gebhart/patrepeval huggingface dataset:
EH Domains and Their Ligands (2004)

This chapter contains sections titled: Introduction EH Domain-containing Proteins Peptide Ligands Cellular Ligands Structures of the Domain and Its Ligands Evolutionary Origins of the EH Domain Functions of the EH Domain References
Synthesis and applications of high-performance P-chiral phosphine ligands (2021)

Metal-catalyzed asymmetric synthesis is one of the most important methods for the economical and environmentally benign production of useful optically active compounds. The success of the asymmetric transformations is significantly dependent on the structure and electronic properties of the chiral ligands coordinating to the center metals, and hence the development of highly efficient ligands, especially chiral phosphine ligands, has long been an important research subject in this field. This review article describes the synthesis and applications of P-chiral phosphine ligands possessing chiral centers at the phosphorus atoms. Rationally designed P-chiral phosphine ligands are synthesized by the use of phosphine-boranes as the intermediates. Conformationally rigid and electron-rich P-chiral phosphine ligands exhibit excellent enantioselectivity and high catalytic activity in various transition-metal-catalyzed asymmetric reactions. Recent mechanistic studies of rhodium-catalyzed asymmetric hydrogenation are also described.
Long-term live cells observation of internalized fluorescent Fe@C nanoparticles in constant magnetic field (2019)

Non-toxic, biologically compatible superparamagnetic fluorescent MFMNPs can be further used for biological application such as delivery of biologically active compounds both inside the cell and inside the whole organism, magnetic separation, and magnetic resonance imaging (MRI) diagnostics.
High-Yield Growth of Carbon Nanotubes on Composite Fe/Si/O Nanoparticle Catalysts: A Car−Parrinello Molecular Dynamics and Experimental Study (2010)

Single-walled carbon nanotubes (SWCNTs) have recently been synthesized at high catalyst yield (∼90%) using a composite iron/silicon-oxide nanoparticle catalyst in a gas-phase diffusion flame environment. Since catalyst yields without silicon are less than 10%, the role of silicon in improving catalyst yield must be studied to understand the molecular-scale factors that govern carbon nanotube nucleation and growth. In this work, Car−Parrinello molecular dynamics simulations are employed to investigate the structure of Fe/Si and Fe/Si/O nanoparticle catalysts at synthesis temperatures (1300 K). The simulations show that silicon is uniformly dispersed on the iron surface when oxygen is not present, but covers only one hemisphere of the particle surface when oxygen is present to form a silica “cap”. These results are consistent with the results of substrate synthesis and the phase diagram of this Fe/Si/O system. The structure of the catalyst particle when oxygen and silicon are present thus facilitates the preferential decomposition of a carbon precursor on the Fe-rich side of the particle. On the basis of this finding, SWCNTs will nucleate preferentially on Fe/Si/O with segregated phases compared to catalyst particles with a uniform surface composition that typically become encapsulated in carbon before nucleation can occur. High catalyst yields are also demonstrated on Fe/Al/O catalysts, which indicate that high yields are not specific to the presence of silicon in the particle. The results of this study support the hypothesis that the addition of silicon or aluminum, in the presence of oxygen, to iron oxide-based catalysts results in a nonuniform surface composition that facilitates SWCNT nucleation.
Microorganisms in vortices: a microfluidic setup (2006)

A method is presented to create microscale vortices using a microfluidic setup specifically designed to investigate the response of swimming microorganisms. Stable, small-scale vortices were generated in the side cavity of a microchannel by the shear stress in the main flow. The generation of a vortex was found to depend on the cavity's geometry, in particular its depth, aspect ratio, and opening length. Using video-microscopy, the position and orientation of individual bacteria and algae swimming in vortices of various strengths were tracked. Elongated cells were found to align with the streamlines in a strong vortex. The experimental system provides quantitative single-cell information on the interaction between microorganisms and their fluid dynamical environment.
Underfill adhesion to BCB (Cyclotene/sup TM/) bumping and redistribution dielectrics (2000)

The adhesion of several commercial underfills (Dexter Hysol FP4511, FP4527, and CNB775-34) to BCB (CYCLOTENE 4022, 4024) has been studied through die shear testing and subsequent failure analysis. Die shear values range between 69-30 MPa. Failure analysis by optical microscopy, profilometry and XPS spectroscopy indicates mixed mode failure at various interfaces. From the die shear data collected before and after 24 h water boil for Cyclotene 4022 and 4024 (with AP3000 adhesion promoter) and underfillers FP 4511 and 4527 we find the die shear strength decreases an average of 11% for the four comparisons. Adhesion promoters based on vinyltriacetoxysilane or 3-amino-propyltriethoxysilane show equivalent die shear performance. Substrate surface cleaning based on UV ozone treatment reveals oxidation of the BCB surface which by SIMS analysis remains <0.1 /spl mu/m deep after 10 min of treatment.
Language-Independent Information Flow Tracking Engine for Program Comprehension Tools (2017)

Program comprehension tools are often developed for a specific programming language. Developing such a tool from scratch requires significant effort. In this paper, we report on our experience developing a language-independent framework that enables the creation of program comprehension tools, specifically tools gathering insight from deep dynamic analysis, with little effort. Our framework is language independent, because it is built on top of Truffle, an open-source platform, developed in Oracle Labs, for implementing dynamic languages in the form of AST interpreters. Our framework supports the creation of a diverse variety of program comprehension techniques, such as query, program slicing, and back-in-time debugging, because it is centered around a powerful information-flow tracking engine. Tools developed with our framework get access to the information-flow through a program execution. While it is possible to develop similarly powerful tools without our framework, for example by tracking information-flow through bytecode instrumentation, our approach leads to information that is closer to source code constructs, thus more comprehensible by the user. To demonstrate the effectiveness of our framework, we applied it to two of Truffle-based languages namely Simple Language and TruffleRuby, and we distill our experience into guidelines for developers of other Truffle-based languages who want to develop program comprehension tools for their language.
[Influenza A/H5N1 virus outbreaks and prepardness to avert flu pandemic]. (2007)

This review emphasizes the need to improve the knowledge of the biology of H5N1 virus, a candidate for causing the next influenza pandemic. In-depth knowledge of mode of infection, mechanisms of pathogenesis and immune response will help in devising an efficient and practical control strategy against this flu virus. We have discussed limitations of currently available vaccines and proposed novel approaches for making better vaccines against H5N1 influenza virus. They include cell-culture system, reverse genetics, adjuvant development. Our review has also underscored the concept of therapeutic vaccine (anti-disease vaccine), which is aimed at diminishing 'cytokine storm' seen in acute respiratory distress syndrome and/or hemophagocytosis.
Associations between sensitization to Staphylococcus aureus enterotoxins and Th2/eosinophilic inflammation and uncontrolled asthma (2014)

Background : Sensitization to Staphylococcus aureus enterotoxin (SE) is a known risk factor for asthma susceptibility and severity. However, detailed roles of SE sensitization in asthma, particularly in non-atopic asthma, remain unclear. Aims : To clarify clinical implications of SE sensitization in patients with asthma. Methods : In 224 patients with asthma (average age 62.3 years, 171 females) receiving inhaled corticosteroids, specific IgE against SEA or B (SEA/B-IgE) and common aeroallergens were determined. Non-atopic asthma was defined as the absence ( Results : A total of 84 (54%) of atopic patients and 21 (31%) of non-atopic patients were sensitized to SEA/B. Patients who were sensitized to SEA/B showed higher levels of serum total IgE, eosinophil cationic protein and periostin, more frequent sensitization to aeroallergens, and worse asthma control than those without sensitization to SEA/B. Sensitization to SEA/B was marginally associated with the most intensive treatment. In non-atopic patients (n=67), those who were sensitized to SEA/B were significantly older and showed higher levels of serum total IgE and periostin, and a greater annual decline in lung function than non-atopic patients without SEA/B sensitization. Conclusions : Sensitization to SEA/B contributes to persistent Th2/eosinophilic inflammation and poor disease control in patients with asthma. This sensitization may partly explain Th2 inflammation and greater lung function decline in “intrinsic” asthma.
Integrated Fare Card System Synthesis Report (2007)

The Massachusetts Bay Transportation Authority has developed a contactless fare card system to automate the collection of fares along its rail and bus route services. At the same time, there are indications that other regional transit authorities as well as other transportation providers in the Commonwealth are considering new technologies to streamline their payment collection and processing activities. A major question being raised is: Are there merits to the development of an integrated system so that multiple fare payments could be collected in a coordinated manner by two or more regional transit authorities with a single card or other medium? An objective of this research project is to address this question by identifying the benefits and challenges associated with the development and deployment of such an integrated fare card and payment system. The anticipated benefits of an integrated fare card system include user convenience; equity and fairness; improved data collection; cost sharing; and reductions in operating costs and increases in revenue. Challenges identified include personal identification security; administrative issues; technology concerns;service coordination issues; and system affordability. Based on the results and conclusions of this synthesis, recommendations have been developed and proposed to serve as a set of guidelines in assisting integrated fare card stakeholders as they move forward with consideration of an integrated fare card system.
Sparse representations for image decomposition with occlusions (1996)

We study the problem of how to detect "interesting objects" appeared in a given image, I. Our approach is to treat it as a function approximation problem based on an over-redundant basis, and also account for occlusions, where the basis superposition principle is no longer valid. Since the basis (a library of image templates) is over-redundant, there are infinitely many ways to decompose I. We are motivated to select a sparse/compact representation of I, and to account for occlusions and noise. We then study a greedy and iterative "weighted L/sup p/ Matching Pursuit" strategy, with O<p<1. We use an L/sup p/ result to compute a solution, select the best template, at each stage of the pursuit.
Stereoselective Synthesis of Pseudopeptide Microbial Agent AI-77-B (2001)

[structure: see text]. An efficient and highly stereoselective synthesis of the gastroprotective natural product AI-77-B is described. The stereocenters of the hydroxy amino acid moiety were generated by an ester-derived titanium-enolate-mediated syn-aldol reaction, a Curtius rearrangement, and application of Dondoni's aldehyde homologation. Condensation with the dihydroisocoumarin fragment and subsequent deprotecting transformations furnished optically active AI-77-B.
Broad Tuning of Whispering-Gallery Modes in Microdisks (2010)

Silicon microdisks with dynamically-tunable resonance spectra are achieved with narrow, in-plane silicon electrical contacts in a single lithographic step. Electrical current is passed through the devices to enable thermal tuning via joule heating. A 14nm wavelength shift is demonstrated with 1.6mW power consumption in devices with &gt;20nm free spectral ranges and quality factors exceeding 20,000. Spectral shifts of several modal linewidths can be achieved with tuning powers below 100µW.
Differential effects of angiotensin II on cardiorespiratory reflexes mediated by nucleus tractus solitarii – a microinjection study in the rat (1999)

1. The effect of microinjecting angiotensin II (ANGII) into the nucleus of the solitary tract (NTS) on both baroreceptor and peripheral chemoreceptor reflexes was compared. 2. Experiments were performed in a working heart-brainstem preparation of rat. Baroreceptors were stimulated by raising perfusion pressure and chemoreceptors were activated with aortic injections of sodium cyanide (0.025 %, 25-75 microl). Reflex changes in phrenic nerve activity and heart rate were measured after bilateral NTS microinjection (50 nl) of ANGII (0.5-5000 fmol). 3. NTS microinjection of 5 fmol ANGII elicited a transient (28.2 +/- 6 s; mean +/- s.e.m.) bradycardia (-18 +/- 3 beats min-1), and decreased phrenic nerve activity cycle length and amplitude (P < 0.05). At higher doses of ANGII a similar respiratory response was seen but heart rate changes were inconsistent. 4. The baroreceptor reflex bradycardia was depressed significantly by NTS microinjections of ANGII (5-5000 fmol) in a dose-dependent manner with the reflex gain decreasing from 1.7 +/- 0.16 to 0.66 +/- 0.1 beats min-1 mmHg-1 (P < 0.01) at 5000 fmol. Although the chemoreceptor reflex bradycardia was depressed at a low dose of ANGII (5 fmol), all higher doses (50-5000 fmol) produced a dose-dependent potentiation of the reflex bradycardia (maximally +64 +/- 8 %). The respiratory component was unaffected. The effects of ANGII on both reflexes were blocked by an ANGII type 1 (AT1) receptor antagonist, losartan (20 microM). 5. The potentiating action of ANGII on the chemoreceptor reflex cardiac response was abolished by a neurokinin type 1 (NK1) receptor blocker (CP-99,994, 5 microM) but this had no effect on the baroreceptor reflex. 6. AT1 receptors in the NTS can depress the baroreceptor reflex bradycardia which is independent of NK1 receptors. The ANGII effect on the cardiac component of the chemoreceptor reflex is bi-directional being inhibited at low concentrations and potentiated at higher concentrations; the latter involves NK1 receptors and presumably results from release of substance P.
Architecture for on-die interconnect (2023)

In an embodiment, an apparatus includes: a plurality of islands configured on a semiconductor die, each of the plurality of islands having a plurality of cores; and a plurality of network switches configured on the semiconductor die and each associated with one of the plurality of islands, where each network switch includes a plurality of output ports, a first set of the output ports are each to couple to the associated network switch of an island via a point-to-point interconnect and a second set of the output ports are each to couple to the associated network switches of a plurality of islands via a point-to-multipoint interconnect. Other embodiments are described and claimed.
Numerical Investigation of Freestream Turbulence Effect on Flow through Low-Pressure Turbine Cascade (2022)

View Video Presentation: https://doi.org/10.2514/6.2022-3412.vid The low-pressure turbine drives the fan which produces most of the thrust in high-bypass turbojet engines. Understanding the effect of freestream turbulence on the flow physics and total pressure loss is important for designers. A method was implemented for introducing resolved freestream turbulence with specified turbulence spectrum, integral turbulent length scale, and turbulence intensity in large-eddy simulations. The method is tested for isotropic homogeneous turbulence and for a zero-pressure gradient turbulent boundary layer. Freestream turbulence is then introduced in a large-eddy simulation of a linear cascade with high-lift airfoils. For a chord Reynolds number of 30,000, Klebanoff streaks are observed for the favorable pressure gradient suction side boundary layer and flow separation from the suction surface is suppressed.
A methodology for the design and evaluation of advanced automotive electrical power systems (1997)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1997.
Inherited Causes of Clonal Hematopoiesis of Indeterminate Potential in TOPMed Whole Genomes (2019)

ABSTRACT Age is the dominant risk factor for most chronic human diseases; yet the mechanisms by which aging confers this risk are largely unknown. 1 Recently, the age-related acquisition of somatic mutations in regenerating hematopoietic stem cell populations was associated with both hematologic cancer incidence 2–4 and coronary heart disease prevalence. 5 Somatic mutations with leukemogenic potential may confer selective cellular advantages leading to clonal expansion, a phenomenon termed ‘Clonal Hematopoiesis of Indeterminate Potential’ (CHIP). 6 Simultaneous germline and somatic whole genome sequence analysis now provides the opportunity to identify root causes of CHIP. Here, we analyze high-coverage whole genome sequences from 97,691 participants of diverse ancestries in the NHLBI TOPMed program and identify 4,229 individuals with CHIP. We identify associations with blood cell, lipid, and inflammatory traits specific to different CHIP genes. Association of a genome-wide set of germline genetic variants identified three genetic loci associated with CHIP status, including one locus at TET2 that was African ancestry specific. In silico -informed in vitro evaluation of the TET2 germline locus identified a causal variant that disrupts a TET2 distal enhancer. Aggregates of rare germline loss-of-function variants in CHEK2 , a DNA damage repair gene, predisposed to CHIP acquisition. Overall, we observe that germline genetic variation altering hematopoietic stem cell function and the fidelity of DNA-damage repair increase the likelihood of somatic mutations leading to CHIP.
An ionic liquid process for mercury removal from natural gas (2015)

Efficient scrubbing of mercury vapour from natural gas streams has been demonstrated both in the laboratory and on an industrial scale, using chlorocuprate(II) ionic liquids impregnated on high surface area porous solid supports, resulting in the effective removal of mercury vapour from natural gas streams. This material has been commercialised for use within the petroleum gas production industry, and has currently been running continuously for three years on a natural gas plant in Malaysia. Here we report on the chemistry underlying this process, and demonstrate the transfer of this technology from gram to ton scale.
Computational and statistical group theory : AMS Special Session Geometric Group Theory, April 21-22, 2001, Las Vegas, Nevada : AMS Special Session Computational Group Theory, April 28-29, 2001, Hoboken, New Jersey (2002)

Uniform growth, actions on trees and $GL_2$ by R. C. Alperin and G. A. Noskov Centralisers of involutions in black box groups by A. V. Borovik Measuring sets in infinite groups by A. V. Borovik, A. G. Myasnikov, and V. Shpilrain Quantum one-way automata and finitely generated groups by E. M. Freden Spectral properties of a torsion-free weakly branch group defined by a three state automation by R. I. Grigorchuk and A. Zuk Malnormal subgroups of free groups by T. Jitsukawa Variants of product replacement by C. R. Leedham-Green and S. H. Murray Weakly amenable groups by D. V. Osin The Knuth-Bendix procedure for strings and large rewriting systems by C. C. Sims.
Partial Discharge Tests in DC Applications: A Review (2020)

The wide spreading of solar power generation stations, far off-shore wind farms, electric vehicles charging stations, as well as the high voltage DC power transmission systems has dramatically increased the development of DC power grid, which in turn calls new challenges to the partial discharge (PD) detections under DC voltage (DC-PD). Although PD diagnosis has been well studied and under industrial practice for decades, the experiences in AC-PD tests cannot be directly transplanted in the DC-PD applications. The mechanism of the initiation and recurrence of DC-PD differs from the situation under AC voltage. The testing and analyzing of DC-PD confront various challenges which are not presented in the AC applications. In the recent decades, more and more researchers have been focusing in the field of utilizing DC-PD diagnosis to verify the insulation design and to evaluate the dielectric deterioration under DC voltages. This paper gives a brief review of the published studies on DC-PD diagnosis. The review covers the PD signal generation, detection and data processing under DC voltages.
A ${c}$ -Axis-Aligned Crystalline In-Ga-Zn Oxide FET With a Gate Length of 21 nm Suitable for Memory Applications (2019)

We fabricated a field-effect transistor (FET) with a gate length of 21 nm whose channel material is a c-axis-aligned crystalline In-Ga-Zn oxide (CAAC-IGZO). A CAAC-IGZO FET with a gate length of 21 nm has an extremely low off-state leakage current, a practical driving capability, and tolerance against high temperatures. CAAC-IGZO FETs enable low-power integrated circuits, such as logic and memory in high-temperature environments. Performance estimation of a memory cell using the CAAC-IGZO FET with a gate length of 21 nm revealed that a write time of less than 1 ns and a data retention time of more than 1 h would be possible at 85 °C.