gebhart/patrepeval huggingface dataset:
Self-modulated taper drawing of silica nanowires (2005)

We report a self-modulated taper-drawing process for fabricating silica nanowires with diameters down to 20?nm. Long amorphous silica nanowires obtained with this top-down approach present extraordinary uniformities that have not been achieved by any other means. The measured sidewall roughness of the wires goes down to the intrinsic value of 0.2?nm, along with a diameter uniformity better than 0.1%. The wires also show high strength and pliability for patterning under optical microscopes. The ability to prepare and manipulate highly uniform silica nanowires may open up new opportunities for studying and using low-dimensional silica material on a nanometre scale.
A Framework for Structural Input/Output and Control Configuration Selection in Large-Scale Systems (2013)

This paper addresses problems on the structural design of control systems taking explicitly into consideration the possible application to large-scale systems. We provide an efficient and unified framework to solve the following major minimization problems: (i) selection of the minimum number of manipulated/measured variables to achieve structural controllability/observability of the system, and (ii) selection of the minimum number of feedback interconnections between measured and manipulated variables such that the closed-loop system has no structurally fixed modes. Contrary to what would be expected, we show that it is possible to obtain a global solution for each of the aforementioned minimization problems using polynomial complexity algorithms in the number of the state variables of the system. In addition, we provide several new graph-theoretic characterizations of structural systems concepts, which, in turn, enable us to characterize all possible solutions to the above problems.
Effects of an Antihypertensive Combination Based on the Long-Acting Calcium Channel Blocker Benidipineon Vascular and Renal Events (2015)

Background: The Combination Therapy of Hypertension to Prevent Cardiovascular Events (COPE) trial compared three regimens based on the calcium channel blocker (CCB) benidipine.Hypertensive outpatients between the ages of 40–85 years who did not achieve the target blood pressure (<140/90 mmHg) with 4 mg/day of benidipine received an additional angiotensin receptor blocker (ARB), β-blocker, or thiazide. The analysis included 3,293 patients who received an ARB (n = 1,110), β-blocker (n = 1,089), or thiazide (n = 1,094) in addition to benidipine and were followed for a median of 3.61 years. The COPE trial demonstrated a significantly higher incidence of hard cardiovascular composite endpoints and of fatal or non-fatal strokes in the benidipine-β-blocker group than in the benidipine-thiazide group (P = 0.0201, P = 0.0109, respectively). Objective and Methods: In this pre-specified sub-analysis, we further evaluated treatment effects of the three benidipine-based regimens on vascular and renal events. Results: We observed a total of 10 vascular events(0.8 per 1,000 person-years) including 9 cases ofperipheral artery disease (0.8 per 1,000 person-years) and 1 aortic dissection (0.1 per 1,000 person-years). We also observed a total of 7 renal events (0.6 per 1,000 person-years).Few differences were observed among the three treatment groups regarding vascular and renal events (vascular events, P = 0.29; renal events, P = 0.16, Log-rank test). Conclusions: This sub-analysis of the COPE trial demonstrated that blood pressure-lowering therapy with benidipine combined with an ARB, β-blocker, or thiazide diuretic was similarly effective in the prevention of vascular and renal events in hypertensive outpatients.
Correlation and Interpretation of Microseismic Responses using Pressure Measurements in Offset Observation Wells (2015)

Abstract Interpretation of the microseismic data acquired during hydraulic fracture treatments is based on a variety of techniques that make use of the locations, times, and source parameters of the detected events, in conjunction with the stimulation treatment data. It is sometimes possible to observe trends or changes in the microseismic data that correspond to the surface pressure measurements; however this aspect of interpretation becomes problematic due the variability of fluid friction, slurry density, perforation restrictions, and other near-wellbore pressures when computing bottom hole fracturing pressure. An interpretation technique is proposed that uses pressure measurements in observation wells that are offset to the treatment well during microseismic interpretations. The observation well can be any well with open perforations in close proximity to the treatment well. The observation well pressures are not affected by the many complicating factors that are encountered when estimating pressure in the fracture from the surface pressure measured in the treatment well. Example data from field observations are used to demonstrate that the detection of microseismic events near an observation well and corresponding detection of fluid pressure from the fracture in the observation well validates the calculated event locations. The relationship between fracture pressure, the state of stress, and microseismic responses is discussed using Mohr-Coulomb failure criteria. Observation-well pressures and microseismic events are also used to identify instances where reservoir pressure depletion near the observation well affects surface operations at the treatment well. The results of the study show that reliable measurements of fracture pressure for use in microseismic interpretations can be obtained from offset observation wells, and where reservoir pressure depletion causes deviations from expected fracture behavior. The results also show that microseismic responses are directly related to fracture pressure, and not simply the presence of fracturing fluid itself, leading to an improved understanding of the conditions under which microseismic events occur.
Novel mass reflow method for organic substrates (2015)

The warp of an organic substrate is a major challenge for bond and assembly (B&A) operations. A portable vacuum fixture that eliminates the warp by holding the substrate perfectly flat during the chip attach process is introduced in this paper. Excellent C4 height uniformity with increased B&A yield is achieved by this novel method. The fixture also makes it possible to utilize all electrically good substrates irrespective of their incoming shape. Furthermore, the electrical performance of the substrate is no longer constrained by the need to modify its circuit design to reduce the warp. The vacuum fixture is designed to be compatible with an industry standard mass reflow oven. The design of the fixture is described along with the manufacturing challenges that were faced. A transient thermal model, leveraged to optimize the thermal mass of the fixture by a factor of two, is presented. The performance of the fixture is compared to other mechanical techniques used for clamping substrates flat. The fixture's unique ability to shape the substrate to match the warp of the chip at reflow temperatures is discussed. Finally, application of the technique to challenging chip-attach cases is explored.
Astrocyte-targeted gene delivery of interleukin 2 specifically increases brain-resident regulatory T cell numbers and protects against pathological neuroinflammation (2022)

Abstract The ability of immune-modulating biologics to prevent and reverse pathology has transformed recent clinical practice. Full utility in the neuroinflammation space, however, requires identification of both effective targets for local immune-modulation and a delivery system capable of crossing the blood-brain-barrier. The recent identification and characterization of a small population of regulatory T cells (Tregs) resident in the brain presents one such potential therapeutic target. Here we identified brain IL2 levels as a limiting factor for brain-resident Tregs. We developed a gene-delivery approach for astrocytes, with a small-molecule on-switch to allow temporal control, and enhanced production in reactive astrocytes to spatially-direct delivery to inflammatory sites. Mice with brain-specific IL2 delivery were protected from traumatic brain injury, stroke and multiple sclerosis models, without impacting the peripheral immune system. These results validate brain-specific IL2 gene-delivery as effective protection against neuroinflammation, and provide a versatile platform for delivery of diverse biologics to neuroinflammatory patients.
Supplementary Dataset S2 from Copy Number Loss of 17q22 Is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer (2023)

&lt;p&gt;Supplementary Dataset S2 shows the list of copy number loss genes.&lt;/p&gt;
Sub-Tg Cross-Linking of a Polyimide Membrane for Enhanced CO2 Plasticization Resistance for Natural Gas Separation (2011)

Decarboxylation-induced thermal cross-linking occurs at elevated temperatures (∼15 °C above glass transition temperature) for 6FDA–DAM:DABA polyimides, which can stabilize membranes against swelling and plasticization in aggressive feed streams. Despite this advantage, such a high temperature might result in collapse of substructure and transition layers in the asymmetric structure of a hollow fibers based on such a material. In this work, the thermal cross-linking of the 6FDA–DAM:DABA at temperatures much below the glass transition temperature (∼387 °C by DSC) was demonstrated. This sub-Tg cross-linking capability enables extension to asymmetric structures useful for large scale membranes. The resulting polymer membranes were characterized by swelling in known solvents for the un-cross-linked materials, TGA analysis, and permeation tests of aggressive gas feed stream at higher pressure. The annealing temperature and time clearly influence the degree of cross-linking of the membranes, and results in a slight difference in selectivity for membranes under various cross-linking conditions. Results indicate that the sub-Tg thermal cross-linking of 6FDA–DAM:DABA dense film membrane can be carried out completely even at a temperature as low as 330 °C. Permeabilities were tested for the polyimide membranes using both pure gases (He, O2, N2, CH4, CO2) and mixed gases (CO2/CH4). The selectivity of the cross-linked membrane can be maintained even under very aggressive CO2 operating conditions that are not possible without cross-linking. Moreover, the plasticization resistance was demonstrated up to 700 psia for pure CO2 gas or 1000 psia for 50% CO2 mixed gas feeds.
Serine Residues 338 and 339 in the Carboxyl-Terminal Tail of the Type II Gonadotropin-Releasing Hormone Receptor Are Critical for β-Arrestin-Independent Internalization (2004)

Cloned mammalian type II GnRH receptors have a carboxyl-terminal tail in contrast to the mammalian type I GnRH receptors, which uniquely lack a carboxyl-terminal tail. Because this domain mediates internalization of many serpentine receptors, the internalization pathway of the marmoset monkey type II GnRH receptor and the functional role of the carboxyl-terminal tail in internalization was studied. The internalization pathway of the type II GnRH receptor was investigated in COS-1 cells by coexpressing G protein-coupled receptor kinases (GRKs), dynamin-1, and beta-arrestins. Internalization of the receptor requires GRKs and dynamin but does not require beta-arrestin. The type II GnRH receptor can also internalize via beta-arrestin in the presence of exogenous beta-arrestins, suggesting that the receptor can use two distinct internalization pathways. Receptor internalization appears to occur via clathrin-coated pits and caveolae because disruption of either structure inhibits internalization. Progressive truncations of the carboxyl-terminal tail identified a region containing serine residues 338 and 339 as critical for receptor internalization. Substitution of these serine residues with alanine residues inhibited internalization, whereas substitutions with glutamic acid residues rescued internalization. Furthermore, a dominant-negative GRK2 did not inhibit internalization of receptors having these serine substitutions, although it inhibited internalization of the wild-type receptor. These results together identify serine residues 338 and 339 in the carboxyl-terminal tail as critical for internalization of the type II GnRH receptor and suggest that these residues undergo phosphorylation by GRKs. However, neither of these residues, nor the carboxyl-terminal tail, is required for beta-arrestin-dependent internalization.
Influence of Cations on Activated‐Sludge Effluent Quality (2001)

Laboratory experiments and field tests were conducted to determine the effect of inorganic cations on effluent from activated-sludge systems. Laboratory experiments showed that monovalent cations tend to increase the concentration of solution biological polymers (biopolymers), whereas divalent cations tend to retain the biopolymers in the floc. Biopolymers in solution affect effluent chemical oxygen demand (COD). Coagulation tests were performed on the effluent with ferric chloride. Ferric hydroxide can coagulate protein through possible adsorptive interactions and may be responsible for some biopolymer retention in the flocs. In the field study, it was found that sodium ions in the influent wastewater caused an increase in proteins and polysaccharides in solution, thereby increasing the effluent COD concentration of the treated municipal wastewater. The attachment or release of these microbially derived organic biopolymers and recalcitrant influent substrate may depend on the monovalent-to-divalent cation ratio and the concentration of iron. Modeling of effluent organics in the activated-sludge process can be enhanced through incorporation of concepts that take into account the partitioning (between floc and solution) of microbial biopolymers and influent recalcitrant substrate.
Genomics-Based Molecular Epidemiology of Campylobacter jejuni Isolates from Feedlot Cattle and from People in Alberta, Canada (2008)

Feedlot cattle in Alberta, Canada, have been identified as reservoirs for Campylobacter jejuni, an important human pathogen. Oligonucleotide DNA microarrays were used as a platform to compare C. jejuni isolates from feedlot cattle and human clinical cases from Alberta. Comparative genomic hybridization (CGH) analysis was performed on 87 isolates (46 bovine, 41 human) obtained within the same geographical regions and time frame. Thirteen CGH clusters were obtained based on overall comparative genomic profile similarity. Nine CGH clusters contained human and cattle isolates, three contained only human isolates, and one contained only cattle isolates. The study isolates clustered regardless of temporal or geographical frameworks. In addition, array genes (n = 1,399) were investigated on a gene-by-gene basis to see if any were unequally distributed between human and cattle sources or between clusters dominated by either human or cattle isolates ("human enriched" versus "cattle enriched"). Using Fisher's exact test with the Westfall and Young correction for these comparisons, a small number of differentially distributed genes were identified. Our findings suggest that feedlot cattle and human C. jejuni strains are very similar and may be endemic within Alberta. Further, the common distribution of human clinical and bovine C. jejuni isolates within the same genetically based clusters suggests that dynamic and important transmission routes between cattle and human populations may exist.
A General Approach Toward the Synthesis of 8‐Acylamidopyrazolo[1,5‐a]‐1,3,5‐triazines. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Abstract 16587: Racial Differences in Circulating Natural Killer Cells in Peripartum Cardiomyopathy: Results of the NHLBI Sponsored IPAC Investigation (2013)

Introduction: Peripartum cardiomyopathy (PPCM) is a major cause of maternal morbidity and mortality and the etiology remains unknown. Cellular immunity is altered in pregnancy and the puerperium, and in subjects with acute cardiomyopathy. We examined peripheral cell subsets and the role of NK (natural killer) cells in the NHLBI sponsored IPAC investigation. Method: IPAC (Investigation of Pregnancy Associated Cardiomyopathy) is a multicenter investigation of myocardial recovery in PPCM. Women presenting with an LVEF Results: For the IPAC cohort of women with PPCM, (mean age=30 ± 6 % NYHA class I/II/III/IV=12/46/24/17, and % race= 66 white, 30 black, 4 other) LVEF was 0.34 ± 0.11 at entry and 0.51 ± 0.11 at 6 months. LVEF was lower in blacks compared to whites at entry (p=0.002) and 6 months (p=0.02). The % NK cells (CD3-CD56+CD16+) was decreased in PPCM compared to PP early (6.8± 4.3 vs. 11.9± 5.0, p=0.001) and at 2 months (8.5± 4.6 vs.11.7± 9.6, p=0.03). The % NK was also decreased in DCM early after presentation (4.6± 2.2) compared to NC (p=0.049) and PP (p=0.02) and persisted at 2 month follow up (4.9± 3.7). In contrast, no differences were observed in the percentage of CD3+CD4+ or CD3+CD8+ T-cell populations among the 4 groups at any time point. In comparison by race, the decrease in %NK cells in PPCM was similar early (B/W= 5.9± 3.7/6.8± 4.2, p=0.48) but persisted at 2 months only in blacks (B/W=5.7± 3.4/9.8± 5.0, p=0.002). Conclusions: The percentage of NK cells is significantly decreased in PPCM subjects compared to healthy PP women. A change in immune cell % was not observed in the major T-cell classes. In comparisons of PPCM subjects by race, this decline in NK cells resolved by 2 months in whites, but persisted in blacks. The role of NK cells in the pathogenesis of PPCM and in racial differences in recovery requires further investigation.
Vascular endothelial growth factor signaling in development and disease (2018)

Vascular endothelial growth factors (VEGFs) are best known for their involvement in orchestrating the development and maintenance of the blood and lymphatic vascular systems. VEGFs are secreted by a variety of cells and they bind to their cognate tyrosine kinase VEGF receptors (VEGFRs) in endothelial cells to elicit various downstream effects. In recent years, there has been tremendous progress in elucidating different VEGF/VEGFR signaling functions in both the blood and lymphatic vascular systems. Here, and in the accompanying poster, we present key elements of the VEGF/VEGFR pathway and highlight the classical and newly discovered functions of VEGF signaling in blood and lymphatic vessel development and pathology.
Knockdown of ALR (MLL2) Reveals ALR Target Genes and Leads to Alterations in Cell Adhesion and Growth (2006)

ALR (MLL2) is a member of the human MLL family, which belongs to a larger SET1 family of histone methyltransferases. We found that ALR is present within a stable multiprotein complex containing a cohort of proteins shared with other SET1 family complexes and several unique components, such as PTIP and the jumonji family member UTX. Like other complexes formed by SET1 family members, the ALR complex exhibited strong H3K4 methyltransferase activity, conferred by the ALR SET domain. By generating ALR knockdown cell lines and comparing their expression profiles to that of control cells, we identified a set of genes whose expression is activated by ALR. Some of these genes were identified by chromatin immunoprecipitation as direct ALR targets. The ALR complex was found to associate in an ALR-dependent fashion with promoters and transcription initiation sites of target genes and to induce H3K4 trimethylation. The most characteristic features of the ALR knockdown cells were changes in the dynamics and mode of cell spreading/polarization, reduced migration capacity, impaired anchorage-dependent and -independent growth, and decreased tumorigenicity in mice. Taken together, our results suggest that ALR is a transcriptional activator that induces the transcription of target genes by covalent histone modification. ALR appears to be involved in the regulation of adhesion-related cytoskeletal events, which might affect cell growth and survival.
Synthesis of porphyrins bearing uracyl groups and their assembly induced by melamine derivatives (2007)

Abstract Self‐assembled porphyrins via noncovalent bonding have attracted wide‐ranging researchers in material science. We reported herein the synthesis of the tetraphenyl porphyrin derivatives bearing uracyl groups as acceptor–donor–acceptor (ADA) type hydrogen bonding units, through the condensation of 5,10‐ or 5,15‐bis (3‐amino‐4‐ethylhexylphenyl) porphyrin derivatives with 6‐carboxyuracyl derivatives. When two porphyrins having uracyl groups at the different substituted positions were respectively mixed with a melamine derivative in benzene, 1 H NMR spectra showed that the 5,15 substituted uracyl porphyrin formed a hydrogen‐bonded suprastructure with the melamine derivative as a complementary molecule to the uracyl moiety, although the other 5,10‐substituted uracylporphyrin could not form such a structure. The SEM observation indicated that the mixture with the 5,15‐substituted uracyl porphyrin and the melamine with long alkyl chains formed a sheet‐like structure. Copyright © 2007 John Wiley &amp; Sons, Ltd.
Molecular dissection of the beta subunit of F1-ATPase into peptide fragments. (1992)

Abstract Partial digestion of the native beta subunit of F1-ATPase from the thermophilic Bacillus strain PS3 by three different proteases produced a limited number of peptide fragments. In most cases, the peptides remained associated, and the gross structure of the beta subunit was not destroyed. Furthermore, most peptides were able to reassociate into the form of the beta subunit after denaturating urea treatment. Therefore, the cleaved sites are most likely located in water-exposed loop regions in the tertiary structure of the protein. Almost all peptides were analyzed, and 17 cleaved sites were determined. From the analysis of the distribution of cleaved sites and deletions or insertions in the multiple amino acid sequence alignment of proteins homologous to the beta subunit, locations of five loops and four candidate loops in the beta subunit are suggested. There are two large loops in the central region of the beta subunit sequence, and dicyclohexylcarbodiimide-reactive Glu190 is located in one of them. Tyr341, involved in putative catalytic ATP binding, is also found in one of the loops. Then, taking cleaved sites as a reference, two kinds of expression plasmids, each of which carried genes of two complementary peptide fragments, 1-193 and 198-473 or 1-284 and 285-473, were constructed and expressed in Escherichia coli. For each plasmid, two peptides were coexpressed, associated into a stable beta subunit form in E. coli cells, and purified without dissociation. When these beta subunits were denatured by urea and applied to polyacrylamide gel without denaturant, a protein band with the same mobility as that of the beta subunit appeared, indicating that reassociation of peptide fragments into the form of the beta subunit occurred upon removal of urea. These beta subunits retained the ability to reconstitute the alpha 3 beta 3 gamma complexes even though the efficiency of reconstitution and the recovered ATPase activities were decreased. These complexes were stable at high or low temperature, and ATPase activities were sensitive to inhibition by N3-.