gebhart/patrepeval huggingface dataset:
A large-scale detailed neuronal model of electrical stimulation of the dentate gyrus and perforant path as a platform for electrode design and optimization (2016)

Owing to the dramatic rise in treatment of neurological disorders with electrical micro-stimulation it has become apparent that the major technological limitation in deploying effective devices lies in the process of designing efficient, safe, and outcome specific electrode arrays. The time-consuming and low-fidelity nature of gathering test data using experimental means and the immense control and flexibility of computational models, has prompted us and others to build models of electrical stimulation of neural networks that can be simulated in a computer. Because prior work has been focused on single cells, very small networks, or non-biological models of neural tissue, it was expedient that we take advantage of our, 4,040 processor, computing cluster to construct a large-scale 3-dimensional emulation of hippocampal tissue using detailed neuronal models with explicit and unique morphologies. This model, when paired with an equivalent circuit method of estimating voltage signal attenuation throughout anisotropic resistive tissue, can be used to predict tissue response to an exhaustive set of stimulation and tissue conditions: electrode geometry, array geometry, static dielectric properties of tissue, stimulation pulse features, etc. Preliminary experiments demonstrate that this system is capable of yielding neuronal responses with striking similarities to experimental results. This work provides an avenue to qualitative evaluation of electrode arrays, and more meaningful modeling of local field potentials in terms of their contributing sources and sinks.
TRAF1: Lord Without A RING (2002)

Tumor necrosis factor (TNF) receptor-associated factors (TRAFs) constitute a family of adaptor proteins that associate with the cytosolic tail of particular TNF-family receptors (TNFR) and regulate cytokine signaling by linking TNFRs with downstream protein kinases, ubiquitin ligases, and other effector proteins. A total of six members of this family (TRAF1-6) have been identified in mammals. TRAF1 is unique among TRAFs because it lacks a RING finger domain present in TRAF2-6 that has been shown to be required for TRAF2- and TRAF6-mediated activities. TRAF1 also has the most restricted expression among TRAFs, and is found almost exclusively in activated lymphocytes, dendritic cells, and certain epithelia. Recent evidence obtained from TRAF1(-/-) mice shows that TRAF1-deficient T cells are hyper-responsive to TNF-alpha, having increased T cell receptor (TCR)-dependent T cell proliferation rates in vitro. Also, these TRAF1(-/-) mice had increased sensitivity to TNF-alpha-induced skin necrosis in vivo. These results support a role for TRAF1 as a negative regulator of signaling by certain TNF-family receptors. This review summarizes current knowledge about TRAF1, focusing on the new information provided by these TRAF1-deficient mice. Also, the pros and cons of TRAFs as potential targets for drug discovery are discussed.
Photonic Crystal Microcavity Enhanced LEDs (2005)

Novel microcavities are fabricated that consist of GaAs microdisks (-3 l m diameter) sandwiched betwecn AlAs cladding, bounded by a circular grating of deeply etched air trenches.An enutting layer of I d s quantum dots is insend in GaAs.The prating acts as a 4thorder Bragg reflector for the in-plane cavity, so that some 2nd-order diffraclion towards air can occur.This allows to Microdirks modes usually requlre lugh azimuthal number 1 to be confined through toral internal reflection, while drum-like modes with low-azimuthal number I only see the poorer norms1 reflection at the semiconductor-air interface (30%).In our cavity, the circular Bragg mirror ic
An Adaptive Base Plane Filtering Algorithm for Inter-plane Estimation of RGB Images in HEVC RExt (2014)

This letter proposes an adaptive base plane filtering algorithm for the inter-plane estimation of RGB images in HEVC RExt. Because most high-frequency components of RGB images have low inter-plane correlation, our proposed scheme adaptively removes the high-frequency components of the base plane in order to enhance the inter-plane estimation accuracy. The experimental results show that the proposed scheme provides average BD rate gains of 0.6%, 1.0%, and 1.2% in the G, B, and R planes, respectively, with slightly decreased complexity, as compared to the previous inter-plane filtering method.
Exploiting Substrate Diversity for Preparing Synthetically Valuable Sulfoxides via Asymmetric Hydrogenative Kinetic Resolution (2020)

A detailed study is disclosed on the Rh‐mediated hydrogenative kinetic resolution of α,β‐unsaturated sulfoxides with alkyl and aryl substituents at the α‐, E ‐ and Z ‐positions of the double bond. This stereoselective catalytic methodology has enabled the preparation of highly enantioenriched (or even enantiopure) alkyl and aryl‐substituted (un)saturated sulfoxides via a simple and efficient synthetic operation. Moreover, the application of the hydrogenative KR to the preparation of valuable optically active sulfoxide‐containing building blocks or biologically active intermediates is described.
Comparison of epoxides on grafting collagen to polyurethane and their effects on cellular growth (1998)

The current study investigated the effects of vary epoxides on linking capacity of collagen to carboxyl-group-enriched polyurethane (PU) and the consequent effects on the growth of endothelial cells. Epoxides of EX-810, 1,4BDE, DER732, DER331, and DER332 were initially reacted with the carboxyl groups of PU substrates at 110 degrees C for 20 h. Free epoxy rings of epoxide-PU substrates, characterized by Fourier transform infrared spectroscopy and quantified by titration with HCl and NaOH, were available for collagen grafting. The amounts of collagen grafted were in accordance with the amounts of free epoxy rings detected and correlated with the growth of endothelial cells on the substrates. Our results indicated that epoxides with shorter aliphatic intermediate chain can graft more collagen to the epoxide-PU substrates than epoxides with longer intermediate chain or with aromatic groups. Epoxides were also demonstrated to be nontoxic linking agents for biomaterials.
A Novel Microfluidic Whole Cell Biosensor Based on Electrochemical Detection for Water Toxicity Analysis (2008)

Over the last few years, the physical dimensions of microchip devices have decreased, enhancing the interest in the integration of various devices and complex operations onto a compatible "lab on a chip" system with desirable characteristics and capabilities. This work presents a novel µ-fluidics whole cell biosensor for water toxicity analysis. The biosensor is based on bacterial cells genetically "tailored" to generate an electrochemical bio-signal in the presence of toxic materials. The µ-chip was electrochemically characterized, and demonstrated the potential toxicity analysis with a model toxicant. A novel concept of bacterial biosensors deposition by means of electrophoretic force was examined for the first time. Preliminary results demonstrated the ability to detect electrochemical signal generated by the deposited bacterial cells indicating the potential use for patterning of bacterial cells on solid-state surfaces for the use in bio-sensing.
ToF depth image motion blur detection using 3D blur shape models (2012)

Time-of-flight cameras produce 3D geometry enabling faster and easier 3D scene capturing. The depth camera, however, suffers from motion blurs when the movement from either camera or scene appears. Unlike other noises, depth motion blur is hard to eliminate by any general filtering methods and yields the serious distortion in 3D reconstruction, typically causing uneven object boundaries and blurs. In this paper, we provide a through analysis on the ToF depth motion blur and a modeling method which is used to detect a motion blur region from a depth image. We show that the proposed method correctly detects blur regions using the set of all possible motion artifact models.
The functional relevance of the lectin-like activities of cytokines : TNF as an illustrative example (2002)

Mammalian cytokines modulate the activity of the immune system. It is generally accepted that the action of cytokines results from their binding to specific receptors. However, many cytokines were shown to contain two domains. The first domain defines indeed the receptor-binding site. The second domain localized at the opposite to the receptor-binding site is necessary for the expression of the full biological activity of the cytokine. However, the exact function of the latter domain remains largely unknown. Recent evidences have shown that second domain of cytokines displays lectin-like activity allowing interaction of the cytokines with glycosaminoglycans on the cell surface of mammalian cells, thereby resulting in modulation of their biological activities. In addition, it has been suggested that the lectin-like domains of cytokines represent pathogen-specific recognition sites that can contribute to their elimination. This review focuses on the physiological relevance of the lectin-like activity of cytokines during the innate immune response in mammals, using TNF as an illustrative example.
Genomic-based signatures of chemosensitivity and ER/HER2 status in biologic replicate breast cancer samples (2008)

11068 Background: Genome-wide expression profiling has now been extensively used for research on breast cancer biology and led to many new insights regarding disease heterogeneity. However, clinical applications require an understanding of various technical considerations, including the extent to which a random sample provides a representative measure of the patient’s tumor. Using genome- scale expression data derived from cancer cell lines and tumor biopsies, we have developed signatures for predicting response to specific cytotoxic chemotherapies. Our objective in this study is to assess the concordance of chemosensitivity predictions and of microarray-based classifiers of ER and HER2 status in a series of multiple samples from individual breast cancer biopsies. Methods: Patients with multiple frozen cores were identified in the Duke Breast SPORE tissue repository. Cores were assessed for percent invasive cancer cellularity, primary tumor size, and standard biomarker assessments. RNA was hybridized to Affymetrix H133 Plus 2.0 microarrays, Gene expression based signatures were generated according to previously identified predictors of sensitivity to adriamycin and docetaxel (Potti et al, Nat Med, 2006). Predefined cutoffs of 0.60 are applied to each signature. Genomic predictors of hormone receptor status were applied to post- processed array data, and compared to single-patient measures from IHC/FISH. Results: Of 14 patients, 1 had quadruplicate samples, 12 had triplicate samples, and 1 had doublet samples. In an overall assignment of being most sensitive to adriamycin, most sensitive to docetaxel, or resistant to both agents, complete concordance was observed in 9 of 14 cases. Intra-class correlation coefficients for the adriamycin and docetaxel signatures were 86% and 92%, respectively. Genomic signatures of ER status showed complete concordance in 13 of 14 patients and >95% agreement with IHC. Genomic-predictors of HER2 status were inconsistent across biological replicates. Conclusions: For replicate frozen core samples, chemosensitivity signatures and ER status appear robust and reproducible. Since cores represent biologic replicates, discordant cases may due to true heterogeneity within cancers from the individual patients. No significant financial relationships to disclose.
Infections in children with acute myeloid leukemia: increased mortality in relapsed/refractory patients (2019)

The aim of this nationwide study was to describe the epidemiology and profile of bacterial infections (BI), invasive fungal disease (IFD) and viral infections (VI) in patients with <i>de novo</i> and relapsed/refractory (rel/ref) acute myeloid leukemia (AML). Within the studied group of 250 children with primary AML, at least one infectious complication (IC) was diagnosed in 76.0% (<i>n</i> = 190) children including 85.1% (<i>n</i> = 504) episodes of BI, 8.3% (<i>n</i> = 49) - IFD and 6.6% (<i>n</i> = 39) - VI. Among 61 patients with rel/ref AML, at least one IC was found in 67.2% (<i>n</i> = 41) of children including 78.8% (<i>n</i> = 78) of BI, 14.1% (<i>n</i> = 14) of IFD and 7.1% (<i>n</i> = 7) of VI. In all AML patients, within BI Gram-negative strains were predominant. Half of these strains were multi-drug resistant. Characteristics of IFD and VI were comparable for de novo and rel/ref AML. The infection-related mortality was significantly higher, while survival from infection was significantly lower in patients with rel/ref disease.
Surface Cleaning and Passivation of Chalcogenide Thin Films Using S(NH<sub>4</sub>)<sub>2</sub> Chemical Treatment (2014)

Chalcopyrite ternary and kesterite quaternary thin films, such as Cu (In,Ga)(S,Se) 2 and Cu 2 ZnSn (S,Se) 4 generically referred to as CIGSSe and CZTSSe, respectively, have become the subject of considerable interest and study for semiconductor devices in recent years [1,2]. These materials are of particular interest for use as an absorber layer in photovoltaic devices. In thin film solar cells, the p-type CIGSSe or CZTSSe layer is combined with an n-type semiconductor thin film such as CdS buffer layer to form the p-n heterojunction of the device. The synthesis process of the CIGSSe or CZTSSe absorber layer requires temperatures ranging between 400 and 600 °C to form the photoactive chalcopyrite or kesterite phases [3,4]. During the synthesis process, the formation of trace amounts of binary/ternary compositions ( i.e. , undesirable secondary or impurity phases consisting of selenides, oxides, carbonates, etc.) may occur. These trace amounts of impurity phases may form at the nascent absorber surfaces, which could negatively affects the photovoltaic conversion efficiencies of solar cells [5-7]. Therefore, prior to the deposition of the CdS buffer layer, there is a need to clean the CIGSSe or CZTSSe surfaces to remove any possible traces of such impurities.
From JSON to JSEN through Virtual Languages (2021)

In this paper we describe a data format suitable for storing and manipulating executable language statements that can be used for exchanging/storing programs, executing them concurrently and extending homoiconicity of the hosting language. We call it JSEN, JavaScript Executable Notation, which represents the counterpart of JSON, JavaScript Object Notation. JSON and JSEN complement each other. The former is a data format for storing and representing objects and data, while the latter has been created for exchanging/storing/executing and manipulating statements of programs. The two formats, JSON and JSEN, share some common properties, reviewed in this paper with a more extensive analysis on what the JSEN data format can provide. JSEN extends homoiconicity of the hosting language (in our case JavaScript), giving the possibility to manipulate programs in a finer grain manner than what is currently possible. This property makes definition of virtual languages (or DSL) simple and straightforward. Moreover, JSEN provides a base for implementing a type of concurrent multitasking for a single-threaded language like JavaScript.
In Vivo Study of Stainless Steel and Ti-13Nb-13Zr Bone Plates in a Sheep Model (1997)

A sheep study was performed to compare the in vivo performance of bone plates of 316L stainless steel and a new titanium alloy, titanium + 13% niobium + 13% zirconium (Ti-13Nb-13Zr), which had been subjected to a diffusion hardening treatment to produce a blue, wear resistant surface. Bone plates and screws of stainless steel and diffusion hardened Ti-13Nb-13Zr were implanted in adult sheep, in one group (with unosteotomized femurs) for 16 weeks, and in the other (with osteotomized femurs) for 8 weeks. At harvest, the diffusion hardened Ti-13Nb-13Zr devices had superior fixation strength, with greater screw torque out strength and fewer loose screws. In the osteotomized animals, the femurs with diffusion hardened Ti-13Nb-13Zr plates had higher torsional strength after removal of the implants; however, the difference was not statistically significant. In the unosteotomized animals, the torsional strength of the femurs was identical for both materials. There was a slightly reduced incidence of infection (bacterial adhesion) for the sheep with diffusion hardened Ti-13Nb-13Zr implants. In a parallel in vitro study, the magnetic resonance imaging compatibility of Ti-13Nb-13Zr was significantly superior to that of stainless steel. This indicates that diffusion hardened Ti-13Nb-13Zr may be an attractive alternative material for osteosynthesis.
Table S2 from Theranostic Radiolabeled Anti-CD20 sdAb for Targeted Radionuclide Therapy of Non-Hodgkin Lymphoma (2023)

&lt;p&gt;Ex vivo biodistribution of 14 anti-hCD20 sdAbs and non-target control sdAb (ctrl sdAb), radiolabeled with 99mTc, in Daudi. Results are expressed as % IA/g {plus minus} SD (n = 3 per SdAb). T/M: Tumor-to-Muscle ratio; T/B: Tumor-to-Blood ratio.&lt;/p&gt;
Uniaxial Strain Controlling Magnetic Anisotropy in (Ga,Mn)As (2007)

A theoretical study of magnetocrystalline anisotropy controlled by in-plane lattice symmetry distortions is presented. The uniaxial strain, only presumed by earlier studies in order to model the observed uniaxial magnetic anisotropy, has recently become an experimentally accessible parameter. We show that the lithographically induced strain can compete with intrinsic symmetry breaking, easy axes can take general in-plane directions, and anisotropy fields scale linearly with strain for typical experimental strain magnitudes. Our results are in qualitative agreement with experimental results.
Nipah Virus V and W Proteins Have a Common STAT1-Binding Domain yet Inhibit STAT1 Activation from the Cytoplasmic and Nuclear Compartments, Respectively (2004)

In previous reports it was demonstrated that the Nipah virus V and W proteins have interferon (IFN) antagonist activity due to their ability to block signaling from the IFN-alpha/beta receptor (J. J. Rodriguez, J. P. Parisien, and C. M. Horvath, J. Virol. 76:11476-11483, 2002; M. S. Park et al., J. Virol. 77:1501-1511, 2003). The V, W, and P proteins are all encoded by the same viral gene and share an identical 407-amino-acid N-terminal region but have distinct C-terminal sequences. We now show that the P protein also has anti-IFN function, confirming that the common N-terminal domain is responsible for the antagonist activity. Truncation of this N-terminal domain revealed that amino acids 50 to 150 retain the ability to block IFN and to bind STAT1, a key component of the IFN signaling pathway. Subcellular localization studies demonstrate that the V and P proteins are predominantly cytoplasmic whereas the W protein is localized to the nucleus. In all cases, STAT1 colocalizes with the corresponding Nipah virus protein. These interactions are sufficient to inhibit STAT1 activation, as demonstrated by the lack of STAT1 phosphorylation on tyrosine 701 in IFN-stimulated cells expressing P, V, or W. Therefore, despite their common STAT1-binding domain, the Nipah virus V and P proteins act by retaining STAT1 in the cytoplasm while the W protein sequesters STAT1 in the nucleus, creating both a cytoplasmic and a nuclear block for STAT1. We also show that the IFN antagonist activity of the P protein is not as strong as that of V or W, perhaps explaining why Nipah virus has evolved to express these two edited products.
Supplementary Table S4 from RLY-4008, the First Highly Selective FGFR2 Inhibitor with Activity across <i>FGFR2</i> Alterations and Resistance Mutations (2023)

&lt;p&gt;In vivo exposures of pan-FGFRi in mouse studies&lt;/p&gt;
Polarization state generator: a polarimeter calibration standard (2011)

A polarization state generator (PSG) was built to generate light having a degree of linear polarization (DoLP) varying from 0.0005 to 0.4 with 0.0005 uncertainty. The PSG operates by tilting a plane parallel SF11 glass plate in a nearly unpolarized beam. The DoLP of collimated, unpolarized light passing through a plane parallel plate over a defined range of field angles can be calculated from theory, and the PSG was intended to act as a calibration standard based on this calculation. Several effects make the DoLP distribution as a function of field and tilt plate difficult to model to the desired 0.0005 uncertainty: source DoLP and intensity nonuniformity, lens surface diattenuation, and errors in optical alignment. Because of these effects, modeled DoLP was not used as a standard. Instead, DoLP was characterized with repeatability of 0.0005.
The surgical approach for revision total knee arthroplasty (2016)

A key to the success of revision total knee arthroplasty (TKA) is a safe surgical approach using an exposure that minimises complications. In most patients, a medial parapatellar arthrotomy with complete synovectomy is sufficient. If additional exposure is needed, a quadriceps snip performed through the quadriceps tendon often provides the additional exposure required. It is simple to perform and does not alter the post-operative rehabilitative protocol. In rare cases, in which additional exposure is needed, or when removal of a cemented long-stemmed tibial component is required, a tibial tubercle osteotomy (TTO) may be used. Given the risk of post-operative extensor lag, a V-Y quadricepsplasty is rarely indicated and usually considered only if TTO is not possible.
Predicting taxi pickups in cities (2017)

In this paper we use machine learning to evaluate the predictability of taxi pickups in New York City's busiest neighborhoods using data available from the Taxi and Limousine Commission and from Twitter. We found that these pickups can be accurately forecast, and we show which features work well for forecasts, including geotagged Twitter posts in some cases.
Improving bilateral control feedback by using novel velocity and acceleration estimation methods in FPGA (2012)

The bilateral control that is used in medical or industrial applications needs to offer rapid processing and precision. The Field Programmable Gate Array (FPGA) helps in this regard. The algorithms of velocity and acceleration estimation require a short processing time in implementation than do conventional estimation methods. Bilateral control is implemented in common and differential modes for force servoing and position regulator, respectively. Position, velocity and acceleration (PVA) feedback in the differential mode enhance position tracking in the bilateral control. The bilateral robot system is implemented using ball screw mechanisms.
A New Method for End-Fire Array Gain Optimization Using Spherical Wave Expansion (2022)

This work presents an analysis of the radiating properties of lossy antennas using the Spherical Wave Expansion (SWE) theory. A new formula to predict the gain of uniformly-spaced end-fire arrays based on the dissipation factor is proposed. The latter allows an analytical synthesis of the complex excitation coefficients associated with the array elements to achieve supergain characteristics. Similar studies have been previously dealt with (super)directivity optimization, characterized by high sensitivity and severe gain attenuations, when the dimensions of the array are considerably reduced. In this context, the proposed study shows a significant improvement of the antenna gain and efficiency compared to synthesis procedures having an objective of the directivity maximization.