bluuebunny/crossref_metadata_2025_split huggingface dataset:
Convergent Bacterial Microbiotas in the Fungal Agricultural Systems of Insects
Authors: Aylward Frank O. , Suen Garret , Biedermann Peter H. W. , Adams Aaron S. , Scott Jarrod J. , Malfatti Stephanie A. , Glavina del Rio Tijana , Tringe Susannah G. , Poulsen Michael , Raffa Kenneth F. , Klepzig Kier D. , Currie Cameron R. 
Published: November 2014

ABSTRACT

The ability to cultivate food is an innovation that has produced some of the most successful ecological strategies on the planet. Although most well recognized in humans, where agriculture represents a defining feature of civilization, species of ants, beetles, and termites have also independently evolved symbioses with fungi that they cultivate for food. Despite occurring across divergent insect and fungal lineages, the fungivorous niches of these insects are remarkably similar, indicating convergent evolution toward this successful ecological strategy. Here, we characterize the microbiota of ants, beetles, and termites engaged in nutritional symbioses with fungi to define the bacterial groups associated with these prominent herbivores and forest pests. Using culture-independent techniques and the
in silico
reconstruction of 37 composite genomes of dominant community members, we demonstrate that different insect-fungal symbioses that collectively shape ecosystems worldwide have highly similar bacterial microbiotas comprised primarily of the genera
Enterobacter
,
Rahnella
, and
Pseudomonas
. Although these symbioses span three orders of insects and two phyla of fungi, we show that they are associated with bacteria sharing high whole-genome nucleotide identity. Due to the fine-scale correspondence of the bacterial microbiotas of insects engaged in fungal symbioses, our findings indicate that this represents an example of convergence of entire host-microbe complexes.

IMPORTANCE
The cultivation of fungi for food is a behavior that has evolved independently in ants, beetles, and termites and has enabled many species of these insects to become ecologically important and widely distributed herbivores and forest pests. Although the primary fungal cultivars of these insects have been studied for decades, comparatively little is known of their bacterial microbiota. In this study, we show that diverse fungus-growing insects are associated with a common bacterial community composed of the same dominant members. Furthermore, by demonstrating that many of these bacteria have high whole-genome similarity across distantly related insect hosts that reside thousands of miles apart, we show that these bacteria are an important and underappreciated feature of diverse fungus-growing insects. Because of the similarities in the agricultural lifestyles of these insects, this is an example of convergence between both the life histories of the host insects and their symbiotic microbiota.
Bioinformatic Genome Comparisons for Taxonomic and Phylogenetic Assignments Using
Aeromonas
as a Test Case
Authors: Colston Sophie M. , Fullmer Matthew S. , Beka Lidia , Lamy Brigitte , Gogarten J. Peter , Graf Joerg 
Published: November 2014

ABSTRACT

Prokaryotic taxonomy is the underpinning of microbiology, as it provides a framework for the proper identification and naming of organisms. The “gold standard” of bacterial species delineation is the overall genome similarity determined by DNA-DNA hybridization (DDH), a technically rigorous yet sometimes variable method that may produce inconsistent results. Improvements in next-generation sequencing have resulted in an upsurge of bacterial genome sequences and bioinformatic tools that compare genomic data, such as average nucleotide identity (ANI), correlation of tetranucleotide frequencies, and the genome-to-genome distance calculator, or
in silico
DDH (
is
DDH). Here, we evaluate ANI and
is
DDH in combination with phylogenetic studies using
Aeromonas
, a taxonomically challenging genus with many described species and several strains that were reassigned to different species as a test case. We generated improved, high-quality draft genome sequences for 33
Aeromonas
strains and combined them with 23 publicly available genomes. ANI and
is
DDH distances were determined and compared to phylogenies from multilocus sequence analysis of housekeeping genes, ribosomal proteins, and expanded core genes. The expanded core phylogenetic analysis suggested relationships between distant
Aeromonas
clades that were inconsistent with studies using fewer genes. ANI values of ≥96% and
is
DDH values of ≥70% consistently grouped genomes originating from strains of the same species together. Our study confirmed known misidentifications, validated the recent revisions in the nomenclature, and revealed that a number of genomes deposited in GenBank are misnamed. In addition, two strains were identified that may represent novel
Aeromonas
species.

IMPORTANCE
Improvements in DNA sequencing technologies have resulted in the ability to generate large numbers of high-quality draft genomes and led to a dramatic increase in the number of publically available genomes. This has allowed researchers to characterize microorganisms using genome data. Advantages of genome sequence-based classification include data and computing programs that can be readily shared, facilitating the standardization of taxonomic methodology and resolving conflicting identifications by providing greater uniformity in an overall analysis. Using
Aeromonas
as a test case, we compared and validated different approaches. Based on our analyses, we recommend cutoff values for distance measures for identifying species. Accurate species classification is critical not only to obviate the perpetuation of errors in public databases but also to ensure the validity of inferences made on the relationships among species within a genus and proper identification in clinical and veterinary diagnostic laboratories.
Prevalence and management of gastrointestinal manifestations in Silver–Russell syndrome
Authors: Marsaud Céline , Rossignol Sylvie , Tounian Patrick , Netchine Irène , Dubern Béatrice 
Published: November 2014

ObjectivesSilver–Russell syndrome (SRS) is an imprinted disorder characterised by intrauterine growth retardation, relative macrocephaly, failure to thrive, typical facial phenotype and frequent body asymmetry. Feeding difficulties are frequently noted, but no study described evolution of gastrointestinal signs during infancy and their management in SRS. The aim of this study was to describe these abnormalities in a large cohort of children with SRS.DesignWe included 75 patients (median age 24.3 months (5.1–135.2)) in the study. We retrospectively analysed nutritional status before growth hormone therapy, the frequency of gastrointestinal signs, such as gastroesophageal reflux (GER), vomiting, constipation and feeding difficulties, and nutritional management.ResultsMaternal uniparental disomy for chromosome 7 was found in 10 patients and 11p15 hypomethylation in 65 patients. Malnutrition (defined as a weight/expected weight for height ratio <80%) was detected in 70% of the children. Gastrointestinal signs were found in 77%, including severe vomiting before the age of 1 year in 50% of cases, persistent vomiting from the age of 1 year in 29% of cases and constipation in 20% of cases. Severe GER was diagnosed in 55% of children by 24 h oesophageal pH-metry. Feeding difficulties were described in 65% of cases, with indications for dietary enrichment in 49%. Enteral nutrition by gastrostomy was indicated in 22% of cases.ConclusionsDigestive signs (GER, constipation) and malnutrition are frequent in children with SRS. The systematic exploration and management of these signs are crucial to improve the nutritional status of these children before initiating growth hormone therapy.
Health literacy issues in the care of Chinese American immigrants with diabetes: a qualitative study
Authors: Leung Angela Yee Man , Bo Ai , Hsiao Hsin-Yi , Wang Song Song , Chi Iris 
Published: November 2014

ObjectivesTo investigate why first-generation Chinese immigrants with diabetes have difficulty obtaining, processing and understanding diabetes related information despite the existence of translated materials and translators.DesignThis qualitative study employed purposive sampling. Six focus groups and two individual interviews were conducted. Each group discussion lasted approximately 90 min and was guided by semistructured and open-ended questions.SettingData were collected in two community health centres and one elderly retirement village in Los Angeles, California.Participants29 Chinese immigrants aged ≥45 years and diagnosed with type 2 diabetes for at least 1 year.ResultsEight key themes were found to potentially affect Chinese immigrants' capacity to obtain, communicate, process and understand diabetes related health information and consequently alter their decision making in self-care. Among the themes, three major categories emerged: cultural factors, structural barriers, and personal barriers.ConclusionsFindings highlight the importance of cultural sensitivity when working with first-generation Chinese immigrants with diabetes. Implications for health professionals, local community centres and other potential service providers are discussed.
Merging Query Results From Local Search Engines for Georeferenced Objects
Authors: Dragut Eduard C. , Dasgupta Bhaskar , Beirne Brian P. , Neyestani Ali , Atassi Badr , Yu Clement , Meng Weiyi 
Published: November 2014

The emergence of numerous online sources about local services presents a need for more automatic yet accurate data integration techniques. Local services are georeferenced objects and can be queried by their locations on a map, for instance, neighborhoods. Typical local service queries (e.g., “French Restaurant in The Loop”) include not only information about “what” (“French Restaurant”) a user is searching for (such as cuisine) but also “where” information, such as neighborhood (“The Loop”). In this article, we address three key problems: query translation, result merging and ranking. Most local search engines provide a (hierarchical) organization of (large) cities into neighborhoods. A neighborhood in one local search engine may correspond to sets of neighborhoods in other local search engines. These make the query translation challenging. To provide an integrated access to the query results returned by the local search engines, we need to combine the results into a single list of results.
Our contributions include: (1) An integration algorithm for neighborhoods. (2) A very effective business listing resolution algorithm. (3) A ranking algorithm that takes into consideration the user criteria, user ratings and rankings. We have created a prototype system, Yumi, over local search engines in the restaurant domain. The restaurant domain is a representative case study for the local services. We conducted a comprehensive experimental study to evaluate Yumi. A prototype version of Yumi is available online.
l-Arginine Depletion Blunts Antitumor T-cell Responses by Inducing Myeloid-Derived Suppressor Cells
Authors: Fletcher Matthew , Ramirez Maria E. , Sierra Rosa A. , Raber Patrick , Thevenot Paul , Al-Khami Amir A. , Sanchez-Pino Dulfary , Hernandez Claudia , Wyczechowska Dorota D. , Ochoa Augusto C. , Rodriguez Paulo C. 
Published: November 2014

Abstract
Enzymatic depletion of the nonessential amino acid l-Arginine (l-Arg) in patients with cancer by the administration of a pegylated form of the catabolic enzyme arginase I (peg-Arg I) has shown some promise as a therapeutic approach. However, l-Arg deprivation also suppresses T-cell responses in tumors. In this study, we sought to reconcile these observations by conducting a detailed analysis of the effects of peg-Arg I on normal T cells. Strikingly, we found that peg-Arg I blocked proliferation and cell-cycle progression in normal activated T cells without triggering apoptosis or blunting T-cell activation. These effects were associated with an inhibition of aerobic glycolysis in activated T cells, but not with significant alterations in mitochondrial oxidative respiration, which thereby regulated survival of T cells exposed to peg-Arg I. Further mechanistic investigations showed that the addition of citrulline, a metabolic precursor for l-Arg, rescued the antiproliferative effects of peg-Arg I on T cells in vitro. Moreover, serum levels of citrulline increased after in vivo administration of peg-Arg I. In support of the hypothesis that peg-Arg I acted indirectly to block T-cell responses in vivo, peg-Arg I inhibited T-cell proliferation in mice by inducing accumulation of myeloid-derived suppressor cells (MDSC). MDSC induction by peg-Arg I occurred through the general control nonrepressed-2 eIF2α kinase. Moreover, we found that peg-Arg I enhanced the growth of tumors in mice in a manner that correlated with higher MDSC numbers. Taken together, our results highlight the risks of the l-Arg–depleting therapy for cancer treatment and suggest a need for cotargeting MDSC in such therapeutic settings. Cancer Res; 75(2); 275–83. ©2014 AACR.
Notch1 Mutations Are Drivers of Oral Tumorigenesis
Authors: Izumchenko Evgeny , Sun Kai , Jones Sian , Brait Mariana , Agrawal Nishant , Koch Wayne , McCord Christine L. , Riley David R. , Angiuoli Samuel V. , Velculescu Victor E. , Jiang Wei-Wen , Sidransky David 
Published: November 2014

Abstract
Disruption of NOTCH1 signaling was recently discovered in head and neck cancer. This study aims to evaluate NOTCH1 alterations in the progression of oral squamous cell carcinoma (OSCC) and compare the occurrence of these mutations in Chinese and Caucasian populations. We used a high-throughput PCR-based enrichment technology and next-generation sequencing (NGS) to sequence NOTCH1 in 144 samples collected in China. Forty-nine samples were normal oral mucosa from patients undergoing oral surgery, 45 were oral leukoplakia biopsies, and 50 were chemoradiation-naïve OSCC samples with 22 paired-normal tissues from the adjacent unaffected areas. NOTCH1 mutations were found in 54% of primary OSCC and 60% of premalignant lesions. Importantly, almost 60% of patients with leukoplakia with mutated NOTCH1 carried mutations that were also identified in OSCC, indicating an important role of these clonal events in the progression of early neoplasms. We then compared all known NOTCH1 mutations identified in Chinese patients with OSCC with those reported in Caucasians to date. Although we found obvious overlaps in critical regulatory NOTCH1 domains alterations and identified specific mutations shared by both groups, possible gain-of-function mutations were predominantly seen in Chinese population. Our findings demonstrate that premalignant lesions display NOTCH1 mutations at an early stage and are thus bona fide drivers of OSCC progression. Moreover, our results reveal that NOTCH1 promotes distinct tumorigenic mechanisms in patients from different ethnical populations. Cancer Prev Res; 8(4); 277–86. ©2014 AACR.
See related perspectives, p. 259 and p. 262
Relationship of the Distance Between Non-PCI Hospitals and Primary PCI Centers, Mode of Transport, and Reperfusion Time Among Ground and Air Interhospital Transfers Using NCDR’s ACTION Registry-GWTG
Authors: Nicholson Benjamin D. , Dhindsa Harinder S. , Roe Matthew T. , Chen Anita Y. , Jollis James G. , Kontos Michael C. 
Published: November 2014

Background—
ST-segment myocardial infarction patients frequently present to non-percutaneous coronary intervention (PCI) hospitals and require interhospital transfer for primary PCI. The effect of distance and mode of transport to the PCI center and the frequency that recommended primary PCI times are met are not clear.

Methods and Results—

Data from the ACTION Registry
®
-GWTG™ were used to determine the distance between the Non-PCI and PCI center and first door time to balloon time based on transfer mode (ground and air) for patients having interhospital transfer for primary PCI. From July 1, 2008, to December 31, 2012, 17 052 ST-segment myocardial infarction patients were transferred to 413 PCI hospitals. The median distance from the non-PCI hospital to the primary PCI center was 31.9 miles (Q1, Q3: 19.1, 47.9; ground 25.2 miles; air 43.9 miles;
P
<0.001). At distances <40 miles, ground transport was the primary transport method, whereas at distances >40 miles air transport predominanted. Median first door time to balloon time time for patients transferred for primary PCI was 118 minutes (Q1, Q3: 95 152), with time for patients transported by air significantly longer (median 124 versus 113 minutes; respectively,
P
<0.001) than for patients transported by ground. Fifty-three percent of patients had a first door time to balloon time ≤120 minutes, with only 20% ≤90 minutes. A first door time to balloon time ≤120 minutes was more likely in ground than in air transport patients (57.0% versus 45.6%;
P
<0.001).

Conclusions—
Interhospital transfer for primary PCI is associated with prolonged reperfusion times. These delays should prompt increased consideration of fibrinolytic therapy, emergency medical services hospital bypass protocols, and improved systems of care for ST-segment myocardial infarction patients requiring transfer.
Disdrometer Network Observations of Finescale Spatial–Temporal Clustering in Rain
Authors: Jameson A. R. , Larsen M. L. , Kostinski A. B. 
Published: November 2014

Abstract
The spatial clustering of drops is a defining characteristic of rain on all scales from centimeters to kilometers. It is the physical basis for much of the observed variability in rain. The authors report here on the temporal–spatial 1-min counts using a network of 21 optical disdrometers over a small area near Charleston, South Carolina. These observations reveal significant differences between spatial and temporal structures (i.e., clustering) for different sizes of drops, which suggest that temporal observations of clustering cannot be used to infer spatial clustering simply using by an advection velocity as has been done in past studies. It is also shown that both spatial and temporal clustering play a role in rain variability depending upon the drop size. The more convective rain is dominated by spatial clustering while the opposite holds for the more stratiform rain.
Like previous time series measurements by a single disdrometer but in contradiction with widely accepted drop size distribution power-law relations, it is also shown that there is a linear relation between 1-min averages of the rainfall rate R over the network and the average total number of drops Nt. However, the network (area) R–Nt relation differs from those derived strictly from time series observations by individual disdrometers. These differences imply that the temporal and spatial size distributions and their variabilities are not equivalent.
The Dissipation of Trapped Lee Waves. Part I: Leakage of Inviscid Waves into the Stratosphere
Authors: Durran Dale R. , Hills Matthew O. G. , Blossey Peter N. 
Published: November 2014

Abstract
Leaky trapped mountain lee waves are investigated by examining the structure of individual linear modes in multilayer atmospheres. When the static stability and cross-mountain wind speed are constant in the topmost unbounded layer, modes that decay exponentially downstream also grow exponentially with height. This growth with height occurs because packets containing relatively large-amplitude waves follow ray paths through the stratosphere, placing them above packets entering the stratosphere farther downstream that contain relatively low-amplitude waves. Nevertheless, if the trapped wave train is generated by a compact source, all waves disappear above some line parallel to the group velocity that passes just above the source region.
The rate of downstream decay due to leakage into the stratosphere is strongly dependent on the atmospheric structure. Downstream dissipation is often significant under realistic atmospheric conditions, which typically include elevated inversions and strong upper-tropospheric winds. On the other hand, idealized profiles with constant Scorer parameters throughout each of two tropospheric layers can exhibit a wide range of behaviors when capped by a third stratospheric layer with typical real-world static stability. Assuming the Scorer parameter in the stratosphere is a little larger than the minimum value necessary to allow a particular mode to propagate vertically, the rate of downstream decay is more sensitive to changes in the height of the tropopause than to further increases in the stability of the stratosphere. Downstream decay is minimized when the tropopause is high and the horizontal wavelength is short.
Development and Formation Mechanism of the Southeast Asian Winter Heavy Rainfall Events around the South China Sea. Part I: Formation and Propagation of Cold Surge Vortex*
Authors: Chen Tsing-Chang , Tsay Jenq-Dar , Matsumoto Jun , Alpert Jordan 
Published: November 2014

Abstract
Examination of the development of cold season heavy rainfall/flood (HRF) events around the South China Sea (SCS) from their parent cold surge vortices (CSVs) shows three new development processes. First, the formation mechanism of the parent CSV of an HRF event [CSV(HRF)] has a preference as to geographic location, flow type of the cold surge inside the SCS, and time of day. The surface trough east of the Philippines, Taiwan, and southern Japan island chain in late fall and the near-equator trough across Borneo in winter facilitate the CSV(HRF) formation in two regions—the vicinity of the Philippines and Borneo. The formation of the Philippine (Borneo) CSV(HRF) occurs at 0600 UTC (0000 UTC) with involvement from the Philippine Sea (PHS)-type (SCS type) of cold surge flow. Second, the flow type of the cold surge determines the CSV(HRF) propagation across the South China Sea. The PHS-type (SCS type) facilitates (hinders) the CSV(HRF) westward propagation. This occurs because the easterly (northerly) flow is greater than (less than) the northerly (easterly) flow at the maximum isotach location of the cold surge flow associated with CSV(HRF) and is centered east of the demarcation line for propagation. This flow-type contrast is substantiated by the vorticity budget analysis for CSV(HRF). The positive 925-hPa vorticity tendency is located west of (coincident with) the 925-hPa vorticity center for the PHS-type (SCS type) of cold surge. Third, the CSV(HRF) development into a HRF event is achieved through multiple interactions of former vortices with sequential cold surges across the South China Sea. The first two CSV(HRF) development processes are reported herein; the last process is presented in Part II.