gebhart/patrepeval huggingface dataset:
Abstract 13067: Depression and 5-Year Stroke Risk in Patients With Atrial Fibrillation (2016)

Introduction: Stroke is a leading cause of death and permanent disability in patients with Atrial Fibrillation (AF). Depression is highly prevalent and previous studies have suggested that it is associated with a significantly increased risk of stroke morbidity and mortality in the general population. Here, we report the impact of depressive mood on the risk of stroke among patients with AF. Hypothesis: Depression increases the risk of stroke among patients with AF. Methods: We enrolled 5976 patients diagnosed with AF at the hospitals and clinics of the University of Pittsburgh Medical Center from January 2006 to November 2013. Depression status was determined by chart review of physicians’ diagnoses. Stroke incidence in each group is summarized with Kaplan-Meier curves; Cox proportional-hazards models were used to assess the relationship between depression and stroke risk when accounting for potential confounders. Results: Of the 5976 patients, 681 (11.4%) had diagnosis of depression. Patients were followed for a median of 39 months (range 1-60), during which there were 200 total strokes (35 in patients with depression). Risk of stroke was higher in patients with diagnosed depression (7.5% vs 4.7%, HR=1.70, 95% CI: 1.18-2.45, p=0.004, Figure). Even after controlling for several known stroke risk factors (age, sex, alcohol and tobacco use, congestive heart failure, previous stroke, diabetes, hypertension, vascular diseases, COPD and anticoagulant use), depressed patients had higher incidence of stroke (HR=1.45, 95% CI 0.99-2.11, p=0.054). Conclusion: Diagnosis of depression is associated with increased risk of ischemic stroke in patients with Atrial Fibrillation. Clinical trials remain necessary to establish whether screening AF patients for depression and then providing effective anti-depressive treatment can reduce the incidence of stroke and improve clinical outcomes.
Guided self-assembly of Si-containing block copolymer with a topcoat surface treatment (2014)

Directed self-assembly (DSA) of block copolymers (BCPs) is one of candidate for next generation patterning technique. Many good demonstrations of DSA have been reported using polystyrene-block-poly(methyl methacrylate) (PS-b- PMMA) these days. On the other hands, BCPs which show high chi parameter are being developed because the BCPs can be formed smaller features than PS-b-PMMA. Si-containing BCPs are one of them. Moreover Si-containing BCPs show higher etch selectivity than PS-b-PMMA because of higher etch resistance of Si-containing block. Unfortunately, while Si-containing BCPs can be aligned by solvent annealing, they but cannot be aligned perpendicular to the substrate by thermal annealing. Because Si-containing block which has low surface energy achieves maximum interaction with air interface by forming a top parallel wetting layer to the substrate. One solution to control of surface energy on top surface is the use of Top-Coat (TC). It has been already demonstrated that TC with Si-containing BCP could form perpendicular pattern. The challenges are TC coating onto BCP film and TC stripping after annealing. In order to solve these problems, polarity-changeable type TC has been developed. The effect of TC materials to generate finger print of BCP has been reported. However, this TC process should combine with DSA process to form aligned patterns. Graphoepitaxy is one of the DSA technique to align BCP pattern using guide pattern. In this technique, the characteristic of guide pattern side wall is very important to control BCP pattern alignment for the Graphoepitaxy process. Also, in order to establish the process, there are two key parameters for the materials. One is BCP and guide pattern should have enough resistance to TC solvent through TC coating process. The other is TC can be removed easily with basic aqueous solution before BCP patterning. In this report, a detail of examination for TC Graphoepitaxy process will be discussed.
O1‐08‐01: THE NIH‐EXAMINER IS SENSITIVE TO COGNITIVE CHANGES IN ASYMPTOMATIC AND MILDLY SYMPTOMATIC FAMILIAL FRONTOTEMPORAL DEMENTIA (2018)

At least 20% of cases of frontotemporal dementia (FTD) are caused by dominantly inherited mutations. As pharmaceutical agents are developed to treat familial FTD, mutation carriers in the presymptomatic and mildly symptomatic stages offer a unique opportunity for dementia prevention. There is a need for validated clinical endpoints that are sensitive to change in these early stages. The NIH-EXAMINER is a battery of executive function tests that is sensitive to early changes in sporadic FTD. We investigated whether the NIH-EXAMINER battery could detect longitudinal changes in cognition in mutation carriers before conversion to dementia. 52 mutation carriers (C9orf72, MAPT and GRN) with at least two acquisitions of EXAMINER data and a global Clinical Dementia Rating Scale (CDR) score < 1 (mean age=50.15; SD=12.82), were compared to 36 non-mutation carrier family members (mean age=49.37; SD=13.7). The NIH-EXAMINER yields an executive function (EF) composite, which includes measures of cognitive control, working memory and verbal fluency. We fitted linear mixed effects models (LME) with the EF composite score as the outcome variable and a random intercept for subject. We evaluated baseline differences and differential rates of decline between carriers and noncarriers by specifying a group*time interaction, covarying for age, education and gender. We fit a LME model to assess whether longitudinal changes in the EF composite were associated with changes in clinical symptomology (CDR Sum of Boxes, CDR-SB). We compared these results to Trail Making Test Part B (Trails B), a paper-and-pencil executive measure. Unstandardized regression coefficients (b) are reported below Carriers performed worse than noncarriers at baseline (b=-.32, p=.015), and there was a significant group*time interaction (b=-.14, p=.044), indicating that carriers had a more negative slope over time. Decreasing longitudinal EF performance was associated with increased clinical symptomology (CDR-SB,b=-.24, p<.001). The interaction coefficient was in the same direction but reduced by 30% when we restricted the analysis to carriers with CDR = 0 (b=-.09, p=.208). In contrast, carriers and noncarriers did not differ at baseline (b=31.33, p=.194) or in their rate of change on Trails B (b=13.51, p=.616). In familial FTD mutation carriers, the NIH-EXAMINER is sensitive to cognitive changes that precede conversion to dementia.
Moving Obstacle Avoidance based on Speed Control without Changing Trajectory of Autonomous Mobile Robot (2003)

走行軌道を変更せずに, 加減速により自律移動ロボットが移動障害物を回避する方法を提案する。本手法では, 回避前と回避後の自律移動ロボットの速度を等速にし, 最小限の加減速で移動障害物を回避する。
Nanotechnologies in Food Packaging (2010)

The main function of food packaging is to protect and preserve the food, to maintain its quality and safety, and to reduce food waste. Other desirable attributes have come to the fore recently including packaging that is sustainable with a low environmental footprint, is “active” and/or is “intelligent.” As materials and applications of nanotechnologies can help meet these requirements, they are rapidly becoming a commercial reality in the area of food packaging. Example applications include the enhancement of mechanical properties to allow development of further light-weight materials, and using nanocomposites or nanocoatings to improve barrier properties. An especially interesting area of application is using nanotechnology products to increase the performance of some biobased and biodegradable materials so that they can be used for a wider range of food applications and not only dry foods. There are also a number of products under development for active packaging – which can release or absorb chemicals – or as intelligent (smart) packaging materials that incorporate nano-sensors. Consequently, nanotechnology products and applications could revolutionise some areas of the food packaging sector, providing innovative, sustainable, strong, lightweight and active and intelligent materials. Market uptake will however be impeded by any uncertainties on consumer and environmental safety. Based on theoretical considerations, and the results of limited testing that has been carried out so far, the expectation is that due to the fixed or embedded nature of nanomaterials in plastics, they are not likely to pose a significant risk to the consumer. However, further research addressing the safety issues of nanotechnologies is needed.
ExSPAnder: a universal repeat resolver for DNA fragment assembly (2014)

http://bioinf.spbau.ru/en/spades
Alumina-Supported Vanadium Nanoparticles:  Structural Characterization and CO Adsorption Properties (2004)

Alumina-supported vanadium particles were prepared under ultrahigh vacuum (UHV) conditions and characterized with respect to their structural and CO adsorption properties. As supporting oxide, we used a thin, well-ordered alumina film grown on NiAl(110). This allows the application of scanning tunneling microscopy (STM), infrared reflection-absorption spectroscopy (IRAS), and X-ray photoelectron spectroscopy (XPS) without charging effects. Vanadium evaporation under UHV conditions leads to the growth of nanometer-sized particles which strongly interact with the alumina support. At very low vanadium coverages, these particles are partially incorporated into the alumina film and get oxidized through the contact to alumina. Low-temperature CO adsorption in this coverage regime permits the preparation of isolated vanadium carbonyls, of which we have identified mono-, di-, and tricarbonyls of the V(CO)(y)() type. A charge-frequency relationship was set up which allows one to quantify the extent of charge transfer from vanadium to alumina. It turns out that this charge transfer depends on the V nucleation site.
HNRNPM controls circRNA biogenesis and splicing fidelity to sustain prostate cancer cell fitness (2020)

ABSTRACT Cancer cells are differentially dependent on the splicing machinery compared to normal untransformed cells. The splicing machinery thus represents a potential therapeutic target in cancer. To identify splicing factors important for prostate cancer cell (PCa) cell growth, we performed a parallel pooled shRNA screen on in vitro passaged cells and in vivo xenografted PCa tumor lines. Our screen revealed HNRNPM as a potential regulator of PCa cell growth. RNA- and eCLIP-sequencing data suggest that HNRNPM is bound to transcripts of key homeostatic genes and that loss of HNRNPM binding in a subset of these genes results in aberrant exon inclusion and exon back-splicing events in target transcripts. In both linear and circular mis-spliced transcripts, HNRNPM appears to preferentially bind to GU-rich elements in long flanking proximal introns. Mimicry of HNRNPM dependent linear splicing events using splice-switching antisense oligonucleotides (SSOs) was sufficient to inhibit cell growth in HNRNPM expressing cells. This suggests that prostate cancer cell dependence on HNRNPM is likely a result of mis-splicing of key homeostatic coding and non-coding genes. Taken together, our data reveal a role for HNRNPM in supporting prostate cancer cell fitness, and also as a potential therapeutic target in PCa.
Fluids beat granular in soil trials (2004)

Data indicate that fluid&#13;\nfertilizers are superior to granular for&#13;\ndelivery of phosphorus (P) for crop&#13;\nnutrition in calcareous soils. Field&#13;\nand glasshouse experiments have&#13;\ndemonstrated in southern Australian&#13;\nsoils the benefits of fluid formulations&#13;\nfor crop nutrition. Experiments were&#13;\nperformed using similar fertilizer&#13;\nproducts delivered either in fluid or&#13;\ngranular form to calcareous soils.&#13;\nIsotopic and spectroscopic techniques&#13;\nwere used to characterize reactions.&#13;\nGranular fertilizers were found to be&#13;\ninferior to fluids (even with the same&#13;\nformulations) due to the precipitation&#13;\nof insoluble Ca/Al phosphates similar&#13;\nto crandallite in the fertilization zone&#13;\n(i.e., in and around the granule). As&#13;\ndetermined by isotopic dilution&#13;\nstudies, P diffusion from the&#13;\nincorporation zone was inhibited with&#13;\ngranular applications and the ability&#13;\nof P in the fertilized zone was also&#13;\nreduced when P was applied in&#13;\ngranular form. Fixation of applied P is&#13;\nminimized when fertilizers are supplied&#13;\nin fluid form. Some formulations may&#13;\nhave the added advantage of&#13;\nliberating fixed P in the soil-to-plant&#13;\navailable forms.
Data from Therapy of Established Tumors with Rationally Designed Multiple Agents Targeting Diverse Immune–Tumor Interactions: Engage, Expand, Enable (2023)

&lt;div&gt;Abstract&lt;p&gt;Immunotherapy of immunologically cold solid tumors may require multiple agents to engage immune effector cells, expand effector populations and activities, and enable immune responses in the tumor microenvironment (TME). To target these distinct phenomena, we strategically chose five clinical-stage immuno-oncology agents, namely, (i) a tumor antigen–targeting adenovirus-based vaccine (Ad-CEA) and an IL15 superagonist (N-803) to activate tumor-specific T cells, (ii) OX40 and GITR agonists to expand and enhance the activated effector populations, and (iii) an IDO inhibitor (IDOi) to enable effector-cell activity in the TME. Flow cytometry, T-cell receptor (TCR) sequencing, and RNA-sequencing (RNA-seq) analyses showed that in the CEA-transgenic murine colon carcinoma (MC38-CEA) tumor model, Ad-CEA + N-803 combination therapy resulted in immune-mediated antitumor effects and promoted the expression of costimulatory molecules on immune subsets, OX40 and GITR, and the inhibitory molecule IDO. Treatment with Ad-CEA + N-803 + OX40 + GITR + IDOi, termed the pentatherapy regimen, resulted in the greatest inhibition of tumor growth and protection from tumor rechallenge without toxicity. Monotherapy with any of the agents had little to no antitumor activity, whereas combining two, three, or four agents had minimal antitumor effects. Immune analyses demonstrated that the pentatherapy combination induced CD4&lt;sup&gt;+&lt;/sup&gt; and CD8&lt;sup&gt;+&lt;/sup&gt; T-cell activity in the periphery and tumor, and antitumor activity associated with decreased regulatory T-cell (Treg) immunosuppression in the TME. The pentatherapy combination also inhibited tumor growth and metastatic formation in 4T1 and LL2-CEA murine tumor models. This study provides the rationale for the combination of multimodal immunotherapy agents to engage, enhance, and enable adaptive antitumor immunity.&lt;/p&gt;&lt;/div&gt;
Towards xBGAS on CHERI: Supporting a Secure Global Memory (2023)

Modern computing systems embrace heterogeneous system architectures to meet high-performance computing requirements. As a result, the Extended Base Global Address Space (xBGAS) project introduced an extension to the RISCV instruction set architecture (ISA) to provide extended addressing capabilities. Although the xBGAS project is currently implemented on the RISC-V ISA, the project’s central vision is to include a broad domain of ideas that is not dependent on any single microarchitecture. Therefore, demonstrating the existing xBGAS benchmarks on the ARM ISA would enable working on a real system prototype. The ARM Morello platform is intended as an industrial demonstrator of a capability architecture using Capability Hardware Enhanced RISC Instructions (CHERI). Consequently, understanding the CHERI semantics and identifying the desired features for xBGAS are crucial for making xBGAS portable across platforms. In this work, we investigate creating a software-based xBGAS solution for the Morello platform by porting the xBGAS runtime onto the ARM ISA. First, we revisit the basics of the xBGAS project and the CHERI project to learn what the security benefits of CHERI on xBGAS are by taking advantage of CHERI capabilities. Then, we explore the implementation of the CHERI capabilities and Morello simulators to discuss an adaptation of the scalable xBGAS runtime library to support other ISAs such as ARM.
MONITORING GRINDING EFFECTIVENESS (2005)

This article discusses the use of a Grinding Quality Index (GQI) for assessing the effectiveness of rail grinding. The GQI is essentially an indicator of the degree of difference between the actual rail profile and the desired rail profile. These profiles are a function of grinding approach and the location. By comparing these pre- and post-grind figures, the effectiveness of the rail grinding treatment can be determined. High-accuracy, laser-based measurement systems are used to determine rail profiles. These tools examine the “after” rail head profiles that are ground into the rail head and compare them with the desired profile. The article details how the GQI can also be used for grinding planning and prioritization. Recent experience using the GQI is also discussed
Pocket Laser Rangefinder (2001)

Abstract : Presentation given at the 2001 Joint Services Small Arms Symposium, 13-16 August 2001, sponsored by the National Defense Industrial Association.
Demystifying Graph Databases: Analysis and Taxonomy of Data Organization, System Designs, and Graph Queries (2019)

Graph processing has become an important part of multiple areas of computer science, such as machine learning, computational sciences, medical applications, social network analysis, and many others. Numerous graphs such as web or social networks may contain up to trillions of edges. Often, these graphs are also dynamic (their structure changes over time) and have domain-specific rich data associated with vertices and edges. Graph database systems such as Neo4j enable storing, processing, and analyzing such large, evolving, and rich datasets. Due to the sheer size of such datasets, combined with the irregular nature of graph processing, these systems face unique design challenges. To facilitate the understanding of this emerging domain, we present the first survey and taxonomy of graph database systems. We focus on identifying and analyzing fundamental categories of these systems (e.g., triple stores, tuple stores, native graph database systems, or object-oriented systems), the associated graph models (e.g., RDF or Labeled Property Graph), data organization techniques (e.g., storing graph data in indexing structures or dividing data into records), and different aspects of data distribution and query execution (e.g., support for sharding and ACID). 51 graph database systems are presented and compared, including Neo4j, OrientDB, or Virtuoso. We outline graph database queries and relationships with associated domains (NoSQL stores, graph streaming, and dynamic graph algorithms). Finally, we describe research and engineering challenges to outline the future of graph databases.
Concurrent Generation of Functional Smooth Muscle and Endothelial Cells via a Vascular Progenitor (2013)

Smooth muscle cells (SMCs) and endothelial cells (ECs) are typically derived separately, with low efficiencies, from human pluripotent stem cells (hPSCs). The concurrent generation of these cell types might lead to potential applications in regenerative medicine to model, elucidate, and eventually treat vascular diseases. Here we report a robust two-step protocol that can be used to simultaneously generate large numbers of functional SMCs and ECs from a common proliferative vascular progenitor population via a two-dimensional culture system. We show here that coculturing hPSCs with OP9 cells in media supplemented with vascular endothelial growth factor, basic fibroblast growth factor, and bone morphogenetic protein 4 yields a higher percentage of CD31(+)CD34(+) cells on day 8 of differentiation. Upon exposure to endothelial differentiation media and SM differentiation media, these vascular progenitors were able to differentiate and mature into functional endothelial cells and smooth muscle cells, respectively. Furthermore, we were able to expand the intermediate population more than a billion fold to generate sufficient numbers of ECs and SMCs in parallel for potential therapeutic transplantations.
Ongoing Myocardial Injury in Stable Severe Heart Failure (2004)

Abnormal cTnT concentrations were detected in >50% of outpatients with advanced CHF. This ongoing myocardial necrosis was a strong predictor of worsening CHF, suggesting a role of cTnT-based monitoring to identify high-risk patients.
Brain white matter structural properties predict transition to chronic pain (2013)

Neural mechanisms mediating the transition from acute to chronic pain remain largely unknown. In a longitudinal brain imaging study, we followed up patients with a single sub-acute back pain (SBP) episode for more than 1 year as their pain recovered (SBPr), or persisted (SBPp) representing a transition to chronic pain. We discovered brain white matter structural abnormalities (n=24 SBP patients; SBPp=12 and SBPr=12), as measured by diffusion tensor imaging (DTI), at entry into the study in SBPp in comparison to SBPr. These white matter fractional anisotropy (FA) differences accurately predicted pain persistence over the next year, which was validated in a second cohort (n=22 SBP patients; SBPp=11 and SBPr=11), and showed no further alterations over a 1-year period. Tractography analysis indicated that abnormal regional FA was linked to differential structural connectivity to medial vs lateral prefrontal cortex. Local FA was correlated with functional connectivity between medial prefrontal cortex and nucleus accumbens in SBPr. As we have earlier shown that the latter functional connectivity accurately predicts transition to chronic pain, we can conclude that brain structural differences, most likely existing before the back pain-inciting event and independent of the back pain, predispose subjects to pain chronification.
Synthesis of 7‐Oxo‐1,2,3,4,6,7,12,12b‐octahydroindolo[2,3‐<i>a</i>]quinolizine (2018)

A short synthesis of 7‐oxo‐1,2,3,4,6,7,12,12b‐octahydroindolo[2,3‐ a ]quinolizine from 2‐acetylpyridine and phenylhydrazine is described. Ring C is forged using 2‐chloro‐ N , N‐ dimethylacetamide. This derivative of the natural alkaloid 1,2,3,4,6,7,12,12b‐octahydroindolo[2,3‐ a ]quinolizine is an inhibitor of the ZipA–FtsZ protein–protein complex, which is a novel antibacterial target.
Electron energy and electric field estimates in sprites derived from ionized and neutral <b><i>N</i></b><sub>2</sub> emissions (2002)

During the EXL98 aircraft mission, sprites and blue jets were observed by narrow band cameras that measure the N 2 + 1NG (0,1) band at 4278Å and the N 2 2PG (0,0) band at 3370Å. We discuss the observations (∼1km resolution), instrumental and atmospheric corrections, and altitude profiles of ionized (1NG) and neutral (2PG) emission observed during a specific sprite. The ratio of ionized‐to‐neutral emission indicates a relative enhancement of ion emission below 55km. Characteristic electron energies ( E Ch ) and electric fields ( E ) are derived from these emission ratios using excitation rates computed from a model that solves the Boltzmann equation as a function of electric field. Up to 55km E follows the breakdown field ( E k ) and E Ch is ∼2.2eV. Above 55km E drops below E k and E Ch drops to ∼1.75eV near 60km.