gebhart/patrepeval huggingface dataset:
Downregulation of SP‐R210 <sub>L</sub> Alters the Macrophage Epigenetic Chromatin Landscape Associated with Changes in Transcription Factor Binding (2019)

Alveolar macrophages are the first immune cells to come into contact with air‐borne pathogens such as influenza. Previous studies demonstrated that the surfactant protein A (SP‐A) receptor, SP‐R210, also known as MYO18A, regulates the immune functions of macrophages through the action of two isoforms; a long form SP‐R210 L (L), and a short form SP‐R210 S (S). Stable knockdown of L in RAW264.7 cells (abbreviated as DN) revealed alterations in mRNA expression of innate immune receptors and responsiveness to various inflammatory stimuli. To elucidate the intrinsic functions of the L isoform, the present study addressed the hypothesis that L modulates macrophage gene transcription through epigenetic modification of chromatin. We thus utilized chromatin immunoprecipitation and sequencing (ChIP‐seq) to determine the impact of L depletion on histone modification marks H3K4me3, H3K9me3, and H3K27me3 and binding of transcription factors PU.1 and NFκB subunit RelA, which regulate macrophage differentiationand inflammatory responses, respectively. Pulled‐down sequences were visualized on the UCSC genome browser to identify the spatial relation between enriched sequences. This analysis showed reduced PU.1 binding at genes associated with macrophage differentiation and intercellular communication between innate and adaptive immune cells, such as interleukin 18 (IL‐18) and colony‐stimulating factor receptors (CSF1R, CSF2RB) in DN cells. Additionally, differences in PU.1 binding were reflected in similar suppression of H3K4me3 marks in DN cells. Further analysis by ChIPpeakAnno and ChIPseeker and ingenuity pathway analysis, however, revealed enrichment in genes that regulate TNFα and interferon (IFN) signaling in DN cells. Collectively, these findings support the idea that the L isoform of SP‐R210 regulates chromatin architecture and accessibility of transcription factors at genes with discrete roles in macrophage differentiation and activation. Support or Funding Information This work was supported by HL128746, The Children's Miracle Network, and the Department of Pediatrics, Penn State University College of Medicine This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Transcriptional Regulation of Mouse δ-Opioid Receptor Gene (1999)

Previously, the existence of dual promoters was reported in mouse mu-opioid receptor (mor) gene, with mor transcription in the mouse brain predominantly initiated by the proximal promoter. In this study, we further analyzed the proximal promoter region, base pairs -450 to -249, to identify cis-DNA regulatory elements and trans-acting protein factors that are important for mor promoter activity. The results revealed that a mor inverted GA (iGA) motif and a canonical Sp1 binding site are required for the promoter activity. Using electrophoretic mobility shift analysis, we identified nuclear proteins that specifically bind to the mor iGA motif and that are immunologically related to Sp1 and Sp3. Mutation of the mor iGA motif, resulting in a loss of Sp binding, led to a 50% decrease in activity. Mutation of the canonical Sp1 binding site yielded a lesser (approximately 25%) loss of activity. Mutation of both motifs together resulted in an approximately 70% decrease in activity. In cotransfection assays using Drosophila SL2 cells, Sp1 trans-activated the promoter in a manner dependent on the presence of mor iGA and canonical Sp1 binding motifs. Sp3 can also trans-activate the promoter, and furthermore, Sp1 and Sp3 can trans-activate the mor promoter additively. Our results suggest that combined or cooperative interaction of Sp transcription factors within the proximal promoter is necessary for activation of mor gene transcription.
Coherence of supercontinua generated by ultrashort pulses compressed in optical fibers (2008)

Femtosecond fiber lasers together with nonlinear fibers are compact, reliable, all-fiber supercontinuum sources. Maintaining an all-fiber configuration, however, necessitates pulse compression in an optical fiber, which can lead to nonlinearities for subhundred femtosecond, nanojoule pulses. In this work we show that using large-mode-area fibers for pulse compression mitigates the nonlinearity, resulting in compressed pulses with significantly reduced satellite pulses. Consequently, supercontinua generated with these pulses are shown to have as much as a 10 dB increase in coherence fringe contrast. By using a hybrid highly nonlinear fiber-photonic crystal fiber, the continuum can be extended to visible wavelengths while still maintaining high coherence.
Fluid shear stress activates YAP1 to promote cancer cell motility (2017)

Mechanical stress is pervasive in egress routes of malignancy, yet the intrinsic effects of force on tumour cells remain poorly understood. Here, we demonstrate that frictional force characteristic of flow in the lymphatics stimulates YAP1 to drive cancer cell migration; whereas intensities of fluid wall shear stress (WSS) typical of venous or arterial flow inhibit taxis. YAP1, but not TAZ, is strictly required for WSS-enhanced cell movement, as blockade of YAP1, TEAD1-4 or the YAP1-TEAD interaction reduces cellular velocity to levels observed without flow. Silencing of TEAD phenocopies loss of YAP1, implicating transcriptional transactivation function in mediating force-enhanced cell migration. WSS dictates expression of a network of YAP1 effectors with executive roles in invasion, chemotaxis and adhesion downstream of the ROCK-LIMK-cofilin signalling axis. Altogether, these data implicate YAP1 as a fluid mechanosensor that functions to regulate genes that promote metastasis.
Rules and Principles in Cognitive Diagnosis (2013)

One of psychology's central goals is the description of human behavior. However, it has become increasingly clear that psychology faces several complications in its pursuit of that goal. The most important of these complications is that individual differences appear to be an essential aspect of the human condition. Different people have different experiences and thus acquire different knowledge and skills. Moreover, the behavior of even a single human varies over time as he gains more experience and more expertise.
Vector Control and Dynamics of AC Drives (1996)

Abstract This book presents a detailed but easily understood development of the complex variable form of the equations describing AC machines. These equations are then extended to incorporate inverter models and a number of examples of inverter-machine dynamics are presented. A section on constant speed behaviour includes development of the conventional equivalent circuits and an extensive treatment of the constant speed eigenvalues and switching transients. Vector control and field orientation concepts are first introduced in terms of their steady state properties. This allows anyone with a basic understanding of steady state machine behaviour to understand and appreciate the potential of field orientation and to actually start using the book immediately. This is followed by a full dynamic analysis of vector controlled systems including conventional indirect and direct field orientation and less conventional systems that orient to air gap or stator flux rather than rotor flux. A chapter on the important types of current regulators is also included. The final two chapters deal with vector control and field orientation system performance in relation to tuning errors, saturation effects, selection of flux levels to optimize performance and the question of optimization in the field weakening mode.
Integrated Combinatorial Synthesis, Characterization, and Test Platform for Lithium-Ion Battery Cathode Materials (2023)

An integrated combinatorial synthesis, characterization, and testing methodology and platform is proposed and developed for high-throughput exploration of Li-ion rechargeable battery cathode chemistries. This article describes the design of the platform’s combinatorial synthesis part and its prototype performance. A key design element is a multi-gear powertrain with a unique milling-force adjustable pestle that ensures high compatibility with varying types of electrode materials. To demonstrate the prototype, LiNiO 2 was prepared via a solid-state route under various operating conditions. We evaluated the effects of processing parameters, including milling force and mixing speed, on the synthesized electrode’s physical properties and electrochemical behavior. The synthesized LiNiO 2 materials show excellent electrochemical performance comparable to manually synthesized LiNiO 2 .
Ubiquitin Ligase RNF146 Regulates Tankyrase and Axin to Promote Wnt Signaling (2011)

Canonical Wnt signaling is controlled intracellularly by the level of β-catenin protein, which is dependent on Axin scaffolding of a complex that phosphorylates β-catenin to target it for ubiquitylation and proteasomal degradation. This function of Axin is counteracted through relocalization of Axin protein to the Wnt receptor complex to allow for ligand-activated Wnt signaling. AXIN1 and AXIN2 protein levels are regulated by tankyrase-mediated poly(ADP-ribosyl)ation (PARsylation), which destabilizes Axin and promotes signaling. Mechanistically, how tankyrase limits Axin protein accumulation, and how tankyrase levels and activity are regulated for this function, are currently under investigation. By RNAi screening, we identified the RNF146 RING-type ubiquitin E3 ligase as a positive regulator of Wnt signaling that operates with tankyrase to maintain low steady-state levels of Axin proteins. RNF146 also destabilizes tankyrases TNKS1 and TNKS2 proteins and, in a reciprocal relationship, tankyrase activity reduces RNF146 protein levels. We show that RNF146, tankyrase, and Axin form a protein complex, and that RNF146 mediates ubiquitylation of all three proteins to target them for proteasomal degradation. RNF146 is a cytoplasmic protein that also prevents tankyrase protein aggregation at a centrosomal location. Tankyrase auto-PARsylation and PARsylation of Axin is known to lead to proteasome-mediated degradation of these proteins, and we demonstrate that, through ubiquitylation, RNF146 mediates this process to regulate Wnt signaling.
<i>Strongyloides</i> coinfection in COVID‐19 patients treated with corticosteroids: A systematic review (2023)

The COVID-19 pandemic linked to the virus SARS-CoV-2, which began in China, affected ∼765 million people as of 30 April 2023. The widespread use of corticosteroids for the symptomatic treatment of COVID-19 could lead to the reactivation of infections of opportunistic pathogens, including Strongyloides. We sought to determine the clinical symptoms and demographic characteristics of SARS-CoV-2-Strongyloides co-infection, particularly in patients with severe disease and being treated with immunosuppressive drugs. To do this, we undertook a systematic review of the literature, and searched public accessible scientific databases-the Web of Science, Scopus, PubMed/Medline and Embase -for eligible studies (1 December 2019 to 30 August 2022). The review protocol is registered in PROSPERO (CRD42022377062). Descriptive statistical analyses were used to present the clinical and laboratory parameters of the co-infection; for this, we calculated prevalence using the following formula: positive cases/total number of cases × 100. Of a total of 593 studies identified, 17 studies reporting 26 co-infected patients met the criteria for inclusion in this review. The median age of these patients was 55.14 years. Most of cases (53.8%) were treated with dexamethasone, followed by methylprednisolone (26.9%). Eighteen of 26 patients were immigrants living in European countries or the USA; most of these immigrants originated from Latin America (58%) and South-East Asia (11%). The commonest symptoms of co-infection were abdominal pain (50%), fever (46.1%), dyspnoea (30.7%) and cough (30.7%), and frequently reported laboratory findings were high absolute eosinophil count (38.4%), high white blood cell count (30.7%), high C-reactive protein (23.0%) and high neutrophil count (19.2%). Two of the 26 patients (7.7%) had fatal outcomes. Most of the SARS-CoV-2-Strongyloides coinfected cases were immigrants living in developed countries, emphasising the need for clinicians in these countries to be aware of clinical and laboratory parameters associated with such co-infections, as well as the key importance of rapid and accurate diagnostic tests for timely and effective diagnosis and patient management.
Retinal vessel diameters and risk of hypertension: the Multiethnic Study of Atherosclerosis (2009)

Findings from this multiethnic population confirm that narrower retinal arteriolar diameter and wider venular diameter are associated with the development of hypertension independent of traditional risk factors.
Data from Oncogenic &lt;i&gt;ALK&lt;/i&gt; Fusion in Rare and Aggressive Subtype of Colorectal Adenocarcinoma as a Potential Therapeutic Target (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Chromosomal translocations in the anaplastic lymphoma kinase (&lt;i&gt;ALK&lt;/i&gt;) gene have been identified as oncogenic drivers in lung adenocarcinomas and other tumors, recently including rare cases of colorectal carcinoma. We identified a patient with refractory metastatic colorectal carcinoma harboring a &lt;i&gt;STRN&lt;/i&gt;–&lt;i&gt;ALK&lt;/i&gt; gene fusion who achieved an exceptional clinical benefit to the ALK inhibitor ceritinib. Our goal was to further define the clinicopathologic features of &lt;i&gt;ALK&lt;/i&gt;-rearranged colorectal carcinoma in a large cohort.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Clinical cases of colorectal carcinoma evaluated by comprehensive genomic profiling (CGP) or by ALK immunohistochemistry (IHC) were reviewed retrospectively. FISH and microsatellite instability (MSI) analyses were performed.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Nine colorectal carcinoma cases harbored &lt;i&gt;ALK&lt;/i&gt; gene fusions. Six cases were identified by CGP of 3,157 colorectal carcinoma (0.2%) and three by IHC of 2,980 colorectal carcinoma (0.1%). The &lt;i&gt;ALK&lt;/i&gt; fusions involved known &lt;i&gt;ALK&lt;/i&gt; partners &lt;i&gt;EML4, C2orf44, CAD&lt;/i&gt;, and the novel &lt;i&gt;STRN, PPP1R21, SENPF, MAPRE3&lt;/i&gt;, and &lt;i&gt;PRKAP1B&lt;/i&gt; partners. These advanced-stage colorectal carcinomas lacked mutations in other oncogenic drivers, predominantly involved the proximal colon, and often exhibited MSI and mucinous phenotype. The index patient was treated with the ALK inhibitor ceritinib, resulting in a marked decrease in size of a skin metastasis, and resolution by computerized tomography of all contrast enhancing tumor. After 9 months of treatment, biopsy of progressive disease demonstrated a &lt;i&gt;KRAS&lt;/i&gt; mutation, consistent with acquired resistance to ceritinib.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Colorectal carcinoma harboring &lt;i&gt;ALK&lt;/i&gt; fusions represent a rare aggressive subtype of colorectal carcinoma with distinct clinicopathologic features. This report provides the first clinical evidence that such patients may benefit from targeted monotherapy with ALK inhibitors. &lt;i&gt;Clin Cancer Res; 22(15); 3831–40. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Automatic selection of high-order transformations in the IBM XL FORTRAN compilers (1997)

The IBM ASTI optimizer provides the foundation for high-order transformations and automatic shared-memory parallelization in the latest IBM XL FORTRAN (XLF) compilers for RS/6000™ and PowerPC® uniprocessors and symmetric multiprocessors (SMPs), and for automatic distributed-memory parallelizationin the IBM XL High-Performance FORTRAN (XLHPF) compiler for the SP2™ distributed-memory multiprocessor. In this paper, we describe how the transformer component of the ASTI optimizer automatically selects high-order transformations for a given input program and a target uniprocessor, so as to improve utilization of the memory hierarchy (including cache and registers) and instruction-level parallelism. Our solution is centered on a quantitative approach in which optimization problems are formulated using quantitative cost models. The loop and data transformations currently employed by the ASTI transformer for optimizing uniprocessor performance are loop distribution, loop interchange, loop reversal, loop skewing, loop tiling/blocking (with compiler-selected tile sizes), loop fusion, unrolling of multiple loops (with compiler-selected unroll factors), and scalar replacement of selected array references. The design and initial implementation of the ASTI optimizer were completed during the 1991-1993 time period. To the best of our knowledge, the ASTI transformer is the first system to perform automatic selection of this wide range of transformations using a cost-based framework.
Fast CNN-Based Document Layout Analysis (2017)

Automatic document layout analysis is a crucial step in cognitive computing and processes that extract information out of document images, such as specific-domain knowledge database creation, graphs and images understanding, extraction of structured data from tables, and others. Even with the progress observed in this field in the last years, challenges are still open and range from accurately detecting content boxes to classifying them into semantically meaningful classes. With the popularization of mobile devices and cloud-based services, the need for approaches that are both fast and economic in data usage is a reality. In this paper we propose a fast one-dimensional approach for automatic document layout analysis considering text, figures and tables based on convolutional neural networks (CNN). We take advantage of the inherently one-dimensional pattern observed in text and table blocks to reduce the dimension analysis from bi-dimensional documents images to 1D signatures, improving significantly the overall performance: we present considerably faster execution times and more compact data usage with no loss in overall accuracy if compared with a classical bidimensional CNN approach.
SMS-20: Effect of Crack-healing Applied Stress on Fracture Strength and Threshold Stress during Crack-healing Treatment(SMS-III: SMART MATERIALS AND STRUCTURES, NDE) (2005)

ing, it would be very desireble fbr structural integrity, From the 2beve points of vievv, a new methedology to gvarantee the structural integrity of ceramic components using in-situ crack-healing ability was proposed and the usafulness was cliscussed "sing the test results in terms ef crackhealing behavier and proof test theory by the authors.
The patient with rhabdomyolysis: Have you considered quail poisoning? (2004)

THE CASES Patient 1: A 62-year-old woman was admitted with nausea, vomiting, weakness and leg muscle pain. The symptoms had begun 7 hours after a meal of fresh roasted quail. She was not taking any medications, had no allergies to food or medications and did not use alcohol, cigarettes or illicit
Flow cytometric characterization of acute myeloid leukemia: IV. Comparison to the differentiation pathway of normal hematopoietic progenitor cells. (1992)

Gradual increase of CD38 on cells expressing CD34 characterizes the early cell differentiation pathway of normal human hematopoietic progenitors. In this study the coordinated expression pattern of CD34 and CD38 was assessed on leukemic blasts from bone marrow aspirates of 95 patients with newly diagnosed acute myeloid leukemia (AML). Expression was divided into six categories analogous to the differentiation pathway of normal bone marrow. The CD38 antigen was expressed on the leukemic cells of all patients and CD34+ leukemic cells were found in 79 patients (83%). In 93 patients, the leukemic cells were found along the differentiation pathway defined by CD34 and CD38. In 33 of the 93 patients, a part of the CD34+ cells did not express the CD38 antigen (categories 1 and 2). In another 33 patients, all CD34+ cells expressed CD38 (categories 3 and 4). In the remaining 27 patients, only cells were found which dimly expressed CD34 or did not express CD34 (categories 5 and 6). Of the 93 patients, 88 were treated with intensive chemotherapy according to the protocol of the German AML Cooperative Group. Of these, 21 died early and were not evaluable for treatment response. Complete remission was achieved in 14 of 22 patients (64%) in categories 1 and 2, in 19 of 26 patients (73%) in categories 3 and 4, and in 18 of 19 patients (95%) in categories 5 and 6. The event-free survival was significantly longer in patients of categories 5 and 6 compared to patients in categories 1 and 2 (p less than 0.01) and categories 3 and 4 (p less than 0.05), respectively. We conclude that in the majority of AML patients the immunophenotype of leukemic cells follows the early cell differentiation pathways defined by coordinated expression of CD34 and CD38 similar to that of normal hematopoietic progenitors. The presence of cells in the late cell differentiation stages (CD34+/-, CD38 /+) identifies patients with a higher complete remission rate and longer complete remission duration.
&lt;title&gt;What is MRT and how do I get one?&lt;/title&gt; (1991)

Although minimum resolvable temperature difference (MRTD) measurements of forward looking infrared (FLIR) systems have been around for a long time, there is still a lot of confusion and misunderstanding about the measurement techniques. C2NVEO has been performing the measurement since the middle 1970s in its image evaluation facility (IEF). The IEF is generally considered to be the standard of the free world for FLIR measurements. This paper provides a basic understanding of the measurement state-of-the-art of MRTD for first- and second-generation FLIR systems. Concepts and theory behind the measurement are addressed and equipment requirements as well as observer training are reviewed. A discussion of the challenges of evaluating new systems such as staring arrays and second-generation digital FLIRs and the requirements for both horizontal and vertical MRTD measurements is also provided. A discussion of effects at automating the measurement is provided.
A Multi-Physics Finite Element Analysis of Round Pin High Power Connectors (2010)

In the past decade, the general public's means of transportation has begun to undergo a radical transformation, moving away from only using gasoline and moving toward using a combination of gasoline and electricity. One parameter that shouldn't stand in the way is the overall reliability of the electric vehicle, which is dependent upon the electric connections between the power source and the motor. Using a multi-physics finite element software package and multiscale predictions of electrical and thermal contact resistance, a model was constructed to predict the behavior of a round pin, high power connector under normal vehicle operating conditions. To test the validity of the model, an experiment was devised to measure connector resistance and temperature. The theoretical and experimental results showed the same trends. The possible influence of fretting was also considered by artificially increasing the contact resistance. The model shows that for increasing current and increasing electrical contact resistance, that current becomes more concentrated along the path it travels through the connector. This constriction of current could lead to much higher surface temperatures than the model currently predicts, resulting in thermally induced softening or distortion in the connector.
Growth heterogeneity in fish farming: simulation of feeding behaviour and growth through an individualized based model (IBM) (2009)

National audience