gebhart/patrepeval huggingface dataset:
Lightness dependencies and the effect of texture on suprathreshold lightness tolerances (2000)

A psychophysical experiment was performed to determine the effects of lightness dependency on suprathreshold lightness tolerances. Using a pass/fail method of constant stimuli, lightness tolerance thresholds were measured using achromatic stimuli centered at CIELAB L* = 10, 20, 40, 60, 80, and 90 using 44 observers. In addition to measuring tolerance thresholds for uniform samples, lightness tolerances were measured using stimuli with a simulated texture of thread wound on a card. A texture intermediate between the wound thread and the uniform stimuli was also used. A computer-controlled CRT was used to perform the experiments. Lightness tolerances were found to increase with increasing lightness of the test stimuli. For the uniform stimuli this effect was only evident at the higher lightnesses. For the textured stimuli, this trend was more evident throughout the whole lightness range. Texture had an effect of increasing the tolerance thresholds by a factor of almost 2 as compared to the uniform stimuli. The intermediate texture had tolerance thresholds that were between those of the uniform and full-textured stimuli. Transforming the results into a plot of threshold vs. intensity produced results that were more uniform across the three conditions. This may indicate that CIELAB is not the best space in which to model these effects. © 2000 John Wiley & Sons, Inc. Col Res Appl, 25, 241–249, 2000
Exploring the Therapeutic Efficacy of Glioma Vaccines Based on Allo- and Syngeneic Antigens and Distinct Immunological Costimulation Activators (2012)

The efficacy of a various immunotherapeutic immunisation strategies for malignant glioma brain cancer was evaluated in the syngeneic CNS-1 Lewis rat glioma model. A prototype glioma cancer vaccine, which was composed of multivalent antigens derived from allogeneic and syngeneic cells and lysates, formed the prototype preparation of antigens. These antigens reflect the autologous antigens derived from the patient's surgically removed tumor tissue, as well as allogeneic antigens form glioma tumor tissue surgically removed from donor patients. This antigen mixture provides a broad spectrum of tumor associated antigens (TAA) and helps to prevent escape of tumor immune surveillance when given as a vaccine. This antigen preparation was administered in a therapeutic setting with distinct single or multiple co-stimulation-favouring immunostimulants and evaluated for inhibition of tumor growth. Our prototype vaccine was able to arrest progression of tumor growth when co-delivered in a specific regimen together with the costimulating multi-TLR agonist, Bacille Calmette Guerin (BCG) and interleukin-2, or with the Toll-Like receptor (TLR) 7/8 activator resiquimod.
ChemInform Abstract: PREPARATION AND REARRANGEMENT OF TRICHOTHECANE‐LIKE COMPOUNDS. SYNTHESIS OF APLYSIN AND FILIFORMIN (1981)

Abstract Die Herstellung der Verbindungen (I)‐(III) wird beschrieben.
Application of the Refracted Near-Field Technique to Multimode Planar and Channel Waveguides in Glass (1986)

Article Application of the Refracted Near-Field Technique to Multimode Planar and Channel Waveguides in Glass was published on September 1, 1986 in the journal Journal of Optical Communications (volume 7, issue 3).
supplementary figure 1 from Efficacy of Anti-mesothelin Immunotoxin RG7787 plus Nab-Paclitaxel against Mesothelioma Patient–Derived Xenografts and Mesothelin as a Biomarker of Tumor Response (2023)

&lt;p&gt;Semiquantitative assessment of mesothelin expression using H-score in mesothelioma patient derived xenografts.&lt;/p&gt;
Micro-fluidic based Detection Platform for Rapid Pathogen Characterization in Water (2012)

We prototyped a compact micro-fluidic based flow cytometer for pathogen detection in water. The system uses a pin-photodiode for detection and yielded a detection limit of ~500MEPE, sufficient to reliably identify and count specifically-tagged pathogens.
Search for Large Extra Dimensions in Dielectron and Diphoton Production (2001)

We report a search for effects of large extra spatial dimensions in pp collisions at a center-of-mass energy of 1.8 TeV with the D0 detector, using events containing a pair of electrons or photons. The data are in good agreement with the expected background and do not exhibit evidence for large extra dimensions. We set the most restrictive lower limits to date, at the 95% C.L. on the effective Planck scale between 1.0 and 1.4 TeV for several formalisms and numbers of extra dimensions.
Filamentous Microorganisms Affiliated with Uncultured Bacterial Group at Phylum Level: Microbes as Causative Agent for Filamentous Bulking of Methanogenic Sludge Granules (2005)

Filamentous anaerobic sludge bulking was observed in an upflow anaerobic sludge blanket (UASB) reactor treating high-strength wastewater discharged from a sugar-manufacturing factory. In the bulking sludge, a number of thick filamentous cells were found, which were considered to be the causative agent for the bulking. To identify these filamentous cells, we applied an rRNA-based approach to the filamentous microbes. 16S rRNA gene analysis revealed that the filaments are uncultivated microbes affiliated with a clone cluster at the phylum level. In situ hybridization using a 16S rRNA-targeted oligonucleotide probe specific for the phylum KSB3 showed that the microbes were abundantly present in the bulking sludge. In addition, in situ hybridization analysis of normal granules (before bulking) indicated that the microbes are also abundant in healthy sludge granules ; the microbes are the major population on the surface of healthy sludge granules. This finding indicates that these filamentous microbes normally reside on the surface of granules, and that they outgrow the granules due to certain environmental changes, resulting in the filamentous bulking of sludge granules.
Metabolite Regulation of Nuclear Localization of Carbohydrate-response Element-binding Protein (ChREBP) (2016)

The carbohydrate-response element-binding protein (ChREBP) is a glucose-responsive transcription factor that plays an essential role in converting excess carbohydrate to fat storage in the liver. In response to glucose levels, ChREBP is regulated by nuclear/cytosol trafficking via interaction with 14-3-3 proteins, CRM-1 (exportin-1 or XPO-1), or importins. Nuclear localization of ChREBP was rapidly inhibited when incubated in branched-chain α-ketoacids, saturated and unsaturated fatty acids, or 5-aminoimidazole-4-carboxamide ribonucleotide. Here, we discovered that protein-free extracts of high fat-fed livers contained, in addition to ketone bodies, a new metabolite, identified as AMP, which specifically activates the interaction between ChREBP and 14-3-3. The crystal structure showed that AMP binds directly to the N terminus of ChREBP-α2 helix. Our results suggest that AMP inhibits the nuclear localization of ChREBP through an allosteric activation of ChREBP/14-3-3 interactions and not by activation of AMPK. AMP and ketone bodies together can therefore inhibit lipogenesis by restricting localization of ChREBP to the cytoplasm during periods of ketosis.
Precision adiabatic scanning calorimetry of a nematic – ferroelectric nematic phase transition (2021)

In high-resolution adiabatic scanning calorimetry (ASC) experiments, data for the temperature dependence of the specific enthalpy, h(T), and of the specific heat capacity, cp(T), are simultaneously obtained, from which the order of the phase transition and critical behaviour can be evaluated. ASC was applied to study the nematic to ferroelectric nematic phase transition (N–NF) in the liquid crystal molecule 4-[(4-nitrophenoxy)carbonyl]phenyl 2,4-dimethoxybenzoate (RM734). The N–NF was found to be very weakly first order with a latent heat Δh = 0.115 ± 0.005 J/g. The pretransitional specific heat capacity behaviour is substantially larger in the high-temperature N phase than in the low-temperature NF phase. In both phases the power-law analysis of cp(T) resulted in a critical exponent α = 0.50 ± 0.05 and amplitude ratio ANF/AN = 0.42 ± 0.03. The very small latent heat and the value of α indicate that the N–NF transition is close to a tricritical point. This is confirmed by a value of the order parameter exponent β ≈ 0.25, recently obtained from electric polarisation measurements. Invoking two-scale-factor universality, it follows from the low value of ANF/AN ratio that the size of the critical fluctuations is much larger in the NF phase than in the N phase.
Data from Efficacy of BET Bromodomain Inhibition in Kras-Mutant Non–Small Cell Lung Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Amplification of &lt;i&gt;MYC&lt;/i&gt; is one of the most common genetic alterations in lung cancer, contributing to a myriad of phenotypes associated with growth, invasion, and drug resistance. Murine genetics has established both the centrality of somatic alterations of &lt;i&gt;Kras&lt;/i&gt; in lung cancer, as well as the dependency of mutant &lt;i&gt;Kras&lt;/i&gt; tumors on MYC function. Unfortunately, drug-like small-molecule inhibitors of KRAS and MYC have yet to be realized. The recent discovery, in hematologic malignancies, that bromodomain and extra-terminal (BET) bromodomain inhibition impairs &lt;i&gt;MYC&lt;/i&gt; expression and MYC transcriptional function established the rationale of targeting &lt;i&gt;KRAS&lt;/i&gt;-driven non–small cell lung cancer (NSCLC) with BET inhibition.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We performed functional assays to evaluate the effects of JQ1 in genetically defined NSCLC cell lines harboring &lt;i&gt;KRAS&lt;/i&gt; and/or &lt;i&gt;LKB1&lt;/i&gt; mutations. Furthermore, we evaluated JQ1 in transgenic mouse lung cancer models expressing mutant &lt;i&gt;kras&lt;/i&gt; or concurrent mutant &lt;i&gt;kras&lt;/i&gt; and &lt;i&gt;lkb1&lt;/i&gt;. Effects of bromodomain inhibition on transcriptional pathways were explored and validated by expression analysis.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Although JQ1 is broadly active in NSCLC cells, activity of JQ1 in mutant KRAS NSCLC is abrogated by concurrent alteration or genetic knockdown of &lt;i&gt;LKB1&lt;/i&gt;. In sensitive NSCLC models, JQ1 treatment results in the coordinate downregulation of the &lt;i&gt;MYC&lt;/i&gt;-dependent transcriptional program. We found that JQ1 treatment produces significant tumor regression in mutant &lt;i&gt;kras&lt;/i&gt; mice. As predicted, tumors from mutant &lt;i&gt;kras&lt;/i&gt; and &lt;i&gt;lkb1&lt;/i&gt; mice did not respond to JQ1.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; Bromodomain inhibition comprises a promising therapeutic strategy for &lt;i&gt;KRAS&lt;/i&gt;-mutant NSCLC with wild-type LKB1, via inhibition of MYC function. Clinical studies of BET bromodomain inhibitors in aggressive NSCLC will be actively pursued. &lt;i&gt;Clin Cancer Res; 19(22); 6183–92. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Automation of High-Throughput Combinatorial Protein MicroCrystallization Trials (2000)

A major bottleneck for protein structure determination using x-ray diffraction is the difficulty in finding conditions for crystallization and optimizing those conditions for the production of high-quality crystals. Hundreds of crystallization trials are typically necessary to find optimized crystallization conditions, but these are limited by the amount of protein sample available. Our goal was to increase the number of crystallization trials while at the same time reducing the amount of protein sample required, all in a high-throughput mode. These design goals suggested automation of all key protocols.Begun in the spring of 1998 at the request of personnel now at NIFG, the BioInstrumentation Group at LBNL undertook to increase the throughput of protein crystallization trials by an order of magnitude while reducing protein usage per trial by 90%. In order to achieve this goal, two completely automated robotic systems were designed and constructed with initial testing of the completed system in the spring of 1999. Joining a combinatorial approach with parallel processes, protein samples are screened against a coarse array of up to 480 unique solutions at a rate of eight seconds/trial. This compares with a rate of one to two minutes/trial either by commercial robots or manual methods. Along with the increased throughput, protein usage was reduced up to 50-fold where only 20 nanoliters of protein/trial were needed to grow crystals compared to current best practices using one microliter of protein. Based on sub-optimal growth conditions identified by hits from the coarse screen, a second system narrows in on the optimal conditions by synthesizing a new two-dimensional array of solutions out of 72 stock chemicals and new crystallization trials begin. By automating crystal growth trials, effort previously spent on manual trial preparation is freed to work on other aspects of proteomic research.
1,3‐Dioxolane: A Strategy to Improve Electrode Interfaces in Lithium Ion and Lithium‐Sulfur Batteries (2018)

Abstract Batteries with increased specific energy will play a crucial role in future electrical energy. Indeed, high specific energy means increased driving ranges in electric vehicles and can also improve the efficient use of the renewable energy. Lithium batteries, including lithium ion batteries (LIBs), with a high specific energy can be achieved with the use of high‐potential and/or high specific capacity cathodes. We exploit the ability of 1,3‐dioxolane (DOL) to polymerize at voltages higher than 4 V to produce a protective polymer layer in situ on two different cathodes. Specifically, DOL was polymerized on high‐voltage LiNi 0.5 Mn 1.5 O 4 (LNMO) and on high‐capacity sulfur electrodes in order to reduce the electrode/electrolyte interface reactivity of these cathode materials and to improve cycling performance.
Influence of family demographic factors on social communication questionnaire scores (2018)

Screeners are used to help identify children who are more likely to have ASD than their peers. Ideally screeners should be accurate for different groups of children and families. This study examined how well the Social Communication Questionnaire (SCQ) predicts ASD. We found that male sex, lower household income, lower maternal education and Black race were associated with higher SCQ scores. In this study an SCQ cut-point of 11 worked best across the different sociodemographic groups in our sample.
Network Analysis and Forensics (2022)

Wireshark has been one of the important tools for network analysis and troubleshooting. Wireshark gives complete visibility of how a packet is treated at various stages of its propagation from one application endpoint to the other over the network. This visibility powers a network operator to understand what an application is doing. If it’s behaving as expected or there is an unexpected malicious attempt to disrupt the network, application, and IT resources.
Transport in carbon nanotubes: Contact models and size effects (2010)

Abstract We present electronic transport calculations for single wall carbon nanotubes (CNTs) using two highly idealized models to describe the electrodes and their contact to the CNT. In the first model we use CNT‐electrodes and in the second one we apply the wide‐band approximation, neglecting any atomic structure within the electrodes. The single orbital tight‐binding approximation is used to describe the electronic structure of the CNTs. This enables us to apply highly efficient decimation techniques to reduce the size of the finite central Hamiltonian. Semi‐infinite CNT‐electrodes can be included iteratively using a similar method. Electronic transport calculations are carried out within the Landauer formalism.
Analysis of energy dissipation in stirred suspension polymerisation reactors using computational fluid dynamics (2011)

Abstract This work evaluates the spatial distribution of normalised rates of droplet breakage and droplet coalescence in liquid–liquid dispersions maintained in agitated tanks at operation conditions normally used to perform suspension polymerisation reactions. Particularly, simulations are performed with multiphase computational fluid dynamics (CFD) models to represent the flow field in liquid–liquid styrene suspension polymerisation reactors for the first time. CFD tools are used first to compute the spatial distribution of the turbulent energy dissipation rates (ε) inside the reaction vessel; afterwards, normalised rates of droplet breakage and particle coalescence are computed as functions of ε. Surprisingly, multiphase simulations showed that the rates of energy dissipation can be very high near the free vortex surfaces, which has been completely neglected in previous works. The obtained results indicate the existence of extremely large energy dissipation gradients inside the vessel, so that particle breakage occurs primarily in very small regions that surround the impeller and the free vortex surface, while particle coalescence takes place in the liquid bulk. As a consequence, particle breakage should be regarded as an independent source term or a boundary phenomenon. Based on the obtained results, it can be very difficult to justify the use of isotropic assumptions to formulate particle population balances in similar systems, even when multiple compartment models are used to describe the fluid dynamic behaviour of the agitated vessel. © 2011 Canadian Society for Chemical Engineering
Aggregation promotes cell viability, proliferation, and differentiation in anin vitromodel of injection cell therapy (2011)

Many cell therapy approaches aim to deliver high-density single-cell suspensions to diseased or injured sites in the body. Long term clinical success will in part be dependent on the cells that remain viable and that assume correct functionality post-administration. The research presented in this paper focuses on the potential of cell aggregate delivery to generate a more supportive environment for cells than single cell suspensions. An in vitro model of injection delivery of C2C12 myoblast cells showed a significant difference in cell function and phenotype between adhesive collagen and non-adhesive alginate, indicating that in vitro assays based on this approach can discriminate between cell-cell/cell-matrix interactions and could be valuable when assessing cell therapy systems. Contrary to single cells, aggregates maintain viability, cellular activity, and phenotype beyond that of single cells, even in non-adhesive matrices, enabling delivery of higher cell densities with enhanced proliferative and differentiation capacity.
A small molecule RIG-I agonist serves to adjuvant broad multifaceted influenza virus vaccine immunity (2022)

Abstract Retinoic acid-inducible gene I (RIG-I) is essential for activating host cell innate immunity to regulates the immune response against many RNA viruses. We identified a small molecule compound, KIN1148, that directly binds RIG-I to drive IRF3activation to impart the expression of IRF3-target genes, including specific immunomodulatory cytokines and chemokines. KIN1148 does not lead to ATPase activity or compete with ATP for binding but activates RIG-I to induce antiviral gene expression programs distinct from type I interferon (IFN) treatment. When administered in combination with a vaccine against influenza A virus (IAV), KIN1148 induces both neutralizing antibody and broadly cross-protective IAV-specific T cell responses compared to vaccination alone, which induces comparatively poor responses. This robust KIN1148-adjuvanted immune response protects mice from lethal H1N1 and H5N1 IAV challenge. Importantly, KIN1148 also augments human CD8 + T cell activation. Thus, we have identified a small molecule RIG-I agonist that serves as an effective adjuvant in inducing non-canonical RIG-I activation for induction of innate immune programs that enhance adaptive immune protection of antiviral vaccination. Summary Hemann, et. al. identify a small-molecule RIG-I agonist (KIN1148) that directly binds RIG-I for non-canonical activation and adjuvants pandemic and avian influenza virus vaccination. KIN1148 augments broadly neutralizing antibody and T cell responses in mice and enhances human DC maturation and CD8 + T cell activation.
A Novel Automethylation Reaction in the Aspergillus nidulans LaeA Protein Generates S-Methylmethionine (2013)

The filamentous fungi in the genus Aspergillus are opportunistic plant and animal pathogens that can adapt to their environment by producing various secondary metabolites, including lovastatin, penicillin, and aflatoxin. The synthesis of these small molecules is dependent on gene clusters that are globally regulated by the LaeA protein. Null mutants of LaeA in all pathogenic fungi examined to date show decreased virulence coupled with reduced secondary metabolism. Although the amino acid sequence of LaeA contains the motifs characteristic of seven-β-strand methyltransferases, a methyl-accepting substrate of LaeA has not been identified. In this work we did not find a methyl-accepting substrate in Aspergillus nidulans with various assays, including in vivo S-adenosyl-[methyl-(3)H]methionine labeling, targeted in vitro methylation experiments using putative protein substrates, or in vitro methylation assays using whole cell extracts grown under different conditions. However, in each experiment LaeA was shown to self-methylate. Amino acid hydrolysis of radioactively labeled LaeA followed by cation exchange and reverse phase chromatography identified methionine as the modified residue. Point mutations show that the major site of modification of LaeA is on methionine 207. However, in vivo complementation showed that methionine 207 is not required for the biological function of LaeA. LaeA is the first protein to exhibit automethylation at a methionine residue. These findings not only indicate LaeA may perform novel chemistry with S-adenosylmethionine but also provide new insights into the physiological function of LaeA.
Population Pharmacokinetic Analysis from First-in-Human Data for HDAC Inhibitor, REC-2282 (AR-42), in Patients with Solid Tumors and Hematologic Malignancies: A Case Study for Evaluating Flat vs. Body Size Normalized Dosing (2021)

FFM was identified as a significant covariate on CL; however, it explained only a very small portion of the IIV; major factors contributing significantly to REC-2282 pharmacokinetic variability remain unidentified.
Table S2 from TAS0728, A Covalent-binding, HER2-selective Kinase Inhibitor Shows Potent Antitumor Activity in Preclinical Models (2023)

&lt;p&gt;The list of 68 non-kinase targets tested in a panel of binding assays&lt;/p&gt;