cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 6: Table S4. of Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants
Creators: name: Alcon-Giner, Cristina
name: Shabhonam Caim
name: Suparna Mitra
name: Ketskemety, Jennifer
name: Wegmann, Udo
name: Wain, John
name: Gusztav Belteki
name: Clarke, Paul
name: Hall, Lindsay
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Computational Biology

description: DNA yield from different DNA extraction methods. (PDF 306Â kb)
Engineered presentation of neural cell adhesion molecules for directed neural and neural stem cell behaviors
Creators: name: Cherry, Jocie Fatima
Publisher: name: No Publisher Supplied
Year: 2013

description: Neurotraumatic injuries result in an irreplaceable cell loss and concomitant deficit in motor and sensory functions. Cell transplantation therapies could potentially address the deficit of neuronal tissues, but remain challenged by limited survival, organization, and integration of transplanted cells. Substrates designed to present specific neurotrophic cues, in precise configurations are candidates for maintaining cell differentiation in vitro and enhancing integration and survival of transplanted cells in vivo. The goal of this dissertation was to design biologically active interfaces based on key developmental neural cell adhesion molecules previously shown to promote neuritogenesis, neuronal differentiation, and survival of neural cells. Specifically, this thesis focuses on modulating the display of protein fragments derived from L1 cell adhesion molecule and N-cadherin and examining cellular responses.    We investigated the efficacy of L1-derived peptide sequences displayed via non-permissive human albumin nanoparticles, which elicited modest neuronal adhesion and neurite outgrowth of primary neurons. In contrast, substrate-bound L1-Fc chimera promoted enhanced neuronal responses. Following this result, we utilized protein A to maximize L1-Fc effectiveness and yield a systematically oriented, multivalent presentation compared to passive adsorption methods. Protein A-presented L1-Fc, displayed from polymeric substrates, greatly improved neurite outgrowth of spinal cord and cerebellar neurons and neuronal differentiation of human embryonic stem cell-derived neural stem cells (hESC-NSCs), compared to L1-Fc presented from the cationic polymer, poly-D-lysine. Next, we sought to address limitations of L1 functionalized substrates, namely, inadequate L1-mediated cell adhesion and limited lineage restriction of hESC-NSCs. To this end, we investigated the effects of presenting N-cadherin-Fc and L1-Fc on differentiation, neurite outgrowth, and survival of hESC-NSCs. Low density N-cadherin substrates promoted greater neuronal differentiation and survival of hESC-NSCs. Enhanced neurite outgrowth and neuronal differentiation was observed in hESC-NSCs cultured on N-cadherin-/L1-Fc substrates, demonstrating the synergistic effect of these two fragments. Findings from this thesis support the paradigm of designing stem cell-bioactive materials by fine-tuning surface concentrations and microscale organization of ligands that regulate different stages of neural development. Such materials could be candidates for recapitulating the microenvironment in the context of biomimetic materials for neural developmental models as well as transplantation devices for neural tissue engineering.
PERFORMANCE AUDITING IN RWANDAN HOSPITALS: MEASURING OPERATIONAL EFFICIENCY AND PATIENT OUTCOMES
Creators: name: 1Kwame Mensah, 2Mbonigaba Celestin &3Youssef El Mansouri, 4Liam Anderson
Publisher: name: Zenodo
Year: 2013

description: This study investigates the role of performance auditing in enhancing operational efficiency and improving patient outcomes in Rwandan hospitals. Employing a mixed-methods approach, data from ten public hospitals between 2008 and 2012 were analyzed using thematic analysis and descriptive statistics. The study reveals a significant improvement in operational metrics: hospital bed occupancy rates increased from 75% to 82% (p<0.01), and bed turnover rates rose from 30 to 38 (p<0.01). Patient outcomes also improved, with maternal mortality rates decreasing from 540 to 400 per 100,000 live births and infant mortality rates declining from 62 to 46 per 1,000 live births (p<0.001). Despite these gains, workforce expansion lagged behind increasing patient admissions (p=0.03). The study concludes that performance auditing is an effective mechanism for improving resource utilization and healthcare delivery but recommends targeted workforce development, standardization of auditing metrics, and investment in health management systems to sustain progress.
Additional file 5: Table S3. of Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants
Creators: name: Alcon-Giner, Cristina
name: Shabhonam Caim
name: Suparna Mitra
name: Ketskemety, Jennifer
name: Wegmann, Udo
name: Wain, John
name: Gusztav Belteki
name: Clarke, Paul
name: Hall, Lindsay
Publisher: name: Figshare
Year: 2017
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Computational Biology

description: Bifidobacterium strains used for validating primers 530F-926R using PCR (PDF 198Â kb)
Synthesis of superbase and correlation between gas phase acidity and pKa study of ionic liquid
Creators: name: Chu, Pingcheng
Publisher: name: No Publisher Supplied
Year: 2013

description: Since chemical reactions involving proton transfer as a key mechanism step become prevalent, development of Brønsted bases has been the intense focus in terms of catalyzing proton transfer reactions. Lambert et al. found and confirmed one cyclopropenimine as a strong superbase by measuring its pKa in acetonitrile for the first time. Based on that, we calculated several cyclopropenimine’s proton affinity (PA) which are much higher than all the volatile reference superbases we’ve ever used. It means that if we could obtain those very basic superbases, they would be used as reference bases to bracket PAs of highly basic compounds. Herein, we tried to design and synthesize cyclopropenimine-based superbases and investigated their tunability of PA by modifying various electron withdrawing and donating groups. The corresponding calculation results are consistent with our proposal that cyclopropenimine superbase with EWG decrease PA while EDG increase PA. We also tried to measure PA of one cyclopropenimine superbase that we synthesized by Cooks kinetics method.  The other project focuses on a special class of ionic liquid which is known as green solvent with several advantages over traditional organic solvent. This new type of ionic liquid is imidazolium-based ionic liquid with tunable aryl and alkyl substituents which was designed by Strassner et al.. They named this category of ionic liquid as tunable aryl-alkyl ionic liquids (TAAILs). The reason we are interested in them is looking into the correlation between TAAILs’ aqueous property and their theoretical acidity in gas phase and solution. If there was some correlation, we could predict imidazolium compounds’ pKa’s by their gas phase property. Based upon this conjecture, we measured different TAAILs’ acidity by LCQ bracketing method on mass spectrometry, calculated their free energy in solution phase as well as in gas phase and developed two methods to measure their pKa’s in solution. Their acidity results demonstrate that those TAAILs with electron-withdrawing groups on para-position of phenyl substituent have high acidity while other TAAILs with electron-donating para-substituent have low acidity. Besides, I successfully obtained the pKa value of one TAAILs as 25.4 in water via H/D exchange kinetics experiment on NMR.
The ups and downs of electrical activity in the brain
Creators: name: Clarke, Stephen G.
Publisher: name: No Publisher Supplied
Year: 2013

description: Action potentials (APs) are travelling waves of electrical activity in neurons composed of a rapid increase in membrane potential called a depolarization, followed by a repolarizing phase returning the membrane to a resting potential. Although APs are often thought of as all-or-nothing events, this is not necessarily the case. The AP waveform is generated by voltage-gated sodium and potassium channels whose composition, density and activity vary between and within neurons based on the function and output of that neuron. In addition to signal propagation, the purpose of an AP is to initiate the cascade of neurotransmitter release, beginning with the opening of voltage-gated calcium channels activated by the AP. Here, we set out to better determine how AP waveforms affect calcium influx and subsequent neurotransmitter release. The patch clamp technique has emerged as the best method to measure and study macroscopic electrical activity in neurons. Presynaptic APs at most synapses in the brain are difficult to study due to the small size of most presynaptic terminals. However, the calyx of Held synapse in the mammalian auditory brainstem is large enough to allow patch clamp recordings. In mouse brain slices, perfused with sodium and potassium channel blockers, various  iii  voltage protocols were tested to determine how modulation of AP kinetics alter calcium activity.  First, various depolarization and repolarization rates were studied with test pulses of equivalent stimulus duration at 1 ms, showing that a repolarization/depolarization ratio between 1.5 and 2.3 is optimal for eliciting calcium influx. Additionally, depolarizations that follow the AP were studied and found to have no appreciable effect on calcium activity within the physiological range for AP durations in this neuron. However, if the repolarization rate is sufficiently fast, these currents were found to significantly alter the timing and magnitude of calcium influx. Finally, the AP was shown to minimize calcium channel inactivation to promote consistent and reliable neurotransmitter release. These findings will serve as the starting point for future work performing simultaneous pre- and postsynaptic patch clamp recordings to study transmission. This work promotes a better understanding of how AP kinetics affect calcium channel activity and thus neurotransmission.
A partitioning explanation of the denomination effect
Creators: name: Colby, Helen
Publisher: name: No Publisher Supplied
Year: 2013

description: Five studies examined the mechanisms by which large denomination bills reduce consumer willingness to make discretionary purchases.  The first study demonstrated the denomination effect, in which large denomination bills can act as spending deterrents. Study 2 examined consumer perception of large denominations as an effective tool for monitoring spending and reducing discretionary consumption. Study 3 compared fungibility, processing fluency, and partitioning explanations for the effect, finding the strongest support for a partitioning based explanation.  Study 4 provided additional evidence for the partitioning explanation, demonstrating that large denomination bills are as effective as envelopes in deterring spending.  Study 5 demonstrated the effect in a real-world spending situation.
Zischkaita serrana Moura 2003
Creators: name: Groll, Elisa Von
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Chrysomelidae
Zischkaita
Zischkaita serrana

description: Zischkaita serrana Moura, 2003
Moura, 2003: 643, figs 1–7.
Holotype ♂, BRAZIL, Rio Grande do Sul: Cambará do Sul, 19.XII.1994, A. Bonaldo col. (MCNZ 219.974). Paratypes: ♂, BRAZIL, Rio Grande do Sul: Cambará do Sul, 19.XII.1994, A. Bonaldo col. (MCNZ 219.975); ♀, São Francisco de Paula (PRO-MATA), 02.V.1997, A. F. Franceschini col. (MCNZ 219.963); 2♂, 4♀, São Francisco de Paula (PRO-MATA), 19–22.III.1998, L. Moura col. (MCNZ 219.971, 219.972, 219.964, 219.965, 219.966, 219.967).
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 459, DOI: 10.11646/zootaxa.4318.3.2, http://zenodo.org/record/887750
Sminthurus nigromaculatus Tullberg 1871
Creators: name: Mayvan, Mahmood Mehrafrooz
name: Greenslade, Penelope
name: Sadeghi-Namaghi, Hussein
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Collembola
Symphypleona
Sminthuridae
Sminthurus
Sminthurus nigromaculatus

description: Sminthurus nigromaculatus Tullberg, 1871
– Sminthurus viridis var. nigromaculata Tullberg, 1871: 145.
KS: Ghahramaninezhad et al. 2013; MAZ: Yoosefi Lafooraki & Shayanmehr 2013a, b; Yoosefi Lafooraki 2014.
Ecology and habitat in Iran: soil of meadows.
General distribution: Holarctic, but probably wider (Fjellberg 2007).
description: Published as part of Mayvan, Mahmood Mehrafrooz, Greenslade, Penelope & Sadeghi-Namaghi, Hussein, 2023, An annotated checklist of the Collembola (Hexapoda) from Iran, pp. 1-101 in Zootaxa 5275 (1) on page 59, DOI: 10.11646/zootaxa.5275.1.1, http://zenodo.org/record/7898948
A requirement model of local news WAP/WEB application for rural community
Creators: name: AL-msie'deen, Ra'fat
name: Frijat, Ahmad
Publisher: name: figshare
Year: 2025
Subjects: classificationCode: 461201
subject: Automated software engineering
classificationCode: 461202
subject: Empirical software engineering
classificationCode: 461299
subject: Software engineering not elsewhere classified

description: Mobile news service can be obtained easily and provide flexibility to access the rural news criteria at any time in any location. This research introduces a prototype “local news WAP/WEB application” that provides the people in the rural communities with the appropriate news services that could help those people to view the various news via this prototype. By using this prototype, the user of this service from the rural communities can easily get necessary information that makes those users in touch with the different news updating in these areas. The proposed prototype provides the user to post the occurred news related for these areas.
A requirement model of local news WAP/WEB application for rural community
Creators: name: AL-msie'deen, Ra'fat
Publisher: name: figshare
Year: 2025
Subjects: classificationCode: 461201
subject: Automated software engineering
classificationCode: 461202
subject: Empirical software engineering
classificationCode: 461299
subject: Software engineering not elsewhere classified

description: Mobile news service can be obtained easily and provide flexibility to access the rural news criteria at any time in any location. This research introduces a prototype “local news WAP/WEB application” that provides the people in the rural communities with the appropriate news services that could help those people to view the various news via this prototype. By using this prototype, the user of this service from the rural communities can easily get necessary information that makes those users in touch with the different news updating in these areas. The proposed prototype provides the user to post the occurred news related for these areas.
Yingaresca limonensis
Creators: name: Groll, Elisa Von
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Chrysomelidae
Yingaresca
Yingaresca limonensis

description: Yingaresca limonensis (Bechyné, 1997)
Bechyné, 1997:292 (Ophraella); Moura, 2016:46 (comb. nov.).
Paratypes ♂, ♀, VENEZUELA, Aragua: El Limón, 2.III.1951, 15.III.1951, F. Fernández Yépez col. (MCNZ 238.233, 238.234).
Yingaresca magdalia (Bechyné, 1997)
Bechyné, 1997:293 (Ophraella); Moura, 2016:46 (comb. nov.).
Paratypes: ♀, VENEZUELA, Aragua: Carmen de Cura, 350 m, 11.VII.1966, Fernández Yépez & J. Rosales col. (MCNZ 238.235); ♀, Lara: Duaca, 19.II.1965, J. & B. Bechyné col. (MCNZ 238.236);
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 460, DOI: 10.11646/zootaxa.4318.3.2, http://zenodo.org/record/887750
Experimental studies of mercury oxidation by anaerobic bacteria
Creators: name: Colombo, Matthew Jordan
Publisher: name: No Publisher Supplied
Year: 2013

description: Mercury is a toxic element with complex biogeochemistry. Bacteria influence mercury fate and transport in the environment by contributing to mercury sorption, reduction, and methylation. While these biogeochemical reactions have been well studied, the role of bacteria in mercury oxidation is poorly understood. In this dissertation, the oxidation of elemental mercury by anaerobic bacteria is documented in detail.    The oxidation and methylation of elemental mercury by Desulfovibrio desulfuricans ND132 is described in Chapter 2. Bulk chemical analyses, derivatization reactions, and X-ray absorption spectroscopy showed that D. desulfuricans ND132 oxidized elemental mercury to divalent mercury and produced methylmercury when provided with elemental mercury as its sole mercury source. X-ray absorption spectroscopy demonstrated that the majority of cell-associated mercury was oxidized and covalently bound to organic sulfur. This work reveals previously unrecognized mercury transformations by anaerobic bacteria that may be important in anoxic aquatic settings.    Other phylogenetically and metabolically diverse anaerobic bacteria were then investigated for their mercury oxidation abilities in Chapter 3. Geothrix fermentans H5, Shewanella oneidensis MR-1, and Cupriavidus metallidurans AE104 all oxidized elemental mercury to divalent mercury. Heat-inactivation of the cells did not diminish mercury oxidation ability, indicating that the bacteria do not have to be metabolically active to oxidize mercury. X-ray absorption spectroscopy also revealed that oxidized mercury was bound to cellular thiol groups. The results of this study suggest that mercury oxidation may be widespread among bacteria and be mediated by a passive cellular mechanism.    Chapter 4 presents preliminary data demonstrating the fractionation of mercury stable isotopes during microbial mercury oxidation, in which the light isotopes preferentially accumulate in the oxidized product. Fractionation appeared to be mass dependent since no odd isotope anomalies or deviations from theoretical fractionation laws were observed. The data, considered in light of past experimental and theoretical work, suggests that isotope fractionation was the result of a kinetic isotope effect. This study provides initial insight into isotope fractionation during mercury oxidation and guides future efforts to detect this reaction in the environment.
Coronabrotica amazonensis Moura 2010
Creators: name: Groll, Elisa Von
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Chrysomelidae
Coronabrotica
Coronabrotica amazonensis

description: Coronabrotica amazonensis Moura, 2010
Moura, 2010:30, figs 1–9.
Paratype ♂, BRAZIL, Amazonas: (Rodovia AM 1, km 104), VI.1968, without colector (MCNZ 237.345).
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 460, DOI: 10.11646/zootaxa.4318.3.2, http://zenodo.org/record/887750
Sminthurus viridis Linnaeus 1758
Creators: name: Mayvan, Mahmood Mehrafrooz
name: Greenslade, Penelope
name: Sadeghi-Namaghi, Hussein
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Collembola
Symphypleona
Sminthuridae
Sminthurus
Sminthurus viridis

description: Sminthurus viridis Linnaeus, 1758
– Podura viridis Linnaeus, 1758: 608.
KH: Farrahbakhsh 1961; NK: Mehrafrooz Mayvan et al. 2021; KS: Ghahramaninezhad et al. 2013; Kahrarian 2015, 2019; LO: Moradi et al. 2018, 2019; MAZ: Yoosefi Lafooraki & Shayanmehr 2013a, b; Yoosefi Lafooraki 2014.
Ecology and habitat in Iran: soil of alfalfa and wheat crops.
Remarks: this species can be known as a pest on alfalfa plant.
General distribution: cosmopolitan (Fjellberg 2007).
description: Published as part of Mayvan, Mahmood Mehrafrooz, Greenslade, Penelope & Sadeghi-Namaghi, Hussein, 2023, An annotated checklist of the Collembola (Hexapoda) from Iran, pp. 1-101 in Zootaxa 5275 (1) on page 59, DOI: 10.11646/zootaxa.5275.1.1, http://zenodo.org/record/7898948
Institutional innovation in global health
Creators: name: Da Silva, Anna
Publisher: name: No Publisher Supplied
Year: 2013

description: This dissertation examines the changes in global governance of vaccine preventable diseases precipitated by the transformations of national infrastructures and international institutions since the 1990s. Neoliberal policies promoted by the transnational elites prompted privatization of healthcare and decline in public healthcare expenditures and resulted in concentration of economic and political power, crumbling of the welfare state, and deepening inequalities. Emergence in public health of a new institutional form -- Public-Private Partnership (PPP), signals a reconfiguration of the governance space.  I focus on one such PPP -- the Global Alliance for Vaccines and Immunization (GAVI). GAVI’s philanthropic goals are balanced against accountability to its partners. Collaborating with the pharmaceutical industry to further its philanthropic objectives, GAVI mediates the market’s pull by effecting state policies. I document the vectors of power that GAVI both exerts and is subjected to in its institutional entanglement with the states, multilateral agencies, and the industry. These mechanisms of influence are functionally different from market pressures or ‘soft’ rules of traditional multilateral organizations and forge new paths for exercising power within PPPs.    Finally, I examine the networks of vaccine trade between countries from 1996 to 2010. Trade networks retain a pronounced core-periphery structure, and the majority of countries lack capacity for vaccine production. Over time some traditionally strong vaccine producers scale down, and some export-oriented developing countries, -- scale up their vaccine production. Congruent with the industrial convergence hypothesis, I find that industry late-comers no longer accrue significant returns and that some of the formerly dominant vaccine-exporting countries engage in innovative funding ventures, such as GAVI’s Advanced Market Commitment (AMC). AMC creates stable demand for new patent-protected and expensive vaccines, subsidizing the industry. I also find that industrial growth does not always reduce inequality for populations most affected by endemic diseases. I take a closer look at India as a country which houses both a thriving vaccine-producing industry and a third of the world’s un-immunized children, and examine the rift between capital accumulation and state decision making.
Legal roles and moral duties
Creators: name: Da Silva, Michael
Publisher: name: No Publisher Supplied
Year: 2013

description: This thesis examines the relationship between the moral rules that apply to all persons by virtue of their humanity (‘universal moral rules’) and the rules they must follow to continue serving in particular (often socially important) roles (‘role responsibilities’). It provides a general framework for what to do if universal moral rules and role responsibilities conflict, focusing particularly on the role of lawyer and similarly state-involving professions. It argues that ideally constituted roles will not create duties to infringe universal moral rules and defends the general priority of universal moral rules when a role’s non-ideal constitution leads to conflict.  It then offers a limited exception to the general priority of universal moral rules that applies when a role can only be performed if one violates a universal moral rule and the role is necessary for a well-developed society to maintain a certain level of functioning, but suggests one ought to regret the bad effects of acting under that exception.
Additional file 7: Figure S1. of Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants
Creators: name: Alcon-Giner, Cristina
name: Shabhonam Caim
name: Suparna Mitra
name: Ketskemety, Jennifer
name: Wegmann, Udo
name: Wain, John
name: Gusztav Belteki
name: Clarke, Paul
name: Hall, Lindsay
Publisher: name: Figshare
Year: 2017
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Inorganic Chemistry
subject: Hematology
subject: Computational Biology

description: Shannon diversity index on 16S rRNA gene sequencing data analysed using OTU and PE protocol. Shannon diversity index was calculated using 16S rRNA bacterial community profiles for sample AP1E (ELBW infant without probiotic supplementation) and sample V3 J (term infant). a Shannon diversity indexes comparison of three different 16S rRNA libraries (27F-519R (region V1 + V2 + V3), 530F-926R (region V4 + V5) and 926F-1394R (region V6 + V7 + V8)) using OTU and PE protocol pipelines for sample AP1E (preterm no supplementation). b Shannon diversity indexes comparison of three different 16S rRNA libraries (27F-519R (region V1 + V2 + V3), 530F-926R (region V4 + V5) and 926F-1394R (region V6 + V7 + V8)) using OTU and PE protocol pipelines for sample V3 J (term infant). (PDF 74 kb)
Statistical mechanics of nucleosomes
Creators: name: Chereji, Răzvan V.
Publisher: name: No Publisher Supplied
Year: 2013

description: Eukaryotic cells contain long DNA molecules (about two meters for a human cell) which are tightly packed inside the micrometric nuclei. Nucleosomes are the basic packaging unit of the DNA which allows this millionfold compactification. A longstanding puzzle is to understand the principles which allow cells to both organize their genomes into chromatin fibers in the crowded space of their nuclei, and also to keep the DNA accessible to many factors and enzymes. With the nucleosomes covering about three quarters of the DNA, their positions are essential because these influence which genes can be regulated by the transcription factors and which cannot.     We study physical models which predict the genome-wide organization of the nucleosomes and also the relevant energies which dictate this organization. In the last five years, the study of chromatin knew many important advances. In particular, in the field of nucleosome positioning, new techniques of identifying nucleosomes and the competing DNA-binding factors appeared, as chemical mapping with hydroxyl radicals, ChIP-exo, among others, the resolution of the nucleosome maps increased by using paired-end sequencing, and the price of sequencing an entire genome decreased.    We present a rigorous statistical mechanics model which is able to explain the recent experimental results by taking into account nucleosome unwrapping, competition between different DNA-binding proteins, and both the interaction between histones and DNA, and between neighboring histones. We show a series of predictions of our new model, all in agreement with the experimental observations.
Lilophaea sulina von Groll & Moura 2016
Creators: name: Groll, Elisa Von
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Chrysomelidae
Lilophaea
Lilophaea sulina

description: Lilophaea sulina von Groll & Moura, 2016
von Groll & Moura, 2016:196, figs 1–11.
Holotype ♂, BRAZIL, Rio Grande do Sul: Canela (Usina de Canastra), 20.XI.1997, M. A. Marques col. (MCNZ 160.195). Paratypes: ♀, BRAZIL, Paraná, Morretes, 13.I.1995, A. Franceschini col. (MCNZ 158.086); ♂, ♀, Rio Grande do Sul: Derrubadas (Parque Estadual do Turvo, estrada p/ Yucumã), 20.X.2004, L. Moura col. (MCNZ 229.519, 230.113); ♀, Derrubadas (Pq. Est. Turvo), 28.X.2003, L. Moura col. (MCNZ 226.675); ♀, Derrubadas (Campestre), 22.X.2007, L. Schmidt col. (MCNZ 229.489); ♀, Canela, 20.X.1997, M. A. Marques col. (MCNZ 160.192); ♂, 7♀, Canela (Usina da Canastra), 15.XII.1999, Franceschini, Bonaldo & Silva col. (MCNZ 238.251, 238.252, 238.256–238.261); ♂, Canela (Barragem dos Bugres), 25.XI.1996, L. Moura col. (MCNZ 238.254); ♂, (Barragem dos Bugres), 25.XI.1996, Franceschini col. (MCNZ 238.253); ♀, 14.II.1999, Franceschini, Bonaldo & Silva col. (MCNZ 238.262); ♂, 2♀, S. F. de Paula (Passo do Inferno), 16.XII.1999, Franceschini, Bonaldo & Silva col. (MCNZ 238.255, 238.263, 238.264); 2♀, Maquiné (Estação Experimental Fepagro), 10–12.I.2006, collected by fogging (MCNZ 238.265, 238.266); ♀, Maquiné (Garapiá), 13.XII.2007, L. Moura col. (MCNZ 238.267); ♀, Torres (Parque Estadual de Itapeva), 12.I.2005, R. Ott col. (MCNZ 232.507).
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 460, DOI: 10.11646/zootaxa.4318.3.2, http://zenodo.org/record/887750
Bayesian model averaging with exponentiated least square loss
Creators: name: Dai, Dong
Publisher: name: No Publisher Supplied
Year: 2013

description: Given a  finite family of functions, the goal of model averaging is to construct  a procedure that mimics the function from this family that is the closest to an  unknown regression function. More precisely, we consider a general regression  model with fi xed design and measure the distance between functions by mean  squared error (MSE) at the design points. In this thesis, we propose a new  method Bayesian model averaging with exponentiated least square loss (BMAX)  to solve the model averaging problem optimally in a minimax sense.
Additional file 8: of Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants
Creators: name: Alcon-Giner, Cristina
name: Shabhonam Caim
name: Suparna Mitra
name: Ketskemety, Jennifer
name: Wegmann, Udo
name: Wain, John
name: Gusztav Belteki
name: Clarke, Paul
name: Hall, Lindsay
Publisher: name: Figshare
Year: 2017
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Computational Biology

description: Number of reads obtained by PE and QIIME for samples V3Â J and AP1E. (PDF 76Â kb)
Scolytocis fritzplaumanni Lopes-Andrade 2008
Creators: name: Groll, Elisa Von
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Ciidae
Scolytocis
Scolytocis fritzplaumanni

description: Scolytocis fritzplaumanni Lopes-Andrade, 2008
Lopes-Andrade, 2008:28, figs 82–84, 91, 94A, 95A, 96–97, 101.
Paratypes: 30 specimens, BRAZIL, Rio Grande do Sul: São Francisco de Paula (FLONA SFP), 10.X.2006, L. V. Graf col. (MCNZ 237.987–238.016).
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 460, DOI: 10.11646/zootaxa.4318.3.2, http://zenodo.org/record/887750
Additional file 9: Figure S2. of Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants
Creators: name: Alcon-Giner, Cristina
name: Shabhonam Caim
name: Suparna Mitra
name: Ketskemety, Jennifer
name: Wegmann, Udo
name: Wain, John
name: Gusztav Belteki
name: Clarke, Paul
name: Hall, Lindsay
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Inorganic Chemistry

description: Rarefaction curves 16S rRNA gene sequencing data. Rarefaction curves representing number of species (leaves) detected at genus level versus number of reads sampled. Three different 16S rRNA gene sequencing data were used for this study: i) green curves represent sequencing data from 16S rRNA library prepared using primers 27F-519R, ii) red curves represent sequencing data from 16S rRNA library prepared using primers 530F-926R and iii) blue curves represent sequencing data from 16S rRNA library prepared using primers 926F-1394R. Rarefaction curves are labelled with numbers to differentiate among the samples used in the study: 1 (V2A.530F), 2 (V2A.926F), 3 (V3 J.926F), 4 (AP8C.530F), 5 (V2AJ.27F), 6 (AP5D.530F), 7 (P35C.530F), 8 (V3 J.530F), 9 (P29F.530F), 10 (P31B.530F), 11 (P30N.530F), 12 (AP25E.530F), 13 (AP25E.926F), 14 (AP25E. 27F), 15 (AP8C.926F), 16 (P35C.926F), 17 (V3 J.27F), 18 (P31B.926F), 19 (AP1E.530F), 20 (P31B.27F), 21(P29F.27F), 22 (P30N.27F), 23 (AP5D.926F), 24 (AP5D.27F), 25 (P29F.926F), 26 (AP1E.926F),27 (AP1E.27F), 28 (AP8C.27F), 29 (P30N.926F), 30 (P35C.27F). Numbers 12, 13 and 14 correspond to sample AP25E where majority of sequenced reads assigned at family level (i.e. Enterobacteriaceae). (PDF 62 kb)
Assessing data deposits in an institutional repository (U of T Dataverse in Borealis)
Creators: name: Dearborn, Dylanne
name: Lefresne, Jasmine
name: Lui, Lok Hei
Publisher: name: Zenodo
Year: 2024

description: U of T Dataverse, the University of Toronto's data repository, is one of the largest institutional dataverse collections in Borealis with over 1000 published datasets. It currently follows a self-deposit model that allows U of T researchers to deposit and publish their data without intervention unless requested. Considering increased usage of the repository and new and developing data deposit policies, we conducted an assessment of U of T Dataverse to (1) review the quality of published datasets, and (2) understand who is using the repository. This was accomplished by analyzing the monthly Borealis metrics and conducting a quality assessment of select datasets’ structure and associated metadata. Ultimately, this assessment will be used to help conceptualize curation services and identify resources to develop that would enable high-quality data deposits. In this presentation we will discuss our approach to this assessment, preliminary findings, and how this project will shape our approach to service and resource development. Overall, this project will allow us to better understand disciplinary trends relating to who is (and isn’t) using U of T Dataverse, help develop clear processes and guidelines, and inform training and departmental outreach. Longer-term, it will help us estimate the effort and time required to provide curation services, inform priorities for repository development, and help us anticipate the impact any change in national policy may have in demand for institutional services.
Sminthurus wahlgreni Stach 1920
Creators: name: Mayvan, Mahmood Mehrafrooz
name: Greenslade, Penelope
name: Sadeghi-Namaghi, Hussein
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Collembola
Symphypleona
Sminthuridae
Sminthurus
Sminthurus wahlgreni

description: Sminthurus wahlgreni Stach, 1920
– Sminthurus wahlgreni Stach, 1920: 207.
KH: Ramezani & Mossadegh 2016; Ramezani et al. 2020.
Ecology and habitat in Iran: soil of wheat fields and date-palm orchard.
General distribution: Eastern and Central Europe (Bretfeld 1999) and Iran.
description: Published as part of Mayvan, Mahmood Mehrafrooz, Greenslade, Penelope & Sadeghi-Namaghi, Hussein, 2023, An annotated checklist of the Collembola (Hexapoda) from Iran, pp. 1-101 in Zootaxa 5275 (1) on page 59, DOI: 10.11646/zootaxa.5275.1.1, http://zenodo.org/record/7898948
MOESM2 of Darwin Day in deep time: promoting evolutionary science through paleontology
Creators: name: Sheffield, Sarah
name: Bauer, Jennifer
Publisher: name: Figshare
Year: 2017
Subjects: subject: Molecular Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy

description: Additional file 2. Sample letter sent to various departments on UT campus to request funding for Darwin Day events.
Lipothrix lubbocki
Creators: name: Mayvan, Mahmood Mehrafrooz
name: Greenslade, Penelope
name: Sadeghi-Namaghi, Hussein
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Collembola
Symphypleona
Sminthuridae
Lipothrix
Lipothrix lubbocki

description: Lipothrix lubbocki (Tullberg, 1872)
– Sminthurus lubbocki Tullberg, 1872: 33.
MAZ: Mehrafrooz Mayvan et al. 2015a; Yahyapour et al. 2019.
Ecology and habitat in Iran: soil and leaf litter in forest.
General distribution: Palaearctic (Fjellberg 2007; Bendjaballah et al. 2018).
Genus Neosminthurus Mills, 1934
description: Published as part of Mayvan, Mahmood Mehrafrooz, Greenslade, Penelope & Sadeghi-Namaghi, Hussein, 2023, An annotated checklist of the Collembola (Hexapoda) from Iran, pp. 1-101 in Zootaxa 5275 (1) on page 60, DOI: 10.11646/zootaxa.5275.1.1, http://zenodo.org/record/7898948
Abiliella galbina Opitz 2016
Creators: name: Groll, Elisa Von
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Cleridae
Abiliella
Abiliella galbina

description: Abiliella galbina Opitz, 2016
Opitz, 2016:157, figs 3, 14, 18–25, 28, 35, 39, 40.
Holotype ♂, BRAZIL, Santa Catarina: Imbituba (Praia do Rosa), 01.I.2001, R. Araujo coll. (MCNZ). Paratypes: 1 specimen, BRAZIL, Santa Catarina: Imbituba (Praia do Rosa), 01.I.2001 (MCNZ); 1 specimen, BRASIL, Santa Catarina: Praia do Rosa, 28–30.XII.2001 (MCNZ).
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 460, DOI: 10.11646/zootaxa.4318.3.2, http://zenodo.org/record/887750
Development of redox-neutral reaction cascades for amine functionalization and synthesis of bimetallic bisoxazoline complexes
Creators: name: Das, Deepankar
Publisher: name: No Publisher Supplied
Year: 2013

description: Activation of moderately reactive C‒H bonds by metal-catalyzed processes has attracted lot of attention because it can give access to complex structures from simple starting materials. Outlined within this dissertation are our efforts to develop alternative redox-neutral approaches for functionalization of relatively unreactive C‒H bonds without requiring the use of expensive metal catalysts, oxidants or other additives. Unique reactivity patterns of in situ formed azomethine ylides for non-pericyclic annulation reactions with pendant nucleophiles were studied. We were able to establish that the redox isomerization from an external iminium ion to an internal iminium ion proceeds through the intermediacy of azomethine ylides. The challenges are summarized and the work was further expanded to the direct, redox-neutral, three-component amine α-alkynylation and α-phosphonation. This approach offers an expeditious route to synthetically and pharmacologically useful building blocks.    Design and synthesis of bimetallic complexes of chiral bisoxazoline ligands was also undertaken for use in asymmetric transformations. These complexes can potentially chelate a single functional group by binding to two metal centers and could result in a higher degree of activation of the substrate.
A theory of laws of nature, dispositions, and chances
Creators: name: Demarest, Heather
Publisher: name: No Publisher Supplied
Year: 2013

description: What are the fundamental properties of the world? What is chance? What are the laws of nature? These questions may seem isolated, but in my dissertation, A Theory of Laws, Dispositions, and Chances, I show how they are connected by developing a new account that unifies traditionally disparate elements. I defend the anti-Humean claim that there are some fundamental, modal features in the world—such as chance and dispositional properties. But, I also defend the Humean claim that the laws of nature merely describe the world, rather than govern it.    According to my view, which I call the Propensity Best System Account (PBSA), some of the fundamental properties are dispositional—these properties are called potencies if they are deterministic, and propensities if they are chancy. And the laws of nature systematize all of the possible distributions of those properties. The PBSA provides a new way of interpreting a probability measure over all of the possible initial states of the universe: as a fundamental chance that grounds all subsequent chances.    I argue that the PBSA accords well with scientific practice. Laws that systematize the distribution of properties suit the importance scientists place on simplicity and informativeness when they describe the regularities in the world. Potencies and propensities, which are necessarily connected to the behavior of the entities that instantiate them, are faithful to the scientific principle that the best way to learn about a system is by studying its characteristic behavior in different (stimulus) conditions.    The PBSA avoids many of the serious objections that face traditional, best system accounts of the laws of nature and chance. For instance, the PBSA yields the right results for the laws of nature in both simple worlds and in improbable worlds. I argue that the PBSA is a promising theory of chance whether the dynamical laws of nature are deterministic or probabilistic and it can be formulated for consistency with classical mechanics or for consistency with quantum mechanics.
The Latinization of Orlando
Creators: name: Delerme, Simone Pierre
Publisher: name: No Publisher Supplied
Year: 2013

description: Taking into consideration the South’s historically powerful racial binary, this project examines the Hispanic migration to Central Florida, and the ways that race and class based identities and distinctions are formulated and experienced in new destinations of Hispanic migration. Based on two years of ethnographic fieldwork, this project combines traditional anthropological methodologies with innovative textual analysis to interweave data gathered through participant observation, informal and semi-structured interviews, archival research, census data, and new media. Organized into seven thematic chapters, this dissertation addresses: Hispanic migration, community development, and homeownership; language ideologies and racialization; and social class formation and distinctions.
Profundiconus teramachii
Creators: name: Tenorio, Manuel J.
name: Puillandre, Nicolas
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Mollusca
Gastropoda
Neogastropoda
Conidae
Profundiconus
Profundiconus teramachii

description: Profundiconus cf. teramachii (Kuroda, 1956)
Fig. 16C–H, M
Asprella (Endemoconus) teramachii Kuroda, 1956: 8, pl. 1 fig. 4.
Conus teramachii – R̂ckel et al. 1995b: 145, pl. 26 fig. 1.
Profundiconus teramachii – Tucker & Tenorio 2013: 391. — Monnier et al. 2018a: 137.
Material examined
2 lots (2 specimens). See Supp. file 1.
Type material
Holotype JAPAN • 115 mm; Tosa; ca 914 m depth; THTA.
Figured material
NEW CALEDONIA • 89.3 mm; Plateau des Chesterfield, off New Caledonia, stn CP364; 19º45′ S, 158º47′ E; 675 m depth; 19 Oct. 1986; MUSORSTOM 5 expedition; MNHN (Fig. 16C–D) • 72.4 mm; Vanuatu, off New Caledonia, stn CP992; 18º52′ S, 168º55′ E; 748‒775 m depth; 24 Sep. 1994; MUSORSTOM 8 expedition; MNHN (Fig. 16E–F) • 67.5 mm; Loyalty Islands (Fig. 16M).
Geographical distribution and bathymetry
Japan to Taiwan, Melanesia (Papua New Guinea and Solomon Islands), N of New Zealand (Wanganella Bank, Raoul Island, Kiwi Seamount), Queensland, Coral Sea (Lansdowne Bank), Vanuatu, Fiji, typically at depths between 250 and 800 m. Some specimens collected by the Valdivia during the Deutsche Tiefsee-Expedition came from depths as great as 1134 m (R̂ckel et al. 1995b). The conspecificity of the populations from New Zealand (Marshall 1981) and New Caledonia, and possibly Fiji (Moolenbeek et al. 2008), with the nominal taxon is doubtful.
Remarks
Shell moderately large to large (it may attain lengths beyond 120 mm). Protoconch multispiral. The radular tooth of P. teramachii and P. cf. teramachii (Fig. 16M) is morphologically similar to that of P. puillandrei (Fig. 12M). Only two specimens of P. cf. teramachii were obtained, one from Plateau des Chesterfield (Fig. 16C–D), and another from off Vanuatu (Fig. 16E–F). These specimens exhibit a high, turriculated spire, with nodules crossed by several strong spiral cords, and are similar to specimens from Wanganella Bank in New Zealand (Fig. 16G–H). Many specimens of P. teramachii from Papua New Guinea, Solomon Islands (Fig.16B) and Taiwan (Fig. 16A) have been sequenced but no individuals from New Caledonia or New Zealand were present in the sample. After many years of sampling in deep water around New Caledonia, very few specimens of these teramachii -like individuals have been collected, indicative of the scarcity of this species in the surveyed areas. The conspecificity of the populations from New Caledonia and New Zealand with the taxon P. teramachii needs to be confirmed using DNA studies. Nodulose specimens of P. puillandrei (i.e., Fig. 12H) might be misidentified as P. cf. teramachii.
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 24-26, DOI: 10.5852/ejt.2023.896.2291, http://zenodo.org/record/8405510
Applications of the 4 mm dynamic shear rheometer geometry for the forensic evaluation of bituminous materials
Creators: name: Derewecki, Kristen E.
Publisher: name: No Publisher Supplied
Year: 2013

description: The current asphalt binder performance grading system requires the use of multiple pieces of testing equipment to determine high, intermediate and low temperature properties.  To properly grade an asphalt binder, numerous hours of labor must be expended to run through all of the required aging and testing.  Additionally when creating master curves to compare stiffness and phase angle with respect to frequency, multiple pieces of equipment are required.  This not only creates inefficiencies with respect to time and money, but also brings an approximation into the data as opposed to a direct reading.  In order to forensically evaluate asphalt binders, the asphalt must be extracted and recovered from roadway cores.  During the extraction/ recovery process the amount of binder required results in coring a considerable amount of the road in question as well as running through an expensive and time consuming chemically intensive process to extract the bituminous material.  This paper investigates the potential of the 4 mm Dynamic Shear Rheometer geometry and its potential applications in evaluating binder properties for all failure mechanisms without the need for additional equipment and reducing the amount of asphalt required.