gebhart/patrepeval huggingface dataset:
Attomole amino acid determination by capillary zone electrophoresis with thermooptical absorbance detection (1989)

Attomole quantities of 4-(dimethylamino)azobenzene-4'-sulfonyl chloride derivatized amino acids are separated by using capillary zone electrophoresis in a mixed acetonitrile/aqueous buffer system. Detection is performed with an on-column thermooptical absorbance detection technique based on a 130-mW argon ion pump laser. Detection limits for the concentration of analyte injected onto the column range from 5 x 10(-8) M for methionine to 5 x 10(-7) M for aspartic acid. Only 37 amol of methionine and 450 amol of aspartic acid are contained within the subnanoliter injection volume. It is interesting to note that these limits are a factor of 4 superior to the best fluorescence detection limit reported for chromatographic separation of amino acids. A subnanoliter sample of derivatized human urine was analyzed with this technique; quantities of amino acids contained within the sample are 3 orders of magnitude greater than the detection limit.
Analysis of Ikaros tumor suppressor function in BCR-ABL1+ pre-B ALL reveals conserved target genes and biological pathways (2016)

Abstract Inactivation of the transcriptional factor Ikaros (IKZF1) correlates with poor prognosis in progenitor B-cell acute lymphoblastic leukemia (pre-B ALL), and is a hallmark of the BCR-ABL1+ subgroup of pre-B ALL. Ikaros is a critical regulator of hematopoietic development and required for B-cell development, however the mechanisms by which Ikaros functions as a tumor suppressor in pre-B ALL remain poorly understood. We analyzed recently developed mouse models of BCR-ABL1+ pre-B ALL containing targeted deletions of Ikaros DNA-binding zinc finger domains together with a new model of inducible expression of WT Ikaros in IKZF1-mutant human BCR-ABL1+ pre-B ALL. We found that both the mouse and human Ikaros-mutated leukemic cells displayed a less mature cell surface phenotype and failed to downregulate the developmentally restricted cell surface receptors c-kit and CD34, respectively. In addition, Ctnnd1, a gene that is also expressed in earlier hematopoietic progenitor cells and normally downregulated as cells differentiate down the B-cell lineage, was found to be a conserved Ikaros target gene, with increased expression in Ikaros-mutated leukemic cells. RNA sequencing defined the Ikaros target genes in both mouse and human Ikaros-mutated pre-B ALL cells and revealed additional conserved target genes and biological functions. Loss of Ikaros tumor suppression was associated with deregulated adhesion pathways and stem-cell signatures. Furthermore, our results presented herein suggest that Ikaros mediates tumor suppressor function, at least in part, by enforcing proper developmental-stage specific expression of multiple genes involved in a network of cadherin-dependent, Rho-regulated Wnt/b-catenin pathways.
Development of an Extremely High Thermal Conductivity TIM for Large Electronics Packages in the 4th Industrial Revolution Era (2020)

The capability and diversity of high-performance microprocessors is increasing with each process technology generation to meet increasing application demands. The cooling designs for these chips must deal with larger temperature gradients across the die than previous generations. Dissipation of the thermal energy from heat generating parts to a heat sink via conduction occurs through a thermal interfacial material (TIM). One of the most important parameters of TIMs is their thermal conductivity that impacts the efficiency of the thermal management. Therefore, in this study, three new different types of TIMs with high thermal conductivity (> 20W/mK) were examined. In this paper, workability and reliability test results will be shown for metal sheet TIM (60W/mK), graphite sheet TIM (24W/mK) and silver (Ag) sintered TIM (50W/mK) materials. All test package sizes are covered with 52.5-mm body size or 45-mm body size for large package with > 45-mm body size in a flip chip ball grid array (FCBGA) package. The reliability test items are high-temperature storage (HTS) @ 150'C 1000hrs, temperature cycling (TC) `B' 1000X and unbiased highly accelerated stress test (uHAST) for 96hrs. Open/short (O/S) test, scanning acoustic tomography (SAT) or X-ray analysis data are reported. Post reliability test, lid pull test results will be shown as well.
Structural and functional analysis of cloned DNA segments containing the replication and incompatibility regions of a miniplasmid derived from a copy number mutant of NR1 (1979)

A 1.45-megadalton segment of DNA cloned from a miniplasmid derived in vivo from a copy number mutant of the R plasmid NR1 has been shown to contain all functions essential for incompatibility and autonomous plasmid replication in Escherichia coli. Specific endonuclease cleavage sites within this DNA segment that localize functions required for replication have been mapped. A 0.45-megadalton fragment that specifies the FII incompatibility of NR1 has been identified within the replication region, and DNA fragments containing this incompatibility region, but lacking other functions required for replication, have been cloned.
A voltammetric electronic tongue for detecting energetic compounds in water (2012)

A voltammetric electronic tongue was developed for detecting energetic compounds in water, providing a rapid, real time method. For the presented study, a glassy carbon electrode, a platinum electrode, and a gold electrode were used to analyze target explosives, nitrotoluene, nitrobenzene, 2,4-dinitrotoluene, and 2,4,6-trinitrotoluene in water. A compact potentiostat was developed to conduct cyclic voltammetry and for extracting data from the electrode sensor array. Finally, pattern recognition methods, such as principal components analysis and a decision tree method are presented for interpretation and discrimination of results.
Computational engineering of small molecules to treat infectious diseases (2017)

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, 2017.
Spinel Magnesium Ferrite: Rationalization of Diversity in Spinel MgFe2O4 Surfaces (Adv. Mater. Interfaces 22/2019) (2019)

Spinel magnesium ferrite (MgFe2O4) is a prospective anode material for lithium ion batteries. Here, the extensive density functional calculations enable the rationalization of the essential effect of magnesium ions in tuning the spinel structures of MgFe2O4 and provide design principles to optimize the battery performance. More details can be found in article number 1901218 by Haoyue Guo, Ping Liu, and co-workers.
Regional and systemic hemodynamic responses following the creation of a murine arteriovenous fistula (2011)

The study of hemodynamic alterations following the creation of an arteriovenous fistula (AVF) is relevant to vascular adaptive responses and hemodialysis access dysfunction. This study examined such alterations in a murine AVF created by anastomosing the carotid artery to the jugular vein. AVF blood flow was markedly increased due to reduced AVF vascular resistance. Despite such markedly increased basal blood flow, AVF blood flow further increased in response to acetylcholine. This AVF model exhibited increased cardiac output and decreased systemic vascular resistance; the kidney, in contrast, exhibited decreased blood flow and increased vascular resistance. Augmentation in AVF blood flow was attended by increased arterial heme oxygenase-1 (HO-1) mRNA and protein expression, the latter localized to smooth muscle cells of the AVF artery; AVF blood flow was substantially reduced in HO-1(-/-) mice compared with HO-1(+/+) mice. Finally, in a murine model of a representative disease known to exhibit impaired hemodynamic responses (sickle cell disease), the creation of an AVF was attended by decreased AVF flow and impaired AVF function. We conclude that this AVF model exhibits markedly increased AVF blood flow, a vasodilatory reserve capacity, increased cardiac output, decreased renal blood flow, and a dependency on intact hemodynamic responses, in general, and HO-1 expression, in particular, in achieving and maintaining AVF blood flow. We suggest that these findings support the utility of this model in investigating the basis for and the consequences of hemodynamic stress, including shear stress, and the pathobiology of hemodialysis AVF dysfunction.
Intact Acute Cardiorenal and Humoral Responsiveness Following Chronic Subcutaneous Administration of the Cardiac Peptide BNP in Experimental Heart Failure (2006)

In experimental CHF, chronic SQ BNP administration did not result in the development of tolerance as demonstrated by increases in both plasma cGMP and UcGMPV following acute administration of SQ BNP. This may have important clinical implications, suggesting that chronic BNP administration does not lead to the development of tolerance to acute BNP administration.
Reciprocity theorem for nonlocal optics: completion of proof and application to spectroscopic analysis (2010)

The problem of optical reciprocity in the long wavelength limit is considered in terms of the symmetry for the scalar Green's function under the Neumann boundary conditions, for materials with nonlocal and anisotropic dielectric responses. This extends the previous works in the literature which were limited either to the Dirichlet conditions or to cases of perfect conductor and local dielectric response. Application of this symmetry principle to the analysis of surface-enhanced spectroscopy for a molecule near a metallic nanoparticle is demonstrated, accounting for the nonlocal response of the particle.
Using DCT-based Approximate Communication to Improve MPI Performance in Parallel Clusters (2019)

Communication overheads in distributed systems constitute a large fraction of the total execution time, and limit the scalability of applications running on these systems. We propose a DCT-based approximate communication scheme that takes advantage of the error resiliency of several widely-used applications, and improves communication efficiency by substantially reducing message lengths. Our scheme is implemented into the Message Passing Interface (MPI) library. When evaluated on several representative MPI applications on a real cluster system, it is seen that the fraction of total execution time devoted to communication reduces from 59% to 23%, even accounting for the computational overhead required for DCT encoding. For many communication-intensive applications, it is shown that our approximate communication scheme effectively speeds up the total execution time without much loss in quality of the result.
Identification and validation of a multivariable prediction model based on blood plasma and serum metabolomics for the distinction of chronic pancreatitis subjects from non-pancreas disease control subjects (2021)

This is the first study that identifies and independently validates a metabolomic signature in plasma and serum for the diagnosis of CP in large, prospective cohorts. The results could provide the basis for the development of the first routine laboratory test for CP.
Immunoglobulin G Fc receptor polymorphisms do not correlate with response to chemotherapy or clinical course in patients with follicular lymphoma (2009)

Recently, immunoglobulin G Fc receptor (FcgammaR) polymorphisms have been found to correlate with the clinical response to rituximab or idiotype vaccine in patients with follicular lymphoma. Two critical questions are whether the FcgammaR polymorphisms correlate with the clinical outcomes after chemotherapy alone in patients with follicular lymphoma and whether they can be explained by linking to underlying biology of follicular lymphoma. This is an important issue because the clinical decisions about the use of antibody therapy may be based on the FcgammaR polymorphisms of these patients. Here, we analyzed the FcgammaRIIIa 158 V/F, FcgammaRIIa 131 H/R, and FcgammaRIIb 232 I/T polymorphisms in a group of 188 patients with follicular lymphoma who were treated with chemotherapy without rituximab initially. In the current study, FcgammaR polymorphisms neither correlated with response rate or time to progression after induction chemotherapy, nor with time to the initial therapy or overall survival after diagnosis. Our results confirm that the correlation between FcgammaR polymorphisms and clinical outcome is specific to immunotherapy such as rituximab and idiotype vaccination, and not due to any effect on the underlying clinical behavior of the disease or chemotherapy response.
Logic Gating by Macrocycle Displacement Using a Double‐Stranded DNA [3]Rotaxane Shuttle (2014)

Abstract Molecular interlocked systems with mechanically trapped components can serve as versatile building blocks for dynamic nanostructures. Here we report the synthesis of unprecedented double‐stranded (ds) DNA [2]‐ and [3]rotaxanes with two distinct stations for the hybridization of the macrocycles on the axle. In the [3]rotaxane, the release and migration of the “shuttle ring” mobilizes a second macrocycle in a highly controlled fashion. Different oligodeoxynucleotides (ODNs) employed as inputs induce structural changes in the system that can be detected as diverse logically gated output signals. We also designed nonsymmetrical [2]rotaxanes which allow unambiguous localization of the position of the macrocycle by use of atomic force microscopy (AFM). Either light irradiation or the use of fuel ODNs can drive the threaded macrocycle to the desired station in these shuttle systems. The DNA nanostructures introduced here constitute promising prototypes for logically gated cargo delivery and release shuttles.
Carbonylation of Aryl Chlorides with Oxygen Nucleophiles at Atmospheric Pressure. Preparation of Phenyl Esters as Acyl Transfer Agents and the Direct Preparation of Alkyl Esters and Carboxylic Acids (2008)

A mild, functional group tolerant method of the preparation of phenyl esters from aryl chlorides via palladium-catalyzed carbonylation is described using atmospheric pressure of carbon monoxide. Phenyl esters are shown to be useful acylating agents, delivering libraries of carbonyl derivatives, including alkyl, allyl and thioesters, under very mild conditions. Direct preparation of alkyl esters and carboxylic acids is also demonstrated, providing the first method for the preparation of methyl and ethyl esters from aryl chlorides without pressured reactors.
Holographic reciprocity law failure (1984)

Previous authors have reported a falloff in diffraction efficiency of reconstructed images in multiple-exposure holograms. We call this phenomenon holographic reciprocity law failure. We propose an explanation for this phenomenon based on latent image formation in photographic materials and discuss a method for superimposing holograms that reconstruct images of equal brightness.
Genetic blueprint of the zoonotic pathogen Toxocara canis (2015)

Toxocara canis is a zoonotic parasite of major socioeconomic importance worldwide. In humans, this nematode causes disease (toxocariasis) mainly in the under-privileged communities in developed and developing countries. Although relatively well studied from clinical and epidemiological perspectives, to date, there has been no global investigation of the molecular biology of this parasite. Here we use next-generation sequencing to produce a draft genome and transcriptome of T. canis to support future biological and biotechnological investigations. This genome is 317 Mb in size, has a repeat content of 13.5% and encodes at least 18,596 protein-coding genes. We study transcription in a larval, as well as adult female and male stages, characterize the parasite's gene-silencing machinery, explore molecules involved in development or host-parasite interactions and predict intervention targets. The draft genome of T. canis should provide a useful resource for future molecular studies of this and other, related parasites.
Crossbow (2009)

This paper describes a new architecture for achieving network virtualization using virtual NICs (VNICs) as the building blocks. The VNICs can be associated with dedicated and independent hardware lanes that consist of dedicated NIC and kernel resources. Hardware lanes support dynamic polling, which enables the fair sharing of bandwidth with no performance penalty. VNICs ensure full separation of traffic for virtual machines within the host. A collection of VNICs on one or more physical machines can be connected to create a Virtual Wire by assigning them a common attribute such as a VLAN tag.
Phased subarrays for low cost C-Scan applications (2006)

The performance of subarray processing as a means of reducing overall beamforming computational load for a low cost C-Scan imaging device is analyzed. Unlike the case encountered in B-Mode imaging, the C-Scan format is characterized by a large channel count (4096 in this case) and very short data record lengths. Additionally, unlike the case in B-Mode, there is no essential need for realtime processing of 'streaming' received channel data. Thus, the C-Scan image format benefits greatly from a subarray processing approach in which partial sums are 'reused' with modified differential delays to form multiple beamformed image pixels. For the design configuration considered here, a subarray aperture of 4x4 elements would be approximately optimal and yielded an approximately 12 - 15 fold reduction in overall beamforming computational load. The actual number of beamforming sums is also influenced by the selected pixel spacing and the range over which partially summed apertures can be steered. Keywords-; Beamforming; Ultrasound Imaging; 2D Array; Phased subarray
Excited-state structure and photochemical ring-opening dynamics of 1,3,5-cyclo-octatriene from absolute resonance Raman intensities (1994)

Absolute resonance Raman cross sections are measured for 1,3,5-cyclo-octatriene (COT) in cyclohexane with excitation from 325 to 200 nm. These intensities and the absorption spectrum are modeled using a fully thermalized time-correlator theory to quantitate the excited-state equilibrium geometry displacements along 19 Raman-active normal modes. The resonance Raman spectra show significant intensity in low-frequency modes corresponding to planarization of the eight-membered ring. The 140 cm−1 twist-boat planarization (Δ=4.6) and the 339 cm−1 ring deformation (Δ=1.6) are particularly strong. However, no intensity is observed in modes which project onto the predicted disrotatory ring-opening motion, such as the nontotally symmetric CH2 twist fundamental or its overtone. Analysis of the fluorescence quantum yield (φF=2×10−6) gives an excited state lifetime on the order of ∼30 fs. These results show that ring planarization is the first step in the disrotatory ring opening of COT followed by rapid depopulation of the initially prepared state to a lower-lying excited electronic state upon which the actual ring opening occurs. Comparison of these results with the excited-state dynamics of other pericyclic systems suggests that pericyclic rearrangements occur only once a planar structure is established and that the bond rearrangement occurs predominantly on a low-lying, optically forbidden excited state.
Enhanced Renal Afferent Arteriolar Reactive Oxygen Species and Contractility to Endothelin-1 Are Associated with Canonical Wnt Signaling in Diabetic Mice (2018)

Increased ROS, notably H2O2 contributes to enhanced afferent arteriolar responses to ET-1 in diabetes, which is closely associated with Wnt signaling. Antioxidant pharmacological strategies targeting Wnt signaling may improve vascular function in diabetic nephropathy.
Oxidative Polymerization of 2,6‐Dimethylphenol To Form Poly(2,6‐dimethyl‐1,4‐phenyleneoxide) in Water (2004)

Green polymerization: The simple stirring of 2,6-dimethylphenol with an excess of oxidant or a catalytic amount of a copper complex in an alkaline aqueous solution yields poly(2,6-dimethyl-1,4-phenyleneoxide), a commercially important polymer (see scheme). The formed polymer was easily separated as an off-white powder by filtration. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2004/z52764_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
In Vivo Stability and Photodynamic Efficacy of Fluorinated Bacteriopurpurinimides Derived from Bacteriochlorophyll-a (2006)

The stable bacteriopurpurinimide (788 nm, epsilon: 38,600 in CH2Cl2), obtained by reducing the corresponding unstable Schiff base (803 nm, epsilon: 50,900 in CH2Cl2) that was isolated by reacting bacteriopurpurin methyl ester with 3,5-bis-(trifluoromethyl)benzylamine, produced promising photosensitizing efficacy. 1H NMR, mass spectrometry, and HPLC analyses confirmed the structures of new bacteriopurpurinimides and the metabolic product. The preliminary in vivo photosensitizing efficacy of this stable bacteriopurpurinimide was determined in C3H mice bearing radiation induced fibrosarcoma tumors as a function of variable drug doses. A drug dose of 1.0 micromol/kg and light exposure of 135 J/cm2 (75 mW/cm2; 24 h postinjection) at 796 nm for 30 min produced a 60% long-term tumor cure (3/5 mice were tumor-free on day 90). Colocalization study of the stable bacteriopurpurinimide with MitoTracker Green confirmed some mitochondrial localization. The fluorescein-exclusion assay and histological staining of CD31 confirmed vascular stasis at various time points post-PDT (post photodynamic therapy). The treatment parameters (time for maximum drug uptake and wavelength for light irradiation) were determined by in vivo reflectance spectroscopy.
Amyloid precursor protein selective gamma-secretase inhibitors for treatment of Alzheimer's disease (2010)

The discordant in vivo activity of ELN318463 suggests that the potency of gamma-secretase inhibitors in AD transgenic mice should be corroborated in wild-type mice. The discovery of ELN475516 demonstrates that it is possible to develop APP selective gamma-secretase inhibitors with potential for treatment for AD.
Role of agglomeration in the early stages of papillar stone formation. (1994)

Possible effects of crystal agglomeration on the early stages of calcium oxalate papillar stone formation are evaluated. The collecting ducts are filled with liquid that flows laminarly as established through hydrodynamical and physicochemical considerations. Under such conditions, agglomeration due to laminar shear forces proceeds. Agglomeration of calcium oxalate monohydrate crystals present in urine at a concentration typical for clinically observed crystalluria cannot result in the formation of a particle sufficiently large enough to be retained in the Bellini's duct and become a papillar stone nidus (nucleus). Formation of such an aggregate during the passage time of urine through the duct requires an unrealistically high concentration of crystals in urine, one that exceeds the normal content of urinary oxalate by several orders of magnitude. Aggregates obstructing the Bellini's duct as assumed in the free particle theory cannot represent a major factor in stone formation. This conclusion is corroborated by experimental results and other observations.
Relationship between indium tin oxide surface treatment and hole injection in C60 modified devices (2006)

The effect of indium tin oxide (ITO) surface treatment on hole injection in organic light-emitting diode with C60 as a buffer layer on ITO was studied. Double surface dipole layer was induced on oxygen plasma treated ITO surface, while no dipole formation was observed on ITO without surface treatment. Interfacial energy barrier between ITO and hole transport layer was reduced by 0.4eV by C60 modification on oxygen plasma treated ITO surface, while there was no change of interfacial energy barrier by C60 on ITO without surface treatment.