gebhart/patrepeval huggingface dataset:
Light promotes regeneration and functional recovery and alters the immune response after spinal cord injury (2005)

Our results demonstrate that light, delivered transcutaneously, improves recovery after injury and suggests that light will be a useful treatment for human SCI.
A survey on RFID security and provably secure grouping-proof protocols (2010)

RFID security is a relatively new research area. Within less than a decade, a large number of research papers dealing with security issues of RFID technology have appeared. In the first part of this paper, we attempt to summarise current research in the field of RFID security and discuss some of their open issues. In the second part of this paper, we address some of the open problems we suggested in the first part. In particular, we deal with scalability problem of existing grouping-proof protocols for RFID tags. In addition, we also present the first security definition for a secure grouping-proof protocol for RFID tags. The definition is then used to analyse the security of our proposed grouping-proof protocol which employs a (n, n)-secret sharing scheme to solve the scalability problem of previous protocols.
AG-348 (Mitapivat), an allosteric activator of red blood cell pyruvate kinase, increases enzymatic activity, protein stability, and ATP levels over a broad range of PKLR genotypes (2020)

Pyruvate kinase (PK) deficiency is a rare hereditary disorder affecting red cell (RBC) glycolysis, causing changes in metabolism including a deficiency in ATP. This affects red cell homeostasis, promoting premature removal of RBCs from the circulation. In this study we characterized and evaluated the effect of AG-348, an allosteric activator of PK that is currently in clinical trials for treatment of PK deficiency, on RBCs and erythroid precursors from PK-deficient patients. In 15 patients ex vivo treatment with AG-348 resulted in increased enzymatic activity in all patient cells after 24 hours (mean increase 1.8-fold, range 1.2-3.4). ATP levels increased (mean increase 1.5-fold, range 1.0-2.2) similar to control cells (mean increase 1.6-fold, range, 1.4-1.8). Generally, PK thermostability was strongly reduced in PK-deficient RBCs. Ex vivo treatment with AG-348 increased residual activity 1.4 to >10-fold than residual activity of vehicle-treated samples. Protein analyses suggests that a sufficient level of PK protein is required for cells to respond to AG-348 treatment ex-vivo, as treatment effects were minimal in patient cells with very low or undetectable levels of PK-R. In half of the patients, ex vivo treatment with AG-348 was associated with an increase in RBC deformability. These data support the hypothesis that drug intervention with AG-348 effectively upregulates PK enzymatic activity and increases stability in PK-deficient RBCs over a broad range of PKLR genotypes. The concomitant increase in ATP levels suggests that glycolytic pathway activity may be restored. AG-348 treatment may represent an attractive way to correct the underlying pathologies of PK deficiency. (AG-348 is currently in clinical trials for the treatment of PK deficiency. ClinicalTrials.gov: NCT02476916, NCT03853798, NCT03548220, NCT03559699).
Fast and Accurate Positioning Technique Using Ultrasonic Phase Accordance Method (2005)

An innovative measurement technique for use by positioning systems using ultrasonic signals was developed. The advantage of this technique is that it can accurately identify the relative distance and orientation between devices by using an one-time ultrasonic packet. It is therefore especially useful for ubiquitous computing applications where people with mobile devices continuously change their positions in indoor environments. The technique, which is named phase accordance method, uses two or more carriers in ultrasonic communication. A special ultrasonic burst signal, called sync pattern in the header part of the communication packet gives the base point of the time measurement. The whole time difference calculation is then carried out using this base point. An experiment based on the proposed method proved that the technique attains remarkable performance, namely, errors of less than plusmn 1 mm in three meter distance measurements and less than 0.5 degree errors in the zero, ten, twenty, and thirty degree measurements.
A cDNA fragment of hepatitis C virus isolated from an implicated donor of post-transfusion non-A, non-B hepatitis in Japan (1989)

Recently, a cDNA from the hepatitis C virus (HCV) RNA genome has been isolated in the USA from a chronically infected chimpanzee. In order to isolate HCV cDNA derived from human material, RNA was extracted from plasma of a Japanese blood donor implicated in post-transfusion non-A, non-B hepatitis and HCV cDNA was synthesized and amplified by the PCR method using HCV-specific oligonucleotide primers. The cDNA fragment, 583 nucleotides long, showed 79.8% homology at the nucleotide level and 92.2% homology at the amino acid level compared with the prototype HCV cDNA. These results provides further evidence to show that HCV is closely associated with the development of post transfusion non-A, non-B hepatitis.
Recognition of synthetic polypeptides corresponding to the N‐ and C‐terminal fragments of Plasmodium falciparum Exp‐1 by T‐cells and plasma from human donors from African endemic areas (2002)

The present work describes the recognition of three synthetic polypeptides encompassing the N- and C-terminal regions of the transmembrane Exp-1 protein of the parasite Plasmodium falciparum by plasma and peripheral blood mononuclear cells from naturally exposed individuals living in African endemic areas. The three polypeptides comprise the sequences 23-105, 73-162 and 101-162, and overlap at the transmembrane domain (73-105). Thus, they permitted characterization of the immune response specific to the N- and C-terminal domains in an independent fashion. Two different populations were evaluated, one in the village of Safo in Mali and the other in the villages of Somnaway, Kabortenga and Toussouktenga in Burkina Faso. Antibodies to the sequence 73-162 of Pf Exp-1 were found in 70% of adult Mali donors and in all of the donors tested from Burkina Faso. Strikingly, the N-terminal fragment Pf Exp-1 23-105 was only weakly recognized by a few donors. Evaluation of the T-cell response indicated that the peptide Pf Exp-1 23-105 was more potent than Pf Exp-1 73-162 in inducing a proliferative response. A correlation between peptide-specific interferon-gamma and interleukin-6 production and proliferation to peptide Pf Exp-1 23-105 was observed. Further studies are needed to evaluate this molecule as a vaccine candidate.
HTRA1 (High Temperature Requirement A Serine Peptidase 1) Gene Is Transcriptionally Regulated by Insertion/Deletion Nucleotides Located at the 3′ End of the ARMS2 (Age-related Maculopathy Susceptibility 2) Gene in Patients with Age-related Macular Degeneration (2014)

Dry age-related macular degeneration (AMD) accounts for over 85% of AMD cases in the United States, whereas Japanese AMD patients predominantly progress to wet AMD or polypoidal choroidal vasculopathy. Recent genome-wide association studies have revealed a strong association between AMD and an insertion/deletion sequence between the ARMS2 (age-related maculopathy susceptibility 2) and HTRA1 (high temperature requirement A serine peptidase 1) genes. Transcription regulator activity was localized in mouse retinas using heterozygous HtrA1 knock-out mice in which HtrA1 exon 1 was replaced with β-galactosidase cDNA, thereby resulting in dominant expression of the photoreceptors. The insertion/deletion sequence significantly induced HTRA1 transcription regulator activity in photoreceptor cell lines but not in retinal pigmented epithelium or other cell types. A deletion construct of the HTRA1 regulatory region indicated that potential transcriptional suppressors and activators surround the insertion/deletion sequence. Ten double-stranded DNA probes for this region were designed, three of which interacted with nuclear extracts from 661W cells in EMSA. Liquid chromatography-mass spectrometry (LC-MS/MS) of these EMSA bands subsequently identified a protein that bound the insertion/deletion sequence, LYRIC (lysine-rich CEACAM1 co-isolated) protein. In addition, induced pluripotent stem cells from wet AMD patients carrying the insertion/deletion sequence showed significant up-regulation of the HTRA1 transcript compared with controls. These data suggest that the insertion/deletion sequence alters the suppressor and activator cis-elements of HTRA1 and triggers sustained up-regulation of HTRA1. These results are consistent with a transgenic mouse model that ubiquitously overexpresses HtrA1 and exhibits characteristics similar to those of wet AMD patients.
PDR5, a novel yeast multidrug resistance conferring transporter controlled by the transcription regulator PDR1. (1994)

The complete sequence of the pleiotropic drug resistance gene PDR5 from Saccharomyces cerevisiae is reported and analyzed. PDR5 encodes a 160-kDa protein with a predicted duplicated six membrane-span domain and a repeated putative ATP-binding domain. PDR5 shares this structural feature with the mammalian multidrug resistance pumps as well as the functional capacity of conferring resistance to various inhibitors upon amplification (Leppert, G., McDevitt, R., Falco, S. C., Van Dyk, T. K., Ficke, M. B., and Golin, J. (1990) Genetics 125, 13-20). The yeast PDR5 is thus a new member of the ABC (ATP-binding cassette) protein superfamily. Mutations in another yeast pleiotropic drug resistance gene, PDR1, encoding a putative transcription regulator (Balzi, E., Chen, W., Ulaszewski, S., Capieaux, E., and Goffeau, A. (1987) J. Biol. Chem. 262, 16871-16879), increase markedly the mRNA levels of the PDR5 and STE6 genes. The multidrug resistance mutations pdr1-3 and pdr1-6 also lead to considerable overexpression of the PDR5 plasma membrane protein.
A benchmark for RGB-D visual odometry, 3D reconstruction and SLAM (2014)

We introduce the Imperial College London and National University of Ireland Maynooth (ICL-NUIM) dataset for the evaluation of visual odometry, 3D reconstruction and SLAM algorithms that typically use RGB-D data. We present a collection of handheld RGB-D camera sequences within synthetically generated environments. RGB-D sequences with perfect ground truth poses are provided as well as a ground truth surface model that enables a method of quantitatively evaluating the final map or surface reconstruction accuracy. Care has been taken to simulate typically observed real-world artefacts in the synthetic imagery by modelling sensor noise in both RGB and depth data. While this dataset is useful for the evaluation of visual odometry and SLAM trajectory estimation, our main focus is on providing a method to benchmark the surface reconstruction accuracy which to date has been missing in the RGB-D community despite the plethora of ground truth RGB-D datasets available.
Friction Identification and Compensation in Robotic Manipulators (2007)

In this paper, friction identification and friction compensation in the joints of a robotic manipulator are studied. The friction force is modeled using a single-state dynamic model that is utilized in the friction compensation algorithm. A new method for identifying the parameters of the aforementioned model in a robotic manipulator is presented. To evaluate the performance of this method, two different manipulators with different friction characteristics are examined. A 2-DOF manipulator that is used for high-speed micrometer precision manipulation and a 4-DOF macromanipulator that is used for long-reach positioning tasks are considered. It is shown that despite the different nature of the two manipulators, the same method can effectively improve the speed, accuracy, and smoothness of the manipulation in both cases.
The challenge of protein structure determination—lessons from structural genomics (2007)

The process of experimental determination of protein structure is marred with a high ratio of failures at many stages. With availability of large quantities of data from high-throughput structure determination in structural genomics centers, we can now learn to recognize protein features correlated with failures; thus, we can recognize proteins more likely to succeed and eventually learn how to modify those that are less likely to succeed. Here, we identify several protein features that correlate strongly with successful protein production and crystallization and combine them into a single score that assesses "crystallization feasibility." The formula derived here was tested with a jackknife procedure and validated on independent benchmark sets. The "crystallization feasibility" score described here is being applied to target selection in the Joint Center for Structural Genomics, and is now contributing to increasing the success rate, lowering the costs, and shortening the time for protein structure determination. Analyses of PDB depositions suggest that very similar features also play a role in non-high-throughput structure determination, suggesting that this crystallization feasibility score would also be of significant interest to structural biology, as well as to molecular and biochemistry laboratories.
Substrate specificity of vaccinia virus thymidylate kinase (2005)

Anti-poxvirus therapies are currently limited to cidofovir [(S)-1-(3-hydroxy-2-phosphonylmethoxypropyl)cytosine], but drug-resistant strains have already been characterized. In the aim of finding a new target, the thymidylate (TMP) kinase from vaccinia virus, the prototype of Orthopoxvirus, has been overexpressed in Escherichia coli after cloning the gene (A48R). Specific inhibitors and alternative substrates of pox TMP kinase should contribute to virus replication inhibition. Biochemical characterization of the enzyme revealed distinct catalytic features when compared to its human counterpart. Sharing 42% identity with human TMP kinase, the vaccinia virus enzyme was assumed to adopt the common fold of nucleoside monophosphate kinases. The enzyme was purified to homogeneity and behaves as a homodimer, like all known TMP kinases. Initial velocity studies showed that the Km for ATP-Mg2+ and dTMP were 0.15 mm and 20 microM, respectively. Vaccinia virus TMP kinase was found to phosphorylate dTMP, dUMP and also dGMP from any purine and pyrimidine nucleoside triphosphate. 5-Halogenated dUMP such as 5-iodo-2'-deoxyuridine 5'-monophosphate (5I-dUMP) and 5-bromo-2'-deoxyuridine 5'-monophosphate (5Br-dUMP) were also efficient alternative substrates. Using thymidine-5'-(4-N'-methylanthraniloyl-aminobutyl)phosphoramidate as a fluorescent probe of the dTMP binding site, we detected an ADP-induced conformational change enhancing the binding affinity of dTMP and analogues. Several thymidine and dTMP derivatives were found to bind the enzyme with micromolar affinities. The present study provides the basis for the design of specific inhibitors or substrates for poxvirus TMP kinase.
Peptides corresponding to the second repeated sequence in MAP-2 inhibit binding of microtubule-associated proteins to microtubules (1990)

Bovine brain high molecular weight microtubule-associated proteins (MAPs) can be displaced from assembled tubules by peptides corresponding to the second of three nonidentical repeated sequences in mouse MAP-2. The octadecapeptide m2 (VTSKCGSLKNIRHRPGGG) can release MAP-1b from MAP-containing microtubules, and the extended second-sequence peptide m2' (VTSKCGSLKNIRHRPGGGRVK) displaces MAP-1a and MAP-1b as well as MAP-2a and MAP-2b. Peptides m2 and m2' stimulate tubulin polymerization in the absence of MAPs or microtubule-stabilizing agents, and m2' acts as a competitive inhibitor of radiolabeled MAP-2 binding. The dissociation constant for MAP-2 binding to taxol-stabilized tubules was 3.4 microM in the absence of m2' and 14 microM in the presence of 1.5 mM of the m2' peptide. We estimate that the inhibition constant for peptide m2' is about 0.5 mM, about 100 times lower than for the Km of MAP-2. These observations suggest that the second repeated sequence in MAP-2 may represent an important recognition site for MAP binding to microtubules and that other structural features within MAP-2 may reinforce the strength of MAP-microtubule interactions.
A Lattice Study of the Glueball Spectrum (2001)

Glueball spectrum is studied using an improved gluonic action on asymmetric lattices in the pure gauge theory. The smallest spatial lattice spacing is about 0.08 fm which makes the extrapolation to the continuum limit more reliable. In particular, attention is paid to the scalar glueball mass which is known to have problems in the extrapolation. Converting our lattice results to physical units using the scale set by the static quark potential, we obtain the following results for the glueball masses: for the scalar glueball mass and for the tensor glueball.
Baricitinib plus Remdesivir for Hospitalized Adults with Covid-19 (2020)

Baricitinib plus remdesivir was superior to remdesivir alone in reducing recovery time and accelerating improvement in clinical status among patients with Covid-19, notably among those receiving high-flow oxygen or noninvasive ventilation. The combination was associated with fewer serious adverse events. (Funded by the National Institute of Allergy and Infectious Diseases; ClinicalTrials.gov number, NCT04401579.).
Generation of Endoderm Lineages from Pluripotent Stem Cells (2016)

Definitive endoderm is the cellular precursor to respiratory- and digestive-related organs such as lungs, stomach, liver, pancreas and intestine. Endodermal lineage cells derived from pluripotent stem cells (PSCs) in vitro are a potentially unlimited resource for regenerative medicine. These cells are useful tools for studying the physiology, pathogenesis and medical therapies involving these tissues, and great progress has been achieved in PSCs differentiation protocols. In this review, we will focus on the most common and/or advanced differentiation strategies currently used in generating endodermal lineage cells from PSCs. A brief discussion about the effect of early definitive endoderm differentiation on the final development products will follow.
Heterologous Protein Production by Filamentous Fungi (1991)

There are clearly many facets to successful production of heterologous proteins from filamentous fungi. The objectives are to exploit the natural ability of some species to secrete high levels of protein. The heterologous target proteins produced in a fungal host must be acceptable to the public and be economic to produce, i.e. the targets must be authentic (in structure and activity) and be produced in high yield to necessary levels of purity. The appearance of heterologous products from fungi on the market is testament to some success but, equally, there are considerable limitations in our ability to produce desired yields of many target proteins. We endorse the view of van den Hondel, Punt and van Gorcom (1991) that for the commercial production of heterologous proteins from filamentous fungi more information is required on transcriptional control, introns, mRNA stability and processing, translational efficiency, protein secretion, glycosylation and proteolysis. In addition, there is scope for yield improvement based on a better understanding of the physiology of growth/product secretion coupled to appropriate bioreactor operation. The authenticity of product is an aspect which will assume increasing importance, particularly for therapeutic proteins. The level at which the structures and functional activity of heterologous proteins are assessed will ultimately be determined by legislation. The analytical methods currently available are not always sufficient, for example, to reveal folded structures, and most proteins are not amenable to analysis by two-dimensional NMR. The authenticity of target heterologous proteins will also need to be assessed in relation to the glycosylation level and pattern. This is not easily done and explains the paucity of detailed information published to date on glycosylation of fungal proteins. Novel engineered proteins are already being produced from filamentous fungi where expression is an aid to investigation of structure-function relationships. Commercial production of such engineered proteins will require approval subject to a range of stringently applied tests and analyses. This imposes an even greater need to be able to specify and control, in a rational manner, the structures of recombinant proteins. The research needs for realization of improved yields are equally important in assuring authenticity of product. It is encouraging that progress is being made on all fronts, primarily with Aspergillus spp. and T. reesei, but also with other species, such as N. crassa.
Gene targeting the myf‐5 locus with nlacZ reveals expression of this myogenic factor in mature skeletal muscle fibres as well as early embryonic muscle (1996)

We have introduced the nlacZ reporter gene into the locus of the myogenic factor gene myf-5 by homologous recombination in embryonic stem (ES) cells. Targeted ES clones were injected into precompaction morula, and the β-galactosidase expression pattern was monitored. These mice permit the sensitive visualization of myf-5 expression throughout the embryo, and provide a standard for comparing it with that seen with different myf-5/nlacZ transgenes. Thus, in a comparison using ES cells in chiameric embryos containing the targeted or randomly integrated myf-5/nlacZ construct, we demonstrate that 5.5 kbp of myf-5 upstream flanking sequence including exon1 and most of intron1 directs some skeletal muscle expression, but this is neither qualitatively nor quantitatively equivalent to that of the endogenous gene. Myf-5 is expressed early, before terminal myogenesis takes place in the medial half of the somite, and subsequently it is a major myogenic factor as skeletal muscle forms. All skeletal muscle shows β-galactosidase activity, even after birth, indicating that myf-5 expression is not confined to primary myotubes, which are derived from embryonic myoblasts, but is also present in muscles containing different adult fibre types. The presence of myf-5 transcripts from the endogenous gene in older muscle was confirmed by in situ hybridization. These results suggest that the myf-5 gene is not activated in only a subset of muscle cells and are consistent with the results on the MyoD knockout mice. © 1996 Wiley-Liss, Inc.
Ad hoc wireless multicast with mobility prediction (2003)

An ad hoc wireless network is an infrastructureless network composed of mobile hosts. The primary concerns in ad hoc networks are bandwidth limitations and unpredictable topology changes. Thus, efficient utilization of routing packets and immediate recovery of route breaks are critical in routing and multicasting protocols. A multicast scheme, on-demand multicast routing protocol (ODMRP), has been recently proposed for mobile ad hoc networks. ODMRP is a reactive (on-demand) protocol that delivers packets to destinations on a mesh topology using scoped flooding of data. A number of enhancements can be applied to improve the performance of ODMRP. In this paper, we propose a mobility prediction scheme to help select stable routes and to perform rerouting in anticipation of topology changes. We also introduce techniques to improve transmission reliability and eliminate route acquisition latency. The impact of our improvements is evaluated via simulation.