bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finger puzzles
Authors: Schmitt R. W. 
Published: January 2012

AbstractSalt fingers are a form of double-diffusive convection that can occur in a wide variety of fluid systems, ranging from stellar interiors and oceans to magma chambers. Their amplitude has long been difficult to quantify, and a variety of mechanisms have been proposed. Radko & Smith (J. Fluid Mech., this issue, vol. 692, 2012, pp. 5–27) have developed a new theory that balances the basic growth rate with that of secondary instabilities that act on the finite amplitude fingers. Their approach promises a way forward for computationally challenging systems with vastly different scales of decay for momentum, heat and dissolved substances.
Subaqueous barchan dunes in turbulent shear flow. Part 2. Fluid flow
Authors: Charru F. , Franklin E. M. 
Published: January 2012

AbstractWe report an experimental study of the turbulent flow above a barchan dune in a channel, from particle image velocimetry measurements, for Reynolds numbers ranging from 9000, just below the threshold for particle motion, up to 24 000, where the dune moves. Two calculations of the speed-up over the dune are compared, the usual ‘same-elevation’ and the more relevant ‘Lagrangian’, showing that the latter is smaller by a factor of two. The two-layer structure of the flow disturbance – an essentially inviscid outer layer and a turbulent inner layer of thickness ${\delta }_{i} $ – is assessed. In the outer layer, streamline curvature is shown to be responsible for half of the Lagrangian speed-up, from the comparison of the velocity measurements with two Bernoulli calculations. In the inner layer, detailed measurements of the velocity and stresses are provided, down to ${y}^{+ } \approx 1$, and the momentum budget is discussed. The Reynolds shear stress decreases monotonically towards the dune surface, according to the standard mixing-length closure, whereas the total shear stress increases strongly in the viscous sublayer. Along the dune surface, the shear stress increases up to the crest where it reaches twice its unperturbed value. A good estimate of the surface stress is provided by a parabolic fit of the inner velocity profile matching the outer flow at ${y}_{d} \approx {\delta }_{i} $. Doubling the Reynolds number, the surface shear stress and the speed-up decrease by ∼30 %. The implications of these results on the dune motion, presented in Part 1 of this study (Franklin & Charru, J. Fluid Mech., vol. 675, 2011, pp. 199–222), are finally discussed.
Reproductive biology ofTephroseris longifoliasubsp. moravica, an endemic taxon of European importance
Authors: Janišová Monika , Škodová Iveta , Hegedüšová Katarína 
Published: January 2012

AbstractTephroseris longifoliasubsp.moravica(Asteraceae) is an endangered narrow endemic taxon recently recorded from nine sites in Slovakia and the Czech Republic. We provide the first consistent information on its reproductive biology – mating system, seed output, germination, seedling emergence and survival. Based on results from isolation, hybridization and emasculation experiments on different subspecies,T. longifolias.l. should be treated as an allogamous taxon without apomictic reproduction. Five populations ofT. l.moravicawere studied in detail for seed output and germination characteristics. The output of well-developed seeds per flowering shoot was estimated to be 592 (1125 seeds per flowering plant). A granivorous butterfly,Phycitodes albatella(family Pyralidae), was identified as a pest, reducing seed output by 18–28%. Germination (reaching 30–62% after dry storage for 4 months) rapidly decreased with storage in room conditions. Deep freeze storage increased germination, although not significantly. Seeds obtained from natural populations had higher germination percentages and germinated faster than seeds from cultivated plants. Seedling emergencein situwas very low (0.9–2.06% of the sown seeds) without significant differences among sites.
Interstage feeding and weight gain in infants following the Norwood operation: can we change the outcome?
Authors: Uzark Karen , Wang Yu , Rudd Nancy , Elixson E. Marsha , Strawn Jennifer , Nieves Jo Ann , Smith Cathy , Staveski Sandra , O'Brien Patricia , Tong Elizabeth , Ittenbach Richard 
Published: January 2012

AbstractBackgroundPoor weight gain is common in infants after Stage I Norwood operation and can negatively impact outcomes.ObjectivesThe purpose of this study was to examine the impact of feeding strategy on interstage weight gain.MethodsIn a multi-centre study, 158 infants discharged following the Norwood operation were enrolled prospectively. Weight and feeding data were obtained at 2-week intervals. Differences between feeding regimens in average daily weight gain and change in weight-for-age z-score between Stage I discharge and Stage II surgery were examined.ResultsDischarge feeding regimens were oral only in 52%, oral with tube supplementation in 33%, and by nasogastric/gastrostomy tube only in 15%. There were significant differences in the average daily interstage weight gain among the feeding groups – oral only 25.0 grams per day, oral/tube 21.4 grams per day, and tube only 22.3 grams per day – p = 0.019. Tube-only-fed infants were significantly older at Stage II (p = 0.004) and had a significantly greater change in weight-for-age z-score (p = 0.007). The overall rate of weight gain was 16–32 grams per day, similar to infant norms. The rate of weight gain declined over time, with earlier decline observed for oral- and oral/tube-fed infants (less than 15 grams per day at 5.4 months) in comparison with tube-only-fed infants (less than 15 grams per day at 8.6 months).ConclusionFollowing Stage I Norwood, infants discharged on oral feeding had better average daily weight gain than infants with tube-assisted feeding. The overall weight gain was within the normal limits in all feeding groups, but the rate of weight gain decreased over time, with an earlier decline in infants fed orally.
Lattices in Filtered (φ, N)-modules
Authors: Liu Tong 
Published: January 2012

AbstractLetpbe a prime. We construct and study integral and torsion invariants, such as integral and torsion Weil–Deligne representations, associated to potentially semi-stable representations and torsion potentially semi-stable representations respectively. As applications, we prove the compatibility between local Langlands correspondence and Fontaine's construction for Galois representations attached to Hilbert modular forms, and Néron–Ogg–Shafarevich criterion of finite level for potentially semi-stable representations.
Perugia and the plots of theMonobiblos
Authors: Breed Brian W. 
Published: January 2012

There is, alas, no secret code or mystical number lurking in the text of Propertius' first book of elegies which, if discovered, could reveal essential truths about the book. Or at least there is none that I can claim to have found. The search for some key to unlock secrets of meaning and authorial design is a well-known phenomenon of the interpretation of Roman poetry books, and Propertius' ‘single book’ has featured prominently in such investigations. The present paper does not put forth a new structural scheme for understanding theMonobiblosor another description of numerical patternings in it, nor does it insist that a true appreciation of the book's ‘architecture’ is essential for understanding its meaning. Instead, it has the goal of considering how the book format affects the experience of reading and the interpretation of this one important work of Roman poetry in light of its generic identity and the literary-historical context in which it was produced.In particular, I am interested in describing how the book format makes available to readers of the Monobiblos a sense that even in the absence of a single narrative spanning all of the poems of the book it is nevertheless possible to supplement them so that something like a plot or story emerges. I first consider how this sense of a possible plot or plots arises in the reading process, looking also at how some previous influential studies of the Monobiblos have relied upon various ways of construing a story or plot for the book.
Propertiana
Authors: Trappes–Lomax John 
Published: January 2012

The study of Propertius has been greatly facilitated by the publication by Stephen Heyworth of his Oxford Text and of his Cynthia. Many problems are now resolved or at any rate as near resolution as they are likely to be in the absence of some unexpected MS discovery. Other problems remain, and this very corrupt text will no doubt continue to provoke attempts at emendation; here are three. All citations are taken from Heyworth's OCT; references to comment by Heyworth are to his Cynthia.Goold (1999) translates ‘the sea, locked out from shadowy Avernus’. Heyworth points out that since Agrippa's harbour works of 37 BC this was no longer the case, and that the meaning should be ‘enclosed by shady Avernus’. No doubt, but the natural meaning of claudo ab is' ‘to shut off from’; cf. Liv. 30.24.9 ea [insula] sinum ab alto claudit. The correct meaning can best be obtained by altering ab to in:By opening up Avernus to sea-going vessels Agrippa has permitted the sea to enter the lake; cf. Suet. Aug. 16.1 portum Iulium apud Baias immisso in Lucrinum et Auernum lacum mari effecit; Verg. Geong. 2.164 Tyrrhenusque fretis immittitur aestus Auernis. The corruption could either be a trivial accident or else the deliberate work of a literal-minded scribe who could not see why it should be desirable to have the sea disporting itself inside a harbour.
Horace and historians
Authors: Woodman A. J. 
Published: January 2012

In ‘the only coherent piece of autobiography which we possess from Horace's pen’, as Fraenkel has called it, the poet wrote these famous lines (Epist.2.2.49–52):unde simul primum me dimisere Philippi,decisis humilem pinnis inopemque paterni 50et laris et fundi paupertas impulit audaxut uersus facerem.As soon as Philippi discharged me thence, poverty drove me grounded as I was, with my wings clipped, and deprived of my ancestral home and farm—boldly to produce verses.As is remarked by Lyne, however, ‘Horace here omits an intervening and prosaic stage’. The evidence for this omission comes from Suetonius' biography of the poet, in which the same period of Horace's life is described slightly differently: ‘uictisque partibus uenia impetrata scriptum quaestorium comparauit. ac primo Maecenati … insinuatus…’ (‘after the defeat of his party and a successful request for pardon he procured the position ofscriba quaestorius. And having first become involved with Maecenas…’). What was the exact sequence of events? Lyne, like Brink, proposes that Horace after Philippi derived income from his position asscriba quacstoriusand that this in turn enabled him to write the poetry which eventually brought him to Maecenas' attention. Nisbet, on the other hand, thinks that Horace's early poetry elicited subsidies from ‘grandees like Pollio and Messalla’ and that these provided him with the wherewithal to buy his position asscriba, from which he was effectively relieved by his later association with Maecenas.
‘Collectors’ as stakeholders in Mycenaean governance: property and the relations between the ruling class and the state
Authors: Kyriakidis E. 
Published: January 2012

There is a considerable body of literature concerned with the clarification of the role of the so-called ‘collectors’ in Mycenaean administration. In this article, a new interpretation will be proposed that offers a possible solution to the major points of dispute in the debate. This new interpretation has far-reaching consequences for our views of Mycenaean governance.Although previous research has been summarized several times elsewhere—most recently and efficiently by Lupack (2008, 86–96) and before her by Bennet (1992, 65–89), we shall here review the key themes which are of particular relevance to the interpretation proposed below.
Tracking energy transfer between light harvesting complex 2 and 1 in photosynthetic membranes grown under high and low illumination
Authors: Lüer Larry , Moulisová Vladimíra , Henry Sarah , Polli Dario , Brotosudarmo Tatas H. P. , Hoseinkhani Sajjad , Brida Daniele , Lanzani Guglielmo , Cerullo Giulio , Cogdell Richard J. 
Published: January 2012

Energy transfer (ET) between B850 and B875 molecules in light harvesting complexes LH2 and LH1/RC (reaction center) complexes has been investigated in membranes of
Rhodopseudomonas palustris
grown under high- and low-light conditions. In these bacteria, illumination intensity during growth strongly affects the type of LH2 complexes synthesized, their optical spectra, and their amount of energetic disorder. We used a specially built femtosecond spectrometer, combining tunable narrowband pump with broadband white-light probe pulses, together with an analytical method based on derivative spectroscopy for disentangling the congested transient absorption spectra of LH1 and LH2 complexes. This procedure allows real-time tracking of the forward (LH2 → LH1) and backward (LH2←LH1) ET processes and unambiguous determination of the corresponding rate constants. In low-light grown samples, we measured lower ET rates in both directions with respect to high-light ones, which is explained by reduced spectral overlap between B850 and B875 due to partial redistribution of oscillator strength into a higher energetic exciton transition. We find that the low-light adaptation in
R. palustris
leads to a reduced elementary backward ET rate, in accordance with the low probability of two simultaneous excitations reaching the same LH1/RC complex under weak illumination. Our study suggests that backward ET is not just an inevitable consequence of vectorial ET with small energetic offsets, but is in fact actively managed by photosynthetic bacteria.
A Mutant in theADH1Gene ofChlamydomonas reinhardtiiElicits Metabolic Restructuring during Anaerobiosis
Authors: Magneschi Leonardo , Catalanotti Claudia , Subramanian Venkataramanan , Dubini Alexandra , Yang Wenqiang , Mus Florence , Posewitz Matthew C. , Seibert Michael , Perata Pierdomenico , Grossman Arthur R. 
Published: January 2012

AbstractThe green alga Chlamydomonas reinhardtii has numerous genes encoding enzymes that function in fermentative pathways. Among these, the bifunctional alcohol/acetaldehyde dehydrogenase (ADH1), highly homologous to the Escherichia coli AdhE enzyme, is proposed to be a key component of fermentative metabolism. To investigate the physiological role of ADH1 in dark anoxic metabolism, a Chlamydomonas adh1 mutant was generated. We detected no ethanol synthesis in this mutant when it was placed under anoxia; the two other ADH homologs encoded on the Chlamydomonas genome do not appear to participate in ethanol production under our experimental conditions. Pyruvate formate lyase, acetate kinase, and hydrogenase protein levels were similar in wild-type cells and the adh1 mutant, while the mutant had significantly more pyruvate:ferredoxin oxidoreductase. Furthermore, a marked change in metabolite levels (in addition to ethanol) synthesized by the mutant under anoxic conditions was observed; formate levels were reduced, acetate levels were elevated, and the production of CO2 was significantly reduced, but fermentative H2 production was unchanged relative to wild-type cells. Of particular interest is the finding that the mutant accumulates high levels of extracellular glycerol, which requires NADH as a substrate for its synthesis. Lactate production is also increased slightly in the mutant relative to the control strain. These findings demonstrate a restructuring of fermentative metabolism in the adh1 mutant in a way that sustains the recycling (oxidation) of NADH and the survival of the mutant (similar to wild-type cell survival) during dark anoxic growth.
Adipokine profile in glucocorticoid‐treated patients: baseline plasma leptin level predicts occurrence of lipodystrophy
Authors: Fardet Laurence , Antuna‐Puente Barbara , Vatier Camille , Cervera Pascale , Touati Amel , Simon Tabassome , Capeau Jacqueline , Fève Bruno , Bastard Jean‐Philippe 
Published: January 2012

SummaryContextGlucocorticoid therapy may result in adipose tissue redistribution of unknown pathophysiology.ObjectivesTo evaluate the effects of glucocorticoids on adipokine levels and adipose tissue inflammation. To compare the results in patients with or without glucocorticoid‐induced lipodystrophy (GIL) after 3 months of therapy.Design and settingProspective monocentric study.PatientsAdult patients initiating systemic, high‐dose prednisone therapy for at least 3 months. Blood samples and subcutaneous abdominal adipose tissue biopsies were collected at baseline and month 3. The presence of GIL after 3 months of therapy was assessed using standardized photography.ResultsThirty‐two patients were enrolled. Blood samples and subcutaneous abdominal adipose tissue were available at baseline and month 3 for 30 patients [median age: 61 (38–79) years, 77% women]. Among those 30 patients, 15 were classified as GIL+ and 15 were GIL− at month 3. Between baseline and month 3, adiponectin and leptin levels increased in the overall population while the level of resistin remained unchanged. At baseline, leptin level was higher [19·3 (8·3–31·1) vs 4·5 (2·4–11·3) μg/l, P = 0·006] and resistin level lower [7·1 (6·3–12·4) vs 10·4 (8·0–21·7) μg/l, P = 0·05] in GIL+ than in GIL− patients. Baseline leptin level was predictive of GIL occurrence. Receiver operating characteristic curve analysis demonstrated that the best diagnostic accuracy was obtained with a baseline leptin cut‐off of 5·9 μg/l (sensitivity: 93%, specificity: 60%). At month 3, leptin and adiponectin levels increased more in the GIL+ than in the GIL− group, as did the number of anti‐inflammatory M2 macrophages in subcutaneous abdominal fat.ConclusionGlucocorticoid‐induced lipodystrophy is associated with a different adipokine profile both before and after glucocorticoid therapy. Serum leptin level prior to glucocorticoid therapy is highly predictive of GIL occurrence.
SoMART: a web server for plant miRNA, tasiRNA and target gene analysis
Authors: Li Feng , Orban Ryan , Baker Barbara 
Published: January 2012

SummaryPlant microRNAs (miRNAs) and trans‐acting small interfering RNAs (tasiRNAs) play important roles in a variety of biological processes. Bioinformatics prediction and small RNA (sRNA) cloning are the most important approaches for identification of miRNAs and tasiRNAs and their targets. However, these approaches are not readily accessible to every researcher. Here we present SoMART, a web server for miRNA/tasiRNA analysis resources and tools, which is designed for researchers who are interested in identifying miRNAs or tasiRNAs that potentially regulate genes of interest. The server includes four sets of tools: ‘Slicer detector’ for detecting sRNAs targeting input genes, ‘dRNA mapper’ for detecting degradome (d)RNA products derived from input genes, ‘PreMIR detector’ for identifying miRNA precursors (MIRs) or tasiRNA precursor (TASs) of input sRNAs, and ‘sRNA mapper’ for mapping sRNAs onto input genes. We also developed a dRNA‐seq protocol to achieve longer dRNA reads for better characterization of miRNA precursors by dRNA mapper. To validate the server function and robustness, we installed sRNA, dRNA and collected genomic DNA or transcriptome databases from Arabidopsis and solanaceous plants, and characterized miR172‐mediated regulation of the APETALA2 gene in potato (Solanum tuberosum) and demonstrated conservation of MIR390‐triggered TAS3 in tomato (Solanum lycopersicum). More importantly, we predicted the existence of MIR482‐triggered TAS5 in tomato. We further tested and confirmed the efficiency and accuracy of the server by analyses of 21 validated miRNA targets and 115 miRNA precursors in Arabidopsis thaliana. SoMART is available at http://somart.ist.berkeley.edu.
Ecological radiation with limited morphological diversification in salamanders
Authors: BLANKERS T. , ADAMS D. C. , WIENS J. J. 
Published: January 2012

AbstractA major goal of evolutionary biology is to explain morphological diversity among species. Many studies suggest that much morphological variation is explained by adaptation to different microhabitats. Here, we test whether morphology and microhabitat use are related in plethodontid salamanders, which contain the majority of salamander species, and have radiated into a striking diversity of microhabitats. We obtained microhabitat data for 189 species that also had both morphometric and phylogenetic data. We then tested for associations between morphology and microhabitat categories using phylogenetic comparative methods. Associations between morphology and ecology in plethodontids are largely confined to a single clade within one subfamily (Bolitoglossinae), whereas variation in morphology across other plethodontids is unrelated to microhabitat categories. These results demonstrate that ecological radiation and morphological evolution can be largely decoupled in a major clade. The results also offer a striking contrast to lizards, which typically show close relationships between morphology and microhabitat.
Morphological differentiation correlates with ecological but not with genetic divergence in aGehyragecko
Authors: SISTROM M. , EDWARDS D.L. , DONNELLAN S. , HUTCHINSON M. 
Published: January 2012

AbstractBody size affects life history, the ecological niche of an organism and its interactions with other organisms. Resultantly, marked differences in body size between related organisms are often an indication of a species boundary. This is particularly evident in theGehyra variegataspecies complex of geckos, which displays differential body sizes between genetically divergent species, but high levels of intraspecific morphological conservatism. We report on aGehyrapopulation that displays extraordinary body size differentiation in comparison with otherG. variegataspecies. We used morphological and environmental data to show this population is phenotypically and ecologically distinct from its parapatric congenerGehyra lazelliand that morphology and ecology are significantly correlated. Contrastingly, mtDNA analysis indicates paraphyly between the two groups, and allele frequencies at six microsatellite loci show no population structure concordant with morpho‐/ecotype. These results suggest either ecological speciation or environmentally induced phenotypic polymorphism, in an otherwise morphologically conservative group.