cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Macrobiotus harmsworthi Murray 1907
Creators: name: Guil, Noemí
Publisher: name: Zenodo
Year: 2008
Subjects: Biodiversity
Taxonomy
Animalia
Tardigrada
Eutardigrada
Parachela
Macrobiotidae
Macrobiotus
Macrobiotus harmsworthi

description: Macrobiotus harmsworthi Murray 1907
This species is differentiated from Macrobiotus richtersi by having a larger microplacoid which is located a shorter distance from the third macroplacoid. The anterior band of teeth of the buccal armature (several rows of small teeth at the anterior band, one row of teeth at the posterior band, and a transversal crest system) was weak in the majority of the specimens examined (90%), and was often not visible. Two types of lunule margins were observed on the double-claws at the fourth pair of legs: irregular (only two specimens, possibly old ones, accordingly to Ramazzotti & Maucci 1983) or smooth (49 specimens). Two eggs were studied with conic-shaped structures, and reticulated egg surface. Ocular spots were observed in 4% of specimens, 90% had no ocular spots (in 6% it was not possible to determine their presence or absence). Mean body size was 589 μm (SD 124), range 330 to 880 μm. This species is considered cosmopolitan (McInnes 1994). In the Iberian Peninsula, it has been recorded for Spain (Rodríguez Roda 1951, 1952; Mihelčič 1954; Maucci & Durante Pasa 1984), Andorra (Maucci & Durante Pasa 1984) and Portugal (Fontoura 1981; Maucci & Durante Pasa 1984, 1985). Macrobiotus harmsworthi was found at 11 sampling points (Table 3) in MR and LF samples.
description: Published as part of Guil, Noemí, 2008, New records and within-species variability of Iberian tardigrades (Tardigrada), with comments on the species from the Echiniscus blumi-canadensis series, pp. 1-30 in Zootaxa 1757 on page 20, DOI: 10.5281/zenodo.181845
Additional file 8: Table S5. of Persistence, impacts and environmental drivers of covert infections in invertebrate hosts
Creators: name: InĂŞs Fontes
name: Hartikainen, Hanna
name: Williams, Chris
name: Okamura, Beth
Publisher: name: Figshare
Year: 2017
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Colony infection intensity. (DOCX 13Â kb)
Macrobiotis hystricogenitus Maucci 1978
Creators: name: Guil, Noemí
Publisher: name: Zenodo
Year: 2008
Subjects: Biodiversity
Taxonomy
Animalia
Tardigrada
Eutardigrada
Parachela
Macrobiotidae
Macrobiotis
Macrobiotis hystricogenitus

description: Macrobiotis cf. hystricogenitus Maucci 1978
Smooth cuticle with a fine dot sculpture in the ventral region. Weak buccal armature, showing only a transverse crest system, was observed in the 13 specimens found. Two rod-shaped macroplacoids and a large microplacoid were present within the pharyngeal bulb; first macroplacoid two times as long as the second macroplacoid, and with median constriction. Double-claws with long common tract, short secondary branch inserted to the main branch in a right angle and big lunules, which had smooth margins in the three first pairs of legs (Fig. 7 A), and big teeth in the fourth pair of legs. All seven specimens from spring collection (found in leaf litter, Retama sphaerocarpa) showed hystricogenitus double-claws with an additional spur inserted at the same level as the secondary branch (arrows in Fig.7 B); I have considered these specimens as Macrobiotus hystricogenitus since the rest of the morphology corresponded to this species. This additional spur could be considered as particular alterations because they were present only in some legs and with no pattern. Ocular spots were observed in nine specimens, and were not present in four specimens. Mean body size was 886 μm (SD 211), range 550 to 1210 μm. This species has been cited for Europe and Asia. It is the first time the species is recorded for the Iberian Peninsula (Table 2). Macrobiotus hystricogenitus was found only at one site (Table 3), in autumn and in spring.
description: Published as part of Guil, Noemí, 2008, New records and within-species variability of Iberian tardigrades (Tardigrada), with comments on the species from the Echiniscus blumi-canadensis series, pp. 1-30 in Zootaxa 1757 on page 22, DOI: 10.5281/zenodo.181845
Additional file 13: Figure S6. 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: Microbiology
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Primer alignment study of the most common bacterial taxa found in ELBW (P29F). a Representation of primers used in this study along the 16S bacterial rRNA gene. b Primer alignment study using 16S rRNA gene from Bifidobacterium bifidum CP 010412 (isolated from Infloran) and the most common bacterial taxa found in an ELBW infant (P29F) with supplementation (Staphylococcus epidermis NR_074995, Enterobacter cloacae CP012165 and Enterococcus faecalis CP014949). We also included two strains of Bifidobacterium as control samples (B.infantis M58738.1 and B.longum ATCC 156697) All sequences are represented in 5′-3’orientation using UPAC nucleotide code, where Y = C or T, R = A or G, K = G or T, M = A or C (PDF 299 kb)
Macrobiotus macrocalix Bertolani & Rebecchi 1993
Creators: name: Guil, Noemí
Publisher: name: Zenodo
Year: 2008
Subjects: Biodiversity
Taxonomy
Animalia
Tardigrada
Eutardigrada
Parachela
Macrobiotidae
Macrobiotus
Macrobiotus macrocalix

description: Macrobiotus macrocalix Bertolani & Rebecchi 1993
A total of 116 specimens and 106 eggs were isolated from MR samples. This species, belonging to the hufelandi group, showed animals and eggs morphologies as in the original description (Bertolani & Rebecchi 1993). Some specimens showed weak buccal armature with a clearly visible transverse crest system yet powerless anterior and posterior bands of teeth. Smooth or irregular lunule margins in the double-claws at the fourth pair of legs. Ocular spots were in 40% of the total specimens, while in 60% it was not possible to determine their presence or absence. Body size range was 242 to 1012 μm, mean 568 μm (SD 165). This species has been cited only for Europe. This is the first time it has been found in the Iberian Peninsula (Table 2). Macrobiotus macrocalix was observed at seven sampling points (Table 3).
description: Published as part of Guil, Noemí, 2008, New records and within-species variability of Iberian tardigrades (Tardigrada), with comments on the species from the Echiniscus blumi-canadensis series, pp. 1-30 in Zootaxa 1757 on page 22, DOI: 10.5281/zenodo.181845
Numerical methods for probabilistic constrained optimization problem where random variables have degenerate continuous distribution
Creators: name: Myndyuk, Olga
Publisher: name: No Publisher Supplied
Year: 2016

description: Several probabilistic constrained problems (single commodity stochastic network design  problem and water reservoir problem) are formulated and solved by use of different numerical  methods. The distribution considered are degenerate normal and uniform distributions.  The network design problem is to find optimal node and arc capacities under some deterministic  and probabilistic constraints that ensure the satisfiability of all demands on a  given probability level. The large number of feasibility inequalities is reduced to a much  smaller number of them and an equivalent reformulation takes us to a specially structured  semi-infinite LP. This, in turn, is solved by a combination of inner and outer algorithms  providing us with both lower and upper bounds for the optimum at each iteration. The flood control and serially linked reservoir network design with consecutive k-out-of-n type  reliability problems are formulated, simplified and solved. Alternative, derivative-free methods,  are proposed and implemented. Various numerical examples are presented and solution  methods software library is developed.
Orexita speculata
Creators: name: Sekerka, Lukáš
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Chrysomelidae
Orexita
Orexita speculata

description: Orexita speculata (Boheman, 1862)
Coptocycla speculata Boheman, 1862: 390 (original description).
Orexita plagipennis Spaeth, 1911: 257 (original description), syn. nov.
Type localities. Coptocycla speculata: ‘ Ega ad fluvium Amazonum’ [= Brazil, Amazonas, Tefé]; Orexita plagipennis: ‘Columbia’.
Type material examined. Coptocycla speculata: HOLOTYPE: pinned (teneral specimen), ‘Type [w, p, s, c, rf] || Ega. [hw] | Bates [hw] | Baly Coll. | 1905—54. [w, p, cb] || Coptocycla | speculata | Boh | Ega, Upper Amazons [w, hw by Baly, cb] || Named by | Boheman | Type | Coll Bates | 97 [hw by Baly on underside of preceding label]’ (BMNH).
Orexita plagipennis: SYNTYPE (MMUE). [Examined but label data not recorded].
Remarks. SPAETH (1911) transferred C. speculata to Orexita but noted that it was unknown to him. Orexita speculata was so far known only from a single and partially scletotized specimen. It is characterised by coarse and sparse punctation of elytra extending on explanate margin and colouration very similar to O. tripartita (Champion, 1894). However, it has a stouter body like O. plagipennis and in my opinion it is conspecific with the latter as both differ only in colouration.
SPAETH (1911) stated that O. plagipennis is closest to O. wagneri but differs in 1) colouration as it is mostly black with yellow anterior margin of pronotum and red oval spot situated around midlength of explanate margin of each elytron; 2) significantly larger size; 3) less rounded anterior margin of the pronotum; 4) smaller and not fully rectangular basal corners of the pronotum; and 5) broader, in proportion to its width shorter pronotum. All these characters, except of the colouration, are identical to O. speculata and hence I synonymize it with the latter species. On the other hand the differences between O. plagipennis and O. wagneri are rather minor and might easily be subject to intraspecific variability. However, I retain O. speciosa (= O. plagipennis) as a valid taxon until I obtain more material for comparative purposes. See additional comments under O. wagneri.
Distribution. Brazil: Amazonas (BOHEMAN 1862), Colombia (SPAETH 1911), and Peru: Loreto (BOROWIEC & TAKIZAWA 2011).
description: Published as part of Sekerka, Lukáš, 2016, Taxonomic and nomenclatural changes in Cassidinae (Coleoptera: Chrysomelidae), pp. 275-344 in Acta Entomologica Musei Nationalis Pragae 56 (1) on pages 314-315, DOI: 10.5281/zenodo.5305725
Additional file 14: Figure S7. 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: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: PCR amplification using primers 530F-926R on 8 Bifidobacterium strains. PCR amplification targeting the bacterial 16S rRNA gene using primers 530F-926R on Bifidobacterium collection strains. DNA extracted from B. bifidum (isolated from the commercial probiotic supplementation) and seven different Bifidobacterium NCIMB collection strains, was amplified using primers 530F-926R. Positive controls for this study were a faecal metagenomic sample and a L. acidophilus strain (isolated from the probiotic supplementation). Pure water was used as negative control. Amplicon samples were run on 1% agarose gel for 30Â min at 100Â V. DNA was visualised under UV light after staining with ethidium bromide. All tested samples gave a PCR product. (PDF 351Â kb)
Queer disruptions
Creators: name: Moussawi, Ghassan
Publisher: name: No Publisher Supplied
Year: 2016

description: My dissertation addresses the changing historical meanings of sexual practices and identities, and the effects of political turmoil and conflict on the experiences of LGBTQ individuals in post-war Beirut. Drawing on ethnographic observations, life history interviews and content analysis, I rethink how claims of modernity and progress operate by focusing on queer sexualities in Beirut since the year 2005. Dominant Euro-American understandings of coming out and LGBTQ visibility are often used as indicators of non-Western societies’ modernity and progress. My work complicates this stance, illustrating how queer lives in Beirut unsettle and disrupt binaries of visibility/invisibility and tradition/progress. In addition, I show how dominant narratives of modernity view the emergence of “gay rights” in the Middle East as a marker of progress, without taking into account local exclusionary practices. I examine public discourses, personal narratives, and collective organizing strategies in a number of different contexts.  Unlike much research that focuses on how sexuality emerges as the most salient marker of difference in LGBT people’s personal narratives, my research illustrates that LGBT individuals in Beirut emphasize how gender, class, and sectarian identities act as their primary modes of visible self-making. Rather than treating queer visibility as a hallmark of progress, individuals devise strategies of visibility such as creating and living in what they refer to as “imagined bubbles.” Queer Beirutis’ strategies vary across different family and social contexts and are shaped by political turmoil, regional instability, and sectarian conflict. Using a feminist intersectional lens, I highlight how various queer social circles contest, yet unwittingly reproduce, the exclusionary practices of Beirut’s cosmopolitanism that sideline gender-nonnormative and transgender persons, as well as migrant workers and refugees. Marginalized queer Beirutis, particularly working-class and gender-nonconforming individuals, question Beirut’s cosmopolitanism and carve out new understandings of queer visibilities that challenge dominant understandings of modernity and progress.
Additional file 15: Figure S8. 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: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Infectious Diseases
subject: FOS: Health sciences

description: Melting curves of PCR amplicons from probiotic strains and bacterial preterm isolates. a Melting curves of PCR amplicons from probiotic strains (Bifidobacterium bifidum and Lactobacillus acidophilus) and bacterial preterm isolates (Enterococcus faecium and Streptococcus infantarius). Primers used to generate these amplicons were 530F-926R targeting region (V4 + V5). Bifidobacterium bifidum displayed the highest melting temperature. b Melting curve of PCR amplicon obtained from a mixed DNA sample (5 ng of Bifidobacterium bifidum, 5 ng of Lactobacillus acidophilus, 5 ng of Enterococcus faecium and 5 ng of Streptococcus infantarius). Primers used to generate these amplicons were 530F-926R targeting region (V4 + V5). Peak name (2) presents a melting temperature (Tm) similar to the melting temperature (Tm) obtained for B. bifidum. (PDF 100 kb)
"With a publick spirit"
Creators: name: Morgan Smith, Sarah Augusta
Publisher: name: No Publisher Supplied
Year: 2016

description: “With a Publick Spirit”: Community and Commitment in New England, 1630-1689 engages in a critical analysis of the core principles of New England’s civic identity from its founding through roughly the first two and a half generations of political development. It explores the complex relationship between the problem of sustaining revolutionary founding commitments and the concept of civic education as character formation in seventeenth century New England. The subject presents the opportunity to study the critical intersection of theory and practice and argues that these early decades were crucial for the establishment of a particularly American concept of civic formation, and thus, for the development of American political thought on the nature of citizenship.    At the heart of the project is a reflection on the civic virtues necessary for founding and maintaining a political society, the ways that they can be encouraged through civic institutions such as schools and legal systems, and the potential dangers when such virtues are either deficient or carried to excess by the citizenry. I argue that the April Revolution in Boston of 1689 demonstrates that the Puritans were successful in transferring their founding commitments to subsequent generations, and that this success stemmed from their utilization of an approach to civic formation that emphasized the importance of civic knowledge and virtue as prerequisite to civic engagement.     The problem of Puritan New England is very much an American problem, and in the conclusion, I argue that the Puritan approach to civic formation recurs in the history of American political thought in ways that have proven particularly useful when the nation’s founding principles seemed most threatened. In contrast, I point to the inadequacies of two major strains of the thought within the American tradition that diverge from the Puritan model of civic formation to successfully perpetuate the commitments of the national founding. Finally, I suggest some of the ways in which an adaptation of the Puritan mode of civic education may be useful for shaping present-day debates about civic education.
Additional file 17: Figure S10. 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: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Physiology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: Shotgun functional profiles from two ELBW infants with /without supplementation and a term infant. Radial tree displaying shotgun functional profiles from an ELBW infant with no supplementation (sample AP8C, represented by the number 2 in the figure) an ELBW infant with supplementation (sample P29F, represented by the number 3 in the figure) and a term baby sample (sample V3Â J, represented by the number 1 in the figure). Functional analysis was performed using the KEGG pathway analysis. (PDF 126Â kb)
Additional file 14: Figure S7. 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: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences

description: PCR amplification using primers 530F-926R on 8 Bifidobacterium strains. PCR amplification targeting the bacterial 16S rRNA gene using primers 530F-926R on Bifidobacterium collection strains. DNA extracted from B. bifidum (isolated from the commercial probiotic supplementation) and seven different Bifidobacterium NCIMB collection strains, was amplified using primers 530F-926R. Positive controls for this study were a faecal metagenomic sample and a L. acidophilus strain (isolated from the probiotic supplementation). Pure water was used as negative control. Amplicon samples were run on 1% agarose gel for 30Â min at 100Â V. DNA was visualised under UV light after staining with ethidium bromide. All tested samples gave a PCR product. (PDF 351Â kb)
Macrobiotus pallarii Maucci 1954
Creators: name: Guil, Noemí
Publisher: name: Zenodo
Year: 2008
Subjects: Biodiversity
Taxonomy
Animalia
Tardigrada
Eutardigrada
Parachela
Macrobiotidae
Macrobiotus
Macrobiotus pallarii

description: Macrobiotus pallarii Maucci 1954
I have collected 191 specimens and 30 eggs from all habitats but MT. Cuticle showed very small pores, sometimes difficult to observe. Animal and egg morphologies corresponded to descriptions in Ramazzotti & Maucci (1983). Lunules on the fourth pair of legs had teeth in one-third of the populations. I found between 14 and 26 processes per egg and between 6 and 12 polygonal areas at the base of each process. Body size ranged from 330 to 1342 μm, mean 723 μm (SD 193). The species has been cited for Europe, Asia and America. In the Iberian Peninsula, it has been recorded for Spain (Lewin Osorio 1984). Macrobiotus pallarii was found at 30 sampling points (Table 3).
description: Published as part of Guil, Noemí, 2008, New records and within-species variability of Iberian tardigrades (Tardigrada), with comments on the species from the Echiniscus blumi-canadensis series, pp. 1-30 in Zootaxa 1757 on page 23, DOI: 10.5281/zenodo.181845
Macrobiotus persimilis Binda & Pilato 1972
Creators: name: Guil, Noemí
Publisher: name: Zenodo
Year: 2008
Subjects: Biodiversity
Taxonomy
Animalia
Tardigrada
Eutardigrada
Parachela
Macrobiotidae
Macrobiotus
Macrobiotus persimilis

description: Macrobiotus persimilis Binda & Pilato 1972
This species showed cuticle with pores. The anterior band of teeth was not visible in all specimens; however, the posterior band of teeth and the transverse crest system were strong. This species, from the hufelandi group, had a small microplacoid. Lunules on the fourth pair of legs had such small teeth that in some specimens they appeared as irregular margins. I have found 16 animals and 3 eggs (in two out if three samples) only in MR samples, however four specimens from the sample without eggs had exactly the same morphology as the other Macrobiotus persimilis found. In this case, the specimens from site 31 (Table 3) should be named as Macrobiotus cf. persimilis. Eleven specimens had ocular spots while it was not possible to determine their presence or absence in five animals. Mean body size was 815 μm (SD 305), range 418 to 1375 μm. The species has been cited for Europe, Asia, America, Africa and Oceania. In the Iberian Peninsula, it has been recorded for Portugal (Maucci & Durante Pasa 1985) and Spain (Maucci & Durante Pasa 1984), but this is the first time to be found in Madrid (Table 2). Macrobiotus persimilis was collected at three sampling points (Table 3).
description: Published as part of Guil, Noemí, 2008, New records and within-species variability of Iberian tardigrades (Tardigrada), with comments on the species from the Echiniscus blumi-canadensis series, pp. 1-30 in Zootaxa 1757 on page 23, DOI: 10.5281/zenodo.181845
Additional file 16: Figure S9. 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: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Comparison of bacterial profiles analysed by shotgun and 16S rRNA gene sequencing data using QIIME pipeline. Normalised data and relative abundance of the bacterial taxa was represented in percentages of number of reads. Bar colours represent different genus taxa, and bar lengths signify the relative abundance of each taxon. 16S rRNA bacterial profiles are named according to the different 16S rRNA hypervariable region amplified: (i) (V1 + V2 + V3, primers 27F-519R), (ii) (V4 + V5, primers 530F-926R) and (iii) (V6 + V7 + V8, primers 926F-1394R). a Bacterial community profiles determined by shotgun and 16S rRNA gene sequencing from an ELBW infant (sample AP8C) with no supplementation. b Bacterial community profiles determined by shotgun and 16S rRNA gene sequencing from an ELBW infant (sample P29F) with supplementation. c Bacterial community profiles determined by shotgun and 16S rRNA gene sequencing from a term baby (sample V3 J). More detailed information on the number of reads obtained by shotgun and 16S rRNA gene sequencing data can be found in Additional file 20. (PDF 36 kb)
Additional file 18: Figure S11. 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: 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: Inorganic Chemistry
subject: 111714 Mental Health
subject: FOS: Health sciences

description: PCoA plots based on 16S rRNA gene sequencing and shotgun data. a PCoA based on 16S rRNA gene sequencing data analysed using PE protocol. b PCoA based on 16S rRNA gene sequencing data analysed using QIIME. Blue circles represent sequencing data of preterm without supplementation (AP8C), yellow circles data of preterm with supplementation (P29F), and green circles data of term baby (V3 J). Each sample was analysed using three different 16S rRNA gene libraries (.27F, targets region (V1 + V2 + V3), .530F targets region (V4 + V5), and .926F targets region (V6 + V7 + V8)). Samples ended with (_shotgun) represents shotgun data used as ‘gold standard’ in this study. Samples from region (V4 + V5) presented the most distinct distribution when compared with shotgun data. More details of primers used for preparing these 16S rRNA libraries can be found in Methods section. (PDF 76 kb)
Noninvasive aortic pressure derivation from peripheral arterial sites
Creators: name: Mohan, Priya
Publisher: name: No Publisher Supplied
Year: 2016

description: In the United States approximately 73 million people 20 and older, i.e. 1 in every 3 person, suffer from high blood pressure. Hypertensive subjects have significantly increased stiffness in their arteries, making it harder for blood to flow through.  Anti-hypertensive drugs such as beta blockers and calcium channel blockers are used for their treatment with the aim to lower blood pressure through reducing vascular stiffness or increasing arterial compliance. The efficacy of the drugs’ effects on each patient cannot be accurately determined by the commonly used blood pressure cuff, which provides just systolic and diastolic pressures. In order to accurately diagnose certain severe cases of cardiovascular disorders, invasive and costly catheterization is performed. This thesis develops a model-based noninvasive diagnostic technique for personalized treatment. The methodology utilizes noninvasively measured peripheral artery pulse waveforms as an input to a transfer function in order to compute central aortic pressure waveforms. This is because aortic pressure cannot be obtained directly by noninvasive means and large vessel compliance or stiffness is critical in determining proper function and treatment of hypertensive patients. A cardiovascular system model allows critical parameters, such as large artery compliance and blood pressure augmentation index, to be readily computed.  Many research groups have attempted to produce the aortic waveform noninvasively, while some have succeeded, most of the existent models have flaws which limit the accuracy of the synthesized waveforms. Therapeutic drug efficacy can be easily monitored at regular intervals through this new model-based noninvasive hypertension evaluation system. This project also evaluates the preferred site for noninvasive blood pressure measurements such as radial artery, carotid artery and femoral artery through comparison of their respective transfer functions. Evaluating the physiological advantages of the various peripheral arterial sites for noninvasive blood pressure measurements, radial arterial sites seems to be ideal as it provides best stability during tonometry due to its anatomical advantage of bone packing in the area and increased accessibility compared to other sites such as carotid and femoral. The scope of the thesis limits direct comparison of noninvasively derived with directly invasively measured aortic pressure waveform. Future testing of this step will allow the eventual system to have many advantages, in that it is noninvasive, accurate and low-cost, and affords personalized care for hypertensive patients.
Targeting the PI3K/Akt/mTOR pathway in traumatic brain injury and developmental disease
Creators: name: Nikolaeva, Ina
Publisher: name: No Publisher Supplied
Year: 2016

description: The PI3K/Akt/mTOR signaling pathway mediates many aspects of cell growth and regeneration. Dysregulation of the pathway during development or following injury can lead to severe symptoms, including behavioral disorders, intellectual disability and seizures. We investigated the effects of excess PI3K/Akt/mTOR signaling in the mouse brain during embryonic development and following traumatic brain injury; we then tested out known inhibitors of the pathway for their potential to prevent or reverse the resulting damage. Here, we described the time course and cell specificity of mTORC1 signal activation in the mouse hippocampus after moderate controlled cortical impact (CCI), and identified an early neuronal peak of activity that occurs within few hours after injury. We suppressed this peak activity by a single injection of the mTORC1 inhibitor rapamycin one hour after CCI, and showed that this acute treatment significantly diminishes the extent of neuronal death and astrogliosis within 24 hours after injury. We investigated two other suppressor compounds of the pathway, mTORC1 inhibitor RAD001 and Akt inhibitor MK-2206, in an in vitro mouse model of excess developmental PI3K/Akt/mTOR activity; increased signaling in this pathway is associated with multiple brain overgrowth disorders in humans. We used excitatory neuron-specific gene deletion of the PI3K antagonist Pten as a method for disinhibiting the pathway. We established Pten-mutant forebrain neuronal cultures as an in vitro model of brain overgrowth that may facilitate the identification of pharmacological treatments. We found that Pten-mutant neurons exhibit dramatic cellular hypertrophy, including increased soma size and dendrite complexity, which can be reversed partially with mTORC1 inhibitor RAD001 and fully with Akt inhibitor MK-2206. Our findings suggest that acute Akt and mTORC1 inhibition may offer viable therapeutic approaches for preventing or reversing pathologies caused by excess PI3K/Akt/mTOR signaling, both in the developing and healing brain.
Additional file 19: 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: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Computational Biology

description: Number of reads detected by PE and QIIME pipelines for the different hypervariable regions. (PDF 181Â kb)
Additional file 20: 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: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Number of reads shotgun and 16S rRNA data (PE versus QIIME). (PDF 286Â kb)
Moduli of Bridgeland stable objects on an Enriques surface
Creators: name: Nuer, Howard J.
Publisher: name: No Publisher Supplied
Year: 2016

description: We construct projective moduli spaces of semistable objects on an Enriques surface for generic Bridgeland stability condition. On the way, we prove the non-emptiness of $M_{H,Y}^s(v)$, the moduli space of Gieseker stable sheaves on an Enriques surface $Y$ with Mukai vector $v$ of positive rank with respect to a generic polarization $H$. In the case of a primitive Mukai vector on an unnodal Enriques surface, i.e. one containing no smooth rational curves, we prove irreducibility of $M_{H,Y}(v)$ as well. Using Bayer and Macr`{i}'s construction of a natural nef divisor associated to a stability condition, we explore the relation between wall-crossing in the stability manifold and the minimal model program for Bridgeland moduli spaces. We give three applications of our machinery to obtain new information about the classical moduli spaces of Gieseker-stable sheaves:    1) We obtain a region in the ample cone of the moduli space of Gieseker-stable sheaves over Enriques surfaces.    2) We determine the nef cone of the Hilbert scheme of $n$ points on an unnodal Enriques surface in terms of its half-pencils and the Cossec-Dolgachev $phi$-function.    3) We recover some classical results on linear systems on unnodal Enriques surfaces and obtain some new ones about $n$-very ample line bundles.
Aerosol liquid water
Creators: name: Nguyen, Thien Khoi V.
Publisher: name: No Publisher Supplied
Year: 2016

description: Particle-phase liquid water is a ubiquitous and abundant component of atmospheric aerosols and influences hydrological cycling, fate and transport of trace species, visibility, human health, and regional climate. Aerosol water mass concentrations are functions of relative humidity (RH), temperature, and aerosol concentration and composition. Previous studies focused on inorganic species, and their relationships to particle hygroscopicity are included in atmospheric models. But there is a dearth of field studies and related ambient information pertaining to water modulation by organic compounds and vice versa. The extent to which water facilitates transfer of biogenically derived carbon from the gas to particle phase to form secondary organic aerosol (SOA), which contributes to the fine particle matter (PM2.5) burden, is poorly constrained. My dissertation aims to 1) better understand the chemical and thermodynamic controls on aerosol water in the Southeast U.S., an area known to contain high concentrations of SOA, through instrument development and field measurements, 2) quantify the temporal, spatial, and aloft trends in aerosol water through observational estimates, and 3) reconcile discrepancies between existing surface and satellite measurements of PM across the continental U.S. using aerosol water. My field measurements of aerosol water found a minimum of 7% water in particles by volume and a diel cycle in water content controlled, in part, by aerosol hygroscopicity, that ranged from 1-5 µg m-3. Next, semi-observational estimates of aerosol water by an inorganic thermodynamic model discovered that aerosol water mass has decreased in the Southeast by 79% between 2001-2012. Similar reductions of biogenically derived SOA mass in the area are consistent with an aerosol water-mediated mechanism and the correlation in water and SOA mass is statistically robust. Finally, estimates of aerosol water across the continental U.S. yield seasonal differences that were highest in the Southeast and modulated by aerosol chemistry and not RH. Near surface trends in aerosol water are qualitatively similar to space-based aerosol optical thickness measurements and potentially resolve surface and satellite PM measurements. Ultimately, this work contributes to improving our understanding of the connections among aerosol water, biogenic and anthropogenic emissions, and biogenic SOA formed in the presence of anthropogenic perturbations.
Additional file 17: Figure S10. 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: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Physiology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences

description: Shotgun functional profiles from two ELBW infants with /without supplementation and a term infant. Radial tree displaying shotgun functional profiles from an ELBW infant with no supplementation (sample AP8C, represented by the number 2 in the figure) an ELBW infant with supplementation (sample P29F, represented by the number 3 in the figure) and a term baby sample (sample V3Â J, represented by the number 1 in the figure). Functional analysis was performed using the KEGG pathway analysis. (PDF 126Â kb)
Macrobiotus recens Cuenot 1932
Creators: name: Guil, Noemí
Publisher: name: Zenodo
Year: 2008
Subjects: Biodiversity
Taxonomy
Animalia
Tardigrada
Eutardigrada
Parachela
Macrobiotidae
Macrobiotus
Macrobiotus recens

description: Macrobiotus recens Cuénot 1932
I isolated 17 specimens and 11 eggs, found in all samples, from LF and MR samples. Cuticle with small round pores. Buccal armature had a strong posterior band of teeth, a weak anterior band of teeth, not always clearly visible on light microscopy, and a transverse crest system. We have found irregular margins for lunules in the fourth pair of legs in the majority of specimens but small teeth in some specimens from two samples in LF and MR. Eggs had cone-shaped processes, sometimes bifid, with rough surface, and granulated egg surface between the processes. We have observed ocular spots in seven specimens but they were not present in ten specimens. Mean body size was 879 μm (SD 229), range 484 to 1320 μm. This species has been cited for Europe, Asia, America and Oceania. In the Iberian Peninsula, it has been recorded for Portugal (Maucci 1979; Fontoura 1981, 1982; Maucci & Durante Pasa 1984, 1985) and Spain (Maucci & Durante Pasa 1984), but this is the first time this species have been found in Madrid (Table 2). Macrobiotus recens was detected at four of the sampling points (Table 3).
description: Published as part of Guil, Noemí, 2008, New records and within-species variability of Iberian tardigrades (Tardigrada), with comments on the species from the Echiniscus blumi-canadensis series, pp. 1-30 in Zootaxa 1757 on page 23, DOI: 10.5281/zenodo.181845
Additional file 2: Table 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: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry

description: Primers used in 16S rRNA sequencing library. (PDF 137Â kb)
Additional file 1: Table S13. 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: 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: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Computational Biology

description: Subject details and metadata. (PDF 202Â kb)
Additional file 18: Figure S11. 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: 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: Inorganic Chemistry
subject: Mental Health

description: PCoA plots based on 16S rRNA gene sequencing and shotgun data. a PCoA based on 16S rRNA gene sequencing data analysed using PE protocol. b PCoA based on 16S rRNA gene sequencing data analysed using QIIME. Blue circles represent sequencing data of preterm without supplementation (AP8C), yellow circles data of preterm with supplementation (P29F), and green circles data of term baby (V3 J). Each sample was analysed using three different 16S rRNA gene libraries (.27F, targets region (V1 + V2 + V3), .530F targets region (V4 + V5), and .926F targets region (V6 + V7 + V8)). Samples ended with (_shotgun) represents shotgun data used as ‘gold standard’ in this study. Samples from region (V4 + V5) presented the most distinct distribution when compared with shotgun data. More details of primers used for preparing these 16S rRNA libraries can be found in Methods section. (PDF 76 kb)
Physonota pellucida Wagener 1877
Creators: name: Sekerka, Lukáš
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Chrysomelidae
Physonota
Physonota pellucida

description: Physonota pellucida Wagener, 1877
Physonota pellucida Wagener, 1877: 61 (original description).
Physonota perampla Champion, 1894: 167 (original description), syn. nov.
Type localities. Physonota pellucida: ‘ Demerara’ [= former Dutch colony, nowadays part of Guyana]; P. perampla: ‘ Nicaragua: Chontales; Costa Rica: Santa Clara’.
Type material examined. Physonota pellucida: SYNTYPE: 1 ♂, pinned, ‘ Demerara | Schmidt. [w, hw, s] || TYPUS [pi, p, cb] || pellucida | Wag. Typus [w, hw by Spaeth, cb,] || pellucida [hw] | Spaeth det. [w, p, cb] || Manchester Museum | SYNTYPE [blue, p, cb]’ (MMUE).
Physonota perampla: SYNTYPES: 1 ♂, pinned, ‘ Chontales. | Nicaragua. | T. Belt. [w, p, cb] || Type [w, p, s, c, rf] || Physonota | perampla | Ch. [w, hw by Champion, s] || Sp. figured. [w, p, cb] || Godman-Salvin | Coll., Biol. | Centr.-Amer. [w, p, cb]’ (BMNH); 1 ♀, pinned, ‘ Chontales. | Nicaragua. | T. Belt. [w, p, cb] || Physonota | perampla, | Ch. [w, hw by Champion, s] || Godman-Salvin | Coll., Biol. | Centr.-Amer. [w, p, cb]’ (BMNH); 1 ♀, pinned, ‘ CHONTALES, | E.M.Janson [w, p, cb, bf] || Physonota | perampla, | Ch [w, hw by Champion, s] || 1905—54. [w, p, cb]’ (BMNH); 1 ♂, pinned (tenereal specimen missing abdomen and right antenna), ‘ Physonota | perampla, | Ch. [w, hw by Champion, s] || Baly Coll. | 1905—54. [w, p, cb]’ (BMNH); 1 ♀, pinned, ‘ CHONTALES | E.M.Janson [w, p, cb, bf] || Physonota | perampla | cotype! Ch [w, hw by Champion, s] || Champion | seripsit [w, hw by Spaeth, cb] || PARATYPUS [red, p, cb] || Manchester Museum | SYNTYPE [blue, p, cb]’ (MMUE).
Remarks. CHAMPION (1894) described Physonota perampla from series of six specimens and stated that Physonota pellucida ‘about equals it in size; but differs in several particulars from the insect here described [P. perampla]’. Both taxa were only listed in catalogues except BOROWIEC (2002) who recorded P. perampla as new to Colombia. I have examined types of both taxa and they are identical with no difference hence I synonymize P. perampla with P. pellucida.
I was unable to locate the syntype from Costa Rica in the BMNH collections although Champion explicitly stated that it came from the museum material.
Distribution. Colombia (BOROWIEC 2002), Costa Rica, Nicaragua (CHAMPION 1894) and Guyana (WAGENER 1877).
description: Published as part of Sekerka, Lukáš, 2016, Taxonomic and nomenclatural changes in Cassidinae (Coleoptera: Chrysomelidae), pp. 275-344 in Acta Entomologica Musei Nationalis Pragae 56 (1) on page 316, DOI: 10.5281/zenodo.5305725