be a viable therapeutic option against GBM exhibiting hyperactivation of Jak2.
Ultrathin Nanowires—A Materials Chemistry Perspective (2008)

Abstract The recent years have seen an explosive interest in one‐dimensional nanostructures, as testified by the number of citations this field has accrued; as customary, its blossoming was enabled by chemical breakthroughs that allowed the reproducible and affordable synthesis of such structures., The limitations of those syntheses was in the diameter of the nanowires that it could produce (hardly &lt; 10 nm), and in the use of expensive and low‐yield techniques, such as chemical vapor deposition (CVD). This paper attempts to summarize the very recent chemical breakthroughs that have allowed the production of ultrathin nanowires, often in solution, and often in gram‐scale quantities. By no means is this a comprehensive coverage of the field, which can in part be found in other excellent reviews, , but a selection of those contributions that we feel would most help put this emerging field in perspective. We will review the various synthetic strategies, their pros and cons, and we will give our best guesses as to the future directions of the field and what we can expect from it.
ChemInform Abstract: CONCERNING THE USE OF POLYMER BASED PHOTOSENSITIZERS (1974)

Abstract Chlormethylierte Copolymere (I) aus Styrol und Divinylbenzol reagieren mit p‐Benzoylbenzoesäure (II) in Gegenwart von Triäthylamin zu den Estern (III), die z.B. durch Umesterung in Gegenwart von Methanol wiederum gespalten werden können.
Atomic Layer Deposition Preparation of Pd Nanoparticles on a Porous Carbon Support for Alcohol Oxidation (2011)

To reduce the loading of noble metals on fuel cell catalysts a synthesis method providing evenly distributed nanoparticles on the support surface is needed. Narrow size distribution palladium nanoparticles were prepared on a porous carbon support by atomic layer deposition (ALD), and their activity for ethanol and isopropanol oxidation was studied electrochemically in alkaline media. Palladium particles had smaller average particle sizes on the support material resulting in ∼50 mV lower onset potential and 2.5 times higher mass activity for alcohol oxidation compared with a commercial catalyst. The results indicate that the use of ALD allows the preparation of a noble metal nanoparticle catalyst, and this catalyst can provide similar mass activity with lower catalyst loading than current commercial fuel cell catalysts. This would significantly reduce the cost of the cell and provide a competitive advantage compared with other power sources.
From No Expression to High-Level Soluble Expression in Escherichia coli by Screening a Library of the Target Proteins with Randomized N-Termini (2008)

For structural studies by x-ray crystallography and nuclear magnetic resonance it is important for the target protein to be available in large quantity and high purity. Escherichia coli expression systems remain the most versatile and convenient means to produce a large quantity of recombinant proteins. Unfortunately, some proteins fail to be expressed in E. coli or are expressed in an insoluble form. To overcome the difficulty of no expression or expression at a very low level, a simple and efficient approach of screening a library of variants of a target protein with randomized N-termini was devised. In this method, a few N-terminal residues are randomized by designing a mixture of oligonucleotides for the forward PCR primer and we fuse the library in front of green fluorescent protein, which serves as a reporter for the target protein expression level and folding yield. In favorable cases this approach can result in high-level soluble expression of recombinant proteins in E. coli. This chapter describes the results of a test of this approach with a bacterial protein (the HI0952 gene product) that is not well expressed in E. coli.
Supplementary Data S3 from Disabled Homolog 2 Controls Prometastatic Activity of Tumor-Associated Macrophages (2023)

&lt;p&gt;Description of the functional status of WT and Dab2 KO macrophages. Related to Fig. 1C-D&lt;/p&gt;
An oomycete effector protein induces shade avoidance in Arabidopsis and attenuates salicylate signaling by binding to host proteins of the RADICAL-INDUCED CELL DEATH1 family (2017)

Abstract The oomycete pathogen Hyaloperonospora arabidopsidis ( Hpa ) causes downy mildew disease on Arabidopsis . During infection, Hpa like other biotrophic pathogens, suppresses activation of plant innate immunity by translocating effector proteins into host cells. Some of these effectors localize to the host cell nucleus where they may manipulate transcriptional reprogramming of plant defense genes. Here we report that the nuclear-localized Hpa effector HaRxL106, when expressed in Arabidopsis , induces shade avoidance and attenuates the transcriptional response to the defense signaling molecule salicylic acid. HaRxL106 interacts with RADICAL-INDUCED CELL DEATH1 (RCD1) and loss of RCD1 function renders Arabidopsis resilient against HaRxL106-mediated suppression of immunity. To further characterize the molecular functions of RCD1 we solved a crystal structure of RCD1’s Poly-(ADP-ribose)-Polymerase (PARP) domain and, based on non-conservation of amino acids constituting the active site of canonical PARPs, conclude that RCD1 has no PARP activity. We report that RCD1-type proteins are phosphorylated and identified histone-modifying Mut9-like kinases (MLKs) as RCD1-interacting proteins. A mlk1,3,4 triple mutant exhibits stronger SA-induced defense marker gene expression compared to wild-type plants. Our data suggest that HaRxL106 suppresses Arabidopsis innate immunity by manipulating the function(s) of RCD1 in the host cell nucleus and point towards a role of RCD1 as a transcriptional co-regulator that integrates signals from light and pathogen sensors.
Hierarchical Policy Learning for Hybrid Communication Load Balancing (2021)

Due to the uneven demographic distribution and people’s daily activities, communication systems usually experience highly imbalanced load across different cells. This imbalance leads to unsatisfied users in the congested cells and under-utilized resources in the less-loaded cells. To deal with this issue, existing work migrates the load from heavily loaded cells to lightly loaded cells, by either handing over active mode User Equipment (UEs) to other serving cells, or re-selecting the camping cells for idle mode UEs. In this paper, we further advance the research on Load Balancing (LB) with a hybrid control of both active and idle UEs. This task is challenging, due to the conflicts between Active-UE LB (AULB) and Idle-UE LB (IULB) policies. To overcome this challenge, we propose a Hierarchical Policy Learning (HPL) framework, which coordinates the actions between LB policies with a two-level learning structure. In this way, HPL produces AULB and IULB policies that are better aligned with each other. Extensive simulation results illustrate the efficiency and efficacy of the proposed HPL.
Distributed coding of multispectral images (2017)

Compression of multispectal images is of great importance in an environment where resources such as computational power and memory are scarce. To that end, we propose a new extremely low-complexity encoding approach for compression of multispectral images, that shifts the complexity to the decoding. Our method combines principles from compressed sensing and distributed source coding. Specifically, the encoder compressively measures blocks of the band of interest and uses syndrome coding to encode the bitplanes of the measurements. The decoder has access to side information, which is used to predict the bitplanes and to decode them. The side information is also used to guide the reconstruction of the image from the decoded measurements. Our experimental results demonstrate significant improvement in the rate-distortion trade-off when compared to coding schemes with similar complexity.