gebhart/patrepeval huggingface dataset:
Retraining of Human Gait - Are Lightweight Cable-Driven Leg Exoskeleton Designs Effective? (2018)

Exoskeletons for gait training commonly use a rigid-linked "skeleton" which makes them heavy and bulky. Cable-driven exoskeletons eliminate the rigid-linked skeleton, providing a lighter and transparent design. Current cable-driven exoskeletons are aimed only at gait assistance by providing short bursts of forces to the leg during walking. It has not yet been shown if these designs are suitable for gait retraining, where rehabilitative forces need to be continuously applied to the leg in response to errors from a desired movement. The goal of this study is to investigate if a cable-driven leg exoskeleton can retrain the gait of human users. Nine healthy subjects were trained by a cable-driven leg exoskeleton to walk in a new gait pattern with 30% increase in step height from their natural gait. After 40 min of training, the gait of the subjects became significantly closer to the target gait than before the training. In three different post-training sessions, the step height of the subjects increased by 22%, 29%, and 31% on an average. In a fourth post-training session, when the subjects were instructed to ignore the training and walk naturally, the step height remained increased by 11%. These results confirm the potential of cable-driven designs in gait training applications.
Patient-Reported Outcomes Measurement Information System instruments: outperforming traditional quality of life measures in patients with back and neck pain (2019)

PROMIS correlates strongly with traditional disability measures in patients with back pain and neck pain. For both back and neck pain, the PROMIS-PF required patients to answer significantly fewer questions to achieve similar granularity. There were no significant differences in ceiling and floor effects for NDI or ODI when compared with the PROMIS-PF instrument.
Automated 3-D method for the correction of axial artifacts in spectral-domain optical coherence tomography images (2011)

The 3-D spectral-domain optical coherence tomography (SD-OCT) images of the retina often do not reflect the true shape of the retina and are distorted differently along the x and y axes. In this paper, we propose a novel technique that uses thin-plate splines in two stages to estimate and correct the distinct axial artifacts in SD-OCT images. The method was quantitatively validated using nine pairs of OCT scans obtained with orthogonal fast-scanning axes, where a segmented surface was compared after both datasets had been corrected. The mean unsigned difference computed between the locations of this artifact-corrected surface after the single-spline and dual-spline correction was 23.36 ± 4.04 μm and 5.94 ± 1.09 μm, respectively, and showed a significant difference (p < 0.001 from two-tailed paired t-test). The method was also validated using depth maps constructed from stereo fundus photographs of the optic nerve head, which were compared to the flattened top surface from the OCT datasets. Significant differences (p < 0.001) were noted between the artifact-corrected datasets and the original datasets, where the mean unsigned differences computed over 30 optic-nerve-head-centered scans (in normalized units) were 0.134 ± 0.035 and 0.302 ± 0.134, respectively.
Perfluorodiacyl peroxides: a class of free radical sources with a wide range of thermal decomposition temperatures (2006)

Perfluorodiacyl peroxides are an important class of perfluorinated peroxides. Thermal decompositions of selected temperature range perfluorinated peroxides have been analyzed in terms of stability of the radical products. In the temp of 0-90 C, all these peroxides undergo first-order decomposition in diluted solutions. EPR analyses provide important information in order to prove the structure of the oncoming perfluorinated radicals. Correlations between thermal stability and radical structures have been supposed
Extracellular adenosine controls NKT‐cell‐dependent hepatitis induction (2014)

Extracellular adenosine regulates inflammatory responses via the A2A adenosine receptor (A2AR). A2AR deficiency results in much exaggerated acute hepatitis, indicating nonredundancy of adenosine-A2AR pathway in inhibiting immune activation. To identify a critical target of immunoregulatory effect of extracellular adenosine, we focused on NKT cells, which play an indispensable role in hepatitis. An A2AR agonist abolished NKT-cell-dependent induction of acute hepatitis by concanavalin A (Con A) or α-galactosylceramide in mice, corresponding to downregulation of activation markers and cytokines in NKT cells and of NK-cell co-activation. These results show that A2AR signaling can downregulate NKT-cell activation and suppress NKT-cell-triggered inflammatory responses. Next, we hypothesized that NKT cells might be under physiological control of the adenosine-A2AR pathway. Indeed, both Con A and α-galactosylceramide induced more severe hepatitis in A2AR-deficient mice than in WT controls. Transfer of A2AR-deficient NKT cells into A2AR-expressing recipients resulted in exaggeration of Con A-induced liver damage, suggesting that NKT-cell activation is controlled by endogenous adenosine via A2AR, and this physiological regulatory mechanism of NKT cells is critical in the control of tissue-damaging inflammation. The current study suggests the possibility to manipulate NKT-cell activity in inflammatory disorders through intervention to the adenosine-A2AR pathway.
Principal component analysis of general patterns of HIV-1 replicative fitness in different drug environments (2010)

To detect general patterns and temporal trends of HIV-1 resistance, we apply principal component analysis (PCA) to in vitro fitness data. Twenty-eight thousand virus samples, obtained between 2002 and 2008, were assayed for fitness in 16 to 21 selective environments. Fitness measurements are based on replication capacity (RC), which quantifies in vitro viral replication in a single cycle of infection. RC is determined both in the absence of drugs and in the presence of 6-7 nucleoside analog reverse transcriptase inhibitors (NRTIs), 3-4 non-nucleoside reverse transcriptase inhibitors (NNRTIs), and 6-9 protease inhibitors (PIs). PCA shows remarkable structure in RC across the different environments, which reveals differences in the patterns of resistance and cross-resistance between drugs or between drug classes. To probe the causes of the observed patterns, we develop a model to generate simulated data and subject these simulated data to an equivalent analysis. By comparing the outcomes of PCA on the original and the simulated data, we quantify which part of the total variance of the original data is due to non-specific effects, class-specific effects, and drug-specific effects of resistance mutations. We find that relative fitness is mainly drug-independent and that drug-specific effects are substantially bigger than class-specific effects for NRTIs, but not for NNRTIs or PIs. The observed patterns remain remarkably stable over the period of observation. Comparison with known potent combination therapies suggests that PCA helps to identify combinations that act synergistically in preventing the emergence of resistance.
LISA Mission and System architectures and performances (2009)

In the context of the LISA Mission Formulation Study, the LISA System was studied in detail and a new baseline architecture for the whole mission was established. This new baseline is the result of trade-offs on both, mission and system level. The paper gives an overview of the different mission scenarios and configurations that were studied in connection with their corresponding advantages and disadvantages as well as performance estimates. Differences in the required technologies and their influence on the overall performance budgets are highlighted for all configurations. For the selected baseline concept, a more detailed description of the configuration is given and open issues in the technologies involved are discussed.
ChemInform Abstract: OXIDATIVE ADDITION AND REDUCTIVE ELIMINATION REACTIONS INVOLVING PLATINUM METALLACYCLES (1978)

Abstract Die thermische Zersetzung der Titelverbindungen (I), gezeigt am Beispiel des Tributylphosphinkomplexes (Ia), liefert in Dichlormethan‐ oder Dibrommethanlösung Cycloalkane und Alkene, die sich von dem metallacyclischen Teil ableiten und homologe Cycloalkane und Alkene, die durch Einlagerung einer Methylengruppe des Lösungsmittels entstehen.
Connections between sparse estimation and robust statistical learning (2013)

Recent literature on robust statistical inference suggests that promising outlier rejection schemes can be based on accounting explicitly for sparse gross errors in the modeling, and then relying on compressed sensing ideas to perform the outlier detection. In this paper, we consider two models for recovering a sparse signal from noisy measurements, possibly also contaminated with outliers. The models considered here are a linear regression model, and its natural one-bit counterpart where measurements are additionally quantized to a single bit. Our contributions can be summarized as follows: We start by providing conditions for identification and the Cramér-Rao Lower Bounds (CRLBs) for these two models. Then, focusing on the one-bit model, we derive conditions for consistency of the associated Maximum Likelihood estimator, and show the performance of relevant l1-based relaxation strategies by comparing against the theoretical CRLB.
Long-Range Communication Network in the Type 1B Bone Morphogenetic Protein Receptor (2015)

Protein-protein interactions are recognized as a fundamental phenomenon that is intimately associated with biological functions and thus are ideal targets for developing modulators for regulating biological functions. A challenge is to identify a site that is situated away from but functionally connected to the protein-protein interface. We employed bone morphogenetic proteins (BMPs) and their receptors as a model system to develop a strategy for identifying such a network of communication. Accordingly, using computational analyses with the COREX/BEST algorithm, we uncovered an overall pattern connecting various regions of BMPR-1B ectodomain, including the four conserved residues in the protein-protein interface. In preparation for testing the long-range effects of mutations of distal residues for future studies, we examined the extent of measurable perturbation of the four conserved residues by determination of the conformation and relative affinities of these BMPR-1B mutants for ligands BMP-2, -6, and -7 and GDF-5. Results suggest no significant structural changes in the receptor but do suggest that the four residues play different roles in defining ligand affinity and both intra- and intermolecular interactions play a role in defining ligand affinity. Thus, these results established two primary but necessary goals: (1) the baseline knowledge of perturbation of conserved interfacial residues for future reference and (2) the ability of the computational approach to identify the distal residues connecting to the interfacial residues. The data presented here provide the foundation for future experiments to identify the effects of distal residues that affect the specificity and affinity of BMP recognition. Protein-protein interactions are integral reactions in essentially all biological activities such as gene regulation and age-related development. Often, diseases are consequences of the alteration of these intermacromolecular interactions, which are thus recognized as a legitimate target for developing modulators for regulating biological functions. One approach is to design ligands that bind to the protein-protein interface. Another is to identify an allosteric site, an advantage of which is bypassing the potential challenge in competing for high-affinity interfacial interactions or a specific interface in a superassembly of multiple macromolecules. However, a challenge of this approach is identifying a site that is situated away from but functionally connected to the protein-protein interface.
ChemInform Abstract: CHEMOSELECTIVITY IN THE CONJUGATE ADDITION OF ALLYLSILANE TO MICHAEL ACCEPTORS (1983)

Abstract Aus dem ungesättigten Keton (I) erhält man bei der Reaktion mit Allyltrimethylsilan (II) in Gegenwart von Titantetrachlorid die isomereneSubstitutionsprodukte (III), während in Gegenwart von Fluorid‐Ionen aus (I) und (II) Gemische aus (III) und den Dienolen (IV) erhalten werden.
Controlled synthesis and characterization of the elusive thiolated Ag55cluster (2014)

A stable, Ag55 cluster protected with 4-(tert-butyl)benzyl mercaptan (BBSH) was synthesized which exhibits two prominent absorption bands with maxima at 2.25 and 2.81 eV. A molecular ion peak at m/z 11 500 ± 20 in matrix assisted laser desorption ionization mass spectrum (MALDI MS), assigned to Ag55(BBS)31 was observed. Electrospray ionization (ESI MS) shows a prominent trication along with higher charged species. An analogous Ag55(PET)31 (PET = 2-phenylethanethiol, in the thiolate form) was also synthesized under optimized conditions which proves the amenability of this cluster and the synthetic methodology to other ligands.
Simulation und Optimierung der Mehrstoff‐Rektifikation (1987)

Abstract Simulation and optimization of multicomponent distillation . Different methods for simulating multicomponent distillation columns are presented and compared with respect to the effort required and the accuracy that may be obtained. Inclusion of mass transfer kinetics based on the laws of multicomponent diffusion in the models significantly increases computer time, but the additional accuracy in the prediction of concentration profiles may justify this effort also in design practice. In particular, the unusual behaviour of concentration profiles due to multidiffusion effects can only be explained by such improved models. The new methods of multicriteria optimization offer substantial advantages over a scalar‐optimization and, in addition to economic criteria, also allow inclusion of aspects of operational safety and of environmental requirements.
ChemInform Abstract: (Trichloromethyl)benzene: A Versatile Reagent for the Preparation of Substituted Benzophenones. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Noble metal alloy clusters in the gas phase derived from protein templates: unusual recognition of palladium by gold (2013)

Matrix assisted laser desorption ionization of a mixture of gold and palladium adducts of the protein lysozyme (Lyz) produces naked alloy clusters of the type Au24Pd(+) in the gas phase. While a lysozyme-Au adduct forms Au18(+), Au25(+), Au38(+) and Au102(+) ions in the gas phase, lysozyme-Pd alone does not form any analogous cluster. Addition of various transition metal ions (Ag(+), Pt(2+), Pd(2+), Cu(2+), Fe(2+), Ni(2+) and Cr(3+)) in the adducts contributes to drastic changes in the mass spectrum, but only palladium forms alloys in the gas phase. Besides alloy formation, palladium enhances the formation of specific single component clusters such as Au38(+). While other metal ions like Cu(2+) help forming Au25(+) selectively, Fe(2+) catalyzes the formation of Au25(+) over all other clusters. Gas phase cluster formation occurs from protein adducts where Au is in the 1+ state while Pd is in the 2+ state. The creation of alloys in the gas phase is not affected whether a physical mixture of Au and Pd adducts or a Au and Pd co-adduct is used as the precursor. The formation of Au cores and AuPd alloy cores of the kind comparable to monolayer protected clusters implies that naked clusters themselves may be nucleated in solution.
Patient-oriented gene set analysis for cancer mutation data (2010)

Recent research has revealed complex heterogeneous genomic landscapes in human cancers. However, mutations tend to occur within a core group of pathways and biological processes that can be grouped into gene sets. To better understand the significance of these pathways, we have developed an approach that initially scores each gene set at the patient rather than the gene level. In mutation analysis, these patient-oriented methods are more transparent, interpretable, and statistically powerful than traditional gene-oriented methods.
Transport of soluble species through tuff core (1997)

This letter report presents and summarizes the results of flow and tracer tests using a core sample of Topopah Spring tuff containing a saw-cut fracture. A dilute Na-Cl-HCO{sub 3} solution containing Br{sup -} or I{sup -} tracer was eluted through the core under constant flow conditions (0.1, 0.2, 2.0 mL/h) and at three temperatures (23, 59, 92 {degrees}C). A more complete analysis of these data and the implications of these results for transport of soluble species in the Topopah Spring tuff in the Near Field Environment (NFE) will be reported in the synthesis on Integrated Testing activities to be included in the NFE report.
Current and voltage ADC using a differential pair of single-electron bipolar avalanche transistors (2009)

Single-electron bipolar avalanche transistors (SEBATs) enable current sensing by electron counting at room temperature. Here, differential SEBAT circuits combining the functions of amplification and analog-to-digital (A/D) conversion are proposed and characterized for two applications: Low-current A/D conversion and differential voltage A/D conversion. Charge detection efficiencies in the order of 30% are reached, allowing for the direct A/D conversion of currents in the 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-13</sup> A range. An equivalent of the differential pair is used as a differential voltage ADC.
Proteolytic Activity-Independent Activation of the Immune Response by Gingipains from Porphyromonas gingivalis (2022)

Porphyromonas gingivalis, a keystone pathogen in periodontitis (PD), produces cysteine proteases named gingipains (RgpA, RgpB, and Kgp), which strongly affect the host immune system. The range of action of gingipains is extended by their release as components of outer membrane vesicles, which efficiently diffuse into surrounding gingival tissues. However, away from the anaerobic environment of periodontal pockets, increased oxygen levels lead to oxidation of the catalytic cysteine residues of gingipains, inactivating their proteolytic activity. In this context, the influence of catalytically inactive gingipains on periodontal tissues is of significant interest. Here, we show that proteolytically inactive RgpA induced a proinflammatory response in both gingival keratinocytes and dendritic cells. Inactive RgpA is bound to the cell surface of gingival keratinocytes in the region of lipid rafts, and using affinity chromatography, we identified RgpA-interacting proteins, including epidermal growth factor receptor (EGFR). Next, we showed that EGFR interaction with inactive RgpA stimulated the expression of inflammatory cytokines. The response was mediated via the EGFR-phosphatidylinositol 3-kinase (PI3K)-protein kinase B (AKT) signaling pathway, which when activated in the gingival tissue rich in dendritic cells in the proximity of the alveolar bone, may significantly contribute to bone resorption and the progress of PD. Taken together, these findings broaden our understanding of the biological role of gingipains, which in acting as proinflammatory factors in the gingival tissue, create a favorable milieu for the growth of inflammophilic pathobionts. <b>IMPORTANCE</b> Gingipain cysteine proteases are essential virulence factors of Porphyromonas gingivalis, an oral bacterium implicated in development of periodontitis. Gingipains diffusing from anaerobic periodontal pockets lose proteolytic activity in the oxygenated environment of gingival tissues. We found that despite the loss of activity, gingipains still elicit a strong inflammatory response, which may contribute to the progression of periodontitis and bone resorption. Moreover, we identified the host molecules utilized by the pathogen as receptors for proteolytically inactivated gingipains. The broad distribution of those receptors in human tissue suggests their involvement in systemic diseases associated with periodontal pathogens.
Synthesis and Properties of Oligonucleotides Having a Phosphorus Chiral Center by Incorporation of Conformationally Rigid 5‘-Cyclouridylic Acid Derivatives (2000)

This paper describes the design and synthesis of a conformationally rigid dimer building block Umpc3Um as a chiral center at the phosphate group with the S/N junction where c3 refers to a propylene bridge linked between the uracil 5-position and 5'-phosphate group of pUm. The extensive H1 NMR analysis of Umpc3Um suggests that the 5'-upstream Um has predominantly a C2'-endo conformation and the pc3Um moiety exists almost exclusively in a C3'-endo conformation. The absolute configuration of the diastereomers Umpc3Um(fast) (8a) and Umpc3Um(slow) (8b) was determined by CD spectroscopy as well as computer simulations. The oligonucleotides U4[Umpc3Um(fast)]U4 (13a) and U4[Umpc3Um(slow)]U4 (13b) incorporating 8a and 8b were synthesized by use of the phosphoramidite building blocks 11a and 11b, respectively. The Tm experiments of the duplexes formed between these modified oligomers and the complementary oligomers imply that the modified oligomer 13a having Umpc3Um(fast) has the Sp configuration at the chiral phosphoryl group.
Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in C. elegans (2014)

RNA granules have been likened to liquid droplets whose dynamics depend on the controlled dissolution and condensation of internal components. The molecules and reactions that drive these dynamics in vivo are not well understood. In this study, we present evidence that a group of intrinsically disordered, serine-rich proteins regulate the dynamics of P granules in C. elegans embryos. The MEG (maternal-effect germline defective) proteins are germ plasm components that are required redundantly for fertility. We demonstrate that MEG-1 and MEG-3 are substrates of the kinase MBK-2/DYRK and the phosphatase PP2A(PPTR-½). Phosphorylation of the MEGs promotes granule disassembly and dephosphorylation promotes granule assembly. Using lattice light sheet microscopy on live embryos, we show that GFP-tagged MEG-3 localizes to a dynamic domain that surrounds and penetrates each granule. We conclude that, despite their liquid-like behavior, P granules are non-homogeneous structures whose assembly in embryos is regulated by phosphorylation.
Supplementary Figure 3 from Oncolytic Vaccinia Virus Disrupts Tumor-Associated Vasculature in Humans (2023)

&lt;p&gt;Supplementary Figure 3 PDF file - 83K, Normal fibroblasts (GM38 cells) do not express VEGFR2 and are not sensitized to JX-594 infection upon incubation with VEGF&lt;/p&gt;