gebhart/patrepeval huggingface dataset:
Make or break for mitochondria (2013)

Ensuring that mitochondrial DNA is successfully divided between daughter mitochondria involves a complex series of interactions with the endoplasmic reticulum and a variety of enzymes.
New results for coaxial re-entrant cavity with partially dielectric filled gap (1992)

Resonant frequencies, Q-factor and electromagnetic field intensity are presented for a set of varied parameters of a coaxial re-entrant cavity with a gap partially filled with a dielectric. The cavity is analyzed using the mode matching technique. The numerical results are found to be in good agreement with experimental data. Based on the numerical results, a scheme for mode identification is proposed and the mode transition is discussed. Furthermore, the equivalent gap capacitances are obtained and compared with the results from an existing formula which has been modified for the dielectric loaded gap.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Development of a DOE/Optimization CAE Method to Simultaneously Improve Side ImpactOccupant Restraint System Performance for Multiple Test Modes (2007)

The automotive industry today faces the challenge of developing a single side impact occupant restraint system to meet performance requirements for multiple crashworthiness test modes. The side air bag, door liner, and vehicle side body structure are key systems that affect the injury criteria of the occupant. This paper discusses how DOE/optimization methods are used to quickly develop a specification for the side air bag and door liner that meets occupant injury criteria for three different side impact test modes. The work detailed in this paper focuses on occupant protection assessment based on three different CAE side impact sled models using ES2-re, DOT-SID and SID-2s, dummy models to evaluate the new FMVSS 214, SINCAP and SICE test modes. Ten design variables were selected from air bag and door liner parameters which include mass flow rates, vent areas, two variables that define the location of the bag, and material/thickness of the door liner. Occupant injury parameters such as rib deflections/accelerations, pelvis accelerations/forces, and abdomen forces were selected as the responses. As the first step, a latin hypercube DOE method was used to evaluate sensitivity of the design variables to occupant injury parameters. Based on the DOE dominant design variables, optimization criteria and methods were established for the next step. Key injury criteria for each test mode were selected as the constraints. A self adaptive evolution (SAE) global optimization method was used to carry out automated simultaneous simulations. Based on the optimization results eleven feasible design specifications were found. Out of these candidates the optimum design was selected for further evaluation.
The Clone Wars – Revenge of the Metastatic Rogue State: The Sarcoma Paradigm (2012)

Ewing sarcoma (ES) is the second most common bone tumor affecting primarily adolescents and young adults. Despite recent advances in biological understanding, intensification of chemotherapeutic treatments, and progress in local control with surgery and/or radiation therapy, patients with metastatic or recurrent ES continue to have a dismal prognosis with less than 20% overall survival. All ES is likely metastatic at diagnosis although our methods of detection and classification may not account for this. Progressive disease may arise via a combination of: (1) selection of chemotherapy-resistant clones in primary tumor, (2) signaling from bone or lung microenvironments that may attract tumor cells to distant locations, and/or (3) genetic changes within the ES cells themselves due to DNA-damaging chemotherapeutic agents or other "hits." These possibilities and the evidence base to support them are explored.
Reactions of K-region oxides of carcinogenic and noncarcinogenic aromatic hydrocarbons. Comparative studies on reactions with nucleophiles and acid-catalyzed reactions. (1978)

Several K-region arene oxides of carcinogenic and noncarcinogenic polycyclic aromatic hydrocarbons were synthesized, and their reactivities with various nucleophiles and their acid-catalyzed reactions were discussed. Relationship between these chemical reactivities and mutagenicity was also discussed.
Performance evaluation of a multiprocessor in a real time environment (1976)

Thesis. 1976. Sc.D.--Massachusetts Institute of Technology. Dept. of Aeronautics and Astronautics.
Fluorinated Phospholipid-Based Vesicles as Potential Drug Carriers: Encapsulation/Sustaining of Drugs and Stability in Human Serum (1994)

The release of entrapped 5(6)-carboxyfluorescein from fluorinated vesicles in a buffer or in human serum is considerably less than that from hydrogenated liposomes. The presence of a fluorinated core inside the liposomal membrane definitely reduces its permeability. In some cases, the stability of liposomes made from fluorinated phospholipids alone is better than that of egg phosphatidylcholine cholesterol 1/1 vesicles, which are among the least permeable and most stable hydrogenated liposomes.
Mixed Precision Training (2017)

Deep neural networks have enabled progress in a wide variety of applications. Growing the size of the neural network typically results in improved accuracy. As model sizes grow, the memory and compute requirements for training these models also increases. We introduce a technique to train deep neural networks using half precision floating point numbers. In our technique, weights, activations and gradients are stored in IEEE half-precision format. Half-precision floating numbers have limited numerical range compared to single-precision numbers. We propose two techniques to handle this loss of information. Firstly, we recommend maintaining a single-precision copy of the weights that accumulates the gradients after each optimizer step. This single-precision copy is rounded to half-precision format during training. Secondly, we propose scaling the loss appropriately to handle the loss of information with half-precision gradients. We demonstrate that this approach works for a wide variety of models including convolution neural networks, recurrent neural networks and generative adversarial networks. This technique works for large scale models with more than 100 million parameters trained on large datasets. Using this approach, we can reduce the memory consumption of deep learning models by nearly 2x. In future processors, we can also expect a significant computation speedup using half-precision hardware units.
ChemInform Abstract: Absolute Stereochemistry of Pentacecilides, New Inhibitors of Lipid Droplet Formation in Mouse Macrophages, Produced by Penicillium cecidicola FKI‐3765‐1. (2010)

Abstract The structure of the new pentacecilide D (Id), produced by Penicillium cecidicola FKI‐3765‐1 is determined.
Autologous Bone Marrow Transplantation (1995)

Autologous bone marrow transplantation has become a very popular and successful treatment for many patients with lymphomas and other malignancies. The current indications, pretreatment regimes, and laboratory manipulations are discussed as well as the application of gene transfer to eliminate selected genetic diseases and detect disease relapse.
Physical properties and gas solubilities in selected fluorinated ethers (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhysical properties and gas solubilities in selected fluorinated ethersMin K. Tham, Robert D. Walker Jr., and Jerome H. ModellCite this: J. Chem. Eng. Data 1973, 18, 4, 385–386Publication Date (Print):October 1, 1973Publication History Published online1 May 2002Published inissue 1 October 1973https://pubs.acs.org/doi/10.1021/je60059a011https://doi.org/10.1021/je60059a011research-articleACS PublicationsRequest reuse permissionsArticle Views192Altmetric-Citations31LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
An FPGA-based Switch-mode Power Amplifier using Boundary Control to achieve High System Bandwidth (2019)

Power amplifiers are critical components for Power Hardware-in-the-Loop (PHIL) applications with the requirement of low cost, high bandwidth and fast dynamic response. This paper proposes an innovative combination of a GaN device and boundary controller implemented in an FPGA to realize a high bandwidth power amplifier providing fast dynamic responses. The transient time and system bandwidth have been discussed, analyzed and verified by experiment results. In this paper, the control strategy, the implementation of a physical power amplifier and the experimental results are presented. The Power Amplifier achieves a 27 kHz average switching frequency with an output power of 100W and amplifier gain of 50. The results show the dynamic response of the system is close to the theoretical best performance under certain parameters and it can track the changes of the reference in tens of microseconds. The system reaches the highest potential system bandwidth.
Gene expression signatures in non-small cell lung cancer (NSCLC) according to cigarette smoking history (2008)

22082 Background: Epidemiological and experimental studies confirm that cigarette smoking is the principal causal agent of lung cancer. It is estimated that about 2–5% of all lung cancer patients (pts) have never smoked. A knowledge on molecular features of lung cancers not related to smoking might lead to better understanding of their carcinogenesis and allow development of new therapeutic targets. In this study we compared gene expression signatures in non-smoking vs smoking NSCLC pts. Methods: Study group included 70 NSCLC pts, of those 25 never-smokers (WHO criteria) and 45 current or past smokers (mean 49.7 pack-years, range 6–130). All pts underwent curative pulmonary resection. There were more women among non-smokers (p=0.003), whereas other major characteristics did not significantly differ between both groups. Qualitative RT-PCR analysis was performed on mRNA derived from snap frozen tumor specimens. Expression of 27 genes: potentially related to smoking, including kinase receptors, sex hormone receptors, transcription factors and genes involved in HPV infection pathways was investigated. 18S rRNA subunit, POLR2A, ESD and YAP1 were used as normalization genes. Gene expressions were compared by parametric permutation test with Benjamini-Hochberg correction for multiple comparisons (False Discovery Rate assessment). Results: In univariate analysis 3 genes were particularly overexpressed in tumors of non-smokers: RRAD (p=0.0002), TGF-beta receptor-2 (TGFBR2; p=0.002) and progesterone receptor (PgR; p=0.007). TGF-beta receptor-3 (TGFBR3; p=0.02), SOX9 (p=0.02) and androgen receptor (AR; p=0.03) were also significantly overexpressed in these tumors. After correction for the impact of sex, histopathology, stage of disease, and multiple comparisons, RRAD and TGFBR2 were independently correlated with smoking history. Conclusions: NSCLC in non-smokers is characterized by a specific gene expression signature. Overexpression of TGFBR2 provides the basis for developing new targeted therapies. No significant financial relationships to disclose.
Motion separating based whole body motion planning for humanoid robots using a gradient descent method (2008)

This paper introduces whole body motion planning for humanoid robots that is fundamentally important for functioning of humanoid robots within the living space of humans. Humanoid robots have multiple degrees of freedom (DOF). Because of this multi-DOF structure, whole body motion planning of humanoid robots is difficult and complex. In this paper, we separated whole body motion of humanoid robots into several partial motions. Separating whole body motion into several partial motions, we can overcome the difficulty and complexity of whole body motion planning for humanoid robots with high degrees of freedom. Each separated partial motion has only 6 DOF: X, Y, Z, Pitch, Yaw, and Roll. Based on these low-degrees of freedom, we can utilize efficient motion planning algorithm. As an algorithm of partial motion planning, the gradient-descent method was used. The correctness and efficiency of our algorithm was established by conducting simulations and experiments on the humanoid robot simulator and physical humanoid robot using the whole body motion planning algorithm developed in this research.
Applying key phrase extraction to aid invalidity search (2011)

Invalidity search poses different challenges when compared to conventional Information Retrieval problems. Presently, the success of invalidity search relies on the queries created from a patent application by the patent examiner. Since a lot of time is spent in constructing relevant queries, automatically creating them from a patent would save the examiner a lot of effort. In this paper, we address the problem of automatically creating queries from an input patent. An optimal query can be formed by extracting important keywords or phrases from a patent by using Key Phrase Extraction (KPE) techniques. Several KPE algorithms have been proposed in the literature but their performance on query construction for patents has not yet been explored. We systematically evaluate and analyze the performance of queries created by using state-of-the-art KPE techniques for invalidity search task. Our experiments show that queries formed by KPE approaches perform better than those formed by selecting phrases based on tf or tf-idf scores.
Incorporating Audio Cues into Dialog and Action Scene Extraction (2003)

In this paper, we present an approach to extract scenes in video. The approach is top-down and uses video editing rules and audio cues to extract simple dialog and action scenes. The underlying model is a finite state machine coupled with audio cues that are determined using an audio classifier.
Soluble Sema4D in Plasma of Head and Neck Squamous Cell Carcinoma Patients Is Associated With Underlying Non-Inflamed Tumor Profile (2021)

Semaphorin 4D (Sema4D) is a glycoprotein that is expressed by several tumors and immune cells. It can function as a membrane bound protein or as a cleaved soluble protein (sSema4D). We sought to investigate the translational potential of plasma sSema4D as an immune marker in plasma of patients with head and neck squamous cell carcinoma (HNSCC). Paired peripheral blood and tumor tissue samples of 104 patients with HNSCC were collected at the same time point to allow for real time analysis. Scoring of the histological inflammatory subtype (HIS) was carried out using Sema4D immunohistochemistry on the tumor tissue. sSema4D was detected in plasma using direct ELISA assay. Defining elevated sSema4D as values above the 95<sup>th</sup> percentile in healthy controls, our data showed that sSema4D levels in plasma were elevated in 25.0% (95% CI, 16.7-34.9%) of the patients with HNSCC and showed significant association with HIS immune excluded (HIS-IE) (p = 0.007), Sema4D<sup>+ve</sup> tumor cells (TCs) (p = 0.018) and PD-L1<sup>+ve</sup> immune cells (ICs) (p = 0.038). A multi-variable logistic regression analysis showed that HIS was significantly (P = 0.004) associated with elevated sSema4D, an association not explained by available patient-level factors. Using the IO-360 nanoString platform, differential gene expression (DGE) analysis of 10 HNSCC tumor tissues showed that patients with high sSema4D in plasma (HsS4D) clustered as IFN-<i>γ</i> negative tumor immune signature and were mostly HIS-IE. The IC type in the HsS4D paired tumor tissue was predominantly myeloid, while the lymphoid compartment was higher in the low sSema4D (LsS4D). The Wnt signaling pathway was upregulated in the HsS4D group. Further analysis using the IO-360, 770 gene set, showed significant non-inflamed profile of the HsS4D tumors compared to the LsS4D. In conclusion, our data reveals an association between sSema4D and the histological inflammatory subtype.
High-resolution imaging of progressive articular cartilage degeneration (2006)

The objective of this study was to develop and verify a new technique for monitoring the progression of osteoarthritis (OA) by combining a rat model with the imaging modality optical coherence tomography (OCT). Time-sequential, in vivo, OCT imaging was performed on the left femoral condyles of 12 Wistar rats following sodium-iodoacetic acid-induced OA progression. The right femoral condyles (untreated) were also imaged and served as controls. Imaging was performed on days 0, 10, 20, 30, and 60 with an OCT system capable of acquiring images at four frames per second and an axial resolution of 5 microm. Progressive changes were analyzed using an OA scoring system. OCT successfully identified progressive cartilage degeneration as well as alteration of the cartilage/bone interface. Significant changes to both of these structures were observed in the sodium-iodoacetic acid-injected condyles. Structural changes detected with OCT were confirmed histologically. OCT in combination with a well-known model used in arthritis research represents a powerful tool for following degenerative joint disease progression in a given animal by detecting changes to the cartilage/bone interface and articular cartilage.
Acute dose of fructooligosaccharide significantly increases calcium absorption in lower gut (2010)

Increasing calcium (Ca) absorption during adolescent growth may help increase peak bone mass. Previous data show that short chain fructooligosaccharides (scFOS) increase fractional Ca absorption (Fxabs) from a single meal in adults (Fukushima et al. 2002). This study examined the acute effect of scFOS on Ca absorption in 15 adolescent girls in a cross‐over design separated by a 3 week washout period. Fasting urine and blood samples were collected. Breakfast was served containing 230 mg Ca plus ~15 mg 44 Ca, a stable isotope, combined with either 0 or 3 g scFOS, in a nutritional drink. One h later, 5 mg 43 Ca was infused intravenously. After 3 h, the final blood sample was drawn. A controlled diet was provided and urine was collected for 24‐h. Fxabs was measured from isotope ratios in 3 h serum and 5, 16, and 24 h urine. Fxabs estimated from urine was plotted vs. time and area under the curve (AUC) was calculated. In a linear model including treatment sequence and baseline serum Ca concentration, the effect of scFOS on serum Fxabs did not differ from control (p=0.66). However, the effect of scFOS supplementation measured by urine AUC became significant by 16 hours (p&lt;0.05) using the same model. Thus the positive effect of scFOS on Ca absorption may be due to increased absorption in the lower gastrointestinal tract warrants further study. This study was sponsored by GTC Nutrition and Abbott Nutrition, Abbot Laboratories.
Generation of Rhesus Macaque-Tropic HIV-1 Clones That Are Resistant to Major Anti-HIV-1 Restriction Factors (2013)

Human immunodeficiency virus type 1 (HIV-1) replication in macaque cells is restricted mainly by antiviral cellular APOBEC3, TRIM5α/TRIM5CypA, and tetherin proteins. For basic and clinical HIV-1/AIDS studies, efforts to construct macaque-tropic HIV-1 (HIV-1mt) have been made by us and others. Although rhesus macaques are commonly and successfully used as infection models, no HIV-1 derivatives suitable for in vivo rhesus research are available to date. In this study, to obtain novel HIV-1mt clones that are resistant to major restriction factors, we altered Gag and Vpu of our best HIV-1mt clone described previously. First, by sequence- and structure-guided mutagenesis, three amino acid residues in Gag-capsid (CA) (M94L/R98S/G114Q) were found to be responsible for viral growth enhancement in a macaque cell line. Results of in vitro TRIM5α susceptibility testing of HIV-1mt carrying these substitutions correlated well with the increased viral replication potential in macaque peripheral blood mononuclear cells (PBMCs) with different TRIM5 alleles, suggesting that the three amino acids in HIV-1mt CA are involved in the interaction with TRIM5α. Second, we replaced the transmembrane domain of Vpu of this clone with the corresponding region of simian immunodeficiency virus SIVgsn166 Vpu. The resultant clone, MN4/LSDQgtu, was able to antagonize macaque but not human tetherin, and its Vpu effectively functioned during viral replication in a macaque cell line. Notably, MN4/LSDQgtu grew comparably to SIVmac239 and much better than any of our other HIV-1mt clones in rhesus macaque PBMCs. In sum, MN4/LSDQgtu is the first HIV-1 derivative that exhibits resistance to the major restriction factors in rhesus macaque cells.
Network Traffic Analysis With Query Driven Visualization SC 2005 HPC Analytics Results (2005)

Our analytics task is to identify, characterize, and visualize anomalous subsets of as large of a collection of network connection data as possible. We use a combination of HPC resources, advanced algorithms, and visualization techniques. To effectively and efficiently identify the salient portions of the data, we rely on a multistage workflow that includes data acquisition, summarization (feature extraction), novelty detection, and classification. Once these subsets of interest have been identified and automatically characterized, we use a stateof- the-art high-dimensional query system to extract this data for interactive visualization. Our approach is equally useful for other large-data analysis problems where it is more practical to identify interesting subsets of the data for visualization than it is to render all data elements. By reducing the size of the rendering workload, we enable highly interactive and useful visualizations.
Anderson localization and quantum Hall effect: Numerical observation of two-parameter scaling (2015)

A two-dimensional disordered system of noninteracting fermions in a homogeneous magnetic field is investigated numerically. By using a modified Landau gauge, we explore the renormalization group flow of the longitudinal and Hall conductances and find that the flow is consistent with the predictions of Pruisken and Khmelnitskii. The extracted critical exponents agree with the results obtained by using transfer matrix methods. The necessity of a second scaling parameter is also demonstrated in the level curvature distribution. Near the critical point the distribution slightly differs from the prediction of random matrix theory, in agreement with previous works. Close to the quantum Hall fixed points the distribution is lognormal since here states are strongly localized.