gebhart/patrepeval huggingface dataset:
The Biochemistry and Structural Biology of Plant Cell Wall Deconstruction (2010)

The cell walls of plants are the most abundant source of organic carbon on the planet. This photosynthetically fixed carbon is recycled by microbial enzymes that convert cell wall polysaccharides to monosaccharides and oligosaccharides, a process that is of biological and industrial importance ([
Encyclopedia of Reagents for Organic Synthesis, Second Edition (2009)

Aaron Van Dyke (with T.F. Jamison) is a contributing author, ""[(1S,2S,5R)-5-Methyl-2-(1-methylethyl)cyclohexyl] diphenylphosphine". Book description: At last, the long anticipated second edition of the highly successful Encyclopedia of Reagents for Organic Synthesis (EROS) is publishing in print in March 2009. With its wealth of valuable information, excellent editorial leadership and methodical classification, EROS has become the authoritative reference source on reagents and catalysts. This makes EROS vital reading for everybody working in organic synthesis. It has wide appeal, with relevance not only to Organic Chemists, but also to Inorganic, Physical and Analytical Chemists, Materials Scientists, Chemical Engineers, Biochemists, Medicinal and Pharmaceutical Chemists and Pharmacologists. In short, it is an essential product for all academic and industrial chemistry laboratories and libraries.
Design of microstrip-fed series array of dielectricresonator antennas (1995)

An experimental procedure for designing a microstrip-fed series array of dielectric resonator antennas is presented. The procedure was used to design a 10 element array with a Taylor amplitude distribution. A gain of 13.2 dBi was measured at 8.2 GHz with maximum sidelobe levels of –17.5 dB. The cross-polarisation levels were also measured to be quite low, at ~20 dB below the peak.
Biocompatibility of a polymer patch for rotator cuff repair (2006)

Both mechanical and biological factors influence the high re-tear rate after rotator cuff repair. Mechanical factors have largely been addressed by the introduction of better implants and modification of suture configuration, but further improvements are needed to address the often poor tissue quality of the degenerated rotator cuff tendons. Current biological solutions provide only short-term reinforcement and have been associated with pseudo-infectious reactions. This pre-clinical animal study investigates the biological response to a novel polycarbonate polyurethane patch used for tissue augmentation in a rat rotator cuff repair model. Bilateral defects were created in the supraspinatus tendons of 12 Sprague Dawley rats. One side was repaired with a patch as a tissue augmentation device. The contralateral side acted as internal control without patch augmentation. After 6 weeks the tissues were harvested and underwent histologic and histomorphometric analyses. Histological evaluation demonstrated no inflammatory reaction; histomorphometry revealed tissue ingrowth of 79.9%. In conclusion, the polycarbonate polyurethane patch for tissue extension or augmentation in rotator cuff repair has demonstrated no inflammatory response and excellent tissue integration in a rat rotator cuff repair model.
Pennisetum squamulatum: Is the Predominant Cytotype Hexaploid or Octaploid? (2006)

Apomixis is a mode of asexual reproduction where maternal clones are produced through seeds. Consequently, genetic segregation is prevented in hybrid progenies. Pennisetum squamulatum has been used to transfer apomixis into the related sexual species Pennisetum glaucum by the introgression of an apospory-specific genomic region (ASGR)-carrier chromosome. Crosses between P. glaucum and P. squamulatum or Pennisetum purpureum have been relatively easy to make even though P. squamulatum has been reported to have a different basic chromosome number than the other 2 species (9 vs. 7) and to be hexaploid (2n = 6x = 54). Our extensive examination of one accession had shown a chromosome number of 2n = 56. In order to determine if there was a variation among accessions, we counted the number of chromosomes in 5 accessions of P. squamulatum using centromeric and 18S-5.8S-26S rDNA probes as molecular cytological markers. Our results showed that P. squamulatum is most likely octaploid with a basic chromosome number of 7 (2n = 8x = 56) and may belong to the secondary gene pool of Pennisetum. Moreover, a morphologically similar ASGR-carrier chromosome that confers apomixis was observed in all accessions.
E-beam inspection for combination use of defect detection and CD measurement (2012)

This paper proposes a combination use of e-beam inspection (EBI) for defect detection and CD Uniformity (CDU) measurement. The experiments are based on 14nm FinFET device manufactured on SOI substrate. A 5nm pixel size is utilized to perform hot spot inspection on SRAM pattern and N/P FET pattern after gate etching, spacer formation, and SiGe epitaxy process respectively. CDU measurement results match well with process split in gate etching and spacer formation process. Protrusion defect is detected after SiGe epitaxy process, and a dependency between protrusion defects with the thickness of spacer is found.
LMI1195 PET neuronal imaging: Evaluation of cardiac denervation, re-innervation and associated susceptibility to arrhythmia (2011)

1103 Objectives Regional cardiac sympathetic denervation (RCSD) has been associated with cardiac arrhythmia in heart failure patients. LMI1195 is a newly developed 18F labeled cardiac neuronal imaging agent which takes advantages of the high spatial resolution and quantification offered by PET. This study evaluated if LMI1195 cardiac imaging could be used to measure RCSD, subsequent re-innervation and potential RCSD association with arrhythmia susceptibility. Methods RCSD rabbits were developed by applying phenol directly on the surface of the left ventricular wall during a sternotomy. Two and twelve weeks following the procedure, LMI1195 cardiac imaging (1.5 mCi, iv) was performed. The myocardium with radioactivity ≥ 50% maximum was quantified as an innervated region for comparison. To evaluate the susceptibility to arrhythmia in these rabbits, cardiac changes induced by dofetilide (a delayed IKr inhibitor, 10 and 40 µg/kg iv) were assessed by measuring ECG including heart rate (HR), QTc interval (corrected by Fridericia method) and frequency of arrhythmia. Results Cardiac imaging showed homogeneous myocardial uptake of LMI1195 in sham-denervated rabbits and reduced regional levels in RCSD rabbits at 2 weeks post surgery (innervated region: 21276±3100 vs. 12970±1108 voxels respectively). The denervated region was reduced at 12 weeks (innervated region: 16812±503 voxels) indicating re-innervation. Imaging with flurpiridaz F 18 (a PET perfusion imaging agent) in these rabbits showed normal myocardial distribution without perfusion interruption after the RCSD procedure. Dofetilide induced QTc prolongation, frequency of premature ventricular contraction and torsade de pointes were more prominent in the RCSD group than in the control. However, the changes in HR were comparable in the two groups. Conclusions LMI1195 cardiac imaging can be use in detection of RCSD and re-innervation. The RCSD increases susceptibility of drug induced QTc prolongation and arrhythmia
STRUCTURE AND ELECTRONIC PROPERTIES OF SP 2 /SP 3 MIXED NANO-CARBON SYSTEMS (2002)

Structures and electronic properties are presented for three types of sp 2 /sp 3 mixed nano-carbon systems. Nano-diamond/nano-graphite conversion takes place around 1600°C, which changes the magnetism from sp 3 -defect-dominated one to π-edge state originating one. Fluorination in the initial stage, which prefers edge carbon sites of nano-graphites, destroys the π-edge states, and the succeeding fluorination generates sp 3 -defects with surrounding σ-non-bonding state at the interior carbon sites. Diamond-like-carbon has non-equilibrium sp 2 /sp 3 mixed structure with atomic scale disorders, which is easily converted to 3D random network of nano-graphite domains by heat-treatment.
The elevated ratio of interferon gamma-/ interleukin-4-positive T cells found in synovial fluid and synovial membrane of rheumatoid arthritis patients can be changed by interleukin-4 but not by interleukin-10 or transforming growth factor beta (1999)

The Th1 pattern in the joint of RA patients demonstrated at the single-cell level may be important for the pathogenesis of RA and may provide a target for future immunotherapy. Our data suggest a therapeutic role for IL-4.
Cancer-Associated Glycosphingolipid Antigens: Their Structure, Organization, and Function (1998)

Experimental and human cancers are often characterized by the presence of tumor-associated glycosphingolipid (GSL) antigens defined by monoclonal antibodies. Major progress has been made during the past two decades on structural identification of these antigens. None of these structures are truly 'tumor-specific'. However, many of the antibodies show preferential or 'specific' reactivity with tumors, based on organizational differences of membrane GSLs in tumor cells versus normal cells. Clustered GSL antigens organized with transducer molecules in microdomain have been found recently to comprise a structural and functional unit involved in tumor cell adhesion coupled with signal transduction. Some of the GSL antigens have been identified as adhesion molecules recognized by carbohydrate-binding proteins or by complementary carbohydrates on target cells. Such adhesion, coupled with signaling, may initiate the metastatic process. Elucidating the mechanism of this initial adhesion/signaling step may lead to discovery of therapeutic agents that disrupt adhesion ('antiadhesion therapy') or normalize signaling ('ortho-signaling therapy'). Tumor-associated GSL antigens are also a target in immunotherapy of tumors, including development of antitumor vaccines.
Specific proteoglycans as potential causative agents and relevant targets for therapeutic intervention in Alzheimer's disease and other amyloidosis (1997)

(1997). Specific proteoglycans as potential causative agents and relevant targets for therapeutic intervention in Alzheimer's disease and other amyloidosis. Amyloid: Vol. 4, No. 2, pp. 135-141.
Clostridial neurotoxins: from toxins to therapeutic tools? (1991)

Tetanus toxin and botulinum toxins are powerful neurotoxins which block neurotransmitter release through an unknown mechanism my means of their light chains. The heavy chains provide the machinery for neuroselective binding, internalization, retrograde intraaxonal transport, and translocation of the L-chains into the cytosole. We have cloned and sequenced the structural genes of tetanus toxin and of five serologically distinct botulinum toxins to identify structurally and functionally conserved subdomains. The minimum essential domains of the L-chains of tetanus and botulinum toxin type A were identified by combined in vitro transcription and microinjection of L-chain specific mRNA into identified presynaptic neurons of Aplysia californica. In addition, a nontoxic mutant of tetanus was generated by replacing histidine(237) by a proline residue. The development of nontoxic neuroselective transporter molecules carrying various marker enzymes is discussed.
Metabolic pathway for poly(3-hydroxybutyrate-co-3-hydroxyvalerate) formation in Nocardia corallina: inactivation of mutB by chromosomal integration of a kanamycin resistance gene (1996)

The gene encoding the large subunit of the methylmalonyl-coenzyme A (CoA) mutase in Nocardia corallina (mutBNc) was cloned. A 4.3-kbp BamHI fragment containing almost the entire mutBNc was identified by Southern hybridization experiments employing a digoxigenin-labeled probe deduced from mutB of Streptomyces cinnamonensis, mutBNc was interrupted by insertion of a kanamycin resistance gene block (mutB::kan or mutB::neo) and introduced into N. corallina to obtain mutB-negative strains by homologous recombination. Four of sixteen kanamycin-resistant clones occurred via double-crossover events and harbored only the interrupted mutBNc. These exhibited no growth on odd-chain fatty acids in the presence of kanamycin but exhibited wild-type growth on even-chain fatty acids, glucose, and succinate. Whereas the wild type of N. corallina accumulates a copolyester of 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV) containing more than 60 mol% 3HV from most carbon sources, mutB-negative strains accumulated poly(3HB-co-3HV) containing only 2 to 6 mol% 3HV. Methylmalonyl-CoA mutase activity was not found in these clones. Therefore, this study provides strong evidence that the majority of 3HV units in poly(3HB-co-3HV) accumulated by N. corallina are synthesized via the methylmalonyl-CoA pathway.
Analyzing features for activity recognition (2005)

Human activity is one of the most important ingredients of context information. In wearable computing scenarios, activities such as walking, standing and sitting can be inferred from data provided by body-worn acceleration sensors. In such settings, most approaches use a single set of features, regardless of which activity to be recognized. In this paper we show that recognition rates can be improved by careful selection of individual features for each activity. We present a systematic analysis of features computed from a real-world data set and show how the choice of feature and the window length over which the feature is computed affects the recognition rates for different activities. Finally, we give a recommendation of suitable features and window lengths for a set of common activities.
Prognostic value of circulating KL‐6 in idiopathic pulmonary fibrosis (2006)

These results suggest that initial evaluation of serum KL-6 level can predict survival in patients with IPF.
Heterogeneity in the Histidine-brace Copper Coordination Sphere in Auxiliary Activity Family 10 (AA10) Lytic Polysaccharide Monooxygenases (2016)

Copper-dependent lytic polysaccharide monooxygenases (LPMOs) are enzymes that oxidatively deconstruct polysaccharides. The active site copper in LPMOs is coordinated by a histidine-brace. This utilizes the amino group and side chain of the N-terminal His residue with the side chain of a second His residue to create a T-shaped arrangement of nitrogen ligands. We report a structural, kinetic, and thermodynamic appraisal of copper binding to the histidine-brace in an auxiliary activity family 10 (AA10) LPMO from Streptomyces lividans (SliLPMO10E). Unexpectedly, we discovered the existence of two apo-SliLPMO10E species in solution that can each bind copper at a single site with distinct kinetic and thermodynamic (exothermic and endothermic) properties. The experimental EPR spectrum of copper-bound SliLPMO10E requires the simulation of two different line shapes, implying two different copper-bound species, indicative of three and two nitrogen ligands coordinating the copper. Amino group coordination was probed through the creation of an N-terminal extension variant (SliLPMO10E-Ext). The kinetics and thermodynamics of copper binding to SliLPMO10E-Ext are in accord with copper binding to one of the apo-forms in the wild-type protein, suggesting that amino group coordination is absent in the two-nitrogen coordinate form of SliLPMO10E. Copper binding to SliLPMO10B was also investigated, and again it revealed the presence of two apo-forms with kinetics and stoichiometry of copper binding identical to that of SliLPMO10E. Our findings highlight that heterogeneity exists in the active site copper coordination sphere of LPMOs that may have implications for the mechanism of loading copper in the cell.
Unnatural Amino Acid Mutagenesis:  A Precise Tool for Probing Protein Structure and Function (2004)

The first general method for the biosynthetic incorporation of unnatural amino acids into proteins was reported in 1989. The ensuing years have seen the solid development and subsequent implementation of "unnatural amino acid mutagenesis" in a number of groundbreaking studies. Over 100 different amino acids have been incorporated into dozens of soluble and transmembrane proteins, using both cell-extract and cell-intact translation systems. The approach has provided insights into ligand-binding sites, conformational changes, and protein-protein interactions with a level of precision simply unparalleled by conventional mutagenesis. Here, the methodology is outlined, significant applications of the approach are summarized, and recent major improvements in the method are discussed. The future will likely see many more investigators utilizing this approach to manipulate proteins as it realizes its promise of becoming a tool with enormous potential.
Polarized transport of the polymeric immunoglobulin receptor in transfected rabbit mammary epithelial cells. (1990)

A cDNA for the rabbit low Mr polymeric immunoglobulin (poly-Ig) receptor was expressed in an immortalized rabbit mammary cell line. The intracellular routing of the receptor and its cell surface expression was analyzed in stably transfected cells grown on permeable supports. Initially the cells formed a monolayer with no transmural electrical resistance. All monolayer cells expressed the poly-Ig receptor and cytokeratin 7 filaments characteristic of luminal mammary cells but absent in myoepithelial cells. Within 7 d in culture, the cells underwent cytodifferentiation and formed a bilayer with a transepithelial electrical resistance of approximately 500 omega x cm2. Upper layer cells formed tight junctions with adjacent cells and gap junctions with basal cells. Expression of the poly-Ig receptor and cytokeratin 7 was restricted to the cells from the upper layer. The kinetics of receptor biosynthesis and processing was similar to that reported for rabbit mammary gland and rat liver. The receptor was cleaved at the apical cell surface and release of secretory component into the apical medium occurred with a half-time of approximately 2 h. Selective cell surface trypsinization combined with pulse-chase experiments served to determine at which cell surface domain newly synthesized receptor appeared first. The receptor was digested with a half-time of approximately 60 min with trypsin present in the basolateral medium and 90 min with apical trypsin. These data are consistent with selective targeting of newly synthesized receptor to the basolateral surface. The results indicate that transcytosis of the receptor from basolateral to apical membrane in the presence or the absence of its ligand requires approximately 30 min. Cleavage of the receptor by endogenous protease is not concomitant with its appearance at the apical surface, but requires additional time, thus explaining the presence of intact receptor on the apical membrane.
Neuroprotective Actions of Neurosteroids (2011)

Neurosteroids were initially defined as steroid hormones locally synthesized within the nervous tissue. Subsequently, they were described as steroid hormone derivatives that devoid hormonal action but still affect neuronal excitability through modulation of ionotropic receptors. Neurosteroids are further subdivided into natural (produced in the brain) and synthetic. Some authors distinguish between hormonal and regular neurosteroids in the group of natural ones. The latter group, including hormone metabolites like allopregnanolone or tetrahydrodeoxycorticosterone, is devoid of hormonal activity. Both hormones and their derivatives share, however, most of the physiological functions. It is usually very difficult to distinguish the effects of hormones and their metabolites. All these substances may influence seizure phenomena and exhibit neuroprotective effects. Neuroprotection offered by steroid hormones may be realized in both genomic and non-genomic mechanisms and involve regulation of the pro- and anti-apoptotic factors expression, intracellular signaling pathways, neurotransmission, oxidative, and inflammatory processes. Since regular neurosteroids show no affinity for steroid receptors, they may act only in a non-genomic mode. Multiple studies have been conducted so far to show efficacy of neurosteroids in the treatment of the central and peripheral nervous system injury, ischemia, neurodegenerative diseases, or seizures. In this review we focused primarily on neurosteroid mechanisms of action and their role in the process of neurodegeneration. Most of the data refers to results obtained in experimental studies. However, it should be realized that knowledge about neuroactive steroids remains still incomplete and requires confirmation in clinical conditions.
TRPV2 Enhances Axon Outgrowth through Its Activation by Membrane Stretch in Developing Sensory and Motor Neurons (2010)

Thermosensitive TRP (thermo TRP) channels are well recognized for their contributions to sensory transduction, responding to a wide variety of stimuli including temperature, nociceptive stimuli, touch, and osmolarity. However, the precise roles for the thermo TRP channels during development have not been determined. To explore the functional importance of thermo TRP channels during neural development, the temporal expression was determined in embryonic mice. Interestingly, TRPV2 expression was detected in spinal motor neurons in addition to the dorsal root ganglia from embryonic day 10.5 and was localized in axon shafts and growth cones, suggesting that the channel is important for axon outgrowth regulation. We revealed that endogenous TRPV2 was activated in a membrane stretch-dependent manner in developing neurons by knocking down the TRPV2 function with dominant-negative TRPV2 and TRPV2-specific shRNA and significantly promoted axon outgrowth. Thus, for the first time we revealed that TRPV2 is an important regulator for axon outgrowth through its activation by membrane stretch during development.
Pectin-Based Injectable Biomaterials for Bone Tissue Engineering (2011)

A variety of natural polymers and proteins are considered to be 3D cell culture structures able to mimic the extracellular matrix (ECM) to promote bone tissue regeneration. Pectin, a natural polysaccharide extracted from the plant cell walls and having a chemical structure similar to alginate, provides interesting properties as artificial ECM. In this work, for the first time, pectin, modified with an RGD-containing oligopeptide or not, is used as an ECM alternative to immobilize cells for bone tissue regeneration. The viability, metabolic activity, morphology, and osteogenic differentiation of immobilized MC3T3-E1 preosteoblats demonstrate the potential of this polysaccharide to keep immobilized cells viable and differentiating. Preosteoblasts immobilized in both types of pectin microspheres maintained a constant viability up to 29 days and were able to differentiate. The grafting of the RGD peptide on pectin backbone induced improved cell adhesion and proliferation within the microspheres. Furthermore, not only did cells grow inside but also they were able to spread out from the microspheres and to organize themselves in 3D structures producing a mineralized extracellular matrix. These promising results suggest that pectin can be proposed as an injectable cell vehicle for bone tissue regeneration.
Analysis of bacterial survival after exposure to reactive oxygen species or antibiotics (2016)

The redox balance in a variety of Gram-negative bacteria was explored using redox sensitive GFP (roGFP2), J. van der Heijden et al. doi:10.1016/j.freeradbiomed.2015.11.029[1]. This data article provides Supporting material to further investigate the relationship between Salmonella typhimurium survival and oxidative stress. The first set of data presented in this article, shows the percentage of surviving bacteria after exposure to hydrogen peroxide. The second set of data shows the concentration of hydrogen peroxide that was produced by S. Typhimurium in different growth phases. The last set of data shows the percentage of surviving S. Typhimurium bacteria after exposure to different antibiotics.