gebhart/patrepeval huggingface dataset:
Mapping Molecular Networks Using Proteomics: A Vision for Patient-Tailored Combination Therapy (2005)

Mapping tumor cell protein networks in vivo will be critical for realizing the promise of patient-tailored molecular therapy. Cancer can be defined as a dysregulation or hyperactivity in the network of intracellular and extracellular signaling cascades. These protein signaling circuits are the ultimate targets of molecular therapy. Each patient's tumor may be driven by a distinct series of molecular pathogenic defects. Thus, for any single molecular targeted therapy, only a subset of cancer patients may respond. Individualization of therapy, which tailors a therapeutic regimen to a tumor molecular portrait, may be the solution to this dilemma. Until recently, the field lacked the technology for molecular profiling at the genomic and proteomic level. Emerging proteomic technology, used concomitantly with genomic analysis, promises to meet this need and bring to reality the clinical adoption of molecular stratification. The activation state of kinase-driven signal networks contains important information relative to cancer pathogenesis and therapeutic target selection. Proteomic technology offers a means to quantify the state of kinase pathways, and provides post-translational phosphorylation data not obtainable by gene arrays. Case studies using clinical research specimens are provided to show the feasibility of generating the critical information needed to individualize therapy. Such technology can reveal potential new pathway interconnections, including differences between primary and metastatic lesions. We provide a vision for individualized combinatorial therapy based on proteomic mapping of phosphorylation end points in clinical tissue material.
Down-regulation of MBD4 contributes to hypomethylation and overexpression of CD70 in CD4+ T cells in systemic lupus erythematosus (2017)

Our results indicated that downregulation of MBD4 contributed to overexpression and hypomethylation of the CD70 gene in SLE CD4<sup>+</sup> T cells. This modulation of MBD4 may provide a novel therapeutic approach for SLE.
Cover Image (2017)

The cover image, by Enrica Vescarelli et al., is based on the In Vitro Research Autophagy activation is required for myofibroblast differentiation during healing of oral mucosa, DOI: 10.1111/jcpe.12767.
Enantioselective Chemoenzymatic Synthesis of the S-Enantiomer of the Systemic Fungicide Fenpropimorph (1995)

Chemoenzymatic synthesis of the S-(-)-enantiomer of fenpropimorph (S)-1 in high optical and chemical purity is described. One feature of this process entails the enantioselective acetylation of prochiral 1,3-propanediol 4 by Pseudomonas sp. lipases, and subsequent transformation of the monoacetate (R)-5 into the final product by the selected order of transformations that comprise; chlorination or tosylation under non-racemizing conditions, hydrogenolysis of the resulting chloromethyl or tosyl group in (+)-6 and (+)-8, second chlorination of (-)-9, and alkylation of cis-3,5-dimethylmorpholine by 1-chloropropane derivative (+)-10. This sequence of reactions affords (S)-1, the more active enantiomer in the commercialized racemic mixture with systemic fungicidal activity.
Multi-Port DC Microgrids: Online Parameter Adaptation in Model Predictive Control (2018)

This paper investigates control of multi-port DC microgrids with a fast transient response and online parameter adaptation. This DC microgrid can handle connection and disconnection of several energy generation units (e.g., fuel cell or photovoltaic units) and battery energy storage units to provide a DC load. To control several unidirectional and bidirectional converters of this microgrid, a scalable model predictive control (MPC) with online parameter adaptation capability is proposed. This adaptive model predictive control (AMPC), which provides fast MPC control for both inner and outer control loops, obviates the need to have a good knowledge about system parameters (as required by conventional MPC controllers). The estimated values of system parameters are deployed in the MPC controllers to ensure fast transient response of the system. This controller increases the scalability of the system to add or remove new power units with unknown parameters. Simulation case studies validate the proposed controller structure.
Microfabrication Of Photonic Crystal Mirrors For Optoelectronic Devices. (1997)

Photonic bandgap crystals are expected to be useful in defining microcavities for modifying spontaneous emission and as high reflectivity mirrors. Here, we use these photonic crystals as end-mirrors of edge-emitting GRINSCH lasers. These single quantum well lasers were grown by molecular beam epitaxy (MBE) and consist of waveguide structures which are in excess of 1.5 micrometers in thickness. To define a high-reflectivity photonic crystal mirror on the edge of these laser stripes, we use a surface mask of PMMA on top of an epitaxially deposited AIAs masking layer. After electron beam exposure of the resist and definition of the 100nm diameter holes through the GaAs cap layer and the 200 nm thick AIAs mask layer, high temperature field oxidation of the AIAs is performed at 340°C for 1.5 hours. This oxidizes the AIAs and forms a very robust etch mask. The hexagonal arrays of 100nm holes are then transferred to a depth of 2 microns through the laser waveguide structure so as to overlap with the optical field in the laser (Figure 1). The output mirror for the laser stripe consists of a standard cleaved facet.
Mass Spectrometric Determination of the Effect of Surface Deactivation on Membranes Used for In-Situ Sampling of Cerebrospinal Fluid (CSF) (2018)

In this paper, a strategy for structured monitoring of surface modifications to control protein adsorption to membrane structures is presented. The already established on-surface enzymatic digestion (oSED) method combined with nano-liquid chromatography and tandem mass spectrometry (LC-MS/MS) analysis was employed for the analysis of proteins in ventricular cerebrospinal fluid (vCSF) from neurointensive care patients. Protein adsorption was studied by in-situ sampling in a temporally resolved manner on both immobilized native and Pluronic-deactivated membranes. Deactivation was significantly reducing the protein adsorption but it also induced novel selective properties of the surface. The proposed versatile strategy will facilitate protein-biomaterial, protein-polymer, protein-protein interaction studies in the future.
Characteristics of CO<sub>2</sub> Laser Welded TRIP Steel Sheet (2011)

Characteristics of CO 2 laser welded 1000 MPa grade Transformation Induced Plasticity steel plate were investigated under different welding power, welding speed and shield gas. Decreasing welding power, increasing welding speed or using mixed shield gas (Ar+He) all reduced the porosity in the weld metal (WM). The weld metal and HAZ near the WM had maximum hardness. In tensile strength test of load perpendicular to the weld axis, the specimens had same tensile properties as that of the raw material. For the load parallel with the weld axis, the specimens prepared with Ar had equal yield strength (YS) and tensile strength (TS) to that of the raw material. But the elongation was lower than that of the raw material. The specimens prepared with shield gas He had higher YS, TS and lower elongation compared with that of the raw material. The welded joint had lower formability than that of the raw material. The formability of specimens prepared with low welding power or mixed shield gas Ar+He was improved compared with that of the specimens prepared using high power or single shield gas Ar.
Would You Like A Chart With That? Incorporating Visualizations into Conversational Interfaces (2019)

Conversational interfaces, such as chatbots, are increasing in prevalence, and have been shown to be preferred by and help users to complete tasks more efficiently than standard web interfaces in some cases. However, little is understood about if and how information should be visualized during the course of an interactive conversation. This paper describes studies in which participants report their preferences for viewing visualizations in chat-style interfaces when answering questions about comparisons and trends. We find a significant split in preferences among participants; approximately 40% prefer not to see charts and graphs in the context of a conversational interface. For those who do prefer to see charts, most preferred to see additional supporting context beyond the direct answer to the question. These results have important ramifications for the design of conversational interfaces to data.
ChemInform Abstract: Bicyclo[2.2.0]hex‐1(4)‐ene. (1986)

Abstract Thermolysis of the tosylhydrazone (I) under reduced pressure gives a mixture of (II) and (III); the ratio of both components is dependent on the pressure.
Isolation of a Chromium Hydride Single-Component Ethylene Polymerization Catalyst (2008)

Reaction of the divalent complex [(t-Bu)NPN(t-Bu)]2Cr (1) with different stoichiometric ratios of Al(i-Bu)3 afforded {μ-[(t-Bu)NP(i-Bu)N(t-Bu)]Al(i-Bu)2}2Cr (2) and [{(i-Bu)P{μ-N(t-Bu)}2Al(i-Bu)2}Cr(μ-H)]2 (3) as part of the same reaction sequence. Complex 2 arises from association of alane and the two ligands via alkylation of the P atom and retention of the AlR2 unit. Complex 3 appears to be generated from subsequent dissociation of one alkylated ligand and possible transfer of an i-Bu group to Cr followed by β-H elimination or transfer of a hydride originating from isobutyl elimination of the aluminum-containing residue. Both species are potent ethylene polymerization catalysts with no need for further activation. It is assumed that 2 is transformed in situ into 3 under the influence of ethylene. Reactions with ethylene carried out in the presence of excess of Al(i-Bu)3 switch the selectivity completely toward selective trimerization.
Intraoperative femoral head dislodgement during total hip arthroplasty: a report of four cases (2017)

Dislodgment of trial femoral heads and migration into the pelvis during total hip arthroplasty is a rarely reported complication with limited published cases. There are three primary mechanisms of femoral head separation: dislodgement during reduction attempt, disassociation from anterior dislocation while assessing anterior stability, and during dislocation after implant trialing. If the trial femoral migrates beyond the pelvic brim, it is safer to finish the total hip arthroplasty and address the retained object after repositioning or in a planned second procedure with a general surgeon. We recommend operative retrieval since long-term complications from retention or clinical results are lacking.
Supplemental Figure 2 from Baseline Plasma Tumor Mutation Burden Predicts Response to Pembrolizumab-based Therapy in Patients with Metastatic Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Overall response to pembrolizumab monotherapy (n=31, left) and combination therapy (n=34*, right).&lt;/p&gt;
Injuries in Underbody Blast Fatalities: Identification of Five Distinct Mechanisms of Head Injury (2022)

Previous research has shown that injuries to the head and neck were prevalent in 73% of all mounted fatalities of underbody blast. The mechanisms that cause such injuries to the central nervous system (CNS) are not yet known. The aim of this study was to identify the head and spinal injuries in fatalities due to underbody blast (UBB) and then develop hypotheses on the causative mechanisms. All U.K. military fatalities from UBB with an associated head injury that occurred during 2007-2013 in the Iraq and Afghanistan conflicts were identified retrospectively. Computed tomography post-mortems (CTPMs) were interrogated for injuries to the head, neck, and spine. All injuries were documented and classified using a radiology classification. Pearson's chi-square and Fisher's exact tests were used to show a relationship between variables and form a hypothesis for injury mechanisms. There were 50 fatalities from UBB with an associated head injury. Of these, 46 had complete CTPMs available for analysis. Chi-square and Fisher's exact tests showed a relationship between lateral ventricle blood and injuries to the abdomen and thorax. Five partially overlapping injury constellations were identified: 1.multiple-level spinal injury with skull fracture and brainstem injury, 2.peri-mesencephalic hemorrhage, 3.spinal and brainstem injury, 4.parenchymal contusions with injury to C0-C1, and 5.an "eggshell" pattern of fractures from direct impact. These injury constellations can now be used to propose injury mechanisms to develop mitigation strategies or clinical treatments.
Size Matters: Body Composition and Outcomes in Maintenance Hemodialysis Patients (2006)

In hemodialysis patients a low body mass index (BMI) is correlated with an unfavorable clinical outcome, a phenomenon known as "reverse epidemiology". Mechanisms underlying this observation are unclear. We propose the following: uremic toxin generation occurs predominantly in visceral organs and the mass of key uremiogenic viscera (gut, liver) relative to body weight is higher in small people. Consequently, the rate of uremic toxin generation per unit of BMI is higher in patients with a low BMI. Body water, mainly determined by muscle mass, serves as a dilution compartment for uremic toxins. Therefore, the concentration of uremic toxins is higher in small subjects. Uremic toxins are taken up by adipose and muscle tissues, subsequently metabolized and stored. Thus, the larger the ratio of fat and muscle mass to visceral mass, the lower the concentration of uremic toxins and the better the survival. To test this hypothesis, studies on uremic toxin kinetics in relation to body composition are needed.
Assessment of nitric oxide signals by triiodide chemiluminescence (2007)

Nitric oxide (NO) bioactivity is mainly conveyed through reactions with iron and thiols, furnishing iron nitrosyls and S-nitrosothiols with wide-ranging stabilities and reactivities. Triiodide chemiluminescence methodology has been popularized as uniquely capable of quantifying these species together with NO byproducts, such as nitrite and nitrosamines. Studies with triiodide, however, have challenged basic ideas of NO biochemistry. The assay, which involves addition of multiple reagents whose chemistry is not fully understood, thus requires extensive validation: Few protein standards have in fact been characterized; NO mass balance in biological mixtures has not been verified; and recovery of species that span the range of NO-group reactivities has not been assessed. Here we report on the performance of the triiodide assay vs. photolysis chemiluminescence in side-by-side assays of multiple nitrosylated standards of varied reactivities and in assays of endogenous Fe- and S-nitrosylated hemoglobin. Although the photolysis method consistently gives quantitative recoveries, the yields by triiodide are variable and generally low (approaching zero with some standards and endogenous samples). Moreover, in triiodide, added chemical reagents, changes in sample pH, and altered ionic composition result in decreased recoveries and misidentification of NO species. We further show that triiodide, rather than directly and exclusively producing NO, also produces the highly potent nitrosating agent, nitrosyliodide. Overall, we find that the triiodide assay is strongly influenced by sample composition and reactivity and does not reliably identify, quantify, or differentiate NO species in complex biological mixtures.
Soliton pulse compression in chalcogenide fiber Bragg gratings (1999)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text G. Lenz, B. J. Eggleton, M. E. Lines, R. E. Slusher, N. M. Litchinitser, J. S. Sanghera, and I. D. Aggarwal, "Soliton pulse compression in chalcogenide fiber Bragg gratings," in Nonlinear Guided Waves and Their Applications, OSA Technical Digest (Optica Publishing Group, 1999), paper ThB4. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Microglia from Mice Transgenic for a Provirus Encoding a Monocyte-Tropic HIV Type 1 Isolate Produce Infectious Virus and Display in Vitro and in Vivo Upregulation of Lipopolysaccharide-Induced Chemokine Gene Expression (2003)

A large body of evidence has indicated that microglia are the predominant cellular location for HIV-1 in the brains of HIV-1-infected individuals and play a direct role in the development of HIV-1-associated dementia (HAD). Therefore, investigation of the mechanism by which HIV-1-infected microglia contribute to the development of HIV-associated dementia should be facilitated by the creation of a mouse model wherein microglia carry replication-competent HIV-1. To circumvent the inability of HIV-1 to infect mouse cells, we developed a mouse line that is transgenic for a full-length proviral clone of a monocyte-tropic HIV-1 isolate, HIV-1(JR-CSF) (JR-CSF mice), whose T cells and monocytes produce infectious HIV-1. We detected expression of the long terminal repeat-regulated proviral transgene in the microglia of these transgenic mice and demonstrated that it was increased by in vitro and in vivo stimulation with lipopolysaccharide. Furthermore, microglia isolated from JR-CSF mouse brains produced HIV-1 that was infectious in vitro and in vivo. We examined the effect that carriage of the HIV-1 provirus had on chemokine gene regulation in the brains of these mice and demonstrated that MCP-1 gene expression by JR-CSF mouse microglia and brains was more responsive to in vitro and in vivo stimulation with lipopolysaccharide than were microglia and brains from control mice. Thus, this study indicates that the JR-CSF mice may represent a new mouse model to study the effect of HIV-1 replication on microglia function and its contribution to HIV-1-associated neurological disease.
Evaluation of fine particle formation by CVD in laminar-flow aerosol reactor. (1990)

層流エアロゾル反応器 (LFAR) での, ガスの化学反応による微粒子の生成が理論および実験的に検討された.実験ではチタンテトライソプロポキシド (TTIP) の蒸気を含むガスが加熱管に層流で導入され, 均一核生成により発生した微粒子の個数濃度および粒度分布が種々の条件下で測定され, TTIP蒸気濃度, 反応器の温度分布, キャリアガスの影響が明らかにされた.理論解析では, 微粒子の生成を簡略化反応凝集モデルで評価し, モノマー, クラスターおよび微粒子のブラウン凝集, ブラウン拡散, 層流による輸送を表すエアロゾルの一般動力学的方程式が数値的に解かれた.実験結果は, 理論計算結果と傾向的によく一致し, TTIP蒸気, モノマー, クラスターおよび微粒子の壁への沈着は, 反応温度が低いほど, 供給TTIP蒸気濃度が低いほど, キャリアガス分子の平均自由行程が大きくなるほど大きくなることが明らかにされた.
Choose, Not Hoard: Information-to-Model Matching for Artificial Intelligence in O-RAN (2022)

Open Radio Access Network (O-RAN) is an emerging paradigm, whereby virtualized network infrastructure elements from different vendors communicate via open, standardized interfaces. A key element therein is the RAN Intelligent Controller (RIC), an Artificial Intelligence (AI)-based controller. Traditionally, all data available in the network has been used to train a single AI model to be used at the RIC. This article introduces, discusses, and evaluates the creation of multiple AI model instances at different RICs, leveraging information from some (or all) locations for their training. This brings about a flexible relationship between gNBs, the AI models used to control them, and the data such models are trained with. Experiments with real-world traces show how using multiple AI model instances that choose training data from specific locations improve the performance of traditional approaches following the hoarding strategy.
Introduction of a Metal-dependent Regulatory Switch into an Enzyme (1989)

A cysteine has been introduced into the hydrophobic binding pocket of staphylococcal nuclease via oligonucleotide-directed mutagenesis. The L89C mutation does not significantly alter the catalytic activity or specificity of the nuclease yet provides a metal-dependent switch for regulating enzymatic activity. The L89C mutant can be inactivated by addition of mercuric or cupric salts and subsequently reactivated by addition of chelating agents. This work may provide a general strategy for regulating the catalytic activity of other enzymes or the binding affinity of proteins to DNA or other proteins.
ALD and MLD Surface Coatings for Performance and Safety Enhancement of Li-Ion Batteries (2010)

Abstract not Available.
Partitioning Roles of Side Chains in Affinity, Orientation, and Catalysis with Structures for Mutant Complexes:  Asparagine-229 in Thymidylate Synthase, (1996)

Thymidylate synthase (TS) methylates only dUMP, not dCMP. The crystal structure of TS.dCMP shows sCMP 4-NH2 excluded from the space between Asn-229 and His-199 by the hydrogen bonding and steric properties and Asn-229. Consequently, 6-C of dCMP is over 4 A from the active site sulfhydryl. The Asn-229 side chain is prevented from flipping 180 degrees to and orientation the could hydrogen bond to dCMP by a hydrogen bond network between conserved residues. Thus, the specific binding of dUMP by TS results from occlusion of competing substrates by steric and electronic effects of residues in the active site cavity. When Asn-229 is replaced by a cysteine, the Cys-229 S gamma rotates out of the active site, and the mutant enzyme binds both dCMP and dUMP tightly but does not methylate dCMP. Thus simply admitting dCMP into the dUMP binding site of TS is not sufficient for methylation of dCMP. Structures of nucleotide complexes of TS N229D provide a reasonable explanation for the preferential methylation of dCMP instead of dUMP by this mutant. In TS N229D.dCMP, Asp-229 forms hydrogen bonds to 3-N and 40NH2 of dCMP. Neither the Asp-229 carboxyl moiety nor ordered water appears to hydrogen bond to 4-O of dUMP. Hydrogen bonds to 4-O (or 4-NH2) have been proposed to stabilize reaction intermediates. If their absence in TS N229D.dUMP persists in the ternary complex, it could explain the 10(4)-fold decrease in kcat/Km for dUMP.
Damage engineering of boron-based low energy ion implantations on ultrashallow junction fabrications (2010)

Combination of transmission electron microscopy and secondary ion mass spectrometry methods and device characteristics are used to successfully study damage engineering of the B-based low energy ion implants. The depths and densities of the amorphizing (a-Si) layer (surface lattice damage) and the end of range (EOR) damage are found to correlate to ion mass (amu) and implant energy, which are scalable to the molecular ion implants and ultralow energy) implants. The B11 beam-line implant shows thinner both a-Si and EOR depths due to its smaller amu and lower energy, and the damage are well annealed under the current annealing conditions. The BF2 beam-line implant shows severe surface lattice damage by more amorphizing due to its larger amu and higher energy, and needs more thermal budget to annealing (recrystallizing). The B2H6 plasma doping (PLAD) shows moderate a-Si layer and less EOR damage than beam-line ones which attributes to B deposition as a screen so that there are no direct ion bombardments on Si wafer substrate. The BF3 PLAD shows similar damage behavior to the BF2 beam-line implant but with less lattice damage. The device performance evaluation confirms that the device processed by B2H6 PLAD shows better ION versus IOFF characteristics than those processed by BF2 and C2B10H12 molecular beam-line implants due to less damage and more complete annealing.