gebhart/patrepeval huggingface dataset:
Pixel-wise programmability enables dynamic high-SNR cameras for high-speed microscopy (2023)

High-speed wide-field fluorescence microscopy has the potential to capture biological processes with exceptional spatiotemporal resolution. However, conventional cameras suffer from low signal-to-noise ratio at high frame rates, limiting their ability to detect faint fluorescent events. Here, we introduce an image sensor where each pixel has individually programmable sampling speed and phase, so that pixels can be arranged to simultaneously sample at high speed with a high signal-to-noise ratio. In high-speed voltage imaging experiments, our image sensor significantly increases the output signal-to-noise ratio compared to a low-noise scientific CMOS camera (~2-3 folds). This signal-to-noise ratio gain enables the detection of weak neuronal action potentials and subthreshold activities missed by the standard scientific CMOS cameras. Our camera with flexible pixel exposure configurations offers versatile sampling strategies to improve signal quality in various experimental conditions.
Extreme Insulin Resistance in Ataxia Telangiectasia (1978)

The syndrome of ataxia telangiectasia is associated with glucose intolerance and insulin resistance. We examined the status of insulin receptors on circulating monocytes and on cultured fibroblasts from two siblings with ataxia telangiectasia and severe insulin resistance. 125I-insulin binding to monocytes of the two patients consistently demonstrated an 80 to 85 per cent decrease in receptor affinity. In contrast, the defect in receptor affinity was not expressed on the patients' cultured fibroblasts or on monocytes or fibroblasts obtained from unaffected family members. Whole plasma and immunoglobulin-enriched fractions of plasma from the patients inhibited the normal binding of insulin to its receptors on cultured human lymphocytes (IM -9 line) and on human placental membranes. We conclude that the insulin resistance in the two siblings with ataxia telangiectasia was associated with defects in the affinity of the receptors for insulin, probably caused by circulating inhibitors of insulin binding.
Evidence for different pyoverdine-mediated iron uptake systems among Pseudomonas aeruginosa strains (1989)

Fourteen strains of Pseudomonas aeruginosa (P. aeruginosa ATCC 15692, P. aeruginosa ATCC 27853, and 12 clinical isolates) were checked for the production of pyoverdine and for pyoverdine-mediated iron uptake. Under iron restriction, two isolates produced undetectable amounts of pyoverdine, but all the other strains produced a compound with physicochemical properties identical or close to those of the pyoverdine of P. aeruginosa ATCC 15692 (strain PAO1). The pyoverdines were purified and tested for their growth-promoting activity and for their ability to facilitate 59Fe uptake in homologous experiments involving each pyoverdine and its producing strain, as well as in heterologous systems involving all the other strains. The results of both types of experiments suggested the existence of three specificity groups. This was confirmed by analysis of the amino acid composition of the pyoverdines, which differed for each group. A partially purified polyclonal antiserum raised against a major 80-kilodalton (kDa) iron-regulated outer membrane protein (IROMP) of P. aeruginosa PAO1 recognized the 80-kDa IROMPs from P. aeruginosa PAO1 and the clinical isolates belonging to the same group, whereas the IROMPs from the strains belonging to the two other groups were not detected. A second antiserum raised against the P. aeruginosa ATCC 27853 80-kDa IROMP gave similar results by reacting specifically with the 80-kDa IROMP from the strains belonging to this group. Thus, together with the already known pyoverdine from P. aeruginosa PAO1, two new types of pyoverdines produced by strains belonging to this species were characterized.
A chikungunya virus–like particle vaccine induces broadly neutralizing and protective antibodies against alphaviruses in humans (2023)

Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes epidemics of acute and chronic musculoskeletal disease. Here, we analyzed the human B cell response to a CHIKV-like particle-adjuvanted vaccine (PXVX0317) from samples obtained from a phase 2 clinical trial in humans (NCT03483961). Immunization with PXVX0317 induced high levels of neutralizing antibody in serum against CHIKV and circulating antigen-specific B cells up to 6 months after immunization. Monoclonal antibodies (mAbs) generated from peripheral blood B cells of three PXVX0317-vaccinated individuals on day 57 after immunization potently neutralized CHIKV infection, and a subset of these inhibited multiple related arthritogenic alphaviruses. Epitope mapping and cryo-electron microscopy defined two broadly neutralizing mAbs that uniquely bind to the apex of the B domain of the E2 glycoprotein. These results demonstrate the inhibitory breadth and activity of the human B cell response induced by the PXVX0317 vaccine against CHIKV and potentially other related alphaviruses.
Hieroglyph: Hierarchical Glia Graph Skeletonization and Matching (2020)

Automatic 3D reconstruction of glia morphology is a powerful tool necessary for investigating the role of microglia in neurological disorders in the central nervous system. Current glia skeleton reconstruction techniques fail to capture an accurate tracing of the processes over time, useful for the study of the microglia motility and morphology in the brain during healthy and diseased states. We propose Hieroglyph, a fully automatic temporal 3D skeleton reconstruction algorithm for glia imaged via 3D multiphoton microscopy. Hieroglyph yielded a 21% performance increase compared to state of the art automatic skeleton reconstruction methods and outperforms the state of the art in different measures of consistency on datasets of 3D images of microglia. The results from this method provide a 3D graph and digital reconstruction of glia useful for a myriad of morphological analyses that could impact studies in brain immunology and disease.
Biomaterial and Biofilm Interactions with the Pulp-Dentin Complex-on-a-Chip (2021)

Calcium silicate cements (CSCs) are the choice materials for vital pulp therapy because of their bioactive properties, promotion of pulp repair, and dentin bridge formation. Despite the significant progress made in understanding CSCs' mechanisms of action, the key events that characterize the early interplay between CSC-dentin-pulp are still poorly understood. To address this gap, a microfluidic device, the "tooth-on-a-chip," which was developed to emulate the biomaterial-dentin-pulp interface, was used to test 1) the effect of CSCs (ProRoot, Biodentine, and TheraCal) on the viability and proliferation of human dental pulp stem cells, 2) variations of pH, and 3) release within the pulp chamber of transforming growth factor-β (TGFβ) as a surrogate of the bioactive dentin matrix molecules. ProRoot significantly increased the extraction of TGFβ (<i>P</i> < 0.05) within 24 to 72 h and, along with Biodentine, induced higher cell proliferation (<i>P</i> > 0.05), while TheraCal decreased cell viability and provoked atypical changes in cell morphology. No correlation between TGFβ levels and pH was observed. Further, we established a biofilm of <i>Streptococcus mutans</i> on-chip to model the biomaterial-biofilm-dentin interface and conducted a live and dead assay to test the antimicrobial capability of ProRoot in real time. In conclusion, the device allows for direct characterization of the interaction of bioactive dental materials with the dentin-pulp complex on a model of restored tooth while enabling assessment of antibiofilm properties at the interface in real time that was previously unattainable.
Delay Tolerant Networking - Bundle Protocol Simulation (2006)

In this paper, we report on the addition of MACHETE bundle protocol model needed to support DTN research. To illustrate the use of MACHETE with the additional BP model, we provide an example simulation and benchmark its performance. We demonstrate the use of the bundle protocol and discuss statistics gathered concerning the total time needed to simulate numerous bundle transmissions
Malignant Involvement of the Peripheral Nervous System in Patients with Cancer: Multimodality Imaging and Pathologic Correlation (2014)

The clinical and imaging evaluation of peripheral neuropathies in patients with cancer is challenging. It is critically important to differentiate malignant invasion of the peripheral nervous system from nonmalignant causes, such as radiation-induced neuritis, neuropathy associated with chemotherapy, and inflammatory neuropathies. Contrast material-enhanced magnetic resonance (MR) imaging is the initial noninvasive test of choice; however, interpretation can be challenging when the anatomic features are distorted by prior surgery, radiation, or both. Fluorine 18 ((18)F)-fluorodeoxyglucose (FDG) positron emission tomography (PET)/computed tomography (CT) is an imaging adjunct to MR imaging that is particularly helpful for evaluating peripheral nerves because the metabolic activity depicted with (18)F-FDG PET/CT helps differentiate malignant from benign disease and assists in making certain management decisions. For example, sites of high (18)F-FDG activity in a peripheral nerve can be targeted to increase the diagnostic yield of a biopsy because malignant involvement of peripheral nerves can be patchy. Of note, (18)F-FDG PET/CT can show clinically unsuspected metastases elsewhere in the body. If cancer is found, (18)F-FDG PET/CT allows excellent assessment of treatment response. (18)F-FDG PET/CT is also useful in evaluating primary nerve sheath tumors in that such tumors with low metabolic activity on FDG PET/CT images are unlikely to be malignant, although the specificity is limited. It is essential to have a good understanding of the imaging characteristics of benign and malignant causes of peripheral neuropathy if (18)F-FDG PET/CT is to be used effectively for accurate diagnosis.
Towards tracking a row of discrete targets with AUVs using Markov Decision Processes and probabilistic techniques (2008)

While complete searches of an area are the standard method currently used by the U.S. Navy for detecting and determining the extent of a field of discrete underwater targets of interest, there are situations where time constraints or mission objectives prohibit a complete search. Furthermore, in many situations it is unnecessary to detect all targets within a field of targets of interest, but is sufficient to determine the area over which the field extends. In this paper we present a novel search procedure for determining the extent of a line of targets within an area for use with AUVs. This method uses a Markov decision process coupled with belief propagation. Monte Carlo simulations indicate that this algorithm out-performs the standard search techniques for determining the endpoints of a line of targets when the metric is time.
Sequential transcriptional waves and NF-κB-driven chromatin remodeling direct drug-induced dedifferentiation in cancer (2019)

Abstract Drug-induced dedifferentiation towards a drug-tolerant persister state is a common mechanism cancer cells exploit to escape therapies, posing a significant obstacle to sustained therapeutic efficacy. The dynamic coordination of epigenomic and transcriptomic programs at the early-stage of drug exposure, which initiates and orchestrates these reversible dedifferentiation events, remains largely unexplored. Here we employ high-temporal-resolution multi-omics profiling, information-theoretic approaches, and dynamic system modeling to probe these processes in BRAF -mutant melanoma models and patient specimens. We uncover a hysteretic transition trajectory of melanoma cells in response to oncogene inhibition and subsequent release, driven by the sequential operation of two tightly coupled transcriptional waves, which orchestrate genome-scale chromatin state reconfiguration. Modeling of the transcriptional wave interactions predicts NF-κB/RelA-driven chromatin remodeling as the underlying mechanism of cell-state dedifferentiation, a finding we validate experimentally. Our results identify critical RelA-target genes that are epigenetically modulated to drive this process, establishing a quantitative epigenome gauge to measure cell-state plasticity in melanomas, which supports the potential use of drugs targeting epigenetic machineries to potentiate oncogene inhibition. Extending our investigation to other cancer models, we identify oxidative stress-mediated NF-κB/RelA activation as a common mechanism driving cellular transitions towards drug-tolerant persister states, revealing a novel and pivotal role for the NF-κB signaling axis in linking cellular oxidative stress to cancer progression.
Influence of chromium (III), cobalt (II) and their mixtures on cell metabolic activity (2021)

Abstract Chromium (III) and cobalt (II) are necessary elements required for the proper functioning of the organism, but their excess can cause toxic effects. They are the basic components of implants and are also commonly used in medicine as components of dietary supplements, vitamin and mineral products and energy drinks. The aim of this study was to investigate the effect of cobalt (II) and chromium (III) and their combination on BJ cells. In the study, BJ cells were exposed to CoCl 2 or CrCl 3 at concentrations ranging from 100 to 1400 µM, and the cytotoxicity of chromium (III) and cobalt (II) and their mixtures was assessed by MTT reduction, LDH release and NRU assays. The outcome of this work reveals the cytotoxic effects of chromium (III) and cobalt (II) and their mixtures on BJ cells. In the cytotoxicity assays, at low concentrations of CoCl 2 and CrCl 3 , stimulation of cell proliferation was observed. In higher concentrations, the cell viability decreased for the tested line in all the assays. During the simultaneous incubation of fibroblasts with 200 µM of CrCl 3 and 1000 µM of CoCl 2 , antagonism was observed: chromium (III) at the concentration of 200 µM induced protection from cobalt (II) toxicity; in the case of interaction of chromium chloride at 1000 µm and cobalt chloride at 200 µM, the protective effect of CrCl 3 on CoCl 2 was not observed. In the latter case, synergism between these elements was noted. Our work indicates that cobalt (II) and chromium (III) show cytotoxic properties. These metals have a destructive effect on the cell membrane, lysosomes and mitochondria, which leads to disorders of cell metabolism.
Hip decompression combined with bone marrow concentrate and platelet-rich plasma for corticosteroid-induced osteonecrosis of the femoral head (2021)

At seven years, hip decompression augmented with BMAC and PRP provided a 67% survivorship free from THA in patients with corticosteroid-induced ON. Ideal candidates for this procedure are patients with low preoperative Kerboul angles and can stop corticosteroid treatment prior to decompression. Cite this article: <i>Bone Jt Open</i> 2021;2(11):926-931.
Evaluation of Potential Optical Amplifier Concepts for Coherent Mode Multiplexing (2011)

Fiber capacity increase by coherent mode multiplexing requires inline optical amplification for cost and energy efficiency. Erbium doped and distributed Raman fiber amplifier concepts are evaluated concerning their suitability for this function with promising perspectives.
Heterojunction Transistors: Negative Transconductance Heterojunction Organic Transistors and their Application to Full‐Swing Ternary Circuits (Adv. Mater. 29/2019) (2019)

In article number 1808265, Jae-Joon Kim and co-workers introduce a new heterojunction transistor structure to implement a high-performance ternary inverter circuit. The proposed heterojunction transistor provides a novel switching behavior of p-type off, p-type subthreshold region, negative transconductance region, and p-type on, which leads to full-VDD-to-GND-swing ternary-circuit operation.
Guarding Machine Learning Hardware Against Physical Side-Channel Attacks (2021)

Machine learning (ML) models can be trade secrets due to their development cost. Hence, they need protection against malicious forms of reverse engineering (e.g., in IP piracy). With a growing shift of ML to the edge devices, in part for performance and in part for privacy benefits, the models have become susceptible to the so-called physical side-channel attacks. ML being a relatively new target compared to cryptography poses the problem of side-channel analysis in a context that lacks published literature. The gap between the burgeoning edge-based ML devices and the research on adequate defenses to provide side-channel security for them thus motivates our study. Our work develops and combines different flavors of side-channel defenses for ML models in the hardware blocks. We propose and optimize the first defense based on Boolean masking. We first implement all the masked hardware blocks. We then present an adder optimization to reduce the area and latency overheads. Finally, we couple it with a shuffle-based defense. We quantify that the area-delay overhead of masking ranges from 5.4$\times$ to 4.7$\times$ depending on the adder topology used and demonstrate first-order side-channel security of millions of power traces. Additionally, the shuffle countermeasure impedes a straightforward second-order attack on our first-order masked implementation.
ChemInform Abstract: A Unified Total Synthesis of the Immunomodulators (‐)‐Rapamycin and (‐) ‐27‐Demethoxyrapamycin: Assembly of the Common C(1‐20) Perimeter and Final Elaboration. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Inferring when Puf4 acquired RNA targets related to Saccharomycotina Puf3 targets. (2015)

&lt;p&gt;Prevalence of putative Puf3 and Puf4 binding sites in the orthologs of Saccharomycotina Puf3 targets in early diverging Pezizomycotina species. A putative binding site is inferred based on the presence of sequences matching the Puf3 or the Pezizomycotina Puf4 motif. Listed under motif results is the percentage of RNAs with a binding site sequence in the 3' UTR. The odds-ratio represents the enrichment of orthologs of Saccharomycotina Puf3 target RNAs containing a binding site sequence compared to the prevalence in all other RNAs. The &lt;i&gt;p&lt;/i&gt;-value was computed using Fisher's exact test and was Bonferroni corrected. A colored oval in the "Inferred Binding By" column indicates significant enrichment of Puf3 or Puf4 sites in each species. The light green oval for Puf4 indicates borderline significance. The cladogram on the left represents a parsimonious model with color along a branch indicating the binding of Puf3 (gold) or Puf4 (green) to the orthologs of Saccharomycotina Puf3 targets (see &lt;a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002307#pbio.1002307.s031" target="_blank"&gt;S21 Fig&lt;/a&gt; for an alternative model). A colored oval within the cladogram denotes a gain in binding, and a red X over an oval denotes a loss of binding. Literature results were used to derive the relationships of species within Orbiliomycetes [&lt;a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002307#pbio.1002307.ref086" target="_blank"&gt;86&lt;/a&gt;,&lt;a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002307#pbio.1002307.ref087" target="_blank"&gt;87&lt;/a&gt;] and Pezizomycetes [&lt;a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002307#pbio.1002307.ref088" target="_blank"&gt;88&lt;/a&gt;–&lt;a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002307#pbio.1002307.ref091" target="_blank"&gt;91&lt;/a&gt;].&lt;/p&gt;
A FACILE SYNTHESIS OF THE PRODRUG 2,5-BIS(4-0-METHOXYAMIDINOPHENYL)FURAN AND ANALOGS (2003)

A convenient synthesis of the prodrug 2,5-bis(4-o-methoxyamidinophenyl)furan and analogs using 2,5-bis(tri-/i-butylstannyl)furan and palladium catalyzed cross-coupling reactions is described.
Reliability of Timber Fender Systems in Waterfront Facilities (2001)

Due to the deterioration of existing timber fender systems in waterfront facilities, high performance, composite replacement components for these structures are in demand. The performance criteria for these replacement components must meet or exceed the performance of existing timber systems. For this reason, a reliability analysis of existing timber fender systems has been performed to establish (1) the level of performance in existing timber fender systems; and (2) target performance levels for new composite replacement components. The design of waterfront fender systems is based on energy considerations. The most widely used and accepted method for determining the applied energy created by the docking ship is the kinetic energy method. Based on the applied kinetic energy of the docking ship and the response of the timber elements, a load model was developed to investigate the effect of several parameters on the system reliability. Investigations were conducted to determine the effect of variability and correlation among material properties on structural reliability. Results showed that as variability decreases and correlation increases, reliability increases. The effect of load-duration assumptions on the structural reliability was also investigated to illustrate the differences in existing fender system design criteria and current timber design standards. The results of the analysis on the timber systems are being used to set a standard for wood-plastic composite elements that will be used as replacement components in these systems.
Real-time augmented face (2004)

This real-time augmented reality demonstration relies on our tracking algorithm described in V. Lepetit et al (2003). This algorithm considers natural feature points, and then does not require engineering of the environment. It merges the information from preceding frames in traditional recursive tracking fashion with that provided by a very limited number of reference frames. This combination results in a system that does not suffer from jitter and drift, and can deal with drastic changes. The tracker recovers the full 3D pose of the tracked object, allowing insertion of 3D virtual objects for augmented reality applications.
Coupled deformation and mass-transport processes in solid polymers (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCoupled deformation and mass-transport processes in solid polymersRuben G. Carbonell and Giulio C. SartiCite this: Ind. Eng. Chem. Res. 1990, 29, 7, 1194–1204Publication Date (Print):July 1, 1990Publication History Published online1 May 2002Published inissue 1 July 1990https://doi.org/10.1021/ie00103a018Request reuse permissionsArticle Views221Altmetric-Citations49LEARN 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 (1 MB) Get e-Alertsclose Get e-Alerts