gebhart/patrepeval huggingface dataset:
Axonal Protective Role of LINGO-1 Blockade in the Visual System: Results From a Study in Rats and Design of a Phase 2 Clinical Trial for BIIB033, an Anti-LINGO-1 Monoclonal Antibody, in Subjects With a First Episode of Acute Optic Neuritis (P2.262) (2014)

OBJECTIVE: To establish the potential for BIIB033, a monoclonal antibody to LINGO-1, as axonal protective therapy in the visual system. BACKGROUND: Acute optic neuritis (AON) is characterized by inflammatory damage to the myelin sheath and axons comprising the optic nerve and is frequently the first manifestation of MS. In humans, and~20% of retinal nerve fibers are lost after an AON episode. LINGO-1 (leucine-rich repeats and immunoglobulin domain-containing neurite outgrowth inhibitor receptor-interacting protein-1) is a component of CNS signaling complexes that suppress axonal repair/remyelination. Blocking LINGO-1 improves remyelination in animal models, thereby providing a rationale for evaluating BIIB033 in a Phase 2 study for AON. DESIGN/METHODS: The optic nerve crush rat model of axonal degeneration was used to investigate the protective role of anti-LINGO-1 (or vehicle) in the absence of autoimmune inflammation. Anti LINGO-1 was given intravitreally or at the crush site. Tissue was processed for visualization and quantification. The length of labeled axons that had regrown beyond the crush site was measured. For the clinical trial, eligible individuals (N=80) are being randomized to BIIB033 or placebo every 4 weeks for 20 weeks to assess whether BIIB033 prevents optic nerve axonal degeneration when given <28 days before the first episode of unilateral AON. Participants are undergoing serial measurements of retinal ganglion cell (RGC) fibers and layers by spectral domain optical coherence tomography (ClinicalTrials.gov #NCT01721161). RESULTS: In the optic nerve crush study, LINGO-1 was expressed in RGCs. Axonal degeneration was reduced in anti-LINGO-1-treated rats; vehicle-treated rats showed axonal degeneration and collapse of RGC fibers. Blocking LINGO-1 induced axonal regeneration versus controls. The clinical trial will determine whether protective effects in optic nerve and RGCs occur using systemic administration of BIIB033. CONCLUSIONS: Blocking LINGO-1 improved axonal regeneration in a rat model of optic nerve axonal injury. A Phase 2 study is underway to examine the neuroprotective efficacy of BIIB033 after AON in the clinic. Study Supported by: Biogen Idec
P0775 IMPORTANCE OF ILEOCECAL VALVE (ICV) ON THE PROGNOSIS OF PATIENTS WITH SHORT BOWEL SYNDROME. (2004)

Introduction: Patients with short bowel syndrome has their prognosis related to the amount of bowel remaining. To compare progression of children and young adults with Short Bowel Syndrome (SBS) with Ileal Cecal Valve (ICV) (group I) or without ICV (group II). Methods: The patients followed for SBS since 1990 were included on this study. Sixteen patients, 6 with ICV (GI) and 10 without ICV (GII). The pathologies that caused the intestinal loss were: GI 2 w/ necrotysing enterocholitis; 2 gastrosquisis; 1 jejunal atresia e 1 mesenteric trombosis. On the GII: 3 gastrosquisis; 2 acidentals; 1 apple peel; 1 Hirschsprung disease; 1 necrotysing enterocholitis; 1 jejunal atresia; 1 Crohn’s disease. Results: There was no significant diference (p0,05) for age: GI median 87,5 months and on GII 41,5 moths. The time on parenteral nutrition (PN) was not different (media): GI 15,5 mo and GII 19,2 mo, as well as the number of semi-implatable catheters (media): GI 1,5 e GII 2,3. The amount of remained intestine didn’t show significant difference (media): GI 55,33 cm e GII 49 cm. There was difference between groups related to the number of deaths (GI=0; GII=4); clinical evolution (GI 6 adaptation obtained; GII 2 adaptation obtained, 3 still on PN). Hepatic complications: Group I: 1 with cholestasis resolved that presented afterward with biliary litiasis, acute cholecistitis and he was submitted to cholecistectomy; 1 has biliary litiasis and 4 never had hepatic problems. Group II: 7 have abnormal liver enzymes, 1 had biliary litiasis (was submitted to cholecistectomy) and 1 never had hepatic problems. Conclusion: This study showed that patients with Short Bowel Syndrome who had lost the ileal-cecal valve have more frequent hepatic complications and higher mortality.
Purification and characterization of an allergen from celery immunochemically related to an allergen present in several other plant species. Identification as a profilin (1992)

The purification of a 15 kD allergen from celery was obtained by a four step procedure. Evidence for at least two isoallergenic forms was obtained after analysis by two-dimensional-electrophoresis. A rabbit polyclonal antibody raised against this purified allergen allowed us to confirm our precedent results on the occurrence of allergenically and molecular mass-related components in celery and birch and mugwort pollens. In addition such components were also present in numerous other species like Cynodon dactylon, Sorghum halopense, Poa pratensis, Ambrosia elatior and in apple and carrot. The 15 kD allergen was identified as profilin by use of a specific rabbit polyclonal antibody that recognized a recombinant birch profilin. In addition, the purified celery allergen binds IgE from sera of patients allergic to birch profilin. These results reinforce the concept of profilin as a panallergen responsible in some patients for cross-allergic manifestations to various and unrelated species of grasses, weeds, trees, vegetables and fruits.
High performance NEMS devices for sensing applications (2015)

NEMS based sensors open several opportunities for integrated solutions in emerging domains as chemical analysis and life science. With critical dimensions ranging between 10 and 100 nm, those devices can be made at the VLSI scale, possibly co-integrated with CMOS and are well suited for autonomous, highly sensitive or dense sensors. Several applications will be presented, as complex gas portable recognitions systems, mass spectrometry, or bio-sensors.
Translation equivalence in free groups (2004)

Motivated by the work of Leininger on hyperbolic equivalence of homotopy classes of closed curves on surfaces, we investigate a similar phenomenon for free groups. Namely, we study the situation when two elements $g,h$ in a free group $F$ have the property that for every free isometric action of $F$ on an $\mathbb{R}$-tree $X$ the translation lengths of $g$ and $h$ on $X$ are equal. We give a combinatorial characterization of this phenomenon, called translation equivalence, in terms of Whitehead graphs and exhibit two difference sources of it. The first source of translation equivalence comes from representation theory and $SL_2$ trace identities. The second source comes from geometric properties of groups acting on real trees and a certain power redistribution trick. We also analyze to what extent these are applicable to the tree actions of surface groups that occur in the Thurston compactification of the Teichmuller space.
Evaluated kinetic and photochemical data for atmospheric chemistry: Volume V – heterogeneous reactions on solid substrates (2010)

Abstract. This article, the fifth in the ACP journal series, presents data evaluated by the IUPAC Subcommittee on Gas Kinetic Data Evaluation for Atmospheric Chemistry. It covers the heterogeneous processes on surfaces of solid particles present in the atmosphere, for which uptake coefficients and adsorption parameters have been presented on the IUPAC website in 2009. The article consists of an introduction and guide to the evaluation, giving a unifying framework for parameterisation of atmospheric heterogeneous processes. We provide summary sheets containing the recommended uptake parameters for the evaluated processes. Four substantial appendices contain detailed data sheets for each process considered for ice, mineral dust, sulfuric acid hydrate and nitric acid hydrate surfaces, which provide information upon which the recommendations are made.
Designed U7 snRNAs inhibit DUX4 expression and improve FSHD-associated outcomes in DUX4 overexpressing cells and FSHD patient myotubes (2020)

Facioscapulohumeral muscular dystrophy (FSHD) arises from epigenetic changes that de-repress the <i>DUX4</i> gene in muscle. The full-length DUX4 protein causes cell death and muscle toxicity, and therefore we hypothesize that FSHD therapies should center on inhibiting full-length <i>DUX4</i> expression. In this study, we developed a strategy to accomplish <i>DUX4</i> inhibition using U7-small nuclear RNA (snRNA) antisense expression cassettes (called U7-asDUX4). These non-coding RNAs were designed to inhibit production or maturation of the full-length <i>DUX4</i> pre-mRNA by masking the <i>DUX4</i> start codon, splice sites, or polyadenylation signal. In so doing, U7-asDUX4 snRNAs operate similarly to antisense oligonucleotides. However, in contrast to oligonucleotides, which are limited by poor uptake in muscle and a requirement for lifelong repeated dosing, U7-asDUX4 snRNAs can be packaged within myotropic gene therapy vectors and may require only a single administration when delivered to post-mitotic cells <i>in vivo</i>. We tested several U7-asDUX4s that reduced <i>DUX4</i> expression <i>in vitro</i> and improved DUX4-associated outcomes. Inhibition of <i>DUX4</i> expression via U7-snRNAs could be a new prospective gene therapy approach for FSHD or be used in combination with other strategies, like RNAi therapy, to maximize <i>DUX4</i> silencing in individuals with FSHD.
Three-sided pyramid wavefront sensor, part II: preliminary demonstration on the new comprehensive adaptive optics and coronagraph test instrument testbed (2022)

The next generation of giant ground and space telescopes will have the light-collecting power to detect and characterize potentially habitable terrestrial exoplanets using high-contrast imaging for the first time. This will only be achievable if the performance of the Giant Segment Mirror Telescopes (GSMTs) extreme adaptive optics (ExAO) systems are optimized to their full potential. A key component of an ExAO system is the wavefront sensor (WFS), which measures aberrations from atmospheric turbulence. A common choice in current and next-generation instruments is the pyramid wavefront sensor (PWFS). ExAO systems require high spatial and temporal sampling of wavefronts to optimize performance and, as a result, require large detectors for the WFS. We present a closed-loop testbed demonstration of a three-sided pyramid wavefront sensor (3PWFS) as an alternative to the conventional four-sided pyramid wavefront (4PWFS) sensor for GSMT-ExAO applications on the innovative comprehensive adaptive optics and coronagraph test instrument (CACTI). The 3PWFS is less sensitive to read noise than the 4PWFS because it uses fewer detector pixels. The 3PWFS has further benefits: a high-quality three-sided pyramid optic is easier to manufacture than a four-sided pyramid. We describe the design of the two components of the CACTI system, the adaptive optics simulator and the PWFS testbed that includes both a 3PWFS and 4PWFS. We detail the error budget of the CACTI system, review its operation and calibration procedures, and discuss its current status. A preliminary experiment was performed on CACTI to study the performance of the 3PWFS to the 4PWFS in varying strengths of turbulence using both the raw intensity and slopes map signal processing methods. This experiment was repeated for a modulation radius of 1.6 and 3.25 λ / D. We found that the performance of the two wavefront sensors is comparable if modal loop gains are tuned.
New chiral ligands bearing two N-heterocyclic carbene moieties at a dioxolane backbone. Gold, palladium and rhodium complexes as enantioselective catalysts (2010)

Biscarbene ligands with two imidazolin-2-ylidene moieties at a chiral dioxolane backbone were used as ligands for gold, rhodium and palladium complexes. All new complexes showed varying degrees of enantioselectivity toward hydrogenation of prochiral alkenes with ees up to 95%.
Direct immobilization of gangliosides onto gold-carboxymethyldextran sensor surfaces by hydrophobic interaction: applications to antibody characterization (1998)

We describe a novel immobilization technique to investigate interactions between immobilized gangliosides (GD3, GM1, and GM2) and their respective antibodies, antibody fragments, or binding partners using an optical biosensor. Immobilization was performed by direct injection onto a carboxymethyldextran sensor chip and did not require derivatization of the sensor surface or the ganglioside. The ganglioside appeared to bind to the sensor surface by hydrophobic interaction, leaving the carbohydrate epitope available for antibody or, in the case of GM1, cholera toxin binding. The carboxyl group of the dextran chains on the sensor surface did not appear to be involved in the immobilization as evidenced by equivalent levels of immobilization following conversion of the carboxyl groups into acyl amino esters, but rather the dextran layer provided a hydrophilic coverage of the sensor chip which was essential to prevent nonspecific binding. This technique gave better reactivity and specificity for anti-ganglioside monoclonal antibodies (anti-GD3: KM871, KM641, R24; and anti-GM2: KM966) than immobilization by hydrophobic interaction onto a gold sensor surface or photoactivated cross-linking onto carboxymethydextran. This rapid immobilization procedure has facilitated detailed kinetic analysis of ganglioside/antibody interactions, with the surface remaining viable for a large number of cycles (>125). Kinetic constants were determined from the biosensor data using linear regression, nonlinear least squares and equilibrium analysis. The values of kd, ka, and KAobtained by nonlinear analysis (KAKM871 = 1.05, KM641 = 1.66, R24 = 0.14, and KM966 = 0.65 x 10(7) M-1) were essentially independent of concentration and showed good agreement with data obtained by other analytical methods.
Chemistry of Si-SiO2 interface trap annealing (1988)

The kinetics and chemistry of Si-SiO2 interface trap annealing are examined in detail. Measurements of interface trap density Dit as a function of anneal time were performed with several process variables as parameters: oxide thickness, anneal ambient, temperature, bulk carrier type, metallization damage, and orientation. Experiments were carried out using rapid thermal processing and capacitance-voltage measurements of aluminum gate metal-oxide-semiconductor capacitors. Anneal temperature and crystal orientation have the strongest effect on the kinetics. 〈100〉 interfaces can be described by a power-law temporal variation; 〈111〉 kinetics are slightly more complicated. In both cases the experimentally observed anneal behavior is in conflict with the commonly used second-order surface recombination model. We propose a two-reaction model involving atomic hydrogen dimerization and hydrogen/interface trap reactions. This model sucessfully predicts anneal kinetics over a temperature range of 170–500 °C, representing a 106 dynamic range in anneal rates. The difference in anneal behavior between 〈111〉 and 〈100〉 interfaces is explained by postulating different trap anneal mechanisms for the Pb0 and Pb1 defect centers. This hypothesis is supported by trap production kinetics induced by extended anneals.
Optimum DMT-based transceivers for multiuser communications (2003)

The paper considers discrete multitone (DMT) modulation for multiuser communications when multiple users are supported by the same system, a zero-padding redundancy is employed at the transmitter output, and linear redundancy removal is used at the channel output. These users may have differing quality of service (QoS) requirements, as quantified by bit rate and symbol-error rate specifications, and are each assigned an equal number of subchannels. Our goal is to minimize the transmitted power, given the QoS specifications and subject to the knowledge of the channel and the second-order statistics of the colored interference at the receiver input. In particular, we find an optimum bit-loading scheme that distributes the bit rate transmitted across the various subchannels belonging to each user, and, subject to this bit allocation, we determine the precise subchannels assigned to each user, the optimum transceiver characterized by the input/output block transforms, and the redundancy removal operation. A major conclusion is that even though the optimum bit-rate allocation differs from the single-user case, the optimum transceiver does not. Further, it is determined entirely by the channel and interference conditions, and is unaffected by the QoS requirements.
quEEGNet: Quantum AI for Biosignal Processing (2022)

In this paper, we introduce an emerging quantum machine learning (QML) framework to assist classical deep learning methods for biosignal processing applications. Specifically, we propose a hybrid quantum-classical neural network model that integrates a variational quantum circuit (VQC) into a deep neural network (DNN) for electroencephalogram (EEG), electromyogram (EMG), and electrocorticogram (ECoG) analysis. We demonstrate that the proposed quantum neural network (QNN) achieves state-of-the-art performance while the number of trainable parameters is kept small for VQC.
IFN-gamma Limits Peripheral T cell Expansion of Extrathymic T cells. (89.18) (2007)

Abstract When overexpressed under the p56Lck proximal promotor, Oncostatin M induces extrathymic T cell development in the lymph nodes. During LCMV infection, extrathymic (ET) T cells produce copious amounts of IFN-γ and their expansion is precocious but of limited amplitude because of early apoptosis. Moreover, ET T cells show significant apoptosis in uninfected mice. Hence, we sought to understand why ET T cells are more susceptible to apoptosis than thymic T cells. We found that the mitochondrial apoptotic pathway is likely involved in apoptosis of CD4+ ET T cells because of lower Il-7Rα and Bcl-2 levels compared to thymic T cells. In contrast, this deficit was not seen in CD8+ ET T cells. However, CD8+ ET T cells displayed higher Fas and active caspase 8 expression indicating apoptosis via the death receptor pathway. Moreover, we found that ET T cells and thymic T cells in homeostatic peripheral expansion (HPE) shared many similarities: memory phenotype, accelerated turnover and increased susceptibility to apoptosis. Moreover, spontaneous IFN-γ secretion by CD8+ ET T cells leading to massive accumulation in sera was observed. Finally, we found that CD8+ T cell survival was restored during HPE induced with ifngR−/−T cells as well as in ifng−/−ET T cells compared to IFN-γ-responsive T cells. Taken together, these results show that IFN-γ regulates apoptosis of ET T cells T cells in HPE and thereby limits their accumulation in vivo.
SHARC: A streaming model for FPGA accelerators and its application to Saliency (2011)

Reconfigurable hardware such as FPGAs are being increasingly employed for accelerating compute-intensive applications. While recent advances in technology have increased the capacity of FPGAs, lack of standard models for developing custom accelerators creates issues with scalability and compatibility. We present SHARC - Streaming Hardware Accelerator with Run-time Configurability, for an FPGA-based accelerator. This model is at a lower-level compared to existing stream processing models and provides the hardware designer with a flexible platform for developing custom accelerators. The SHARC model provides a generic interface for each hardware module and a hierarchical structure for parallelism at multiple levels in an accelerator. It also includes a parameterization and hierarchical run-time reconfiguration framework to enable hardware reuse for flexible yet high throughput design. This model is very well suited for compute-intensive applications in areas such as real-time vision and signal processing, where stream processing provides enormous performance benefits. We present a case-study by implementing a bio-inspired Saliency-based visual attention system using the proposed model and demonstrate the benefits of run-time reconfiguration. Experimental results show about 5X speedup over an existing CPU implementation and up to 14X higher Performance-per-Watt over a relevant GPU implementation.
Effect of Backbone Chemistry on the Structure of Polyurea Films Deposited by Molecular Layer Deposition (2017)

An experimental investigation into the growth of polyurea films by molecular layer deposition was performed by examining trends in the growth rate, crystallinity, and orientation of chains as a function of backbone flexibility. Growth curves obtained for films containing backbones of aliphatic and phenyl groups indicate that an increase in backbone flexibility leads to a reduction in growth rate from 4 to 1 Å/cycle. Crystallinity measurements collected using grazing incidence X-ray diffraction and Fourier transform infrared spectroscopy suggest that some chains form paracrystalline, out-of-plane stacks of polymer segments with packing distances ranging from 4.4 to 3.7 Å depending on the monomer size. Diffraction intensity is largely a function of the homogeneity of the backbone. Near-edge X-ray absorption fine structure measurements for thin and thick samples show an average chain orientation of ∼25° relative to the substrate across all samples, suggesting that changes in growth rate are not caused by differences in chain angle but instead may be caused by differences in the frequency of chain terminations. These results suggest a model of molecular layer deposition-based chain growth in which films consist of a mixture of upward growing chains and horizontally aligned layers of paracrystalline polymer segments.
Genes Involved in miRNA Biogenesis Are Not Downregulated in SARS-CoV-2 Infection (2023)

miRNAs, small non-coding RNAs that regulate gene expression, are involved in various pathological processes, including viral infections. Virus infections may interfere with the miRNA pathway through the inhibition of genes involved in miRNA biogenesis. A reduction in the number and the levels of miRNAs expressed in nasopharyngeal swabs of patients with severe COVID-19 was lately observed by us, pointing towards the potential of miRNAs as possible diagnostic or prognostic biomarkers for predicting outcomes among patients with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. The objective of the present study was to investigate whether SARS-CoV-2 infection influences the expression levels of messenger RNAs (mRNAs) of key genes involved in miRNA biogenesis. mRNA levels of <i>AGO2</i>, <i>DICER1</i>, <i>DGCR8</i>, <i>DROSHA</i>, and Exportin-5 (<i>XPO5</i>) were measured by quantitative reverse-transcription polymerase chain reaction (RT-qPCR) in nasopharyngeal swab specimens from patients with COVID-19 and controls, as well as in cells infected with SARS-CoV-2 in vitro. Our data showed that the mRNA expression levels of <i>AGO2</i>, <i>DICER1</i>, <i>DGCR8</i>, <i>DROSHA</i>, and <i>XPO5</i> were not significantly different in patients with severe COVID-19 when compared to patients with non-severe COVID-19 and controls. Similarly, the mRNA expression of these genes was not affected by SARS-CoV-2 infection in NHBE and Calu-3 cells. However, in Vero E6 cells, <i>AGO2</i>, <i>DICER1</i>, <i>DGCR8</i>, and <i>XPO5</i> mRNA levels were slightly upregulated 24 h after infection with SARS-CoV-2. In conclusion, we did not find evidence for downregulation of mRNA levels of miRNA biogenesis genes during SARS-CoV-2 infection, neither ex vivo nor in vitro.