gebhart/patrepeval huggingface dataset:
Effect of Humoral Immune Responses on Controlling Viremia during Primary Infection of Rhesus Monkeys with Simian Immunodeficiency Virus (2003)

Cellular immune responses mediated by CD8+ lymphocytes exert efficient control of virus replication during primary simian immunodeficiency virus (SIV) infection. However, the role that antibodies may play in the early control of virus replication remains unclear. To evaluate how antibody responses may affect virus replication during primary SIVmac infection, we depleted rhesus monkeys of B cells with anti-CD20 antibody. In normal rhesus monkeys immunized with tetanus toxoid, anti-CD20 treatment and resulting depletion of B cells inhibited the generation of antitetanus antibodies, while tetanus-specific T-cell responses were preserved. During the first 4 weeks after inoculation with SIVmac251, development of SIV-specific neutralizing antibody was delayed, and titers were significantly lower in B-cell-depleted monkeys than control-antibody-treated monkeys. Despite the lower neutralizing antibody titers, the levels of plasma SIV RNA and the linear slope of the decline seen in B-cell-depleted monkeys did not differ from that observed in monkeys treated with control antibody. However, beginning at day 28 after SIV infection, the B-cell-depleted monkeys showed a significant inverse correlation between neutralizing antibody titers and plasma virus level. These results suggest that the rapid decline of peak viremia that typically occurs during the first 3 weeks of infection was not significantly affected by SIV-specific antibodies. However, the inverse correlation between neutralizing antibodies and plasma virus level during the postacute phases of infection suggests that humoral immune responses may contribute to the control of SIV replication.
Probing Thermal Stability of Li-Ion Battery Ni-Rich Layered Oxide Cathodes by means of Operando Gas Analysis and Neutron Diffraction (2020)

Thermal stability is a crucial parameter that must be considered within the overall performance metrics of Ni-rich layered oxide cathodes. While the intrinsic structural stability of the cathode materials under thermal conditions is important, it is also critical to consider their reaction with electrolytes. In this paper, operando gas analysis, ex situ neutron diffraction, and differential scanning calorimetry were combined to give a broader picture of the thermal stability of Ni-rich NMC cathodes. Li1–xNi0.8Mn0.1Co0.1O2 (NMC811) composite materials with four different states of charge were investigated with and without the presence of an electrolyte. It has been found that electrolyte can greatly accelerate both the structural and thermal decomposition of the cathode materials. A higher state of charge will also make cathode materials more susceptible to thermal shock. Without an electrolyte, O2 release inducing a structural change from layered to rock salt was the major observation during thermal runaway. However, all samples retained some levels of layered structure after annealing up to 300 °C without the electrolyte. In comparison, almost all the O3-type layered phase transformed to the rock-salt phase for the cathode materials heated with the electrolyte at the same experimental conditions. Moreover, the amount of CO2 increased by nearly two orders of magnitude when annealing cathode materials with electrolyte in operando gas analysis experiments. More delithiated NMC811 samples released larger amounts of CO2 at earlier onset temperatures, resonating well with the differential scanning calorimetry (DSC) results showing that more delithiated samples release more heat during thermal shock.
Growth control and metabolism (2012)

mTOR is the target of the immunosuppressive drug rapamycin and the central component of a nutrient-and hormone-sensitive signaling pathway that regulates cell growth and proliferation. We now appreciate that this pathway becomes deregulated in many human cancers and has an important role in the control of metabolism and aging. We have identified two distinct mTORcontaining proteins complexes, one of which regulates growth through S6K and another that regulates cell survival through Akt. These complexes, mTORC1 and mTORC2, define both rapamycin-sensitive and insensitive branches of the mTOR pathway. I will discuss new results from our lab on the regulation and functions of the mTORC1 and mTORC2 pathways.
Conceptual design of laser fusion reactor KOYO-fast – Concepts of reactor system and laser driver (2006)

We have carried out the design studies of KOYO-Fast laser fusion power plant, using fast ignition cone targets, DPSSL lasers, and LiPb liquid wall chambers. Using fast ignition targets, we could design a middle sized 300 MWe reactor module, with 200 MJ fusion pulse energy and 4 Hz rep-rates, and 1200MWe modular power plants with 4 reactor modules and a 16 Hz laser driver. The liquid wall chambers with free surface cascade flows are proposed for cooling surface quickly enough to a 4 Hz pulse operation. We examined the potential ofYb-YAG ceramic lasers operated at 150 ∼ 225 K for both implosion and heating laser systems required for a 16-Hz repetition and 8 % total efficiency.
Genetic analysis of two Arabidopsis DNA polymerase epsilon subunits during early embryogenesis (2005)

Accurate DNA replication is one of the most important events in the life of a cell. To perform this task, the cell utilizes several DNA polymerase complexes. We investigated the role of DNA polymerase epsilon during gametophyte and seed development using forward and reverse genetic approaches. In Arabidopsis, the catalytic subunit of this complex is encoded by two genes, AtPOL2a and AtPOL2b, whereas the second largest regulatory subunit AtDPB2 is present as a unique complete copy. Disruption of AtPOL2a or AtDPB2 resulted in a sporophytic embryo-defective phenotype, whilst mutations in AtPOL2b produced no visible effects. Loss of AtDPB2 function resulted in a severe reduction in nuclear divisions, both in the embryo and in the endosperm. Mutations in AtPOL2a allowed several rounds of mitosis to proceed, often with aberrant planes of division. Moreover, AtDPB2 was not expressed during development of the female gametophyte, which requires three post-meiotic nuclear divisions. Since a consensus binding site for E2F transcription factors was identified in the promoter region of both genes, the promoter-reporter fusion technique was used to show that luciferase activity was increased at specific phases of the cell cycle in synchronized tobacco BY-2 cells. Our results support the idea that fertilization may utilize the mechanisms of cell cycle transcriptional regulation of genes to reactivate the divisions of the oosphere and central cell.
On sustainability and digital fabrication with concrete (2022)

Digital fabrication with concrete has been touted as an avenue to more sustainable construction through more material efficient design, but notably has produced materials with higher carbon footprints and a strong likelihood of reduced durability compared to standard construction. In this short article, a relationship to give a sense of the environmental impact of a structure is introduced, and it is emphasized that shape efficiency is the only unique environmental benefit that digital concrete brings. However, efforts should still continue to bring digital concrete more in line with standard concrete, especially through incorporation of large aggregates and better characterizing the durability. Finally, it is shown that while most 3D printed concretes appear to be overdesigned due to processing requirements, the use of aluminum based accelerators in a 2K system can be beneficial in decoupling buildability from structural strength, allowing greater freedom to lower carbon footprints in mix design.
Cover Picture: A Different Reaction Pathway for the Reduction of Aromatic Nitro Compounds on Gold Catalysts (Angew. Chem. Int. Ed. 38/2007) (2007)

The chemoselective reduction …︁…︁ of functionalized aromatic compounds into the corresponding anilines is important for the industrial preparation of dyes, pharmaceuticals, and pesticides (see cover picture). The anilines are typically produced by metal-catalyzed reduction of aromatic nitro compounds. In their Communication on page 7266 ff., A. Corma and co-workers propose a reaction route for the hydrogenation of aromatic nitro compounds on Au/TiO2 that accounts for the high chemoselectivity and efficiency observed.
A Prospective Comparative Study of ASCA and pANCA in Chinese and Caucasian IBD Patients (2004)

This study identified that pANCA is more sensitive in Caucasian than Chinese UC and that ASCA IgA has a low yield in Chinese CD. pANCA and ASCA are useful for differentiating between UC and CD in both populations, and ASCA IgG and IgA titers have potential use in determining the risk of developing complicated CD.
P53-induced microRNA-107 inhibits HIF-1 and tumor angiogenesis (2010)

The pathway involving the tumor suppressor gene TP53 can regulate tumor angiogenesis by unclear mechanisms. Here we show that p53 regulates hypoxic signaling through the transcriptional regulation of microRNA-107 (miR-107). We found that miR-107 is a microRNA expressed by human colon cancer specimens and regulated by p53. miR-107 decreases hypoxia signaling by suppressing expression of hypoxia inducible factor-1beta (HIF-1beta). Knockdown of endogenous miR-107 enhances HIF-1beta expression and hypoxic signaling in human colon cancer cells. Conversely, overexpression of miR-107 inhibits HIF-1beta expression and hypoxic signaling. Furthermore, overexpression of miR-107 in tumor cells suppresses tumor angiogenesis, tumor growth, and tumor VEGF expression in mice. Finally, in human colon cancer specimens, expression of miR-107 is inversely associated with expression of HIF-1beta. Taken together these data suggest that miR-107 can mediate p53 regulation of hypoxic signaling and tumor angiogenesis.
Reactions Radicals and Resistance: A Tale of Mechano-Chemistry at Sliding Contacts. (2015)

Abstract not provided.
A New Formation-Evaluation Technique for the Lower Tertiary in South Texas—Predicting Production in Low-Permeability, Fine-Grained Sandstones (2006)

Summary The lower Tertiary Wilcox, Yegua, and Vicksburg formations are prolific natural gas plays in south Texas that have been extensively drilled and produced from low-permeability, fine-grained sandstones. It is not unusual to encounter several potential pay zones in each well. What is lacking is a proven formation-evaluation method to determine the highest-productivity water-free producing zones from multiple intervals that can be casually identified on the logs as hydrocarbon-bearing. Connate-water resistivity (Rw) determination is not a major problem, given that many water-bearing sands are usually present. Accurately estimating true clay content, porosity, irreducible water volumes, and permeability present the greatest challenges. A new spectroscopy-based petrophysical interpretation methodology has been developed that makes use of several unique measurements, namely quantitative elemental concentrations and lithology logs obtained from capture gamma ray spectroscopy devices in open or cased wells. These measurements allow us to more accurately define the clay content, mineralogy, and matrix properties of each potential zone. One significant finding obtained from these measurements is the occurrence of calcite cements detected in many sands that cause a pessimistic density porosity to be computed if not accounted for. This calcite cementation appears to vary dramatically in a lateral sense, indicating that its presence should not be used to condemn an entire layer as being too tight for production, nor provide irrefutable evidence of the expected ability of the layer to contain a hydraulic fracture. The enhanced elemental and mineralogical analyses provided by the spectroscopy measurements also allow for more accurate bulk volume irreducible water calculations and a means to correct the neutron porosity for clay and matrix effects. By comparing irreducible water volume to bulk volume hydrocarbon, an accurate prediction of water production can be determined. Oil- and gas-bearing intervals can be identified easily from crossover of the matrix-corrected neutron porosity when used in conjunction with the matrix-corrected density porosity. Results are illustrated with several case studies from wells recently drilled and now producing from the Wilcox, Yegua, and Vicksburg formations.
A TEM Study of Alkaline-Earth Metal Hexaboride Nanowires (2008)

Extended abstract of a paper presented at Microscopy and Microanalysis 2008 in Albuquerque, New Mexico, USA, August 3 – August 7, 2008
Near-Infrared Surface-Enhanced Raman Scattering (NIR SERS) on Colloidal Silver and Gold (1994)

Near-infrared surface-enhanced Raman scattering (NIR SERS) was detected with high sensitivity for two model compounds, crystal violet and the DNA base adenine, adsorbed on silver and gold colloidal particles in aqueous solutions. The NIR SERS spectra were measured with a fiber-optic probe with the use of a Ti:sapphire laser at 850 nm as the excitation source and a charge-coupled device (CCD) as the detection system. In a step to achieve the optimal electromagnetic SERS-enhancement conditions, silver and gold sols were modified to shift their extinction spectra more to the NIR region. Surface enhancement factors for both crystal violet and adenine were estimated to be on the order of 10 6 and 10 8 for gold and silver, respectively. A larger enhancement factor was observed for adenine with NIR excitation than with visible excitation. The benefits of NIR SERS and its potential applications are discussed.
SPRED: Spatially Distributed Laser Fault Injection Resilient Design (2023)

Computing systems’ hardware implementation is vulnerable to physical attacks. One of the most powerful tools in the arsenal of physical attacks is laser fault injection (LFI), which can successfully compromise an embedded cryptographic implementation even with a single fault. Several countermeasures have been proposed to prevent and detect LFI attacks. However, these schemes cannot protect a multi-spot laser fault injection setup alone. Vulnerabilities can be addressed in such circumstances using a multi-layer or defense-in-depth approach. Defense-in-depth refers to implementing several independent countermeasures within a device to provide aggregated protection against various attack vectors. In this paper, we introduce a multi-layer countermeasure where the proposed approach protects an LFI attack detector against multi-spot LFI attacks. We design and simulate a spatially distributed multi-gate driven design, called SPRED, to prevent single and multi-spot LFI attacks. Simulation results show that the distribution of gates in SPRED forces an attacker to use higher laser power and a thinner wafer to inject a fault.
Core Count vs Cache Size for Manycore Architectures in the Cloud (2010)

The number of cores which fit on a single chip is growing at an exponential rate while off-chip main memory bandwidth is growing at a linear rate at best. This core count to off-chip bandwidth disparity causes per-core memory bandwidth to decrease as process technology advances. Continuing per-core off-chip bandwidth reduction will cause multicore and manycore chip architects to rethink the optimal grain size of a core and the on-chip cache configuration in order to save main memory bandwidth. This work introduces an analytic model to study the tradeoffs of utilizing increased chip area for larger caches versus more cores. We focus this study on constructing manycore architectures well suited for the emerging application space of cloud computing where many independent applications are consolidated onto a single chip. This cloud computing application mix favors small, power-efficient cores. The model is exhaustively evaluated across a large range of cache and core-count configurations utilizing SPEC Int 2000 miss rates and CACTI timing and area models to determine the optimal cache configurations and the number of cores across four process nodes. The model maximizes aggregate computational throughput and is applied to SRAM and logic process DRAM caches. As an example, our study demonstrates that the optimal manycore configuration in the 32nm node for a 200 mm^2 die uses on the order of 158 cores, with each core containing a 64KB L1I cache, a 16KB L1D cache, and a 1MB L2 embedded-DRAM cache. This study finds that the optimal cache size will continue to grow as process technology advances, but the tradeoff between more cores and larger caches is a complex tradeoff in the face of limited off-chip bandwidth and the non-linearities of cache miss rates and memory controller queuing delay.
Design, synthesis, pharmacological characterization of a fluorescent agonist of the P2Y 14 receptor (2020)

The P2Y14R is a G(i/o)-coupled receptor of the P2Y family of purinergic receptors that is activated by extracellular UDP and UDP-glucose (UDPG). In an earlier report we described a P2Y14R fluorescent probe, MRS4174, based on the potent and selective antagonist PPTN, a naphthoic acid derivative. Here, we report the design, preparation, and activity of an agonist-based fluorescent probe MRS4183 (11) and a shorter P2Y14R agonist congener, which contain a UDP-glucuronic acid pharmacophore and BODIPY fluorophores conjugated through diaminoalkyl linkers. The design relied on both docking in a P2Y14R homology model and established structure activity relationship (SAR) of nucleotide analogs. 11 retained P2Y14R potency with EC50 value of 0.96 nM (inhibition of adenylyl cyclase), compared to parent UDPG (EC50 47 nM) and served as a tracer for microscopy and flow cytometry, displaying minimal nonspecific binding. Binding saturation analysis gave an apparent binding constant for 11 in whole cells of 21.4±1.1 nM, with a t1/2 of association at 50 nM 11 of 23.9 min. Known P2Y14R agonists and PPTN inhibited cell binding of 11 with the expected rank order of potency. The success in the identification of a new P2Y14R fluorescent agonist with low nonspecific binding illustrates the advantages of rational design based on recently determined GPCR X-ray structures. Such conjugates will be useful tools in expanding the SAR of this receptor, which still lacks chemical diversity in its collective ligands.
The role of neutral and ionized oxygen defects in the emission of tin oxide nanocrystals for near white light application (2015)

Tin oxide (SnO2) nanocrystals (NCs) based phosphor was synthesized by a green chemistry microwave-assisted hydrothermal method at different reactor pressures. The x-ray diffraction analysis showed that a single rutile SnO2 phase with a tetragonal lattice structure was formed. The photoluminescence emission was measured for He-Cd laser excitation at 325 nm and it showed a broad band emission from 400 to 800 nm for all the synthesized reactor pressures. The broad emission spectra were due to the creation of various oxygen and tin defects as confirmed by x-ray photoelectron spectroscopy data. The origin of the emission in the SnO2 NCs is discussed with the help of an energy band diagram. Analysis suggests that the visible emission of SnO2 NCs is due to a transition of an electron from a level close to the conduction band edge to a deeply trapped hole in the SnO2 NCs. The NCs were found to be suitable for warm near white light emission device applications.
Abstract 2326: The first crystal structure of a telomeric quadruplex DNA with a metal-containing ligand (2011)

Abstract The inhibition of telomerase function in cancer cells via induction of a higher-order four-stranded quadruplex arrangement in the telomeric DNA substrate, requires the participation of a quadruplex-stabilizing ligand. We showed several years ago that certain metal complexes could fulfil this role and not only have selectivity for a quadruplex arrangement but had significant biological activity. We now report on the crystal structures of square-planar nickel (II) and copper (II) complexes containing salphen ligands with a human telomeric quadruplex. The structures show that the metal complexes are bound on an external G-quartet face of the quadruplex, and that the metal itself is positioned above the potassium-containing ion channel of the quadruplex, providing important stabilization. The planar groups of the ligand are stacked onto guanine bases, and the charged amino side-chains are positioned in the grooves of the quadruplex. These features are enabling the available structure-activity data to be rationalized and will be discussed in terms of the design of future complexes with enhanced activity. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2326. doi:10.1158/1538-7445.AM2011-2326
Rio Tinto as a niche for acidophilus enzymes of industrial relevance (2023)

Lignocellulosic residues are amongst the most abundant waste products on Earth. Therefore, there is an increasing interest in the utilization of these residues for bioethanol production and for biorefineries to produce compounds of industrial interest. Enzymes that breakdown cellulose and hemicellulose into oligomers and monosaccharides are required in these processes and cellulolytic enzymes with optimum activity at a low pH area are desirable for industrial processes. Here, we explore the fungal biodiversity of Rıo Tinto, the largest acidic ecosystem on Earth, as far as the secretion of cellulolytic enzymes is concerned. Using colorimetric and industrial substrates, we show that a high proportion of the fungi present in this extremophilic environment secrete a wide range of enzymes that are able to hydrolyze cellulose and hemicellulose at acidic pH (4.5-5). Shotgun proteomic analysis of the secretomes of some of these fungi has identified different cellulases and hemicellulolytic enzymes as well as a number of auxiliary enzymes. Supplementation of pre-industrial cocktails from Myceliophtora with Rio Tinto secretomes increased the amount of monosaccharides released from corn stover or sugar cane straw. We conclude that the Rio Tinto fungi display a good variety of hydrolytic enzymes with high industrial potential.
Corepressor SMRT is required to maintain Hox transcriptional memory during somitogenesis (2018)

Nuclear hormone receptors (NRs), such as retinoic acid receptors (RARs), play critical roles in vertebrate development and homeostasis by regulating target gene transcription. Their activity is controlled by ligand-dependent release of corepressors and subsequent recruitment of coactivators, but how these individual receptor modes contribute to development are unknown. Here, we show that mice carrying targeted knockin mutations in the corepressor Silencing Mediator of Retinoid and Thyroid hormone receptor (SMRT) that specifically disable SMRT function in NR signaling (SMRT<sup>mRID</sup>), display defects in cranial neural crest cell-derived structures and posterior homeotic transformations of axial vertebrae. SMRT<sup>mRID</sup> embryos show enhanced transcription of RAR targets including Hox loci, resulting in respecification of vertebral identities. Up-regulated histone acetylation and decreased H3K27 methylation are evident in the Hox loci whose somitic expression boundaries are rostrally shifted. Furthermore, enhanced recruitment of super elongation complex is evident in rapidly induced non-Pol II-paused targets in SMRT<sup>mRID</sup> embryonic stem cells. These results demonstrate that SMRT-dependent repression of RAR is critical to establish and maintain the somitic Hox code and segmental identity during fetal development via epigenetic marking of target loci.