gebhart/patrepeval huggingface dataset:
Dexterous Control of Seven Functional Hand Movements Using Cortically-Controlled Transcutaneous Muscle Stimulation in a Person With Tetraplegia (2018)

Individuals with tetraplegia identify restoration of hand function as a critical, unmet need to regain their independence and improve quality of life. Brain-Computer Interface (BCI)-controlled Functional Electrical Stimulation (FES) technology addresses this need by reconnecting the brain with paralyzed limbs to restore function. In this study, we quantified performance of an intuitive, cortically-controlled, transcutaneous FES system on standardized object manipulation tasks from the Grasp and Release Test (GRT). We found that a tetraplegic individual could use the system to control up to seven functional hand movements, each with >95% individual accuracy. He was able to select one movement from the possible seven movements available to him and use it to appropriately manipulate all GRT objects in real-time using naturalistic grasps. With the use of the system, the participant not only improved his GRT performance over his baseline, demonstrating an increase in number of transfers for all objects except the <i>Block</i>, but also significantly improved transfer times for the heaviest objects (videocassette (<i>VHS</i>), <i>Can</i>). Analysis of underlying motor cortex neural representations associated with the hand grasp states revealed an overlap or non-separability in neural activation patterns for similarly shaped objects that affected BCI-FES performance. These results suggest that motor cortex neural representations for functional grips are likely more related to hand shape and force required to hold objects, rather than to the objects themselves. These results, demonstrating multiple, naturalistic functional hand movements with the BCI-FES, constitute a further step toward translating BCI-FES technologies from research devices to clinical neuroprosthetics.
Iterative receiver for clipped GFDM signals (2014)

Multicarrier communication is a well-known and widely used method in the current wireless or wired data transmission. Orthogonal Frequency Division Multiplexing (OFDM) is the leading technology in this area and is implemented in various forms in almost every current broadband communication systems. It has a number of advantages, but also few significant shortcomings. Especially the high out-of-band radiation and high peak-to-average ratio (PAPR). For that reason, it is inconvenient to employ OFDM in particular applications, e.g. Cognitive Radio (CR). The Generalized Frequency Division Multiplexing (GFDM) is a novel non-orthogonal multicarrier waveform design method, which can be considered as an alternative to OFDM in some scenarios. However, also GFDM can suffer from high PAPR. In this article, we will show that clipping can be conveniently used for PARP reduction of GFDM signals. But, on the other hand, clipping causes nonlinear degradation of the signal and that means worse bit error ratio (BER). One of the solutions to this problem is to use iterative reception for nonlinear noise mitigation. Therefore, the main goal of the article is to propose an iterative receiver structure for deliberately clipped GFDM signals. The simulations show that the BER performance of the GFDM system, undergoing clipping as PARP reduction technique, can be significantly improved using the proposed iterative receiver.
Delay-hopped transmitted-reference RF communications (2003)

Previously, the authors have invented and experimented with a new radio communications scheme called delay-hopped transmitted-reference (DHTR) radio. This technique can function either as an impulse radio, or can employ a more traditional spread-spectrum carrier such as broadband noise. The DHTR method is well-suited to short-range transmissions in a high multipath environment, and, in contrast to time-modulated impulse radio, is easy to synchronize at the receiver. Finally, DHTR receivers and transmitters are not highly complex, and can be implemented in a cost-effective way.
Importance of the inducible costimulator molecule for the induction of allergic immune responses and its decreased expression on T helper cells after venom immunotherapy (2004)

The inducible costimulator (ICOS), a newly identified member of the CD28 receptor family that is induced after T-cell activation, and its ligand (ICOSL), being expressed on activated monocytes and dendritic cells play a key role in T-cell-mediated immune responses. As ICOS costimulation also seems to regulate T helper 2 effector cells, the aim of this study was to analyse the function of this molecule in allergic immune responses and their specific therapy, mainly venom immunotherapy (VIT). CD4+ T cells from grass pollen-, or bee or wasp venom-allergic donors were stimulated in the presence of autologous mature dendritic cells, which were pulsed with different allergen doses. In this system, costimulation of ICOS strongly enhanced the production of the T helper 2 cytokines interleukin (IL)-4, IL-5 and IL-10 and, to a lesser extent, secretion of the T helper 1 cytokine, interferon-gamma. Expression of ICOS on CD4+ T cells was induced, in a dose-dependent manner, after a few days of stimulation with allergen-pulsed dendritic cells, reaching a peak on day 6. The upregulation of ICOS after stimulation with venom allergens was significantly reduced after VIT. Addition of exogenous IL-10 (which is induced during VIT) to the co-cultures before VIT also led to an inhibition of ICOS expression, while blocking of IL-10 in co-cultures after VIT partially restored the expression of ICOS. These data indicate that the inhibition of T cells after immunotherapy also involves decreased induction of the costimulatory molecule ICOS, which, in turn, seems to be dependent on the presence of IL-10, also associated with the inhibited status of T cells after VIT. This makes the ICOS-ICOSL pathway a potential target for therapeutic intervention in T helper 2-mediated diseases, such as allergic diseases.
In vitro transcribed guide RNAs trigger an innate immune response via the RIG-I pathway (2018)

Abstract CRISPR-Cas9 genome editing is revolutionizing fundamental research and has great potential for the treatment of many diseases. While editing of immortalized cell lines has become relatively easy, editing of therapeutically relevant primary cells and tissues can remain challenging. One recent advancement is the delivery of a Cas9 protein and an in vitro transcribed (IVT) guide RNA (gRNA) as a precomplexed ribonucleoprotein (RNP). This approach allows editing of primary cells such as T cells and hematopoietic stem cells, but the consequences beyond genome editing of introducing foreign Cas9 RNPs into mammalian cells are not fully understood. Here we show that the IVT gRNAs commonly used by many laboratories for RNP editing trigger a potent innate immune response that can be several thousand times stronger than benchmark immune stimulating ligands. IVT gRNAs are recognized in the cytosol through the RIG-I pathway but not the MDA5 pathway, thereby triggering a type I interferon response. Removal of the 5’-triphosphate from gRNAs ameliorates inflammatory signaling and prevents the loss of viability associated with genome editing in hematopoietic stem cells. The potential for Cas9 RNP editing to induce a potent antiviral response indicates that care must be taken when designing therapeutic strategies to edit primary cells. Abbreviations Cas CRISPR-associated CIP calf intestinal alkaline phosphatase CRISPR clustered, regularly interspaced, short palindromic repeat dCas9 nuclease-dead Cas9 HEK293 Human embryonic kidney cells 293 HEK293T Human embryonic kidney cells 293 SV40 large T antigen HeLa Henrietta Lacks cells HSPCs CD34 + human hematopoietic stem and progenitor cells IFNAR1 Interferon Alpha And Beta Receptor Subunit 1 IFNβ/IFNB1 Interferon beta ISG15 Interferon-stimulated gene 15 IVT – in vitro transcribed KO knockout MAVS mitochondrial activator of virus signaling MDA5/IFIH1 melanoma differentiation-associated gene 5/ Interferon Induced with Helicase C Domain 1 PAMP pathogen-associated molecular pattern RIG-I/DDX58 retinoic acid-inducible gene I/ DExD-H-box helicase 58 gRNA guide RNA SPRI solid phase reversible immobilization WT wild type
Effects of the glucosphingolipid synthesis inhibitor, PDMP, on lysosomes in cultured cells. (1994)

The glucosphingolipid synthesis inhibitor, 1-phenyl-2-decanoylamino-3-morpholino-1-propanol (PDMP) has a wide range of effects on cell physiology and morphology. Here, we studied the effects of high concentrations of PDMP on cells in culture and found that fluorescent analogs of PDMP targeted to the lysosomes of Chinese hamster ovary (CHO) cells. Overnight incubation of the cells in the presence of drug induced enlargement ("vacuolization") of the lysosomes. PDMP was toxic at high concentrations (> 30 microM); this finding was used to select CHO cells that exhibited increased resistance to PDMP (PDMPR cells). The PDMPR cells were approximately 2-fold more resistant to PDMP than the parental cells (CHO-P). PDMPR cells were resistant to a number of other drugs that are also lipophilic and possess a titratable amino group. The multidrug resistance exhibited by the PDMPR cells was distinct from that observed in cells (MDR cells) that overproduce the plasma membrane drug pump, P-glycoprotein. In addition, MDR cells were extremely sensitive to PDMP.
Excitability and contractility of skeletal muscle engineered from primary cultures and cell lines (2001)

The purpose of this study was to compare the excitability and contractility of three-dimensional skeletal muscle constructs, termed myooids, engineered from C2C12 myoblast and 10T1/2 fibroblast cell lines, primary muscle cultures from adult C3H mice, and neonatal and adult Sprague-Dawley rats. Myooids were 12 mm long, with diameters of 0.1-1 mm, were excitable by transverse electrical stimulation, and contracted to produce force. After approximately 30 days in culture, myooid cross-sectional area, rheobase, chronaxie, resting baseline force, twitch force, time to peak tension, one-half relaxation time, and peak isometric force were measured. Specific force was calculated by dividing peak isometric force by cross-sectional area. The specific force generated by the myooids was 2-8% of that generated by skeletal muscles of control adult rodents. Myooids engineered from C2C12-10T1/2 cells exhibited greater rheobase, time to peak tension, and one-half relaxation time than myooids engineered from adult rodent cultures, and myooids from C2C12-10T1/2 and neonatal rat cells had greater resting baseline forces than myooids from adult rodent cultures.
Cellular interaction in germinal centers. Roles of CD40 ligand and B7-2 in established germinal centers (1995)

Costimulatory interactions between T and B lymphocytes are crucial for T cell activation and B cell proliferation and differentiation. We have compared the roles of CD40L and B7-2 in the initiation and maturation of humoral immunity by administering anti-CD40 ligand (L) or anti-B7-2 Ab during the early (days -1 to 3) or late (days 6-10) phases of primary responses to thymus-dependent (Td) and -independent (Ti) Ags. Germinal center (GC) formation in response to a Td Ag was inhibited completely by the early administration of anti-CD40L or anti-B7-2 Abs. Later in the response, established GCs remained sensitive to anti-CD40L but were resistant to treatment with anti-B7-2. However, Ig hypermutation was reduced dramatically in GCs of anti-B7-2-treated mice and humoral memory was impaired. Early administration of anti-CD40L reduced serum Ab levels to approximately 10% of controls, whereas early treatment with anti-B7-2 reduced Ab production by only 50%. Later treatments with either Ab had no effect on Ab production. Response to a type II Ti Ag was more resistant than Td responses to interruption of costimulatory interactions. Our findings suggest that the costimulatory roles of CD40:CD40L and B7-2:CD28/CTLA-4 differ in the GC; administration of anti-CD40L abrogates an established GC reaction, whereas Ab to B7-2 suppresses Ig hypermutation and entry into the B cell memory compartment. Once B cells have entered the differentiation pathway to Ab production, neither CD40L nor B7-2 is necessary for their continued differentiation and persistence.
IRAK4 in TLR/IL‐1R signaling: Possible clinical applications (2008)

A member of the IL-1 receptor (IL-1R)-associated kinase (IRAK) family, IRAK4, has been shown to play an essential role in Toll-like receptor (TLR)-mediated signaling. IRAK4 kinase-inactive knockin mice have been shown to be completely resistant to LPS- and CpG-induced shock, due to impaired TLR-mediated induction of pro-inflammatory cytokines and chemokines. A reduction of LPS-, R848- and IL-1-mediated mRNA stability contributes to the reduced cytokine and chemokine production in bone marrow (BM)-derived macrophages from IRAK4 kinase-inactive knockin mice: however, not all of the TLR/IL-1R signaling events are ablated in IRAK4 kinase-inactive knockin mice. A paper in this issue of the European Journal of Immunology shows that, while JNK activation is significantly impaired, NF-kappaB and IRF3 activation are retained in the absence of IRAK4 kinase activity. These residual TLR/IL-1R-induced signaling events allow the production of some cytokines and chemokines (including TNFalpha and CXCL1); at early times after the stimulation and induction of a group of TLR-mediated MyD88/IRAK4-independent genes in IRAK4 kinase-inactive knockin cells. Therefore, pharmacological blocking of IRAK4 kinase activity will retain some levels of host defence, while reducing the levels and duration of inflammatory responses, which should provide beneficial therapies for sepsis and chronic inflammatory diseases.
Regulation of proliferation and cytokine expression of bone marrow fibroblasts: role of c-myb. (1993)

The c-myb protooncogene plays a major role in regulating the process of in vitro and in vivo hematopoiesis via its activity as transcriptional regulator in hematopoietic progenitor cells. Since the bone marrow microenvironment appears to regulate in vivo hematopoiesis by maintaining the growth of multipotent progenitors via secretion of specific cytokines, we asked whether c-myb is also required for the proliferation of and/or cytokine production by stromal cells that generate fibroblast-like colonies (fibroblast colony-forming units [CFU-F]). Using the reverse transcriptase polymerase chain reaction technique, we detected low levels of c-myb mRNA transcripts in human normal bone marrow fibroblasts. Treatment of these cells with c-myb antisense oligodeoxynucleotides caused downregulation of c-myb expression, decreased in the number of marrow CFU-F colonies (approximately 54% inhibition) and in the cell number within residual colonies (approximately 80%), and downregulation of granulocyte/macrophage colony-stimulating factor (GM-CSF) and stem cell factor (SCF) mRNA expression. Transfection of T98G glioblastoma cells, in which expression of c-myb, GM-CSF, and SCF mRNAs is undetectable or barely detectable, with a plasmid containing a full-length c-myb cDNA under the control of the SV40 promoter induced the expression of biologically active SCF and GM-CSF in these cells. Regulation of GM-CSF expression by c-myb was due in part to transactivation of the GM-CSF promoter. These results indicate that, in addition to regulating hematopoietic cell proliferation, c-myb is also required for proliferation of and cytokines synthesis by bone marrow fibroblasts.
HLA class II genotype influences the type of liver injury in drug-induced idiosyncratic liver disease (2004)

Drug-induced idiosyncratic liver disease (DIILD) depends largely on host susceptibility factors. Small studies support the genetic influence of human leukocyte antigen (HLA) class II molecules on the predisposition to DIILD. We sought associations between HLA-DRB and -DQB alleles and DIILD considered collectively or according to the biochemical expression of liver damage. We studied a total of 140 patients with a definitive or probable diagnosis of DIILD, as assessed with the Council for International Organizations of Medical Sciences scale, with 635 volunteer bone marrow and blood donors serving as controls. HLA-DRB1* and -DQB1* genotyping was performed by hybridization with sequence-specific oligonucleotides after genomic amplification. The group with DIILD did not differ from control subjects with regard to the distribution of HLA-DRB and -DQB antigens. The frequencies of alleles DRB1*15 (35.4% vs. 18.6% of controls; P =.002; odds ratio [OR] 2.31) and DQB1*06 (61.5% vs. 40.8%; P =.001; OR 2.32) were significantly increased in patients with the cholestatic/mixed type of liver damage in comparison to healthy subjects. By contrast, frequencies of alleles DRB1*07 (16.9% vs. 35.4%; P =.003; OR 0.37) and DQB1*02 (32.3% vs. 55.8%; P =.0003; OR 0.39) were significantly decreased. In conclusion, there is no association between any specific HLA allele and the propensity to develop DIILD. However, the genetic influence associated with HLA class II alleles appears to play a role in the biochemical expression of liver injury in cholestatic/mixed hepatotoxicity and may explain why a given drug may cause different patterns of liver damage.
Coexpression of CD15 and CD20 by Reed-Sternberg cells in Hodgkin's disease. (1991)

The immunophenotype of the Reed-Sternberg cells in Hodgkin's disease is heterogeneous among different cases; this heterogeneity has contributed to the continuing uncertainty regarding the normal counterpart of the Reed-Sternberg cell. In this study, the authors demonstrate coexpression of the B-cell marker, CD20, and the granulocyte associated antigen, CD15, by Reed-Sternberg cells in three of 20 cases of nodular sclerosis and mixed cellularity Hodgkin's disease using a double-labelling technique in one case and staining of serial sections in three cases. Additionally, the authors found that expression of CD20 occurred more often in tumors with a monomorphous proliferation of mononuclear and binucleate Hodgkin's and Reed-Sternberg cells, without numerous eosinophils or polymorphonuclear neutrophils. In contrast, expression of CD15 by Reed-Sternberg cells was associated with a greater granulocyte infiltrate. The presence or absence of fibrosis, plasma cells, and histiocytes did not correlate with antigen expression. These results suggest that there may be a continuum of antigen expression by Reed-Sternberg cells, with some cells expressing CD20, some CD15, and others expressing both antigens; cells coexpressing both CD15 and CD20 may represent an unstable intermediate in the process of antigen switching. The possibility that antigen expression by the neoplastic cells in a given case may modulate depending on the background infiltrate could explain the heterogeneity of immunophenotype among cases of Hodgkin's disease.
Antibody-Mediated Targeting of siRNA via the Human Insulin Receptor Using Avidin−Biotin Technology (2008)

Delivery of short interfering RNA (siRNA) to cells in culture, and in vivo, is possible with combined use of a receptor-specific monoclonal antibody (mAb) and avidin-biotin technology. In the present studies, the luciferase gene is transiently expressed in human 293 epithelial cells. The siRNA delivery system is composed of the siRNA, monobiotinylated on the 3'-terminus of the sense strand, and a conjugate of streptavidin (SA) and a mAb to the human insulin receptor (HIR). Exposure of cells to 3'-biotinyl-siRNA bound to the HIRMAb/SA conjugate, but not to unconjugated SA, avidin, or the HIRMAb, causes a >90% reduction in luciferase gene expression. The receptor-targeted siRNA effect is maximal at 48 h after delivery of the siRNA to the cells, and the effect is lost by 7 days after a single application of the targeted siRNA in culture. The KI of the receptor-targeted siRNA inhibition of gene expression is 30.5 +/- 11.7 nM, and significant inhibition is observed with siRNA concentrations as low as 3 nM. In conclusion, the combination of a receptor-specific targeting ligand, such as the HIRMAb, and avidin-biotin technology allows for high affinity capture of the monobiotinylated siRNA by the targeting mAb. The siRNA is effectively delivered to the cytosol of cells, and knockdown of gene expression with the HIRMAb/SA delivery system is comparable to RNA interference effects obtained with cationic polyplexes. Whereas the use of cationic polyplexes in vivo is problematic, the bond between the targeting mAb and the siRNA is stable with avidin-biotin technology, and RNAi effects at distant sites such as brain are observed in vivo following an intravenous administration of the targeted siRNA.
The PilZ Domain Is a Receptor for the Second Messenger c-di-GMP (2006)

The ubiquitous bacterial second messenger c-di-GMP controls exopolysaccharide synthesis, flagella- and pili-based motility, gene expression, and interactions of bacteria with eukaryotic hosts. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets have remained unknown. Recently, Amikam and Galperin (Amikam, D., and Galperin, M. (2006) Bioinformatics 22, 3-6) hypothesized that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding. This hypothesis has been tested here using the Escherichia coli PilZ domain protein YcgR, its individual PilZ domain and the PilZ domain from Gluconacetobacter xylinus BcsA. YcgR was purified and found to bind c-di-GMP tightly and specifically, Kd 0.84 microm. Individual PilZ domains from YcgR and BcsA also bound c-di-GMP, albeit with lesser affinity, indicating that PilZ is sufficient for binding. The site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding. It is suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilize the bound ligand and initiate the downstream signal transduction cascade. While the identity of the downstream partner(s) of YcgR remains unknown, it is shown that YcgR regulates flagellum-based motility in a c-di-GMP-dependent manner. The inactivation of ycgR improves swimming and swarming motility of the poorly motile yhjH mutants of Salmonella enterica serovar Typhimurium UMR1. Therefore, biochemical and genetic evidence presented here establishes PilZ as a long sought after c-di-GMP-binding domain and YcgR as a c-di-GMP receptor affecting motility in enterobacteria.
Elevated nucleosome levels in systemic inflammation and sepsis* (2003)

Patients with severe sepsis and septic shock have elevated plasma levels of nucleosomes. We suggest that apoptosis, probably resulting from exposure of cells to excessive amounts of inflammatory mediators, might by involved in the pathogenesis of multiple organ dysfunction syndrome.
Acoustic investigation of cavitation noise from offset ink film splitting (2006)

The acoustic signal from the nip during film splitting between inked rollers and on ink transfer to paper was investigated on laboratory scale, using two sheet-fed offset inks (based on mineral o ...
Simultaneous correction of the influence of skin color and fat on tissue spectroscopy by use of a two-distance fiber-optic probe and orthogonalization technique (2005)

We have demonstrated simultaneous correction for the optical interference of skin and fat in tissue spectra by using a two-distance fiber-optic probe. We obtained the correction by orthogonalizing the spectra collected at a long source-detector distance (SD) to the spectra collected at a short SD and mapped to the long SD space. The method was validated in tissuelike three-layer phantoms as well as preliminarily in human tissue. After the correction, a partial-least-squares model of the phantoms showed enhanced prediction performance.