gebhart/patrepeval huggingface dataset:
Silicon µPCR Chip for Forensic STR Profiling with Hybeacon Probe Melting Curves (2019)

Abstract The demand to perform forensic DNA profiling outside of centralized laboratories and on the crime scene is increasing. Several criminal investigations would benefit tremendously from having DNA based information available in the first hours rather than days or weeks. However, due to the complexity and time-consuming nature of standard DNA fingerprinting methods, rapid and automated analyses are hard to achieve. We here demonstrate the implementation of an alternative DNA fingerprinting method in a single microchip. By combining PCR amplification and HyBeacon melting assays in a silicon Lab-on-a-chip (LoC), a significant step towards rapid on-site DNA fingerprinting is taken. The small form factor of a LoC reduces reagent consumption and increases portability. Additional miniaturization is achieved through an integrated heating element covering 24 parallel micro-reactors with a reaction volume of 0.14 µl each. The high level of parallelization allows the simultaneous analysis of 4 short tandem repeat (STR) loci and the amelogenin gender marker commonly included in forensic DNA analysis. A reference and crime scene sample can be analyzed simultaneously for direct comparison. Importantly, by using industry-standard semiconductor manufacturing processes, mass manufacturability can be guaranteed. Following assay design and optimization, complete 5-loci profiles could be robustly generated on-chip that are on par with those obtained using conventional benchtop real-time PCR thermal cyclers. Together, our results are an important step towards the development of commercial, mass-produced, portable devices for on-site testing in forensic DNA analysis.
Effect of ruthenium red on the bronchoconstriction induced by capsaicin and by selective tachykinin receptor agonists in anaesthetized guinea‐pig (1992)

1. The effect of systemic administration of ruthenium red on bronchospasm induced by acetylcholine, capsaicin or selective tachykinin receptor agonists ([Sar9]SP sulfone or [beta Ala8]-neurokinin A (NKA)-(4-10) for NK-1 and NK-2 receptors, respectively) was studied in anaesthetized guinea-pigs. 2. The bronchospasm induced by capsaicin was reduced by ruthenium red, which did not affect the response induced by acetylcholine. Atropine, which totally blocked the response to acetylcholine, also partially blocked the bronchospasm induced by capsaicin. 3. The inhibitory action of atropine and ruthenium red on the bronchospasm produced by capsaicin was additive, independently from the order of administration of the two antagonists. 4. Ruthenium red induced an increase in [Sar9]SP sulfone-bronchospasm and a marked enhancement of the bronchomotor response to [beta Ala8]NKA-(4-10). This latter was antagonized by the prior administration of the selective NK-2 receptor antagonist MEN 10,376. 5. Pretreatment with guanethidine or propranolol increased the airway constriction induced by [beta Ala8]NKA-(4-10). Furthermore, pretreatment with guanethidine prevented the enhancement induced by ruthenium red, showing that activation of NK-2 receptors influences the sympathetic bronchodilator drive to the airways. 6. It is concluded that ruthenium red antagonizes selectively the in vivo excitatory effect of capsaicin in guinea-pig airways. Furthermore, the additivity of the blocking action of ruthenium red and atropine indicates that two distinct mechanisms take place in bronchospastic response to i.v. capsaicin in this species.
Dominant edge direction based fast intra mode decision in the H.264/AVC encoder (2009)

The H.264/AVC video coding standard uses an intra prediction mode with 4×4 and 16×16 blocks for luma and 8×8 blocks for chroma. This standard uses the rate distortion optimization (RDO) method to determine the best coding mode based on the compression performance and video quality. This method offers a large improvement in coding efficiency compared to other compression standards, but the computational complexity is greater due to the various intra prediction modes. This paper proposes a fast intra mode decision algorithm for real-time encoding of H.264/AVC based on the dominant edge direction (DED). The DED is extracted using pixel value summation and subtraction in the horizontal and vertical directions. By using the DED, three modes instead of nine are chosen for RDO calculation to decide on the best mode in the 4×4 luma block. For the 16×16 luma and the 8×8 chroma, only two modes are chosen instead of four. Experimental results show that the entire encoding time saving of the proposed algorithm is about 67% compared to the full intra search method with negligible loss of quality.
Robust optimization of the laser induced damage threshold of dielectric mirrors for high power lasers (2018)

We report on a numerical optimization of the laser induced damage threshold of multi-dielectric high reflection mirrors in the sub-picosecond regime. We highlight the interplay between the electric field distribution, refractive index and intrinsic laser induced damage threshold of the materials on the overall laser induced damage threshold (LIDT) of the multilayer. We describe an optimization method of the multilayer that minimizes the field enhancement in high refractive index materials while preserving a near perfect reflectivity. This method yields a significant improvement of the damage resistance since a maximum increase of 40% can be achieved on the overall LIDT of the multilayer.
Correlates of the country differences in the infection and mortality rates during the first wave of the COVID-19 pandemic: Evidence from Bayesian model averaging (2020)

In the initial wave of the COVID-19 pandemic we observed great discrepancies in both infection and mortality rates between countries. Besides the biological and epidemiological factors, a multitude of social and economic criteria also influence the extent to which these discrepancies appear. Consequently, there is an active debate regarding the critical socio-economic and health factors that correlate with the infection and mortality rates outcome of the pandemic. Here, we leverage Bayesian model averaging techniques and country level data to investigate the potential of 28 variables, describing a diverse set of health and socio-economic characteristics, in being correlates of the final number of infections and deaths during the first wave of the coronavirus pandemic. We show that only few variables are able to robustly correlate with these outcomes. To understand the relationship between the potential correlates in explaining the infection and death rates, we create a Jointness Space. Using this space, we conclude that the extent to which each variable is able to provide a credible explanation for the COVID-19 infections/mortality outcome varies between countries because of their heterogeneous features.
Multi-to-Single Knowledge Distillation for Point Cloud Semantic Segmentation (2023)

3D point cloud semantic segmentation is one of the fundamental tasks for environmental understanding. Although significant progress has been made in recent years, the performance of classes with few examples or few points is still far from satisfactory. In this paper, we propose a novel multi-to-single knowledge distillation framework for the 3D point cloud semantic segmentation task to boost the performance of those hard classes. Instead of fusing all the points of multi-scans directly, only the instances that belong to the previously defined hard classes are fused. To effectively and sufficiently distill valuable knowledge from multi-scans, we leverage a multilevel distillation framework, i.e., feature representation distillation, logit distillation, and affinity distillation. We further develop a novel instance-aware affinity distillation algorithm for capturing high-level structural knowledge to enhance the distillation efficacy for hard classes. Finally, we conduct experiments on the SemanticKITTI dataset, and the results on both the validation and test sets demonstrate that our method yields substantial improvements compared with the baseline method. The code is available at https://github.com/skyshoumeng/M2SKD.
Biological Markers and Alzheimer Disease: A Canadian Perspective (2010)

Decreased beta-amyloid(1-42) and increased phospho-tau protein levels in the cerebrospinal fluid (CSF) are currently the most accurate chemical neurodiagnostics of sporadic Alzheimer disease (AD). A report (2007) of the Third Canadian Consensus Conference on the Diagnosis and Treatment of Dementia (2006) recommended that biological markers should not be currently requisitioned by primary care physicians in the routine investigation of subjects with memory complaints. Consideration for such testing should prompt patient referral to a specialist engaged in dementia evaluations or a Memory Clinic. The specialist should consider having CSF biomarkers (beta-amyloid(1-42) and phospho-tau) measured at a reputable facility in restricted cases presenting with atypical features and diagnostic confusion, but not as a routine procedure in all individuals with typical sporadic AD phenotypes. We submit that developments in the field of AD biomarker discovery since publication of the 3rd CCCDTD consensus data do not warrant revision of the 2007 recommendations.
Resilience Analysis of Distributed Wireless Spiking Neural Networks (2021)

&amp;lt;p&amp;gt;Spiking neural networks (SNN) are expected to enable several use-cases in future communication networks (beyond 5G and 6G), as edge AI and battery-constrained systems can leverage the fast computation and high-power efficiency offered by SNNs. In this work we consider a Distributed Wireless SNN (DW-SNN) system and we analyze its performance in terms of inference accuracy and total neural activity when radio losses are applied to spikes transferred during the inference phase. Our aim is to understand how radio losses impact performance when considering different SNN spike communication types, i.e., input, excitatory, and inhibitory spikes. Then we evaluate the impact of different traffic prioritization approaches among SNN spikes when considering a shared channel capacity being available for SNN activity. From these analyses, we derive some key insights and features that can be considered when applying a DW-SNN and handling it&amp;rsquo;s traffic over wireless communication systems. Finally, we report a prototype implementation of DW-SNN using custom-built IoT components, which we use to further investigate different coverage scenarios.&amp;lt;/p&amp;gt;
Reduction Sensitive Lipid Conjugates of Tenofovir: Synthesis, Stability, and Antiviral Activity (2016)

The therapeutic value of numerous small molecules hinges on their ability to permeate the plasma membrane. This is particularly true for tenofovir (TFV), adefovir, and other antiviral nucleosides that demonstrate potent antiviral activity but poor bioavailability. Using TFV as a model substrate, we hybridized two disparate prodrug strategies to afford novel reduction-sensitive lipid conjugates of TFV that exhibit subnanomolar activity toward HIV-1 and are stable in human plasma for more than 24 h with a therapeutic index approaching 30000. These compounds significantly rival the clinically approved formulation of TFV and revitalize the potential of disulfide-bearing prodrugs which have seen limited in vitro and in vivo success since their debut over 20 years ago. We further demonstrate the utility of these conjugates as a tool to indirectly probe the enzymatic hydrolysis of phosphonomonoesters that may further advance the development of other prodrug strategies for nucleosides, peptides, and beyond.
A design for small time-delay control circuit for DPWM- POL (2010)

Digital-controlled switching mode power supplies (SMPS) are popular in the fields of relatively large power supply system. The digital controller is consisted of DSPs or microprocessors performing with software. By contrast, such as on-board SMPSs, adapting digital controller isn't still popular because of its cost or response characteristics even if the controllers are constructed by FPGA or custom LSI which is hardware-logic base. This paper will discuss about the proposed hardware logic type digital controller for on-board SMPS, which is very simple and unique design. And, accuracy improved output voltage detection method for the proposed digital controller is proposed. The some experiments are done. And the results show the validity of the proposed circuits.
Off-Target Networks Derived from Ligand Set Similarity (2009)

Chemically similar drugs often bind biologically diverse protein targets, and proteins with similar sequences or structures do not always recognize the same ligands. How can we uncover the pharmacological relationships among proteins, when drugs may bind them in defiance of bioinformatic criteria? Here we consider a technique that quantitatively relates proteins based on the chemical similarity of their ligands. Starting with tens of thousands of ligands organized into sets for hundreds of drug targets, we calculated the similarity among sets using ligand topology. We developed a statistical model to rank the resulting scores, which were then expressed in minimum spanning trees. We have shown that biologically sensible groups of targets emerged from these maps, as well as experimentally validated predictions of drug off-target effects.
Gene Expression Signatures Associated With Immune and Virological Responses to Therapeutic Vaccination With Dendritic Cells in HIV-Infected Individuals (2019)

The goal of HIV therapeutic vaccination is to induce HIV-specific immune response able to control HIV replication. We previously reported that vaccination with <i>ex vivo</i> generated Dendritic Cells (DC) loaded with HIV-lipopeptides in HIV-infected patients (<i>n</i> = 19) on antiretroviral therapy (ART) was well-tolerated and immunogenic. Vaccine-elicited HIV-specific T cell responses were associated with improved control of viral replication following antiretroviral interruption (ATI from w24 to w48). We show an inverse relationship between HIV-specific responses (production of IL-2, IL-13, IL-21, IFN-g, CD4 polyfunctionality, i.e., production of at least two cytokines) and the peak of viral load during ATI. Here we have performed an integrative systems vaccinology analysis including: (i) post vaccination (w16) immune responses assessed by cytometry, cytokine secretion, and Interferon-γ ELISPOT assays; (ii) whole blood and cellular gene expression measured during vaccination; and (iii) viral parameters following ATI, with the objective to disentangle the relationships between these markers and to identify vaccine signatures. During vaccination, 69 gene expression modules out of 260 varied significantly including (by order of significance) modules related to inflammation (Chaussabel Modules M3.2, M4.13, M4.6, M5.7, M7.1, M4.2), plasma cells (M4.11) and T cells (M4.1, 4.15). Cellular immune responses were positively correlated to genes belonging to T cell functional modules (M4.1, M4.15) at w16 and negatively correlated to genes belonging to inflammation modules (M7.1, M5.7, M3.2, M4.13, M4.2). More specifically, we show that prolonged increased abundance of inflammatory gene pathways related to toll-like receptor signaling (especially TLR4) are associated with both lower vaccine immune responses and control of viral replication post ATI. Further comparison of DC vaccine gene signatures with previously reported non-HIV vaccine signatures, such as flu and pneumococcal vaccines, revealed common pathways across vaccines. Overall, these results show that too long duration and too high intensity of vaccine inflammatory responses hamper the magnitude of effector responses.
Clinical Cell Therapy Guidelines for Neurorestoration (IANR/CANR 2017) (2018)

Cell therapy has been shown to be a key clinical therapeutic option for central nervous system diseases or damage. Standardization of clinical cell therapy procedures is an important task for professional associations devoted to cell therapy. The Chinese Branch of the International Association of Neurorestoratology (IANR) completed the first set of guidelines governing the clinical application of neurorestoration in 2011. The IANR and the Chinese Association of Neurorestoratology (CANR) collaborated to propose the current version "Clinical Cell Therapy Guidelines for Neurorestoration (IANR/CANR 2017)". The IANR council board members and CANR committee members approved this proposal on September 1, 2016, and recommend it to clinical practitioners of cellular therapy. These guidelines include items of cell type nomenclature, cell quality control, minimal suggested cell doses, patient-informed consent, indications for undergoing cell therapy, contraindications for undergoing cell therapy, documentation of procedure and therapy, safety evaluation, efficacy evaluation, policy of repeated treatments, do not charge patients for unproven therapies, basic principles of cell therapy, and publishing responsibility.
Full reference video quality estimation for videos with different spatial resolutions (2014)

Full reference video quality estimators (QEs) either resize the input video or the reference video to compute the quality when these videos have different spatial resolutions. This resizing operation causes several limitations. Multiscale Image Quality Estimator (MIQE) [1] overcomes those limitations for images but it does not consider the temporal characteristics of video. In this work, we develop a video quality estimator that integrates MIQE with the motion information to estimate the quality. We also perform subjective tests to compare the proposed algorithm with the existing QEs. Test results show that the proposed algorithm outperforms other QEs.
The Contribution of Raised Intraneuronal Chloride to Epileptic Network Activity (2015)

Altered inhibitory function is an important facet of epileptic pathology. A key concept is that GABAergic activity can become excitatory if intraneuronal chloride rises. However, it has proved difficult to separate the role of raised chloride from other contributory factors in complex network phenomena, such as epileptic pathology. Therefore, we asked what patterns of activity are associated with chloride dysregulation by making novel use of Halorhodopsin to load clusters of mouse pyramidal cells artificially with Cl(-). Brief (1-10 s) activation of Halorhodopsin caused substantial positive shifts in the GABAergic reversal potential that were proportional to the charge transfer during the illumination and in adult neocortical pyramidal neurons decayed with a time constant of τ = 8.0 ± 2.8s. At the network level, these positive shifts in EGABA produced a transient rise in network excitability, with many distinctive features of epileptic foci, including high-frequency oscillations with evidence of out-of-phase firing (Ibarz et al., 2010). We show how such firing patterns can arise from quite small shifts in the mean intracellular Cl(-) level, within heterogeneous neuronal populations. Notably, however, chloride loading by itself did not trigger full ictal events, even with additional electrical stimulation to the underlying white matter. In contrast, when performed in combination with low, subepileptic levels of 4-aminopyridine, Halorhodopsin activation rapidly induced full ictal activity. These results suggest that chloride loading has at most an adjunctive role in ictogenesis. Our simulations also show how chloride loading can affect the jitter of action potential timing associated with imminent recruitment to an ictal event (Netoff and Schiff, 2002).
Cell Surface Glycoproteins of Human Tumor Cell Lines: Unusual Characteristics of Malignant Melanoma2 (1979)

Cell surface glycoproteins of human tumor cell lines (melanomas and astrocytomas, and ovarian, bladder, stomach, cervical, laryngeal, and renal cancers) were studied by labelling with 1) neuraminidase-galactose oxidase-[3H]borohydride, 2) galactose oxidase-[3H]borohydride, and 3) dilute periodate-[3H]borohydride. The labeled components were examined by polyacrylamide gel electrophoresis and fluorography. Each tumor type had a distinctive pattern of labeled glycoproteins when the results from both procedures 1 and 2 were considered. Cell surface glycoproteins of malignant melanoma could not be labeled by procedure 2, whereas the other cell lines had at least two major glycoproteins that could be labeled by this method. Very similar profiles of melanoma glycoproteins were labeled by procedures 1 and 3. From these results the conclusion was reached that cell surface glycoproteins of melanomas are substituted with sialic acid so that their D-galactose and/or N-acetyl-D-galactosamine residues are available for oxidation by galactose oxidase only after neuraminidase treatment. An alternative explanation that these sugars are sterically accessible to galactose oxidase only after neuraminidase treatment also has to be considered. All melanoma lines studied were characterized by having two major cell surface glycoproteins with molecular weights of 110,000 and 90,000, respectively. Lines, however, varied considerably in their expression of other components. In particular, heterogeneity was shown in the expression of gp220, a component identified as fibronectin by immunoprecipitation with a specific antiserum, and in the expression of gp37/32, a pair of glycoproteins having the characteristics of la-like antigens. Of the other cell lines studied, astrocytomas most closely resembled melanoma in their glycoprotein profiles. The brain tumors, however, had two or three glycoproteins, including gp110, which could be labeled by galactose oxidase-[3H]borohydride without neuraminidase treatment.
Corrosion and Wear Control for Industrial Applications (2013)

Abstract This article focuses on noble and neutral coatings and the requirements necessary to achieve successful industrial applications. These include corrosion and wear control and repair applications in processing and chemical industries, and valve and downhole drilling applications in the petrochemical industry. The article also discusses substrate chemistry and preparation; coating selection process and microstructure; sealing by chemical, post-heat treatments, and laser processing; and thermal spray process alternatives.
Plasminogen Controls Inflammation and Pathogenesis of Influenza Virus Infections via Fibrinolysis (2013)

Detrimental inflammation of the lungs is a hallmark of severe influenza virus infections. Endothelial cells are the source of cytokine amplification, although mechanisms underlying this process are unknown. Here, using combined pharmacological and gene-deletion approaches, we show that plasminogen controls lung inflammation and pathogenesis of infections with influenza A/PR/8/34, highly pathogenic H5N1 and 2009 pandemic H1N1 viruses. Reduction of virus replication was not responsible for the observed effect. However, pharmacological depletion of fibrinogen, the main target of plasminogen reversed disease resistance of plasminogen-deficient mice or mice treated with an inhibitor of plasminogen-mediated fibrinolysis. Therefore, plasminogen contributes to the deleterious inflammation of the lungs and local fibrin clot formation may be implicated in host defense against influenza virus infections. Our studies suggest that the hemostatic system might be explored for novel treatments against influenza.