cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Regulation of expression of copper responsive genes in Sulfolobus solfataricus
Creators: name: Villafañe Martinez, Aramis Alexis
Publisher: name: No Publisher Supplied
Year: 2010

description: Copper is an essential micronutrient, but toxic in excess. Cells must maintain their internal level of copper within a narrow range of concentrations. This is accomplished mainly by copper efflux mediated by ATP-driven copper transporters that are induced at the level of transcription. Sulfolobus solfataricus has the ability to adapt to fluctuations of copper levels in its environment. Two Sulfolobus strains P2 and 98/2, showed different sensitivity to copper To better understand the molecular mechanism behind the organismal response to copper, the expression of the cluster of genes copRTA, which encodes the copper-responsive transcriptional regulator CopR, the copper-binding protein CopT, and CopA, has been investigated. The expression of the copR and copA transcripts was monitored by quantitative real-time RT-PCR. The data showed that only copA was induced by copper. By comparing the patterns of copA expression and cellular copper accumulation, as determined by Inductively Coupled Plasma Optical Emission spectrometry, it was concluded that the level of copA depends on the internal fluctuations of copper. To investigate the role of CopR, a mutant carrying a disruption of the copR gene was created. The mutant strain was uncapable of growth in the presence of excess copper, and under the same conditions no transcription of copA was observed. These data suggested that CopR positively regulates transcription of copA. The knockout mutant strain PBL2070, its parent strain and the mutant complemented with a wild type copy of copR, were compared with respect to their physiological and transcriptional response to copper. Results confirmed that, under copper stress, CopR, activates the transcription of copA, and its presence restores the wild type phenotype resistant to copper. Finally, a reporter system based on the thermostable β-glucuronidase of S. solfataricus was developed to study the promoter of regulated genes. This system was applied to the analysis of the copTA promoter region fused to the S. solfataricus β-glucuronidase reporter. GUS activity assays showed that after copper addition, the activity of GusB was consistent with the transcriptional changes observed for copA under similar conditions. The results provide the basis for a model of the molecular mechanisms of copper homeostasis in Sulfolobus.
Gymnothorax angusticauda
Creators: name: Bogorodsky, Sergey V.
name: Alpermann, Tilman J.
name: Mal, Ahmad O.
name: Gabr, Mohamed H.
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Anguilliformes
Muraenidae
Gymnothorax
Gymnothorax angusticauda

description: Gymnothorax angusticauda (Weber & de Beaufort, 1916)
Material examined. SMF 34962 (1: 38.7 cm)
description: Published as part of Bogorodsky, Sergey V., Alpermann, Tilman J., Mal, Ahmad O. & Gabr, Mohamed H., 2014, Survey of demersal fishes from southern Saudi Arabia, with five new records for the Red Sea, pp. 401-437 in Zootaxa 3852 (4) on page 411, DOI: 10.11646/zootaxa.3852.4.1, http://zenodo.org/record/225360
title: Compact Raman analyzer for recording dissolved gases in liquids with high sensitivity and spectral resolution
Creators: name: Varghese, Philip L.
name: Fink, Manfred F.
Publisher: name: United States Patent and Trademark Office
Year: 2013
Subjects: subject: G01J3/44
subject: G01J3/02
subject: G01J3/0286
subject: G01J3/0291
subject: G01N21/65
subject: G01N21/15
subject: G01N2021/651
subject: 356/301
subject: 356/246

description: A Raman head is provided capable of operating at high surrounding pressures. The Raman head has housing having a first, sealed chamber filled with an incompressible liquid and a second chamber that is open to the surrounding environment. At least one bellows can be used to equalize pressure between the first sealed chamber and the surrounding environment. A planar side of a pair of plano-concave lens is positioned within the first chamber and the concave side of each plano-concave lens is positioned within the second chamber of the Raman head. Light emitted as a result of a laser beam in communication with the pair of plano-concave lens can be analyzed by a Raman analyzer.
Biomechanical modeling and simulation of human eye movement
Creators: name: Wei, Qi
Publisher: name: No Publisher Supplied
Year: 2010

description: Studying human eye movement has significant implications for understanding the oculomotor system and treating vision disorders. Existing models of the oculomotor system either simplify the geometry and mechanics of the orbit, or are restricted to static simulation. In this dissertation, we present a novel three-dimensional (3D) biomechanical modeling framework for simulation of the oculomotor plant that addresses the above limitations. We aim to lay the foundation of a biomechanical simulator that will potentially be used for scientific research on ocular motility and clinical applications.We first propose an efficient method for building subject-specific orbit models from magnetic resonance imaging (MRI). We reconstruct 3D geometric models of the orbit by fitting a generic template model to the MRI data of individual subjects. An automatic fitting process is developed, which combines parametric surface deformation with image feature selection. The accuracy of our method is validated by comparison to manual segmentation. We also present 3D reconstruction of eyeball models from MRI using the template approach with subdivision surface fitting.We then describe a new approach for determining the averaged longitudinal strains of cylindrical soft tissues. Our method does not rely on image features to establish tissue correspondences and uses the incompressibility property of soft tissues. We demonstrate its usefulness by estimating extraocular muscle (EOM) strains from reconstructed models. Simulated sensitivity analysis and validation on MRI of a rubber phantom show its accuracy. Integrating estimated EOM strains as deformation constraints, we register EOM models across eye positions in a physically consistent way.Finally, we develop a 3D dynamic biomechanical model for simulating ocular motility. We model EOMs as "strands," which are modeling elements for musculotendon mechanics. Realistic muscle paths and cross sectional areas of the EOM strands are based on 3D geometric models reconstructed from human subject MRI. Nonlinear EOM mechanics are incorporated and pulley hypotheses are implemented. Simulation of fixations, smooth pursuits, and saccades are demonstrated. The model generates realistic gaze trajectories from neural control signals. We validate our simulator by comparing simulations to experimental data. Our model is the first one that simulates dynamics and includes anatomical and physiological properties.
Ichoria pyrrhonota Zerny 1931
Creators: name: Pinheiro, L. R.
name: Gaal-Haszler, S.
Publisher: name: Zenodo
Year: 2015
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Arctiidae
Ichoria
Ichoria pyrrhonota

description: pyrrhonota Zerny, 1931
(Fig. 38)
Ichoria pyrrhonota Zerny, 1931b: 11 (Taf. 1, fig. 14). Holotype female [by monotypy]: [BRAZIL], Santa Catarina, Jaraguá (Fr. Hoffmann), 21.xii.1929; with two labels: printed label “Sta. Catarina, Jaraguá, Fr. Hoffmann” on underside with handwriting “ 21.xii. ’29”, and handwritten label “ Ichoria pyrrhonota Zerny ♀ type ”.
Current combination. Ichoria pyrrhonota Zerny, 1931.
Condition of the type. Wings slightly worn.
Remarks. This species resembles the type species of Ichoria Butler, 1876, I. quadrigutta (Walker, 1854) and it is likely correctly positioned in Ichoria.
description: Published as part of Pinheiro, L. R. & Gaal-Haszler, S., 2015, Illustrated catalogue of Neotropical Ctenuchina, Euchromiina and Pericopina types (Lepidoptera, Erebidae, Arctiinae, Arctiini) described by Hans Zerny, with discussion on their taxonomic status, pp. 505-535 in Zootaxa 3925 (4) on page 523, DOI: 10.11646/zootaxa.3925.4.2, http://zenodo.org/record/240540
Pickard, Kate E.R., letter, Camillus, [N.Y.], January 29, 1853, to "Uncle Peter" [Peter Still]
Creators: name: Pickard, Kate E. R.
Publisher: name: No Publisher Supplied
Year: 1853

description: Kate Pickard acknowledges receiving Peter Still’s letter; relates information from her sister Julia, in Tuscumbia or vicinity, regarding a Dr. Hargraves and a Judge Weakley there who are sympathetic to his cause; acknowledges that the higher price of 5,000 dollars quoted to Mr. Thornton for Peter’s enslaved family after the "attempt to run them off" [help them run away] is probably really meant by Maj. McKiernan; counsels Peter not to loose his patience or temper; and quotes from Julia's letter (including some information about people in Tuscumbia).
Chase, Stephen A., letter, Salem, [Mass.?], January 12, 1854, to Robert I? Murray, [New York]
Creators: name: Chase, Stephen A.
Publisher: name: No Publisher Supplied
Year: 1854

description: Letter of introduction for Peter Still written by Stephen A. Chase, which notes, in part, that Still’s tale “unfolds a phase in the history of slavery strongly illustrative of its evils, its oppressions, its injustice and its opposition to all that is good and kind and Christian.”
Pickard, Kate E.R., letter, Camillus, [N.Y.], January 22, 1855, to "Uncle Peter" [Peter Still]
Creators: name: Pickard, Kate E. R.
Publisher: name: No Publisher Supplied
Year: 1855

description: Kate Pickard acknowledges the receipt of Peter Still’s letter; rejoices that Still's family is now free and encourages him to thank God for the same; advises that his children should pursue educations; relates how she learned of the Still family’s reunion; laments that the baby (Still’s grandchild) was left behind in Alabama; wonders if efforts to free the infant will delay the appearance of Still’s narrative; and provides news about her family members.
Gymnothorax randalli Smith & Bohlke 1997
Creators: name: Bogorodsky, Sergey V.
name: Alpermann, Tilman J.
name: Mal, Ahmad O.
name: Gabr, Mohamed H.
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Anguilliformes
Muraenidae
Gymnothorax
Gymnothorax randalli

description: Gymnothorax randalli Smith & Böhlke, 1997
Material examined. SMF 34963 (1: 41.3 cm).
description: Published as part of Bogorodsky, Sergey V., Alpermann, Tilman J., Mal, Ahmad O. & Gabr, Mohamed H., 2014, Survey of demersal fishes from southern Saudi Arabia, with five new records for the Red Sea, pp. 401-437 in Zootaxa 3852 (4) on page 411, DOI: 10.11646/zootaxa.3852.4.1, http://zenodo.org/record/225360
title: System and method for pump variable stroke
Creators: name: Smalling, Richard W.
name: Gohean, Jeffrey R.
name: Pate, Thomas D.
name: Longoria, Raul G.
Publisher: name: United States Patent and Trademark Office
Year: 2013
Subjects: subject: A61N1/362
subject: A61M1/101
subject: A61M1/1005
subject: A61M1/1017
subject: A61M1/1055
subject: A61M1/1081
subject: A61M1/1086
subject: A61M1/1087
subject: A61M2205/33
subject: A61M2205/3303
subject: A61M2205/3334
subject: 417/415
subject: 607/16

description: Systems and methods for providing a variable pumping stroke from a pump comprising a pumping chamber, a pump inlet, a pump outlet, a valving mechanism, and a drive piston. In one embodiment, the pump inlet is in fluid communication with the pumping chamber regardless of the location of the drive piston within the pumping chamber, and the pump outlet is similarly in fluid communication with the pumping chamber regardless of the location of the drive piston within the pumping chamber.
Mononychellus mcgregori
Creators: name: DyamanagoudaK, Poojar
name: K, Kenchappa Rajashekharappa
name: ChinnamadegowdaK, Channegowda
name: MulimaniK, Vidya
name: Flechtmann K, Carlos H. W.
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Trombidiformes
Tetranychidae
Mononychellus
Mononychellus mcgregori

description: Mononychellus mcgregori (Flechtmann & Baker, 1970)
Figs. 1–7
description: Published as part of DyamanagoudaK, Poojar, K, Kenchappa Rajashekharappa, ChinnamadegowdaK, Channegowda, MulimaniK, Vidya & Flechtmann K, Carlos H. W., 2024, New record and redescription of invasive cassava green mite, Mononychellus mcgregori (Flechtmann & Baker) in India on cassava, Manihot esculenta Crantz, pp. 879-890 in Acarologia 64 (3) on page 881, DOI: 10.24349/2n0h-5tye, http://zenodo.org/record/14670239
Effect of domain size and interface characteristics on the impact resistance of selected polymer composites
Creators: name: Viratyaporn, Wantinee
Publisher: name: No Publisher Supplied
Year: 2010

description: Nanocomposite technology has advanced considerably in recent years and excellent engineering properties have been achieved in numerous systems.  In multiphase materials the enhancement of properties relies heavily on the nature at the interphase region between polymer domains and nanoparticle reinforcements.  Strong adhesion between the phases provides excellent load-transfer and good mechanical elastic modulus and strength, whereas weak interaction contributes to crack deflection mechanisms and toughness.  Polymer molecules are large and the presence of comparably sized filler particles affects chain gyration, which in turn influences the conformation of the polymer and the properties of the composite. Nanoparticles were incorporated into a poly(methyl methacrylate) matrix by means of in situ free radical (bulk) polymerization.  Aluminum oxide and zinc oxide nanoparticles were added to study the effects of particle chemistry and shape on selected mechanical properties such as impact resistance, which showed significant improvement at a certain loading of zinc oxide.  The elongated shape of zinc oxide particles appears to promote crack deflection processes and to introduce a pull-out mechanism similar to that observed in fiber composite systems.  Moreover, the thermal stability of PMMA was improved with the addition of nanoparticles, apparently by steric hindrance of polymer chain motion and a second mechanism related to the dipole inducing effect of the oxide particles.  The sensitivity of infrared spectroscopy to changes in molecular dipoles was used to study the nature of the polymer/particle interface.  The results revealed some interesting aspects of the secondary bonds between polymers and oxides.  Raman spectroscopy was used to investigate the extent of polymerization and changes in polymer conformation.  A degree of polymerization of 93% was achieved in neat PMMA, and even when 5.0 v/o of PGMEA was introduced into the system no monomer was detected.  However, when nanoparticles were included in the system, the ability of these surfaces to absorb active species reduced the degree of polymerization to about 87%.  Furthermore, the syndiotactic sequence increases with the addition of nanoparticles as a consequence of enhanced accessibility to both the metal oxide surface and the dispersing solvent within the system.
title: Machine division
Creators: name: Swartzlander, Earl E.
name: Kong, Inwook
Publisher: name: United States Patent and Trademark Office
Year: 2013
Subjects: subject: G06F7/535
subject: G06F2207/5355
subject: 708/653

description: Techniques are generally described that include methods, devices, systems and/or apparatus for dividing a numerator by a denominator. Some example methods may include selecting a first numerical factor stored in an electronic storage media. The first numerical factor may be multiplied by a numerator at least in part using a first logic circuit configured to perform multiplication. The first numerical factor may also be multiplied by a denominator. A second numerical factor may be calculated based, at least in part, on an approximation of a square of the difference between unity and the product of the first numerical factor and the denominator. The second numerical factor may be multiplied by the product of the numerator and the first numerical factor at least in part using the first logic circuit, to generate an approximation of a quotient of the numerator and the denominator.
title: General signaling protocol for chemical receptors in immobilized matrices
Creators: name: Neikirk, Dean P.
name: Shear, Jason B.
name: McDevitt, John T.
name: Anslyn, Eric V.
Publisher: name: United States Patent and Trademark Office
Year: 2003
Subjects: subject: B01L3/50276
subject: B01L2200/0668
subject: B01L2300/0636
subject: B01L2300/0819
subject: B01L2300/0877
subject: B01L2400/049
subject: G01N21/77
subject: G01N21/253
subject: G01N21/6452
subject: G01N21/78
subject: G01N2021/7786
subject: 435/288.7
subject: 435/287.2

description: A system for the rapid characterization of multi-analyte fluids, in one embodiment, includes a light source, a sensor array, and a detector. The sensor array is formed from a supporting member into which a plurality of cavities may be formed. A series of chemically sensitive particles are, in one embodiment positioned within the cavities. The particles may be configured to produce a signal when a receptor coupled to the particle interacts with the analyte. Using pattern recognition techniques, the analytes within a multi-analyte fluid may be characterized.
Gymnothorax reticularis Bloch 1795
Creators: name: Bogorodsky, Sergey V.
name: Alpermann, Tilman J.
name: Mal, Ahmad O.
name: Gabr, Mohamed H.
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Anguilliformes
Muraenidae
Gymnothorax
Gymnothorax reticularis

description: Gymnothorax reticularis Bloch, 1795
Material examined. SMF 34964 (1: 36.0 cm).
description: Published as part of Bogorodsky, Sergey V., Alpermann, Tilman J., Mal, Ahmad O. & Gabr, Mohamed H., 2014, Survey of demersal fishes from southern Saudi Arabia, with five new records for the Red Sea, pp. 401-437 in Zootaxa 3852 (4) on page 411, DOI: 10.11646/zootaxa.3852.4.1, http://zenodo.org/record/225360
Between market and movement
Creators: name: Wilson, Bradley R.
Publisher: name: No Publisher Supplied
Year: 2010

description: Over the past two decades, social movements transformed the retail marketplace in the United States into a dynamic site for protest and reform.  Product certification has become a central means for negotiating and resolving conflicts between social movement and market actors.  The Fair Trade movement has been pivotal in the evolution of market-oriented campaigns in the United States by pioneering product certification and ensuring market penetration through mobilization of NGO and grassroots activist support.  Fair Trade Certified coffee is the flagship product of the Fair Trade movement in the United States.  What has made the Fair Trade movement unique among market-oriented social movement campaigns is that it presents retailers and consumers with an alternative to traditional boycotts - the purchasing of third party certified Fair Trade labeled products. This dissertation explores the tension between the product marketing and social movement imperatives of the Fair Trade coffee buycott campaign through multi-sited ethnographic research conducted within the United States - the largest coffee consuming country in the world - and Nicaragua - site of the first Fair Trade coffee exchanges in Central America.  Over the course of two years of field study (2005-2007), I observed and interviewed U.S. activists who worked on the front-lines of buycott campaigns in the United States and Nicaraguan coffee farmers who labored in the fields that supply Fair Trade Certified coffee to U.S. retailers.
title: Treatment of neoplastic tissue by water-soluble texaphyrine metal complexes
Creators: name: Sessler, Jonathan L.
name: Hemmi, Gregory W.
name: Mody, Tarak D.
Publisher: name: United States Patent and Trademark Office
Year: 1998
Subjects: subject: A61K51/0485
subject: A61K41/0009
subject: A61K41/0038
subject: A61K41/0076
subject: A61K47/546
subject: A61K49/0021
subject: A61K49/0036
subject: A61K49/0058
subject: A61K49/04
subject: A61K49/106
subject: A61K51/1093
subject: A61L2/0011
subject: C07D487/22
subject: C07H17/02
subject: C07H21/00
subject: 514/185
subject: 534/11
subject: 534/15
subject: 534/16
subject: 540/145
subject: 540/465
subject: 540/472

description: The present invention relates to the use of water-soluble texaphyrin-diamagnetic metal complexes retaining lipophilicity as photosensitizers in the treatment of benign and malignant neoplastic tissue.
Abrochia spitzi Zerny 1931
Creators: name: Pinheiro, L. R.
name: Gaal-Haszler, S.
Publisher: name: Zenodo
Year: 2015
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Arctiidae
Abrochia
Abrochia spitzi

description: spitzi Zerny, 1931
(Figs. 39 and 64)
Abrochia spitzi Zerny, 1931b: 15 (Taf. 1, fig. 3). Lectotype hereby designated, female, BRAZIL, São Paulo, Ipiranga (R. Spitz), with two labels: one printed label “Sao Paulo, Ypiranga, R. Spitz, 14.vi. [19]22, and handwritten label “ Abrochia spitzi Zerny type ♀”. Two paralectotypes, females, with the exact same labels as the lectotype, but for the dates, which are “ 10.vi. [19]22” for the first female and “ii.[19]28” for the second.
Current combination. Pseudosphex spitzi (Zerny, 1931).
Condition of the types. Lectotype. Right hindwing and forelegs slightly damaged. Paralectotypes. Female from 1922 with the left antenna missing, and female from 1928 with the right antenna missing.
Remarks. This species was described from the three specimens mentioned above. Simmons and Weller (2006) ressurected Myrmecopsis, including in it several species that were previously placed in Pseudosphex (see notes on fuscus and deceptans). However, they did not treat Abrochia spitzi or its putative sister species, Pseudosphex nivaca (Dukinfield-Jones, 1914). The two characters found by Simmons and Weller (2006) to be autapomorphic for Myrmecopsis do not occur in P. spitzi. This species may be closest to Cercocladia Draudt, 1915, but until further studies are made, it should remain in Pseudosphex, as incorrect as this placement may be.
Simmons and Weller (2006) incorrectly mentioned Pseudosphex Hübner, 1818 as a junior synonym of Chrysostola Herrich-Schäffer, 1855, whereas the opposite is true, and for this reason this species is treated here under Pseudosphex.
description: Published as part of Pinheiro, L. R. & Gaal-Haszler, S., 2015, Illustrated catalogue of Neotropical Ctenuchina, Euchromiina and Pericopina types (Lepidoptera, Erebidae, Arctiinae, Arctiini) described by Hans Zerny, with discussion on their taxonomic status, pp. 505-535 in Zootaxa 3925 (4) on page 523, DOI: 10.11646/zootaxa.3925.4.2, http://zenodo.org/record/240540
Latency/accuracy trade-offs during sequences of saccades
Creators: name: Wu, Chia-Chien
Publisher: name: No Publisher Supplied
Year: 2010

description: For many motor behaviors, the more time devoted to planning a movement, the higher the spatial accuracy. To determine whether trade-offs between planning time and accuracy apply to saccadic eye movements, the present study investigated whether Fitts's Law, which holds that movement time depends on traveled distance and the required level of precision, applies to sequences of saccades. Saccades were made in sequence to 4 stationary target circles. Target eccentricities and target sizes varied. The time to scan the targets increased with Fitts's Index of Difficulty (ID), (defined as log 2 (2S / D), where S is target separation and D is target diameter), showing that Fitts's Law can apply to sequences of saccades. The increase was due mainly to a greater frequency of secondary saccades, rather than to increases in the latency of primary saccades. Analyses of saccadic accuracy showed that subjects used secondary saccades, rather than prolonging saccadic latency, to improve landing accuracy. Even where subjects were explicitly asked to increase saccadic latency (Experiment 2), the spatial distribution of landing positions of primary saccades did not change. These results showed that increasing the time available for saccadic planning did not improve the spatial precision of saccades. Saccades differ from some other motor behaviors, where optimal performance depends on trading off the duration of primary movements with the occurrence of corrections (Meyer et al., 1988). For saccades, the only apparently viable strategy to improve accuracy is to issue more corrections.
title: Method of phosphate ester hydrolysis
Creators: name: Miller, Richard A.
name: Dow, William C.
name: Sessler, Jonathan L.
name: Wright, Meredith
name: Magda, Darren
Publisher: name: United States Patent and Trademark Office
Year: 1998
Subjects: subject: A61K41/0038
subject: A61K47/546
subject: A61K49/0021
subject: A61K49/0054
subject: B01J31/1658
subject: B01J31/1815
subject: B01J31/061
subject: B01J2531/025
subject: B01J2531/38
subject: C07D487/22
subject: C07H21/00
subject: 435/6.12
subject: 435/6.1
subject: 514/1
subject: 514/44A
subject: 536/22.1
subject: 536/23.1
subject: 536/24.3
subject: 536/25.32

description: A method of phosphate ester hydrolysis including incubating a solution of an aqueous phosphate ester with a metallotexaphyrin complex under conditions and for a time sufficient to hydrolyze the phosphate ester. The metal is a metal cation having catalytic activity for ester bond hydrolysis in aqueous solution. Phosphate ester substrates include nucleic acid such as RNA, phosphoric anhydrides, phospholipids, and alkyl phosphate esters.
NMR characterization of intrinsically disordered alpha-synuclein
Creators: name: Wu, Kuen-Phon
Publisher: name: No Publisher Supplied
Year: 2010

description: A broad range of human diseases arise from the loss of the native function of a specific peptide or protein. The pathological conditions of these diseases are generally referred to as protein misfolding and aggregation problem. An increasing number of misfolded proteins are associated with the deposition of protein aggregation in the brain cells resulting in neurodegenerative diseases, for example, the aggregated α-synuclein (αSyn) in sporadic Parkinson’s disease. αSyn is an intrinsically disordered protein and the aggregation kinetics are sensitive to the changes of amino acids and chemical environments. The structural conversion of αSyn from an unfolded monomeric ensemble to a well-ordered fibril remains unclear. In this work, nuclear magnetic resonance (NMR) was applied to characterize the aggregation-prone species including homologous mouse αSyn and human αSyn at low pH. Comparison of human and mouse αSyn at pH 7.4 and at supercooled aqueous solution presents a less compact mouse αSyn ensemble with transient inter-chain interactions at the N-terminal region. Characterization of αSyn conformational ensembles at both neutral and low pH shows that the altered charge distribution at low pH changes the structural properties of these ensembles and leads to rapid aggregation. Paramagnetic relaxation enhancement (PRE) experiments using mixed isotope (15N) and spin labeled αSyn further illustrate different intermolecular contacts of low-populated transient complex at neutral and low pH. A head-to-tail αSyn complex transiently stabilized by the electrostatic interactions at neutral pH is observed while a tail-to-tail αSyn complex via hydrophobic interactions at low pH is seen. This work provides novel structural insight into the molecular conversion of αSyn at the very early nucleation state.In addition to understanding the aggregation mechanism of αSyn, an approach that deconvolutes the strong modulation of fast hydrogen exchange (HX) rates on the transverse relaxation rate (R2) of disordered proteins is also presented. This work shows an HX-free R2 profile of αSyn at pH 7.4 and provides an opportunity to understand NMR relaxation of disordered proteins or unstructured loop regions in folded proteins at fast HX conditions such as high pH or high temperature.
Uroconger lepturus Richardson 1845
Creators: name: Bogorodsky, Sergey V.
name: Alpermann, Tilman J.
name: Mal, Ahmad O.
name: Gabr, Mohamed H.
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Anguilliformes
Congridae
Uroconger
Uroconger lepturus

description: Uroconger lepturus (Richardson, 1845)
Material examined. SMF 34965 (3: 23.7–38.6 cm); SMF 34967 (1: 27.3 cm); KAUMM 21 (1: 13.4 cm); KAUMM 22 (2: 28.8–30.4 cm).
description: Published as part of Bogorodsky, Sergey V., Alpermann, Tilman J., Mal, Ahmad O. & Gabr, Mohamed H., 2014, Survey of demersal fishes from southern Saudi Arabia, with five new records for the Red Sea, pp. 401-437 in Zootaxa 3852 (4) on page 411, DOI: 10.11646/zootaxa.3852.4.1, http://zenodo.org/record/225360
title: Phosphoramidite derivatives of texaphyrins
Creators: name: Sessler, Jonathan L.
name: Iverson, Brent L.
name: Crofts, Shaun P.
name: Magda, Darren
name: Sansom, Petra I.
Publisher: name: United States Patent and Trademark Office
Year: 1997
Subjects: subject: A61K47/546
subject: C07H21/00
subject: 534/15
subject: 534/11
subject: 534/13
subject: 534/16
subject: 536/17.1
subject: 536/17.3
subject: 536/17.4
subject: 540/145
subject: 540/465
subject: 540/472

description: The invention is directed to a method of incorporating expanded porphyrins, and particularly of incorporating a sapphyrin or a texaphyrin, before, during, or after chemical synthesis of an oligomer to form an expanded porphyrin-oligonucleotide conjugate, and particularly a sapphyrin- or texaphyrin-oligonucleotide conjugate. This method includes reacting derivatized nucleotides and a sapphyrin or a texaphyrin in a desired order in an automated or manual DNA synthesizer having a solid support to form a sapphyrin- or a texaphyrin-oligonucleotide conjugate.
Epimeria (Drakepimeria) d'Acoz & Verheye 2017, subgen. nov.
Creators: name: d'Acoz, Cédric d'Udekem
name: Verheye, Marie L.
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Malacostraca
Amphipoda
Epimeriidae
Epimeria

description: Incertae sedis: Epimeria (Drakepimeria) subgen. nov. sp. 2
Epimeria sp. – Andres 1985: 127, fig. 10, 11A.
Distribution
South Shetland Islands: Clarence Island, 0– 145 m.
Remark
The description of Epimeria sp. by Andres (1985) is based on two tiny (7 mm) male specimens. It exhibits similarities with E. leukhoplites sp. nov., E. reoproi and E. vaderi, of which the description is based on much larger specimens. It is likely that Andres’ (1985) specimens are juveniles of one of these species.
description: Published as part of d'Acoz, Cédric d'Udekem & Verheye, Marie L., 2017, Epimeria of the Southern Ocean with notes on their relatives (Crustacea, Amphipoda, Eusiroidea), pp. 1-553 in European Journal of Taxonomy 359 on page 65, DOI: 10.5852/ejt.2017.359, http://zenodo.org/record/3855694
Ammothella stauromata Child 1982
Creators: name: Bamber, Roger N.
Publisher: name: Zenodo
Year: 2004
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Pycnogonida
Pantopoda
Ammotheidae
Ammothella
Ammothella stauromata

description: Ammothella stauromata Child, 1982
Child, 1982, 271–273, fig. 1.
Material: New Caledonia, 1 subadult specimen (MNHN­Py 1049), station 1418, Baie de Santal: east of Easo Point; sand and weed on wharf, 20º46.9'S 167º07.9'E, 1­5 m, November 2000; Lifou workshop.
Remarks: This small subadult has the tall, slender, middorsal trunk tubercles on the first three trunk segments, small tubercles on the lateral processes and first coxa, a large, blunt, eyed ocular tubercle, and auxiliary claws almost as long as the main claw as described by Child (1982). The juvenile features of the specimen include ovigers present as mere buds and a lack of trunk segmentation. This species is known throughout this region from the Philippines to Polynesia and the Great Barrier Reef, and from the littoral zone to 11 m depth.
description: Published as part of Bamber, Roger N., 2004, Pycnogonids (Arthropoda: Pycnogonida) from French Cruises to Melanesia, pp. 1-27 in Zootaxa 551 on page 3, DOI: 10.5281/zenodo.157770
Muraenesox cinereus Forsskal 1775
Creators: name: Bogorodsky, Sergey V.
name: Alpermann, Tilman J.
name: Mal, Ahmad O.
name: Gabr, Mohamed H.
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Anguilliformes
Muraenesocidae
Muraenesox
Muraenesox cinereus

description: Muraenesox cinereus (Forsskål, 1775)
Material examined. SMF 34970 (2: 52.8–66.4 cm); KAUMM 39 (1: 43.8 cm).
description: Published as part of Bogorodsky, Sergey V., Alpermann, Tilman J., Mal, Ahmad O. & Gabr, Mohamed H., 2014, Survey of demersal fishes from southern Saudi Arabia, with five new records for the Red Sea, pp. 401-437 in Zootaxa 3852 (4) on page 411, DOI: 10.11646/zootaxa.3852.4.1, http://zenodo.org/record/225360
Imputation of automatic control algorithms and estimation in high-dimensional linear regression
Creators: name: Ye, Fei
Publisher: name: No Publisher Supplied
Year: 2010

description: This thesis contains two parts. In the first part, we study a semiparametric imputation method to simulate a time series of blood glucose level under certain closed-loop control algorithm of a diabetic patient equipped with a continuous glucose monitor and an insulin pump, from the "frozen" measurements under self-adjusted open-loop control. The Star One data set provided by Medtronic Inc illustrates the feasibility of a simple PID algorithm, as an example of automatic control algorithms, in controlling blood glucose levels from the perspective of reducing the A1c level and controlling hypoglycemia risk.In the second part, we consider L1-penalized selection of variables and estimation of regression coefficients in a high-dimensional linear model. Under an L0 sparsity condition on the regression coefficients, we sharpen an upper bound of Candes and Tao (2007) for the L2 loss of the Dantzig selector and extend it to the Lq loss and the Lasso. By allowing q equals infinity, our bound implies the variable selection consistency of threshold Dantzig selectors. For the estimation of regression coefficients in Lr balls, we provide minimax lower bounds for the Lq risk and the tail quantiles of the Lq loss as well as sufficient conditions on the design matrix and penalty level for the Dantzig and Lasso estimators to attain these minimax rates.
Compact Modelling of Memristors Toward Analog Neuromorphic Circuit Simulations
Creators: name: Ratier, Thomas Ratier
name: Delvenne, Jean-Charles
name: Flandre, Denis
name: Van Brandt, Leopold
Publisher: name: Zenodo
Year: 2024
Subjects: Neuromorphic Computing
Memristor

description: Motivation: Neuromorphic Computing❑ Computation limitation (Von NeumannBottleneck).❑ Energy hungry.❑ Binary information.❑ Computation and Memory separation.
Ichoria thyrassia Zerny 1931
Creators: name: Pinheiro, L. R.
name: Gaal-Haszler, S.
Publisher: name: Zenodo
Year: 2015
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Arctiidae
Ichoria
Ichoria thyrassia

description: thyrassia Zerny, 1931
(Fig. 40)
Ichoria thyrassia Zerny, 1931b: 10 (Taf. 1, fig. 29). Holotype male [fixed by monotypy], COLOMBIA, Rio Aguacatal, 2000m (Fassl); with two labels: printed label “Rio Aguacatal, Colomb., W. Cord., 2000m, coll. Fassl” and handwritten label “ Ichoria thyrassia Zerny ♂ type”.
Current combination. Ichoria thyrassia Zerny, 1931.
Condition of the type. Wings slightly worn.
Remarks. This species probably does not belong in a monophyletic concept of Ichoria. It resembles Chrostosoma decisa (Walker, [1865]).
description: Published as part of Pinheiro, L. R. & Gaal-Haszler, S., 2015, Illustrated catalogue of Neotropical Ctenuchina, Euchromiina and Pericopina types (Lepidoptera, Erebidae, Arctiinae, Arctiini) described by Hans Zerny, with discussion on their taxonomic status, pp. 505-535 in Zootaxa 3925 (4) on page 523, DOI: 10.11646/zootaxa.3925.4.2, http://zenodo.org/record/240540
title: Raman spectrometer
Creators: name: Fink, Manfred F.
name: Robinson, John C.
name: Buell, Walter F.
Publisher: name: United States Patent and Trademark Office
Year: 1998
Subjects: subject: G01N21/65
subject: G01J3/44
subject: 356/301
subject: 359/885
subject: 372/32

description: An improved Raman spectrometer is provided, having, in a preferred embodiment, a light source comprising an injection-locked laser diode array, a multipass cell to multiply the intensity of the light source, a dynamic gas sample focusing system, and an atomic vapor filter to remove the Rayleigh scattered light. The laser diode arrays are tuned to match an absorption band of the atomic vapor filter. The Raman scattered light passes virtually unattenuated through the filter to be recorded by a Fourier transform spectrometer or other spectrometer. This invention permits higher sensitivity and resolution than prior art Raman spectrometers, in particular permitting identification and measurement of Raman emissions that occur at low wave numbers. The light source of this invention can also be used in conjunction with optical notch filters and photodetectors to permit detection and measurement of preselected species in a sample.
Partitioning problems in discrete and computational geometry
Creators: name: Zhao, Jihui
Publisher: name: No Publisher Supplied
Year: 2010

description: Many interesting problems in Discrete and Computational Geometry involve partitioning. A main question is whether a given set, or sets, may be separated into parts satisfying certain properties. Sometime we also need to find an efficient way to do it - in other words an algorithm. In this thesis, we discuss several of problems and results of this kind.First we give a combinatorial proof of the existence and the uniqueness of the generalized ham-sandwich cut for well separated point sets in R^d, that have the weak general position property. The combinatorial proof allows us to derive an O(n(log n)^d−3) running time algorithm to find a generalized cut for d given well separated point sets in R^d.A second problem concerns the 6-way partition of a given convex set in R^2 using 3 lines. We reopen an old question and show that when the direction of one line is fixed, there is unique partition such that 6 regions have the same area. In the Voronoi game two players A and B each play n points in a compact set S in R^d. They obtain scores equal to the total volume of the Voronoi cells of their points. There are one round and alternating versions of the game. We give the player A's best strategy to minimize the area of player B's one(first) Voronoi cell.
Rehabilitation and kinesiological analysis of motor control in grasp
Creators: name: Yungher, Don
Publisher: name: No Publisher Supplied
Year: 2010

description: Rehabilitation of grasp following brain injury remains a challenge that is seldom completely successful. Current biofeedback protocols for fine motor rehabilitation are generally limited to single-muscle or single-joint movements, and their application to Activities of Daily Living (ADL) is constrained by the simplicity of motions feasible during training. Herein, a novel biofeedback device, termed Proprioception-Augmenting and Measurement Interface (PAMI) was used to train thumb-index opposition, a task relevant to ADL.  PAMI uses a novel method to non-invasively measure muscle forces in the arm during grasp, using Surface Muscle Pressure (SMP).     The efficacy of PAMI training was assessed using a standard therapeutic test, the 9-hole peg test. In addition, the neural control features of grasp were examined using motor variance analysis. Features of the PAMI signal were extracted from recorded signals and compared to clarify the mechanisms by which PAMI aids rehabilitation.  Variability analysis of recorded SMP signals measured the effect of PAMI biofeedback on the coordination of muscle activity in impaired and healthy persons.  Training with the PAMI device was shown to be effective in the short-term improvement of fine motor function for brain injured participants (p
Design and analysis of amino acid supplementation in hepatocyte culture using in vitro experiment and mathematical modeling
Creators: name: Yang, Hong
Publisher: name: No Publisher Supplied
Year: 2010

description: Extracorporeal bioartificial liver (BAL) devices, involving primary hepatocytes, represent a promising option to provide temporary support for patients with liver failure. Current use of BAL is primary challenged by development of techniques for long-term culture of hepatocytes during plasma exposure, as occurs during clinical application. Previous in vitro studies and mathematical modeling analysis have shown that supplementation of amino acids to the plasma enhances liver-specific functions and reduces lipid accumulation. However, further improvement would be enhanced greatly by development of a rational strategy to design the profile of amino acid supplementation and by better understanding of the metabolic objectives of hepatocytes, and how they vary as a function of amino acid supplementation. In order to address these issues, a rational design approach was first developed using flux balance analysis (FBA) to determine a profile of amino acid supplementation to achieve a specific cellular objective (urea production) in cultured hepatocytes exposed to plasma. Experiments based on the designed supplementation showed that both urea and albumin production were increased compared with previously reported (empirical) amino acid supplementation. However, the experimental values did not match our theoretical prediction mainly due to the insufficient constraints imposed to the modeling. In an attempt to improve the model accuracy, we incorporated pathway energy balance (PEB) constraints, and amino acids transport constraints. It is found that both PEB and transport constraints significantly reduce the feasible region of the flux space. Moreover, metabolic objective prediction (MOP) model reveals that hepatocytes respond to variations in available amino acid supplementation by changing their metabolic objectives and pathway utilization. In particular, the analysis shows that fatty acid oxidation is vital to reduce the rate of lipid accumulation and to increase liver-specific functions with amino acid supplementation.This study leads to a better understanding of amino acid supplementation effects on hepatocytes during plasma exposure based on the integration of in vitro experiments and mathematical modeling. The approach enables the metabolic manipulation of hepatocytes with rationally designed amino acid supplementation to improve the targeted liver cell functionality and improve the long-term technique of hepatocytes applied for BAL devices.
Amblygaster sirm Walbaum 1792
Creators: name: Bogorodsky, Sergey V.
name: Alpermann, Tilman J.
name: Mal, Ahmad O.
name: Gabr, Mohamed H.
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Clupeiformes
Clupeidae
Amblygaster
Amblygaster sirm

description: Amblygaster sirm (Walbaum, 1792)
Material examined. SMF 34968 (2: 10.2–14.6 cm); KAUMM 24 (1: 9.7 cm).
description: Published as part of Bogorodsky, Sergey V., Alpermann, Tilman J., Mal, Ahmad O. & Gabr, Mohamed H., 2014, Survey of demersal fishes from southern Saudi Arabia, with five new records for the Red Sea, pp. 401-437 in Zootaxa 3852 (4) on page 412, DOI: 10.11646/zootaxa.3852.4.1, http://zenodo.org/record/225360
The packaging of DNA in chromatin
Creators: name: Zheng, Guohui
Publisher: name: No Publisher Supplied
Year: 2010

description: The mechanical properties of DNA play a key role in its biological processing, determining how the long, thin, double-helical molecule responds to the binding of proteins and functions in confined spaces within a cell. In eukaryotes, about 75-90% of genomic DNA exists in the form of nucleosomes, which are the fundamental units of DNA packaging in chromatin and the primary determinate of DNA accessibility. The structure of chromatin undergoes various changes that depend, at least in part, upon the requirements of gene expression and other functional environments. The dynamics of DNA packaging in chromatin is thus fundamental to numerous biological processes.The flexibility of DNA is important in packaging DNA over lengths comparable to its persistence length during genetic processing and the sequence-dependent properties of DNA determine the positioning of nucleosomes in the genome and the sites of binding of enzymes and transcription factors. In addition, understanding the correlation between DNA flexibility and histone-DNA interactions inside the nucleosome is essential for unraveling currently unsolved mechanisms of gene regulation. Furthermore, although many experimental techniques have emerged to examine the overall structure of chromatin fibers, the internal arrangement of DNA and histones remains unclear. Thus an appropriate computational model able to incorporate experimental observations is key to interpretation of the folding and unfolding of chromatin.The major goal of this thesis is to understand some of biophysical mechanisms involved in the packaging of DNA into chromatin using computational techniques at multi-scales: (i) to determine the sequence-dependent flexibility of DNA by developing DNA deformation analysis tools and databases; (ii) to design DNA spatial configurations using knowledge-based Monte-Carlo sampling; (iii) to map protein-DNA recognition inside nucleosomes in terms of realistic molecular treatments; and (iv) to interpret the internal structure of chromatin fibers and examine chromatin looping using novel modeling and simulation methods.
Epimeria (Drakepimeria) d'Acoz & Verheye 2017, subgen. nov.
Creators: name: d'Acoz, Cédric d'Udekem
name: Verheye, Marie L.
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Malacostraca
Amphipoda
Epimeriidae
Epimeria

description: Epimeria (Drakepimeria) subgen. nov. sp. 1
Distribution
Ross Sea, 151– 300 m.
Remarks
This undescribed species, which is similar to E. leukhoplites sp. nov. (see key) was discovered in the Ross Sea by A.-N. Lörz. It will be described as new in a forthcoming paper by M. Verheye, A.- N. Lörz & C. d’Udekem d’Acoz.
description: Published as part of d'Acoz, Cédric d'Udekem & Verheye, Marie L., 2017, Epimeria of the Southern Ocean with notes on their relatives (Crustacea, Amphipoda, Eusiroidea), pp. 1-553 in European Journal of Taxonomy 359 on page 65, DOI: 10.5852/ejt.2017.359, http://zenodo.org/record/3855694