cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
MOESM3 of A systematic review and diagnostic test accuracy meta-analysis of the validity of anion gap as a screening tool for hyperlactatemia
Creators: name: Glasmacher, Stella
name: Stones, William
Publisher: name: Figshare
Year: 2017
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Science Policy

description: Additional file 3: Table S1. Characteristics of included studies. HL (hyperlactatemia), ICU (intensive care unit), NA (data not available).
Arc protein expression within discrete subfields of the hippocampus following trace fear conditioning
Creators: name: Hudgins, Caleb Deneb
Publisher: name: No Publisher Supplied
Year: 2013

description: A growing body of evidence suggests not only that the dorsal and ventral subregions of the hippocampus contribute differentially to some forms of memory, but that the contribution of the discrete subfields (CA1, CA3) within the hippocampus may also be dissociable.   In the present study, we examined the regional distribution of learning-related Arc (activity-related cytoskeletal protein) expression following training in hippocampal-dependent trace fear conditioning.  .  We have recently shown that trace fear conditioning enhances Arc protein levels, and that both trace fear conditioning and the associated learning-related enhancement of Arc can be blocked by infusing either Arc antisense oligodeoxynucleotides (ODNs) or the NMDA receptor antagonist APV into the dorsal or ventral hippocampus prior to training.   Thus while NMDAr –dependent Arc expression in both dorsal and ventral hippocampus appears to be critically involved in the acquisition of trace fear conditioning,  the extent to which Arc is differentially expressed within the discrete subfields of the hippocampus following learning has yet to be characterized.  Different groups of subjects were either trained in our auditory trace fear conditioning paradigm, a modified trace fear conditioning paradigm with pre-exposure to the conditioning context, received simple exposure the novel training context, or served as home-cage, handled control subjects. Consistent with our earlier findings, the present results suggest a substantial percent increase in Arc expression in both the dorsal and ventral hippocampus following either trace fear conditioning paradigm.  With respect to the regional distribution of Arc, expression was greater in CA3 relative to CA1 in the dorsal hippocampus, whereas expression increased in both CA1 and CA3 in ventral hippocampus compared to home cage controls.  Interestingly animals exposed to the novel training context also exhibited increased levels of Arc protein expression in patterns similar to those of animals trained in trace fear conditioning, though to a lesser extent.  When considered together with our previous data regarding learning-related Arc expression and the known anatomical connections between the hippocampus and the amygdala, these results further support a dissociable role of NMDA mediated Arc expression, not just along the dorsal-ventral axis, but within the discrete subfields of both hippocampal subregions.
Conasprella (Endemoconus) howelli
Creators: name: Tenorio, Manuel J.
name: Puillandre, Nicolas
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Mollusca
Gastropoda
Neogastropoda
Conidae
Conasprella
Conasprella howelli

description: Conasprella (Endemoconus) howelli (Iredale, 1929)
Figs 38A–H, L–M, 39
Conus howelli Iredale, 1929: 182, pl. 40 figs 1, 8.
Conus howelli – R̂ckel et al. 1995b: no. 277, pl. 58 figs 25–28.
Endemoconus howelli – Tucker & Tenorio 2013: 223.
Conasprella howelli – Monnier et al. 2018a: 212.
Material examined
13 lots (15 specimens). See Supp. file 1.
Type material
Holotype AUSTRALIA • 26.5 mm; Montague Island, New South Wales; AMS C.57711 (Fig. 38A).
Other material
NEW CALEDONIA • 21.5 mm; off S New Caledonia, Banc Kaimon Maru, stn DW8; 24°45′ S, 168°08′ E; 233 m depth; 21 May 1987; SMIB 3 expedition; MNHN (Fig. 38B) • 13.7 mm; Norfolk Ridge, off New Caledonia, stn DW159; 24º46′ S, 168º08′ E; 241‒245 m depth; 28 Jan. 1993; SMIB 8 expedition; MNHN (Fig. 38C, L) • 15.1 mm; same collection data as for preceding; MNHN (Fig. 38D) • 17.1 mm; Loyalty Ridge, off New Caledonia, stn DW85; 22º20′ S, 168º43′ E; 260 m depth; 13 Sep. 1989; SMIB 5 expedition; MNHN (Fig. 38E) • 19.3 mm; Norfolk Ridge, east coast, off New Caledonia, stn DW170‒172; 21°43′ S, 166°36′ E; 315‒327 m depth; 29 Jan. 1993; SMIB 8 expedition; MNHN (Fig. 38F) • 24.2 mm; Norfolk Ridge, off New Caledonia, stn DW159; 24º46′ S, 168º08′ E; 241‒245 m depth; 28 Jan. 1993; SMIB 8 expedition; MNHN (Fig. 38G) • 16.3; SE Île des Pins, off New Caledonia, stn DW4741; 22°52′ S, 167°41′ E; 210 m depth; 23 Aug. 2016; KANACONO expedition; MNHNIM- 2018-12306 (Fig. 38H) • 12.7 mm; Norfolk Ridge, off New Caledonia, stn DW159; 24º46′ S, 168º08′ E; 241‒245 m; 28 Jan. 1993; SMIB 8 expedition (Fig. 38M).
Geographical distribution and bathymetry
Eastern Australia (New South Wales and Queensland) to N New Zealand (Lord Howe Island, Wanganella Bank) at depths between 50 to 295 m. In New Caledonia, specimens have been sampled in locations in Norfolk Ridge, Loyalty Ridge and Coral Sea (Kelso Bank), at depths between 100 and 400 m, but ocassionally beyond 500 m deep.
Remarks
Shell small to medium-sized (maximum shell length 49 mm), conical with a moderate to high, stepped spire. Multispiral protoconch of about 4 whorls (Fig. 38L). Teleoconch sutural ramp concave, with closely spaced radial threads. Radular tooth (Fig. 38M) typical of Conasprella, with a short barb and a pointed blade covering about one third of the anterior section, which is much shorter than the posterior section. Shaft fold present. Basal spur is present. Specimens from New Caledonia are similar to those from Australia and New Zealand. This species has not been examined using DNA.
description: Published as part of Tenorio, Manuel J. & Puillandre, Nicolas, 2023, Revision of the deep-water cone snail fauna from New Caledonia (Gastropoda, Conoidea), pp. 1-134 in European Journal of Taxonomy 896 on page 53, DOI: 10.5852/ejt.2023.896.2291, http://zenodo.org/record/8405510
Hox Transcriptional Regulation of Breast Tumor Angiogenesis
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: The growth of human tumors beyond a few millimeters is dependent on the growth of new blood vessels (angiogenesis). The new vessels act to supply nutrients to the tumor and to provide routes for tumor cells to spread (metastasize) to other areas of the body. Our laboratory has been investigating the role of a group of genes (HOX) in the growth of the cells that form blood vessels, endothelial cells. Homeobox-containing, or "HOX," genes are responsible for the major body structures in early development. Fruit flies with a particular mutation in one of their many HOX genes, for example, will develop an anatomically normal leg-in the spot where an antenna should be. Human HOX genes are expressed during embryogenesis and early development where they act as master transcriptional (gene expression) regulators. HOX genes are also expressed in normal adult cells, potentially in a tissue specific manner involving maintenance of the normal phenotype. In cancer, mis-expression of many HOX genes have been shown, indicating an involvement of these transcriptional regulators in carcinogenesis and metastasis.

 We wish to investigate the effects of modulating the levels of two HOX (HOX D3 and HOX D10) in human endothelial cells. We will use a mouse model of angiogenesis to study human endothelial cells, which are modified to express high levels of HOX D10 or are deficient in HOX D3 for their ability to form new blood vessels in response to breast tumor cells. To identify the genes that HOX D10 regulates in order to coordinate the process of angiogenesis, we will use a technique to link HOX D10 protein to the DNA in endothelial cells and then isolate this DNA and identify the respective gene. We will also examine the effect of breast tumor cells on the expression of HOX D 10 and HOX D3 genes by culturing these cells together in gels made from the proteins that support and surround cells (the extracellular matrix).

 One of the major limitations of many current animal tumor angiogenesis models is that the angiogenic responses being studied are those that arise from the host animal (i.e., mouse, chick embryo) and not vessels of human origin. However, in these proposed studies we will be able to study the ability of genetically manipulated human endothelial cells to form new blood vessels in response to human breast tumor cells in mice. In addition, this project is unique in that it will characterize naturally occurring HOX genes as an alternative method to limit new blood vessel growth in response to breast tumor cells in order to ultimately inhibit breast tumor growth and metastasis.
Lithium diamidobinaphthyl catalysts for asymmetric hydroamination
Creators: name: Hurd, Lisa
Publisher: name: No Publisher Supplied
Year: 2013

description: Lithium catalyzed intramolecular hydroamination of unactivated alkenes has been known for over 20 years, although growth in this field has been limited. Deduction of structure activity relationships for these systems is a challenge because of their complex solution behavior. A series of axially chiral C2-symmetric diamidobinaphtyl dilithium salts given by the formula [{C10H6N(CH2CH2X)}2Li2]n where n = 2, 6 for X = NMe2, n = 2 for X = OMe, and n = 1 for X = NEt2 or N(CH2)5 were synthesized.  Solid state characterization of these dilithium salts free of outside donor solvents allowed ligands to direct aggregation based on their steric hindrance and flexibility. All complexes showed π interactions between lithium and the naphthyl rings playing a significant role in the stabilization of the metal center. The complexes based on the sterically least demanding N-dimethyl-substituted ligand [{C10H6N(CH2CH2NMe2)}2Li2]n crystallize as a dimer in enantiopure form and as a hexameric cycle in racemic form.  When used in combination with excess LiCH2SiMe3 various gem-dialkyl substituted aminopentenes were cyclized in up to 6&% ee at 22°C. Cyclization of aminopentene at 40°C was also performed producing 2-methylpyrrolidine in up to 64% ee. The precatalysts were studied using DOSY, &Li and variable temperature NMR spectroscopy. DOSY NMR spectroscopy suggests that solutions of (rac)-64 and (R)-64 exist as a mixture of monomers and dimers at 25°C, while (R)-65 and (R)-66 are monomeric. Addition of one equivalent LiCH2SiMe3 to (R)-64 resulted in a sharpening of 1H NMR spectra and produced a single peak in the &Li NMR spectra, suggesting the formation of a new mixed aggregate, (R)-69.  Kinetic studies for the cyclization of C-(1-allyl-cyclohexyl)-methylamine demonstrated a first order rate dependence on substrate and catalyst concentrations. A first order rate dependence on LiCH2SiMe3 was also observed, with enantioselectivity decreasing linearly as the concentration of LiCH2SiMe3 was increased. (R)-&0 is a general representation of components found in the rate limiting transition state for the hydroamination/cyclization of C-(1-allyl-cyclohexyl)-methylamine. Solid state characterization of (R)-64 with two equivalents of 3-methyl-2-aza-spiro[4.5]decane bound to it revealed the formation of a monomeric species, (R)-68.
Anomiopus andrei Canhedo 2006
Creators: name: Groll, Elisa Von
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Scarabaeidae
Anomiopus
Anomiopus andrei

description: Anomiopus andrei Canhedo, 2006
Canhedo, 2006:478, figs 713–721, 810.
Paratype ♂, BRAZIL, Acre: Rio Branco (Fazenda Catuaba), II.1987, F. Z. Vaz-de-Mello col. (MCNZ 234.811).
description: Published as part of Groll, Elisa Von, 2017, Catalogue of Coleoptera type specimens housed in the collection of the Museu de Ciências Naturais, Fundação Zoobotânica do Rio Grande do Sul, Brazil, pp. 439-473 in Zootaxa 4318 (3) on page 463, DOI: 10.11646/zootaxa.4318.3.2, http://zenodo.org/record/887750
Tityopsis rolandoi Kovařík, Stockmann, Šťáhlavský & Yong, 2024, sp. n.
Creators: name: Kovařík, František
name: Stockmann, Mark
name: Šťáhlavský, František
name: Yong, Sheyla
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Scorpiones
Buthidae
Tityopsis
Tityopsis rolandoi

description: Tityopsis rolandoi sp. n.
(Figures 1–50, 53–58, Table 1)
description: Published as part of Kovařík, František, Stockmann, Mark, Šťáhlavský, František & Yong, Sheyla, 2024, Tityopsis rolandoi sp. n. (Scorpiones: Buthidae) from Cuba, pp. 1-15 in Euscorpius 400 on page 5, DOI: 10.5281/zenodo.14660689
Anomiopus birai Canhedo 2006
Creators: name: Groll, Elisa Von
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Scarabaeidae
Anomiopus
Anomiopus birai

description: Anomiopus birai Canhedo, 2006
Canhedo, 2006:428, figs 399–414, 791.
Paratype ♀, PARAGUAI, Cordillera: Naranjo, 06.IV.1996, R. C. Aguilar col. (MCNZ 234.813).
description: Published as part of Groll, Elisa Von, 2017, Catalogue of Coleoptera type specimens housed in the collection of the Museu de Ciências Naturais, Fundação Zoobotânica do Rio Grande do Sul, Brazil, pp. 439-473 in Zootaxa 4318 (3) on page 463, DOI: 10.11646/zootaxa.4318.3.2, http://zenodo.org/record/887750
The nonequilibrium dynamics of quantum integrable models
Creators: name: Iyer, Deepak
Publisher: name: No Publisher Supplied
Year: 2013

description: The primary goals of this dissertaion are to describe and elucidate a new formalism to study the out of equilibrium dynamics of integrable models, and to apply this formalism to some specific problems. In particular, I describe the “quench dynamics” of a gas of interacting bosons in one dimension, and provide details of some preliminary work on the isotropic Heisenberg chain. The formalism, based on earlier work by Yudson, provides a way of getting around some of the difficulties involved in calculating the time evolution of arbitrary initial states evolved with integrable Hamiltonians.    In addition to this, I aim to discuss some of the general aspects of quench dynamics in quantum systems. The description of the nonequilibrium dynamics of a given system depends significantly on initial states, and the time scales at which the system is probed compared with the various inherent time scales in the system. I present the experimental context and motivation for these studies, and survey the existing techniques and efforts at understanding the relaxation of systems that are far from their equilibrium states or ground states.
Effect of temperature abuse on freeze-thaw characteristics and microbial quality of frozen army rations
Creators: name: Jagadeesan Sankaran, Karthikeyan
Publisher: name: No Publisher Supplied
Year: 2013

description: Frozen army rations for the deployed US army units are manufactured in the US and shipped to army bases in various countries. The transportation usually takes 3 to 5 months and the frozen rations are stored at -18 °C in large containers. Under ideal conditions, the frozen food items are expected to have a frozen shelf-life of 9 months. In reality, the food items might get exposed to severe temperature abuse during transportation, which may lead to microbial spoilage and/or quality loss. The aim of this study was to predict the effect of external temperature fluctuations on the temperature distribution and the microbial quality of frozen army rations during storage and transportation.                 An army breakfast menu box containing five different food items, was selected for conducting this research. Commercial software COMSOL® Multiphysics was used to numerically predict the thermal behavior of the food items under varied external temperature conditions. Freeze-thaw properties of each food item were obtained using component data and Differential Scanning Calorimetry (DSC), which were then used in the numerical simulation of heat transfer with phase change. Apparent Specific Heat (ASH) method was used to account for the latent heat of a phase change during thawing and refreezing. The predictive model was validated in terms of variation of temperature with time at selected locations in a gel-based model food system and in a real food system. Microbial quality was used as the primary parameter that determined the shelf-life of food. ComBase database was used to identify the most prone microorganism and to obtain its growth kinetics.     Microbial kinetics data was incorporated in the numerical simulation program to predict the microbial quality of army rations during two temperature abuse scenarios: (i) constant high external temperature exposure and (ii) freezer breakdown. Numerical predictions suggested that the food items which was exposed to surrounding constant temperatures of (20, 25, 30, 35, and 40) °C, can be allowed to stay at those temperatures for a maximum time of (29, 20, 15, 12, and 9) h, respectively, and in the case of freezer failure, the food items can be allowed to stay in the broken freezer for a maximum time of 186 hours, to ensure food safety.
Additional file 1: Figure S1. of Gene expression profiling of upregulated mRNAs in granulosa cells of bovine ovulatory follicles following stimulation with hCG
Creators: name: Lussier, Jacques
name: Mame Diouf
name: Lévesque, Valérie
name: Sirois, Jean
name: Kalidou Ndiaye
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Physiology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Analyses of the cDNA subtraction efficiency. PCR analysis was performed on the indicated samples using PTGS2 or CYP19A1 specific primers, as described under Materials and Methods. PCR product aliquots were collected at increasing numbers of PCR cycles as indicated. The PTGS2 DNA fragment (418 bp) was detected following 13 PCR cycles in the OF-DF subtracted sample but not until 18 PCR cycles in the corresponding unsubtracted OF sample. The CYP19A1 DNA fragment (520 bp) was detected following 13 PCR cycles in the DF-OF subtracted sample but not until 18 PCR cycles in the corresponding unsubtracted DF sample. PTGS2 or CYP19A1 were not detected in the DF or OF samples, respectively. Figure S2. Representative differential screening results by macroarrays of the OF-DF cDNA library. PCR-amplified cDNA fragments (OF-DF) obtained by SSH were dot-blotted to generate two identical sets of membranes. A total of 940 individual cDNAs were dot-blotted. The macroarrays were then hybridized with two different probe set: subtracted OF-DF cDNAs (A), and reverse subtracted DF-OF cDNAs (B), as described under Materials and Methods. The two upper left hand dots for each membrane served as internal hybridization controls: A1 = CYP19A1 (negative control) and A2 = PTGS2 (positive control) for the OF-DF reaction. The cDNA clones that were found to be differentially expressed in the OF-DF membrane following comparison of hybridization signals among the corresponding spots of the two membranes were further characterized by sequencing. (PDF 275 kb)
The Silence of Inquiry: Forensic Reflections, A Crisis of Perception, and NASA Under Scrutiny
Creators: name: Lehti, Andrew
Publisher: name: figshare
Year: 2025
Subjects: classificationCode: 460404
subject: Digital forensics
classificationCode: 520102
subject: Educational psychology
classificationCode: 500405
subject: Religion, society and culture

description: Science is about inquiry, no matter how absurd. When we can no longer question without an entire faction arming weapons against science, we become no better than those that burned dissenters at the stake.Final Analysis and Conclusion: The photos captured in orbit are determined to be authentic. However, the photos taken on the Moon appear to be staged, with evidence suggesting the use of two distinct sets: one life-sized and one miniature. Drawing from a background in film—a foundational interest prior to pursuing science and truth—several techniques employed in the footage were recognizable. Notably, the most apparent indication is the slowed-down motion in the Moon landing videos, made evident by the drastically altered framerate.
Additional file 4: of Modulating the catalytic activity of AMPK has neuroprotective effects against α-synuclein toxicity
Creators: name: Bobela, Wojciech
name: Nazeeruddin, Sameer
name: Knott, Graham
name: Aebischer, Patrick
name: Schneider, Bernard
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Neuroscience
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology

description: Figure S3. Levels of phospho ACC in primary cortical neurons overexpressing AMPKα and α-syn. (PDF 222 kb)
Anomiopus edmondsi Canhedo 2006
Creators: name: Groll, Elisa Von
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Scarabaeidae
Anomiopus
Anomiopus edmondsi

description: Anomiopus edmondsi Canhedo, 2006
Canhedo, 2006:431, figs 415–430, 792.
Paratype ♂, COLOMBIA, Bolívar: Rio Sipao (110 km E Caiçara), 17.VI–04.VIII.1987, S. & J. Peck col. (MCNZ 234.814).
description: Published as part of Groll, Elisa Von, 2017, Catalogue of Coleoptera type specimens housed in the collection of the Museu de Ciências Naturais, Fundação Zoobotânica do Rio Grande do Sul, Brazil, pp. 439-473 in Zootaxa 4318 (3) on page 463, DOI: 10.11646/zootaxa.4318.3.2, http://zenodo.org/record/887750
Conasprella (Endemoconus) raoulensis
Creators: name: Tenorio, Manuel J.
name: Puillandre, Nicolas
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Mollusca
Gastropoda
Neogastropoda
Conidae
Conasprella
Conasprella raoulensis

description: Conasprella (Endemoconus) raoulensis (Powell, 1958)
Figs 38I–K, 42
Conus (Kermasprella) raoulensis Powell, 1958: 83, pl. 9 fig. 1.
Conus raoulensis – R̂ckel et al. 1995b: no. 256, pl. 55 figs 9–12.
Endemoconus raoulensis – Tucker & Tenorio 2013: 341.
Conasprella raoulensis – Monnier et al. 2018a: 213.
Material examined
2 lots (2 specimens). See Supp. file 1.
Type material
Holotype NEW ZEALAND • 18 mm; off Raoul Island, Kermadec Islands; 75–85 m depth; 3 Mar. 1952; NHMD-91129, previously ZMUC GAS-000805 (Fig. 38I).
Figured material
NEW CALEDONIA • 15.1 mm; Coral Sea, Capel Bank, off New Caledonia, stn DW255; 25º15′ S, 159º55′ E; 280‒295 m depth; 7 Oct. 1986; MUSORSTOM 5 expedition; MNHN (Fig. 38J) • 16.9 mm; Norfolk Ridge, Banc Kaimon Maru, off New Caledonia, stn DW2093; 24º44′ S, 168º09′ E; 230 m depth; 29 Oct. 2003; NORFOLK 2 expedition; MNHN (Fig. 38K).
Geographical distribution and bathymetry
Known from N New Zealand (Wanganella Bank and Kermadec Islands) and Australia (Norfolk Island). Two dead specimens were collected in New Caledonia (Norfolk Ridge) and Coral Sea (Capel Bank) at depths between 200‒ 400 m.
Remarks
Shell small (maximum shell length 22 mm), conical to broadly conical with a moderate to high stepped spire. Teleoconch sutural ramps concave with arcuate radial threads. Last whorl with strongly granulose spiral ribs. Protoconch multispiral of about 4 whorls. Radular morphology unknown. No specimens have been sequenced. The two dead specimens collected off New Caledonia exhibit shell features consistent with those of the holotype for the species.
description: Published as part of Tenorio, Manuel J. & Puillandre, Nicolas, 2023, Revision of the deep-water cone snail fauna from New Caledonia (Gastropoda, Conoidea), pp. 1-134 in European Journal of Taxonomy 896 on pages 58-59, DOI: 10.5852/ejt.2023.896.2291, http://zenodo.org/record/8405510
Inhibition of lung tumorigenesis and cancer cell growth by EGCG and other chemopreventive agents
Creators: name: Jin, Huanyu
Publisher: name: No Publisher Supplied
Year: 2013

description: Lung cancer is the leading cause of cancer death in the United States and the most commonly diagnosed cancer worldwide and smoking is a key risk factor of lung cancer. The purpose of this thesis study is to characterize the mechanisms of 4-(methylnitrosamino)-1-(3-pyridyl)- 1-butanone (NNK)-induced lung tumorigenesis in A/J mice and the inhibitory activities of (−)-epigallocatechin-3-gallate (EGCG) and other chemopreventive agents including tocopherols, myo-inositol and atorvastatin.  DNA methyltransferase 1 (DNMT1), a key enzyme mediating DNA methylation, is known to be activated in cancers, including the mouse lung tumors induced by NNK. However, it is not known how NNK treatment affects the DNMT1 expression. We found that administration of NNK to A/J mice caused elevation of DNMT1 in bronchial epithelial cells at days 1-14. DNMT1 elevation at days 1 and 3 was accompanied by an increase in -H2AX and phospho-AKT (p-AKT), which has been shown to stabilize DNMT1 at the protein level by inhibiting the ubiquitination of DNMT1. Induction of O6-methylguanine, cyclooxygenase-2 (COX-2), superoxide dismutase (SOD) and catalase by NNK treatment was also observed at days 1-14. DNMT1 expression decreased to lower levels at weeks 5-20 in lung tissues, but was highly elevated in lung tumors at week 20. In concordance with DNMT1 elevation, promoter hypermethylation of tumor suppressor genes Cdh13, Prdm2 and Runx3 was observed in lung tissues at day 3 and in lung tumors at week 20. EGCG (0.4% in diet) treatment attenuated the induction of DNMT1, p-AKT and γ-H2AX at days 1 and 3 and inhibited lung tumorigenesis.   EGCG, γ-tocopherol-rich mixture of tocopherols (γ-TmT) and myo-inositol significantly reduced tumor multiplicity and tumor size in the NNK model. The EGCG-generated reactive oxygen species (ROS) caused cell growth inhibition and induction of apoptosis and oxidative DNA damage in vitro. Apoptosis and oxidative DNA damage were also induced in lung tumors by EGCG treatment at the tumor stage. Short-term γ-TmT treatment at the tumor stage induced antioxidant enzymes SOD and glutathione peroxidase. Myo-inositol treatment significantly reduced the level of p-c-Jun in lung tumors.
Additional file 1: Figure S1. of Gene expression profiling of upregulated mRNAs in granulosa cells of bovine ovulatory follicles following stimulation with hCG
Creators: name: Lussier, Jacques
name: Mame Diouf
name: Lévesque, Valérie
name: Sirois, Jean
name: Kalidou Ndiaye
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Physiology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Developmental Biology
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: Analyses of the cDNA subtraction efficiency. PCR analysis was performed on the indicated samples using PTGS2 or CYP19A1 specific primers, as described under Materials and Methods. PCR product aliquots were collected at increasing numbers of PCR cycles as indicated. The PTGS2 DNA fragment (418 bp) was detected following 13 PCR cycles in the OF-DF subtracted sample but not until 18 PCR cycles in the corresponding unsubtracted OF sample. The CYP19A1 DNA fragment (520 bp) was detected following 13 PCR cycles in the DF-OF subtracted sample but not until 18 PCR cycles in the corresponding unsubtracted DF sample. PTGS2 or CYP19A1 were not detected in the DF or OF samples, respectively. Figure S2. Representative differential screening results by macroarrays of the OF-DF cDNA library. PCR-amplified cDNA fragments (OF-DF) obtained by SSH were dot-blotted to generate two identical sets of membranes. A total of 940 individual cDNAs were dot-blotted. The macroarrays were then hybridized with two different probe set: subtracted OF-DF cDNAs (A), and reverse subtracted DF-OF cDNAs (B), as described under Materials and Methods. The two upper left hand dots for each membrane served as internal hybridization controls: A1 = CYP19A1 (negative control) and A2 = PTGS2 (positive control) for the OF-DF reaction. The cDNA clones that were found to be differentially expressed in the OF-DF membrane following comparison of hybridization signals among the corresponding spots of the two membranes were further characterized by sequencing. (PDF 275 kb)
Additional file 2: of Willingness to accept capitation payment system under the Ghana National Health Insurance Policy: do income levels matter?
Creators: name: Sackey, Frank
name: Amponsah, Peter
Publisher: name: Figshare
Year: 2017
Subjects: subject: Medicine
subject: Molecular Biology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Stata inputs command. (DOCX 11 kb)
The food resource management strategies employed by low-income adults in New Jersey
Creators: name: Johnson, Charita J.
Publisher: name: No Publisher Supplied
Year: 2013

description: Food insecurity is a major public health issue by which low-income individuals are disproportionately affected.  Food and nutrition assistance programs, such as the Supplemental Nutrition Assistance Program (SNAP), were created in an attempt to lower food insecurity prevalence among those with limited incomes.  However, many low-income individuals that receive nutrition assistance remain food insecure.  Employing food resource management (FRM) skills may help low-income people stretch their food budgets and ultimately increase their food security.  But, if nutrition educators are to provide impactful education regarding FRM, they must be familiar with the spectrum of practices that can effectively be used by their target audience.  To date, no research has been conducted to catalogue the FRM strategies employed by low-income people, nor to determine which strategies contribute to monetary savings and increased food security.  This investigation was designed to learn what FRM behaviors low-income individuals employ, as a preliminary step towards determining optimal FRM practices for this audience.  Face to face interviews (n=201) were conducted at agencies that serve this target audience throughout New Jersey.  The results from this study demonstrated that there is a large gap between the FRM behaviors taught in nutrition education for low-income people to those that are actually employed, most notably among individuals with children who use multiple strategies to reduce their children’s influences on their food purchases.  Use of a combination of FRM nutrition education and nutrition assistance may decrease the high rates of food insecurity among low-income people.  Further research should be conducted to examine the relative contribution of FRM behaviors in helping low-income people save money and increase their food security.  Research of that type may be rigorous and timely, hence, in the interim nutrition educators should consider teaching the FRM behaviors identified in this work that they feel will be beneficial to their target population.
Identifying SNP correlates of a schizophrenia subtype characterized by poor premorbid functioning and perceptual organization deficits
Creators: name: Joseph, Jamie M.
Publisher: name: No Publisher Supplied
Year: 2013

description: Schizophrenia has been defined as a neurodevelopmental disorder (Weinberger, 198&; Lewis & Levitt, 2002; Javitt & Coyle, 2004). The etiology of schizophrenia is thought to be comprised of a combination of genetic and environmental components. Although the estimated heritability of schizophrenia is 80% (Sullivan et al., 2003); well-known (e.g. psychosocial stressors) and unknown environmental factors have a significant role in the development of this disorder. These factors subsequently lead to epigenetic and neurochemical changes affecting brain structure and function; thus also characterizing schizophrenia as a neural circuitry disorder (Friston & Firth, 1995; Benes, 2000; Lisman et al., 2008).  Visual perceptual organization and premorbid social-sexual functioning impairments are significant cognitive and social deficit traits that are found in many individuals with schizophrenia, and that are strongly correlated with each other. However, the relationship between these phenotypes and the genetic etiology of schizophrenia is not known. Furthermore, clarification of this issue is complicated by heterogeneity of perceptual and social history functioning in the disorder.  Therefore, the aim of this study was to reduce heterogeneity compared to past studies by determining association of this combined phenotype to single nucleotide polymorphisms (SNPs) in genes associated with glutamatergic and GABAergic neurotransmitter systems; the primary hypothesized neurocircuitry of visual perceptual organization in schizophrenia. A combination of clinical assessments, a battery of visual perceptual organization tasks and saliva samples were ascertained in order to determine links between selected phenotypes and genotypes.   The observed relationships among perceptual, clinical, demographic variables are consistent with past findings suggesting a possible patient subtype with poor premorbid social sexual functioning, significant disorganized symptoms, and abnormal visual perceptual functioning. While the contribution of specific SNPs to these phenotypes has not been definitively clarified, the psychosocial developmental and perceptual organization factors analyzed are suggested to interact in schizophrenia spectrum populations and thought to be related to the genetic liability of schizophrenia. Overall, the study data suggest that further study of well-defined phenotypes and potentially associated genetic variants may be useful for future studies in schizophrenia spectrum populations that aim to develop personalized treatments.
Anomiopus foveicollis Canhedo 2006
Creators: name: Groll, Elisa Von
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Scarabaeidae
Anomiopus
Anomiopus foveicollis

description: Anomiopus foveicollis Canhedo, 2006
Canhedo, 2006:377, figs 102–121, 772.
Paratype ♂, PERU, Madre de Dios: Reserva Cuzco Amazonica (15 km NE Puerto Maldonado, 12°33’S, 69°03’W, 200 m), 30.VI.1989, Ashe & Leschen col., “terraform swamp forest, FIT” (MCNZ 234.815).
description: Published as part of Groll, Elisa Von, 2017, Catalogue of Coleoptera type specimens housed in the collection of the Museu de Ciências Naturais, Fundação Zoobotânica do Rio Grande do Sul, Brazil, pp. 439-473 in Zootaxa 4318 (3) on page 463, DOI: 10.11646/zootaxa.4318.3.2, http://zenodo.org/record/887750
Additional file 5: of Modulating the catalytic activity of AMPK has neuroprotective effects against α-synuclein toxicity
Creators: name: Bobela, Wojciech
name: Nazeeruddin, Sameer
name: Knott, Graham
name: Aebischer, Patrick
name: Schneider, Bernard
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Cell Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: Science Policy
subject: Computational Biology

description: Figure S4. Down-regulation of dopaminergic markers in the nigrostriatal system following overexpression of human α-syn and T172Dα1 AMPK subunit. (PDF 1785 kb)
Cognitive influences in the perceptual brain experiments and computational models for the Ames window illusion
Creators: name: Karakatsani, Maria Eleni
Publisher: name: No Publisher Supplied
Year: 2013

description: The current study is part of a more comprehensive project that aims to explore potential differences between schizophrenia (SZ) patients and healthy controls in perceiving depth-inversion illusions (DII). Previous work with two types of DII, namely the hollow mask and the reverse perspective illusions, has indicated that SZ patients tend to rely less on experience and stored knowledge, in this case the experience with faces and linear perspective, than healthy controls. The present study explores how healthy controls perform on variants of the “Ames window illusion” that uses humans’ experience of viewing rectangles. The Ames window is based on a rotating trapezoid, typically rotating about a vertical axis that is located in the middle between the vertically oriented long and short bases. Because the trapezoid is perceived as a slanted rectangle, viewers perceive the Ames window illusion, which is a type of DII: the window appears to oscillate back and forth even though it rotates continuously in the same direction. The most plausible explanation is that viewers perceive the inverse depth when the short base is closer than the large base, because of prior experience in viewing slanted rectangles. We investigated the strength of the illusion by using nine computer-generated windows that were displayed on a screen. The nine windows were designed to vary systematically three key parameters: (1) The long-to-short base ratio; (2) the height-to-short base ratio, and (3) the presence or absence of shadows. These stimuli were used in two experiments to assess illusion strength using two measures: (A) Asking observers to report which base was in front at selected instances, signaled by auditory beeps; (B) Asking observers to indicate reversals in rotation direction. The two measures produced results that had a high degree of correlation, thus confirming the validity of the methods. The data were fed to an optimization algorithm for a model that was based on a linear combination of the weights of the three parameters. The model produced results that were significantly correlated with the experimental data. The next phase will involve experiments with SZ patients, based on the results of the present study.
Anomiopus galileoae Canhedo 2006
Creators: name: Groll, Elisa Von
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Scarabaeidae
Anomiopus
Anomiopus galileoae

description: Anomiopus galileoae Canhedo, 2006
Canhedo, 2006:423, figs 367–384, 789.
Paratype ♂, BRAZIL, Rio Grande do Sul: Marcelino Ramos, X.1939 (MCNZ 234.816).
description: Published as part of Groll, Elisa Von, 2017, Catalogue of Coleoptera type specimens housed in the collection of the Museu de Ciências Naturais, Fundação Zoobotânica do Rio Grande do Sul, Brazil, pp. 439-473 in Zootaxa 4318 (3) on page 463, DOI: 10.11646/zootaxa.4318.3.2, http://zenodo.org/record/887750
Megalops atlanticus Valenciennes 1847
Creators: name: Angulo, Arturo
name: Betts, Joel T.
name: González-Alemán, Néstor J.
name: Castañeda, Edgar
name: Berghe, Eric Van Den
name: Elías, Diego J.
name: Mcmahan, Caleb D.
name: Matamoros, Wilfredo A.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Squamata
Elopiformes
Megalopidae
Megalops
Megalops atlanticus

description: Megalops atlanticus Valenciennes 1847 (Fig. 6F). Tarpon, Atlantic Tarpon; Sábalo, Sábalo Real, Tarpón, Tarpón del Atlántico
Vouchers: UCR 1091-001 (1) and 1092-001 (1). Distribution: Atlantic and Eastern Pacific oceans; from southern Nova Scotia, Canada, to southern Brazil in the western Atlantic, from southern France to Angola in the eastern Atlantic and from southern Guatemala to southern Colombia in the Eastern Pacific; entering estuaries and littoral lagoons and ascending river courses; (Nicaragua) Co, UI, WK, Pr, GM, KP, Es, BF, IM, To, Sa, SJ, RF and LN (Atlantic); 0–31 masl; Per, Dia, Amp. Occurrence and conservation status: Nat; VU A2bd (2019), population trend decreasing. Literature: Meek (1907: 111, as Tarpon atlanticus —synonym; brief description, including an identification key, and information on distribution and ecology), Astorqui (1975: 93; brief description, including illustrations and an identification key, and information on distribution and ecology), Villa (1982: 77, as T. atlanticus —synonym; detailed description, including illustrations and an identification key, and information on distribution and ecology), Bussing (1998: 61; brief description, including illustrations and an identification key, and information on distribution, with a map, and ecology), González-Alemán (2006: 81; brief description, including an illustration, and information on distribution and ecology), Gros & Miguel-Frithz (2010: 153; brief description, including illustrations, and information on distribution and ecology, plus indigenous science and ethnoichthyology), Robertson & Allen (2015: 2522; detailed description, including illustrations, and information on distribution, with a map, and ecology), van den Berghe (2015: 36; listed, including an illustration and information on distribution and ecology), Robertson & Van Tassell (2019: 2522; detailed description, including illustrations, and information on distribution, with a map, and ecology), Castellanos-Galindo et al. (2019: 401; information on distribution, with a map, and ecology) and Angulo (2021: 20; listed, including information on distribution).
description: Published as part of Angulo, Arturo, Betts, Joel T., González-Alemán, Néstor J., Castañeda, Edgar, Berghe, Eric Van Den, Elías, Diego J., Mcmahan, Caleb D. & Matamoros, Wilfredo A., 2023, Continental fishes of Nicaragua: diversity, distribution and conservation status; with an annotated and illustrated checklist of species and an identification guide to families, pp. 1-89 in Zootaxa 5376 (1) on page 14, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Automated bridge deck evaluation using ground penetrating radar scans
Creators: name: Kaur, Parneet
Publisher: name: No Publisher Supplied
Year: 2013

description: Reinforcement concrete (RC) bridge decks are surveyed regularly to ensure that they are safe to use and to determine if they require rehabilitation or replacement. The bridge surveys include evaluating subsurface bridge condition. RC bridges have steel reinforcement bars, also called rebars, embedded in their surface, which are prone to corrosion due to factors like moisture, carbonation, use of deicing salts and aging. By the time the effect of corroded rebars is visible on deck surface in form of cracks, the damage is tremendous. If left unchecked, corroded rebars can deteriorate at a faster and significantly affect bridge integrity. So, it is very important to timely identify and repair deteriorated rebars. Ground Penetrating Radar (GPR) is a widely used non-destructive technology (NDT) for detecting subsurface anomalies in variety of structures including RC bridges. The raw GPR data is represented as images that can be processed for obtaining a deterioration map of a bridge, which indicates the level of corrosion in rebars for the entire bridge. The existing methods to generate the deterioration map using GPR data are semi-automated, time consuming and depends on expertise of the engineer analyzing the data.  In this thesis, we work towards automating the process of obtaining deterioration map of RC bridge decks based on measuring signal attenuation at the upper rebar mat using GPR. Intensity and gradient-based feature vectors were explored to construct a classifier, which can detect the regions of interest (ROI) corresponding to each rebar in images. Each classifier was tested on datasets constructed from two different bridges. Further, the exact location of rebar was found in each ROI. Once all the rebars were detected throughout the bridge, depth-correction of the measured attenuation is applied so that the component of that measured attenuation caused solely by variation in rebar depth does not skew the results. Finally, a deterioration map was generated which indicates the level of corrosion in the bridge. The proposed algorithm was tested on two RC bridges and the deteriorated regions obtained are compared with the results obtained using existing tools.
Anomiopus genieri Canhedo 2006
Creators: name: Groll, Elisa Von
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Scarabaeidae
Anomiopus
Anomiopus genieri

description: Anomiopus genieri Canhedo, 2006
Canhedo, 2006:372, figs 73–88, 770.
Paratypes: ♂, COLOMBIA, Bolívar: Rio Sipao (110 km E Caiçara), 04.VIII.1987, S. & J. Peck col. (MCNZ 234.818); ♂, TRINIDAD: St. George (Simla Res. Stn., 8 km N Arima), 24.VI–08.VII.1993, S. & J. Peck col. (MCNZ 234.817).
description: Published as part of Groll, Elisa Von, 2017, Catalogue of Coleoptera type specimens housed in the collection of the Museu de Ciências Naturais, Fundação Zoobotânica do Rio Grande do Sul, Brazil, pp. 439-473 in Zootaxa 4318 (3) on page 463, DOI: 10.11646/zootaxa.4318.3.2, http://zenodo.org/record/887750
Fungal decomposition dynamics using Fourier transform infrared spectroscopy and atomic force microscopy
Creators: name: Kilic, Jennifer A.
Publisher: name: No Publisher Supplied
Year: 2013

description: I studied the decomposition of leaf material at the hyphal scale of resolution and the chemical and physical changes occurring at the fungal/substrate interface using Fourier transform infrared (FTIR) spectroscopy and atomic force microscopy (AFM).  The chemical composition of 20 fungal isolates was determined using FTIR and FTIR-attenuated total reflectance (FTIR-ATR) microscopy, with the intention of subtracting fungal FTIR spectra from decomposing leaf spectra in a separate experiment.  I found fungi are difficult to differentiate using FTIR spectra.  I performed a twelve month decomposition study placing leaves of white oak, black huckleberry, and pitch pine in leaf litter of the New Jersey pinelands.  FTIR-ATR spectra of the leaves at 10x10 micron areas were taken at 0, 6, and 12 months.  I found leaf chemistry of oak and huckleberry was similar, but different from pine, prior to decomposition.   As decomposition progressed, the chemistry of the leaves appeared to become more similar.  Subtracting fungal spectra from the leaf spectra was not possible and complicated analysis of leaf spectra.  AFM was combined with FTIR-ATR to study the fungal hypha/leaf interface at the level of an individual hypha.  It was not possible to scan a leaf on the AFM, so a flatter substrate was required.  I attempted to cast starch:lignin biofilms as a simple leaf model using published methods, however it was found that during the film making process the lignin may have been degraded.  Instead, manufactured cellophane was used as a model for cellulose.  Three fungal species were grown on cellophane squares, and AFM and FTIR-ATR imaging utilized to determine the chemical and physical properties of the cellophane adjacent to the hyphae.  Fungal species capable of producing cellulase caused a change in the physical characteristics and chemistry of cellophane adjacent to fungal hyphae.  These experiments demonstrate the chemistry of fungal hyphae and decomposing leaves using FTIR-ATR and chemical and physical changes occurring in a substrate during fungal decomposition using FTIR-ATR and AFM.  The novel use of FTIR-ATR and AFM to investigate the fungus/substrate interface at the scale of an individual fungal hypha introduces new methods for studying fungi at this scale of resolution.
Additional file 1: Table S1. of Cooperative antitumor activities of carnosic acid and Trastuzumab in ERBB2+ breast cancer cells
Creators: name: DâAlesio, Carolina
name: Bellese, Grazia
name: Gagliani, Maria
name: Aiello, Cinzia
name: Grasselli, Elena
name: Marcocci, Gianluca
name: Bisio, Angela
name: Tavella, Sara
name: Daniele, Tiziana
name: Cortese, Katia
name: Castagnola, Patrizio
Publisher: name: Figshare
Year: 2017
Subjects: Biochemistry
Developmental Biology
Cancer
Hematology
Computational Biology

description: Antibodies used for immunoblot analysis. (DOCX 78Â kb)