gebhart/patrepeval huggingface dataset:
Upper motor neuron assessment and early diagnosis in ALS (2019)

Considerable neurologic injury has already occurred by the time the first symptom appears in amyotrophic lateral sclerosis (ALS) and, although it is one of the most rapidly progressive of the neurodegenerative diseases, the average time from symptom onset to diagnosis is approximately 9 to 12 months.1,2 Unfortunately, every month of diagnostic delay equates to worsening motor neuron damage and diminished chances that experimental therapies might be effective. The diagnosis of ALS remains a clinical one, supported by electrodiagnostic and other testing, and ALS diagnostic criteria require evidence of both upper motor neuron (UMN) and lower motor neuron (LMN) signs. Because LMN signs are often easier to detect, and UMN signs may not appear until later in the disease course, early diagnosis is challenging, and may be made more so by the fact that progressive LMN weakness can be caused by so many other pure motor disorders (e.g., motor radiculopathy, multifocal motor neuropathy, myasthenia gravis, and the inflammatory myopathies).
Tissue-Engineered Grafts from Human Decellularized Extracellular Matrices: A Systematic Review and Future Perspectives (2018)

Tissue engineering and regenerative medicine involve many different artificial and biologic materials, frequently integrated in composite scaffolds, which can be repopulated with various cell types. One of the most promising scaffolds is decellularized allogeneic extracellular matrix (ECM) then recellularized by autologous or stem cells, in order to develop fully personalized clinical approaches. Decellularization protocols have to efficiently remove immunogenic cellular materials, maintaining the nonimmunogenic ECM, which is endowed with specific inductive/differentiating actions due to its architecture and bioactive factors. In the present paper, we review the available literature about the development of grafts from decellularized human tissues/organs. Human tissues may be obtained not only from surgery but also from cadavers, suggesting possible development of Human Tissue BioBanks from body donation programs. Many human tissues/organs have been decellularized for tissue engineering purposes, such as cartilage, bone, skeletal muscle, tendons, adipose tissue, heart, vessels, lung, dental pulp, intestine, liver, pancreas, kidney, gonads, uterus, childbirth products, cornea, and peripheral nerves. In vitro recellularizations have been reported with various cell types and procedures (seeding, injection, and perfusion). Conversely, studies about in vivo behaviour are poorly represented. Actually, the future challenge will be the development of human grafts to be implanted fully restored in all their structural/functional aspects.
Asymmetric aldol reaction of 2-cyanopropionates catalysed by trans-chelating chiral diphosphine ligand TRAP–rhodium(I) complex (1998)

trans-Chelating chiral diphosphine TRAP ligands bearing P-aromatic groups are effective for RhI-catalysed asymmetric aldol reaction of 2-cyanopropionates with an aldehyde to give the corresponding aldol adduct with up to 93% ee.
FPGA Based on Integration of CMOS and RRAM (2010)

In this paper, a novel CMOS-nano hybrid reconfigurable field-prgrammable gate array architecture (rFPGA) is introduced based on resistive memory (RRAM) devices. Different from the existing crossbar-based CMOS-nano architectures, rFPGA consists of mainly 1T1R RRAM structures that can be fabricated by using a CMOS-compatible process. These devices can efficiently establish FPGA block memories. More importantly, novel RRAM routing switches are developed to replace the CMOS routing switches to achieve significant density enhancement and power reduction. The simulation results demonstrate that 2-D and 3-D rFPGAs provide at least 2 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\times$</tex> </formula> –3 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\times$</tex> </formula> overall improvement in terms of area with 20% lower power consumption, compared with the corresponding CMOS FPGAs.
Multipurpose HTS Coagulation Analysis: Assay Development and Assessment of Coagulopathic Snake Venoms (2017)

Coagulation assays currently employed are often low throughput, require specialized equipment and/or require large blood/plasma samples. This study describes the development, optimization and early application of a generic low-volume and high-throughput screening (HTS) assay for coagulation activity. The assay is a time-course spectrophotometric measurement which kinetically measures the clotting profile of bovine or human plasma incubated with Ca<sup>2+</sup> and a test compound. The HTS assay can be a valuable new tool for coagulation diagnostics in hospitals, for research in coagulation disorders, for drug discovery and for venom research. A major effect following envenomation by many venomous snakes is perturbation of blood coagulation caused by haemotoxic compounds present in the venom. These compounds, such as anticoagulants, are potential leads in drug discovery for cardiovascular diseases. The assay was implemented in an integrated analytical approach consisting of reversed-phase liquid chromatography (LC) for separation of crude venom components in combination with parallel post-column coagulation screening and mass spectrometry (MS). The approach was applied for the rapid assessment and identification of profiles of haemotoxic compounds in snake venoms. Procoagulant and anticoagulant activities were correlated with accurate masses from the parallel MS measurements, facilitating the detection of peptides showing strong anticoagulant activity.
Logic characterization vehicle design for maximal information extraction for yield learning (2014)

A new type of logic characterization vehicle (LCV) that optimizes design, test, and diagnosis for yield learning is described. The Carnegie-Mellon LCV (CM-LCV) uses constant-testability theory and logic/layout regularity to create a parameterized design that exhibits both front- and back-end characteristics of a product-like, customer design. Design and test analysis of various CM-LCV designs (one of which has >4M gates) demonstrates that design time and density, test and diagnosis can all be simultaneously improved. For example, conventional ATPG produces test sets that are 2X larger, produce significantly poorer fault-detection and diagnostic characteristics for standard and advanced fault models, and require runtimes that are several orders of magnitude larger than the simple approach used to generate the constant test set for the CM-LCV. On the design side, a fully designed custom layout is 25% smaller than its synthesized, place-and-routed counterpart.
Dynamics of the actin cytoskeleton in Phytophthora infestans hyphae and infection structures (2015)

The actin cytoskeleton is a dynamic but well organized intracellular framework that is indispensable for the viability of eukaryotic cells. Its functions range from intracellular transport, formation of contractile rings, nuclear segregation, endocytosis and facilitating apical cell expansions. We studied the actin cytoskeleton dynamics in the filamentous oomycete plant pathogen Phytophthora infestans in transgenic lines expressing the actin binding peptide Lifeact-eGFP by fluorescence microscopy. This showed that in hyphae actin filament cables and plaques are cortically localized. The distance between the hyphal tip and the first actin filament plaque correlated strongly with growth velocity. Upon growth termination, actin filament plaques appeared in the hyphal tip. The plaques were nearly immobile with average lifetimes exceeding one hour; much longer (over 500-fold) than the lifetimes of actin patches in fungi. Plaque assembly required ~30 seconds while disassembly took only ~10 seconds. In contrast to actin patches in yeast, plaque disassembly was not accompanied with formation and internalization of endocytic vesicles (Meijer et al. 2014, Cell. Microbiol.). We also investigated the in vivo actin dynamics during early stages of pathogenesis. At the site of contact with the plant cell a condensed transient actin structure was observed that resembles aster-like actin structures formed upon encountering hard surfaces. Our results suggest that the actin cytoskeleton has distinct functions during the P. infestans lifecycle. Future efforts will focus at identifying interactors and key regulators of the actin cytoskeleton and pinpoint features in the actin network that are unique for oomycetes.
Blind separation of surface EMG signals (2002)

Multiple site measurements with surface EMG electrodes can produce a significant amount of cross-talk, which depends on electrode placement. The "blind separation" techniques can be used to reduce that cross-talk. However the conventional techniques are not very effective if the media causes latencies in signal propagation, which is the case of myoelectric potentials. The algorithm proposed here takes into account the latencies of the media and uses FIR decorrelators which significantly reduce the unwanted cross-talk.
Rectangular pulse generation based on pulse reshaping using a superstructured fiber Bragg grating (2001)

We present a technique for the shaping of short pulses based on the use of superstructured fiber Bragg gratings (SSFBGs). We apply this technique to demonstrate the generation of 20-ps rectangular pulses by phase and amplitude profiling of 2.5-ps soliton pulses. Numerical calculations validate our experimental findings.
Odor-related Chronic Somatic Symptoms Are Associated with Self-Reported Asthma and Hay Fever: The Hordaland Health Study. (2015)

The aetiology behind odor-related chronic somatic symptoms (O-RCSS) is unknown, although both immunological and psychiatric causes have been suggested. The aim of this study was to investigate the occurrence of self-reported asthma and hay fever and psychiatric symptoms in individuals having O-RCSS compared to individuals with similar chronic somatic symptoms (CSS) which were not odors-related, and also compared to healthy controls. Data from the Hordaland Health Study were used. 13,799 individuals, 40-45 years, answered a questionnaire including 16 questions related to somatic symptoms. They also indicated if the symptoms were odor-related, and answered questions about asthma and hay fever. Anxiety and depression were measured with the Hospital Anxiety and Depression Scale. 38 (0.6%) men and 106 (1.4%) women had O-RCSS, whereas 88 (1.5%) men and 192 (2.5%) women had CSS. Adjusted logistic regression analyses showed increased odds of self-reported asthma in those with O-RCSS compared to those with CSS (males: 3.81, 1.06-13.8, females: 2.60, 1.05-6.93) and compared to male and female controls (3.56, 1.89-6.68 and 4.81, 1.92-12.1 respectively). Increased odds of self-reported hay fever were in addition seen in females with O-RCSS. There were no differences in psychiatric symptoms between individuals with O-RCSS and CSS, although individuals in both groups showed increased odds compared to male and female controls. Increased occurrence of self-reported asthma was exclusively found among male and females with O-RCSS, compared to CSS and controls. Increased occurrence of psychiatric symptoms was seen both in individuals with O-RCSS and CSS.
Copper-Catalyzed vs Thermal Step Growth Polymerization of Starch-Derived α-Azide−ω-Alkyne Dianhydrohexitol Stereoisomers: To Click or Not To Click? (2009)

International audience
α-L-Fucose: A Potentially Critical Molecule in Pathologic Processes Including Neoplasia (1998)

Alpha-L-fucose is a 6-carbon deoxyhexose that is commonly incorporated into human glycoproteins and glycolipids. It is found at the terminal or preterminal positions of many cell-surface oligosaccharide ligands that mediate cell-recognition and adhesion-signaling pathways. These include such normal events as early embryologic development and blood group recognition and pathologic processes including inflammation, infectious disease recognition, and neoplastic progression. Fucosylated oligosaccharide ligands mediate cell-cell adhesion through binding to cell-surface selectins (calcium-dependent binding proteins) and calcium-dependent interactions with other cell-surface carbohydrate counterligands. A number of fucose-containing "natural ligands" are common to inflammatory and malignant cell processes. We review evidence that alpha-L-fucose is critically important for cell-cell and cell-matrix adhesion in a variety of normal and pathologic processes, particularly neoplasia. Current results suggest that alpha-L-fucose provides the essential structure that enables carbohydrate ligands to bind to selectins and to carbohydrate counterligands and thereby alter cellular homeostasis.
IgE antibody-mediated degranulation of cutaneous mast cells induces thermal pain in mice (118.8) (2012)

Abstract Pain is a key component of inflammation and a public health issue of significance. Mast cell activity has been implicated in pain responses associated with irritable bowel syndrome, migraine headaches, interstitial cystitis, postoperative pain, and endometriosis, but the mechanisms underlying mast cell involvement in pain pathologies are not clear. We show that degranulation of plantar mast cells caused by passive local antibody (IgE anti-DNP/HSA) sensitization and systemic antigen (DNP/HSA) challenge, induces thermal hyperalgesia as well as significant edema, neutrophil influx, and upregulation of IL-1beta and IL-6 proteins in the plantar tissue. Pre-treatment with histamine receptor H2 and H3/4 antagonists significantly abrogates pain, but not edema, associated with IgE/antigen-mediated mast cell degranulation This suggests that while pain has a multifactorial pathophysiology, tissue-resident sentinel mast cells may be a critical initiators of allergen-invoked hyperalgesia in mice.
Reliable Effects Screening: A Distributed Continuous Quality Assurance Process for Monitoring Performance Degradation in Evolving Software Systems (2007)

Developers of highly configurable performance-intensive software systems often use in-house performance-oriented "regression testing" to ensure that their modifications do not adversely affect their software's performance across its large configuration space. Unfortunately, time and resource constraints can limit in-house testing to a relatively small number of possible configurations, followed by unreliable extrapolation from these results to the entire configuration space. As a result, many performance bottlenecks escape detection until systems are fielded. In our earlier work, we improved the situation outlined above by developing an initial quality assurance process called "main effects screening". This process 1) executes formally designed experiments to identify an appropriate subset of configurations on which to base the performance-oriented regression testing, 2) executes benchmarks on this subset whenever the software changes, and 3) provides tool support for executing these actions on in-the-field and in-house computing resources. Our initial process had several limitations, however, since it was manually configured (which was tedious and error-prone) and relied on strong and untested assumptions for its accuracy (which made its use unacceptably risky in practice). This paper presents a new quality assurance process called "reliable effects screening" that provides three significant improvements to our earlier work. First, it allows developers to economically verify key assumptions during process execution. Second, it integrates several model-driven engineering tools to make process configuration and execution much easier and less error prone. Third, we evaluate this process via several feasibility studies of three large, widely used performance-intensive software frameworks. Our results indicate that reliable effects screening can detect performance degradation in large-scale systems more reliably and with significantly less resources than conventional techniques
Constructing Efficient Attribute-Based Broadcast Encryption (2010)

Attribute Based Broadcast Encryption (ABBE) is a novel Broadcast Encryption (BE) approach. Compared to existing BE approaches that requires an explicitly specified decrypters list, ABBE encrypter enforces an expressive access policy composed of one or more attributes. Although ABBE is more flexible and efficient with reduced storage overhead, ciphertext size of current ABBE schemes is linearly proportional to the numbers of attributes. In this paper, we investigate the solution on how to reduce the ABBE's ciphertext size to a constant value. Moreover, we explore the capability of using ABBE in secure many-to-many communication environments.
Spinorphin as an Endogenous Inhibitor of Enkephalin-degrading Enzymes: Roles in Pain and Inflammation (2002)

It is possible that enkephalins are involved in the pain-modulating mechanism in the spinal cord. Enkephalins, however, are short-lived, being rapidly degraded by various endogenous enzymes. Many substances that inhibit enkephalin-degradation have been investigated and it has been reported that some inhibitors (e.g. kelatorphan and RB101) alone showed anti-nociceptive activity. We found an endogenous factor that modulated enkephalin-degrading activity and purified it from bovine spinal cord based on its inhibitory activity toward enkephalin-degrading enzymes. Structural analysis revealed the factor to be Leu-Val-Val-Tyr-Pro-Trp-Thr and it was named spinorphin. It has been found that spinorphin inhibited the activity toward various enkephalin-degrading enzymes from monkey brain, especially dipeptidyl peptidase III (DPPIII, Ki=5.1 x 10(-7) M). Recently we reported that this inhibitor significantly inhibited bradykinin (BK)-induced nociceptive flexor responses. Importantly, the mode of inhibition to BK-responses by spinorphin was different from the case with morphine. The morphine-induced blockade of BK-response was attenuated by pertussis toxin treatment, whereas that of spinorphin was not. We also have reported roles for spinorphin in inflammation. Spinorphin significantly inhibited the functions of polymorphonuclear neutrophils (PMNs) by suppressing the binding of fMLF to its receptor on PMNs. Further, this inhibitor suppressed the carrageenan-induced accumulation of PMN in mouse air pouches after intravenous administration. These results indicate that spinorphin may be an endogenous anti-inflammatory regulator. The possible role of spinorphin and its analog as regulators in pain and inflammation will be discussed.
Identification of <i>Treponema pallidum</i> subspecies <i>pallidum</i> genes encoding signal peptides and membrane‐spanning sequences using a novel alkaline phosphatase expression vector (1991)

Treponema pallidum subspecies pallidum is a pathogenic spirochaete for which there are no systems of genetic exchange. In order to provide a system for the identification of T. pallidum surface proteins and potential virulence factors, we have developed a novel expression vector which confers the utility of TnphoA transposition. The relevant features of this plasmid vector, termed pMG, include an inducible tac promoter, a polylinker with multiple cloning sites in three reading frames, and an alkaline phosphatase (AP) gene lacking the signal sequence-encoding region. Library construction with Sau3A-digested T. pallidum genomic DNA resulted in the creation of functional T. pallidum-AP fusion proteins. Analysis of fusion proteins and their corresponding DNA and deduced amino acid sequences demonstrated that they could be grouped into three categories: (i) those with signal peptides containing leader peptidase I cleavage sites, (ii) those with signal peptides containing leader peptidase II cleavage sites, and (iii) those with non-cleavable hydrophobic membrane-spanning sequences. Triton X-114 detergent phase partitioning of individual T. pallidum-AP fusions revealed several clones whose AP activity partitioned preferentially into the hydrophobic detergent phase. Several of these fusion proteins were subsequently shown to be acylated by Escherichia coli following [3H]-palmitate labelling, indicating their lipoproteinaceous nature. DNA and amino acid sequence analysis of one acylated fusion protein, Tp75, confirmed the presence of a hydrophobic N-terminal signal sequence containing a consensus leader peptidase II recognition site. The DNA sequence of Tp75 also indicates that this is a previously unreported T. pallidum lipoprotein. T. pallidum-AP fusion proteins which partitioned into the hydrophobic detergent phase but did not incorporate palmitate were also identified. DNA and amino acid analysis of one such clone, Tp70, showed no cleavable signal but had a significant hydrophobic region of approximately 20 residues, consistent with a membrane-spanning domain. Immunoblot analysis of T. pallidum-AP fusions detected with a monoclonal antibody specific for AP identified several fusion proteins which migrated as doublets separated in apparent electrophoretic mobility by no more than 3 kDa. [35S]-methionine pulse-chase incorporation showed that the doublet AP fusions represented precursor and processed forms of the same protein. DNA and amino acid sequence analysis of clones expressing processed fusion proteins demonstrated hydrophobic N-terminal signal sequences containing consensus leader peptidase I recognition sites.
The Evolution of Vascular Tissue Engineering and Current State of the Art (2011)

Dacron® (polyethylene terephthalate) and Goretex® (expanded polytetrafluoroethylene) vascular grafts have been very successful in replacing obstructed blood vessels of large and medium diameters. However, as diameters decrease below 6 mm, these grafts are clearly outperformed by transposed autologous veins and, particularly, arteries. With approximately 8 million individuals with peripheral arterial disease, over 500,000 patients diagnosed with end-stage renal disease, and over 250,000 patients per year undergoing coronary bypass in the USA alone, there is a critical clinical need for a functional small-diameter conduit [Lloyd-Jones et al., Circulation 2010;121:e46-e215]. Over the last decade, we have witnessed a dramatic paradigm shift in cardiovascular tissue engineering that has driven the field away from biomaterial-focused approaches and towards more biology-driven strategies. In this article, we review the preclinical and clinical efforts in the quest for a tissue-engineered blood vessel that is free of permanent synthetic scaffolds but has the mechanical strength to become a successful arterial graft. Special emphasis is given to the tissue engineering by self-assembly (TESA) approach, which has been the only one to reach clinical trials for applications under arterial pressure.