bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brief report: Youth pathways out of homelessness – Preliminary findings
Authors: Kidd Sean A. , Karabanow Jeff , Hughes Jean , Frederick Tyler 
Published: September 2013

AbstractWhile there exists an extensive body of knowledge regarding the risks associated with youth homelessness, very little work has addressed the process of exiting street contexts. This paper reports baseline findings from an ongoing longitudinal study assessing factors associated with a successful transition out of homelessness. Fifty‐one formerly homeless youth who obtained stable housing in the past 2 months to 2 years participated in this study which took place in two Canadian urban centres. Findings include poorer functioning across all domains for youth residing in housing contexts without supports, a lack of relationship between psychological and behavioural aspects of community integration, and the central role of self‐concept in mental health and quality of life. These findings suggest the need for ongoing support for youth exiting street spaces and social contexts, with attention to the importance of self‐concept and psychological aspects of community integration.
Pre-emptive virology screening in the pediatric hematopoietic stem cell transplant population
Authors: Evers Patrick D 
Published: September 2013

BACKGROUND AND OBJECTIVES:
Pediatric patients undergoing hematopoietic stem cell transplant (HSCT) are at a uniquely high risk of cytomegalovirus (CMV) and Epstein–Barr virus (EBV) infections. The pre-emptive treatment model whereby asymptomatic post-transplant patients are routinely screened with treatment initiated if found viremic has recently been shown to be superior in terms of patient mortality when compared to deferring laboratory assessment and treatment until symptoms emerge. This study analyzes the cost-effectiveness of the pre-emptive therapy model in patient care dollars per quality-adjusted life years (QALY).

PATIENTS AND METHODS:
Utilization and outcome data were compiled as a retrospective cohort study of 96 pediatric patients receiving HSCT at University of California Los Angeles Pediatric Hematology/Oncology Department between the years 2006 and 2010. Two-decision tree models were constructed for each the preemptive model and the deferred model wherein costs and probability assumptions were based on either previously published literature or calculated from this study cohort.

RESULTS:
The pre-emptive model resulted in a five-year survival of 71%, during which time 4% of patients were found to be EBV viremic, while 33% were found to be CMV viremic. The average actual cost of EBV/CMV virology screening per patient in the cohort following the pre-emptive model was $9699 while the expected cost following the deferred model was $19,284. This results in an incremental cost effectiveness ratio illustrating pre-emptive model cost-savings of $2367/QALY.

CONCLUSION:
These results support the financial viability and prudence of scheduled screening for subclinical viremia for achieving optimal outcomes in a cost-effective manner in the pediatric HSCT population.
Two-layer shallow-water dam-break solutions for gravity currents in non-rectangular cross-area channels
Authors: Ungarish Marius 
Published: September 2013

AbstractWe consider the propagation of a high-Reynolds-number gravity current in a horizontal channel along the horizontal coordinate $x$. The bottom and top of the channel are at $z= 0, H$, and the cross-section is given by the quite general $- {f}_{1} (z)\leq y\leq {f}_{2} (z)$ for $0\leq z\leq H$. We develop a two-layer shallow-water (SW) formulation, and we implement it for the solution of the dam-break problem. The dependent variables are the position of the interface, $h(x, t)$, and the velocity (averaged over the area of the current), $u(x, t)$. The non-rectangular cross-section geometry enters the formulation via $f(h)$ and integrals of $f(z)$ and $zf(z)$, where $f(z)= {f}_{1} (z)+ {f}_{2} (z)$ is the width of the channel. For a given geometry $f(z)$, the free input parameters of the lock-release problem are: (i) the height ratio $H/ {h}_{0} $ of ambient to lock; and (ii) the density ratio of ‘light’ to ‘heavy’ fluids, $R$. We show that the dam-break problem is amenable to solution by the method of characteristics, but various complications (internal jumps, critical restrictions) appear when the return flow in the ambient is significant; these features are not captured by a one-layer shallow-water model. The role of the non-standard geometry in the detection and calculation of the internal and reflected jumps, and on the dam-break flow field, is elucidated. The methodology is illustrated for Boussinesq flow in typical geometries: power-law ($f(z)= b{z}^{\alpha } $, where $b, \alpha $ are positive constants), trapezoidal and circle (full or sector); we solved for full-depth ($H= 1$) and part-depth ($H\gt 1$) lock-release configurations. The approach seems to work well: in all the tested cases, the solution was obtained with simple mathematical and numerical tools (a Runge–Kutta integrator and a secant-method solver); the insights are compatible with our previous understanding of the problem; and the standard (rectangular) case is recovered in the appropriate limit (i.e. when the side-boundaries of the trapezium cross-section are vertical or far apart). A comparison of the speed of propagation with available experiments is also presented, and the agreement is satisfactory. The present solution is a significant generalization of the classical two-layer gravity–current dam-break problem. The classical formulation for a rectangular (or laterally unbounded) channel is now just a particular case, $f(z)= $ const., in the wide domain of cross-sections covered by the new model.
VARIATIONS ON A THEOREM OF DAVENPORT CONCERNING ABUNDANT NUMBERS
Authors: JENNINGS EMILY , POLLACK PAUL , THOMPSON LOLA 
Published: September 2013

AbstractLet$\sigma (n)= {\mathop{\sum }\nolimits}_{d\mid n} d$be the usual sum-of-divisors function. In 1933, Davenport showed that$n/ \sigma (n)$possesses a continuous distribution function. In other words, the limit$D(u): = \lim _{x\rightarrow \infty }(1/ x){\mathop{\sum }\nolimits}_{n\leq x, n/ \sigma (n)\leq u} 1$exists for all$u\in [0, 1] $and varies continuously with$u$. We study the behaviour of the sums${\mathop{\sum }\nolimits}_{n\leq x, n/ \sigma (n)\leq u} f(n)$for certain complex-valued multiplicative functions$f$. Our results cover many of the more frequently encountered functions, including$\varphi (n)$,$\tau (n)$and$\mu (n)$. They also apply to the representation function for sums of two squares, yielding the following analogue of Davenport’s result: for all$u\in [0, 1] $, the limit$$\begin{eqnarray*}\tilde {D} (u): = \lim _{R\rightarrow \infty }\frac{1}{\pi R} \# \biggl\{ (x, y)\in { \mathbb{Z} }^{2} : 0\lt {x}^{2} + {y}^{2} \leq R\text{ and } \frac{{x}^{2} + {y}^{2} }{\sigma ({x}^{2} + {y}^{2} )} \leq u\biggr\}\end{eqnarray*}$$exists, and$\tilde {D} (u)$is both continuous and strictly increasing on$[0, 1] $.
DIRECTIONAL MAXIMAL OPERATORS AND RADIAL WEIGHTS ON THE PLANE
Authors: SAITO HIROKI , TANAKA HITOSHI 
Published: September 2013

AbstractLet $\Omega $ be the set of unit vectors and $w$ be a radial weight on the plane. We consider the weighted directional maximal operator defined by $$\begin{eqnarray*}{M}_{\Omega , w} f(x): = \sup _{x\in R\in \mathcal{B} _{\Omega }}\frac{1}{w(R)} \int \nolimits \nolimits_{R} \vert f(y)\vert w(y)\hspace{0.167em} dy,\end{eqnarray*}$$ where ${ \mathcal{B} }_{\Omega } $ denotes the set of all rectangles on the plane whose longest side is parallel to some unit vector in $\Omega $ and $w(R)$ denotes $\int \nolimits \nolimits_{R} w$. In this paper we prove an almost-orthogonality principle for this maximal operator under certain conditions on the weight. The condition allows us to get the weighted norm inequality $$\begin{eqnarray*}\Vert {M}_{\Omega , w} f\mathop{\Vert }\nolimits_{{L}^{2} (w)} \leq C\log N\Vert f\mathop{\Vert }\nolimits_{{L}^{2} (w)} ,\end{eqnarray*}$$ when $w(x)= \vert x\hspace{-1.2pt}\mathop{\vert }\nolimits ^{a} $, $a\gt 0$, and when $\Omega $ is the set of unit vectors on the plane with cardinality $N$ sufficiently large.
Not just any old pile of dirt: evaluating the use of artificial nesting mounds as conservation tools for freshwater turtles
Authors: Paterson James E. , Steinberg Brad D. , Litzgus Jacqueline D. 
Published: September 2013

AbstractThe viability of freshwater turtle populations is largely dependent on the survivorship of reproducing females but females are frequently killed on roads as they move to nesting sites. Installing artificial nesting mounds may increase recruitment and decrease the risk of mortality for gravid females by enticing them to nest closer to aquatic habitats. We evaluated the effectiveness of artificial nesting mounds installed in Algonquin Park, Canada. Artificial mounds were monitored for 2 years to determine if turtles would select them for nest sites. We also simulated turtle paths from wetlands to nests to determine the probability that females would encounter the new habitat. A transplant experiment with clutches ofChrysemys pictaandChelydra serpentinaeggs compared nest success and incubation conditions in the absence of predation between artificial mounds and natural sites. More turtles than expected used the artificial mounds, although mounds comprised a small proportion of the available nesting habitat and the simulations predicted that the probability of females encountering mounds was low. Hatching success was higher in nests transplanted to artificial mounds (93%) than in natural nests (56%), despite no differences in heat units. Greater use than expected, high hatching success, and healthy hatchlings emerging from nests in artificial mounds suggest promise for their use as conservation tools.
The heptachordal basis of hexachordal theory: on the semiotics of musical notation in the Middle Ages
Authors: MENGOZZI STEFANO 
Published: September 2013

ABSTRACTBy all appearances, the advent of a full-fledged hexachordal system in the late thirteenth century marked the culmination of a radical reconceptualisation of diatonic space that had begun over two centuries earlier with Guido of Arezzo's introduction of the syllables ut re mi fa sol la as an aid to sight-singing. An early witness of the new diatonic configuration is Johannes de Garlandia's Introductio musicae planae (c.1275), which presents the three proprietates per b quadro, per natura and per b molle as a fundamental articulation of the gamut that is necessary for conveying the intervallic distances between the diatonic pitches.A contextual evaluation of the theory of the proprietates, however, indicates that the hexachordal parsing of the gamut was not meant to establish the major sixth as the regulative paradigm of diatonic space (i.e. as a normative scale), but was rather in line with the earlier understanding of the ut-la syllables as an optional aid for singing. The development of hexachordal theory was in fact an implicit confirmation of the heptachordal structure of the gamut that had been in place since around the year 1000 (and arguably earlier), when the cycle of seven A–G letters was first used to label the constituent pitches of the octave.
Resistance and resilience of the forest soil microbiome to logging-associated compaction
Authors: Hartmann Martin , Niklaus Pascal A , Zimmermann Stephan , Schmutz Stefan , Kremer Johann , Abarenkov Kessy , Lüscher Peter , Widmer Franco , Frey Beat 
Published: September 2013

Abstract
Soil compaction is a major disturbance associated with logging, but we lack a fundamental understanding of how this affects the soil microbiome. We assessed the structural resistance and resilience of the microbiome using a high-throughput pyrosequencing approach in differently compacted soils at two forest sites and correlated these findings with changes in soil physical properties and functions. Alterations in soil porosity after compaction strongly limited the air and water conductivity. Compaction significantly reduced abundance, increased diversity, and persistently altered the structure of the microbiota. Fungi were less resistant and resilient than bacteria; clayey soils were less resistant and resilient than sandy soils. The strongest effects were observed in soils with unfavorable moisture conditions, where air and water conductivities dropped well below 10% of their initial value. Maximum impact was observed around 6–12 months after compaction, and microbial communities showed resilience in lightly but not in severely compacted soils 4 years post disturbance. Bacteria capable of anaerobic respiration, including sulfate, sulfur, and metal reducers of the Proteobacteria and Firmicutes, were significantly associated with compacted soils. Compaction detrimentally affected ectomycorrhizal species, whereas saprobic and parasitic fungi proportionally increased in compacted soils. Structural shifts in the microbiota were accompanied by significant changes in soil processes, resulting in reduced carbon dioxide, and increased methane and nitrous oxide emissions from compacted soils. This study demonstrates that physical soil disturbance during logging induces profound and long-lasting changes in the soil microbiome and associated soil functions, raising awareness regarding sustainable management of economically driven logging operations.
Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone
Authors: Ganesh Sangita , Parris Darren J , DeLong Edward F , Stewart Frank J 
Published: September 2013

AbstractMarine oxygen minimum zones (OMZs) support diverse microbial communities with roles in major elemental cycles. It is unclear how the taxonomic composition and metabolism of OMZ microorganisms vary between particle-associated and free-living size fractions. We used amplicon (16S rRNA gene) and shotgun metagenome sequencing to compare microbial communities from large (&gt;1.6 μm) and small (0.2–1.6 μm) filter size fractions along a depth gradient in the OMZ off Chile. Despite steep vertical redox gradients, size fraction was a significantly stronger predictor of community composition compared to depth. Phylogenetic diversity showed contrasting patterns, decreasing towards the anoxic OMZ core in the small size fraction, but exhibiting maximal values at these depths within the larger size fraction. Fraction-specific distributions were evident for key OMZ taxa, including anammox planctomycetes, whose coding sequences were enriched up to threefold in the 0.2–1.6 μm community. Functional gene composition also differed between fractions, with the &gt;1.6 μm community significantly enriched in genes mediating social interactions, including motility, adhesion, cell-to-cell transfer, antibiotic resistance and mobile element activity. Prokaryotic transposase genes were three to six fold more abundant in this fraction, comprising up to 2% of protein-coding sequences, suggesting that particle surfaces may act as hotbeds for transposition-based genome changes in marine microbes. Genes for nitric and nitrous oxide reduction were also more abundant (three to seven fold) in the larger size fraction, suggesting microniche partitioning of key denitrification steps. These results highlight an important role for surface attachment in shaping community metabolic potential and genome content in OMZ microorganisms.
Does dopamine block the spawning of the acroporid coral Acropora tenuis?
Authors: Isomura N. , Yamauchi C. , Takeuchi Y. , Takemura A. 
Published: September 2013

AbstractMost corals undergo spawning after a particular moon phase, but how moon-related spawning is endogenously regulated in corals remains unknown. The objective of the present study was to evaluate whether dopamine (DA) affects spawning in Acropora tenuis. When pieces of four A. tenuis colonies were reared under a natural photoperiod and water temperature, spawning was observed after the predicted moon phase. After exposure to water containing DA at 0.1 μM, pieces of the same colonies only released 5 to 10 bundles. Co-treatment with DA and pimozide (D1 and D2 receptors antagonist), but not domperidone (D2 receptor antagonist), induced mass release of bundles from the colonies. A cross-experiment revealed high fertilization rates between the control colonies (95%) and between the control and DA-treated colonies (90%), suggesting that gametes developed normally in coral tissue. Therefore, DA appears to have an inhibitory effect on the spawning of A. tenuis.
Endoplasmic reticulum-associated ubiquitin-conjugating enzyme Ube2j1 is a novel substrate of MK2 (MAPKAP kinase-2) involved in MK2-mediated TNFα production
Authors: Menon Manoj B. , Tiedje Christopher , Lafera Juri , Ronkina Natalia , Konen Timo , Kotlyarov Alexey , Gaestel Matthias 
Published: September 2013

The p38 MAPK (mitogen-activated protein kinase)/MK2 [MAPKAP (MAPK-activated protein) kinase-2] signalling pathway is a major regulator of stress- and cytokine-induced gene expression at the transcriptional and post-transcriptional level. Using phosphoproteomics we identified the ER (endoplasmic reticulum)-associated ubiquitin-conjugating enzyme Ube2j1 as a potential substrate of MK2. We demonstrate that Ube2j1 is phosphorylated in a cytokine-, cytosolic stress- and LPS (lipopolysaccharide)-induced manner. The cytosolic stress-induced phosphorylation of Ube2j1 proceeds at Ser184, a site described previously to be phosphorylated in response to ER stress, which is located in a perfect MK2 consensus motif. The cytosolic stress-induced phosphorylation of Ube2j1, but not its ER-stress-induced phosphorylation is sensitive to p38/MK2 inhibitors and abrogated in MK2/MK3-deficient cells. In a pull-down assay we demonstrate the interaction of MK2 with Ube2j1 in HEK (human embryonic kidney)-293T cells. Furthermore, MK2 is able to phosphorylate recombinant Ube2j1, but not the S184A mutant in an in vitro kinase assay. These findings strongly suggest that MK2 directly phosphorylates Ube2j1 at Ser184 upon p38-activating stress in vivo. However, ectopically expressed Ube2j1-S184A mutant displays ubiquitinating activity towards the model substrate ER-synthesized T-cell receptor-α similar to that of the wild-type protein. Interestingly, Ube2j1 is phosphorylated in response to LPS also in macrophages and contributes to MK2-dependent TNFα biosynthesis by a so far unknown mechanism.
Functional role of oligomerization for bacterial and plant SWEET sugar transporter family
Authors: Xuan Yuan Hu , Hu Yi Bing , Chen Li-Qing , Sosso Davide , Ducat Daniel C. , Hou Bi-Huei , Frommer Wolf B. 
Published: September 2013

Significance
SWEET sugar transporter homologs from bacteria were identified and named SemiSWEETs. They are small proteins with only three transmembrane domains (TMs); they are too small to create pores by themselves, but likely, they assemble multiple 3-TMs into a complex. SemiSWEETs are related to SWEETs, which play important roles in intercellular and interorgan sugar translocation in plants, and they are found in animals. SWEETs have fused two 3-TM units through a linker. However, SWEETs seem to be too small to transport sugars on their own. Here, we show that SWEET function requires assembly into oligomers, indicating that a pore requires at least an SWEET dimer.
First Report of Phytophthora tentaculata Causing Stem and Root Rot on Celery in China
Authors: Wang T. , Zhao W. , Qi R.-D. 
Published: September 2013

Celery (Apium graveolens) is an important vegetable in China. In August 2012, about 20 to 70% declining plants with root and basal stem rot were observed in Bengbu, Anhui Province, China. Typical symptoms included large dark brown to black water-soaked lesions near the soil line of stems. As the disease progressed, lesions girdled the stem, and plants became brown, wilted, and eventually died. A Phytophthora-like organism was consistently isolated from symptomatic tissues on a selective medium, P5ARP. Resultant isolates were identified as Phytophthora tentaculata based on their morphological features and rDNA sequence. Sporangia, chlamydospores, hyphal swellings, and oospores were produced on V8 agar. Sporangia were ovoid to pyriform, 28.5 to 52.5 × 21.5 to 40.6 μm, average 35.3 × 29.8 μm, with one or occasionally two papillae. Chlamydospores were spherical, 21.3 to 30.2 μm in diameter, average 25.7 μm. The isolates were homothallic, and one or occasionally two paragynous antheridia were attached to the global oogonia (24 to 39 μm in diameter, average 29.5 μm). The internal transcribed spacer region of rDNA was amplified with primer pair ITS1/ITS4 for one isolate (1), and the sequence (GenBank Accession No. KF501392) showed >99% similarity with those P. tentaculata isolates deposited in GenBank (AJ854302.1). Pathogenicity was confirmed by inoculating Shijihuangqin, a local cultivar of celery, with isolate PT12081. The isolate was cultivated on V8 agar at 25°C for 5 to 7 days to produce sporangia. Five 2-month-old, disease-free celery were drench-inoculated with 10 ml of a suspension of 2 × 104 zoospores/ml, and five control plants per pot were treated with sterile water. There were four pots for each of the inoculated and non-inoculated treatments, and the experiment was repeated twice. All plants were maintained at 25°C for 10 days. Symptoms similar to those observed in the field developed 7 days after inoculation. Ten days later, five plants wilted and two or three died in each pot inoculated with PT12081, but the control plants remained symptomless. P. tentaculata was consistently re-isolated from the symptomatic plants. P. tentaculata has been reported to infect Chrysanthemum spp., Delphinium ajacis, Verbena spp., and Origanum vulgare (2,3). To our knowledge, this is the first report of Phytophthora blight caused by P. tentaculata on celery in China. References: (1) H. Guo et al. Plant Dis. 96:1072, 2012. (2) P. Martini et al. Plant Dis. 93:843, 2009. (3) J. Meng and Y. C. Wang. Plant Dis. 92:1365, 2008.
Cell- and Stimulus Type-Specific Intracellular Free Ca2+ Signals in Arabidopsis
Authors: Martí María C. , Stancombe Matthew A. , Webb Alex A.R. 
Published: September 2013

Abstract
Appropriate stimulus-response coupling requires that each signal induces a characteristic response, distinct from that induced by other signals, and that there is the potential for individual signals to initiate different downstream responses dependent on cell type. How such specificity is encoded in plant signaling is not known. One possibility is that information is encoded in signal transduction pathways to ensure stimulus- and cell type-specific responses. The calcium ion acts as a second messenger in response to mechanical stimulation, hydrogen peroxide, NaCl, and cold in plants and also in circadian timing. We use GAL4 transactivation of aequorin in enhancer trap lines of Arabidopsis (Arabidopsis thaliana) to test the hypothesis that stimulus- and cell-specific information can be encoded in the pattern of dynamic alterations in the concentration of intracellular free Ca2+ ([Ca2+]i). We demonstrate that mechanically induced increases in [Ca2+]i are largely restricted to the epidermal pavement cells of leaves, that NaCl induces oscillatory [Ca2+]i signals in spongy mesophyll and vascular bundle cells, but not other cell types, and detect circadian rhythms of [Ca2+]i only in the spongy mesophyll. We demonstrate stimulus-specific [Ca2+]i dynamics in response to touch, cold, and hydrogen peroxide, which in the case of the latter two signals are common to all cell types tested. GAL4 transactivation of aequorin in specific leaf cell types has allowed us to bypass the technical limitations associated with fluorescent Ca2+ reporter dyes in chlorophyll-containing tissues to identify the cell- and stimulus-specific complexity of [Ca2+]i dynamics in leaves of Arabidopsis and to determine from which tissues stress- and circadian-regulated [Ca2+]i signals arise.