gebhart/patrepeval huggingface dataset:
Gait freezing in Parkinson's disease and the stride length sequence effect interaction (2009)

Freezing of gait (FOG) has been identified as one of the main contributors to gait disturbances in Parkinson's disease. While the pathophysiology remains enigmatic, several factors such as step length and the sequence effect (step to step reduction in amplitude) may lead to the occurrence of FOG. It was hypothesized that by reducing step length, FOG episodes would present more frequently if a significant sequence effect (measured as a regression slope) was co-existent in the subject. Twenty-six participants with Parkinson's disease were separated clinically into a freezing (PD + FOG, n = 16) and non-freezing (PD-FOG, n = 10) group, with 10 age-matched control participants. Testing involved walking trials where preferred step length was set at 100%, 75%, 50% and 25% of normalized step length. The number of FOG episodes increased in the 50% condition and further increased in the 25% condition compared to other conditions. The participants with FOG also demonstrated a larger average regression slope, with significant differences in the 75%, 50% and 25% conditions when compared to the PD-FOG and control groups. There were no significant differences when comparing the slope of the PD-FOG and control group, indicating the reduced step length and the sequence effect may have led to the occurrence of FOG. These findings support the possible dual requirement of a reduced step length and a successive step to step amplitude reduction to lead to FOG.
Strategies for developing design spaces for viral clearance by anion exchange chromatography during monoclonal antibody production (2010)

The quality-by-design (QbD) regulatory initiative promotes the development of process design spaces describing the multidimensional effects and interactions of process variables on critical quality attributes of therapeutic products. However, because of the complex nature of production processes, strategies must be devised to provide for design space development with reasonable allocation of resources while maintaining highly dependable results. Here, we discuss strategies for the determination of design spaces for viral clearance by anion exchange chromatography (AEX) during purification of monoclonal antibodies. We developed a risk assessment for AEX using a formalized method and applying previous knowledge of the effects of certain variables and the mechanism of action for virus removal by this process. We then use design-of-experiments (DOE) concepts to perform a highly fractionated factorial experiment and show that varying many process parameters simultaneously over wide ranges does not affect the ability of the AEX process to remove endogenous retrovirus-like particles from CHO-cell derived feedstocks. Finally, we performed a full factorial design and observed that a high degree of viral clearance was obtained for three different model viruses when the most significant process parameters were varied over ranges relevant to typical manufacturing processes. These experiments indicate the robust nature of viral clearance by the AEX process as well as the design space where removal of viral impurities and contaminants can be assured. In addition, the concepts and methodology presented here provides a general approach for the development of design spaces to assure that quality of biotherapeutic products is maintained.
Vaccinia virus morphogenesis is blocked by temperature-sensitive mutations in the F10 gene, which encodes protein kinase 2 (1995)

Four previously isolated temperature-sensitive (ts) mutants of vaccinia virus WR (ts28, ts54, ts61, and ts15) composing a single complementation group have been mapped by marker rescue to the F10 open reading frame located within the genomic HindIII F DNA fragment. Sequencing of the F10 gene from wild-type and mutant viruses revealed single-amino-acid substitutions in the F10 polypeptide responsible for thermolabile growth. Although the ts mutants displayed normal patterns of viral protein synthesis, electron microscopy revealed a profound morphogenetic defect at the nonpermissive temperature (40 degrees C). Virion assembly was arrested at an early stage, with scant formation of membrane crescents and no progression to normal spherical immature particles. The F10 gene encodes a 52-kDa serine/threonine protein kinase (S. Lin and S. S. Broyles, Proc. Natl. Acad. Sci. USA 91:7653-7657, 1994). We expressed a His-tagged version of the wild-type, ts54, and ts61 F10 polypeptides in bacteria and purified these proteins by sequential nickel affinity and phosphocellulose chromatography steps. The wild-type F10 protein kinase activity was characterized in detail by using casein as a phosphate acceptor. Whereas the wild-type and ts61 kinases displayed similar thermal inactivation profiles, the ts54 kinase was thermosensitive in vitro. These findings suggest that protein phosphorylation plays an essential role at an early stage of virion assembly.
Mining Risk Factors in RFID Baggage Tracking Data (2015)

Airport baggage management is a significant part of the aviation industry. However, for several reasons every year a vast number of bags are mishandled (e.g., Left behind, send to wrong flights, gets lost, etc.,) which costs a lot of money to the aviation industry as well as creates inconvenience and frustration to the passengers. To remedy these problems we propose a detailed methodology for mining risk factors from Radio Frequency Identification (RFID) baggage tracking data. The factors should identify potential issues in the baggage management. However, the baggage tracking data are low level and not directly accessible for finding such factors. Moreover, baggage tracking data are highly imbalanced, for example, our experimental data, which is a large real-world data set from the Scandinavian countries, contains only 0.8% mishandled bags. This imbalance presents difficulties to most data mining techniques. The paper presents detailed steps for pre-processing the unprocessed raw tracking data for higher-level analysis and handling the imbalance problem. We fragment the data set based on a number of relevant factors and find the best classifier for each of them. The paper reports on a comprehensive experimental study with real RFID baggage tracking data and it shows that the proposed methodology results in a strong classifier, and can find interesting concrete patterns and reveal useful insights of the data.
the low-temperature crystal structure of the pure-spermine form of Z-DNA reveals binding of a spermine molecule in the minor groove (1994)

The X-ray crystal structure of the pure-spermine form of the left-handed Z-DNA duplex [d(CGCGCG)]2 has been determined at a temperature of -110 degrees C. Whereas the previously described room temperature structure of the pure-spermine form showed only the presence of a single "interhelix" spermine molecule, mediating contacts between neighboring duplexes (Egli et al., 1991), a second "intrahelix" spermine molecule as well as two hydrated sodium ions were found in the structure determined at low temperature. This second spermine molecule binds primarily within the minor groove of two hexamer duplexes that are stacked in an end-to-end fashion in the crystal lattice. Thus, the intrahelix spermine molecule interacts with a single infinite helix. The spine of hydration observed in other structures of Z-DNA hexamers is partially replaced and partially displaced by the intrahelix spermine molecule. In Z-DNA, phosphate groups are relatively closely spaced across the minor groove compared to the right-handed double-helical conformation of B-DNA. The intrahelix spermine molecule decreases cross-groove electrostatic repulsion within the Z-DNA helix, thereby increasing its relative stability. This structure may therefore provide an explanation for the role of spermine as a very effective inducer of the conformational B-DNA to Z-DNA transition with alternating dG-dC sequences in solution.
Pedestrian Dead Reckoning with Particle Filter for handheld smartphone (2016)

Commonly used Global Navigation Satellite Systems (GNSS) are inappropriate as Location Based Services (LBS) in indoor environment. Therefore research teams are developing different systems, which can be used as a suitable alternative. One of options is to use Inertial Navigation System (INS) which consists of inertial sensors and mathematic procedures. This concept has been known for a long time, but with arrival of Microelectro Mechanical System (MEMS) INS found wide use. Smartphones with inertial sensors, such as accelerometers and gyroscopes, allow us to use them as input devices for Pedestrian Dead Reckoning (PDR). In this paper we present PDR by using smartphone sensors. They can be classified as low-cost Inertial Measurement Unit (IMU), and have been compared with more precise and expensive Xsens IMU. Accuracy of inertial sensors has increased in the past few years, but they still cannot alone provide proper accuracy because of many negative effects, such as heading drift due to gyroscope bias. Particle Filter (PF) has been successfully used with map constraints to increase the accuracy of proposed location system. Presented results show that low-cost smartphone IMU combined with PF can be applicable as proper navigation system.
Dispersion analysis of planar metallo-dielectric EBG structures in Ansoft HFSS (2008)

In the paper, the dispersion analysis of planar metallo-dielectric electromagnetic band gap (MD-EBG) structures in Ansoft HFSS is discussed. The attention is turned to critical settings of unit cell modeling for the correct computation of the dispersion diagram. First, a dispersion analysis of the original uniplanar compact photonic band gap (UC-PBG) structure was done, and the results were compared with the literature. Next, a dispersion analysis of a simple, a 3D planar EBG with the 1D periodicity, is presented. The existence of the surface wave band gap, predicted by the dispersion diagram, was verified experimentally.
Microbial cellulose (1991)

Cellulose is probably the most abundant biologically produced polymer and has been important to man for many centuries in the wood, textile and paper industries. It is a major constituent of plant, and some algal and fungal cell walls. It is less widely known that cellulose is also produced by several different types of microorganisms. Cellulose is a homopolymer of glucose in β(1–4) linkage, but is generally found in nature in close association with xylans, other polysaccharides and polymers such as lignin. By contrast, the cellulose synthesized by bacteria is free from contamination with other materials. For this reason bacteria have been studied to elucidate the route of cellulose biosynthesis. The properties deriving from the microfibrillar nature of cellulose produced by microorganisms has led to commercial interest in the material.
Broad Requirement for the Mediator Subunit RGR-1 for Transcription in the Caenorhabditis elegans Embryo (2002)

The Mediator-related transcription co-factors integrate positive and negative inputs and recruit and activate the RNA polymerase II complex. To understand the role of Mediator during transcription, it is important to identify Mediator subunits that are essential for its functions. In the yeast Mediator, the conserved component Rgr1 is associated with multiple subunits that are required for specific activation or repression events. Yeast rgr1 is essential for viability, for certain repression mechanisms, and for activation of heat shock genes, but it is not known whether rgr1 is generally important for transcription. Here we have performed the first analysis of rgr-1 function in a metazoan. We found that in the developing Caenorhabditis elegans embryo rgr-1 is broadly required for transcription and for phosphorylation of both Ser-2 and Ser-5 of the RNA polymerase II C-terminal domain repeat. We conclude that RGR-1 fulfills a critical Mediator function that is broadly essential for metazoan mRNA transcription and that RGR-1 may be required at an early recruitment or initiation step.
microDuMIP: target-enrichment technique for microarray-based duplex molecular inversion probes (2014)

Molecular inversion probe (MIP)-based capture is a scalable and effective target-enrichment technology that can use synthetic single-stranded oligonucleotides as probes. Unlike the straightforward use of synthetic oligonucleotides for low-throughput target capture, high-throughput MIP capture has required laborious protocols to generate thousands of single-stranded probes from DNA microarray because of multiple enzymatic steps, gel purifications and extensive PCR amplifications. Here, we developed a simple and efficient microarray-based MIP preparation protocol using only one enzyme with double-stranded probes and improved target capture yields by designing probes with overlapping targets and unique barcodes. To test our strategy, we produced 11 510 microarray-based duplex MIPs (microDuMIPs) and captured 3554 exons of 228 genes in a HapMap genomic DNA sample (NA12878). Under our protocol, capture performance and precision of calling were compatible to conventional MIP capture methods, yet overlapping targets and unique barcodes allowed us to precisely genotype with as little as 50 ng of input genomic DNA without library preparation. microDuMIP method is simpler and cheaper, allowing broader applications and accurate target sequencing with a scalable number of targets.
Controlled Free-Radical Polymerization: New Breath in a Mature Technology (2005)

Abstract The controlled (or “living”) radical polymerization techniques, nitroxide-mediated radical polymerization, atom transfer radical polymerization, reversible addition fragmentation chain-transfer polymerization, methods based on iniferters are reviewed. For each technique a brief historical profile is given, and the mechanism, features, and applications are discussed. A few examples of the macromolecular architectures that can be achieved through these techniques are reported and some implementations and developments from industrial companies are presented.
Multiagent Bidirectionally-Coordinated Nets: Emergence of Human-level Coordination in Learning to Play StarCraft Combat Games (2017)

Many artificial intelligence (AI) applications often require multiple intelligent agents to work in a collaborative effort. Efficient learning for intra-agent communication and coordination is an indispensable step towards general AI. In this paper, we take StarCraft combat game as a case study, where the task is to coordinate multiple agents as a team to defeat their enemies. To maintain a scalable yet effective communication protocol, we introduce a Multiagent Bidirectionally-Coordinated Network (BiCNet ['bIknet]) with a vectorised extension of actor-critic formulation. We show that BiCNet can handle different types of combats with arbitrary numbers of AI agents for both sides. Our analysis demonstrates that without any supervisions such as human demonstrations or labelled data, BiCNet could learn various types of advanced coordination strategies that have been commonly used by experienced game players. In our experiments, we evaluate our approach against multiple baselines under different scenarios; it shows state-of-the-art performance, and possesses potential values for large-scale real-world applications.
Precise control of end‐tidal carbon dioxide and oxygen improves BOLD and ASL cerebrovascular reactivity measures (2010)

In-depth investigation of cerebrovascular blood flow and MR mechanisms underlying the blood oxygenation level dependent signal requires precise manipulation of the arterial partial pressure of carbon dioxide and oxygen, measured by their noninvasive surrogates, the end-tidal values. The traditional methodology consists of administering a fixed fractional concentration of inspired CO(2), but this causes a variable ventilatory response across subjects, resulting in different values of end-tidal partial pressures of CO(2) and O(2). In this study, we investigated whether fine control of these end-tidal partial pressures would improve stability and predictability of blood oxygenation level dependent and arterial spin labeling signals for studying cerebrovascular reactivity. In 11 healthy volunteers, we compared the MR signals generated by the traditional fixed fractional concentration of inspired CO(2) method to those of an automated feed-forward system, a simpler, safer, and more compact alternative to dynamic end-tidal forcing systems, designed to target constant end-tidal partial pressures of CO(2) and O(2). We found that near square-wave changes in end-tidal partial pressure of CO(2) of 5, 7.5, and 10 mm Hg (+/-1.01 mm Hg within two to three breaths) and constrained changes in the end-tidal partial pressure of O(2) (<10 mm Hg) induced cerebral vascular reactivity measurements with faster transitions, together with improved stability and gradation, than those achieved with the traditional fixed fractional concentration of inspired CO(2) method.
Nitric Oxide and the Regulation of Blood Pressure in the Hypertension-Prone and Hypertension-Resistant Sabra Rat (1996)

We examined the role of nitric oxide (NO) in the inherited resistance or susceptibility to hypertension in the Sabra hypertension-prone (SBH) and hypertension-resistant (SBN) rat. Basal mean arterial blood pressure was significantly greater in SBH than in SBN rats. Phenylephrine elevated blood pressure to a similar extent in both substrains, whereas the NO synthase inhibitor NG-monomethyl-L-arginine (L-NMMA) had a greater pressor effect in SBN rats. The vasoconstrictor potency of phenylephrine was significantly higher in endothelium-intact aortic rings from the SBH rat, whereas the vasoconstrictor potency of L-NMMA was higher in those from the SBN substrain. Acetylcholine-induced endothelium-dependent relaxation was greater in aortic rings from SBN rats. The vasodilator potency of glyceryl trinitrate was significantly higher in aortic rings from SBH rats and was enhanced after endothelium removal. Both the activity of calcium-dependent NO synthase from aortic endothelial cells and the basal concentration of nitrite/nitrate in plasma were significantly greater in SBN than in SBH rats. In normotensive Wistar rats, basal mean arterial blood pressure, the pressor effect of L-NMMA, endothelial NO synthase activity, and plasma nitrite/ nitrate concentrations were all between the values in SBH and SBN rats. These results indicate that a decrease in NO generation plays a role in the susceptibility of SBH rats to hypertension. Furthermore, the resistance to hypertension in the SBN strain may be related to increased NO generation.
Detecting Changes in Suicide Content Manifested in Social Media Following Celebrity Suicides (2015)

The Werther effect describes the increased rate of completed or attempted suicides following the depiction of an individual's suicide in the media, typically a celebrity. We present findings on the prevalence of this effect in an online platform: r/SuicideWatch on Reddit. We examine both the posting activity and post content after the death of ten high-profile suicides. Posting activity increases following reports of celebrity suicides, and post content exhibits considerable changes that indicate increased suicidal ideation. Specifically, we observe that post-celebrity suicide content is more likely to be inward focused, manifest decreased social concerns, and laden with greater anxiety, anger, and negative emotion. Topic model analysis further reveals content in this period to switch to a more derogatory tone that bears evidence of self-harm and suicidal tendencies. We discuss the implications of our findings in enabling better community support to psychologically vulnerable populations, and the potential of building suicide prevention interventions following high-profile suicides.
CDK6 kinase activity is required for thymocyte development (2011)

Cyclin-dependent kinase-6 (CDK6) is required for early thymocyte development and tumorigenesis. To mechanistically dissect the role of CDK6 in thymocyte development, we generated and analyzed mutant knock-in mice and found that mice expressing a kinase-dead Cdk6 allele (Cdk6(K43M)) had a pronounced reduction in thymocytes and hematopoietic stem cells and progenitor cells (Lin⁻Sca-1⁺c-Kit⁺ [LSK]). In contrast, mice expressing the INK4-insensitive, hyperactive Cdk6(R31C) allele displayed excess proliferation in LSK and thymocytes. However, this is countered at least in part by increased apoptosis, which may limit progenitor and thymocyte expansion in the absence of other genetic events. Our mechanistic studies demonstrate that CDK6 kinase activity contributes to Notch signaling because inactive CDK6 kinase disrupts Notch-dependent survival, proliferation, and differentiation of LSK, with concomitant alteration of Notch target gene expression, such as massive up-regulation of CD25. Further, knockout of CD25 in Cdk6(K43M) mice rescued most defects observed in young mice. These results illustrate an important role for CDK6 kinase activity in thymocyte development that operates partially through modulating Notch target gene expression. This role of CDK6 as a downstream mediator of Notch identifies CDK6 kinase activity as a potential therapeutic target in human lymphoid malignancies.
Effect of seed layer on the magnetoresistance characteristics in a-CoNbZr-based spin valves (1998)

We have investigated an amorphous-based spin valve structure of NiO(40 nm)/Co(2)/Cu(t)/Co(1.2)/CoNbZr(20) for the application of magnetic random access memory. The spin valves were prepared on Si(100) by sputtering, and characterized by XRD, VSM, AFM/MFM, and 4-point probe. To improve GMR characteristics by controlling the interfacial structures of the Co/Cu/Co trilayer, we employed NiFe as a seed layer for NiO and achieved a GMR ratio of 10.7%. The spin valves with the seed layer exhibited lower ferromagnetic coupling between the pinned and free layers, lower pinning fields, and higher coercivities of the pinned layer than the spin valves without a seed layer. These phenomena were discussed mainly in terms of interfacial microstructural change as well as Neel's orange peel model.
The dispersive effects of Basset history forces on particle motion in a turbulent flow (1984)

A calculation of the asymptotic particle diffusion coefficient in an unbounded stationary homogeneous turbulent flow is performed for a particle subjected to both added mass and Basset history forces, as well as the normal Stokes drag. The original value obtained by Tchen is shown to be in error by an additional term which for a sphere of diameter d is given by (d2/2πνf)σ, νf being the kinematic viscosity, and σ the covariance of the incipient relative velocity between particle and local fluid. Noticeably this term does not depend upon the particle density. This extra term is consistent with values obtained for the particle diffusion coefficient from a numerical simulation.