gebhart/patrepeval huggingface dataset:
Emergent coordination underlying learning to reach to grasp with a brain-machine interface (2018)

The development of coordinated reach-to-grasp movement has been well studied in infants and children. However, the role of motor cortex during this development is unclear because it is difficult to study in humans. We took the approach of using a brain-machine interface (BMI) paradigm in rhesus macaques with prior therapeutic amputations to examine the emergence of novel, coordinated reach to grasp. Previous research has shown that after amputation, the cortical area previously involved in the control of the lost limb undergoes reorganization, but prior BMI work has largely relied on finding neurons that already encode specific movement-related information. In this study, we taught macaques to cortically control a robotic arm and hand through operant conditioning, using neurons that were not explicitly reach or grasp related. Over the course of training, stereotypical patterns emerged and stabilized in the cross-covariance between the reaching and grasping velocity profiles, between pairs of neurons involved in controlling reach and grasp, and to a comparable, but lesser, extent between other stable neurons in the network. In fact, we found evidence of this structured coordination between pairs composed of all combinations of neurons decoding reach or grasp and other stable neurons in the network. The degree of and participation in coordination was highly correlated across all pair types. Our approach provides a unique model for studying the development of novel, coordinated reach-to-grasp movement at the behavioral and cortical levels. NEW & NOTEWORTHY Given that motor cortex undergoes reorganization after amputation, our work focuses on training nonhuman primates with chronic amputations to use neurons that are not reach or grasp related to control a robotic arm to reach to grasp through the use of operant conditioning, mimicking early development. We studied the development of a novel, coordinated behavior at the behavioral and cortical level, and the neural plasticity in M1 associated with learning to use a brain-machine interface.
Characterization of the Chemical Composition Distribution of Ethylene/1‐Alkene Copolymers with HPLC and CRYSTAF—Comparison of Results (2015)

A series of copolymers of ethylene with propene, 1‐hexene, 1‐octene, and 1‐octadecene is characterized by size‐exclusion chromatography (SEC), nuclear magnetic resonance spectroscopy (NMR), crystallization analysis fractionation (CRYSTAF), and high‐temperature interactive liquid chromatography. Four different solvent pairs are used as the mobile phase, while porous graphite is used as the column packing. The elution volumes of the polymer samples do not correlate with their average molar mass (SEC); however, they correlate with the average chemical composition (NMR). High performance liquid chromatography (HPLC) enables separation of the copolymers over the full range of their composition and independent of their crystallinity. Dependence between the elution volume and the average chemical composition distribution (CCD) of the copolymer is linear and it is a function of the length of branches as well as the type of the mobile phase. The CCDs of copolymers derived from HPLC profiles are similar to, yet broader than the CCDs obtained with CRYSTAF. image
Isolation, differential splicing and protein expression of a DNase on the human X chromosome. (1996)

A systematic search for genes differentially expressed in human tissues resulted in the isolation of a gene encoding a protein with high homology to DNase I. In addition to the recently described cDNA sequence (Parrish et al., 1995) we have isolated a transcript, alternatively spliced in the 5' noncoding region. The gene is located between the QM and the XAP-2 gene in Xq28 and encodes a 302 amino acid protein with 39% identity to human DNase I. Besides a high homology at the nucleotide and amino acid level, most exon-intron boundaries of DNase I and DNase X are identical, indicating that both genes may have evolved from a common ancestor. The predicted function was verified by expression of a recombinant protein in an inducible bacterial system and detection of DNase activity. In contrast to DNase I a 18 kdal amino terminal fragment of the full length 35 kdal protein exhibited DNase activity.
The Size of the Hepatitis Delta Agent (1989)

The size of the hepatitis delta virus was determined by filtration of infectious plasma through polycarbonate membranes and the inoculation of filtrates into chimpanzees. Chimpanzees inoculated with filtrates of 50 nm and 30 nm, but not 15 nm filters, developed delta hepatitis. The minimum size of infectious hepatitis delta virus was estimated to be approximately 30 nm, which is consistent with measurements of particles thought to be the virus.
Measurement of the near infrared absorption of Ge on Si films by differential spectroscopy (2008)

Using a differential method on epitaxially grown Ge films on silicon, we measure the near-infrared absorption and its temperature dependence.
Biocompatibility of Thermally Hydrocarbonized Porous Silicon Nanoparticles and their Biodistribution in Rats (2010)

Porous silicon (PSi) particles have been studied for the effects they elicit in Caco-2 and RAW 264.7 macrophage cells in terms of toxicity, oxidative stress, and inflammatory response. The most suitable particles were then functionalized with a novel (18)F label to assess their biodistribution after enteral and parenteral administration in a rat model. The results show that thermally hydrocarbonized porous silicon (THCPSi) nanoparticles did not induce any significant toxicity, oxidative stress, or inflammatory response in Caco-2 and RAW 264.7 macrophage cells. Fluorescently labeled nanoparticles were associated with the cells surface but were not extensively internalized. Biodistribution studies in rats using novel (18)F-labeled THCPSi nanoparticles demonstrated that the particles passed intact through the gastrointestinal tract after oral administration and were also not absorbed from a subcutaneous deposit. After intravenous administration, the particles were found mainly in the liver and spleen, indicating rapid removal from the circulation. Overall, these silicon-based nanosystems exhibit excellent in vivo stability, low cytotoxicity, and nonimmunogenic profiles, ideal for oral drug delivery purposes.
Revacept, an Inhibitor of Platelet Adhesion in Symptomatic Carotid Stenosis: A Multicenter Randomized Phase II Trial (2022)

gov; Unique Identifier: NCT01645306.
Planning and visualization for a smart meeting room assistant1 (2019)

In this paper, we report on the planning and visualization capabilities of Mr.Jones – a proactive orchestrator and decision-support agent for a collaborative decision making setting embodied by a smart room. The duties of such an agent may range across interactive problem solving with other agents in the environment, developing automated summaries of meetings, visualization of the internal decision-making process, proactive data and resource management, and so on. Specifically, we focus on how the visualization of the planning and plan recognition processes forms a key component of the smart assistant, and establishes transparency in the decision-making process. We also highlight how these processes contribute to the proactive nature of the agent. We demonstrate some of these functionalities in a successful deployment of the system in the CEL – the Cognitive Environments Laboratory at IBM’s T.J. Watson Research Center (Yorktown, USA), and report on emerging deployments of the system that have turned into success stories.
Pupil constriction via the parasympathetic pathway precedes perceptual switch of ambiguous stimuli (2021)

Perceptual rivalry of ambiguous stimuli reflects the interaction of neural activity among multiple cortical regions. However, it remains unclear what drives a spontaneous perceptual alteration. We hypothesized that increased fluctuations in spontaneous neural activity due to arousal reduction drive the perceptual switch. Here, we show that the pupils shrank a few seconds prior to the onset of the spontaneous perceptual switch. Such pupil constriction was not observed before the exogenous perceptual switch. Pharmacological experiments confirmed that the pupil constriction disappeared when the peripheral parasympathetic pathway (pupil sphincter muscle) was blocked, but it remained intact when the peripheral sympathetic pathway (pupil dilator muscle) was manipulated. Furthermore, rapid pupil dilations with behavioral response are also mediated by the peripheral parasympathetic pathway. The present findings suggested that transient arousal drops, as denoted by the autonomic nervous modulation of pupil size, are involved in inducing the spontaneous perceptual switch of bistable stimuli.
Loss of heterozygosity (LOH) as a measure of whole-genome instability in ovarian cancer correlates with clinical outcomes. (2011)

5027 Background: The aim of the study was to assay the amount of loss of heterozygosity (LOH) across the whole genome as a measure of genomic instability in ovarian tumors and to determine the correlation between the fraction of the ovarian cancer genome with LOH and the clinical outcomes of ovarian cancer patients. Methods: We assessed the prevalence of LOH in 100 unselected ovarian cancer tumors using whole genome 500K Single Nucleotide Polymorphism (SNP) arrays (Affymetrix, Inc.). Allele dosage, copy number, and degree of contamination with benign tissue were used to estimate the likelihood of various genotypes in tumor tissue. Regions with the copy number of more than 3 were eliminated from the analysis since LOH data are unreliable when copy number exceeds 3. Results: We found that copy number changes of 1, 2 and 3 composed 12.6%, 45.7% and 21.5% of the genome in ovarian cancer, respectively. These changes contributed to 42.4%, 43.8% and 13.8% of LOH in ovarian cancer, respectively. The average fraction of the whole genome with LOH in ovarian cancer was 35%. The fraction of the genome with LOH was significantly correlated with tumor grade. The fraction of the ovarian cancer genome with LOH was statistically highly correlated with both overall survival (OS;p=3.4x10-6) and progression-free survival (PFS; p=0.0016) after debulking surgery and platinum/taxane-based chemotherapy. In multivariate analyses with clinical variables, only the fraction of the genome with LOH and residual tumor size (RTS) after debulking surgery were independent predictive factors for OS and PFS. Conclusions: Increased fraction of the genome with LOH as a measure of genomic instability in ovarian cancer is a significant and independent negative prognostic factor for both OS and PFS. The validation of the fraction of the ovarian cancer genome with LOH as an independent predictor of RFS and OS in a second ovarian cancer sample set will also be presented at the meeting.
Multiresolution Interblock Interpolation in Direct Volume Rendering (2006)

We present a direct interblock interpolation technique that enables direct volume rendering of blocked, multiresolution volumes. The proposed method smoothly interpolates between blocks of arbitrary block-wise level-of-detail (LOD) without sample replication or padding. This permits extreme changes in resolution across block boundaries and removes the interblock dependency for the LOD creation process. In addition the full data reduction from the LOD selection can be maintained throughout the rendering pipeline. Our rendering pipeline employs a flat block subdivision followed by a transfer function based adaptive LOD scheme. We demonstrate the effectiveness of our method by rendering volumes of the order of gigabytes using consumer graphics cards on desktop PC systems.
Microchip-based homogeneous immunoassay using fluorescence polarization spectroscopy (2008)

We have realized fluorescence polarization immunoassay (FPIA) on a microchip in about 1 minute. FPIA is a homogeneous competitive immunoassay which is based on measuring fluorescence polarization after competitive binding of an analyte and a tracer to an antibody. We constructed a microfluidic FPIA system composed of a newly designed microchip, a laser, a CCD camera and an optical microscope with two specially installed polarizers-one fixed and one rotatable. Theophylline, a typical small drug molecule, was used as a model analyte. Theophylline and fluorescence-labeled theophylline were introduced through different inlets and combined in a 100 microm-wide microchannel where anti-theophylline antibody was added. To optimize the microchip design for FPIA, we investigated the diffusion time of theophylline and the mixing time of theophylline and antibody in this channel, which were 6 s and 36 s, respectively. We successfully carried out a quantitative analysis of theophylline in serum near the therapeutic range in 65 s. In FPIA, a larger tracer-antibody complex emits more polarized fluorescence than the tracer, and therefore, by increasing the antigen concentration in a sample, more polarization relaxation is observed since the tracer-antibody complex concentration is decreased and the tracer concentration is increased. Tracer binding to an antibody is directly measured by spectroscopic techniques without any separation process.This microchip-based FPIA is very simple and rapid, unlike microchip-based heterogeneous immunoassay, because it does not require several processes such as washing and reflowing and immobilizing of antibodies or antigens in the channel. In the future, microchip-based FPIA should find frequent use for point-of-care testing in the clinical field, where conventional FPIA has been used for laboratory tests.
Pulse Wave Analysis of HbA1C Categorized Prediabetes, Type 2 Diabetes and Normo-Glycemic Populations (2018)

Arterial stiffness is a significant risk factor for cardiovascular events and early detection is key for intervention and monitoring. This pathophysiological process is accelerated in type 2 diabetes (T2D), yet the onset of this condition has a limited body of research. PURPOSE: To evaluate (1) arterial stiffness properties via pulse wave analysis (PWA) across a 4-group spectrum, and (2) determine whether waist-to-height-ratio (WHtR), waist circumference (WC) or body mass index (BMI) serves as the best predictor of early changes in PWA pathophysiology. METHODS: PWA was measured in 52 participants across four groups separated by HbA1c values: 13 normo-glycemic (N, 4.0-5.1), 14 high normal (HN, 5.2-5.6), 10 prediabetes (PD, 5.7-6.4) and 13 with T2D (T2D, ≥ 6.5). Brachial, central and peripheral pressures, central and peripheral augmentation index (AIx) data were collected via Sphygmocor using validated methods after overnight caffeine abstinence and a minimum 4-hr fast. Group differences were evaluated via MANCOVAs. HbA1C, WHtR, WC and BMI data were assessed through regression to determine the best predictor. RESULTS: Significant differences were found between N to T2D and HN to T2D for brachial systolic blood pressure (SBP) [F(3,46)=2.743, p<.05], brachial diastolic blood pressure (DBP) [F(3,46)=3.329, p<.028] and brachial mean pressures (MP) [F(3,46)=4.321, p<.009]. Central DBP and MP differed between N to T2D, and HN to PD and T2D groups [DBP:F(3,44)=3.874, p<.015; MP:F(3,44)=3.303, p<.029]. Central pulse pressure (PP) and CAIx showed no differences between groups. Peripheral pressures significantly differed between N and both PD and T2D; HN and both PD and T2D groups for peripheral SBP [F(3,44)=3.007, p<.040], peripheral DBP [F(3,44)=4.316, p<.009] and peripheral MP [F(3,44)=3.487, p<.023], but not PP or PAIx. WHtR and WC were identified as the best predictors of CAIx after adjusting for age and height [R2=.800, F(5,45)=16.023, p<.0005; adj. R2=.640], while PAIx had no significant predictor. CONCLUSIONS: PWA may be effective for identifying differences in multiple brachial, central and peripheral pressure measures across a novel, pre-defined HbA1C spectrum; however, more research needs to be executed to validate these findings. WHtR and WC, but not BMI, effectively predicts CAIx.
1H NMR and conformational analysis of diastereotopic methylene protons in achiral flexible molecules (2021)

Unlike diastereotopic -CH2- protons from chiral compounds, the diastereotopic protons from achiral compounds may not be easily predictable. For molecules with flexible chain this task is even more problematic. Additionally, the assignment from the experimental 1H NMR spectrum of chemical shifts and coupling constants is very frequently uncertain. Nevertheless, computationally, for both chiral and achiral molecules the -CH2- protons diastereotopic nature is evident as well as NMR parameters assignments. In the present paper we examine the NMR parameters calculated as a sum of Boltzmann weighted average of the lowest conformations that fits a window less than 10 kJ/mole. A Spartan20 six steps protocol was chosen to select the lower energy conformations. The NMR conformationally averaged parameters obtained for 2-ethyl-2-hyroxybutanoic acid (EHB) and citric acid (CA), both achiral molecules, and the chiral malic acid (MA) fit acceptable well with the experimental data, although the calculation is done for gas phase (conformations dominated by intermolecular hydrogen bonding) and the experiment was carried out in D2O (conformations controlled by intermolecular hydrogen bonding of highly decorated molecules with OH and COOH that can interact with the solvent). In addition, in the present paper we have examined EHB, CA and MA the lowest energy conformer geometry, Atom in Molecules (AIM) and Natural Bond Orbital protocols to identify the intramolecular hydrogen bonds.
Finite linear algebra (2014)

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Genotoxicity of Different Nanocarriers: Possible Modifications for the Delivery of Nucleic Acids (2013)

The prevention of cyto- and genotoxicity of nanocarriers is an important task in nanomedicine. In the present investigation, we, at the first time using similar experimental conditions, compared genotoxicity of nanocarriers with different composition, architecture, size, molecular weight and charge. Poly(ethylene glycol) polymers, neutral and cationic liposomes, micelles, poly(amindo amine) and poly(propyleneimine) dendrimers, quantum dots, mesoporous silica, and supermagnetic iron oxide (SPIO) nanoparticles were studied. All nanoparticles were used in non-cytotoxic concentrations. However, even in these concentrations, positively charged cationic liposomes, dendrimers, and SPIO nanoparticles induced genotoxicity leading to the significant formation of micronuclei in cells. Negatively charged and neutral nanocarriers were not genotoxic. A strong positive correlation was found between the number of formed micronuclei and the positive charge of nanocarriers. We proposed modifications of both types of dendrimers and SPIO nanoparticles that substantially decreased their genotoxicity and allowed for an efficient intracellular delivery of nucleic acids.
A Methodology for the Characterisation of Leakages in Combinatorial Logic. (2016)

Glitches represent a great danger for hardware implementations of cryptographic schemes. Their intrinsic random nature makes them difficult to tackle and their occurrence threatens side-channel protections. Although countermeasures aiming at structurally solving the problem already exist, they usually require some effort to be applied or introduce non-negligible overhead in the design. Our work addresses the gap between such countermeasures and the naive implementation of schemes being vulnerable in the presence of glitches. Our contribution is twofold: (1) we expand the mathematical framework proposed by Brzozowski and Esik [5] by meaningfully adding the notion of information leakage, (2) thanks to which we define a formal methodology for the analysis of vulnerabilities in combinatorial circuits when glitches are taken into account.
Comparative analysis of the expression of the epstein‐barr virus (EBV) anti‐apoptotic gene BHRF1 in nasopharyngeal carcinoma and EBV‐related lymphoid diseases (2001)

Epstein-Barr virus (EBV) has been identified in a wide range of neoplastic and non-neoplastic disorders. The EBV open reading frame BHRF1 encodes a protein with partial sequence and functional homology to the anti-apoptotic onco-protein Bcl-2 and may therefore have a role in the proliferation of EBV positive cells. We have developed a rat monoclonal antibody against pBHRF1, which can detect BHRF1 in paraffin sections. While a number of mutant versions of BHRF1 were recognised, the monoclonal did not detect the BHRF1 homologue encoded by Herpesvirus papio or two mutants with deletions in the BH2 region. This novel rat monoclonal antibody (6A9) was used to examine tissue sections from 39 cases of non-keratinising undifferentiated nasopharyngeal carcinoma (NPC), 6 cases of metastatic NPC, 7 cases of EBV-positive NPC with squamous differentiation from Chinese patients, 15 cases of EBV-positive post-transplant lymphoproliferative disorder (PTLD), 6 EBV-containing lymphoblastoid cell lines, and 2 cases of oral hairy leukoplakia (OHL). In 11 cases of undifferentiated NPC, RT-PCR data were available for comparison with the immunohistochemistry. Both cases of OHL and two cases of LCL were positive for BHRF1 but none of the PTLD showed positive staining. All cases of undifferentiated NPC were positive for Bcl-2 but only one BHRF1 positive cell was identified in 1 of 39 cases of primary undifferentiated NPC. The 6A9 antibody produced less background staining and no nuclear positivity compared with the commercially available mouse monoclonal 5B11. It is concluded that BHRF1 can not be detected by immunohistochemistry in NPC and therefore it appears not to play a significant anti-apoptotic role in the progression of this EBV-associated tumour. The 6A9 monoclonal appears to be superior to 5B11 for the detection of pBHRF1 in tissue sections. J. Med. Virol. 65:105–113, 2001. © 2001 Wiley-Liss, Inc.
Selective CO Production in Photoelectrochemical Reduction of CO2 with a Cobalt Chlorin Complex Adsorbed on Multiwalled Carbon Nanotubes in Water (2017)

Photoelectrochemical reduction of CO2 occurred using cobalt(II) chlorin (CoII(Ch)) as a cathode active material adsorbed on multiwalled carbon nanotubes as a current collector in combination with a surface-modified BiVO4 photoanode with iron(III) oxide(hydroxide), FeO(OH), to produce CO with 83% Faradaic efficiency at an applied bias voltage of −1.3 V at the CoII(Ch)-modified cathode vs the FeO(OH)/BiVO4/FTO photoanode under visible light irradiation in a CO2-saturated aqueous solution (pH 4.6). The difference in the oxidation potential of the FeO(OH)/BiVO4/FTO electrode under dark and that under light illumination was ∼1.5 V, which was smaller than the band gap of BiVO4 (band gap energy ≈ 2.4 eV), indicating that the FeO(OH)/BiVO4/FTO photoanode lowered the total bias that enabled simultaneous water oxidation and CO2 reduction.
Turbine blade with tuned damping structure (2023)

A turbine blade is provided comprising: a root; an airfoil comprising an external wall extending radially from the root and having a radially outermost portion; and a damping structure. The external wall may comprise first and second side walls joined together to define an inner cavity of the airfoil. The damping structure may be positioned within the airfoil inner cavity and coupled to the airfoil so as to define a tuned mass damper.