bluuebunny/crossref_metadata_2025_split huggingface dataset:
River tributaries as sediment sinks: Processes operating where the Tapajós and Xingu rivers meet the Amazon tidal river
Authors: Fricke Aaron T. , Nittrouer Charles A. , Ogston Andrea S. , Nowacki Daniel J. , Asp Nils E. , Souza Filho Pedro W. M. , da Silva Marcio S. , Jalowska Anna M. 
Published: March 2017

AbstractThe Amazon River is the largest fluvial source of fresh water and sediment to the global ocean and has the longest tidally influenced reach in the world. Two major rivers, the Tapajós and Xingu, enter the Amazon along its tidal reach. However, unlike most fluvial confluences, these are not one‐way conduits through which water and sediment flow downstream towards the sea. The drowned‐river valleys (rias) at the confluences of the Tapajós and Xingu with the Amazon River experience water‐level fluctuations associated not only with the seasonal rise and fall of the river network, but also with semidiurnal tides that propagate as far as 800 km up the Amazon River. Superimposed seasonal and tidal forcing, distinct sediment and temperature signatures of Amazon and tributary waters, and antecedent geomorphology combine to create mainstem–tributary confluences that act as sediment traps rather than sources of sediment. Hydrodynamic measurements are combined with data from sediment cores to determine the distribution of tributary‐derived and Amazon‐derived sediment within the ria basins, characterize the sediment‐transport mechanisms within the confluence areas and estimate rates of sediment accumulation within both rias. The Tapajós and Xingu ria basins trap the majority of the sediment carried by the tributaries themselves in addition to ca 20 Mt year−1 of sediment sourced from the Amazon River. These findings have implications for the interpretation of stratigraphy associated with incised‐valley systems, such as those that dominated the transfer of sediment to the oceans during lowstands in sea level.
microRNA/microRNA* complementarity is important for the regulation pattern of NFYA5 by miR169 under dehydration shock in Arabidopsis
Authors: Du Qingguo , Zhao Meng , Gao Wei , Sun Suzhen , Li Wen‐Xue 
Published: March 2017

SummaryMicroRNAs regulate gene expression at the mRNA and translational levels. Although our previous research showed that expression of miR169 and one of its targets, NFYA5, is down‐ and up‐regulated by drought stress, respectively, the current study shows that expression of both miR169 and NFYA5 are induced by dehydration shock. Unlike overexpression of MIR169a/b, overexpression of MIR169i/l did not decrease NFYA5 transcripts but increased NFYA5 protein levels. NFYA5 protein abundance also increased in mir169a knock‐out mutants and 35S::MIR169l mir169a double mutants. When bulge #11 and bulge #16 in the miR169/miR169* duplex were mutated, both NFYA5 transcripts and the corresponding protein levels were lower in 35S::MIR169l*‐mut transgenic plants than in wild‐type (WT) plants, and the 35S::MIR169l*‐mut transgenic plants were as sensitive to drought stress as the 35S::MIR169a plants. The mRNA and protein levels of NFYA5 did not differ substantially between WT and 35S::MIR169a*‐mut transgenic plants when the two bulges were introduced in the miR169a/miR169a* duplex. Both bulge #11 and bulge #16 in the miR169/miR169* duplex were essential for different regulation patterns of NFYA5 by miR169a and miR169l. These results increase the understanding of regulatory specialization in one MIR family, and also increase our understanding of the importance of microRNA/microRNA* secondary structure.
Small molecules below‐ground: the role of specialized metabolites in the rhizosphere
Authors: Massalha Hassan , Korenblum Elisa , Tholl Dorothea , Aharoni Asaph 
Published: March 2017

SummarySoil communities are diverse taxonomically and functionally. This ecosystem experiences highly complex networks of interactions, but may also present functionally independent entities. Plant roots, a metabolically active hotspot in the soil, take an essential part in below‐ground interactions. While plants are known to release an extremely high portion of the fixated carbon to the soil, less information is known about the composition and role of C‐containing compounds in the rhizosphere, in particular those involved in chemical communication. Specialized metabolites (or secondary metabolites) produced by plants and their associated microbes have a critical role in various biological activities that modulate the behavior of neighboring organisms. Thus, elucidating the chemical composition and function of specialized metabolites in the rhizosphere is a key element in understanding interactions in this below‐ground environment. Here, we review key classes of specialized metabolites that occur as mostly non‐volatile compounds in root exudates or are emitted as volatile organic compounds (VOCs). The role of these metabolites in below‐ground interactions and response to nutrient deficiency, as well as their tissue and cell type‐specific biosynthesis and release are discussed in detail.
Comparisons among MRI signs, apparent diffusion coefficient, and fractional anisotropy in dogs with a solitary intracranial meningioma or histiocytic sarcoma
Authors: Wada Masae , Hasegawa Daisuke , Hamamoto Yuji , Yu Yoshihiko , Fujiwara‐Igarashi Aki , Fujita Michio 
Published: March 2017

AbstractAlthough MRI has become widely used in small animal practice, little is known about the validity of advanced MRI techniques such as diffusion‐weighted imaging and diffusion tensor imaging. The aim of this retrospective analytical observational study was to investigate the characteristics of diffusion parameters, that is the apparent diffusion coefficient and fractional anisotropy, in dogs with a solitary intracranial meningioma or histiocytic sarcoma. Dogs were included based on the performance of diffusion MRI and histological confirmation. Statistical analyses were performed to compare apparent diffusion coefficient and fractional anisotropy for the two types of tumor in the intra‐ and peritumoral regions. Eleven cases with meningioma and six with histiocytic sarcoma satisfied the inclusion criteria. Significant differences in apparent diffusion coefficient value (× 10−3mm2/s) between meningioma vs. histiocytic sarcoma were recognized in intratumoral small (1.07 vs. 0.76) and large (1.04 vs. 0.77) regions of interest, in the peritumoral margin (0.93 vs. 1.08), and in the T2 high region (1.21 vs. 1.41). Significant differences in fractional anisotropy values were found in the peritumoral margin (0.29 vs. 0.24) and the T2 high region (0.24 vs. 0.17). The current study identified differences in measurements of apparent diffusion coefficient and fractional anisotropy for meningioma and histiocytic sarcoma in a small sample of dogs. In addition, we observed that all cases of intracranial histiocytic sarcoma showed leptomeningeal enhancement and/or mass formation invading into the sulci in the contrast study. Future studies are needed to determine the sensitivity of these imaging characteristics for differentiating between these tumor types.
Genome Sequence of Deinococcus marmoris PAMC 26562 Isolated from Antarctic Lichen
Authors: Kim Junghee , Kwon Kae Kyoung , Kim Byung Kwon , Hong Soon Gyu , Oh Hyun-Myung 
Published: March 2017

ABSTRACT

Deinococcus marmoris
strain PAMC 26562 was isolated from
Usnea
sp., a lichen collected from King George Island, Antarctica. We report here the draft genome sequence of strain PAMC 26562, which has xanthorhodopsin and carbon monoxide dehydrogenase genes in addition to major metabolic pathways presented in deinococcal genomes.
Draft Genome Sequence of Propionibacterium avidum Strain UCD-PD2 Isolated from a Feline Anal Sac
Authors: Dahms Petra A. , Martin Alexandra L. , Ganz Holly H. , Eisen Jonathan A. , Coil David A. 
Published: March 2017

ABSTRACT

Here, we present the draft genome sequence of
Propionibacterium
(
Cutibacterium
)
avidum
strain UCD-PD2. The assembly contains 2,667,287 bp in 51 contigs. The strain was isolated from anal sac secretion samples collected from a feral domestic cat (
Felis catus
) as part of a larger project to study the microbiology of cats.
High-Quality Draft Genome Sequence of Francisella tularensis subsp.
holarctica
Strain 08T0073 Isolated from a Wild European Hare
Authors: Busch Anne , Thomas Prasad , Myrtennäs Kerstin , Forsman Mats , Braune Silke , Runge Martin , Tomaso Herbert 
Published: March 2017

ABSTRACT

Here, we report a high-quality draft genome sequence of
Francisella tularensis
subsp.
holarctica
strain 08T0073, isolated from the cadaver of a wild European hare (
Lepus europaeus
) found near Helmstedt, Lower Saxony, Germany, in 2007. In Germany, infected hares are a major source of tularemia in humans.
Draft Genome Sequence of Chromobacterium pseudoviolaceum LMG 3953
T
, an Enigmatic Member of the Genus
Chromobacterium
Authors: Soby Scott D. 
Published: March 2017

ABSTRACT

Chromobacterium pseudoviolaceum
LMG 3953
T
was separated from
Chromobacterium violaceum
in 2009, but little is known of its origin or environmental role. Here, the genome of LMG 3953
T
was sequenced to understand the evolution of the genus
Chromobacterium
. It is not clear from this sequence that
C. pseudoviolaceum
is taxonomically distinct from
C. violaceum
.
A 99.7-dB DR fourth-order sigma–delta modulator for digital gyroscope sensor
Authors: Di Xin-Peng , Chen Wei-Ping , Yin Liang , Liu Xiao-Wei 
Published: March 2017

A fourth-order single-loop 1-bit sigma–delta [Formula: see text] modulator for digital gyroscope sensor interface circuit is presented in this paper. The effects caused by mismatch between parasite capacitors at the input of the operational transconductance amplifier (OTA) and the nonlinear on-resistance of the CMOS switch are analyzed. The chopping technique is adopted to eliminate the flick noise in low frequency. The modulator is fabricated in a standard CMOS 0.5-[Formula: see text] process and the effective area is 2 mm2. The power dissipation is 9.66 mW when the voltage is 5 V. The tested results show that a 93.7-dB peak signal-to-noise-and-distortion ratio (SNDR) and a 99.7-dB dynamic range (DR) are achievable at the sample frequency of 500 kHz for 2 kHz bandwidth. The optimization of the switches used in the first integrator and the parasite capacity is proved to be effective in the design of modulator.
Crafting a national cyberdefense, and preparing to support computational literacy
Authors: Arquilla John , Guzdial Mark 
Published: March 2017

The
Communications
Web site, http://cacm.acm.org, features more than a dozen bloggers in the BLOG@CACM community. In each issue of
Communications
, we'll publish selected posts or excerpts.

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John Arquilla considers how we should interpret the alleged Russian cyberattack on the U.S. Presidential election; Mark Guzdial describes the potential benefits of a 'computing lab.'
Glycans in the intestinal peptide transporter PEPT1 contribute to function and protect from proteolysis
Authors: Stelzl Tamara , Geillinger-Kästle Kerstin E. , Stolz Jürgen , Daniel Hannelore 
Published: March 2017

Despite the fact that many membrane proteins carry extracellular glycans, little is known about whether the glycan chains also affect protein function. We recently demonstrated that the proton-coupled oligopeptide transporter 1 (PEPT1) in the intestine is glycosylated at six asparagine residues (N50, N406, N439, N510, N515, and N532). Mutagenesis-induced disruption of the individual N-glycosylation site N50, which is highly conserved among mammals, was detected to significantly enhance the PEPT1-mediated inward transport of peptides. Here, we show that for the murine protein the inhibition of glycosylation at sequon N50 by substituting N50 with glutamine, lysine, or cysteine or by replacing S52 with alanine equally altered PEPT1 transport kinetics in oocytes. Furthermore, we provide evidence that the uptake of [14C]glycyl-sarcosine in immortalized murine small intestinal (MODE-K) or colonic epithelial (PTK-6) cells stably expressing the PEPT1 transporter N50Q is also significantly increased relative to the wild-type protein. By using electrophysiological recordings and tracer flux studies, we further demonstrate that the rise in transport velocity observed for PEPT1 N50Q is bidirectional. In line with these findings, we show that attachment of biotin derivatives, comparable in weight with two to four monosaccharides, to the PEPT1 N50C transporter slows down the transport velocity. In addition, our experiments provide strong evidence that glycosylation of PEPT1 confers resistance against proteolytic cleavage by proteinase K, whereas a remarkable intrinsic stability against trypsin, even in the absence of N-linked glycans, was detected.NEW & NOTEWORTHY This study highlights the role of N50-linked glycans in modulating the bidirectional transport activity of the murine peptide transporter PEPT1. Electrophysiological and tracer flux measurements in Xenopus oocytes have shown that removal of the N50 glycans increases the maximal peptide transport rate in the inward and outward directions. This effect could be largely reversed by replacement of N50 glycans with structurally dissimilar biotin derivatives. In addition, N-glycans were detected to stabilize PEPT1 against proteolytic cleavage.
The effect of intravenous corticotropin-releasing hormone administration on esophageal sensitivity and motility in health
Authors: Broers Charlotte , Melchior Chloé , Van Oudenhove Lukas , Vanuytsel Tim , Van Houtte Brecht , Scheerens Charlotte , Rommel Nathalie , Tack Jan , Pauwels Ans 
Published: March 2017

Esophageal hypersensitivity is important in gastroesophageal reflux disease (GERD) patients who are refractory to acid-suppressive therapy. Stress affects visceral sensitivity and exacerbates heartburn in GERD. Peripheral CRH is a key mediator of the gut stress response. We hypothesize that CRH increases esophageal sensitivity and alters esophageal motility in health. Esophageal sensitivity to thermal, mechanical, electrical, and chemical stimuli was assessed in 14 healthy subjects after administration of placebo or CRH (100 μg iv). Perception scores were assessed for first perception, pain perception threshold (PPT), and pain tolerance threshold (PTT). Esophageal motility was investigated by high-resolution impedance manometry, before and after CRH and evaluated by distal contractile integral (DCI) and intrabolus pressure (IBP). Pressure flow analysis assessed bolus clearance (impedance ratio), degree of pressurization needed to propel bolus onward (IBP slope), and pressure flow (pressure flow index, PFI). Stress and mood were assessed during the study. Sensitivity to mechanical distention was increased after CRH compared with placebo (PPT: P = 0.0023; PTT: P = 0.0253). CRH had no influence on the other stimulations. DCI was increased for all boluses (liquid, P = 0.0012; semisolid, P = 0.0017; solid, P = 0.0107). Impedance ratio for liquid ( P < 0.0001) and semisolid swallows ( P = 0.0327) decreased after CRH. IBP slope increased after CRH for semisolid ( P = 0.0041) and solid ( P = 0.0003) swallows. PFI increased for semisolid ( P = 0.0017) and solid swallows ( P = 0.0031). CRH increased esophageal sensitivity to mechanical distention, not to the other stimulation modalities. CRH increased esophageal contractility and tone, decreased LES relaxation, increased esophageal bolus pressurization, improved esophageal bolus clearance, and increased pressure flow.NEW & NOTEWORTHY This is the first study to address the effect of corticotropin-releasing hormone (CRH) on esophageal sensitivity and alterations in motility in health. CRH administration increased esophageal sensitivity to mechanical distention. This effect is accompanied by an increase in esophageal contractility and tone and a decrease in lower esophageal sphincter relaxation. CRH increased esophageal bolus pressurization, improved esophageal bolus clearance, and increased pressure flow. The changes in esophageal contractile properties may underlie the increased sensitivity to mechanical distention after CRH.
Transfer to High-Volume Centers Associated With Reduced Mortality After Endovascular Treatment of Acute Stroke
Authors: Rinaldo Lorenzo , Brinjikji Waleed , Rabinstein Alejandro A. 
Published: March 2017

Background and Purpose—
Some have argued that it may be beneficial to expand the availability of endovascular revascularization services to lower-volume hospitals to minimize the morbidity associated with transfer to larger endovascular centers. We compared the outcomes after revascularization of patients directly admitted to a low-volume center and those transferred to a high-volume center.

Methods—
We searched a national database of hospital-reported outcomes for patients who underwent endovascular revascularization for acute ischemic stroke. Hospitals were categorized as low, medium, or high procedural volume hospitals. Outcomes of inpatient admissions were collected and compared on the basis of admission source and hospital procedural volume.

Results—

A total of 118 institutions with 8533 patients were included. Mortality rate (14.9% versus 18.6%;
P
=0.049) and mortality index (1.1 versus 1.6;
P
=0.048) were significantly lower among directly admitted relative to transferred patients. For all patients, there were significant differences in institutional mortality rate (low: 19.7%, medium: 14.9%, high: 9.8%;
P
=0.003) and mortality index (low: 1.5, medium: 1.1, high: 0.8;
P
=0.004) between low-, medium-, and high-volume hospitals. For transferred patients to high-volume centers, both mortality rate (high: 10.0% versus low: 20.4%;
P
=0.005) and mortality index (high: 0.8 versus low: 1.5;
P
=0.034) were significantly lower than that observed for directly admitted patients to low-volume hospitals.

Conclusions—
We report a beneficial effect of treatment at high-volume hospitals in spite of the detrimental effects of transfer. These findings argue for the centralization of care.
Seasonal Poetics: The Dry Season and Autumn Rains among Pre-Islamic Naǧdī and Ḥiǧāzī Tribes
Authors: Miller Nathaniel A. 
Published: March 2017

This article maps out the depiction among pre-Islamic tribes of two seasons, the August ḫarīf rains and the qayẓ dry season. References to the ḫarīf rain are found almost exclusively in southwestern Arabia, Yemen and the Ḥiǧāz. Tribes in these regions evidently began their seasonal migration in August, that is, earlier than tribes of central and northeastern Arabia (Naǧd), where migration began in October and November. The most conspicuous result of this difference is the development of two regional methods of depicting the ẓaʿn, or departure of the beloved’s caravan, in the classical qaṣīda (polythematic ode). Naǧdī tribes set this scene at the beginning of the summer dry season, while the Ḥiǧāzī Huḏayl set it in a rainy season. A sequence of poets within Tamīm developed an idiosyncratic set of vocabulary for developing the early-summer ẓaʿn, just as certain Huḏalī poets developed certain techniques to describe their rainy season ẓaʿn.
Cet article analyse la représentation dans les tribus préislamiques de deux saisons, les pluies d’août (ḫarīf) et la saison sèche (al-qayẓ). Les références à la pluie ḫarīf se trouvent presque exclusivement au sud-ouest de l’Arabie, au Yémen et dans le Ḥiǧāz. Les tribus de ces régions commençaient apparemment leur migration saisonnière en août, plus tôt que les tribus du centre et du nord-est de l’Arabie (Naǧd), où la migration commençait en octobre ou novembre. Le résultat le plus remarquable de cette différence est l’évolution de deux méthodes régionales de la représentation du ẓaʿn, le départ de la caravane de la bien-aimée, dans la qaṣīda classique (ode polythématique). Les tribus du Naǧd plantent le décor de cette scène au début de la saison sèche, tandis que la tribu ḥiǧāzienne Huḏayl la situe à la saison des pluies.
This article is in English.
Hospital-level variation in inpatient cost among children receiving extracorporeal membrane oxygenation
Authors: Barbaro Ryan P. , Boonstra Philip S. , Moler Frank W. , Davis Matthew M. , Prosser Lisa A 
Published: March 2017

Objective: Pediatric extracorporeal membrane oxygenation (ECMO) varies in the way care is provided from hospital to hospital. This variability in hospital ECMO care can be represented by the variation in ECMO costs. We hypothesized that hospitals will demonstrate large variations in case-mix-adjusted ECMO inpatient costs for children requiring ECMO and higher volume hospitals will have lower associated costs. Methods: We retrospectively analyzed the inpatient cost of children receiving ECMO in 2006, 2009 and 2012, using the Healthcare Cost and Utilization Project Kids’ Inpatient Database. We used a hierarchical linear regression model and the intraclass correlation coefficient to quantify how much of the difference in ECMO inpatient costs was associated with the hospital where a child received care. To do this, we adjusted for patient factors, hospital factors and potentially modifiable factors such as complications, procedures and length of stay. Results: The median inflation-adjusted inpatient costs for children requiring ECMO were $183,000, $240,000 and $241,000 in years 2006, 2009 and 2012, respectively. The largest median cost for ECMO cases in a given hospital in a given year ($690,000) was more than 11 times that of the smallest median cost ($60,000). After case-mix adjustment, 27% of the variation in inpatient costs was associated with the hospital where ECMO care was provided. Average hospital costs were not associated with hospital ECMO volume. Conclusions: The large variation in ECMO inpatient costs between hospitals suggests great variation in care between hospitals, which is important because hospitals have a co-existing variation in ECMO survival rates.
Dexamethasone suppresses JMJD3 gene activation via a putative negative glucocorticoid response element and maintains integrity of tight junctions in brain microvascular endothelial cells
Authors: Na Wonho , Shin Jee Y , Lee Jee Y , Jeong Sangyun , Kim Won-Sun , Yune Tae Y , Ju Bong-Gun 
Published: March 2017

The blood–brain barrier (BBB) exhibits a highly selective permeability to support the homeostasis of the central nervous system (CNS). The tight junctions in the BBB microvascular endothelial cells seal the paracellular space to prevent diffusion. Thus, disruption of tight junctions results in harmful effects in CNS diseases and injuries. It has recently been demonstrated that glucocorticoids have beneficial effects on maintaining tight junctions in both in vitro cell and in vivo animal models. In the present study, we found that dexamethasone suppresses the expression of JMJD3, a histone H3K27 demethylase, via the recruitment of glucocorticoid receptor α (GRα) and nuclear receptor co-repressor (N-CoR) to the negative glucocorticoid response element (nGRE) in the upstream region of JMJD3 gene in brain microvascular endothelial cells subjected to TNFα treatment. The decreased JMJD3 gene expression resulted in the suppression of MMP-2, MMP-3, and MMP-9 gene activation. Dexamethasone also activated the expression of the claudin 5 and occludin genes. Collectively, dexamethasone attenuated the disruption of the tight junctions in the brain microvascular endothelial cells subjected to TNFα treatment. Therefore, glucocorticoids may help to preserve the integrity of the tight junctions in the BBB via transcriptional and post-translational regulation following CNS diseases and injuries.