bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Gondwanan legacy in South American biogeography
Authors: Segovia Ricardo A. , Armesto Juan J. 
Published: January 2015

AbstractThe tropical conservatism hypothesis (TCH) suggests that phylogenetic niche conservatism (the tendency for traits to be maintained during diversification) should be the main driver of latitudinal diversity gradients. For example, the tropical–temperate diversity gradient for woody angiosperms should reflect the tropical, older origin of most clades, the constrained evolution of cold tolerance, and the fact that few clades were able to persist in temperate zones after the beginning of the global cooling in the Eocene. Evidence for this explanation has been discussed primarily from a Northern Hemisphere perspective. Recently, two studies have presented diversity and clade–age relationships in South American forests that are inconsistent with the TCH, with older woody families being more frequent at higher latitudes and higher elevations in the Andes. We argue that a broader framework considering the ancient history of the Southern Hemisphere flora and the recent history of the Andean flora can help explain these discordant patterns. Here, we provide an initial discussion of this new perspective, emphasizing the historical development of a unique and rich palaeoflora of Gondwanan ancestry at mid‐ to high latitudes of South America and Antarctica. We suggest that the idea of Austral niche conservatism (ANC) of a warm‐temperate Antarctic–South American biota should be explored further to improve our understanding of biogeographical patterns in the Southern Hemisphere.
Colonic motor abnormalities in slow transit constipation defined by high resolution, fibre‐optic manometry
Authors: Dinning P. G. , Wiklendt L. , Maslen L. , Patton V. , Lewis H. , Arkwright J. W. , Wattchow D. A. , Lubowski D. Z. , Costa M. , Bampton P. A. 
Published: January 2015

AbstractBackgroundSlow transit constipation (STC) is associated with colonic motor abnormalities. The underlying cause(s) of the abnormalities remain poorly defined. In health, utilizing high resolution fiber‐optic manometry, we have described a distal colonic propagating motor pattern with a slow wave frequency of 2–6 cycles per minute (cpm). A high calorie meal caused a rapid and significant increase in this activity, suggesting the intrinsic slow wave activity could be mediated by extrinsic neural input. Utilizing the same protocol our aim was to characterize colonic meal response STC patients.MethodsA fiber‐optic manometry catheter (72 sensors at 1 cm intervals) was colonoscopically placed with the tip clipped at the ascending or transverse colon, in 14 patients with scintigraphically confirmed STC. Manometric recordings were taken, for 2 h pre and post a 700 kCal meal. Data were compared to 12 healthy adults.Key ResultsPrior to and/or after the meal the cyclic propagating motor pattern was identified in 13 of 14 patients. However, the meal, did not increase the cyclic motor pattern (preprandial 7.4 ± 7.6 vs postprandial 8.3 ± 4.5 per/2 h), this is in contrast to the dramatic increase observed in health (8.3 ± 13.3 vs 59.1 ± 89.0 per/2 h; p < 0.001).Conclusions & InferencesIn patients with STC a meal fails to induce the normal increase in the distal colonic cyclic propagating motor patterns. We propose that these data may indicate that the normal extrinsic parasympathetic inputs to the colon are attenuated in these patients.
Digestive, cognitive and hedonic responses to a meal
Authors: Malagelada C. , Accarino A. , Molne L. , Mendez S. , Campos E. , Gonzalez A. , Malagelada J. R. , Azpiroz F. 
Published: January 2015

AbstractBackgroundGut dysfunctions may be associated to digestive symptoms. We hypothesized that the gut can also originate pleasant sensations, and wished to demonstrate the hedonic component of the digestive response to a meal.MethodsHealthy subjects (n = 42) were evaluated during basal fasting conditions and during experimentally induced fullness sensation (either by gastric distension or duodenal nutrient infusion). In each set of studies, a 240 mL test meal (12 kcal broth) and water, as inert control meal, were administered on separate days in a randomized, cross‐over design. Gastric accommodation, the cognitive response and the hedonic dimension (both by 10 score scales) were measured 9 min before and 60 min after the meal.Key ResultsIn basal conditions, the test meal induced a significantly greater gastric relaxation than the control meal (166 ± 28 mL isotonic volume increase 67 ± 14 mL; p = 0.002). Both meals induced epigastric fullness (3.8 ± 0.7 score and 3.2 ± 0.8 score, respectively; p = 0.740), but contrary to the inert meal, with the active meal this conscious sensation had a pleasant dimension (digestive comfort increase by 1.3 ± 0.6 score with active meal vs −1.1 ± 0.6 decrease with inert meal; p = 0.015). Experimentally induced fullness was associated to a decrease in digestive well‐being or abdominal discomfort, which improved only after the active meal but not the inert meal.Conclusions & InferencesWhen appropriate conditions are met, the response to a meal includes a hedonic dimension involving pleasant sensation of digestive well‐being.
A continental view of pine‐associated ectomycorrhizal fungal spore banks: a quiescent functional guild with a strong biogeographic pattern
Authors: Glassman Sydney I. , Peay Kabir G. , Talbot Jennifer M. , Smith Dylan P. , Chung Judy A. , Taylor John W. , Vilgalys Rytas , Bruns Thomas D. 
Published: January 2015

Summary

Ecologists have long acknowledged the importance of seed banks; yet, despite the fact that many plants rely on mycorrhizal fungi for survival and growth, the structure of ectomycorrhizal (ECM) fungal spore banks remains poorly understood. The primary goal of this study was to assess the geographic structure in pine‐associated ECM fungal spore banks across the North American continent.

Soils were collected from 19 plots in forests across North America. Fresh soils were pyrosequenced for fungal internal transcribed spacer (ITS) amplicons. Adjacent soil cores were dried and bioassayed with pine seedlings, and colonized roots were pyrosequenced to detect resistant propagules of ECM fungi.

The results showed that ECM spore banks correlated strongly with biogeographic location, but not with the identity of congeneric plant hosts. Minimal community overlap was found between resident ECM fungi vs those in spore banks, and spore bank assemblages were relatively simple and dominated by Rhizopogon, Wilcoxina, Cenococcum, Thelephora, Tuber, Laccaria and Suillus.

Similar to plant seed banks, ECM fungal spore banks are, in general, depauperate, and represent a small and rare subset of the mature forest soil fungal community. Yet, they may be extremely important in fungal colonization after large‐scale disturbances such as clear cuts and forest fires.
Pimecrolimus in atopic dermatitis: Consensus on safety and the need to allow use in infants
Authors: Luger Thomas , Boguniewicz Mark , Carr Warner , Cork Michael , Deleuran Mette , Eichenfield Lawrence , Eigenmann Philippe , Fölster‐Holst Regina , Gelmetti Carlo , Gollnick Harald , Hamelmann Eckard , Hebert Adelaide A. , Muraro Antonella , Oranje Arnold P. , Paller Amy S. , Paul Carle , Puig Luis , Ring Johannes , Siegfried Elaine , Spergel Jonathan M. , Stingl Georg , Taieb Alain , Torrelo Antonio , Werfel Thomas , Wahn Ulrich 
Published: January 2015

AbstractAtopic dermatitis (AD) is a distressing dermatological disease, which is highly prevalent during infancy, can persist into later life and requires long‐term management with anti‐inflammatory compounds. The introduction of the topical calcineurin inhibitors (TCIs), tacrolimus and pimecrolimus, more than 10 yr ago was a major breakthrough for the topical anti‐inflammatory treatment of AD. Pimecrolimus 1% is approved for second‐line use in children (≥2 yr old) and adults with mild‐to‐moderate AD. The age restriction was emphasized in a boxed warning added by the FDA in January 2006, which also highlights the lack of long‐term safety data and the theoretical risk of skin malignancy and lymphoma. Since then, pimecrolimus has been extensively investigated in short‐ and long‐term studies including over 4000 infants (<2 yr old). These studies showed that pimecrolimus effectively treats AD in infants, with sustained improvement with long‐term intermittent use. Unlike topical corticosteroids, long‐term TCI use does not carry the risks of skin atrophy, impaired epidermal barrier function or enhanced percutaneous absorption, and so is suitable for AD treatment especially in sensitive skin areas. Most importantly, the studies of pimecrolimus in infants provided no evidence for systemic immunosuppression, and a comprehensive body of evidence from clinical studies, post‐marketing surveillance and epidemiological investigations does not support potential safety concerns. In conclusion, the authors consider that the labelling restrictions regarding the use of pimecrolimus in infants are no longer justified and recommend that the validity of the boxed warning for TCIs should be reconsidered.
A comparison of functional magnetic resonance imaging findings in children with and without a history of early exposure to general anesthesia
Authors: Taghon Thomas A. , Masunga Abigail N. , Small Robert H. , Kashou Nasser H. 
Published: January 2015

SummaryBackgroundFunctional magnetic resonance imaging (fMRI) has been used to evaluate the long‐term consequences of early exposure to neurotoxic agents. fMRI shows that different patterns of brain activation occur in ethanol‐exposed subjects performing a go/no‐go response inhibition task. Pharmacologically, ethanol and general anesthetics have similar receptor‐level activity in the brain. This study utilizes fMRI to examine brain activation patterns in children exposed to general anesthesia and surgery during early brain development.MethodsAfter obtaining Nationwide Children's Hospital IRB approval, a surgical database was utilized to identify children aged 10–17 years with a history of at least 1 h of exposure to general anesthetics and surgery when they were between 0 and 24 months of age. Age‐ and gender‐matched children without anesthesia exposure were recruited as a control group. All subjects were scanned while being presented with a go/no‐go response inhibition task. Reaction time and accuracy data were acquired, and the blood‐oxygen‐level‐dependent (BOLD) fMRI signal was measured as a biomarker for regional neuronal activity.ResultsThere were no differences in terms of performance accuracy and response time. The analysis did not reveal any significant activation differences in the primary region of interest (prefrontal cortex and caudate nucleus); however, activation differences were seen in other structures, including the cerebellum, cingulate gyrus, and paracentral lobule.ConclusionsEarly anesthetic exposure and surgery did not affect accuracy, response time, or activation patterns in the primary region of interest during performance of the task. Intergroup differences in activation patterns in other areas of the brain were observed, and the significance of these findings is unknown. fMRI appears to be a useful tool in evaluating the long‐term effects of early exposure to general anesthesia.
Liver transplantation for neonatal hemochromatosis: Analysis of the UNOS database
Authors: Sheflin‐Findling Shari , Annunziato Rachel A. , Chu Jaime , Arvelakis Antonios , Mahon Danielle , Arnon Ronen 
Published: January 2015

AbstractNH is the most common identifiable cause of ALF in the neonate. LT is the definitive treatment for neonates with NH who have failed medical therapy. Our aim was to determine the outcomes of LT in infants with NH. Patients (less than one yr of age) with NH who were listed for LT and patients who underwent LT between 1994 and 2013 were identified from the UNOS database for analysis. Risk factors for death and graft loss were analyzed by multivariate logistic regression. Thirty‐eight infants with NH with a total of 43 transplants were identified. One‐ and five‐yr patient and graft survival were 84.2%, 81.6%, 71.1%, and 68.4%, respectively. The outcomes for NH were not significantly different when compared to the same age‐matched recipients with other causes of ALF. There were no statistically significant risk factors identified for graft loss or death. Ninety infants with NH were listed for LT. Reasons for removal included transplanted (49%), death (27%), too sick to transplant (7%), and improved status (13%). LT for infants with NH has a high rate of graft loss and death; however, outcomes are comparable to the same age‐matched recipients with other causes of ALF.
Microbial Production of Aliphatic (
S
)-Epoxyalkanes by Using Rhodococcus sp. Strain ST-10 Styrene Monooxygenase Expressed in Organic-Solvent-Tolerant Kocuria rhizophila DC2201
Authors: Toda Hiroshi , Ohuchi Takuya , Imae Ryouta , Itoh Nobuya 
Published: January 2015

ABSTRACT

We describe the development of biocatalysis for producing optically pure straight-chain (
S
)-epoxyalkanes using styrene monooxygenase of
Rhodococcus
sp. strain ST-10 (RhSMO). RhSMO was expressed in the organic solvent-tolerant microorganism
Kocuria rhizophila
DC2201, and the bioconversion reaction was performed in an organic solvent-water biphasic reaction system. The biocatalytic process enantioselectively converted linear terminal alkenes to their corresponding (
S
)-epoxyalkanes using glucose and molecular oxygen. When 1-heptene and 6-chloro-1-hexene were used as substrates (400 mM) under optimized conditions, 88.3 mM (
S
)-1,2-epoxyheptane and 246.5 mM (
S
)-1,2-epoxy-6-chlorohexane, respectively, accumulated in the organic phase with good enantiomeric excess (ee; 84.2 and 95.5%). The biocatalysis showed broad substrate specificity toward various aliphatic alkenes, including functionalized and unfunctionalized alkenes, with good to excellent ee. Here, we demonstrate that this biocatalytic system is environmentally friendly and useful for producing various enantiopure (
S
)-epoxyalkanes.
Non-O1/Non-O139 Vibrio cholerae Carrying Multiple Virulence Factors and V. cholerae O1 in the Chesapeake Bay, Maryland
Authors: Ceccarelli Daniela , Chen Arlene , Hasan Nur A. , Rashed Shah M. , Huq Anwar , Colwell Rita R. 
Published: January 2015

ABSTRACT

Non-O1/non-O139
Vibrio cholerae
inhabits estuarine and coastal waters globally, but its clinical significance has not been sufficiently investigated, despite the fact that it has been associated with septicemia and gastroenteritis. The emergence of virulent non-O1/non-O139
V. cholerae
is consistent with the recognition of new pathogenic variants worldwide. Oyster, sediment, and water samples were collected during a vibrio surveillance program carried out from 2009 to 2012 in the Chesapeake Bay, Maryland.
V. cholerae
O1 was detected by a direct fluorescent-antibody (DFA) assay but was not successfully cultured, whereas 395 isolates of non-O1/non-O139
V. cholerae
were confirmed by multiplex PCR and serology. Only a few of the non-O1/non-O139
V. cholerae
isolates were resistant to ampicillin and/or penicillin. Most of the isolates were sensitive to all antibiotics tested, and 77 to 90% carried the El Tor variant hemolysin gene
hlyA
ET
, the actin cross-linking repeats in toxin gene
rtxA
, the hemagglutinin protease gene
hap
, and the type 6 secretion system. About 19 to 21% of the isolates carried the neuraminidase-encoding gene
nanH
and/or the heat-stable toxin (NAG-ST), and only 5% contained a type 3 secretion system. None of the non-O1/non-O139
V. cholerae
isolates contained
Vibrio
pathogenicity island-associated genes. However,
ctxA
,
ace
, or
zot
was present in nine isolates. Fifty-five different genotypes showed up to 12 virulence factors, independent of the source of isolation, and represent the first report of both antibiotic susceptibility and virulence associated with non-O1/non-O139
V. cholerae
from the Chesapeake Bay. Since these results confirm the presence of potentially pathogenic non-O1/non-O139
V. cholerae
, monitoring for total
V. cholerae
, regardless of serotype, should be done within the context of public health.
Enhancing the Secretion Efficiency and Thermostability of a Bacillusderamificans Pullulanase Mutant (D437H/D503Y) by N-Terminal Domain Truncation
Authors: Duan Xuguo , Wu Jing 
Published: January 2015

ABSTRACT

Pullulanase (EC 3.2.1.41), an important enzyme in the production of starch syrup, catalyzes the hydrolysis of α-1,6 glycosidic bonds in complex carbohydrates. A double mutant (DM; D437H/D503Y) form of
Bacillus
deramificans
pullulanase was recently constructed to enhance the thermostability and catalytic efficiency of the enzyme (X. Duan, J. Chen, and J. Wu, Appl Environ Microbiol 79:4072–4077, 2013,
http://dx.doi.org/10.1128/AEM.00457-13
). In the present study, three N-terminally truncated variants of this DM that lack the CBM41 domain (DM-T1), the CBM41 and X25 domains (DM-T2), or the CBM41, X25, and X45 domains (DM-T3) were constructed. Upon expression, DM-T3 existed as inclusion bodies, while 72.8 and 74.8% of the total pullulanase activities of DM-T1 and DM-T2, respectively, were secreted into the medium. These activities are 2.8- and 2.9-fold that of the DM enzyme, respectively. The specific activities of DM-T1 and DM-T2 were 380.0 × 10
8
and 449.3 × 10
8
U · mol
−1
, respectively, which are 0.94- and 1.11-fold that of the DM enzyme. DM-T1 and DM-T2 retained 50% of their activity after incubation at 60°C for 203 and 160 h, respectively, which are 1.7- and 1.3-fold that of the DM enzyme. Kinetic studies showed that the

K
m

values of DM-T1 and DM-T2 were 1.5- and 2.7-fold higher and the
K
cat
/

K
m

values were 11 and 50% lower, respectively, than those of the DM enzyme. Furthermore, DM-T1 and DM-T2 produced
d
-glucose contents of 95.0 and 94.1%, respectively, in a starch saccharification reaction, which are essentially identical to that produced by the DM enzyme (95%). The enhanced secretion and improved thermostability of the truncation mutant enzymes make them more suitable than the DM enzyme for industrial processes.
Role of Tec1 in the Development, Architecture, and Integrity of Sexual Biofilms of Candida albicans
Authors: Daniels Karla J. , Srikantha Thyagarajan , Pujol Claude , Park Yang-Nim , Soll David R. 
Published: January 2015

ABSTRACT

MTL
-homozygous (
a
/
a
or α/α) white cells form a complex sexual biofilm that exhibits the same architecture as that of
MTL
-heterozygous (
a
/α) pathogenic biofilms. However, the former is regulated by the mitogen-activated protein (MAP) kinase pathway, while the latter is regulated by the Ras1/cyclic AMP (cAMP) pathway. We previously demonstrated that in the formation of an
MTL
-homozygous, mature (48 h) sexual biofilm in RPMI 1640 medium, the MAP kinase pathway targets Tec1 rather than Cph1, the latter of which is the target of the same pathway, but for the opaque cell mating response. Here we continued our analysis of the role of Tec1 by comparing the effects of deleting
TEC1
on initial adhesion to silicone elastomer, high-resolution confocal microscopy assessments of the stages and cellular phenotypes during the 48 h of biofilm development, human white cell penetration, and biofilm fragility. We show that although Tec1 plays only a minor role in initial adhesion to the silicone elastomer, it does play a major role in the growth of the basal yeast cell polylayer, vertical extension of hyphae and matrix deposition in the upper portion of the biofilm, final biofilm thickness, penetrability of human white blood cells, and final biofilm integrity (i.e., resistance to fluid flow). These results provide a more detailed description of normal biofilm development and architecture and confirm the central role played by the transcription factor Tec1 in the biofilm model employed here.
Complete Genome Sequences of T4-Like Bacteriophages RB3, RB5, RB6, RB7, RB9, RB10, RB27, RB33, RB55, RB59, and RB68
Authors: Yaung Stephanie J. , Esvelt Kevin M. , Church George M. 
Published: January 2015

ABSTRACT
T4-like bacteriophages have been explored for phage therapy and are model organisms for phage genomics and evolution. Here, we describe the sequencing of 11 T4-like phages. We found a high nucleotide similarity among the T4, RB55, and RB59; RB32 and RB33; and RB3, RB5, RB6, RB7, RB9, and RB10 phages.
Draft Genome Sequence of Nocardia seriolae ZJ0503, a Fish Pathogen Isolated from
Trachinotus ovatus
in China
Authors: Xia Liqun , Cai Jia , Wang Bei , Huang Yucong , Jian Jichang , Lu Yishan 
Published: January 2015

ABSTRACT

Nocardia seriolae
is a pathogen that causes nocardiosis in marine and freshwater fish. Here, we report the draft genome sequence of
N. seriolae
strain ZJ0503, which was isolated from
Trachinotus ovatus
in Guangdong, China.
Whole-Genome Sequence of Quorum-Sensing Vibrio tubiashii Strain T33
Authors: Izzati Mohamad Nur , Yin Wai-Fong , Chan Kok-Gan 
Published: January 2015

ABSTRACT

Vibrio tubiashii
strain T33 was isolated from the coastal waters of Morib, Malaysia, and was shown to possess quorum-sensing activity similar to that of its famous relative
Vibrio fischeri
. Here, the assembly and annotation of its genome are presented.
Insights into the Quorum-Sensing Activity in Aeromonas hydrophila Strain M013 as Revealed by Whole-Genome Sequencing
Authors: Tan Wen-Si , Yin Wai-Fong , Chan Kok-Gan 
Published: January 2015

ABSTRACT

Aeromonas hydrophila
species can be found in warm climates and can survive in different environments. They possess the ability to communicate within their populations, which is known as quorum sensing. In this work, we present the draft genome sequence of A. hydrophila M013, a bacterium isolated from a Malaysian tropical rainforest waterfall.
Draft Genome Sequence of Oenococcus oeni Strain X
2
L (CRL1947), Isolated from Red Wine of Northwest Argentina
Authors: Mendoza Lucía M. , Saavedra Lucila , Raya Raúl R. 
Published: January 2015

ABSTRACT

We report the draft genome sequence of
Oenococcus oeni
strain X
2
L, a potential starter culture of malolactic fermentation, isolated from Malbec wine of Argentina. Genes encoding for enzymes involved in the metabolism of malate, citrate, and nitrogen compounds, as well as aroma compounds, were found in this genome, showing its ability to improve the sensorial characteristics of wines.
Two Metagenomes from Late Pleistocene Northeast Siberian Permafrost
Authors: Krivushin Kirill , Kondrashov Fyodor , Shmakova Lyubov , Tutukina Mariya , Petrovskaya Lada , Rivkina Elizaveta 
Published: January 2015

ABSTRACT
The present study reports metagenomic shotgun sequencing of microbial communities of two ancient permafrost horizons of the Russian Arctic. Results demonstrate a significant difference in microbial community structure of the analyzed samples in general and microorganisms of the methane cycle in particular.