cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Further characterization of metacaspase expression and activity in marine phytoplankton
Creators: name: Liao, Wanjing
Publisher: name: No Publisher Supplied
Year: 2010

description: Metacaspases are considered to be ancestral cysteinyl aspartate specific proteases involved in the initiation and execution of apoptotic programmed cell death (PCD). The widespread presence of metacaspases genes among a variety of phytoplankton, suggests that they play a fundamental role in cell turnover, aquatic food webs, and biogeochemical cycles. Yet, there are still fundamental questions that exist about these enzymes: How does metacaspase diversity relate to different evolutionary plastid lineages? What is their relationship to cell physiology? Are metacaspases associated with caspase activity?Using hydrolysis of a fluorogenic canonical tetrapeptide substrate and western blot analysis, we report on the induction of caspase-like activity and metacaspases-like protein expression from four ecologically and evolutionarily diverse phytoplankton species, including a chlorophyte (Dunaliella tertiolecta), a haptophyte (Isochrysis galbana), a diatom (Thalassiosira weissflogii), and a dinoflagellate (Amphidinium carterae).  These derived eukaryotic lineages represented phytoplankton from primary (D. tertiolecta), secondary (I. galbana and T. weissflogii), and tertiary endosymbiotic (A. carterae) events. Immunohybridization to polyclonal antisera raised against a coccolithophore metacaspase indicated high conservation of caspase-like proteins and an accumulation of metacaspase complexity with evolutionary complexity. An E. huxleyi CCMP1516 (Ehux1516) and EhV86 host-virus model system was used to link dramatic increases in caspase specific activity with protein signatures via a genome-enabled, proteomic approach.  Both the host and virus have sequenced genomes and EhV86 strongly triggered caspase activity. Caspase activation was measured through in vitro cleavage of fluorogenic peptide substrates with up to ~170-fold increase during infection. Subsets of partially purified proteins were associated with enhanced caspase specific activity and displayed hybridization to metacaspase antibodies. Pooled subsets of caspase active fractions from size exclusion chromatography were subjected to both 1D SDS-PAGE and 2D gel electrophoresis (GE) followed by mass spectrometry analysis. SYPRO-Ruby staining of 2D gels yielded approximately 10-17 clearly definable protein spots for caspase active fractions. Seventeen proteins hits, including four from the EhV86 proteome, were homologues to proteases or death related proteins, suggesting these proteins may be responsible for observed caspase activities and some may be virally derived. Further work should focus on validating the activity and function of these gene products.
Pseudosphex fuscus Zerny 1931
Creators: name: Pinheiro, L. R.
name: Gaal-Haszler, S.
Publisher: name: Zenodo
Year: 2015
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Arctiidae
Pseudosphex
Pseudosphex fuscus

description: fuscus Zerny, 1931
(Fig. 31)
Pseudosphex fuscus Zerny, 1931b: 5 (Taf. 1, fig. 11). Holotype male [by monotypy]: COLOMBIA, Muzo, 400–800m (Fassl); with two labels: printed label “Muzo, Colombia, 4–800m coll. Fassl” and handwritten label ” Pseudosphex fuscus Zerny ♂ type ”.
Current combination. Myrmecopsis fuscus (Zerny, 1931).
Condition of the type. Left hindleg broken.
Remarks. Simmons & Weller (2006) transferred this species to Myrmecopsis. Cerda (2008) mentioned M. fuscus when describing a similar species, M. francoisi Cerda, 2008.
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 519, DOI: 10.11646/zootaxa.3925.4.2, http://zenodo.org/record/240540
Adopted papal kin as art patrons in early modern Rome (1592-1676)
Creators: name: Lloyd, Karen Jean
Publisher: name: No Publisher Supplied
Year: 2010

description: This dissertation examines the art patronage of adopted papal nephews in Baroque Rome (1592-1676), exploring the relationship between adoption and the arts in the context of a political system based on clientage and nepotism. When the nephew was not from the same paternal line as the pope, the onus fell on the pope and his nephew to publicly proclaim, thereby reifying, the solidity of their relationship. Adopted nephews used the visual arts to create public displays of the unity of the ruling papal family, to demonstrate allegiance to a new paternal affiliation, and as part of the client system, in which works of art acted as signs of favor.Chapter 1 offers an outline of adoption and its reception based on primary source documents; subsequent chapters are case studies of individual patrons. Cinzio Passeri Aldobrandini's (1551-1610) career demonstrates the essential link between paternity and authority. This chapter presents unpublished documentation regarding Cinzio as a collector and reconsiders the significance of his ties to poet Torquato Tasso.Scipione Caffarelli Borghese's (1577-1632) commissions reiterate the hierarchical relationship between pope and nephew, preempting potential dissent by reaffirming the source and limitations of his authority and proclaiming the unity of the Borghese papacy. The first detailed reading of Guido Reni's 1608 Vatican Palace frescoes anchors this chapter.Contemporary commentary regarding the first true adopted nephew, Camillo Astalli Pamphili (1619-63), illustrates the extent of the resistance to adoption. His few commissions, from Velázquez and Claude Lorrain, present him as a worthy nephew in an attempt to normalize his unprecedented situation. The three adopted nephews of Clement X (1670-76) used their projects to proclaim their crucial role in the Altieri papacy and the illustrious heritage of their Albertoni family roots. From new analyzes of Carlo Maratti's Altieri Palace fresco and its development, to the rediscovery of a lost painting by Baciccio, this chapter highlights the issues at the crux of early modern resistance to adoption: loyalty, memory, and legitimacy. As the first study of adoption and its relationship to the visual arts in Seicento Rome, this dissertation reconstitutes a key component of baroque society and culture.
title: Isolation of binding proteins with high affinity to ligands
Creators: name: Iverson, Brent L.
name: Georgiou, George M.
name: Chen, Gang
name: Hayhurst, Andrew
name: Thomas, Jeffrey G.
Publisher: name: United States Patent and Trademark Office
Year: 2006
Subjects: subject: C12N15/1034
subject: 435/69.1
subject: 435/7.1
subject: 435/69.2
subject: 435/69.3
subject: 435/69.7

description: The invention overcomes the deficiencies of the prior art by providing a rapid approach for isolating binding proteins capable of binding small molecules and peptides via “display-less” library screening. In the technique, libraries of candidate binding proteins, such as antibody sequences, are expressed in soluble form in the periplasmic space of gram negative bacteria, such as Escherichia coli, and are mixed with a labeled ligand. In clones expressing recombinant polypeptides with affinity for the ligand, the concentration of the labeled ligand bound to the binding protein is increased and allows the cells to be isolated from the rest of the library. Where fluorescent labeling of the target ligand is used, cells may be isolated by fluorescence activated cell sorting (FACS). The approach is more rapid than prior art methods and avoids problems associated with the surface-expression of ligand fusion proteins employed with phage display.
Bulacarus FanK & ZhaoK, 2024, gen. nov.
Creators: name: FanK, Qing-Hai
name: ZhaoK, Zeng Qi
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Sarcoptiformes
Histiostomatidae
Bulacarus

description: Bulacarus gen. nov.
Zoobank: 6FFD575B-0792-4035-A67E-D671272998BB
Type species: Bulacarus curvisetus sp. nov. ; monotypic.
Diagnosis and description — As for the family.
Etymology — The name of this genus is derived from the Fijian word bula “,” which means life, health, or greeting, combined with the genus name Acarus “ ”.
description: Published as part of FanK, Qing-Hai & ZhaoK, Zeng Qi, 2024, Establishment of a new mite family, Bulacaridae (Acari: Astigmata), pp. 1003-1018 in Acarologia 64 (4) on page 1006, DOI: 10.24349/183v-eq41, http://zenodo.org/record/14670215
An ecological momentary assessment analysis of relations among coping, affect, and smoking lapse
Creators: name: Minami, Haruka
Publisher: name: No Publisher Supplied
Year: 2010

description: This study used EMA data from smokers engaged in an earnest attempt to quit smoking to assess complex relations among coping, affect, and smoking. Analyses tested hypotheses about the main effects of coping and both mediators and moderators of coping effects on subsequent outcomes of interest (i.e., affect, coping effort, coping efficacy, and smoking behavior). Results of multilevel models indicated that coping does not improve negative affect within 4 hours of coping efforts, but that coping does improve positive affect and increase the odds of engaging in temptation coping in the short-term. Lapses were more likely to happen when recent coping was reported within 48 hours. None of the putative mediators of coping were predictive of later lapse risk as anticipated. Analyses also revealed that pre-quit coping practice moderated the effects of post-quit coping to deal with stressful events on later affect. Moreover, significant moderating gender effects were also found in these relations.
Lophostica mauriciana
Creators: name: Wesołowska, Wanda
Publisher: name: Zenodo
Year: 2000
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Araneae
Salticidae
Lophostica
Lophostica mauriciana

description: Lophostica mauriciana SIMON, 1902
(Figs 1­8) Lophostica mauriciana SIMON 1902: 390­391; 1903: 810.
MATERIAL.
Mauritius island [Ins. Mauricia], 1 female (lectotype; present designation ­ in separate vial), 4 females, 1 male, leg. C. ALLUAUD, Muséum National d’Histoire Naturelle, Paris (19040).
DESCRIPTION.
Measurements (male/female). Carapace: length 4.1/3.5[mm], width 3.4/2.8, height 1.9/1.9. Ocular area: length 1.8/1.6, anterior width 2.4/2.1, posterior width 2.5/2.1. Abdomen: length 3.7/5.5, width 3.1/3.5.
Male. Large salticid. Carapace brown, rounded and convex, rather high. Eye field darker, occupies almost half of carapace length, vicinity of eyes almost black. Clypeus very low, covered with white hairs. Maxillae and labium yellow with brown bases. Sternum orange, scutiform. Chelicerae large, dark brown, promargin with two teeth, retromargin with triple tooth (Fig. 2). Abdomen (partially damaged) brown, spinnerets orange. Legs long and thin, orange­brownish, first pair longest (with very long tibiae). Leg hairs brown; spines long, brown. Pedipalp long, brown, clothed in long hairs. Cymbium long and narrow (Fig. 5). Single tibial apophysis straight and thin (Figs 3­5), bulbus oval, sperm duct course meandering, embolus long and almost straight (Figs 3­4).
Female. Dorsal aspect as in Fig. 1. Colouration of carapace like in male. Abdomen grey with median irregular yellow strip and longitudinal patches laterally. Venter yellowish. Epigyne rounded with large central depression partially separated with narrow ridge (Fig. 6). Initial parts of seminal ducts weakly sclerotized, spermathecae spherical (Figs 7­8).
description: Published as part of Wesołowska, Wanda, 2000, A redescription of Lophostica mauriciana Simon, 1902 (Araneae: Salticidae), pp. 95-98 in Genus 11 on pages 95-98
Using RNA backbone torsions to study RNA structure
Creators: name: Micallef, David Ian
Publisher: name: No Publisher Supplied
Year: 2010

description: Ribonucleic Acid (RNA) is an important cellular macromolecule vital to most if not all life on Earth. RNA has many different roles in the cell, most notably as the intermediary molecule that transfers genetic information from DNA to protein in translation. Recently, additional functions of RNA have been elucidated more clearly, such as catalyzing chemical reactions and regulating gene expression. These exciting new findings have shined a scientific spotlight on the field of RNA structure in order to better understand how the once mundane polynucleotide acts in such myriad ways.An important factor in RNA’s versatile nature is the inherent variation in its chemical structure. The hydroxyl group present on the ribose sugar of a ribonucleic acid makes the corresponding polynucleotide capable of chemical reaction, with itself or with other molecules in the cell. This hyper-reactivity allows RNA to form substantially unique structures, from the hammerhead ribozyme's helical shape from which it takes its name, to the L-shaped conformation common to all transfer RNAs. The problem at hand is thus to study RNA structure and determine if any new patterns can be discovered.The work presented here centered on a collaborative effort to define a set of conformations common to two-nucleotide long sequences of RNA found in structures from the Protein Data Bank (PDB). This work contributed by clustering RNA di-nucleotides by their torsion angle space using a Fast Fourier averaging technique proven to be effective in clustering nucleotide structure. Each group in the collaboration used different methodologies to analyze the same RNA structural data, and yet found similar results. The collaboration ultimately produced a set of 46 consensus conformations defined by the seven dihedral angles of the sugar-to-sugar unit in a di-nucleotide RNA sequence.To utilize this new set of RNA di-nucleotide conformations, a software tool was designed and developed to automatically assign the conformation nomenclature to input RNA structure. The program was successfully tested on the pilot study data. A test study was performed on a unique set of RNA structures. The results of this study demonstrated that the consensus conformation set can in fact be used to classify RNA structure.
Evidence-based recommendations for Atlantic Coast piping plover (Charadrius melodus) conservation and habitat restoration
Creators: name: Maslo, Brooke
Publisher: name: No Publisher Supplied
Year: 2010

description: Conservation action and habitat restoration for threatened and endangered species are often guided by anecdotal evidence.  Limited time and resources are wasted on ineffective strategies, or in some cases, on management that is detrimental to the target species.  Therefore, rigorous scientific study must be easily translatable into pragmatic conservation directives.  For the Atlantic Coast piping plover (Charadrius melodus), a threatened beach-nesting shorebird, two major threats exist for the recovery of the species -- habitat degradation by beach stabilization practices and human disturbance, and intense predation pressure by the introduced red fox (Vulpes vulpes).  This dissertation employs robust statistical methods to: 1) analyze piping plover nesting and foraging behavior, and 2) evaluate the effectiveness of predator exclosures to present evidence-based recommendations for the restoration of breeding habitat and the optimization of reproductive success.Piping plover nests primarily occur in four distinct habitat conditions defined by percent shell and pebble cover, and distance to nearest dunes and high tide line.  Characteristics also vary depending on where the nest is initiated (backshore, overwash fan, primary dune).  I translate these results into practical restoration target parameters and identify threshold values to assist managers in maintaining suitable nesting habitat.  Restoration projects must also include accessible high quality foraging habitat to bolster reproductive success.  Plover chicks foraged at higher rates and spent less time being vigilant or fleeing from threats at restored tidal ponds than at other potential foraging habitats.  This result suggests that the study ponds offered adequate prey biomass, were visited less frequently by humans, and provided proximate refuge from approaching predators.  The foraging models I created were validated externally and are applicable for evaluating future restoration projects.Finally, long-term nest monitoring data indicate that predator exclosures do increase nest hatching success.  Electrified exclosures are effective under certain conditions, but at sites with high fox density and human disturbance, nest abandonment becomes sizeable.  While the direct cause of abandonments remains unclear, these results will assist managers in making informed decisions on using this technique.  These science-based directives can help to create effective habitat designs and conservation strategies for this species.
Additional file 1: of iTACTIC â   implementing Treatment Algorithms for the Correction of Trauma-Induced Coagulopathy: study protocol for a multicentre, randomised controlled trial
Creators: name: Baksaas-Aasen, Kjersti
name: Gall, Lewis
name: Eaglestone, Simon
name: Rourke, Claire
name: Nicole. Juffermans
name: J. Goslings
name: Paal Naess
name: Dieren, Susan Van
name: Ostrowski, Sisse
name: Stensballe, Jakob
name: Maegele, Marc
name: Stanworth, Simon
name: Gaarder, Christine
name: Brohi, Karim
name: Johansson, Per
Publisher: name: Figshare
Year: 2017
Subjects: subject: Space Science
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Protocol version 3.0/14.03.2017. (PDF 2172 kb)
Philonthus trochocerus Hromadka 2013
Creators: name: Mikátová, Šárka
name: Macháčková, Lenka
name: Hájek, Jiří
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Staphylinidae
Philonthus
Philonthus trochocerus

description: Philonthus trochocerus Hromádka, 2013
Philonthus trochocerus Hromádka, 2013b: 13, Figs 26–28.
Two paratypes are deposited in NMPC (ex coll. L. Hromádka):
PA*©A*´YPൾ (unsexed specimen): ‘Tschadsee,AEF., / Insel Iba [sic!],lg. Franz [p] // ex coll. L. Hromádka / National Museum / Prague, Czech Republic [p] // PARATYPUS / PHILONTHUS (s. str.) / trochocerus sp. nov. / Hromádka, det., 2012. [p, red label]’.
PA*©A*´YPൾ (unsexed specimen): ‘Tschadsee,Ile [p] / Iba [hw],AEF/ lg.H. Franz [p] // ex coll. L. Hromádka / National Museum / Prague, Czech Republic [p] // PARATYPUS / PHILONTHUS (s. str.) / trochocerus sp. nov. / Hromádka, det., 2012. [p, red label]’.
Current status. Valid species.
Philonthus turnix Hromádka, 2016 Philonthus turnix Hromádka, 2016a: 104, Figs 16–19.
One paratype is deposited in NMPC (ex coll. L. Hromádka):
PA*©A*´YPൾ (): ‘ DŘC [sic!]; Tsingidi / 2.24. 15.6S 12.58.11.0E / November
2013 / leg.L.J.Niemand [p] // ex coll.L. Hromádka / National Museum
/ Prague, Czech Republic [p] // PARATYPUS / PHILONTHUS (s.str.) / turnix sp. nov. / Hromádka, det. 2015 [p, red label]’.
Current status. Valid species.
description: Published as part of Mikátová, Šárka, Macháčková, Lenka & Hájek, Jiří, 2020, Catalogue of type specimens of beetles (Coleoptera) deposited in the National Museum, Prague, Czech Republic, pp. 353-389 in Acta Entomologica Musei Nationalis Pragae 60 (1) on pages 384-385, DOI: 10.37520/aemnp.2020.021, http://zenodo.org/record/3880030
Morphological evolution of birds recently introduced to islands
Creators: name: Mathys, Blake
Publisher: name: No Publisher Supplied
Year: 2010

description: Evolution was originally considered to be observable only over geological time scales.  It has recently become apparent that evolutionary changes can be detected over contemporary time periods.  Exotic species often experience intense selection, making them good model systems for investigating evolutionary changes over contemporary time.  We often know details of the introductions, such as exact time, location of the source population, founding propagule size, and establishment history.  These details allow us to formulate hypotheses concerning the evolutionary changes expected in these species' exotic ranges.I examined contemporary morphological evolution of passerine birds introduced to islands.  Passerine birds have been introduced to many islands world-wide, making them conducive for examining patterns of insular evolution.  In chapters one and two, I evaluated whether these species conform to the Island Rule, an ecogeographic rule based on the study of native insular species.  It states that, on islands, small species should increase in body size while large species should decrease body size.  All of the species I studied are small, therefore they were expected to increase in body size.  I found equivocal results concerning the Island Rule.  In chapter one, I found that the great kiskadee (Pitangus sulphuratus) follows the Island Rule, as it is larger in its exotic island range than in the native source range.  However, in chapter two, I found no clear Island Rule pattern examining 39 insular populations.  However, I did find a clear pattern of decrease in wing length and increase in tail length.  Although these populations may not be following an overall Island Rule pattern, they are still adapting to their exotic environments.  In chapter three, I evaluated among-island diversification of six passerine species introduced to the Hawaiian archipelago.  Five of these six species show some morphological differentiation between islands, and at least some of this differentiation cannot be accounted for by genetic drift. The results of this dissertation provide further support for the idea that evolutionary divergence can happen over contemporary time scales.  The passerine bird populations examined in these chapters have adapted to local conditions, giving us insights into the genesis of evolutionary diversity.
title: Combinatorial protein library screening by periplasmic expression
Creators: name: Iverson, Brent L.
name: Georgiou, George M.
name: Harvey, Barrett R.
Publisher: name: United States Patent and Trademark Office
Year: 2006
Subjects: subject: C07K2319/034
subject: C12N15/1034
subject: C12N15/1037
subject: C12N15/1086
subject: C40B40/02
subject: 435/69.1
subject: 435/7.1
subject: 435/69.2
subject: 435/69.3
subject: 435/69.7

description: The invention overcomes the deficiencies of the prior art by providing a rapid approach for isolating binding proteins capable of binding small molecules and peptides. In the technique, libraries of candidate binding proteins, such as antibody sequences, are expressed in the periplasm of gram negative bacteria and mixed with a labeled ligand. In clones expressing recombinant polypeptides with affinity for the ligand, the concentration of the labeled ligand bound to the binding protein is increased and allows the cells to be isolated from the rest of the library. Where fluorescent labeling of the target ligand is used, cells may be isolated by fluorescence activated cell sorting (FACS). The approach is more rapid than prior art methods and avoids problems associated with the outer surface-expression of ligand fusion proteins employed with phage display.
Tuneable collagen scaffolds for the directed differentiation of embryonic stem cells toward neural lineages
Creators: name: Monteiro, Gary Albert
Publisher: name: No Publisher Supplied
Year: 2010

description: This thesis aims to develop and understand the role of peptide modified collagen scaffolds in tissue engineering and stem cell differentiation.  The extracellular matrix and microenvironment surrounding cells plays a critical role in controlling phenotypic and genotypic behavior of cells. It is important to elucidate this role in stem cell differentiation to develop regenerative therapies. Here in, we developed a method to alter, positively and negatively, the adhesion migration and reorganization of scaffolds by fibroblast and smooth muscle cells on and in collagen. By grafting an adhesive peptide 'RGD' and a scramble non-adhesive peptide 'RDG' to collagen we were able to modulate in a dose dependent manner the adhesion of cells to collagen and establish the bimodal dependence of migration on adhesion in and on collagen scaffolds.  We then extended this approach to understand the role of cell adhesion on differentiation of stem cells; we assayed the differentiation of sox-1 reporting murine embryonic stem cells on these scaffolds. Sox-1 expression was found to be inversely related to cell-matrix adhesion. Sox-1 reporting stem cells cultured on RDG grafted collagen scaffolds had a significantly greater population of cells that were sox-1 positive relative to controls. However, the difference between conditions was at most 10%.  To further evaluate the ability of matrix cues to guide the differentiation of stem cells we grafted peptide mimics of neural stem cell niche carbohydrates, human natural killer-1 and polysialic acid to collagen and assayed the differentiation of stem cells towards cell types from all three germ layers. Cells cultured on human natural killer-1 and polysialic acid grafted collagen preferentially differentiated towards neuroectoderm lineage cells as indicated by qPCR and Immunohistochemistry. Identifying matrix cues and environments that support and direct the differentiation of stem cell is essential for regenerative medicine. Scaffolds that support and direct the differentiation of stem cells may eventually be used as therapies for degenerative diseases.
Philonthus uhligi Hromadka 2005
Creators: name: Mikátová, Šárka
name: Macháčková, Lenka
name: Hájek, Jiří
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Staphylinidae
Philonthus
Philonthus uhligi

description: Philonthus uhligi Hromádka, 2005
Philonthus (s.str.) uhligi Hromádka, 2005: 112, Figs 29–31.
One paratype is deposited in NMPC (ex coll. L. Hromádka):
PA*©A*´YPൾ ♀) (: ‘R.S.Africa 5.i.1999 [sic!] / Kruger NP: Skukuza / ex elephant dung / ex sample No. 9 / leg. C. Paetel [p, blue label] // ex coll. L. Hromádka / National Museum / Prague, Czech Republic [p] // PARATYPUS / PHILONTHUS (s. str.) / uhligi sp. n. / Hromádka,det. 2005 [p, red label]’.
Current status. Valid species.
description: Published as part of Mikátová, Šárka, Macháčková, Lenka & Hájek, Jiří, 2020, Catalogue of type specimens of beetles (Coleoptera) deposited in the National Museum, Prague, Czech Republic, pp. 353-389 in Acta Entomologica Musei Nationalis Pragae 60 (1) on page 385, DOI: 10.37520/aemnp.2020.021, http://zenodo.org/record/3880030
Additional file 1 of Mapping eQTL by leveraging multiple tissues and DNA methylation
Creators: name: Chaitanya Acharya
name: Kouros Owzar
name: Allen, Andrew
Publisher: name: Figshare
Year: 2017
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Hematology

description: Supplementary material. Supplementary material expanding on 1) Our model, 2) Individual components of our joint score test statistic, 3) Description of various null hypotheses, 4) Null and power simulations of our joint score test statistic, 5) Gibbs et al. dataset preprocessing, 6) Design of our data analysis, 7) KEGG pathway analysis on the results from Gibbs et al brain data, 8) JAGUAR, 9) A potential strategy to combine two models to maximize eQTL discovery, and 10) Reproducibility. (PDF 635 kb)
Analysis and design of quiet hypersonic wind tunnels
Creators: name: Naiman, Hadassah
Publisher: name: No Publisher Supplied
Year: 2010

description: The purpose of the present work is to integrate CFD into the design of quiet hypersonic wind tunnels and the analysis of their performance.  Two specific problems are considered.  The first problem is the automated design of the supersonic portion of a quiet hypersonic wind tunnel.  Modern optimization software is combined with full Navier-Stokes simulations and PSE stability analysis to design a Mach 6 nozzle with maximum quiet test length.  A response surface is constructed from a user-specified set of contour shapes and a genetic algorithm is used to find the "optimal contour", which is defined as the shortest nozzle with the maximum quiet test length.  This is achieved by delaying transition along the nozzle wall.  It is found that transition is triggered by Goertler waves, which can be suppressed by including a section of convex curvature along the contour.  The optimal design has an unconventional shape described as compound curvature, which makes the contour appear slightly wavy.The second problem is the evaluation of a proposed modification of the test section in the Boeing/AFOSR Mach 6 Quiet Tunnel.  The new design incorporates a section of increased diameter with the intention of enabling the tunnel to start in the presence of larger blunt models.  Cone models with fixed base diameter (and hence fixed blockage ratio) are selected for this study.  Cone half-angles from 15° to 75° are examined to ascertain the effect of the strength of the test model shock wave on the tunnel startup.  The unsteady, laminar, compressible Navier-Stokes equations are solved.  The resulting flowfields are analyzed to see what affect the shocks and shear layers have on the quiet test section flow.  This study indicates that cone angles ≤20° allow the tunnel to start.
The assessment of body condition in rabbits
Creators: name: EURCAW-Poultry-SFA
Publisher: name: Zenodo
Year: 2025
Subjects: Rabbit welfare indicators
body condition score
scoring methods

description: Body condition score (BCS) reflects the nutritional status and overall health of rabbits, serving as a key indicator of welfare. Poor BCS in females/does leads to reduced fertility, increased disease risk, metabolic disorders, and insufficient milk production, putting kits at risk of hunger, especially before weaning. Moreover, the BCS helps to assess whether the feeding programme meets growing rabbits’ nutritional needs, but also the management of groups and feeding places. The BCS can be assessed visually or by palpation in breeding and growing rabbits. This factsheet describes four methods for assessing BCS in rabbits.
title: Method for probabilistically classifying tissue in vitro and in vivo using fluorescence spectroscopy
Creators: name: Richards-Kortum, Rebecca R.
name: Ramanujam, Nirmala
name: Mahadevan-Jansen, Anita M.
name: Follen, Michele
name: Utzinger, Urs
Publisher: name: United States Patent and Trademark Office
Year: 2007
Subjects: subject: A61B5/0071
subject: A61B5/0075
subject: A61B5/0084
subject: A61B5/4331
subject: A61B5/7264
subject: G01N21/274
subject: G01N21/6486
subject: G01N2021/6417
subject: G01N2021/6419
subject: G01N2021/6484
subject: Y10S436/813
subject: 436/63
subject: 436/64
subject: 436/813
subject: 600/407
subject: 600/476
subject: 600/477

description: Fluorescence spectral data acquired from tissues in vivo or in vitro is processed in accordance with a multivariate statistical method to achieve the ability to probabilistically classify tissue in a diagnostically useful manner, such as by histopathological classification. The apparatus includes a controllable illumination device for emitting electromagnetic radiation selected to cause tissue to produce a fluorescence intensity spectrum. Also included are an optical system for applying the plurality of radiation wavelengths to a tissue sample, and a fluorescence intensity spectrum detecting device for detecting an intensity of fluorescence spectra emitted by the sample as a result of illumination by the controllable illumination device. The system also include a data processor, connected to the detecting device, for analyzing detected fluorescence spectra to calculate a probability that the sample belongs in a particular classification. The data processor analyzes the detected fluorescence spectra using a multivariate statistical method. The five primary steps involved in the multivariate statistical method are (i) preprocessing of spectral data from each patient to account for inter-patient variation, (ii) partitioning of the preprocessed spectral data from all patients into calibration and prediction sets, (iii) dimension reduction of the preprocessed spectra in the calibration set using principal component analysis, (iv) selection of the diagnostically most useful principal components using a two-sided unpaired student's t-test and (v) development of an optimal classification scheme based on logistic discrimination using the diagnostically useful principal component scores of the calibration set as inputs.
Additional file 1: of Integrative testis transcriptome analysis reveals differentially expressed miRNAs and their mRNA targets during early puberty in Atlantic salmon
Creators: name: K. Skaftnesmo
name: R. Edvardsen
name: T. Furmanek
name: D. Crespo
name: E. Andersson
name: L. Kleppe
name: G. Taranger
name: J. Bogerd
name: R. Schulz
name: A. Wargelius
Publisher: name: Figshare
Year: 2017
Subjects: subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified

description: A detailed description of samples used in the study. (DOCX 6 kb)
title: Portable sensor array system
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: 2008
Subjects: subject: B01L3/0289
subject: B01L3/5025
subject: B01L3/50271
subject: B01L3/50273
subject: B01L3/50276
subject: B01J2219/005
subject: B01J2219/00576
subject: B01J2219/00648
subject: B01J2219/00659
subject: B01J2219/00702
subject: B01J2219/00722
subject: B01L3/5027
subject: B01L3/50270
subject: B01L2200/027
subject: B01L2200/0657
subject: B01L2200/0668
subject: B01L2200/12
subject: B01L2300/0636
subject: B01L2400/0415
subject: B01L2400/049
subject: B01L2400/0633
subject: B01L2400/0638
subject: C07B2200/11
subject: C12Q1/34
subject: C12Q1/37
subject: C40B40/00
subject: G01N21/6452
subject: G01N21/253
subject: G01N21/6428
subject: G01N21/6454
subject: G01N21/6486
subject: G01N21/77
subject: G01N33/54313
subject: G01N33/54366
subject: G01N33/54373
subject: G01N21/6458
subject: G01N2001/021
subject: G01N2021/6417
subject: G01N2021/6421
subject: G01N2021/6432
subject: G01N2021/6439
subject: G01N2021/6441
subject: G01N2021/6482
subject: G01N2035/00158
subject: G01N2035/00564
subject: G01N2201/062
subject: G01N2201/0627
subject: Y02A90/26
subject: Y10S977/924
subject: Y10T436/2575
subject: 422/68.1
subject: 422/82.5
subject: 435/6.19
subject: 435/283.1
subject: 435/287.2
subject: 435/288.5
subject: 506/39
subject: 977/924

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.
Additional file 1: of iTACTIC â   implementing Treatment Algorithms for the Correction of Trauma-Induced Coagulopathy: study protocol for a multicentre, randomised controlled trial
Creators: name: Baksaas-Aasen, Kjersti
name: Gall, Lewis
name: Eaglestone, Simon
name: Rourke, Claire
name: Nicole. Juffermans
name: J. Goslings
name: Paal Naess
name: Dieren, Susan Van
name: Ostrowski, Sisse
name: Stensballe, Jakob
name: Maegele, Marc
name: Stanworth, Simon
name: Gaarder, Christine
name: Brohi, Karim
name: Johansson, Per
Publisher: name: Figshare
Year: 2017
Subjects: subject: Space Science
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Protocol version 3.0/14.03.2017. (PDF 2172 kb)
Agyrta grandimacula Zerny 1931
Creators: name: Pinheiro, L. R.
name: Gaal-Haszler, S.
Publisher: name: Zenodo
Year: 2015
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Arctiidae
Agyrta
Agyrta grandimacula

description: grandimacula Zerny, 1931
(Fig. 32)
Agyrta grandimacula Zerny, 1931b: 21 (Taf. 1, fig. 28). Holotype female [by monotypy]: ECUADOR (don. Study); with two handwritten labels “Study don 1922, Ecuador ” and “ Agyrta grandimacula Zerny ♀ type ”.
Current combination. Agyrta grandimacula Zerny, 1931.
Condition of the type. Wings worn, with slight damage to the internal margin of the left hindwing.
Remarks. Given the similarity in habitus to Phalaena micilia Cramer, 1779, type species of Agyrta Hübner, [1820], (designated by Watson et al. 1980), this species is probably correctly assigned to this genus.
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 520, DOI: 10.11646/zootaxa.3925.4.2, http://zenodo.org/record/240540
Philonthus umbrinoides Smetana 1995
Creators: name: Mikátová, Šárka
name: Macháčková, Lenka
name: Hájek, Jiří
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Staphylinidae
Philonthus
Philonthus umbrinoides

description: Philonthus umbrinoides Smetana, 1995
Philonthus umbrinoides Smetana, 1995: 268, Figs 368–375.
Two paratypes are deposited in NMPC (ex coll. L.
Hromádka):
PA*©A*´YPൾඌ (1, 1 unsexed specimen):‘QUE:Parc Gati- / neau Lac Bour- / geois 14.VI.79 / A.Smetana [p] // ex coll. L. Hromádka / National Museum / Prague, Czech Republic [p] // PARATYPE / Philonthus / umbrinoides / A. Smetana 1993 / CNC No.21953 [p, yellow label]’.
Current status. Valid species, see Hൾ*©MAN (2001b).
description: Published as part of Mikátová, Šárka, Macháčková, Lenka & Hájek, Jiří, 2020, Catalogue of type specimens of beetles (Coleoptera) deposited in the National Museum, Prague, Czech Republic, pp. 353-389 in Acta Entomologica Musei Nationalis Pragae 60 (1) on page 385, DOI: 10.37520/aemnp.2020.021, http://zenodo.org/record/3880030
INTEGRATED REPORTING AS A TOOL FOR IMPROVING FINANCIAL TRANSPARENCY IN RWANDA'S BANKING SECTOR
Creators: name: 1Mbonigaba Celestin, 2Abdourahman Farah & 3Ahmed Mansour, 4Kiuri Daniel
Publisher: name: Zenodo
Year: 2012

description: This study examines the role of Integrated Reporting (IR) in enhancing financial transparency within Rwanda's banking sector, targeting improved governance, stakeholder trust, and accountability. Employing a qualitative research design, it analyzed secondary data from financial reports and conducted interviews with key banking stakeholders. The findings reveal a statistically significant improvement (p < 0.05) in financial disclosure compliance, increasing from 72% in 2008 to 84% in 2012. Adoption of IR also correlated strongly with financial performance, reflected in the rise of Return on Equity (ROE) from 12% to 22% and Return on Assets (ROA) from 2.5% to 4.7%. Despite these advances, challenges remain, including a lack of skilled personnel (reported by 45% of banks) and high implementation costs (40%). Recommendations include capacity-building programs, financial incentives, and technological integration. This research concludes that IR significantly enhances transparency and stakeholder engagement in Rwanda’s banking sector while aligning with global standards.
title: The proline effect and the tryptophan immonium ion assist in de novo sequencing of adipokinetic hormones
Creators: name: König, Simone
name: Marco, Heather G.
name: Gäde, Gerd
Publisher: name: University of Muenster, Institutional Repository MIAMI
Year: 2024
Subjects: subject: 572 Biochemistry

description: Adipokinetic hormones (AKHs) in Arthopoda are characterized by special sequence features including limited choices of amino acid residues in certain positions, such as Trp in position 8. Over 100 different AKHs have been described, but de novo sequencing of novel peptide hormones can be a challenge. In a project of analyzing corpora cardiaca extracts from two fly species, two different moths, a termite and a beetle for their AKHs, we noted specific patterns in the fragmentation spectra of octapeptides in electrospray Q-TOF experiments resulting from the presence of Pro in position 6. The preference for cleavage N-terminal to Pro residues created an abundant y3"-ion, which, in conjunction with the two b-ions resulting from the fragmentation before and after Pro, provided a marker pattern. As Pro6 occurs in about 61% of known AKHs, this information is highly relevant for sequence elucidation. Moreover, the default presence of Trp8 allowed the use of its immonium ion for AKH candidate identification. In addition, we assembled the known AKH sequences from the literature and sequences of AKH-type format found in the Uniprot database in a single online resource. These efforts assisted in the analysis workflow and led to the assignment of two novel AKHs and evidence for the presence of Melme-CC and Dorpa-AKH in the corpus cardiacum of the scarab beetle 'Sinodendron cylindricum'.
description: Finanziert über die DEAL-Vereinbarung mit Wiley, Springer oder Elsevier 2019–2023.
Modeling the growth of Salmonella spp. on cut tomatoes
Creators: name: Pan, Wenjing
Publisher: name: No Publisher Supplied
Year: 2010

description: Tomato-associated Salmonella outbreaks have recently become a significant food safety concern. Temperature abuse of cut tomatoes may have played a role in some of these outbreaks.The purpose of this study was to develop a mathematical model to describe the growth of Salmonella on cut tomatoes at various temperatures.Four Salmonella serotypes (Salmonella Typhimurium, Salmonella Newport, Salmonella Javiana, Salmonella Braenderup) obtained from previous tomato-linked cases of salmonellosis were used in this study. These four serotypes were cultured separately, combined into a cocktail and inoculated onto whole red round tomatoes and allowed to dry overnight. The tomatoes were then cut into pieces and incubated at a predetermined range of temperatures (10, 12.5, 15, 18.5, 20, 22.5, 25, 27.5, 30, and 35°C). Salmonella concentration was measured at specified time intervals to determine the growth curve for Salmonella on cut tomatoes at each temperature. The growth rates were calculated using DMFit and used to build a mathematical model to illustrate the relationship between the growth rates of Salmonella on tomatoes and incubation temperatures from 10-35°C.The resulting model compared favorably with a Salmonella growth model for raw poultry developed by our laboratory. The Pathogen Modeling Program under-predicted growth at low temperatures and over predicted growth at high temperatures. ComBase predicted consistently slower growth rates than were observed in tomatoes, but showed parallel increases in growth rate with increasing temperature.
Musonycteris harrisoni DNA
Creators: name: Basaldúa, Sonia
name: Rodriguez-Pilco, Milena
name: Gutiérrez-Guerrero, Yocelyn
name: Ortega, Jorge
name: Baeza, J. Antonio
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Chiroptera
Phyllostomidae
Musonycteris
Musonycteris harrisoni

description: Sampling of Musonycteris harrisoni, DNA extraction, and sequencing
A muscle tissue sample of Musonycteris harrisoni (specimen ID: GHC216; catalogue number: 16,153) was donated by the Museum of Zoology ̍Alfonso L. Herrera̾, Facultad de Ciencias, Universidad Nacional Autonoma de Mexico, Mexico to the ̍Laboratorio de Bioconservación y Manejo̾, Instituto Politécnico Nacional, Escuela Nacional De Ciencias Biológicas (ENCB), Mexico City, Mexico. The specimen was originally collected in Palma de Cayaco (17°13̾45.5″N, 100°35̾04.6″W), Tecpan de Galena, Guerrero, Mexico.
Genomic DNA (gDNA) was isolated using the DNA Blood and Tissue Kit (Qiagen, Germany) following the manufacturer̾s instructions and shipped to the ̍Vincent J. Coates̾ Genomics Sequencing Laboratory, University of California, Berkeley, for sequencing in a Illumina HiSeq 4000 platform. A total of 203,048,998 pair-end (PE) reads (150 bp) were generated by the facility and made available as fastq files. The totality of these reads was used for mitochondrial genome assembly.
description: Published as part of Basaldúa, Sonia, Rodriguez-Pilco, Milena, Gutiérrez-Guerrero, Yocelyn, Ortega, Jorge & Baeza, J. Antonio, 2023, The mitochondrial genome of the endemic and endangered trumpet-nosed bat Musonycteris harrisoni (Chiroptera: Phyllostomidae), pp. 1206-1219 in Journal of Natural History 57 (21 - 24) on page 1208, DOI: 10.1080/00222933.2022.2150581, http://zenodo.org/record/10014410
Inhibition of colon carcinogenesis by stilbenoids and mechanisms of action
Creators: name: Paul, Shiby
Publisher: name: No Publisher Supplied
Year: 2010

description: Stilbenes are a class of compounds present in small fruits such as grapes and berries and are known to present diverse pharmacological properties which include cholesterol lowering, serum glucose regulation, controlling lifespan and anti-cancer activity. Resveratrol is one of the extensively studied stilbene. Pterostilbene (trans-3, 5-dimethoxy-4’-hydroxystilbene), a structural analog of resveratrol, is present in heartwood of the tree, Pterocarpus marsupium as well as in many small fruits such as blueberries. In an attempt to study the effects of pterostilbene on colon carcinogenesis, we identified that pterostilbene inhibited expression of certain inflammatory genes in the colon and suppressed aberrant crypt foci formation in an azoxymethane (AOM)-induced model of colon carcinogenesis in rats. We also investigated the mechanism of anti-inflammatory action of pterostilbene using cultured HT-29 colon cancer cells. Our studies identified that the p38-ATF2 pathway was significantly inhibited by pterostilbene. More importantly, by silencing the expression of p38α isoform, there was significant reduction in iNOS and COX-2 induction. Interestingly, pterostilbene and the structurally similar compound, resveratrol, targeted different inflammatory pathways in HT-29 colon cells. Pterostilbene given at 40 ppm of the diet of AOM-injected rats lowered the tumor multiplicity of non-invasive adenocarcinomas compared to the control diet. Pterostilbene lowered the β-catenin levels in HT-29 cells which can have implications in the action of the compound against cell proliferation. An evaluation of different structural analogs of pterostilbene revealed some compounds to have greater action than pterostilbene against colon cancer cells. Methoxylation, ester and amino modifications at the 4' position in the B ring conferred greater potency for the molecule against cell proliferation and inflammation in vitro. Amino substitutions and methoxy modifications with trans configuration reduced tumor burden significantly in the HT-29 xenograft tumor model in SCID mice. These compounds were present at higher levels in the serum of the animals compared to the levels of other compounds. In conclusion, stilbenoid class of compounds has promising effects against proliferation and inflammation in both in vivo and in vitro models of colon carcinogenesis.