gebhart/patrepeval huggingface dataset:
Production of Hydrogen for Oil Refining by Thermal Gasification of Biomass: Process Design, Integration and Evaluation (2013)

Hydrogen is an important part of crude oil refining operations since it is required in several units for the desulphurization and upgrading of various oil fractions. At present, most of the refineries meet their hydrogen demand through methane steam reforming, a refinery unit that can represent up to 25% of the plant’s fossil CO2 emissions. Processes based on thermochemical gasification of biomass are promising alternatives for hydrogen production. This thesis presents a process integration study of two distinct biomass-to-hydrogen concepts. The focus is put on the\nintegration of these processes with an existing refinery used as a case study for the identification of promising configurations.\nThe first biomass-to-hydrogen concept is based on indirect, atmospheric steam gasification and proven technologies for gas cleaning and upgrade (IG concept) while the second concept relies on direct, pressurized oxygen-steam blown gasification and more advanced cleaning and upgrading technologies (DG concept). Mass and energy balances for the biorefinery concepts are obtained by process simulation while actual refinery data is used. Simulation results show that based on Higher Heating Values (HHV), the conversion efficiency from biomass to hydrogen is 67% for the IG concept and 65% for the DG concept.\nProcess integration tools are then used to identify promising integration and heat recovery opportunities. The identified process configurations differ in terms of coproducts: in addition to hydrogen, the production of HP steam and/or electricity is investigated. All configurations are compared in terms of energy and exergy efficiency and their environmental impact is assessed by\nmeans of a fossil CO2 balance.\nResults highlight the potential for improvement of process performances by performing biomass drying with low quality refinery excess heat instead of biorefinery excess heat. This integration allows the export of additional HP steam to the refinery or electricity generation through an\nintegrated steam cycle, which increase the efficiency of the biorefinery. The IG concept is found to consistently outperform the DG concept according to both thermodynamic efficiencies. For both concepts, the configuration where HP steam is exported to the refinery appears most promising in a context of decreasing emissions from the European power sector.
FlyBase: enhancing Drosophila Gene Ontology annotations (2008)

FlyBase (http://flybase.org) is a database of Drosophila genetic and genomic information. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. This article describes recent changes to the FlyBase GO annotation strategy that are improving the quality of the GO annotation data. Many of these changes stem from our participation in the GO Reference Genome Annotation Project--a multi-database collaboration producing comprehensive GO annotation sets for 12 diverse species.
Resolvins suppress tumor growth and enhance cancer therapy (2017)

Cancer therapy reduces tumor burden by killing tumor cells, yet it simultaneously creates tumor cell debris that may stimulate inflammation and tumor growth. Thus, conventional cancer therapy is inherently a double-edged sword. In this study, we show that tumor cells killed by chemotherapy or targeted therapy ("tumor cell debris") stimulate primary tumor growth when coinjected with a subthreshold (nontumorigenic) inoculum of tumor cells by triggering macrophage proinflammatory cytokine release after phosphatidylserine exposure. Debris-stimulated tumors were inhibited by antiinflammatory and proresolving lipid autacoids, namely resolvin D1 (RvD1), RvD2, or RvE1. These mediators specifically inhibit debris-stimulated cancer progression by enhancing clearance of debris via macrophage phagocytosis in multiple tumor types. Resolvins counterregulate the release of cytokines/chemokines, including TNFα, IL-6, IL-8, CCL4, and CCL5, by human macrophages stimulated with cell debris. These results demonstrate that enhancing endogenous clearance of tumor cell debris is a new therapeutic target that may complement cytotoxic cancer therapies.
The Effect of an Anti-IgE Monoclonal Antibody on the Early- and Late-Phase Responses to Allergen Inhalation in Asthmatic Subjects (1997)

A humanized murine monoclonal antibody directed to the Fc epsilonR1-binding domain of human IgE (rhuMAb-E25) has been shown to inhibit the binding of IgE to mast cells without provoking mast cell activation. To examine the effects of neutralizing IgE on allergic airway responses, we assessed the effects of 9 wk of treatment with rhuMAb-E25 in a parallel group, randomized, double-blind, placebo-controlled study of 19 allergic asthmatic subjects. We found that treatment with rhuMAb-E25 reduced serum IgE, increased the dose of allergen needed to provoke an early asthmatic response, reduced the mean maximal fall in FEV1 during the early response (30 +/- 10% at baseline to 18.8 +/- 8%, versus 33 +/- 8% at baseline to 34 +/- 4% after placebo; p = 0.01), and reduced the mean maximal fall in FEV1 during the late response (24 +/- 20% at baseline to 9 +/- 10% versus 20 +/- 17% at baseline to 18 +/- 17% after placebo; p = 0.047). We conclude that an anti-IgE monoclonal antibody, which inhibits binding of IgE to its receptor, suppresses the early- and late-phase responses to inhaled allergen in allergic asthmatic subjects. Targeting IgE with rhuMAb-E25 might be a useful treatment for allergic asthma.
Diamond Field-Effect Transistors with 1.3 A/mm Drain Current Density by Al2O3 Passivation Layer (2012)

Using nitrogen-dioxide (NO 2 ) adsorption treatment and Al 2 O 3 passivation technique, we improved drain current ( I DS ) of hydrogen-terminated (H-terminated) diamond field-effect transistors (FETs). The Al 2 O 3 passivation layer also serves as a gate-insulator in a gate region. Maximum I DS ( I DSmax ) of -1.35 A/mm was obtained for the diamond FETs with NO 2 adsorption and the Al 2 O 3 passivation layer. This I DSmax is the highest ever reported for diamond FETs and indicates that the Al 2 O 3 passivation layer can stabilize adsorbed NO 2 , which increases the hole carrier concentration on the H-terminated diamond surface. In RF small-signal characteristics, the diamond FETs with NO 2 adsorption and the Al 2 O 3 passivation layer showed high cutoff-frequency ( f T ) and maximum frequency of oscillation ( f max ) in a wide gate–source voltage ( V GS ) range (&gt;10 V). This is because the Al 2 O 3 gate insulator with a high potential barrier against hole carriers can confine and control the high concentration of hole carriers and then high forward-bias voltage can be applied without noticeable gate leakage current.
双重透视论:研究精神-肉体问题的一般系统方法 (1986)

研究精神和肉体问题的一般系统方法,导源于被称作系统哲学的一般理论结构。这种概念结构将实在与功能和组织联在一起,而不与物质或实体联在一起。它建立在当代科学理论的基础上,力图综合各种科学理论,形成一种揭示实在本性的内容坚实的理论,去回答那些长期存在的哲学问题,自然、人类和社会的问题。
Neoantigen screening identifies broad TP53 mutant immunogenicity in patients with epithelial cancers (2019)

The adoptive cell transfer of select tumor-infiltrating lymphocytes (TILs) for personalized immunotherapy can mediate long-term objective tumor regressions in patients with metastatic melanoma, bile duct, cervix, colon, and breast cancers (1–5). These clinical responses are likely mediated by recognition of mutated gene products termed neoantigens because they are absent in normal tissues. Intratumoral T cell responses to mutated neoantigens identified thus far have been unique to the patient, i.e., they are private mutations not identified in other patients’ tumors, except for a neoepitope arising from the KRASG12D driver mutation (1, 3). However, it is largely unknown whether naturally occurring T cells within tumors recognize other shared mutated neoantigens expressed by cancers of unrelated patients.

Across all cancer types, TP53 is the most commonly mutated gene, but mutations occur throughout the gene with preference in the DNA binding domain (6, 7). Therapeutic approaches evaluating small-molecule inhibitors and T cells targeting both WT and mutant p53 tumors in mouse models have been described (8–11). Preliminary studies provided some evidence that mutated TP53 could be recognized by peripheral blood T cells after in vitro stimulation and in vivo vaccination (12–14). However, evidence of immune responses to mutated TP53 within human tumors is limited even though most tumors will express a TP53 mutation. We previously reported patient-specific neoantigen screening in 7 patients with metastatic ovarian cancer, 2 of whom had mutated TP53 neoantigens restricted by HLA-DRB3*02:02 (15, 16). Here, we developed a novel strategy to systematically and comprehensively analyze intratumoral T cell responses to defined TP53 hot spot mutations independent of other tumor mutations in 133 new patients with multiple tumor types. The goal was to translate these cells or their TCR genes into broadly applicable adoptive cellular therapies for common epithelial malignancies.
Virtual Adversarial Training: A Regularization Method for Supervised and Semi-Supervised Learning (2018)

We propose a new regularization method based on virtual adversarial loss: a new measure of local smoothness of the conditional label distribution given input. Virtual adversarial loss is defined as the robustness of the conditional label distribution around each input data point against local perturbation. Unlike adversarial training, our method defines the adversarial direction without label information and is hence applicable to semi-supervised learning. Because the directions in which we smooth the model are only "virtually" adversarial, we call our method virtual adversarial training (VAT). The computational cost of VAT is relatively low. For neural networks, the approximated gradient of virtual adversarial loss can be computed with no more than two pairs of forward- and back-propagations. In our experiments, we applied VAT to supervised and semi-supervised learning tasks on multiple benchmark datasets. With a simple enhancement of the algorithm based on the entropy minimization principle, our VAT achieves state-of-the-art performance for semi-supervised learning tasks on SVHN and CIFAR-10.
Screening for prostate cancer. A decision analytic view. (1994)

Our analysis does not support using PSA, TRUS, or DRE to screen asymptomatic men for prostatic cancer. Screening may result in poorer health outcomes and will increase costs dramatically. Assessment of comorbidity, risk attitude, and valuation of sexual function may identify individuals who will benefit from screening, but selecting high-prevalence populations will not improve the benefit of screening.
Comparative DNA Sequence Analysis of Wheat and Rice Genomes (2003)

The use of DNA sequence-based comparative genomics for evolutionary studies and for transferring information from model species to crop species has revolutionized molecular genetics and crop improvement strategies. This study compared 4485 expressed sequence tags (ESTs) that were physically mapped in wheat chromosome bins, to the public rice genome sequence data from 2251 ordered BAC/PAC clones using BLAST. A rice genome view of homologous wheat genome locations based on comparative sequence analysis revealed numerous chromosomal rearrangements that will significantly complicate the use of rice as a model for cross-species transfer of information in nonconserved regions.
Techniques to Synchronize and Align Driving Simulator Data (2005)

This paper describes techniques used to overcome issues encountered in collecting and aligning driving simulation data recorded from multiple devices. Driving simulators offer the ability to monitor the driver, vehicle, and environment in situation and in detail that are impracticable for roadway vehicles, but the data is often collected from various independent asynchronous data recording devices. Even when all subsystems properly collect data there exists a high degree of probability that the various data files will not be time aligned, thus resulting in misinterpretation of the data which then results in faulty conclusions about driving behavior or algorithms. The paper describes a data synchronization mechanism and a multistage alignment process whereby data from various subsystems is aligned in a two step process: rough alignment and then optimal alignment within milliseconds. Optimal alignment uses a variation of the dynamic time warping (DTW) algorithm resulting in a single data file (plus video). The paper also presents the results of the alignment process on driving simulator data and also describes an automated data validation technique to ensure the integrity of collected data.
Optimal Depth and Duration of Mild Hypothermia in a Focal Model of Transient Cerebral Ischemia (1998)

Intraischemic mild hypothermia must be maintained for 1 to 2 hours to obtain optimal neuroprotection against ischemic cell death due to necrosis and apoptosis.
Mass spectrometric analysis of cyclosporine metabolites (1986)

Cyclosporine (CsA, mol. wt 1202) is a cyclic undecapeptide with potent immunosuppressive properties which have made it extremely useful for preventing the rejection of transplanted organs. The drug has severe side-effects, however, which may be related to its metabolism. Sensitive methods to determine the structure of metabolites of CsA have, therefore, been developed using mass spectrometric techniques. First, the molecular weight of the metabolite is determined using fast atom bombardment mass spectrometry or thermospray liquid chromatography/mass spectrometry. The metabolite is then hydrolysed to its component amino acids, which are esterified and acylated and identified by gas chromatography/mass spectrometry. To distinguish metabolism at the four identical N-methyl leucines, the metabolite is partially hydrolysed, the resulting peptides are derivatized to the trimethylsilyl-polyamino alcohols, and these in turn are analysed by gas chromatography/mass spectrometry. These procedures have been used to determine the structure of metabolites of CsA isolated from rabbit bile. The determination of the structure of one metabolite carboxylated on the eta-carbon of amino acid 1, and of one metabolite hydroxylated on the eta-carbon of amino acid 1 and on the gamma-carbon of N-methyl leucine 9 is presented. These procedures should be generally useful for the structural analysis of microgram amounts of CsA metabolites and analogs.
Associations between subunit ectodomains promote T cell antigen receptor assembly and protect against degradation in the ER (1993)

The T cell antigen receptor (TCR) is an oligomeric protein complex made from at least six different integral membrane proteins (alpha beta gamma delta epsilon and zeta). The TCR is assembled in the ER of T cells, and correct assembly is required for transport to the cell surface. Single subunits and partial receptor complexes are retained in the ER where TCR alpha, beta, and CD3 delta chains are degraded selectively. The information required for the ER degradation of the TCR beta chain is confined to the membrane anchor of the protein (Wileman et al., 1990c; Bonifacino et al., 1990b). In this study we show that the rapid degradation of the TCR beta chain is inhibited when it assembles with single CD3 gamma, delta, or epsilon subunits in the ER, and have started to define the role played by transmembrane anchors, and receptor ectodomains, in the masking proteolytic targeting information. Acidic residues within the membrane spanning domains of CD3 subunits were essential for binding to the TCR beta chain. TCR beta chains and CD3 subunits therefore interact via transmembrane domains. However, when sites of binding were restricted to the membrane anchor of the TCR beta chain, stabilization by CD3 subunits was markedly reduced. Interactions between membrane spanning domains were not, therefore, sufficient for the protection of the beta chain from ER proteolysis. The presence of the C beta domain, containing the first 150 amino acids of the TCR ectodomain, greatly increased the stability of complexes formed in the ER. For assembly with CD3 epsilon, stability was further enhanced by the V beta amino acids. The results showed that the efficient neutralization of transmembrane proteolytic targeting information required associations between membrane spanning domains and the presence of receptor ectodomains. Interactions between receptor ectodomains may slow the dissociation of CD3 subunits from the beta chain and prolong the masking of transmembrane targeting information. In addition, the close proximity of TCR and CD3 ectodomains within the ER may provide steric protection from the action of proteases within the ER lumen.
The determination of the three-dimensional structure of barley serine proteinase inhibitor 2 by nuclear magnetic resonance, distance geometry and restrained molecular dynamics (1987)

The solution structure of the 64 residue structured domain (residues 20-83) of barley serine proteinase inhibitor 2 (BSPI-2) is determined on the basis of 403 interproton distance, 34 phi backbone torsion angle and 26 hydrogen bonding restraints derived from n.m.r. measurements. A total of 11 converged structures were computed using a metric matrix distance geometry algorithm and refined by restrained molecular dynamics. The average rms difference between the final 11 structures and the mean structure obtained by averaging their coordinates is 1.4 +/- 0.2 A for the backbone atoms and 2.1 +/- 0.1 A for all atoms. The overall structure, which is almost identical to that found by X-ray crystallography, is disc shaped and consists of a central four component mixed parallel and antiparallel beta-sheet flanked by a 13 residue alpha-helix on one side and the reactive site loop on the other.
Analysis of Incident Field Modeling and Incident/Scattered Field Calibration Techniques in Microwave Tomography (2011)

Imaging with microwave tomography systems requires both the incident field within the imaging domain as well as calibration factors that convert the collected data to corresponding data in the numerical model used for inversion. The numerical model makes various simplifying assumptions, e.g., 2-D versus 3-D wave propagation, which the calibration coefficients are meant to take into account. For an air-based microwave tomography system, we study two types of calibration techniques-incident and scattered field calibration-combined with two different incident field models: a 2-D line-source and an incident field from full-wave 3-D simulation of the tomography system. Although the 2-D line-source approximation does not accurately model incident field in our system, the use of scattered field calibration with the 2-D line-source provides similar or better images to incident and scattered field calibration with an accurate incident field. Thus, if scattered field calibration is used, a simple (but inaccurate) incident field is acceptable for our microwave tomography system. While not strictly generalizable, we expect our methodology to be applicable to most other microwave tomography systems.
Triple helix formation by purine-rich oligonucleotides targeted to the human dihydrofolate reductase promoter (1992)

The ability of oligodeoxynucleotides to form specific triple helical structures with critical regulatory sequences in the human dihydrofolate reductase (DHFR) promoter was investigated. A battery of purine-rich oligonucleotides targeted to the two purine.pyrimidine strand biased regions near the DHFR transcription initiation site was developed. The stable triple helical structures formed by binding of the oligonucleotides to the native promoter double helix were dominated by G*G.C triplets, with interspersed C*C.G and A*A.T alignments. Mismatches between the oligonucleotide and the purine-rich strand of the target significantly destabilized third strand binding, and a G*A.T alignment was particularly unfavorable. Formation of a pur.pur.pyr triple helical structure results in a localized limitation of access to the native double helical DNA and produces sequence dependent conformational alterations extending several nucleotides beyond the triplex-duplex boundary. Although they differ only by the insertion of two A.T base pairs, the distal and proximal purine.pyrimidine regions can be targeted individually due to the high degree of sequence specificity of triple helical alignment. Triplex formation overlapping any of three consensus transcriptional regulatory elements and collectively covering 50% of the DHFR core promoter is now possible with this set of oligonucleotides.
Regulation of Cytoplasmic Dynein ATPase by Lis1 (2006)

Mutations in Lis1 cause classical lissencephaly, a developmental brain abnormality characterized by defects in neuronal positioning. Over the last decade, a clear link has been forged between Lis1 and the microtubule motor cytoplasmic dynein. Substantial evidence indicates that Lis1 functions in a highly conserved pathway with dynein to regulate neuronal migration and other motile events. Yeast two-hybrid studies predict that Lis1 binds directly to dynein heavy chains (Sasaki et al., 2000; Tai et al., 2002), but the mechanistic significance of this interaction is not well understood. We now report that recombinant Lis1 binds to native brain dynein and significantly increases the microtubule-stimulated enzymatic activity of dynein in vitro. Lis1 does this without increasing the proportion of dynein that binds to microtubules, indicating that Lis1 influences enzymatic activity rather than microtubule association. Dynein stimulation in vitro is not a generic feature of microtubule-associated proteins, because tau did not stimulate dynein. To our knowledge, this is the first indication that Lis1 or any other factor directly modulates the enzymatic activity of cytoplasmic dynein. Lis1 must be able to homodimerize to stimulate dynein, because a C-terminal fragment (containing the dynein interaction site but missing the self-association domain) was unable to stimulate dynein. Binding and colocalization studies indicate that Lis1 does not interact with all dynein complexes found in the brain. We propose a model in which Lis1 stimulates the activity of a subset of motors, which could be particularly important during neuronal migration and long-distance axonal transport.
Dual regulation of mouse Δ5- and Δ6-desaturase gene expression by SREBP-1 and PPARα (2002)

In the process of seeking sterol regulatory element-binding protein 1a (SREBP-1a) target genes, we identified and cloned a cDNA clone encoding mouse Delta(5)-desaturase (D5D). The hepatic expression of D5D as well as Delta(6)-desaturase (D6D) was highly activated in transgenic mice overexpressing nuclear SREBP-1a, -1c, and -2. Disruption of the SREBP-1 gene significantly reduced the expression of both desaturases in the livers of SREBP-1-deficient mice refed after fasting. The hepatic expression of both desaturases was downregulated by dietary PUFA, which were reported to suppress SREBP-1c gene expression. Sustained expression of hepatic nuclear SREBP-1c protein in the transgenic mice abolished the PUFA suppression of both desaturases. Although these data suggested that SREBP-1c regulates D5D and D6D expression, there was no difference in either the D5D or D6D mRNA level between fasted and refed normal mouse livers, indicating a mechanism for fasting induction of both desaturases. Administration of fibrate, a pharmacological ligand for peroxisome proliferator activating receptor alpha (PPARalpha), caused a significant increase in expression of both desaturases. The data suggested that D5D and D6D expression is dually regulated by SREBP-1c and PPARalpha, two reciprocal transcription factors for fatty acid metabolism, and could be involved in lipogenic gene regulation by producing PUFA.