gebhart/patrepeval huggingface dataset:
Generation and characterization of a bivalent protein boost for future clinical trials: HIV-1 subtypes CR01_AE and B gp120 antigens with a potent adjuvant (2018)

The RV144 Phase III clinical trial with ALVAC-HIV prime and AIDSVAX B/E subtypes CRF01_AE (A244) and B (MN) gp120 boost vaccine regime in Thailand provided a foundation for the future development of improved vaccine strategies that may afford protection against the human immunodeficiency virus type 1 (HIV-1). Results from this trial showed that immune responses directed against specific regions V1V2 of the viral envelope (Env) glycoprotein gp120 of HIV-1, were inversely correlated to the risk of HIV-1 infection. Due to the low production of gp120 proteins in CHO cells (2-20 mg/L), cleavage sites in V1V2 loops (A244) and V3 loop (MN) causing heterogeneous antigen products, it was an urgent need to generate CHO cells harboring A244 gp120 with high production yields and an additional, homogenous and uncleaved subtype B gp120 protein to replace MN used in RV144 for the future clinical trials. Here we describe the generation of Chinese Hamster Ovary (CHO) cell lines stably expressing vaccine HIV-1 Env antigens for these purposes: one expressing an HIV-1 subtype CRF01_AE A244 Env gp120 protein (A244.AE) and one expressing an HIV-1 subtype B 6240 Env gp120 protein (6240.B) suitable for possible future manufacturing of Phase I clinical trial materials with cell culture expression levels of over 100 mg/L. The antigenic profiles of the molecules were elucidated by comprehensive approaches including analysis with a panel of well-characterized monoclonal antibodies recognizing critical epitopes using Biacore and ELISA, and glycosylation analysis by mass spectrometry, which confirmed previously identified glycosylation sites and revealed unknown sites of O-linked and N-linked glycosylations at non-consensus motifs. Overall, the vaccines given with MF59 adjuvant induced higher and more rapid antibody (Ab) responses as well as higher Ab avidity than groups given with aluminum hydroxide. Also, bivalent proteins (A244.AE and 6240.B) formulated with MF59 elicited distinct V2-specific Abs to the epitope previously shown to correlate with decreased risk of HIV-1 infection in the RV144 trial. All together, these results provide critical information allowing the consideration of these candidate gp120 proteins for future clinical evaluations in combination with a potent adjuvant.
A new feedback congestion control policy for long propagation delays (1995)

This paper presents a new feedback congestion control mechanism for the flow control of the best-effort available bit rate (ABR) traffic in ATM networks. This new mechanism belongs to the class of feedback control schemes that ensure no data losses and operate based on simple 'stop' and 'start' signals. A novelty presented by this paper is a methodology which, for a given set of desired properties, leads to the specification of the corresponding control algorithm. For the case of a single connection, the algorithm can operate with the theoretically minimum possible buffer size. Interestingly, the algorithm obtained has a different structure than the previous schemes; it does not operate based on fixed high and low thresholds. A new congestion control mechanism is subsequently derived for the flow control of multiple connections. The new scheme is exercised hop-by-hop and on a per-connection basis. This scheme allows connections to share memory and bandwidth resources efficiently within the network. The performance of the new scheme is also presented, and its statistical multiplexing efficiency is demonstrated. The measures investigated include buffer occupancy, average delay, overhead due to the protocol signals, and sustained throughput. In the case of long propagation delays, the buffer savings achieved by the new scheme are substantial.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Combination of Mass Metrology with Scatterometry to obtain bottom Width of deep Trenches : AM: Advanced Metrology (2022)

Three different in-line metrology techniques are combined to calculate the bottom width of trenches, 3&#x03BC;m and 42&#x03BC;m deep. CD-SEM gives the top critical dimension (CD) of trenches and scatterometry provides the trench depth. An average value for the trench bottom width or bottom CD is obtained from a mass loss determination with a pre- and post-etch measurement, in combination with the available top CD and depth values. This hybrid metrology approach has been demonstrated in case of the 3&#x03BC;m deep trench, where the conventional physical scatterometry modelling with rigorous coupled wave analysis (RCWA) is used to determine the trench depth and shape. The physical RCWA modelling is not applicable to the 42&#x03BC;m deep trenches with a pitch of &#x003E;5&#x03BC;m. Hence, the proposed combined metrology method is verified with SEM cross-sections from wafers with different trench side-wall angles.
A Global-Shutter CMOS Image Sensor With Readout Speed of 1-Tpixel/s Burst and 780-Mpixel/s Continuous (2012)

A 400 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">H</sup> ×256 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</sup> pixels global-shutter high-speed CMOS image sensor including 128 on-chip memories/pixel has been fabricated in a 0.18-μm 2P4M CMOS with pinned photodiode process. The key technologies of this image sensor are as follows: multiple on-chip memories for each pixel, spatial separation of pixel and on-chip memory regions, multiple pixel output wires for each column, in-pixel noise reduction circuits, in-pixel source-follower current-sources and flexibly selectable on-chip memories. This CMOS image sensor achieves 1 Tpixel/s burst video operation, a full resolution of 10 Mfps with 128 frames and a half resolution of 20 Mfps with 256 frames, and 780 Mpixel/s continuous video operation on the same chip. The power consumption at 1 Tpixel/s was 24 W, while the image sensor operates without active cooling.
Synthesis and Characterization of Poly(styrene-co-4-[(tert-butyldimethylsilyl)oxy]styrene) as a Precursor of Hydroxyl-Functionalized Syndiotactic Polystyrene (1999)

The ligand effects of homogeneous Ti-based catalysts for the copolymerization of styrene ([M1]) with 4-[(tert-butyldimethylsilyl)oxy]styrene (TBDMSS; [M2]) were investigated by the UV/visible spectroscopic analysis. Concerning the higher yields from the copolymerization of styrene with TBDMSS, the half-sandwich type of titanocene having π-ligands compared to titanium (IV) butoxide (Ti(OBu)4) having σ-ligands was a more effective catalysts. The silyloxy group exhibiting a negative σ value in the Hammett σ−ρ relationship reduced the activities of titanocenes. The stronger electron-donating substituent on the π-ligand leading to the increase in the catalytic activity in syndiospecific polymerization of styrene contributed to the decrease of the reactivity of the “cationlike” metal center due to both electronic and steric effects. The reactivity ratios, r1 and r2, in the η5-indenyl trichlorotitanium ((Ind)TiCl3)-catalyzed copolymerization of styrene with TBDMSS in the presence of methylaluminoxane (MAO) ([Al]/[Ti] = 2000) were 0.997 and 7.27 from the evaluation of Finmann and Ross, respectively. The r1r2 product value (7.25) indicates that a block type of copolymer may be produced in a relatively high feed range of TBDMSS to styrene.
Novel Layered Organic−Inorganic Hybrid Materials with Bridged Silsesquioxanes as Pillars (2007)

Layered organic−inorganic hybrid materials were synthesized by pillaring with viologen and nitroaniline compounds which are intercalated between magadiite layers. The bridged silsesquioxanes, 4,4‘-bis(trimethoxysilylpropyl)viologen and 4-nitro-N,N‘-bis(3-trimethoxysilyl)propylaniline react with the surface silanol groups of the inorganic layers of silicate, bonding covalently with them. The preparation process was followed by DRX, and the pillarization was corroborated using chemical and thermogravimetrical analyses. The presence of viologen and nitroaniline organic linkers covalently bonded to inorganic layers was confirmed by 13C and 29Si NMR spectroscopy. UV−visible diffuse reflectance permitted to observe the high stabilization achieved by the intercalated organic fragments. Micro- and mesoporosity were also generated because of the existence of interlayer galleries conformed by homogenously distributed organic linkers into the interlayer space. The layered organic−inorganic hybrids exhibited a thermally stable network, and the organic spacers remained after elimination of the swelling agents by acid extraction. The resultant materials can be of interest as sensors and for nonlinear optics.
Polymorphism in Isomeric Dihydroxybenzoic Acids (2010)

Multifunctional molecules are capable of assembling via different supramolecular synthons, or hydrogen bond motifs, between the same or different functional groups, leading to the possibility of polymorphism. We have employed sublimation and melt crystallization to generate two new crystalline polymorphs of 3,5-dihydroxybenzoic acid (DHBA), and a second form for 2,3-dihydroxybenzoic acid and 3,4-dihydroxybenzoic acid each. Since hydroxybenzoic acids tend to give solvate/hydrate crystal structures by solution crystallization, solvent-free methods are necessary to obtain single crystals of unsolvated forms. In addition to guest-free polymorphs, a new hydrate polymorph of 3,4-dihydroxybenzoic acid was crystallized from cold water. Polymorphs of dihydroxybenzoic acids differ in the number of symmetry-independent molecules (Z′), the nature of the hydrogen bond synthon, the molecular packing, and the unit cell parameters. Structural and thermal characterization of polymorphic phases shows that the commercial material matches with the high Z′ phase for 2,3-DHBA, 3,5-DHBA, and 3,4-DHBA hydrate even though a low Z′ crystal structure is known in each case. Solventless crystallization conditions at high temperature are a practical method to generate new guest-free polymorphs and high Z′ crystal structures for high affinity functional group compounds.
The fast atom bombardment mass spectrum and fragmentation pathway ofN-[2-(acetamido)-2-deoxy-β-D-glucopyranosyl]-L-asparagine (1992)

The positive ion fast atom bombardment mass spectrum of the aminoglycan N-[2-(acetamido)-2-deoxy-β-D-glucopyranosyl]-L-asparagine and the collisional activation spectrum of the protonated molecule are presented and its fragmentation scheme is proposed. To gain a further understanding of the mechanisms involved spectra of both methyl-2-(acetamido)-2-deoxy-α-D-glucopyranoside and its trideuteroacetamido analogue have been used.
Weaving Klotho into bile acid metabolism (2005)

Bile acids are natural detergents that assist in the absorption and digestion of fats in the intestine. In liver, the synthesis of bile acids from cholesterol is regulated by multiple signaling cascades that repress transcription of the gene encoding cholesterol 7alpha-hydroxylase (CYP7A1), the rate-limiting enzyme in the classic bile acid synthesis pathway. In this issue of the JCI, Ito and coworkers demonstrate that mice lacking betaKlotho, a membrane protein with 2 putative glycosidase domains, have increased Cyp7a1 mRNA levels and bile acid concentrations. betaKlotho-KO mice also have small gallbladders and are resistant to cholesterol gallstone formation. These findings highlight the central role of betaKlotho in bile acid homeostasis and raise the possibility that this protein could be a pharmacologic target for the treatment of gallstones.
Cloning DNA sequences from influenza viral RNA segments (cDNA strands/cleavage maps/nonstructural protein/matrix protein/hemagglutinin) (2016)

DNA sequences corresponding to gene seg- ments that code for the nonstructural protein, the matrix protein, and the hemagglutinin of influenza A virus (strain A/Udorm/72 (H3N2)) were cloned in Escherichia coli pBR 322. Initially, positive and negative cDNA strands were prepared separately by reverse transcription. The positive strands of cDNA were transcribed from genomic RNA segments by using a specific dodecamer DNA sequence as a primer; the negative strands of cDNA were transcribed from cytoplasmic viral mRNA segments by using an oligo(dT) primer. DNA duplexes corresponding in size to the virus RNA segments were then purified, inserted into the plasmid DNA, and used for transformation of E. coli. The influenza virus-specific DNA sequences isolated from recom- binant plasmid molecules were characterized by mapping re- striction enzyme cleavage sites. In addition, the orientation of cloned DNA was determined with reference to the 3' terminus of viral RNA. The negative-stranded RNA genome of influenza A virus contains eight segments that vary from 0.2 to 0.9 X 106 daltons
Serum Antioxidants, Inflammation, and Total Mortality in Older Women (2005)

The inflammatory cytokine interleukin-6 (IL-6) has been linked to poor health outcomes in older adults. Oxidative stress triggers the production of IL-6, and antioxidant micronutrients play a critical role in decreasing this inflammatory response. The authors sought to identify the relations between serum levels of antioxidant nutrients and IL-6 and mortality in older women. Levels of alpha- and beta-carotene, lycopene, lutein/zeaxanthin, alpha-cryptoxanthin, total carotenoids, retinol, alpha-tocopherol, zinc, and selenium were measured at baseline in 619 participants in Women's Health and Aging Study I (Baltimore, Maryland, 1992-1998). IL-6 was measured at baseline and at follow-up 1 and 2 years later, and all-cause mortality was determined over a 5-year period. Participants with the highest serum levels of alpha-carotene, total carotenoids, and selenium were significantly less likely to be in the highest tertile of serum IL-6 at baseline (p < 0.0001). Those with the lowest levels of alpha- and beta-carotene, lutein/zeaxanthin, and total carotenoids were significantly more likely to have increasing IL-6 levels over a period of 2 years. Those with the lowest selenium levels had a significantly higher risk of total mortality over a period of 5 years (hazard ratio = 1.54, 95% confidence interval: 1.03, 2.32). These findings suggest that specific antioxidant nutrients may play an important role in suppressing IL-6 levels in disabled older women.
Advanced Measurement Post-processing by Equivalent Currents on Small 5G Antennas (2018)

Fifth-Generation (5G) mobile communication demands a wide use of multi beam scanning array antennas, providing effective coverage performances at millimeter waves [1-3]. In particular, when the telecommunication channel is characterized by a reduced signal to noise ratio, an omni like radiation pattern could be generated by the beam scanning antenna system. The testing of the AUT (Antenna Under Test), in such conditions, is typically performed with low directive reference antennas. These antennas can suffer of the interaction with the feeding cable. The measurement postprocessing by the equivalent currents approach (EQC) [4-7], implemented in the MVG software INSIGHT [8], can be used for diagnostic investigations on this kind of reference antennas and to filter undesired currents on the feeding cable. In this paper the EQC approach is applied, for the first time, on diagnostic and filtering of feeding cable on a measurement of a low directive antenna for 5G tests.
Electromagnetic Characteristics of a High Density Motor Drive System Using a Printed Power Circuit Board (2001)

This paper describes a high-density motor drive system in which the power transmission lines are formed by a multi-layer printed board, making it possible to reduce inductance of lines. The structure of the power transmission lines between the converter and the inverter is determined, based on calculations of the magnetic field distribution generated by the differential (normal) mode current, which leads to an increase in radiated emissions due to the common mode current. The printed power circuit is experimentally verified as an effective way to reduce the electric field intensity from the radiation.
Superantigen activation of CD4+ and CD8+ T cells from HIV-infected subjects: role of costimulatory molecules and antigen-presenting cells (APC) (1998)

T cell receptor (TCR) triggering via superantigens induces decreased proliferative responses and increased apoptosis in T cells from HIV-infected patients compared with controls. Our aim was to delineate the role of intrinsic T cell defects, of APC dysfunction and of cytokines and costimulatory signal dysregulation in the deficient responses of CD4+ and CD8+ T cells from HIV+ subjects to the superantigen Staphylococcus enterotoxin A (SEA). Proliferation and IL-2R alpha up-regulation on SEA-stimulated CD4+ and CD8+ T cells in whole blood were reduced in HIV+ subjects with CD4 counts < 500, compared with controls. Neither addition of IL-2, IL-12 or phorbol myristate acetate (PMA) nor neutralization of endogenous IL-10, tumour necrosis factor-alpha (TNF-alpha), TNF-beta or transforming growth factor-beta (TGF-beta) could restore the decreased activation by SEA. Possible intrinsic T cell defects were studied by presenting SEA on HLA-DR-transfected Chinese hamster ovary (CHO) cells, co-expressing LFA3 and/or CD80, to purified T cells. In this system CD8+ T cells from most HIV+ patients were hyporesponsive with regard to IL-2 production, IL-2R alpha up-regulation and proliferation, whereas clearly reduced responses were only shown in CD4+ T cells from AIDS patients. Similarly, apoptosis was increased in CD8+ T cells from all patients, but only in CD4+ T cells from AIDS patients. During HIV infection, the responses to TCR triggering through SEA are deficient in both T cell subsets. The intrinsic defect appears earlier during disease progression in purified CD8+ T than in CD4+ T cells, it occurs in conjunction with both CD2 and CD28 costimulation, and it is correlated with increased levels of apoptosis.
CIA, a Novel Estrogen Receptor Coactivator with a Bifunctional Nuclear Receptor Interacting Determinant (2001)

Coregulators for nuclear receptors (NR) are factors that either enhance or repress their transcriptional activity. Both coactivators and corepressors have been shown to use similar but functionally distinct NR interacting determinants containing the core motifs LxxLL and PhixxPhiPhi, respectively. These interactions occur through a hydrophobic cleft located on the surface of the ligand-binding domain (LBD) of the NR and are regulated by ligand-dependent activation function 2 (AF-2). In an effort to identify novel coregulators that function independently of AF-2, we used the LBD of the orphan receptor RVR (which lacks AF-2) as bait in a yeast two-hybrid screen. This strategy led to the cloning of a nuclear protein referred to as CIA (coactivator independent of AF-2 function) that possesses both repressor and activator functions. Strikingly, we observed that CIA not only interacts with RVR and Rev-ErbAalpha in a ligand-independent manner but can also form complexes with estrogen receptor alpha (ERalpha) and ERbeta in vitro and enhances ERalpha transcriptional activity in the presence of estradiol (E(2)). CIA-ERalpha interactions were found to be independent of AF-2 and enhanced by the antiestrogens EM-652 and ICI 182,780 but not by 4-hydroxytamoxifen and raloxifene. We further demonstrate that CIA-ERalpha interactions require the presence within CIA of a novel bifunctional NR recognition determinant containing overlapping LxxLL and PhixxPhiPhi motifs. The identification and functional characterization of CIA suggest that hormone binding can create a functional coactivator interaction interface in the absence of AF-2.
Penicillium griseofulvum F1959, high-production strain of pyripyropene a, specific inhibitor of acyl-CoA: cholesterol acyltransferase 2. (2008)

Acyl-coenzyme A: cholesterol acyltransferase (ACAT) catalyzes cholesterol esterification and plays an important role in the intestinal absorption of cholesterol, hepatic production of lipoproteins, and accumulation of cholesteryl ester within cells. During the course of screening to find ACAT inhibitors from microbial sources, the present authors isolated pyripyropene A from Penicillium griseofulvum F1959. Pyripyropene A, an ACAT2-specific inhibitor, has already been produced from Aspergillus fumigatus. Yet, Aspergillus fumigatus is a pathogen and only produces a limited amount of pyripyropene A, making the isolation of pyripyropene A troublesome. In contrast, Penicillium griseofulvum F1959 was found to produce approximately 28 times more pyripyropene A than Aspergillus fumigatus, plus this report also describes the ideal conditions for the production of pyripyropene A by Penicillium griseofulvum F1959 and its subsequent purification.
Retinal Analog Study of the Role of Steric Interactions in the Excited State Isomerization Dynamics of Rhodopsin (1996)

The role of intramolecular steric interactions in the isomerization of the 11-cis-retinal chromophore in the photoreceptor protein rhodopsin is examined with resonance Raman and CD spectroscopy combined with quantum yield experiments. The resonance Raman spectra and CD spectra of 13-demethylrhodopsin indicate that its chromophore, an analog in which the nonbonded interaction between the 10-H and the 13-CH3 groups is removed, is less distorted in the C10...C13 region than the native chromophore. The reduced torsional and hydrogen-out-of-plane resonance Raman intensities further indicate that the excited state potential energy surface has a much shallower slope along the isomerization coordinate. This is consistent with the decrease in quantum yield from 0.67 in rhodopsin to 0.47 in 13-demethylrhodopsin. The resonance Raman intensities show that the steric twist is reintroduced by addition of a methyl group at the C10 position. However, the quantum yield of 10-methyl-13-demethylrhodopsin is found to be only 0.35. This is attributed to nonisomorphous protein-analog interactions. The nonbonded interaction between the 10-hydrogen and the 13-methyl group in 11-cis-retinal makes this isomer particularly effective as the light-sensing chromophore in all visual pigments.
Assessment of Semiempirical Quantum Mechanical Methods for the Evaluation of Protein Structures (2007)

The ability to discriminate native structures from computer-generated misfolded ones is key to predicting the three-dimensional structure of a protein from its amino acid sequence. Here we describe an assessment of semiempirical methods for discriminating native protein structures from decoy models. The discrimination of decoys entails an analysis of a large number of protein structures, and provides a large-scale validation of quantum mechanical methods and their ability to accurately model proteins. We combine our analysis of semiempirical methods with a comparison of an AMBER force field to discriminate decoys in conjunction with a continuum solvent model. Protein decoys provide a rigorous and reliable benchmark for the evaluation of scoring functions, not only in their ability to accurately identify native structures but also to be computationally tractable to sample a large set of non-native models.
Supplementary Tables S1-3, Figure S1 from Inhibition of JNK Sensitizes Hypoxic Colon Cancer Cells to DNA-Damaging Agents (2023)

&lt;p&gt;Supplementary Tables S1-3, Figure S1. Table S1. Hypoxia increases signaling through JNK in colon cancer cell lines in a cell-specific manner Table S2. Hypoxia increases resistance to chemotherapy in colon cancer cell lines Table S3. Combination of the JNK inhibitor SP600125 with chemotherapy is synergistic in colon cancer cell lines Figure S1. Effects of oxaliplatin and SN-38 on JNK pathway in oxic conditions.&lt;/p&gt;