gebhart/patrepeval huggingface dataset:
Light-Driven Four-Component Reaction with Boronic Acid Derivatives as Alkylating Agents: An Amine/Imine-Mediated Activation Approach (2023)

Herein, we describe a one-pot aminoalkylation of styrene derivatives with boronic acids (BAs) and boronic acid pinacol esters as radical precursors for the synthesis of complex secondary amines in moderate to high yields through a mild and easily accessible organophotoredox-catalytic four-component reaction. Additionally, we report for the first time in a photoredox process the activation of alkyl boronic acid derivatives by imines, which play a dual role in the reaction as both substrate and Lewis base activator. The protocol applicability was greatly enhanced by its successful adaptation to photoflow reactors.
Identification and localization of renal Na(+)-Ca2+ exchanger by polymerase chain reaction (1992)

The molecular identity of the renal Na(+)-Ca2+ exchanger was determined by a homology-based polymerase chain reaction (PCR) cloning strategy. Rat kidney RNA was amplified by PCR, using oligonucleotide primers based on regions of low degeneracy in the published canine cardiac Na(+)-Ca2+ exchanger cDNA sequence, and the products were subcloned and sequenced. A 452-bp clone (NCX1) was identified, which shares 89% nucleotide and 98% amino acid sequence identity with the canine cardiac exchanger, suggesting that they are products of the same gene. NCX1 was shown, by Northern analysis, to hybridize to an abundant major transcript of 7 kb and a minor one of approximately 14 kb both localized predominantly to kidney cortex. Microdissected tubule PCR analysis revealed that NCX1 was enriched in distal convoluted tubule compared with other cortical nephron segments. Such a location is consistent with a Na(+)-Ca2+ exchanger corresponding to NCX1 playing a major role in active Ca2+ reabsorption at this site.
Short communication. Sequence of msp1alpha gene of Anaplasma marginale Havana isolate and expression in eukaryotic cells (2005)

Bovine anaplasmosis is a disease of worldwide economic importance caused by the rickettsia Anaplasma marginale. Several major surface proteins with conserved gene sequences have been examined as potential candidates for vaccines. One of these proteins, MSP1a, is expressed from the single copy msp1alpha gene. The molecular weight of MSP1a varies among the geographic isolates of A. marginale because of a varying number of tandem repeated peptides of 28-29 amino acids. In the present study, the sequence of the msp1alpha gene of Anaplasma marginale Havana isolate was determined, with a size of 2,043 kb, demonstrating the presence of five tandem repeated regions. This gene was cloned into the eukaryotic expression vector pCIneo, transfected in COS-7 cells and expression verified by immunofluorescence. These data provide a basis for an immunization strategy using the msp1alpha gene in DNA immunization containing single or multiple genes encoding major surface proteins of A. marginale.
Photonic Integration With Epitaxial III–V on Silicon (2018)

We present a brief overview of the various leading platforms for photonic integration. Subsequently, we consider the possibility of a photonic integrated circuit platform utilizing epitaxially grown III-V material on silicon-without the need for wafer bonding, or an externally coupled laser. Finally, a techno-economic analysis contrasting the aforementioned platforms will be presented.
Novel TNF receptor-1 inhibitors identified as potential therapeutic candidates for traumatic brain injury (2018)

Using sleep as a bio-indicator of TNF-R-dependent neuroinflammation, we identified C7 and SGT11 as potential therapeutic candidates for TBI.
Experimental demonstration of increased organic light emitting device output via volumetric light scattering (2004)

A set of experimental measurements of scattering films and organic light emitting devices (OLEDs) is presented. We measure the reflectance, transmission, and emission characteristics of scattering media and OLED devices separately, and use this data as input into a simple radiative transfer model to predict the effect of light scattering on OLED light output. We find quantitative agreement between the radiative transfer model predictions and experimental results. We find that the introduction of volumetric scattering mechanisms increases the output of OLEDs by as much as 40%, which corresponds to over 70% of the light within a typical glass substrate being coupled to air.
O5‐04‐01: A RARE GENETIC VARIANT IN THE PLCG2 GENE IS ASSOCIATED WITH A REDUCED RISK OF ALL MAJOR TYPES OF DEMENTIA AND AN INCREASED RISK TO REACH AN EXTREMELY OLD AGE (2018)

The genetic variant rs72824905-G(p.Pro522Arg) in the PLCG2 gene(Phospholipase C Gamma 2) was previously found to associate with a reduced risk of Alzheimer's disease (AD). We hypothesized that the variant might reduce the risk of other neurodegenerative diseases as PLCG2 plays an important role in innate immune system signaling, and is expressed in microglial cells in brain. Therefore, we tested if the variant associated with a reduced risk of Fronto-temporal Dementia(FTD), Lewy-body dementia (LBD), Progressive Supranuclear Palsy(PSP), Parkinson's Disease(PD) and Amyotrophic Lateral Sclerosis(ALS). Additionally, we investigated if carriers had an increased risk to reach extreme ages in good cognitive health. We determined rs72824905-G genotypes in 2,129 AD, 2,273 FTD patients, 1,075 LBD patients, 625 PSP patients all from European descent(consortia in author list). We genotyped 464 nonagenarians and 268 self-reported cognitively healthy centenarians. Patients and aged cases were compared with population-matched controls(N-max=10,891). Cohorts were analyzed using the score test and if necessary cohorts were meta-analyzed in R with the ‘SeqMeta’ package. One-sided p-values are reported. Association results were extracted from existing meta-analyses of 6,248 PD patients(6,031 controls) and 10,953 ALS patients(20,673 controls). We replicated the protective effect of rs72824905-G on AD(OR=0.49; 95%CI 0.33-0.73, P=2.5×10−4), and we found a similar protective effect on FTD, LBD and PSP(aggregate OR=0.65; 95%CI 0.49-0.86, P=1.4×10−3). The effect was comparable for FTD(OR=0.66, 95%CI 0.48-0.90, P=4.8×10−3), LBD(OR=0.64, 95%CI 0.35-1.19, P=0.08) and PSP(OR=0.71, 95%CI 0.29-1.74, P=0.26). There was no significant effect in the large meta-analysis of PD(OR=0.79, 95%CI 0.56-1.12, P=0.10) or ALS(OR=1.07, 95%CI 0.87-1.33, P=0.26). Lastly, we considered the effect on extreme aging. Carriers of rs72824905-G had 1.65-fold(95%CI 0.91-2.99, P=4.8×10−2) increased chance to become a nonagenarian and 3.2-fold(95%CI 1.49-6.95, P=1.4×10−3) increased chance to become a cognitively healthy centenarian. The amino acid substitution Pro522Arg in PLCG2 reduces the risk of AD and non-AD dementias, as well as increase the risk to reach extreme ages. No evidence of association with PD and ALS was found, despite large sample sizes. We speculate that an improved immune response as consequence of this variant in the PLCG2 gene makes the brain resilient to neurodegenerative processes leading to dementia.
High-contrast grating mirror embedded in acoustic shield for optomechanics (2021)

By enabling high reflectivity from a single layer of dielectric, high-contrast gratings (HCGs) provide an exciting platform for optomechanics. In the interest of enhancing the mechanical quality factor of such devices, we have combined photonic and phononic engineering to fabricate HCG mirrors within a structure containing phononic bandgaps. In this way, we realize optomechanical devices that simultaneously exhibit high reflectivity, ultralow mass, and ultrahigh mechanical quality factors. Our initial devices are designed to trade off optimal acoustic and optical performance. We have incorporated these devices into optical cavities, which we probe in order to determine their optical and mechanical properties.
The Effectiveness of Continuing the Induction Dose of Asacol into the Maintenance Phase (2005)

Purpose: The FDA indicated dosages of Asacol® (mesalamine) delayed-release tablets are 2.4 g/day for the treatment of mild-moderately active ulcerative colitis (UC) and 1.6 g/day for maintenance of remission. There is anecdotal evidence that maintaining the induction dose may be better than dose-reduction to prevent relapse. This study used a naturalistic, retrospective design to compare the outcomes of UC patients maintained on the dose used to induce remission with those whose maintenance dose was reduced. Methods: The medical records from 411 UC patients from 39 geographically dispersed, community gastroenterology practices who had a disease flare between 1999 and 2003 successfully treated with Asacol without requiring steroids were reviewed. The review included the single flare of interest and the subsequent maintenance period. Outcome measures examined were maintenance of remission at 6 and 12 months post-induction, and% rated “normal” on the physician global assessment of symptom severity (PGA) at final data capture. The primary explanatory variable was the relation between maintenance (M) and induction (I) dose, coded as M = I vs. M < I. Other covariates examined were: Final induction dose: grouped on g/day, ≤2.4, 3.2–4.0, ≥4.8 Extent of disease: proctitis+proctosigmoiditis vs. left-sided vs. extensive Severity of disease: mild vs. moderate+severe Prior history: 1st flare vs. subsequent flare without immediately prior maintenance medication vs. subsequent flare while on maintenance medication. Results: In logistic regression analyses, no variables were significantly (p < .05) predictive of maintenance of remission at 6 or 12 months. When the initial PGA was forced into the logistic regression model first, to control for severity of attacks and to assess the impact of the other variables, the only significant predictor of final PGA was M = I vs. M < I (p < .01, OR = 2.21, 95% CI = 1.36–3.58). Results are shown in the table below.Table: No Caption available.Conclusions: Maintaining the same dose of Asacol used to induce remission significantly increased the likelihood of UC patients receiving a physician's global assessment of “normal” at one year post-induction. This finding was consistent across dosage levels and extent of disease.
<title>Real-time system diagnosis with sensors of uncertain quality</title> (2003)

This paper presents a real time approach to the detection and isolation of component failures in largescale systems. The algorithm is given a set of observed test results from multiple sensors, and its main task is to deal with sensor errors (i.e., noise). The probabilities of these missed detections and false alarms are not known a-priori, and must be estimated - ideally along with the accuracies of these estimates - online, within the inference engine. Further, recognizing a practical concern in most real systems, a sparsely instantiated observation vector must not be a problem. The key ingredients to the approach include the Multiple Hypothesis Tracking (MHT) philosophy to complexity management, and a Beta prior distribution on the sensor errors. We provide results illustrating performance in terms of both computational needs and error rate, and show its application both as a filter (i.e., used to "clean" sensor reports) and as a standalone state estimator.
Maximum likelihood estimation in linear models with a Gaussian model matrix (2006)

We consider the problem of estimating an unknown deterministic parameter vector in a linear model with a Gaussian model matrix. We derive the maximum likelihood (ML) estimator for this problem and show that it can be found using a simple line-search over a unimodal function that can be efficiently evaluated. We then discuss the similarity between the ML, the total least squares (TLS), the regularized TLS, and the expected least squares estimators.
Fabrication‐conscious neural network based inverse design of single‐material variable‐index multilayer films (2023)

Multilayer films with continuously varying indices for each layer have attracted great deal of attention due to their superior optical, mechanical, and thermal properties. However, difficulties in fabrication have limited their application and study in scientific literature compared to multilayer films with fixed index layers. In this work we propose a neural network based inverse design technique enabled by a differentiable analytical solver for realistic design and fabrication of single material variable-index multilayer films. This approach generates multilayer films with excellent performance under ideal conditions. We furthermore address the issue of how to translate these ideal designs into practical useful devices which will naturally suffer from growth imperfections. By integrating simulated systematic and random errors just as a deposition tool would into the optimization process, we demonstrated that the same neural network that produced the ideal device can be retrained to produce designs compensating for systematic deposition errors. Furthermore, the proposed approach corrects for systematic errors even in the presence of random fabrication imperfections. The results outlined in this paper provide a practical and experimentally viable approach for the design of single material multilayer film stacks for an extremely wide variety of practical applications with high performance.
Simultaneous In-Process Roughness Control and Tool Wear Monitoring via a Distributed Open Architecture Controller (1998)

Abstract This paper presents in-process roughness control and tool wear monitoring during a machining process. An in-process surface roughness monitoring system which uses ultrasonic sensing techniques was adopted in this research to provide roughness feedback. A roughness model which describes the relationship between surface finish, cutting parameters, and tool flank wear was developed and used as the basis of roughness control and tool wear monitoring. The roughness control and tool wear monitoring scheme was implemented using a distributed open architecture controller which provides an open environment for integration and development. The experimental results show that the tool flank wear can be monitored accurately by surface roughness and the control scheme can effectively compensate for the effect of tool wear and other disturbances to produce a constant surface finish throughout the life of the cutting tool.
Genome-wide interaction analysis identified low-frequency variants with sex disparity in lung cancer risk (2022)

Differences by sex in lung cancer incidence and mortality have been reported which cannot be fully explained by sex differences in smoking behavior, implying existence of genetic and molecular basis for sex disparity in lung cancer development. However, the information about sex dimorphism in lung cancer risk is quite limited despite the great success in lung cancer association studies. By adopting a stringent two-stage analysis strategy, we performed a genome-wide gene-sex interaction analysis using genotypes from a lung cancer cohort including ~ 47 000 individuals with European ancestry. Three low-frequency variants (minor allele frequency < 0.05), rs17662871 [odds ratio (OR) = 0.71, P = 4.29×10-8); rs79942605 (OR = 2.17, P = 2.81×10-8) and rs208908 (OR = 0.70, P = 4.54×10-8) were identified with different risk effect of lung cancer between men and women. Further expression quantitative trait loci and functional annotation analysis suggested rs208908 affects lung cancer risk through differential regulation of Coxsackie virus and adenovirus receptor gene expression in lung tissues between men and women. Our study is one of the first studies to provide novel insights about the genetic and molecular basis for sex disparity in lung cancer development.
Nutritional Solutions to Reduce Risks of Negative Health Impacts of Air Pollution (2015)

Air pollution worldwide has been associated with cardiovascular and respiratory morbidity and mortality, particularly in urban settings with elevated concentrations of primary pollutants. Air pollution is a very complex mixture of primary and secondary gases and particles, and its potential to cause harm can depend on multiple factors-including physical and chemical characteristics of pollutants, which varies with fine-scale location (e.g., by proximity to local emission sources)-as well as local meteorology, topography, and population susceptibility. It has been hypothesized that the intake of anti-oxidant and anti-inflammatory nutrients may ameliorate various respiratory and cardiovascular effects of air pollution through reductions in oxidative stress and inflammation. To date, several studies have suggested that some harmful effects of air pollution may be modified by intake of essential micronutrients (such as B vitamins, and vitamins C, D, and E) and long-chain polyunsaturated fatty acids. Here, we review the existing literature related to the potential for nutrition to modify the health impacts of air pollution, and offer a framework for examining these interactions.
Subpial Thorn-shaped Astrocytes Are Prevalent In Guam ALS/PDC (2021)

Guam amyotrophic lateral sclerosis/parkinsonism-dementia complex is a progressive neurodegenerative disorder characterized by neuronal and glial tau pathologies. With the aim to evaluate aging-related tau astrogliopathy (ARTAG) we examined the collection at the University of Pennsylvania, consisting of blocks of the frontal parietal, temporal, and occipital cortices. Formalin fixed, paraffin-embedded tissue blocks were evaluated using anti-tau antibodies PHF-1 and AT8. In addition to neuronal and oligodendroglial tau pathology, granular/fuzzy astrocytes in the gray matter and thorn-shaped astrocytes (TSAs) in subpial location were also observed. Twenty-one out of 33 cases (63%) showed subpial TSAs diffusely along the cortical surface in one or more cortical regions. Accumulation of TSAs in the depth of the sulci were seen in 41% in the temporal, 7% in the frontal and 14% in parietal cortex. This was not associated with perivascular neuronal tau pathology in the depth of the sulci. Accumulation of TSAs in the depth of cortical sulci in this cohort is approximately 20 times more frequent than reported in a European aging cohort. The presence of subpial TSAs in the depth of cortical sulci in CTE and Guam PDC, and less frequently in aging brains, might suggest common mechanisms. Learning Objectives Describe the spectrum of neuropathology in Guam ALS/PDC Describe the frequency of tau positive cortical subpial thorn-shaped astrocytes
Data from A Phase I Study of Oral ARRY-614, a p38 MAPK/Tie2 Dual Inhibitor, in Patients with Low or Intermediate-1 Risk Myelodysplastic Syndromes (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Data suggest that activity of p38 MAPK and Tie2 kinases is dysregulated in myelodysplastic syndromes (MDS) and may be targets for novel therapies. A phase I study of ARRY-614, an oral dual inhibitor of p38 MAPK and Tie2, was conducted in patients with low or intermediate-1 International Prognostic Scoring System risk MDS to evaluate safety, pharmacokinetics (PK), pharmacodynamics (PD), and preliminary responses by International Working Group 2006 criteria.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Forty-five patients received ARRY-614 either once daily or twice daily in dose escalation (400, 600, 900, or 1,200 mg once daily; 200 or 300 mg twice daily) or expansion cohorts.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The 300 mg twice daily schedule was not tolerated, and an MTD was not reached for once daily dosing. Treatment-related adverse events were primarily grade 1–2, with the most common being rash, diarrhea, dry skin, fatigue and anorexia. Interpatient PK variability was high, although exposure was sufficient to achieve reduction in p38 MAPK activation in bone marrow and in the levels of circulating biomarkers. Disease responses were observed in 14 of 44 (32%) evaluable patients, 13 (93%) of whom had previously been treated with a hypomethylating agent. Responses were observed in all lineages, with 5 patients experiencing bilineage responses. Three of 25 red blood cell transfusion-dependent (TD) patients achieved transfusion independence (TI) and 5 of 7 platelet TD patients achieved TI.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; ARRY-614 was well tolerated and has sufficient activity to warrant further evaluation in this patient population. We recommend 1,200 mg once daily as the optimal dose for further study. &lt;i&gt;Clin Cancer Res; 21(5); 985–94. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Clinical and Radiological Follow-up of Intraneural Perineuriomas (2018)

We found that intraneural perineuriomas only rarely grow in length, do not grow to involve new nerves or nerve divisions, and growth does not correlate with clinical progression. These findings have significant ramifications for management of these tumors.
Retinoic acid induces persistent, RAR?-mediated anti-proliferative responses in Epstein-Barr virus-immortalized b lymphoblasts carrying an activated c-myc oncogene but not in Burkitt's lymphoma cell lines (2000)

We have previously demonstrated that 13-cis-retinoic acid (RA), 9-cis-RA and all-trans-RA (ATRA) powerfully inhibit the proliferation of Epstein-Barr virus-immortalized B-lymphoblastoid cell lines (LCLs). The aim of the present study was to assess whether these compounds are effective at inhibiting the growth of B cells at more advanced stages of lymphomagenesis, including fully transformed B lymphocytes. To this end, c-myc-transfected LCLs (myc-LCLs) and Burkitt's lymphoma (BL) cell lines were used. We report that 13-cis-RA, 9-cis-RA and ATRA also markedly inhibit the proliferation of myc-LCLs by inducing G(0)/G(1) growth arrest as well as enhancing rates of apoptosis. Conversely, all but 1 (DG75) of the 8 BL cell lines investigated were poorly RA-responsive. Moreover, unlike LCLs and myc-LCLs, RA-treated DG75 cells rapidly resumed proliferation upon drug removal. Analysis of cell cycle-regulatory proteins showed that, as in LCLs, strong up-regulation of p27(Kip-1) and increased levels of under-phosphorylated pRb and p130 were detected in RA-treated DG75 cells. While the catalytic activity of all 3 G(1)-associated CDKs (CDK2, CDK4 and CDK6) was strongly inhibited in RA-treated LCLs, only CDK2-associated kinase activity was reduced in DG75 cells arrested in G(0)/G(1) by RA. Moreover, RA-treated DG75 cells failed to show the down-regulation of cyclin D3 observed in LCLs. Use of receptor-selective agonists and antagonists showed that in LCLs and RA-responsive BL cells, RA-induced growth arrest is mainly mediated by RARalpha. The RARalpha-selective agonist Ro 40-6055 was also effective at very low concentrations (10(-10) M). Nevertheless, comparable levels of RARalpha mRNA were found in RA-responsive and -resistant BL cell lines, indicating that mechanisms different from transcriptional deregulation of RARalpha probably underlie the differential responsiveness of BL cells.
Scalable Kernel-Based Minimum Mean Square Error Estimator for Accelerated Image Error Concealment (2016)

Error concealment (EC) is of great importance for block-based video systems, such as digital video broadcasting or video streaming services. In this paper, we propose a novel scalable spatial EC algorithm that aims at obtaining high quality reconstructions with reduced computational burden. The proposed technique exploits the excellent reconstructing abilities of the kernel-based minimum mean square error (K-MMSE) estimator. We propose to decompose this approach into a set of hierarchically stacked layers. The first layer performs the basic reconstruction that the subsequent layers can eventually refine. In addition, we design a layer management mechanism, based on profiles, that dynamically adapts the use of higher layers to the visual complexity of the area being reconstructed. The proposed technique outperforms other state-of-the-art algorithms and produces high quality reconstructions, equivalent to K-MMSE, while requiring around one tenth of its computational time.