gebhart/patrepeval huggingface dataset:
Development of an epitope-based HIV-1 vaccine strategy from HIV-1 lipopeptide to dendritic-based vaccines (2017)

Development of a safe, effective and globally affordable Human Immunodeficiency Virus strain 1 (HIV-1) vaccine offers the best hope for future control of the HIV-1 pandemic. However, with the exception of the recent RV144 trial, which elicited a modest level of protection against infection, no vaccine candidate has shown efficacy in preventing HIV-1 infection or in controlling virus replication in humans. There is also a great need for a successful immunotherapeutic vaccine since combination antiretroviral therapy (cART) does not eliminate the reservoir of HIV-infected cells. But to date, no vaccine candidate has proven to significantly alter the natural history of an individual with HIV-1 infection. Areas covered: For over 25 years, the ANRS (France Recherche Nord&Sud Sida-HIV hépatites) has been committed to an original program combining basic science and clinical research developing an epitope-based vaccine strategy to induce a multiepitopic cellular response against HIV-1. This review describes the evolution of concepts, based on strategies using HIV-1 lipopeptides towards the use of dendritic cell (DC) manipulation. Expert commentary: Understanding the crucial role of DCs in immune responses allowed moving from the non-specific administration of HIV-1 sequences with lipopeptides to DC-based vaccines. These DC-targeting strategies should improve HIV-1 vaccine efficacy.
High-bias backhopping in nanosecond time-domain spin-torque switches of MgO-based magnetic tunnel junctions (2009)

For CoFeB∕MgO-based magnetic tunnel junctions, the switching probability has an unusual dependence on bias voltage V and bias magnetic field H for bias voltage pulse durations t long enough to allow thermally activated reversal. At high junction bias close to 1V, the probability of magnetic switching in spin-torque-driven switches sometimes appears to decrease. This is shown to be due to a backhopping behavior occurring at high bias, and it is asymmetric in bias voltage, being more pronounced in the bias direction for antiparallel-to-parallel spin-torque switch, i.e., in the direction of electrons tunneling into the free layer. This asymmetry hints at processes involving hot electrons within the free-layer nanomagnet.
Genetic or nutritional disorders in homocysteine or folate metabolism increase protein N ‐homocysteinylation in mice (2009)

Genetic disorders of homocysteine (Hcy) or folate metabolism or high-methionine diets elevate plasma Hcy and its atherogenic metabolite Hcy-thiolactone. In humans, severe hyperhomocysteinemia due to genetic alterations in cystathionine beta-synthase (Cbs) or methylenetetrahydrofolate reductase (Mthfr) results in neurological abnormalities and premature death from vascular complications. In mouse models, dietary or genetic hyperhomocysteinemia results in liver or brain pathological changes and accelerates atherosclerosis. Hcy-thiolactone has the ability to form isopeptide bonds with protein lysine residues, which generates modified proteins (N-Hcy-protein) with autoimmunogenic and prothrombotic properties. Our aim was to determine how N-Hcy-protein levels are affected by genetic or nutritional disorders in Hcy or folate metabolism in mice. We found that plasma N-Hcy-protein was elevated 10-fold in mice fed a high-methionine diet compared with the animals fed a normal commercial diet. We also found that inactivation of Cbs, Mthfr, or the proton-coupled folate transporter (Pcft) gene resulted in a 10- to 30-fold increase in plasma or serum N-Hcy-protein levels. Liver N-Hcy-protein was elevated 3.4-fold in severely and 11-fold in extremely hyperhomocysteinemic Cbs-deficient mice, 3.6-fold in severely hyperhomocysteinemic Pcft mice, but was not elevated in mildly hyperhomocysteinemic Mthfr-deficient animals, suggesting that mice have a capacity to prevent accumulation of N-Hcy-protein in their organs. These findings provide evidence that N-Hcy-protein is an important metabolite associated with Hcy pathophysiology in the mouse.
Tin Sulfide Mesh: AFM Imaging of Lamellae and Mesopores (1998)

A novel tin sulfide composite mesostructure is important because of its unique combination of electrical, optical, and liquid-crystalline properties. The atomic force microscopy (AFM) studies of the material reported here suggest that its structure is a tin sulfide mimic of a mesh phase—a two-periodic square mesh surface is illustrated in the Figure—with rhombohedral or monoclinic space symmetry.
Ion ring experiments with applications to the compact toroid program (1985)

We report here the status of the ion ring experimental program at Cornell. Ion rings having 3 x 10/sup 15/. 430 keV protons have been trapped in the Ion Ring Experiment (IREX) in a 0.8 T magnetic field. Trapping was achieved using a static downstream mirror and a fast (1.7 ..mu..sec rise time) gated upstream mirror. Ring protons were detectable for up to 4 ..mu..sec (about 50 times both the ion cyclotron period and the injection pulse duration). On LONGSHOT II, up to 1 kJ of less than or equal to 150 keV ions has been produced in 0.4 to 0.9 ..mu..sec pulses using an active anode plasma source as well as the standard surface flashover source. The LONGSHOT II beam will shortly be formed into a rotating proton layer and injected into a preformed (0.3 m diameter and 2.5 m long) Z-discharge plasma to study axial energy dissipation processes. This proton layer ultimately is to be combined with a compact toroid plasma.
ChemInform Abstract: An Efficient Deoxygenation of 1‐Alkenyl or Alkyl Phenyl Sulfoxides to the Corresponding Sulfides Mediated by Magnesium in Alcohol (1994)

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.
A Complementary Silicon Quantum Dot-EnzymePlatform for Selective Detection of NitroaromaticsCompounds (2021)

To address the issue of poor selectivity in nanotechnology-driven, portable nitroaromatics sensors, we have coupled a ratiometric photoluminescence sensor based on silicon quantum dots and fluorescent proteins with a colorimetric enzyme-based sensor. Together, the sensors allow differentiation of nitroaromatic compounds – specifically, distinguishing acetylcholinergic nerve agents from the explosive compounds explored herein. The combined system can detect 2,4,6-trinitrotoluene, 2,4-dinitrotoluene and 4-nitrophenol with micromolar detection limits and affords subsequent differentiation from the nitro-containing nerve agent paraoxon. This demonstrates the advantage of merging elements of materials chemistry and biochemistry to devise customized sensors which can accurately identify hazardous chemical species.
Benchmarking Adversarial Robustness (2019)

Deep neural networks are vulnerable to adversarial examples, which becomes one of the most important research problems in the development of deep learning. While a lot of efforts have been made in recent years, it is of great significance to perform correct and complete evaluations of the adversarial attack and defense algorithms. In this paper, we establish a comprehensive, rigorous, and coherent benchmark to evaluate adversarial robustness on image classification tasks. After briefly reviewing plenty of representative attack and defense methods, we perform large-scale experiments with two robustness curves as the fair-minded evaluation criteria to fully understand the performance of these methods. Based on the evaluation results, we draw several important findings and provide insights for future research.
Cylindrical ultrasound transducers for intravascular and endolumenal imaging applications (2019)

Conventional ultrasound imaging transducers are fabricated using planar geometries—of materials and in most subsequent processing (bonding, dicing, etc.); this can lead to complications in assembling catheter- or endoscope-based devices, and/or significant inherent limitations in their design and application. Miniature cylindrical transducer devices offer the potential for more straightforward design for 360-deg imaging applications, albeit with unique fabrication challenges. We have developed a novel technique for processing cylindrical ultrasound transducer geometries, and used it to fabricate prototype devices designed for intravascular and endolumenal applications. We created a custom dicing setup allowing a tube of radially poled piezoceramic (PZT-4) as small as 4.6 Fr (1.53 mm diameter) to be cut circumferentially, to a specified depth or completely through the wall of the tube, at precise axial locations. The resulting cylindrical transducer was connected to a function generator and power amplifier, and driven at 7.5 MHz to generate axisymmetric, radially directed acoustic radiation force impulse (ARFI) displacements up to 19 μm in a tissue-mimicking elasticity phantom. This demonstrates that miniature cylindrical transducers can be made to enable 360-deg elasticity imaging of the mechanical properties and structure of tissues, to identify vulnerable atherosclerotic plaques or quantify softening of the cervix prior to labor onset.
Improved Synthesis of γ-Lactones from Cyclopropyl Cyanoesters (2011)

Abstract Cyclopropyl cyanoesters 2 were reliably converted to γ-lactones 4 on treatment with aqueous sulfuric acid. The cyanoesters could be easily prepared from ketones or aldehydes in two steps, making this process particularly attractive from an efficiency standpoint.
Molten Carbonate Fuel Cells (2013)

Molten carbonate fuel cells (MCFCs) are high-temperature fuel cells that stand at the end of more than 35 years of intensive development and are finding increased applications in the field of high-efficiency, clean energy supply. They can provide heat and power at overall efficiencies of 90%, and thanks to their operating principle, they could also be used in the incumbent large-scale application of carbon capture and sequestration (CCS). Despite continuous improvements in the technology, some crucial issues still call for focused research and development before the MCFC achieves full operational reliability, especially in conversion of waste-derived fuels. To gain experience and steepen the learning curve leading to market maturity, cost reduction of components, and manufacturing processes are a priority. Current developments have shown that this is a crucial period in MCFC deployment, with certain developers discontinuing their activities, being stumped by the challenges related to the increase of reliability and cost reduction, where others are registering continuous market growth and first profits since commercialization started, having overcome them.
Abstract A25: Activating alterations of p110 subunits determine PI3K isoform selectivity in prostate cancer (2020)

Abstract Oncogenic activity of PI3K mutated tumors is often dependent on different PI3K isoforms. In breast cancer PI3Kα activating mutations are dominant drivers, whereas in PTEN-deficient prostate cancer such activity is thought to be driven by PI3Kβ. In particular, loss of PTEN function is seen in 40% of metastatic prostate cancer patients, which remains a challenging clinical problem. Recent success of selectively targeting PI3Kα or PI3Kβ to treat disease caused by hyperactivation of PI3K pathway sheds light on further developing such agents to a boarder disease spectrum. Yet relatively little is known about how different PI3K isoforms are selected as dominant drivers in different genetic and pathologic contexts. Here we use multiple prostate cancer cell lines and organoid models to study the mechanisms of PI3K isoform dependency in prostate cancer. We found PI3K isoform dependency is not always correlated with PTEN status across a panel of prostate cancer models in which different levels of PI3K signaling are observed. However, such dependency can be shifted towards either PI3Kα or PI3Kβ in the presence of its corresponding activating alteration, regardless of its original isoform dependency. Interestingly, such PI3K isoform activating alteration is able to further enhance PI3K signal in the setting of PTEN loss. PI3Kα mutant models are more sensitive to the α selective inhibitor BYL719 while PI3Kβ mutant models are more sensitive to the β selective inhibitor AZD8186. Besides, we found that PI3Kα mutant prostate tumors are sensitive to PI3Ksy inhibition by AZD8186 at a high dosage both in vitro and in vivo. High dose of AZD8186 also inhibits PI3K signaling in PI3Kα mutant breast cancer models. These data raise the possibility that the PI3Kβ selective inhibitor AZD8186 can also target PI3Kα at a high dose. In an ongoing clinical trial at MSK, a prostate cancer patient with PI3Kα mutation also responded to PI3Kβ inhibition. This finding reveals a new mechanism of how PI3K activating mutations determine PI3K isoform selectivity regardless of PTEN status. Results from this study also present new opportunities to treat cancer patients with PI3Kα or PI3Kβ inhibition. Citation Format: Zeda Zhang, Ninghui Mao, Young Sun Lee, Dan Li, Neal Rosen, Charles Sawyers, Brett Carver. Activating alterations of p110 subunits determine PI3K isoform selectivity in prostate cancer [abstract]. In: Proceedings of the AACR Special Conference on Targeting PI3K/mTOR Signaling; 2018 Nov 30-Dec 8; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(10_Suppl):Abstract nr A25.
Analysis of a herpes simplex virus type 1 LAT mutant with a deletion between the putative promoter and the 5' end of the 2.0-kilobase transcript (1994)

A herpes simplex virus type 1 strain 17 mutant with a deletion between genomic nucleotides 118880 and 119250 was constructed and called 17 delta Sty. The deletion removes most of a putative secondary LAT promoter (called LAPII) as well as 370 of the first 449 nucleotides of the proposed 8.5-kb transcript believed to be the precursor of 2.0-kb LAT. 17 delta Sty was shown to produce major 2.0-kb LATs in tissue culture. Moreover, trigeminal nerves from latently infected mice contained an intact 1.45- to 2.0-kb LAT as well as the minor LATs which are recognized by probes specific for regions downstream of the 2.0-kb LAT. Finally, 17 delta Sty reactivated with normal kinetics from the trigeminal ganglia of latently infected mice in the explant cocultivation assay and egressed from tissue culture cells as efficiently as wild-type virus. These results clearly show that the region deleted in 17 delta Sty is dispensable for intact 2-kb LAT production, viral egress in tissue culture, and normal reactivation from latently infected neurons in mice.
Gas6 deficiency in recipient mice of allogeneic transplantation alleviates hepatic graft-versus-host disease (2010)

Growth arrest-specific gene 6 (Gas6) is expressed in antigen-presenting cells and endothelial cells (ECs) but not in T cells. When wild-type (WT) or Gas6(-/-) mice received allogeneic non-T cell-depleted bone marrow cells, hepatic graft-versus-host disease (GVHD) was alleviated in Gas6(-/-) recipients regardless of donor genotype, but not in WT recipients. T-cell infiltration was more prominent and diffuse in WT than in Gas6(-/-) recipients' liver. When mice received 0.5 x 10(6) allogeneic T cells with T cell-depleted allogeneic bone marrow, clinical signs indicated that GVHD was less severe in Gas6(-/-) than in WT recipients, as shown by a significant improvement of the survival and reduced liver GVHD. These data demonstrate that donor cells were not involved in the protection mechanism. In addition, lack of Gas6 in antigen-presenting cells did not affect WT or Gas6(-/-) T-cell proliferation. We therefore assessed the response of WT or Gas6(-/-) ECs to tumor necrosis factor-alpha. Lymphocyte transmigration was less extensive through Gas6(-/-) than WT ECs and was not accompanied by increases in adhesion molecule levels. Thus, the lack of Gas6 in ECs impaired donor T-cell transmigration into the liver, providing a rationale for considering Gas6 pathway as a potential nonimmunosuppressive target to minimize GVHD in patients receiving allogeneic hematopoietic stem cell transplantation.
Listening for climatic temperature change in the northeast Pacific: 1983–1989 (1992)

Data are presented from an acoustic experiment designed to detect climatic trends of temperature in the ocean with basin-scale resolution. These data are presented as an intriguing new way to recognize changes in spatially averaged temperature. In 1983, travel times of acoustic signals (133 Hz, 60-ms resolution) were measured over 4000 km between a source and receiver mounted near Oahu and northern California, respectively. In 1987, measurement was begun on the travel times along six additional sections in the northeast Pacific, each at a distance of 3000 to 4000 km. Travel times changed by about ±0.2 s at each receiver at interannual periods. Changes in acoustic travel time exceeding about ±0.03 s are due to changes in the spatially averaged temperature along each section. A change of ±0.03 s is equivalent to a change in spatially averaged temperature of only about ∓0.02 °C in the upper kilometer of the ocean. The dynamical processes responsible for the temperature variability along the acoustic sections are not yet identified. No evidence is seen for a long term change in climate from intermittent data between 1983 and 1989 along a 4000-km section.
NKT sublineage specification and survival requires the ubiquitin-modifying enzyme TNFAIP3/A20 (2016)

Natural killer T (NKT) cells are innate lymphocytes that differentiate into NKT1, NKT2, and NKT17 sublineages during development. However, the signaling events that control NKT sublineage specification and differentiation remain poorly understood. Here, we demonstrate that the ubiquitin-modifying enzyme TNFAIP3/A20, an upstream regulator of T cell receptor (TCR) signaling in T cells, is an essential cell-intrinsic regulator of NKT differentiation. A20 is differentially expressed during NKT cell development, regulates NKT cell maturation, and specifically controls the differentiation and survival of NKT1 and NKT2, but not NKT17, sublineages. Remaining A20-deficient NKT1 and NKT2 thymocytes are hyperactivated in vivo and secrete elevated levels of Th1 and Th2 cytokines after TCR ligation in vitro. Defective NKT development was restored by compound deficiency of MALT1, a key downstream component of TCR signaling in T cells. These findings therefore show that negative regulation of TCR signaling during NKT development controls the differentiation and survival of NKT1 and NKT2 cells.
The DNA-Repair GeneMGMTand the Clinical Response of Gliomas to Alkylating Agents (2001)

To the Editor: Esteller and colleagues (Nov. 9 issue) 1 claim that methylation of the O 6 -methylguanine-DNA methyltransferase ( MGMT ) promoter is associated with improved responsiveness to carmustine and prolonged survival in patients with high-grade gliomas. We believe there are methodologic flaws in the authors' study that call these results into question. First, the patients in the study were treated with a combination of surgery, radiation therapy, and chemotherapy with cisplatin and carmustine. We do not believe the response to carmustine is a discernible end point in this trial, because multiple treatments were administered along with carmustine.
Influence of space-charge on hysteresis loop characteristics of ferroelectric thin films (2008)

Hysteresis loops of Pb(Zr, Ti)O3 (PZT) thin films obtained by using a Sawyer-Tower (ST) circuit are affected by many factors. This paper investigated the influence of space charge on the hysteresis loop of thin-film ferroelectrics, based on the model that polarization consists of two parts: linear and switching polarization. It is found that the space charge affects both the shape and offset of the ideal hysteresis loop. Further investigation shows that the practical hysteresis loop has a close relationship with the equivalent ST circuit parameters: the leakage resistance of the FE film, the equivalent input impedance of the measurement equipment, the signal source, and other similar parameters. The normally assumed symmetric hysteresis loop without any offset is obtained with an ST circuit when the output becomes stable. The hysteresis loop obtained at the initial stage of applied signal depends on the initial status of the FE film, and remnant polarization causes an initial offset that gradually disappears.
Modeling and Designing Components with Locally Controlled Composition (1998)

SFF processes have demonstrated the ability to produce parts with locally controlled composition. In the limit, processes such as 3D Printing,cancreate parts with composition control on thelength scaleiof 100 microns.ToexploitthispC)tential,~e\\ZJnethodsto rnod~l, exchange, and process parts.with local composition needtobe.deyeloped..... Anapproachtc) modeling a part's geometty,.topology, and composition will be presented.· This.approachis based on sUbdividing the solidmodel into sub-regions and associating analytic composition blending functions \\lith each region. These blending functions definethe composition throughout the model as mixtures ofthe primary materials available to·the SEF machine. Various design tools will also be presented, for example, specification of com~ositionasa function of the distance from the surface of a part. Finally,the role of design rules specifying maximum concentrations and concentration.gradients will be discussed.
Maximizing binding capacity for protein A chromatography (2014)

Advances in cell culture expression levels in the last two decades have resulted in monoclonal antibody titers of ≥10 g/L to be purified downstream. A high capacity capture step is crucial to prevent purification from being the bottleneck in the manufacturing process. Despite its high cost and other disadvantages, Protein A chromatography still remains the optimal choice for antibody capture due to the excellent selectivity provided by this step. A dual flow loading strategy was used in conjunction with a new generation high capacity Protein A resin to maximize binding capacity without significantly increasing processing time. Optimum conditions were established using a simple empirical Design of Experiment (DOE) based model and verified with a wide panel of antibodies. Dynamic binding capacities of >65 g/L could be achieved under these new conditions, significantly higher by more than one and half times the values that have been typically achieved with Protein A in the past. Furthermore, comparable process performance and product quality was demonstrated for the Protein A step at the increased loading.
Reproductive Technologies for Male Infertility (2001)

The introduction of intracytoplasmic sperm injection (ICSI) in 1992 has revolutionized the treatment of male infertility (1) and has allowed couples whose only prior options were donor insemination to achieve pregnancies or adoption. Although in vitro fertilization (IVF) and related procedures have been used in the past for the treatment of male infertility, most assisted reproductive technology centers are using ICSI as the primary treatment for male infertility. Table 1 lists the cause of male factor infertility. Only a small minority of such patients are amenable to specific hormonal or pharmacologic therapy. Of these, the most probable candidates are the 1–2% of men with male infertility secondary to hypothalamic-pituitary (gonadotropin) insufficiency. These patients respond well to gonadotropin or GnRH therapy. Specific medical treatment is not available for most patients with testicular or idiopathic causes of male infertility. These patients are candidates for assisted reproductive technologies using oocytes from their spouses or partners. This article reviews the ICSI procedure, its indications, and techniques used to retrieve sperm and the risks and concerns that have been raised in regard to its safety, including the genetic risks to the fetus.