gebhart/patrepeval huggingface dataset:
Interpreting biological variation: seeds, populations and sensitivity thresholds (2018)

Abstract Seeds offer a unique perspective from which to view biology. An individual seed is an autonomous biological entity that must rely on its own resources (and resourcefulness) to persist after dispersal and to time its transition to germination and seedling growth to coincide with environmental opportunities for survival. At the same time, seed biology in agriculture and ecology is determined largely by the behaviours of populations of individual seeds. The percentage of seeds in a population that is in a particular state (e.g. dormant, germinated, dead) at a given time is a fundamental metric of seed biology. This duality of individual diversity underlying consistent population-wide behaviour patterns can be described quantitatively using population-based threshold (PBT) models. While conceptually simple, these models are highly flexible and can describe the wide diversity of responses of seed populations to temperature, water potential, hormones, oxygen, light, ageing and combinations of these factors. This seed behaviour is linked to respiratory rates of individual seeds, indicating that basic metabolic processes within seeds vary among individuals in accordance with PBT principles. Looking more broadly across microbial, plant and animal biology, examples of cellular diversity in hormonal sensitivity, gene expression, developmental responses and signalling abound. This variation often is termed ‘noise’, and analysis efforts are focused on extracting mean signals from this variation to understand regulatory pathways. However, extension of the PBT approach to the cellular and molecular levels suggests that population sensitivity distributions and recruitment phenomena may underlie many fundamental biological processes. Thus, concepts and quantitative approaches developed for the analysis of seed populations can be applied across biological scales from molecules to ecosystems to interpret inherent biological variation and provide mechanistic insights into the nature of biological regulatory systems.
Microwave Properties of Ba 2 Ti 9 O 20 Doped with Zirconium and Tin Oxides (1999)

The effects of solid‐solution additives, their concentration, and the thermal processing schedule on the microstructure evolution and microwave properties of Ba 2 Ti 9 O 20 were studied. The solubility of tin in Ba 2 Ti 9 O 20 was higher than that of zirconium. Both elements facilitated the formation of phase‐pure Ba 2 Ti 9 O 20 resonators. Ba 2 Ti 9 O 20 formed most easily with low dopant concentrations (0.82 mol%) (most impressively for ZrO 2 substitutions). Extended heat treatment (16 h versus 6 h at a temperature of 1390°C) resulted in volatilization of the grain‐boundary liquid phase, which leads to more‐porous resonators that have correspondingly lower permittivities. Increasing the dopant concentration resulted in minor increases in the quality factor; doping with zirconium led to slightly higher values (a maximum of 13900 at a frequency of 3 GHz). Increasing the measurement temperature degraded the quality factor (most precipitously for BaTi 4 O 9 ). The temperature coefficient decreased as the ZrO 2 substitution increased but was largely unaffected by the SnO 2 concentration. Excess TiO 2 in a batch with no other dopants demonstrated degraded microwave properties.
Supplementary Table 3 from A687V EZH2 Is a Driver of Histone H3 Lysine 27 (H3K27) Hypertrimethylation (2023)

&lt;p&gt;Supplementary Table 3: Functional analysis of genes significantly up- and down-regulated in SUP-B8 and NALM-6 cells.&lt;/p&gt;
Retransmission-Based Distributed Video Streaming with a Channel-Adaptive Packet Scheduler (2010)

This paper describes a channel-adaptive packet scheduler for improved error control performance in a peer-cooperative distributed media streaming system. The proposed packet-scheduling algorithm was designed for the case in which streaming server peers rely on an error-recovery strategy using retransmission and application-layer automatic repeat request rather than error protection using forward error correction. The proposed scheduler can maximize retransmission opportunities and reduce the frame loss rate by using the observed channel status from each server peer. Simulation results show that the proposed algorithm enhances error-recovery performance in distributed multimedia streaming better than other schedulers.
Weight Gain Associated With Increased Food Intake and Low Habitual Activity Levels in Male Adolescent Schizophrenic Inpatients Treated With Olanzapine (2002)

Olanzapine-induced weight gain is associated with a general increase in caloric intake.
MPEG-4: Next-Generation Standard for Interactive Media (2002)

The graphics and content creation community will get insight into the opportunities offered by MPEG-4 as an attractive target format for the creation and delivery of rich and interactive media. The media is meant to be delivered to users via a wide range of networks and channels. This includes the Internet, and also broadcast or wireless channels. The list of target reciver devices goes from set-top boxes down to PDAs. MPEG-4 employs and object oriented approach, addressing the seamless and transparent combination of locally stored and remotley accessed media objects into one presentation. This approach is the central point of MPEG-4 and the global convergence theme, where technical aspects of telecommunications, computer and entertainment are merged into a unifying content delivery framework. The course provides general information about the MPEG-4 standard, the technology included and supported as well as examples of applications. Further, since MPEG-4 provides a standardized framework for the transport of interactive content that includes computer graphics techniques next to video and audio, the course provides information and demonstrations of this framework in action. This course provides information and demonstrations about MPEG-4 new media standard, the technology included and supported. It will be emphasized how interactive media evolved under this standard as well as how computer graphics aspects have become part of an international standard that is traditionally associated with video and audio only. This session will be heavily grounded in demonstrations and case studies.
A new minimal solution to the relative pose of a calibrated stereo camera with small field of view overlap (2009)

In this paper we present a new minimal solver for the relative pose of a calibrated stereo camera (i.e. a pair of rigidly mounted cameras). Our method is based on the fact that a feature visible in all four images (two image pairs acquired at two points in time) constrains the relative pose of the second stereo camera to lie on a sphere around this feature, which has a known, triangulated position in the first stereo camera coordinate frame. This constraint leaves three degrees of freedom; two for the location of the second camera on the sphere, and the third for the rotation in the respective tangent plane. We use three 2D correspondences, in particular two correspondences from the left (or right) camera and one correspondence from the other camera, to solve for these three remaining degrees of freedom. This approach is amenable to stereo cameras having a small overlap in their views. We present an efficient solution for this novel relative pose problem, describe the incorporation of our proposed solver into the RANSAC framework, evaluate its performance given noise and outliers, and demonstrate its use in a real-time structure from motion system.
Complete catalytic oxidation of volatile organics (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComplete catalytic oxidation of volatile organicsJames J. SpiveyCite this: Ind. Eng. Chem. Res. 1987, 26, 11, 2165–2180Publication Date (Print):November 1, 1987Publication History Published online1 May 2002Published inissue 1 November 1987https://doi.org/10.1021/ie00071a001RIGHTS & PERMISSIONSArticle Views3903Altmetric-Citations741LEARN 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 InReddit PDF (3 MB) Get e-Alerts Get e-Alerts
Recent developments in x-ray Talbot interferometry at ESRF-ID19 (2010)

In this paper we describe the design of different X-ray Talbot interferometers that have been built at the tomography beamline ID19 of the European Synchrotron Radiation Facility (ESRF) in Grenoble, France, and give a short review of performance characteristics, of current developments, and of the results obtained with these instruments so far. Among the applications so far, soft-tissue imaging has been a particular focus, as demonstrated in a recent paper by Schulz et al. <i>(J. Roy. Soc. Interface</i>, in press).
GLP-1R Agonism Enhances Adjustable Gastric Banding in Diet-Induced Obese Rats (2013)

Bariatric procedures vary in efficacy, but overall are more effective than behavioral and pharmaceutical treatment. Roux-en-Y gastric bypass causes increased secretion of glucagon-like peptide 1 (GLP-1) and reduces body weight (BW) more than adjustable gastric banding (AGB), which does not trigger increased GLP-1 secretion. Since GLP-1-based drugs consistently reduce BW, we hypothesized that GLP-1 receptor (GLP-1R) agonists would augment the effects of AGB. Male Long-Evans rats with diet-induced obesity received AGB implantation or sham surgery. GLP-1R agonism, cannabinoid receptor-1 (CB1-R) antagonism, or vehicle was combined with inflation to evaluate interaction between AGB and pharmacological treatments. GLP1-R agonism reduced BW in both sham and AGB rats (left uninflated) compared with vehicle-treated animals. Subsequent band inflation was ineffective in vehicle-treated rats but enhanced weight loss stimulated by GLP1-R agonism. In contrast, there was no additional BW loss when CB1-R antagonism was given with AGB. We found band inflation to trigger neural activation in areas of the nucleus of the solitary tract known to be targeted by GLP-1R agonism, offering a potential mechanism for the interaction. These data show that GLP-1R agonism, but not CB1-R antagonism, improves weight loss achieved by AGB and suggest an opportunity to optimize bariatric surgery with adjunctive pharmacotherapy.
Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes (2018)

SUMMARY Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin and drivers of ITH across cancer types are poorly understood. To address this question, we extensively characterize ITH across whole-genome sequences of 2,658 cancer samples, spanning 38 cancer types. Nearly all informative samples (95.1%) contain evidence of distinct subclonal expansions, with frequent branching relationships between subclones. We observe positive selection of subclonal driver mutations across most cancer types, and identify cancer type specific subclonal patterns of driver gene mutations, fusions, structural variants and copy-number alterations, as well as dynamic changes in mutational processes between subclonal expansions. Our results underline the importance of ITH and its drivers in tumor evolution, and provide an unprecedented pan-cancer resource of comprehensively annotated subclonal events from whole-genome sequencing data.
Follow-up of Bronchial Precancerous Lesions and Carcinoma in Situ Using Fluorescence Endoscopy (2001)

Little is known about the natural history of precancerous bronchial lesions. Histological changes occurring in 416 bronchial intraepithelial lesions (104 high-risk subjects) were assessed over a 2-yr period, using repeated follow-up autofluorescence endoscopies. During the study, 6 of 36 normal epitheliums became dysplastic; 47 of 152 metaplasia evolved to low-grade dysplasia, two progressed to carcinoma in situ, and one to invasive cancer; 6 of 169 low-grade epithelial lesions progressed to a persistent severe dysplasia; 10 of 27 severe dysplastic lesions and 28 of 32 carcinoma in situ persisted or progressed, respectively (p = 0.0005, severe dysplasia versus carcinoma in situ 24 mo outcome). Carcinoma in situ appeared more frequent in patients with a prior history or concomitant cancer (p = 0.003). Persistence of smoking during the study did not influence high-grade lesion outcome. Progression of low-grade epithelial lesions during the study occurred only in patients with at least a high-grade lesion in another site at baseline (9 of 147 lesions, 6.1%). Our study suggests that low-grade epithelial lesions could be safely followed-up at 2 yr in patients without high-grade lesions at baseline, whereas severe dysplasia should be treated if they persist at 3 mo. Immediate treatment of carcinoma in situ appears warranted.
51.1: A DC‐DC Converter Circuit Integrated into a Poly‐Si TFT LCD Containing a 6‐bit DAC (2003)

Abstract A DC‐DC converter composed of charge pumps and regulators has been integrated into a poly‐Si TFT LCD that also contains a 6‐bit DAC. It has the ability to supply regulated voltages to the 6‐bit DAC and to the LCD's gate driver circuit.
Beyond expert-only parallel programming? (2012)

My parallel-programming education began in earnest when I joined Sequent Computer Systems in late 1990. This education was both brief and effective: within a few short years, my co-workers and I were breaking new ground [MG92, MS93, MS98].1 Nor was I alone: Sequent habitually hired new-to-parallelism engineers and had them producing competent parallel code within a few months. Nevertheless, more than two decades later, parallel programming is perceived to be difficult to teach and learn. Is parallel programming an exception to the typical transitioning of technnology from impossible to expert-only to routine to unworthy of conscious thought?
Fundus autofluorescence related to retinal morphological and functional changes in idiopathic macular holes (2008)

Fundus autofluorescence imaging reflects anatomic changes and represents the dysfunctional retinal area in IMH. The technique provides 2-D images with 3-D information on the retinal morphology of this disease.
p120 Is a Major Substrate of Tyrosine Phosphorylation upon B Cell Antigen Receptor Stimulation and Interacts in Vivo with Fyn and Syk Tyrosine Kinases, Grb2 and Shc Adaptors, and the p85 Subunit of Phosphatidylinositol 3-Kinase (1996)

We and others have demonstrated that the c-cbl proto-oncogene product is one of the earliest targets of tyrosine phosphorylation upon T cell receptor stimulation. Given the similarities in the B and T lymphocyte antigen receptors, and the induction of pre-B leukemias in mice by the v-cbl oncogene, we examined the potential involvement of Cbl in B cell receptor signaling. We demonstrate prominent and early tyrosine phosphorylation of Cbl upon stimulation of human B cell lines through surface IgM. Cbl was associated in vivo with Fyn and, to a lesser extent, other Src family kinases. B cell activation also induced a prominent association of Cbl with Syk tyrosine kinase. A substantial fraction of Cbl was constitutively associated with Grb2 and this interaction was mediated by Grb2 SH3 domains. Tyrosine-phosphorylated Shc, which prominently associated with Grb2, was detected in association with Cbl in activated B cells. Thus, Grb2 and Shc adaptors, which associate with immunoreceptor tyrosine based activation motifs, may link Cbl to the B cell receptor. B cell activation also induced a prominent association between Cbl and the p85 subunit of phosphatidylinositol (PI) 3-kinase resulting in the association of a substantial fraction of PI 3-kinase activity with Cbl. Thus, Cbl is likely to play an important role to couple the B cell receptor to the PI 3-kinase pathway. Our results strongly suggest a role for p120cbl in signaling downstream of the B cell receptor and support the idea that Cbl participates in a general signal transduction function downstream of the immune cell surface receptors.
N-Heterocyclic carbene catalyzed regioselective oxo-acyloxylation of alkenes with aromatic aldehydes: a high yield synthesis of α-acyloxy ketones and esters (2013)

An N-heterocyclic carbene (NHC)-catalyzed reaction of alkenes with aromatic aldehydes providing for a high yield synthesis of α-acyloxy ketones and esters has been described. This unprecedented regioselective oxidative process employs NBS and Et3N in stoichiometric amounts and O2 (1 atm) as an oxidant under ambient conditions in DMSO as a solvent.
Reverse engineering biological networks :applications in immune responses to bio-toxins. (2005)

Our aim is to determine the network of events, or the regulatory network, that defines an immune response to a bio-toxin. As a model system, we are studying T cell regulatory network triggered through tyrosine kinase receptor activation using a combination of pathway stimulation and time-series microarray experiments. Our approach is composed of five steps (1) microarray experiments and data error analysis, (2) data clustering, (3) data smoothing and discretization, (4) network reverse engineering, and (5) network dynamics analysis and fingerprint identification. The technological outcome of this study is a suite of experimental protocols and computational tools that reverse engineer regulatory networks provided gene expression data. The practical biological outcome of this work is an immune response fingerprint in terms of gene expression levels. Inferring regulatory networks from microarray data is a new field of investigation that is no more than five years old. To the best of our knowledge, this work is the first attempt that integrates experiments, error analyses, data clustering, inference, and network analysis to solve a practical problem. Our systematic approach of counting, enumeration, and sampling networks matching experimental data is new to the field of network reverse engineering. The resulting mathematical analyses and computational tools lead to new results on their own and should be useful to others who analyze and infer networks.
Anti-CD20 therapy depletes activated myelin-specific CD8+T cells in multiple sclerosis (2019)

CD8<sup>+</sup> T cells are believed to play an important role in multiple sclerosis (MS), yet their role in MS pathogenesis remains poorly defined. Although myelin proteins are considered potential autoantigenic targets, prior studies of myelin-reactive CD8<sup>+</sup> T cells in MS have relied on in vitro stimulation, thereby limiting accurate measurement of their ex vivo precursor frequencies and phenotypes. Peptide:MHC I tetramers were used to identify and validate 5 myelin CD8<sup>+</sup> T cell epitopes, including 2 newly described determinants in humans. The validated tetramers were used to measure the ex vivo precursor frequencies and phenotypes of myelin-specific CD8<sup>+</sup> T cells in the peripheral blood of untreated MS patients and HLA allele-matched healthy controls. In parallel, CD8<sup>+</sup> T cell responses against immunodominant influenza epitopes were also measured. There were no differences in ex vivo frequencies of tetramer-positive myelin-specific CD8<sup>+</sup> T cells between MS patients and control subjects. An increased proportion of myelin-specific CD8<sup>+</sup> T cells in MS patients exhibited a memory phenotype and expressed CD20 compared to control subjects, while there were no phenotypic differences observed among influenza-specific CD8<sup>+</sup> T cells. Longitudinal assessments were also measured in a subset of MS patients subsequently treated with anti-CD20 monoclonal antibody therapy. The proportion of memory and CD20<sup>+</sup> CD8<sup>+</sup> T cells specific for certain myelin but not influenza epitopes was significantly reduced following anti-CD20 treatment. This study, representing a characterization of unmanipulated myelin-reactive CD8<sup>+</sup> T cells in MS, indicates these cells may be attractive targets in MS therapy.
Detecting total hip replacement prosthesis design on plain radiographs using deep convolutional neural network (2020)

Identifying the design of a failed implant is a key step in the preoperative planning of revision total joint arthroplasty. Manual identification of the implant design from radiographic images is time-consuming and prone to error. Failure to identify the implant design preoperatively can lead to increased operating room time, more complex surgery, increased blood loss, increased bone loss, increased recovery time, and overall increased healthcare costs. In this study, we present a novel, fully automatic and interpretable approach to identify the design of total hip replacement (THR) implants from plain radiographs using deep convolutional neural network (CNN). CNN achieved 100% accuracy in the identification of three commonly used THR implant designs. Such CNN can be used to automatically identify the design of a failed THR implant preoperatively in just a few seconds, saving time and improving the identification accuracy. This can potentially improve patient outcomes, free practitioners' time, and reduce healthcare costs.
Molecular Signaling Design Exploiting Cyclostationary Drift-Diffusion Fluid (2017)

This paper investigates a method to improve performance of diffusive molecular communications between biologically-enabled nanomachines in in-vivo aqueous environment. The proposed method exploits periodic flow, e.g., induced by repeated heart pumping. We make an analysis of channel impulse response (CIR) for such drift- diffusion fluid systems. In order to take the cyclic CIR into account, the proposed method optimizes the release timing and size of information molecules so that highest equalization gain can be achieved. We reveal that error rate performance can be significantly improved with adaptive molecule loading by taking care of the cyclic CIR.
Cochlear partition tuning within the 2nd apical turn of the intact gerbil cochlea (2018)

Our understanding of cochlear amplification has been mainly informed by observations of the high-frequency basal region. Results from the few existing in vivo studies from the low-frequency apical region have suggested that cochlear amplification may be more broadly tuned and not as nonlinear as in the base. The current study explored micromechanics via sound evoked vibrations of the cochlear partition, including the organ of Corti (OoC), the basilar membrane (BM) and the tectorial membrane (TM), within the 2nd apical turn, corresponding to the 2.5 kHz best frequency region, of the gerbil cochlea using volumetric optical coherence tomography vibrometry (VOCTV), imaged non-invasively through the otic capsule bone in vivo. Sound induced radial displacements below 4 kHz showed similarities and differences to the well-established BM transverse responses at high-frequency basal region. Responses showed broader tuning, but similar gains at the best frequency and similar phase accumulation. The distinct difference found was the presence of compressive nonlinear growth with SPL below the best frequency down to 0.1 kHz observed at the outer hair cell (OHC) and reticular laminar (RL) locations but not in the BM or inner hair cell regions. These relative motions provide further insight on how OHC somatic forces are distributed within the cochlear partition.