gebhart/patrepeval huggingface dataset:
Rhodium‐Complex‐Linked Hybrid Biocatalyst: Stereo‐Controlled Phenylacetylene Polymerization within an Engineered Protein Cavity (2014)

Abstract The incorporation of a Rh complex with a maleimide moiety into the cavity of the nitrobindin β‐barrel scaffold by a covalent linkage at the 96‐position (Cys) provides a hybrid biocatalyst that promotes the polymerization of phenylacetylene. The appropriate structural optimization of the cavity by mutagenesis enhances the stereoselectivity of the polymer with a trans content of 82 % at 25 °C and pH 8.0. The X‐ray crystal structure of one of the hybrid biocatalysts at a resolution of 2.0 Å reveals that the Rh complex is located in the β‐barrel cavity without any perturbation to the total protein structure. Crystal structure analysis and molecular modeling support the fact that the stereoselectivity is enhanced by the effective control of monomer access to the Rh complex within the limited space of the protein cavity.
A proposed diagrammatic logic for ontology specification and visualization (2009)

We propose a diagrammatic logic that is suitable for specifying ontologies. We provide a specification of a simple ontology and include examples to show how to place constraints on ontology specifications and define queries. The framework also allows the depiction of instances, multiple ontologies to be related, and reasoning about ontologies. 1.
ChemInform Abstract: Efficient Method for Pinacol Coupling of Aromatic and Aliphatic Ketones by Using Titanium(II) Chloride and Zinc in the Presence of Pivalonitrile. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
MISPEL: A supervised deep learning harmonization method for multi-scanner neuroimaging data (2022)

Abstract Large-scale data obtained from aggregation of already collected multi-site neuroimaging datasets has brought benefits such as higher statistical power, reliability, and robustness to the studies. Despite these promises from growth in sample size, substantial technical variability stemming from differences in scanner specifications exists in the aggregated data and could inadvertently bias any downstream analyses on it. Such a challenge calls for data normalization and/or harmonization frameworks, in addition to comprehensive criteria to estimate the scanner-related variability and evaluate the harmonization frameworks. In this study, we propose MISPEL (Multi-scanner Image harmonization via Structure Preserving Embedding Learning), a supervised multi-scanner harmonization method that is naturally extendable to more than two scanners. We also designed a set of criteria to investigate the scanner-related technical variability and evaluate the harmonization techniques. As an essential requirement of our criteria, we introduced a multi-scanner matched dataset of 3T T1 images across four scanners, which, to the best of our knowledge is one of the few datasets of this kind. We also investigated our evaluations using two popular segmentation frameworks: FSL and segmentation in statistical parametric mapping (SPM). Lastly, we compared MISPEL to popular methods of normalization and harmonization, namely White Stripe, RAVEL, and CALAMITI. MISPEL outperformed these methods and is promising for many other neuroimaging modalities.
Search for CP violation using T-odd correlations in D 0 → K + K −π+π− decays (2014)

A search for CP violation using T -odd correlations is performed using the four-body D 0 K + K - + -decay, selected from semileptonic B decays. The data sample corresponds to integrated luminosities of 1.0 fb -1 and 2.0 fb -1 recorded at the centre-of-mass energies of 7 TeV and 8 TeV, respectively. The CP -violating asymmetry a T -odd CP is measured to be (0.18 0.29 (stat) 0.04 (syst))%. Searches for CP violation in different regions of phase space of the four-body decay, and as a function of the D 0 decay time, are also presented. No significant deviation from the CP conservation hypothesis is found.
Complex biologic heterogeneity of de novo hormone naïve metastatic prostate cancer (HNPCa): Comparison of early progressors and prolonged responders to initial systemic treatment. (2019)

5055 Background: Given the absence of biologically based biomarkers current therapy allocation strategies for men with mHNPCa are based on anatomic distribution and volume of metastases. We sought to determine the strength of the association between clinical predictors (including met volume) and outcomes in men with mHNPCa at extremes of response to initial systemic therapy (ST). Methods: Data from a population screened for a phase II trial of Best ST +/- local therapy in mHNPCa was analyzed (NCT01751438). Pts had to have sustained responses to ST (≥6 mos) in order to be randomized. Early Progressors (EP, castration resistant progression &lt;6 mos from start of ST per PCWG2) were not randomized. Prolonged Responders (PR) were defined as those with progression free survivals (PFS) &gt; median for the 109 randomized pts. Baseline demographics were compared between groups (Fisher’s exact test for categorical and Wilcoxon rank-sum test for continuous variables) and Kaplan Meier estimates of OS determined. Immunohistochemistry and genomic sequencing of untreated tumor biopsies are ongoing. Results: Of 208 screened pts, 27 (13%) were identified as EPs, with a median PFS of 5.9 mos (95%CI: 5.3-6.5). The median PFS for the randomized cohort was 16.8 mos (95%CI: 12.7-37.6). 55 (50%) pts were identified as PRs, with median PFS not reached (NR) at a median follow up of 31 mos (range: 7.5-75). Patients’ demographics are below (Table), grouped by EP and PR cohorts. Median OS was 24.8 mos vs NR in the Eps compared to PRs (p&lt;0.001). Conclusions: The EP group was enriched for high risk features and had a worse outcome. However, 33% of men in the EP group had low volume disease and 22% in the PR group had high volume disease. This suggests that clinical volume is an inadequate predictor of biologic response and highlights the need for biologic sub-typing of de novo mHNPCa. [Table: see text]
Air Revitalization System for Japanese Experiment Module (1988)

&lt;div class="htmlview paragraph"&gt;It is necessary to remove carbon dioxide (CO2) and other contaminant gases generated from the crew and nonmetallic materials to keep the allowable level of them for the long duration life support in the space station. Therefore, the Air Revitalization System (ARS) shall be provided in the space station. The ARS for Japanese Experiment Module (JEM) consists of a regenerative CO2 removal system and a trace contaminant control system (TCCS).&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;A solid amine CO2 removal system has been evaluated as the preferable technology.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;An adsorption and catalytic oxidizing method has been selected for the TCCS.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This paper describes the outline of the investigations and study results of the ARS for JEM implemented on the phase B preliminary study (entrusted by NASDA) and subsequent activity.&lt;/div&gt;
Immunomodulatory Function of Interleukin 28B During Primary Infection With Cytomegalovirus (2014)

We postulate that IL-28B may act as a key regulator of ISG expression during primary CMV infection. IL-28B SNPs may be associated with higher antiviral ISG expression, which results in better replication control.
S0645 Efficacy and Safety of Ustekinumab for Crohn's Disease Through 5 Years: Final Results From the IM-UNITI Long-Term Extension (2020)

INTRODUCTION: Ustekinumab (UST) is approved for treatment of moderate-to-severely active Crohn's disease (CD) and ulcerative colitis. Here we report final results of the IM-UNITI long-term extension (LTE) study, with efficacy and safety through 5 years (yrs) of subcutaneous (SC) UST treatment. METHODS: 1281 patients (pts) entered the maintenance study, including 397 IV UST induction responders, randomized to either SC placebo [PBO], n = 133; UST 90 mg q12w, n = 132; or UST 90 mg q8w, n = 132. Additional nonrandomized pts were assigned to receive UST 90 mg q12w (PBO induction non-responder), UST 90 mg q8w (delayed Wk16 responder to UST), or PBO (PBO induction responder). All pts who entered the LTE at Wk44 continued the same treatment regimen they were receiving at Wk44, including 567 UST-treated pts (237 randomized). 151 PBO-treated pts terminated study participation after study unblinding and analysis of the Wk44 data. RESULTS: Among all pts originally randomized in the maintenance study (ITT analysis), 28.7% and 34.4% of pts were in clinical remission 5 yrs later, at Wk252, on 90 mg UST q12w and q8w, respectively. Approximately half (51.1%) of the pts who entered the LTE completed their final dosing visit. Key results after 5 yrs among pts who entered the LTE, including response and remission overall and in anti-TNF therapy history subsets, are summarized in Table 1. Of the pts who were in clinical remission at wk252, 89.5% who received continuous q12w (34/38) and 93.3% who received continuous q8w (42/45) were not receiving steroids. Antibody to UST rates through Wk272 remained low, occurring in 5.8% (31/532) of randomized pts continuously receiving UST in the LTE (excluding randomized PBO dose adjusters). Safety events (per hundred pt-yrs) were not higher among all UST-treated pts entering the LTE compared with PBO from Wk0 through Wk272 (Table 2). No new deaths were reported after Wk156 (6 reported previously). Six pts had malignancies (excluding NMSC) between Wks156 and 272 (q12w: intraocular melanoma, renal cell carcinoma; q8w: endometrial adenocarcinoma, lentigo maligna melanoma, lobular breast cancer in situ, pancreatic carcinoma). CONCLUSION: Pts receiving SC UST generally maintained clinical response and remission through 5 yrs. Nearly half of anti-TNF-naive pts who responded to UST IV induction were in remission after 5 yrs of SC q8w maintenance treatment. No new safety signals were observed.Table 1Table 2
Pressure Reactive Piston Technology Investigation and Development for Spark Ignition Engines (2005)

&lt;div class="htmlview paragraph"&gt;Variable Compression Ratio (VCR) technology has long been recognized as a method of improving Spark Ignition (SI) engine fuel economy. The Pressure Reactive Piston (PRP) assembly features a two-piece piston, with a piston crown and separate piston skirt which enclose a spring set between them. The unique feature is that the upper piston reacts to the cylinder pressure, accommodating rapid engine load changes passively. This mechanism effectively limits the peak pressures at high loads without an additional control device, while allowing the engine to operate at high compression ratio during low load conditions.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Dynamometer engine testing showed that Brake Specific Fuel Consumption (BSFC) improvement of the PRP over the conventional piston ranged from 8 to 18 % up to 70% load. Knock free full load operation was also achieved. The PRP equipped engine combustion is characterized by reverse motion of the piston crown near top dead center and higher thermal efficiency.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The cycle simulation was modified to investigate the effect of the spring set of PRP engine over a wide range of operation. In addition, the spherical flame interaction with the combustion chamber was newly modeled to calculate the flame entrainment rate of unburned charge. It was found that fuel conversion efficiency was gradually increased with spring preload until the spring could not be compressed any more and peak cylinder pressure was effectively maintained at the level of conventional engine at high loads. In addition, BSFC improvement of PRP engine over the conventional engine increased with engine speed. Overall, the full potential of PRP technology was evaluated and discussed favorably.&lt;/div&gt;
Imaging the dynamics of embryonic development (2010)

The explosion of progress in cell biology, biochemistry, and molecular biology has offered unprecedented knowledge of the components involved complex events such as embryonic development. This poses the challenge of integrating this knowledge of the building blocks into an understanding of the functioning system. Advanced imaging techniques offer important stepping‐stones between disparate approaches, permitting us to spy on the assembly process and to pose questions about cellular and molecular events in the most relevant setting of the intact system. Intravital imaging presents major tradeoffs between the rapidity of data collection and the limited photon budget. We are attempting to advance this tradeoff by constructing more efficient microscopes and creating labeling reagents with greater photostability and brightness such as second harmonic generating nanoparticles. These nanoparticles give sufficient signal for clear imaging down to the single molecule level, even in complex optical environments, and avoid the limitations of quantum dots (blinking and bleaching). Such new labels, combined with new imaging tools, are giving unique insights into the processes of embryonic development.
Alternative ESD Concepts: On‐Chip and Off‐Chip ESD Protection Solutions (2006)

This chapter contains sections titled: Spark Gaps Field Emission Devices Off-Chip Protection and Off-Chip Transient Suppression Devices Package-Level Mechanical ESD Solutions RF Proximity Communications Chip-to-Chip ESD Design Practices Summary and Closing Comments Problems References
Down‐Regulation of c‐neu Receptors by Nerve Growth Factor in PC12 Cells (1995)

A small number of p185c-neu receptors have been found on PC12 cells. These receptors show some basal phosphorylation in quiescent cells. When the cells are treated with nerve growth factor (NGF) for a short time, some increase in phosphorylation is seen, mainly on serine and threonine residues, and this is accompanied by a slight shift in the apparent molecular weight. Epidermal growth factor (EGF) also increases the phosphorylation of p185c-neu, in this case on tyrosine residues. Neither heregulin-beta 1 nor gp30 stimulates the tyrosine phosphorylation of p185c-neu, and neither has a proliferative effect on the cells. Treatment of the cells with NGF for 5 days produces a 70-80% reduction in the number of p185c-neu receptors. This down-regulation does not occur when PC12nnr5 cells, which lack the high-affinity NGF receptor, p140trk, are treated with NGF. The level of p185c-neu mRNA is not altered by NGF treatment, suggesting that the down-regulation is due to either a translational or a posttranslational alteration.
Continuous-relief diffractive optical elements for two-dimensional array generation (1993)

Continuous surface-relief diffractive optical elements for two-dimensional array generation (fan-out) are designed and fabricated. Separable and nonseparable solutions for the two-dimensional element design are compared. The phase-grating microstructures are generated by laser-beam writing lithography in a single exposure step and converted to nickel shims by electroplating, enabling low-cost replicas to be produced by using laboratory and commercial replication processes. Results are presented for a 9 x 9 fan-out diffractive optical element with a measured efficiency of 94% and an overall uniformity within +/-8%; replicas in epoxy have the same efficiency and a uniformity of +/-15%.
Molecular imaging of CXCR4 expression in orthotopic and metastatic models of breast cancer with [64Cu]AMD3100 (2010)

281 Objectives Chemokine receptor (CXCR4) plays a critical role in the homing of cancer cells to distant sites by binding to its ligand CXCL12, which is highly expressed in commonly observed metastastic sites. Neoplastic breast tissue and metastases express elevated levels of CXCR4. Previous observations suggest that CXCR4 levels could be used as a predictive marker of metastatic potential. We demonstrate PET/CT imaging of CXCR4 expression in orthotopic xenografts and in an experimental lung metastasis model of breast cancer with [64Cu]AMD3100. Methods MDA-MB-231(CXCR4low) and DU4475(CXCR4high) breast cancer cells were used to generate orthotopic xenografts. Experimental lung metastasis model was generated by tail vein injection of MDA-MB-231 cells. Whole body PET/CT imaging and biodistribution studies with selected tissue harvesting were carried out at 90 min post injection of [64Cu]AMD3100 in both orthotopic and lung metastasis models. Minimum of three animals were used for all the studies. CXCR4 expression of orthotopic tumors and lung metastases-derived cells was analyzed by flow cytometry, immunohistochemistry, and immunoblot analysis. Results Whole body imaging and biodistribution studies demonstrated selective accumulation of activity in DU4475 tumors compared to MDA-MB-231 tumors. The tumor-to-muscle ratios (Tu/Ms) were 26.24 ± 3.50 and 14.41 ± 0.73 for DU4475 and MDA-MB-231 tumors respectively. Accumulation of radioactivity was similarly observed in the lung metastasis model. The Tu/Ms ratios were 22.99 ± 2.50 and 14.32 ± 2.67 for lung metastases and control animals, respectively. Flow cytometry and immunoblot analysis demonstrated elevated CXCR4 expression in tumor and lung metastases-derived cells. Conclusions Our findings demonstrate the feasibility of imaging CXCR4 expression in breast tumor xenografts, and lung metastases. Research Support U24 CA92871, P50CA10317
Combined angiotensin-converting enzyme inhibition and adrenomedullin in an ovine model of heart failure (2002)

Advances in the treatment of heart failure may require manipulation of neurohumoral responses to cardiac impairment in addition to the established strategy of angiotensin-converting enzyme (ACE) inhibition. Importantly, since new treatments are likely to be used in conjunction with ACE inhibition therapy, the effects of the combination of agents need to be assessed. Adrenomedullin (ADM) is a peptide with potent vasodilator and natriuretic actions. ADM and an ACE inhibitor (captopril) were administered for 3h both separately and together in eight sheep with heart failure. Both ADM and captopril alone reduced arterial pressure, left atrial pressure (greater with captopril) and peripheral resistance, and increased cardiac output (greater with ADM). Compared with either treatment separately, combined ADM+captopril produced directionally similar but significantly greater changes in all haemodynamic variables (particularly falls in blood pressure). ADM increased renal sodium and creatinine excretion and creatinine clearance, and maintained urine output. Captopril and ADM+captopril reduced creatinine excretion and creatinine clearance, while urine volume and sodium excretion were not significantly altered. Plasma renin activity rose with all active treatments, whereas angiotensin II levels rose during ADM, but fell during captopril and ADM+captopril. Aldosterone was reduced by all active treatments. ADM+captopril reduced plasma noradrenaline (norepinephrine). In conclusion, short-term co-treatment with ADM and an ACE inhibitor produced significantly greater decreases in ventricular filling pressures and cardiac afterload, and increases in cardiac output, compared with either treatment alone. Despite the greater falls in blood pressure (and presumably renal perfusion pressure), renal function was maintained at a level similar to that observed with captopril alone.
Crystallographic studies in the pyrrole series. Part II. Crystal and molecular structure of 5,5′-diethoxycarbonyl-3,3′,4,4′-tetraethyldipyrrol-2-ylmethane (1972)

Crystals of the title compound (III) are monoclinic, space group P21/c, with cell dimensions a= 8·655(2), b= 17·781(4), c= 15·465(4)Å and β= 102·70(2)°. The structure was solved by direct methods and refined by block-matrix least-squares techniques to R 0·0713 for 2711 observed reflections. The pyrrole rings are distorted from the C2v symmetry of pyrrole, but the distortion is much less marked than that found earlier with 3-acetyl-5-ethoxycarbonyl-4-ethyl-2-methylpyrrole (I). The two carbonyl groups of (III) are arranged in different orientations with respect to the N⋯H vectors, one syn and the other anti. The molecules are arranged in the crystal lattice as hydrogen-bonded, centrosymmetrically related dimers.
Omphalotins E–I, Five Oxidatively Modified Nematicidal Cyclopeptides from Omphalotus olearius (2009)

Abstract Omphalotins E–I, oxidatively modified cyclic dodecapeptides, were isolated from mycelial extracts of the basidiomycete Omphalotus olearius , and their structures were determined by NMR spectroscopic and MS methods. Four of the five omphalotins contained an unprecedented N ‐hydroxylated tricyclic tryptophan derivative. All compounds exhibited strong and selective nematicidal activity against the plant pathogen Meloidogyne incognita with LD 90 values between 2 and 5 μg mL –1 . Cytotoxic activities were not detected up to 50 μg mL –1 . (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2009)
Excess oxygen defects in layered cuprates (1990)

Neutron powder diffraction has been used to study the oxygen defect chemistry of two non-superconducting layered cuprates, La{sub 1. 25}Dy{sub 0.75}Cu{sub 3.75}F{sub 0.5}, having a T{sup {asterisk}}- related structure, and La{sub 1.85}Sr{sub 1.15}Cu{sub 2}O{sub 6.25}, having a structure related to that of the newly discovered double-layer superconductor La{sub 2-x}Sr{sub x}CaCu{sub 2}O{sub 6}. The role played by oxygen defects in determining the superconducting properties of layered cuprates is discussed. 16 refs., 2 figs.
Hydrogel-Tissue Chemistry: Principles and Applications (2018)

Over the past five years, a rapidly developing experimental approach has enabled high-resolution and high-content information retrieval from intact multicellular animal (metazoan) systems. New chemical and physical forms are created in the hydrogel-tissue chemistry process, and the retention and retrieval of crucial phenotypic information regarding constituent cells and molecules (and their joint interrelationships) are thereby enabled. For example, rich data sets defining both single-cell-resolution gene expression and single-cell-resolution activity during behavior can now be collected while still preserving information on three-dimensional positioning and/or brain-wide wiring of those very same neurons-even within vertebrate brains. This new approach and its variants, as applied to neuroscience, are beginning to illuminate the fundamental cellular and chemical representations of sensation, cognition, and action. More generally, reimagining metazoans as metareactants-or positionally defined three-dimensional graphs of constituent chemicals made available for ongoing functionalization, transformation, and readout-is stimulating innovation across biology and medicine.
A 1.8-pJ/bit 16&#x00D7;16-Gb/s source synchronous parallel interface in 32nm SOI CMOS with receiver redundancy for link recalibration (2015)

A 16×16-Gb/s source-synchronous I/O is reported in 32nm SOI CMOS. The bus-level receiver includes redundant RX lanes to enable lane recalibration with reduced power and area overhead. The I/O also includes an 8:1 TX serializer with 8-phase clocking, and an active-inductor-based RX CTLE whose outputs form current mirrors with the inputs of the RX samplers. A phase rotator based on current-integrating phase interpolator cores is described, with architecture and circuit improvements to performance as compared to prior art. 16-Gb/s link measurements over Megtron-6 traces demonstrate efficiencies of 1.8pJ/bit (0.75" traces) and 1.9pJ/bit (10" traces) with >30% timing margin, with the TX, RX, and PLL operating from 1V supplies.