gebhart/patrepeval huggingface dataset:
Hyperglycosylated Mutants of Human Immunodeficiency Virus (HIV) Type 1 Monomeric gp120 as Novel Antigens for HIV Vaccine Design (2003)

The ability to induce broadly neutralizing antibodies should be a key component of any forthcoming vaccine against human immunodeficiency virus type 1. One potential vaccine candidate, monomeric gp120, has generally failed to elicit such antibodies. We postulated that gp120 might be a better immunogen if it could be engineered to preferentially bind known broadly neutralizing antibodies. In a first study, we found that four alanine substitutions on the perimeter of the so-called Phe-43 cavity of gp120 could reduce binding of weakly neutralizing CD4-binding site antibodies (R. Pantophlet, E. O. Saphire, P. Poignard, P. W. H. I. Parren, I. A. Wilson, and D. R. Burton, J. Virol. 77:642-658, 2003), while slightly enhancing binding of the potent, broadly neutralizing antibody b12. In the present study, we sought to reduce or abolish the binding of a wider range of nonneutralizing antibodies, by incorporating extra N-glycosylation motifs at select positions into the hypervariable loops and the gp120 core. A hyperglycosylated mutant containing seven extra glycosylation sequons (consensus sequences) and the four alanine substitutions described above did not bind an extensive panel of nonneutralizing and weakly neutralizing antibodies, including a polyclonal immunoglobulin preparation (HIVIG) of low neutralizing potency. Binding of b12, at lowered affinity, and of four antibodies to the C1 and C5 regions was maintained. Removal of N- and C-terminal residues in the C1 and C5 regions, respectively, reduced or abolished binding of the four antibodies, but this also adversely affected b12 binding. The hyperglycosylated mutant and its analogues described here are novel antigens that may provide a new approach to eliciting antibodies with b12-like neutralizing properties.
Report- Role of prostaglandin H synthase in activation of acrylonitrile to cyanide. (2018)

The present study aimed at investigating the in-vitro oxidation of acrylonitrile (ACN) to cyanide (CN-) by prostaglandin H synthase (PHS). Detection of CN- is considered a marker for free radical intermediates involved in ACN-induced toxicity. First, most favorable circumstances for ACN oxidation were characterized: pH (4.5), temperature (37ºC) and time of incubation (60 min.). In addition, the concentrations of ACN, PHS and H2O2 in incubation mixtures were assessed for further reaction characterization. The reaction maximum velocity (Vmax) was calculated to be 582.75 pmol CN-/mL/min and the Michaelis-Menten constant (Km) was 149.25 μmol ACN. Adding PHS inhibitors; resveratrol, quercetin, indomethacin or troloc-C to the reaction mixtures significantly reduced the rate of ACN oxidation. In conclusion, the present study demonstrates the ability of PHS to oxidize ACN to CN- and provides a clue for the explanation of ACN target toxicity.
Supplementary Figure S15 from Evolution of Castration-Resistant Prostate Cancer in ctDNA during Sequential Androgen Receptor Pathway Inhibition (2023)

&lt;p&gt;Supplementary Figure S15 shows temporal changes in whole exome copy number profile in patients that had evidence for copy number profile change in 72-gene targeted sequencing&lt;/p&gt;
Biosynthesis of vitamin B12: the site of reduction of precorrin-6x (1991)

It is proved by deuterium labelling and NMR spectroscopy that a hydride equivalent from NADPH is transferred to C-19 of precorrin-6x as this intermediate is converted enzymically into hydrogenobyrinic acid.
Critical roles of transcriptional coactivator MED1 in the formation and function of mouse adipose tissues (2021)

The MED1 subunit has been shown to mediate ligand-dependent binding of the Mediator coactivator complex to multiple nuclear receptors, including the adipogenic PPARγ, and to play an essential role in ectopic PPARγ-induced adipogenesis of mouse embryonic fibroblasts. However, the precise roles of MED1, and its various domains, at various stages of adipogenesis and in adipose tissue have been unclear. Here, after establishing requirements for MED1, including specific domains, for differentiation of 3T3L1 cells and both primary white and brown preadipocytes, we used multiple genetic approaches to assess requirements for MED1 in adipocyte formation, maintenance, and function in mice. We show that MED1 is indeed essential for the differentiation and/or function of both brown and white adipocytes, as its absence in these cells leads to, respectively, defective brown fat function and lipodystrophy. This work establishes MED1 as an essential transcriptional coactivator that ensures homeostatic functions of adipocytes.
Optimal control of the argon-oxygen decarburising steelmaking process (1979)

The argon-oxygen decarburising process is an increasingly important method of stainless-steel manufacture. In the paper, a nonlinear dynamic model is presented which represents approximately the refining process. Finite-dimensional-optimisation techniques are used to calculate an optimal switched control, and infinite-dimensional-gradient methods are applied to discover an optimal continuous strategy. Control is achieved by varying the ratio of argon and oxygen in the supplied gas. Results with a realistic cost function indicate that substantial improvements in operating practice may be achieved. The feasibility of implementing the suggested control schemes is discussed.
Integration of a Microstrip Patch Antenna with a Two-Dimensional Photonic Crystal Substrate (1999)

ABSTRACT We have experimentally and computationally studied the integration of a microstrip patch antenna with a two-dimensional photonic crystal substrate. This antenna was fabricated on a defect in the two-dimensional photonic crystal lattice that localized the energy under the patch antenna. The finite-difference time-domain method was employed to study the characteristics of this antenna. Measurements are in excellent agreement with calculations. The effects of finite size ground planes were also studied. This work can lead to a new design tool for integrating patch antennas with photonic crystal substrates.
Ornithine Aminotransferase versus GABA Aminotransferase: Implications for the Design of New Anticancer Drugs (2014)

Ornithine aminotransferase (OAT) and γ-aminobutyric acid aminotransferase (GABA-AT) are classified under the same evolutionary subgroup and share a large portion of structural, functional, and mechanistic features. Therefore, it is not surprising that many molecules that bind to GABA-AT also bind well to OAT. Unlike GABA-AT, OAT had not been viewed as a potential therapeutic target until recently; consequently, the number of therapeutically viable molecules that target OAT is very limited. In this review the two enzymes are compared with respect to their active-site structures, catalytic and inactivation mechanisms, and selective inhibitors. Insight is offered that could aid in the design and development of new selective inhibitors of OAT for the treatment of cancer.
Mild cognitive impairment and cognitive impairment, no dementia: Part A, concept and diagnosis (2007)

Mild cognitive impairment (MCI) and cognitive impairment, no dementia (CIND) are controversial emerging terms that encompass the clinical state between elderly normal cognition and dementia. This article reviews recent work on the classification of MCI and CIND, their prognosis, and diagnostic approaches and presents evidence‐based recommendations approved at the meeting of the Third Canadian Consensus Conference on the Diagnosis and Treatment of Dementia (CCCDTD3) held in Montreal in March, 2006. New short tools such as the Montreal Cognitive Assessment are making it easier for family physicians to confidently attach the label of MCI.
Mutant P53 vaccination of patients with advanced cancers generates specific immunological responses (2004)

2521 Background: Mutations of the p53 tumor suppressor gene are the most common genetic abnormality implicated in development and progression of various tumors. These mutations produce unique proteins that are processed and displayed as short peptides through HLA molecules on the tumor cell surface. Previously, we have demonstrated that animal vaccination with the mutated P53 peptide can generate specific cytotoxic T lymphocytes that lyse tumor cells expressing mutant p53. Therefore, mutant p53 peptides can be a widely applicable cancer therapy. Methods: Twenty-four patients with advanced malignancies (10 colorectal, 9 ovarian, 2 SCLC, and 3 other) expressing mutant p53 were vaccinated with the specific mutant P53. Autologous Peripheral blood mononuclear cells (PBMCs) were cultured for 48hours in the presence of the peptide and granulocyte-macrophage colony-stimulating factor and then administered to the patients IV. During the second and subsequent cycles, autologous PBMCs were cultures with the mutant peptide and IL-2 for 1 week and then administered IV on day 15 and six mIU/m2/day of subcutaneous interleukin-2 (IL-2) on days 15–19 and 22–26. Phenotype analysis of the vaccine product was done using a flow cytometer (FACS). Results: The overall progression-free survival (PFS) and post-vaccination survival (PVS) were longer than expected at 12.5 and 27.2 months, respectively. Twenty patients out of the twenty four were immunologically evaluated. Elispot assay was the main test used to monitor the immunological response in those patients. Nine patients (45%) showed a statistically significant increase in the level of IFN-γ producing specific T-cells after vaccination with the mutant P53. The difference in the level of IFN-γ producing cells between pre and post vaccination was only significant when the cells were challenged with the mutant P53 and not with the irrelevant peptide. Conclusions: Despite the advanced disease and the poor immunological status of the patients, favorable clinical and immunological responses were detected. We believe that this approach may form a promising treatment modality for a wide variety of cancers in the future. No significant financial relationships to disclose.
Dense Small-Cell Networks: Rethinking the Radio Interface Beyond LTE-Advanced (2014)

In this article, we provide an overview of the 5GETLA radio interface proposal for low latency dense small-cell networks. We discuss the new physical layer parametrization and frame design to support high energy and spectral efficiency in wireless small-cell communications and compare the main param
Upper bound for defragmenting buddy heaps (2005)

Knuth's buddy system is an attractive algorithm for managing storage allocation, and it can be made to operate in real-time. At some point, storage-management systems must either over-provide storage or else confront the issue of defragmentation. Because storage conservation is important to embedded systems, we investigate the issue of defragmentation for heaps that are managed by the buddy system. In this paper, we present tight bounds for the amount of storage necessary to avoid defragmentation. These bounds turn out to be too high for embedded systems, so defragmentation becomes necessary.We then present an algorithm for defragmenting buddy heaps and present experiments from applying that algorithm to real and synthetic benchmarks. Our algorithm relocates less than twice the space relocated by an optimal algorithm to defragment the heap so as to respond to a single allocation request. Our experiments show our algorithm to be much more efficient than extant defragmentation algorithms.
Correction: Corrigendum: Enterobacteria-secreted particles induce production of exosome-like S1P-containing particles by intestinal epithelium to drive Th17-mediated tumorigenesis (2016)

Nature Communications 6: Article number: 6956 (2015); Published 24 April 2015; Updated 11 April 2016 The financial support for this Article was not fully acknowledged. The Acknowledgements should have included the following: Huang-Ge Zhang is supported by a Research Career Scientist (RCS) Award.
Palladin is overexpressed in the non-neoplastic stroma of infiltrating ductal adenocarcinomas of the pancreas, but is only rarely overexpressed in neoplastic cells (2007)

The overexpression of palladin relative to normal pancreas in the majority of pancreatic cancers is limited to non-neoplastic stromal cells. This observation highlights the limitations of relying on bulk tissues when analyzing gene expression. Since palladin is not overexpressed in most pancreatic cancer cells, the overexpression of palladin is not likely to be responsible for pancreatic cancer cells invasive and migratory abilities.
A Numerical Study of an Electrically Assisted Boosting System for Turbocharged Diesel Engines (2019)

Abstract Modern diesel engines are normally turbocharged in order to achieve desired fuel economy and meet emission requirements. The well-known “turbo-lag”, delayed engine torque response to driver’s demand, is the main disadvantage for turbocharged engines operated under transient conditions. In addition, at low engine speed, the peak engine output torque is heavily limited by the available turbine energy. As a result, turbocharged engines have degraded peak torque at low speed and slow transient responses in general. Various technologies (variable geometry turbine, electrically assisted turbocharger, hydraulically assisted turbocharger, etc.) have been developed to improve transient response and low-speed torque performance. This paper presents a numerical study of an electrically assisted boosting (eBoost) system for a turbocharged diesel engine through 1-D simulations. This study focuses on two main areas: the electrical compensation at steady-state and turbo-lag reduction under transient operation. It is shown that the eBoost system is capable of increasing engine fuel economy at mid-speed and greatly improving low-speed peak torque. In addition, the eBoost system improves engine transient performance by reducing response time up to 60%.
High Mobility N‐Type Transistors Based on Solution‐Sheared Doped 6,13‐Bis(triisopropylsilylethynyl)pentacene Thin Films (2013)

An N-Type organic thin-film transistor (OTFT) based on doped 6,13-Bis(triisopropylsilylethynyl)pentacene is presented. A transition from p-type to n-type occurrs with increasing doping concentrations, and the highest performing n-channel OTFTs are obtained with 50 mol% dopant. X-ray diffraction, scanning Auger microscopy, and secondary ionization mass spectrometry are used to characterize the morphology of the blends. The high performance of the obtained transistors is attributed to the highly crystalline and aligned nature of the doped thin films.
Demonstration of Dielectric Optical Magnetic Mirrors Using Phase-locked Infrared Time-domain Spectroscopy. (2016)

Abstract not provided.
Visualization of 180° domain structures in uniaxial ferroelectrics using confocal scanning optical microscopy (2000)

Confocal scanning optical microscopy (CSOM) is used to visualize ferroelectric domain structure in materials with no natural optical contrast between domains. By applying an in-plane ac electric field, the orientation of the in-plane ferroelectric polarization may be determined. Experiments on LiNbO3 single crystals show high-quality images of domain structures. The domain contrast is found to depend on the ac field orientation and the incident light polarization. This investigation demonstrates the utility of CSOM for studying static and dynamic processes of domain structure and the possibility for studying domain kinetics on the nanoscale level.
Using Biomass Gasification Mineral Residue as Catalyst to Produce Light Olefins from CO, CO2, and H2 Mixtures (2022)

The Front Cover shows a coarse solid residue particle, originating from the gasification of biomass, which acts as a solid catalyst to produce high-value chemicals, such as olefins, from mixtures of H2, CO, and CO2. The heart of the developed catalyst material are nanoparticles, consisting of iron carbides and iron metal, together with some alkali elements, such as sodium and potassium. The latter elements act as promotors to boost the production of light olefins. This approach represents an elegant example illustrating how we can apply the concept of materials circularity, in which a waste material is transformed into a functional catalyst material. More information can be found in the Research Article by I. C. ten Have et al.
Blockchain-based trust management collaborative system for transport multi-stakeholder scenarios (2023)

A trend in future networks (i.e., beyond 5G and 6G) is the increasing virtualization and disaggregation of networks (i.e., Open Radio Access Network, network function virtulization/software-defined networking, or disaggregated optical networks, among others). This trend leads to a multi-vendor situation appearing in the telco arena (i.e., hardware suppliers, software function providers, vendors, operators) that communications service providers will need to deal with. This multi-stakeholder scenario complicates provisioning and the established relationships among actors based on operation agreements that define the requirements, penalties, and prices that generate a certain level of trust among them. This new disaggregated scenario implies an increment of possibilities and relationships, requiring agreements to be created in a run-time way. As the agreement is generated ad hoc , selecting a provider is a crucial decision, and so, trust and transparency are keys to help with this decision. As trust is a human/subjective concept, it is necessary to find a way to convert it into an objective parameter that can be used in an analytical field such as network control and management. This paper aims to present a model to compute the reputation of a provider based on a set of specific and measurable parameters and the use of Blockchain to make all of the process transparent and reliable to all players involved. Furthermore, this paper shows the design for a Blockchain-based Trust Manager that can compute and distribute the reputation and trust parameters to define how trustworthy are the multi-stakeholders. Finally, an experimental validation is presented on top of an optical transport network.
Characterization of tungsten–nickel simultaneous Ohmic contacts to p- and n-type 4H-SiC (2015)

Ohmic contacts to p- and n-type 4H-SiC using refractory alloyed W:Ni thin films were investigated. Transfer length measurement test structures to p-type 4H-SiC (NA = 3 × 1020 cm−3) revealed Ohmic contacts with specific contact resistances, ρc, of ~10−5 Ω cm2 after 0.5 h annealing in argon at temperatures of 1000 °C, 1100 °C, 1150 °C, and 1200 °C. Contacts fabricated on n-type 4H-SiC (ND = 2 × 1019 cm−3) by similar methods were shown to have similar specific contact resistance values after annealing, demonstrating simultaneous Ohmic contact formation for W:Ni alloys on 4H-SiC. The lowest ρc values were (7.3 ± 0.9) × 10−6 Ω cm2 for p-SiC and (6.8 ± 3.1) × 10−6 Ω cm2 for n-SiC after annealing at 1150 °C. X-ray diffraction shows a cubic tungsten–nickel–carbide phase in the Ohmic contacts after annealing as well as WC after higher temperatures. Auger electron spectroscopy depth profiles support the presence of metal carbide regions above a nickel and silicon-rich region near the interface. X-ray energy dispersive spectroscopy mapping showed tungsten-rich and nickel-rich regions after annealing at 1100 °C and above. W:Ni alloys show promise as simultaneous Ohmic contacts to p- and n-SiC, offering low and comparable ρc values along with the formation of WxNiyC.
A Salicylate Sympathetic Ink from Consumer Chemicals (2005)

A color-change reaction is described in which invisible writing on paper is made to appear as violet upon being sprayed with a liquid. The reaction uses chemicals readily available on the retail market: aspirin tablets, washing soda, vinegar, iron supplement tablets, and liquid chlorine laundry bleach.Find this demonstration and others in the DigiDemos area of the JCE Digital Library.
Use of amplification of the 8q24 and 20q11–13 loci to predict progression-free survival of advanced epithelial ovarian cancer patients receiving standard therapy (2009)

e16526 Background: The purpose of this study was to identify genes that predict the progression free survival (PFS) of advanced epithelial ovarian cancer (aEOC) receiving standard therapy. Methods: We performed expression analysis using GeneChip (Human Genome U133 plus 2.0 Array) in aEOC cells produced by laser-based microdissection. Thirty three aEOC patients (stage IIc: 4, III: 19, IV: 10; serous adenocarcinoma: 21, endometrioid adenocarcinoma: 5, undifferentiated: 7) were included in this array study. All cases received staging laparotomy, cytoreductive surgery, and adjuvant chemotherapy (carboplatin + paclitaxel) as primary therapy. Results: Class comparison analysis between groups of NED (no evidence of disease) and non-NED identified 46 genes that exhibited significant differences (p &lt; 0.001). Among them, 6 (13%) genes are located in 8q24 and 9 (19.6%) genes are located in 20q11–13. Finally, we focused on 8q24 and 20q11–13 loci, and confirmed array data using real-time quantitative PCR in 94 validation sets. The validation showed that ZNF7, MAF1, ADRM1, and GNAS amplification was related with PFS (p &lt; 0.05, respectively). Conclusions: The amplification of 8q24 and 20q11–13 can predict the PFS of aEOC and these genes may be new biomarkers for aEOC. No significant financial relationships to disclose.
Genetic regulatory network identification using multivariate monotone functions (2011)

We present a method for identification of gene regulatory network topology using a time series of gene expression data. The underlying assumption is that the regulatory effects of a set of regulators to a gene can be described by a multivariate function. The multivariate function is constrained to be continuous, nonnegative and monotonic in each variable. We present necessary and sufficient conditions for the validity of the regulation hypothesis. Checking these conditions can be expressed as a Linear Programming feasibility problem. This paper builds on our previous work, where the regulation is described by a summation of multiple regulator functions, one function for each gene in the regulator set. Our procedure is two phased; the first identifies the correct set of regulators, the second uses the data and the regulator set to generate an appropriate regulator function. This paper focuses on the identification of the correct regulator set. As demonstration, we run our main algorithm on some experimental data from a synthetic gene network in yeast. We are able to show that the correct set of regulators is picked by the algorithm.
Synchronous Pulsed Plasma for Silicon Etch Applications (2010)

This paper investigates the interest of synchronous pulsed plasmas to etch silicon in HBr/O2 chemistries. Using mass spectrometry, ellipsometry and angle resolved X-ray photoelectron spectroscopy, we demonstrate that the radical concentration in the plasma, the etch rate and formation of passivation layers, can be controlled by the RF pulse parameters (frequency and duty cycle). Accordingly, pattern profiles are improved, selectivity to the mask is increased and the silicon recess is reduced from 4 to 0.8 nm when the HBr/O2 plasma lands on thin silicon oxide.