gebhart/patrepeval huggingface dataset:
Agents and networks to model the dynamic interactions of intracellular transport (2017)

Cell biology is increasingly evolving to become a more formal and quantitative science. The field of intracellular transport is no exception. However, it is extremely challenging to formulate mathematical and computational models for processes that involve dynamic structures that continuously change their shape, position and composition, leading to information transfer and functional outcomes. The two major strategies employed to represent intracellular trafficking are based on "ordinary differential equations" and "agent-" based modeling. Both approaches have advantages and drawbacks. Combinations of both modeling strategies have promising characteristics to generate meaningful simulations for intracellular transport and allow the formulation of new hypotheses and provide new insights. In the near future, cell biologists will encounter and hopefully overcome the challenge of translating descriptive cartoon representations of biological systems into mathematical network models.
LIGAMENT LOADING DURING CLINICAL EXAMINATIONS (2008)

Many different clinical examinations are used to assess instability of the glenohumeral joint. Validation of these includes clinical data, follow-up, imaging, and arthroscopy. In spite of these many works, there currently exists no clear unique method for identifying and validation novel clinical examinations. The aim of this study was to use a computational tool to quantify the specificity of clinical examinations in assessing glenohumeral ligament (GHL) pathology. Five GHLs were modelled according to the literature [1]. Physiological kinematics data [2] were applied to simulate 23 clinical examination manoeuvres for the glenohumeral joint. Individual ligament forces were computed as a percentage of the total ligamentous restraint. The 0° abduction anterior-laxity test was most specific for the superior GHL (82.3%). The anterior apprehension in the coronal plane and 90° anterior-laxity tests were specific for the anterior band of the inferior GHL (abIGHL – 100%). Pure scapular plane abduction and the 90° abduction inferior-laxity tests were specific for the axillary pouch of the IGHL (apIGHL – 100%, 89.6%). Specific tests for posterior band of the IGHL were posterior apprehension (95.1%), 0° and 20° abduction posterior-laxity, and 30° to 45° flexion Norwood and Terry test (100% each). The middle GHL did not exhibit any exclusive loading pattern for any of the tests. A secondary insertional morphology was simulated with the abIGHL positioned at the 4 o’clock position as opposed to the 3 o’clock position [1,2,3]. Significant loading differences were computed for the same ligaments during the same tests. This study demonstrates the sensitivity of specific tests for individual GHLs, but provides the significant caveat that ligament loading is significantly influenced by normal anatomical variations.
<title>Improvement of beam-adjustment accuracy by beam-intensity distribution measurement on a second shaping aperture in electron-beam writing systems</title> (2001)

We proposed a new adjustment method for the beam-intensity distribution. On the 2nd shaping aperture plate, a small aperture is positioned sufficiently apart from the aperture for variable shaping. The center of the 1st shaping aperture image is moved to the small aperture by adjusting an alignment coil. The beam current, which passes through the small aperture, is measured by the Faraday cup on the target while the 1st shaping aperture image is scanned over the small aperture by operating the shaping deflector. Using this method the beam-intensity distribution of the 1st shaping aperture image on the 2nd shaping aperture plane is obtained. The beam-intensity distribution obtained is ideally a series of concentric circles and the maximum value is reached at the center circle. The center is shifted when the alignment of the limit aperture at the illumination or at the 1st shaping aperture is incorrect. The position of the maximum in the beam intensity is adjusted to the center of the 1st shaping aperture image. At the beam-current-density of 20 A/cm<SUP>2</SUP>, the slope of the distribution is usually under 1 percent. To evaluate the adjustment accuracy, resist profile of drawn pattern is measured by AFM. The resist profiles in a beam shot coincide well with the beam intensity distribution.
The Combination of Soy Isoflavones and Resveratrol Preserve Bone Mineral Density in Hindlimb-Unloaded Mice (2020)

It is well known that physical inactivity during space flight or prolonged bed rest causes rapid bone loss. Soy isoflavones (ISOs) and resveratrol (RES) have been reported to be useful to maintain a positive balance for bone turnover. Therefore, we examined the combined effects of ISO and RES on bone loss that was induced by hindlimb-unloading in mice. Female eight-week-old ddY mice were divided into the following six groups (<i>n</i> = 6-8 each): normally housed mice, loading mice, hindlimb-unloading (UL) mice fed a control diet, UL mice fed a 0.16% ISO conjugates, UL mice fed a 0.15% RES diet, and UL mice fed a 0.16% ISO and 0.15% RES diet. After three weeks, femoral bone mineral density was markedly decreased in unloading mice. The combination of ISO and RES prevented bone loss and especially maintained the trabecular bone mineral density more effectively compared with cortical bones. ISO and/or RES inhibited the increase in the RANKL/OPG expression ratio in bone marrow cells in UL mice. These results suggest that the combination of ISO and RES had a preventive effect against bone loss induced by hindlimb-unloading in mice. These osteoprotective effects of ISO and RES may result from the inhibition of bone resorption.
Message from the IWCMC 2015 chairs (2015)

It is a great pleasure welcoming all of you to the IEEE International Wireless Communications and Mobile Computing Conference (IEEE IWCMC 2015) in the beautiful Dubrovnik, Croatia! We are indeed delighted that this year's IEEE IWCMC lived up to its goal under the conference theme “Communications for the 21 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">st</sup> Century,” and continues its tradition of providing the premier forum for presentation of research results and experience reporting on the cutting edge research in the general areas of wireless communications and mobile computing. This year, we received more than 700 submissions from 42 countries. Each paper received at least three peer technical reviews, comprised of more than 450 TPC members from academia, government laboratories, and industries. After carefully examining all review reports, the IEEE IWCMC 2015 TPC finally selected about 36% high-quality papers for presentation at the conference and publication in the IEEE IWCMC 2015 proceedings. The conference program starts on Monday August 24 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> with a full day of Tutorials that are free of charge to all our attendees. Then, each day starts with a keynote speaker chosen from renowned world-class leaders in the area-Dr. Giuseppe Bianchi from University of Roma Tor Vergata, Italy, Dr. Mario Gerla from UCLA, and Dr. Slim Alouini from KAUST, highlighting the latest research trends in the wireless communications, mobile computing, and networks. This year, the technical sessions reflect the continued and growing interests in a wide range of spectrum, including wireless communications and networks, cross-layer design and optimization, mobile computing, wireless sensor networks, network security, and use of wireless technologies in social emergency applications. There are two special sessions composed of invited papers from renowned experts from around the world. Outstanding papers will be selected for four Special Issues in well known international journals. Our objective in the future is to reduce the acceptance rate further.
Contrast-enhanced US for the Interventional Radiologist: Current and Emerging Applications (2020)

US is a powerful and nearly ubiquitous tool in the practice of interventional radiology. Use of contrast-enhanced US (CEUS) has gained traction in diagnostic imaging given the recent approval by the U.S. Food and Drug Administration (FDA) of microbubble contrast agents for use in the liver, such as sulfur hexafluoride lipid-type A microspheres. Adoption of CEUS by interventional radiologists can enhance not only procedure guidance but also preprocedure patient evaluation and assessment of treatment response across a wide spectrum of oncologic, vascular, and nonvascular procedures. In addition, the unique physical properties of microbubble contrast agents make them amenable as therapeutic vehicles in themselves, which can lay a foundation for future therapeutic innovations in the field in drug delivery, thrombolysis, and vascular flow augmentation. The purpose of this article is to provide an introduction to and overview of CEUS aimed at the interventional radiologist, highlighting its role before, during, and after frequently practiced oncologic and vascular interventions such as biopsy, ablation, transarterial chemoembolization, detection and control of hemorrhage, evaluation of transjugular intrahepatic portosystemic shunts (TIPS), detection of aortic endograft endoleak, thrombus detection and evaluation, evaluation of vascular malformations, lymphangiography, and percutaneous drain placement. Basic physical principles of CEUS, injection and scanning protocols, and logistics for practice implementation are also discussed. Early adoption of CEUS by the interventional radiology community will ensure rapid innovation of the field and development of future novel procedures. <i>Online supplemental material is available for this article.</i> <sup>©</sup>RSNA, 2020.
Continuous time random walks for the evolution of Lagrangian velocities (2016)

A continuous-time random walk approach is developed that quantifies the evolution of isochrone and equidistant Lagrangian velocities in steady heterogeneous flows. It is based on the Eulerian velocity distribution and predicts particle transport for arbitrary stationary and nonstationary initial conditions.
Synthesizing Metal Nanowires that Detect Molecules (2006)

Abstract not Available.
Long-term exposure to PM2.5 and its components is associated with elevated blood pressure and hypertension prevalence: Evidence from rural adults (2023)

Long-term exposure to PM<sub>2.5</sub> and its components, especially BC and SOIL, was associated with elevated BP and hypertension prevalence in rural adults, and decreasing pollutants may provide additional benefits.
Vapor phase association in acetic and trifluoroacetic acids. Thermal conductivity measurements and molecular orbital calculations (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTVapor phase association in acetic and trifluoroacetic acids. Thermal conductivity measurements and molecular orbital calculationsD. J. Frurip, L. A. Curtiss, and M. BlanderCite this: J. Am. Chem. Soc. 1980, 102, 8, 2610–2616Publication Date (Print):April 1, 1980Publication History Published online1 May 2002Published inissue 1 April 1980https://pubs.acs.org/doi/10.1021/ja00528a015https://doi.org/10.1021/ja00528a015research-articleACS PublicationsRequest reuse permissionsArticle Views346Altmetric-Citations68LEARN 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
Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement (2021)

The SARS-CoV-2 Omicron variant of concern evades antibody mediated immunity with an unprecedented magnitude due to accumulation of numerous spike mutations. To understand the Omicron antigenic shift, we determined cryo-electron microscopy and X-ray crystal structures of the spike and RBD bound to the broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309 (the parent mAb of sotrovimab) and to the human ACE2 receptor. We provide a structural framework for understanding the marked reduction of binding of all other therapeutic mAbs leading to dampened neutralizing activity. We reveal electrostatic remodeling of the interactions within the spike and those formed between the Omicron RBD and human ACE2, likely explaining enhanced affinity for the host receptor relative to the prototypic virus.
Mom1 is a Semi-Dominant Modifier of Intestinal Adenoma Size and Multiplicity in Min/+ Mice (1996)

The intestinal tumor multiplicity in mice heterozygous for ApcMin is strongly modulated by genetic background. On the sensitive C57BL/6J (B6) background, mice develop large numbers of intestinal adenomas. The AKR/J (AKR) strain carries alleles that correlate with a strong reduction in tumor multiplicity. To study the effect of one of these modifiers, Mom1, we have generated a mouse line in which the AKR allele of Mom1 is carried on the sensitive B6 genetic background. This strain was produced by using a marker-assisted selection method to eliminate unlinked AKR alleles more rapidly. The application and efficiency of this method are discussed. We used this strain to determine that Mom1 affects both tumor multiplicity and tumor size in a semi-dominant fashion.
Exposure-Related Effects of Atazanavir on the Pharmacokinetics of Raltegravir in HIV-1-Infected Patients (2010)

Raltegravir (RAL) is primarily metabolized by uridine diphosphate-glucorunosyl transferase 1A1 (UGT1A1). Atazanavir (ATV), a strong inhibitor of UGT1A1, has been shown to increase plasma concentrations of RAL by approximately 50% in healthy volunteers. However, the extent of this interaction has not been studied in HIV-infected patients. A pharmacokinetic study was performed in 22 HIV-infected adults treated with 400 mg RAL plus 300 mg ATV 300 twice a day. Both drugs showed high pharmacokinetic variability (RAL AUC 0-12 7649 ± 4862 ng*h/mL; ATV AUC 0-12 = 19237 ± 13136 ng*h/mL). Notably, RAL trough concentrations were significantly higher compared with those measured in HIV subjects (n = 24) on RAL plus nucleoside reverse transcriptase inhibitors (506 ± 411 versus 177 ± 262 ng/mL, P < 0.01). A significant correlation was found between RAL and ATV area under the curve (AUC) (r = 0.611, P = 0.005). Notably, patients with ATV AUC 0-12 above the mean or with concentrations exceeding the half maximal inhibitory concentration for UGT1A1 had twofold higher RAL AUCs compared with patients with lower ATV exposure. Coadministration of ATV significantly increased plasma concentrations of RAL, especially in HIV-1-infected patients exposed to high concentrations of the protease inhibitor. This pharmacokinetic drug interaction could be handled by routine measurements of ATV trough concentrations and by the assessment of plasma RAL concentrations 2 to 3 hours after the morning drug intake.
AAV8 Gene Therapy for Crigler-Najjar Syndrome in Macaques Elicited Transgene T Cell Responses That Are Resident to the Liver (2018)

Systemic delivery of adeno-associated viral (AAV) vectors has been evaluated for the treatment of several liver diseases, including homozygous familial hypercholesterolemia, ornithine transcarbamylase deficiency, and hemophilia. Here, we evaluated this approach for the treatment of Crigler-Najjar syndrome. We administered wild-type rhesus macaques with 1.0 × 10<sup>13</sup> or 2.5 × 10<sup>13</sup> genome copies/kg of an AAV serotype 8 vector expressing a codon-optimized version of human uridine diphosphate glucuronosyl transferase 1A1 (UGT1A1) from a liver-specific promoter. We extensively studied vector biodistribution, transgene expression, and immune responses following vector administration. All rhesus macaques survived until their scheduled necropsy at day 56 and showed no clinical abnormalities during the course of the study. Macaques administered with either vector dose developed a T cell response to the AAV capsid and/or transgene. We mapped the immunodominant epitope in the human UGT1A1 sequence, and we found no correlation between peripheral and tissue-resident lymphocyte responses. Upon further investigation, we characterized CD107a<sup>+</sup>, granzyme B<sup>+</sup>, CD4<sup>+</sup>, and CD8<sup>+</sup> transgene-specific cellular responses that were restricted to tissue-resident T cells. This study highlights the importance of studying immune responses at the vector transduction site and the limited usefulness of blood as a surrogate to evaluate tissue-restricted T cell responses.
A Role for TLRs in Moraxella-superantigen induced polyclonal B cell activation (2012)

A number of microorganisms are capable of binding immunoglobulins (Igs) in a manner, which excludes binding to conventional antigen binding sites. Interaction of such bacterial proteins with surface immunoglobulins leads to polyclonal activation of B-lymphocytes. A recent example is Moraxella catarrhalis that binds to B lymphocytes in an IgD-dependent manner and induces proliferation and differentiation of B lymphocytes leading to the production of unspecific Igs. The activation is mediated by Moraxella IgD binding protein (MID), which specifically binds to both soluble IgD and the IgD B cell receptor (BCR). Besides cross-linking the BCR, whole Moraxella and outer membrane vesicles (OMVs) engage Toll like receptors (TLRs) to further increase the response. TLR activation leads to initiation of signaling pathways, which evoke a proinflammatory response against the invading microbes. Polyclonal B cell activation has in general been implicated in various phenomenons that are detrimental for the host but beneficial for pathogens, for example, autoimmune manifestations and redirection of the immune system.
Scale-Space Flow for End-to-End Optimized Video Compression (2020)

Despite considerable progress on end-to-end optimized deep networks for image compression, video coding remains a challenging task. Recently proposed methods for learned video compression use optical flow and bilinear warping for motion compensation and show competitive rate-distortion performance relative to hand-engineered codecs like H.264 and HEVC. However, these learning-based methods rely on complex architectures and training schemes including the use of pre-trained optical flow networks, sequential training of sub-networks, adaptive rate control, and buffering intermediate reconstructions to disk during training. In this paper, we show that a generalized warping operator that better handles common failure cases, e.g. disocclusions and fast motion, can provide competitive compression results with a greatly simplified model and training procedure. Specifically, we propose scale-space flow, an intuitive generalization of optical flow that adds a scale parameter to allow the network to better model uncertainty. Our experiments show that a low-latency video compression model (no B-frames) using scale-space flow for motion compensation can outperform analogous state-of-the art learned video compression models while being trained using a much simpler procedure and without any pre-trained optical flow networks.
Nano-Signature of Surface Charge Spatial Distribution of Metal Nanoparticles Irradiated Off-Resonance (2012)

International audience
An Examination of Dummy Head Kinematics Prior to Vehicle Rollover (2001)

&lt;div class="htmlview paragraph"&gt;This report presents two test methods and results of a study involving unrestrained dummies in dynamic rollover tests. Data are presented showing dummy head kinematics in relation to the interior of the vehicle as the vehicle experiences deceleration prior to the trip.&lt;/div&gt;
Revisiting Popularity and Demographic Biases in Recommender Evaluation and Effectiveness (2021)

Recommendation algorithms are susceptible to popularity bias: a tendency to recommend popular items even when they fail to meet user needs. A related issue is that the recommendation quality can vary by demographic groups. Marginalized groups or groups that are under-represented in the training data may receive less relevant recommendations from these algorithms compared to others. In a recent study, Ekstrand et al. investigate how recommender performance varies according to popularity and demographics, and find statistically significant differences in recommendation utility between binary genders on two datasets, and significant effects based on age on one dataset. Here we reproduce those results and extend them with additional analyses. We find statistically significant differences in recommender performance by both age and gender. We observe that recommendation utility steadily degrades for older users, and is lower for women than men. We also find that the utility is higher for users from countries with more representation in the dataset. In addition, we find that total usage and the popularity of consumed content are strong predictors of recommender performance and also vary significantly across demographic groups.
Cytokine-dependent granulocytic differentiation. Regulation of proliferative and differentiative responses in a murine progenitor cell line. (1987)

Human granulocyte colony stimulating factor (G-CSF) can support the survival and short term proliferation of the interleukin 3 (IL 3)-dependent diploid murine hemopoietic progenitor cell line 32D C13. After 8 days in the presence of 30 U/ml of G-CSF and in the absence of IL 3, the great majority of 32D C13 cells becomes positive for myeloperoxidase (a marker that appears at the promyelocytic stage of the granulocytic lineage) and progressively differentiates into lactoferrin-containing neutrophilic granulocytes. Myeloperoxidase mRNA rapidly increases after 24 to 48 hr of treatment with G-CSF, peaks at day 6 and is no longer detectable at day 9 and 12, paralleling the appearance of myeloperoxidase-positive promyelocytes and myelocytes in the culture. After 12 days, 100% of the cells terminally differentiate, and clonogenic assays in IL 3-containing semisolid media indicate that the whole population has irreversibly lost proliferative capability. By using varying concentrations of both murine IL 3 and recombinant human G-CSF, the cultures develop an heterogeneous population of cells representing all the differentiation stages of the myeloid lineage, and the relative ratios of immature proliferating precursors and terminally differentiated cells present in the cultures can be modulated by modifying the concentrations of IL 3 or recombinant human G-CSF. Isobolic curves indicate that IL 3 and G-CSF have an antagonistic effect on the proliferation of 32D C13 cells. Thus, these cells represent a simplified in vitro model of normal granulocytic differentiation whose extent may be modulated completely in the presence of serum by two well-defined growth and differentiation factors: IL 3 and G-CSF.
Predictors of continuous tobacco smoking in a clinical cohort study of Danish laryngeal cancer patients smoking before treated with radiotherapy (2015)

Younger patients, who had an early smoking initiation, a poor performance status, low income and lived alone, were most likely to continue smoking. Continuous smoking was not related to the extent of disease.