gebhart/patrepeval huggingface dataset:
Active Components from Cassia abbreviata Prevent HIV-1 Entry by Distinct Mechanisms of Action (2021)

<i>Cassia abbreviata</i> is widely used in Sub-Saharan Africa for treating many diseases, including HIV-1 infection. We have recently described the chemical structures of 28 compounds isolated from an alcoholic crude extract of barks and roots of <i>C. abbreviata</i>, and showed that six bioactive compounds inhibit HIV-1 infection. In the present study, we demonstrate that the six compounds block HIV-1 entry into cells: oleanolic acid, palmitic acid, taxifolin, piceatannol, guibourtinidol-(4α→8)-epiafzelechin, and a novel compound named as cassiabrevone. We report, for the first time, that guibourtinidol-(4α→8)-epiafzelechin and cassiabrevone inhibit HIV-1 entry (IC<sub>50</sub> of 42.47 µM and 30.96 µM, respectively), as well as that piceatannol interacts with cellular membranes. Piceatannol inhibits HIV-1 infection in a dual-chamber assay mimicking the female genital tract, as well as HSV infection, emphasizing its potential as a microbicide. Structure-activity relationships (SAR) showed that pharmacophoric groups of piceatannol are strictly required to inhibit HIV-1 entry. By a ligand-based in silico study, we speculated that piceatannol and norartocarpetin may have a very similar mechanism of action and efficacy because of the highly comparable pharmacophoric and 3D space, while guibourtinidol-(4α→8)-epiafzelechin and cassiabrevone may display a different mechanism. We finally show that cassiabrevone plays a major role of the crude extract of <i>CA</i> by blocking the binding activity of HIV-1 gp120 and CD4.
Generation-recombination noise in GaN and GaN-based devices (2003)

Generation-recombination (GR) noise in GaN and AlGaN thin films, GaN based Metal Semiconductor Field Effect Transistors (MESFETs), Heterostructure Field Effect Transistors (HFETs) and Schottky diode photodetectors was investigated. AlGaN thin films, AlGaN/GaN HFETs and Schottky barrier Al<sub>0.4</sub>Ga<sub>0.6</sub>N diodes exhibited GR noise with activation energies of 0.8 - 1 eV. AlGaN/GaN HFETs also presented GR noise with activation energies of 1 - 3 meV and 0.24 eV at cryogenic temperatures. No such noise was observed in thin doped GaN films and GaN MESFETs. GR noise with the largest reported activation energy of 1.6 eV was measured in AlGaN/InGaN/GaN Double Heterostructure Field Effect Transistors (DHFETs). We conclude that the local levels responsible for the observed noise in HFETs and DHFETs could be located in AlGaN barrier layers.
Reverse Transfer Learning: Can Word Embeddings Trained for Different NLP Tasks Improve Neural Language Models? (2019)

status: Published
Exploring Regulation of Protein O-Glycosylation in Isogenic Human HEK293 Cells by Differential O-Glycoproteomics (2019)

Most proteins trafficking the secretory pathway of metazoan cells will acquire GalNAc-type O-glycosylation. GalNAc-type O-glycosylation is differentially regulated in cells by the expression of a repertoire of up to twenty genes encoding polypeptide GalNAc-transferase isoforms (GalNAc-Ts) that initiate O-glycosylation. These GalNAc-Ts orchestrate the positions and patterns of O-glycans on proteins in coordinated, but poorly understood ways - guided partly by the kinetic properties and substrate specificities of their catalytic domains, as well as by modulatory effects of their unique GalNAc-binding lectin domains. Here, we provide the hereto most comprehensive characterization of nonredundant contributions of individual GalNAc-T isoforms to the O-glycoproteome of the human HEK293 cell using quantitative differential O-glycoproteomics on a panel of isogenic HEK293 cells with knockout of GalNAc-T genes (<i>GALNT1</i>, <i>T2</i>, <i>T3</i>, <i>T7</i>, <i>T10</i>, or <i>T11</i>). We confirm that a major part of the O-glycoproteome is covered by redundancy, whereas distinct O-glycosite subsets are covered by nonredundant GalNAc-T isoform-specific functions. We demonstrate that the GalNAc-T7 and T10 isoforms function in follow-up of high-density O-glycosylated regions, and that GalNAc-T11 has highly restricted functions and essentially only serves the low-density lipoprotein-related receptors in linker regions (C<sup>6</sup>XXXTC<sup>1</sup>) between the ligand-binding repeats.
ChemInform Abstract: Orally Bioavailable Imidazoazepanes as Calcitonin Gene‐Related Peptide (CGRP) Receptor Antagonists: Discovery of MK‐2918. (2012)

Abstract Fused heterocyclic derivatives of telcagepant are explored with the aim to achieve a lower projected clinical dose.
Transmission of Commercial Low Latency Interfaces Over Hollow-Core Fiber (2015)

For the first time, we successfully demonstrate the transmission of commercial 10- and 100-Gb/s interfaces, both direct detect and coherent, over 2.75 km of hollow-core fiber. The fiber is connected to the transceivers using spliced standard single-mode pigtails. This demonstration solidifies the commercial potential for low latency applications.
An integrative genomic analysis identifies Bhmt2 as a diet-dependent genetic factor protecting against acetaminophen-induced liver toxicity (2009)

Acetaminophen-induced liver toxicity is the most frequent precipitating cause of acute liver failure and liver transplant, but contemporary medical practice has mainly focused on patient management after a liver injury has been induced. An integrative genetic, transcriptional, and two-dimensional NMR-based metabolomic analysis performed using multiple inbred mouse strains, along with knowledge-based filtering of these data, identified betaine-homocysteine methyltransferase 2 (Bhmt2) as a diet-dependent genetic factor that affected susceptibility to acetaminophen-induced liver toxicity in mice. Through an effect on methionine and glutathione biosynthesis, Bhmt2 could utilize its substrate (S-methylmethionine [SMM]) to confer protection against acetaminophen-induced injury in vivo. Since SMM is only synthesized in plants, Bhmt2 exerts its beneficial effect in a diet-dependent manner. Identification of Bhmt2 and the affected biosynthetic pathway demonstrates how a novel method of integrative genomic analysis in mice can provide a unique and clinically applicable approach to a major public health problem.
Optical activity of cholesteric liquid crystals in the pretransitional regime and in the blue phase (1983)

Using the definition due to Landau, we present a closed-form expression for the optical-activity tensor for a cholesteric liquid crystal. The rotatory power is calculated in the pretransitional regime (above the isotropic-cholesteric transition), as well as in the ordered blue phase. The expression obtained for the first case reduces, in the low-chirality limit, to that of Dolganov et al. The result for the blue phase is new, and indicates the possibility of distinguishing between some of the ordered cubic structures that were recently proposed by various workers.
#TwitterSearch (2011)

Social networking Web sites are not just places to maintain relationships; they can also be valuable information sources. However, little is known about how and why people search socially-generated content. In this paper we explore search behavior on the popular microblogging/social networking site Twitter. Using analysis of large-scale query logs and supplemental qualitative data, we observe that people search Twitter to find temporally relevant information (e.g., breaking news, real-time content, and popular trends) and information related to people (e.g., content directed at the searcher, information about people of interest, and general sentiment and opinion). Twitter queries are shorter, more popular, and less likely to evolve as part of a session than Web queries. It appears people repeat Twitter queries to monitor the associated search results, while changing and developing Web queries to learn about a topic. The results returned from the different corpora support these different uses, with Twitter results including more social chatter and social events, and Web results containing more basic facts and navigational content. We discuss the implications of these findings for the design of next-generation Web search tools that incorporate social media.
Supplementary Table Legend from GDC-0941, a Novel Class I Selective PI3K Inhibitor, Enhances the Efficacy of Docetaxel in Human Breast Cancer Models by Increasing Cell Death <i>In Vitro</i> and <i>In Vivo</i> (2023)

&lt;p&gt;PDF file, 56KB.&lt;/p&gt;
Reactivity to tyrosinase: Expression in cancer (melanoma) and autoimmunity (vitiligo) (1996)

Anti-tyrosinase antibodies are found in the sera of patients with diffuse vitiligo, metastatic melanoma and in sera of patients with melanoma and hypopigmentation (MAH). The autoantigen is tyrosinase itself, the enzyme that participates in pigment (melanin) formation by both melanocytes and melanoma cells. The production of autoantibodies in both diseases is associated with the development of white patches on the patients' skin. The presence of these autoantibodies in patients with melanoma may suggest a better prognosis. Cross-antigenicity between melanoma cells and normal melanocytes is most probably the key mechanism leading to the appearance of MAH. Anti-tyrosinase antibodies are absorbed by melanocytes and by melanoma cells in all the 3 situations (melanoma, vitiligo, MAH). However, since the production of antibodies in vitiligo exceeds that in melanoma or MAH, the antibodies are detected in significantly higher levels only in vitiligo. It is suggested here that anti-tyrosinase antibodies may be responsible, or at least participate in destruction of normal melanocytes during the immune response to melanoma antigens. This mechanism may be responsible for the phenomenon of MAH in patients with melanoma, and for the formation of the autoimmune vitiligo. Anti-tyrosinase antibodies may serve for two clinical applications. One is a marker for monitoring and follow up of patients with melanoma treated by immune therapy. The second is active (or passive) immunotherapy. We have recently shown that C57BL/6J mice immunized with tyrosinase generated a high titer of antityrosinase antibodies, and following the inoculation of melanoma cells developed lower number of lung metastases, compared to the unvaccinated control group.
Creation of gallium acid and platinum metal sites in bifunctional zeolite hydroisomerization and hydrocracking catalysts by atomic layer deposition (2020)

Active sites in bifunctional zeolite catalysts were engineered using atomic layer deposition (ALD). Gallium acid and platinum metal sites were introduced to zeolites <italic>via</italic> ALD and investigated for a hydroconversion reaction.
ChemInform Abstract: Enantiospecific Formation of trans‐1,3‐Disubstituted Tetrahydro‐β‐ carbolines by the Pictet‐Spengler Reaction and Conversion of cis Diastereomers into Their trans Counterparts by Scission of the C‐1/N‐2 Bond. (1997)

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.
Temperature dependence of the momentum distribution of positronium inMgF2,SiO2,andH2O (2000)

Temperature dependence of the momentum distribution of delocalized Bloch-positronium in solids is studied. The momentum distribution of the positronium, which is proportional to the energy integration of the spectral function weighted with the Bose distribution, is expressed in terms of the effective mass and the deformation potential of the crystal for positronium. A simple formula for the shape of the positronium peak in the 1D-ACAR spectrum is derived and applied to the analysis of the experimental data for ${\mathrm{MgF}}_{2},$ ${\mathrm{SiO}}_{2},$ and ${\mathrm{H}}_{2}\mathrm{O}$ in wide temperature ranges. An extraordinary broadening of the peak shape is observed for ${\mathrm{MgF}}_{2}.$ It is interpreted as an effect of the umklapp phonon scattering. The diffusion constants of Ps in these materials are also estimated.
Role-Based Self-Appointment for Autonomic Management of Resources (2014)

Resource management in distributed environments, such as Cloud virtualized networks, is one of the main concerns of infrastructure providers. Despite many advantages of centralized solutions (such as the facility of implementation and management), their unique point of failure and the lack of scalability make us consider the use of distributed and autonomic solutions. Beyond this, centralized solutions would be inefficient to deal with dynamic and peak situations. By using simple sets of rules, each autonomic node can independently act and react according to scenario's changes without the knowledge of the whole system status, making autonomic management robust and adaptable. The main goal of this paper is to describe a role-based autonomic mechanism - called Role-Based Self-Appointment (RBSA) - for resource management in distributed environments and its applicability in different scenarios.
Mesakalk – ett miljövänligt material eller skadligt avfall? (2016)

Sweden is experiencing major problems with the management of waste from nearly every industry within the country. There is I big waste of waste materials which are placed in landfill when they have potential of being reused. Landfills usually leach contaminated water leading to the contamination of soils and watercourses. Lime mud from the paper industry is currently at 133 000 tones. The purpose of this paper is to study the Sweden’s environmental legislation to see if it has flaws that may explain why the lime mud is not re-used even though it may have potentially useful properties. The result is based on an analysis of documents of legal provisions and completed schemes interpreted against the mesa content. The answer is that the law is neither an obstacle and opportunities and it is not possible to provide for law neither promotes nor prevents lime reuse. It is also clear that there is little research on the environmental gains and losses that would arise if the mesa came in contact with nature. What is clear is that there is an unclear division of responsibilities between authorities regarding Environmental Protection Agency and the County administrative boards of Sweden that might complicate the reuse of lime mud.
SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma (2021)

To investigate the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the immune population, we coincupi bated the authentic virus with a highly neutralizing plasma from a COVID-19 convalescent patient. The plasma fully neutralized the virus for seven passages, but, after 45 d, the deletion of F140 in the spike N-terminal domain (NTD) N3 loop led to partial breakthrough. At day 73, an E484K substitution in the receptor-binding domain (RBD) occurred, followed, at day 80, by an insertion in the NTD N5 loop containing a new glycan sequon, which generated a variant completely resistant to plasma neutralization. Computational modeling predicts that the deletion and insertion in loops N3 and N5 prevent binding of neutralizing antibodies. The recent emergence in the United Kingdom, South Africa, Brazil, and Japan of natural variants with similar changes suggests that SARS-CoV-2 has the potential to escape an effective immune response and that vaccines and antibodies able to control emerging variants should be developed.
Prior-Guided Metal Artifact Reduction for Iterative X-Ray Computed Tomography (2018)

High-attenuation materials pose significant challenges to computed tomographic imaging. Formed of high mass-density and high atomic number elements, they cause more severe beam hardening and scattering artifacts than do water-like materials. Pre-corrected line-integral density measurements are no longer linearly proportional to the path lengths, leading to reconstructed image suffering from streaking artifacts extending from metal, often along highest-density directions. In this paper, a novel prior-based iterative approach is proposed to reduce metal artifacts. It combines the superiority of statistical methods with the benefits of sinogram completion methods to estimate and correct metal-induced biases. Preliminary results show minimized residual artifacts and significantly improved image quality.
SPARC_Duke_Grill_OT2-OD025340_VagusNerve_IHC_TH v2 (2021)

The protocol describes immunohistochemistry with anti-tyrosine hydroxylase, as it has been applied to cervical and abdominal vagus nerve samples from rats, pigs, and humans.
A Practical Procedure for Reduction of Primary, Secondary and Tertiary Amides to Amines (2013)

Abstract A mild and general procedure for reduction of primary, secondary, and tertiary amides using catalytic triruthenium dodecacarbonyl and 1,1,3,3‐tetramethyldisiloxane as reductant is described. The reaction is tolerant of numerous functional groups, and the amine products can often be isolated by direct crystallization as hydrochloride salts. The catalyst and silane are commercially available, air stable, and inexpensive, making the procedure accessible for both laboratory and large‐scale applications.
Ultra-Thick Electrodes for Li-Ion Battery (2017)

In order to meet the challenge of a transition from fossil fuels to green energies, the rapid development of technology is crucial. A characteristic of energy produced from renewable sources is to be discontinuous in time (e. g. photovoltaic or wind turbines). So, as a result of the development of this kind of systems, it is really important to establish a reliable electric energy storage grid. Nowadays, advanced devices that convert and store energy are the focus of intensive attentions and lithium-ion batteries hold the promise of effective solution for a clean electric future. Nevertheless, the needs to improve performances and reduce costs of Li-ion batteries encourage different research strategies. Among them, an increase in the basis weight of the electrodes active material allows to improve the energy density and to reduce the costs associated with the electrochemical inactive materials (current collectors and separator). The maximum loading achievable by the current industrial reference process, the coating, is limited by the migration of the binder during solvent evaporation phase. Thus, an innovative and effective process, the filtration, is here proposed for the production of ultra-thick electrodes (&gt; 20 mAh / cm² or &gt; 50 mg / cm²). In particular, this research is focused on the adaptation of filtration with the aim to obtain Li-ion battery electrodes and on the development of a pseudo 3D current collector. This innovative current collector is suitable for the filtration process, participates in the transversal electrical conductivity and improves the adhesion of the active layer. The active materials used in this research are commercial LiNiMnCo (NMC) for the cathode and graphite for the anode. The mechanical properties of ultra-thick electrodes are, of course, critical and will be discussed. Moreover, the remarkable mechanical stability along with the improved adhesion of active material layer with the metallic current collector allows electrodes to be pressed and to attain low porosity, resulting in improved energy density and increased electrical conductivity due to a better contact between particles. The electrochemical performances of electrodes based on NMC/graphite and of a full cells composed of these ultra-thick electrodes will be presented. These ultra-thick electrodes feature a volumetric energy density greater than the state of art Li-ion electrodes, making them particularly suitable for stock energy produced from renewable and natural sources, giving the possibility to increase the capacity of future electricity grid. Fig. 1: Ambient temperature galvanostatic cycling behavior of a NMC/graphite ultra-thick cell at different C-rate. Inset shows typical potential vs. specific capacity profile. Figure 1
Increasing processor performance by implementing deeper pipelines (2002)

One architectural method for increasing processor performance involves increasing the frequency by implementing deeper pipelines. This paper will explore the relationship between performance and pipeline depth using a Pentium® 4 processor like architecture as a baseline and will show that deeper pipelines can continue to increase performance.This paper will show that the branch misprediction latency is the single largest contributor to performance degradation as pipelines are stretched, and therefore branch prediction and fast branch recovery will continue to increase in importance. We will also show that higher performance cores, implemented with longer pipelines for example, will put more pressure on the memory system, and therefore require larger on-chip caches. Finally, we will show that in the same process technology, designing deeper pipelines can increase the processor frequency by 100%, which, when combined with larger on-chip caches can yield performance improvements of 35% to 90% over a Pentium® 4 like processor.
Presentation of Text Conversation in real-time and en-bloc form (2011)

This specification defines methods for presentation of a text
conversation with focus on the real-time features. The aim is to give
the participants in a conversation a good opportunity to perceive the
real-time flow of the conversation and also provide a display of the
history of the conversation that makes it easy to read. Both two-party
and multi-party situations are defined.
Surgery Task Load Index in Cardiac Surgery: Measuring Cognitive Load Among Teams (2020)

<i>Background.</i> The most commonly used subjective assessment of perceived cognitive load, the NASA Task Load Index (TLX), has proven valuable in measuring individual load among general populations. The surgery task load index (SURG-TLX) was developed and validated to measure cognitive load specifically among individuals within a surgical team. Notably, the TLX lacks temporal sensitivity in its typical retrospective administration. <i>Objective.</i> This study sought to expand the utility of SURG-TLX by investigating individual measures of cognitive load over time during cardiac surgery, and the relationship between individual and team measures of cognitive load and proxies for surgical complexity. <i>Materials & Methods.</i> SURG-TLX was administered retrospectively in the operating room immediately following each case to approximate cognitive load before, during, and after cardiopulmonary bypass for cardiac surgery team members (surgeon, anesthesiologist, and perfusionist). Correlations were calculated to determine the relationship of individual and team measures of cognitive load over the entire procedure with bypass length and surgery length. <i>Results.</i> Results suggest that perceived cognitive load varies throughout the procedure such that cognitive load during bypass significantly differs compared to before or after bypass, across all 3 roles. While on bypass, results show that anesthesiologists experience significantly lower levels of perceived cognitive load than both surgeons and perfusionists. Correlational analyses reveal that perceived cognitive load of both the surgeon and the team had significant positive associations with bypass length and surgery length. <i>Conclusion.</i> Our findings support the utility of SURG-TLX in real cardiac cases as a measure of cognitive load over time, and on an individual and team-wide basis.