bluuebunny/crossref_metadata_2025 huggingface dataset:
Resource Allocation by the Banking System
Authors: Battilossi Stefano , Gigliobianco Alfredo , Marinelli Giuseppe , Triglia With The Cooperation Of Sandra Natoli and Ivan
Published: January 2014

In Italy's bank-oriented financial system, bank credit is the most important source of external finance for firms. The allocative efficiency of banks is therefore a critical element underlying the overall performance of the economy. This chapter focuses on credit allocation across industrial sectors with different growth opportunities, as revealed by stock market data. We constructed a unique database which includes annual data on bank credit to different sectors and data on listed firms from 1948 to 2009. We assume that average sectoral price/earnings ratios are a proxy for growth opportunities, and that an efficient allocation of credit takes into account the variation of such opportunities. Our results confirm the hypothesis that, after a good start in the Fifties and Sixties, the following two decades, characterized by an excess of regulation (mixed with robust doses of political interference), saw a decline in the performance of the banking system. We also find evidence that after the financial liberalization of the early Nineties the allocative efficiency (across sectors) of the banking system increased. The present structural difficulties of the Italian economy do not depend, therefore, on the ability of the banks to select the industrial sectors to which to lend money.
Stable hovering of a jellyfish-like flying machine
Authors: Ristroph Leif , Childress Stephen
Published: January 2014

Ornithopters, or flapping-wing aircraft, offer an alternative to helicopters in achieving manoeuvrability at small scales, although stabilizing such aerial vehicles remains a key challenge. Here, we present a hovering machine that achieves self-righting flight using flapping wings alone, without relying on additional aerodynamic surfaces and without feedback control. We design, construct and test-fly a prototype that opens and closes four wings, resembling the motions of swimming jellyfish more so than any insect or bird. Measurements of lift show the benefits of wing flexing and the importance of selecting a wing size appropriate to the motor. Furthermore, we use high-speed video and motion tracking to show that the body orientation is stable during ascending, forward and hovering flight modes. Our experimental measurements are used to inform an aerodynamic model of stability that reveals the importance of centre-of-mass location and the coupling of body translation and rotation. These results show the promise of flapping-flight strategies beyond those that directly mimic the wing motions of flying animals.
Synergy of cell–cell repulsion and vacuolation in a computational model of lumen formation
Authors: Boas Sonja E. M. , Merks Roeland M. H.
Published: January 2014

A key step in blood vessel development (angiogenesis) is lumen formation: the hollowing of vessels for blood perfusion. Two alternative lumen formation mechanisms are suggested to function in different types of blood vessels. Thevacuolationmechanism is suggested for lumen formation in small vessels by coalescence of intracellular vacuoles, a view that was extended to extracellular lumen formation by exocytosis of vacuoles. Thecell–cell repulsionmechanism is suggested to initiate extracellular lumen formation in large vessels by active repulsion of adjacent cells, and active cell shape changes extend the lumen. We used an agent-based computer model, based on the cellular Potts model, to compare and study both mechanisms separately and combined. An extensive sensitivity analysis shows that each of the mechanisms on its own can produce lumens in a narrow region of parameter space. However, combining both mechanisms makes lumen formation much more robust to the values of the parameters, suggesting that the mechanisms may work synergistically and operate in parallel, rather than in different vessel types.
Analytical insights into optimality and resonance in fish swimming
Authors: Kohannim Saba , Iwasaki Tetsuya
Published: January 2014

This paper provides analytical insights into the hypothesis that fish exploit resonance to reduce the mechanical cost of swimming. A simple body–fluid fish model, representing carangiform locomotion, is developed. Steady swimming at various speeds is analysed using optimal gait theory by minimizing bending moment over tail movements and stiffness, and the results are shown to match with data from observed swimming. Our analysis indicates the following: thrust–drag balance leads to the Strouhal number being predetermined based on the drag coefficient and the ratio of wetted body area to cross-sectional area of accelerated fluid. Muscle tension is reduced when undulation frequency matches resonance frequency, which maximizes the ratio of tail-tip velocity to bending moment. Finally, hydrodynamic resonance determines tail-beat frequency, whereas muscle stiffness is actively adjusted, so that overall body–fluid resonance is exploited.
Determining optimal fallout shelter times following a nuclear detonation
Authors: Dillon Michael B.
Published: January 2014

In the event of a single, low-yield nuclear detonation in a major urban area, rapidly providing adequate shelter to affected populations could save 10 000–100 000 individuals from a fatal exposure to fallout radiation. However, poorly sheltered individuals may remain at risk. Current guidance and prior studies are not consistent as to the timing and conditions under which poorly sheltered individuals should leave their shelters to evacuate or obtain better shelter. This study proposes methods to determine the optimal shelter time based on information potentially available following a nuclear detonation. For the case in which individuals move to an adequate shelter that can be reached within 15 min, individuals should stay in a poor-quality shelter for at most 30 min after the detonation. If adequate shelter is available nearby (within 5 min), then poorly sheltered individuals should immediately proceed to the better shelter.
Network medicine analysis of chondrocyte proteins towards new treatments of osteoarthritis
Authors: Nacher Jose C. , Keith Benjamin , Schwartz Jean-Marc
Published: January 2014

Osteoarthritis (OA) is a progressive disorder with high incidence in the ageing human population that still has no treatment currently. This disorder induces the breakdown of articular cartilage, leading to the exposure and damage of bone surfaces. For a global understanding of OA development, the systematic integration of known OA-related proteins with protein–protein interaction (PPI) networks is required. In this work, the OA-related interactome was reconstructed using multiple data sources to have the most up-to-date information on OA-related proteins and their interactions. We then combined emergent concepts in network medicine to detect new unclassified OA-related proteins. The mapping of known OA-related proteins with PPI networks showed that these proteins are locally connected to each other and agglomerated in a large component. To expand this module, we applied a diffusion-based algorithm that probabilistically induces more searches in the vicinity of the seed OA-related proteins. As a result, the 10 topmost ranked proteins were connected to the OA disease module, supporting the local hypothesis. We computed structural modules and selected those that had the highest enrichment of OA-related proteins. The identified molecules show a link between structural topology and disease dysfunctionality. Interestingly, the protein Q6EEV6 was highlighted for OA association by both methods, reinforcing the potential involvement of this protein. These results suggest that similar disease-connected modules may exist in different human disorders, which could lead to systematic identification of genes or proteins that have a joint role in specific disease phenotypes.
Sediminibacterium goheungense sp. nov., isolated from a freshwater reservoir
Authors: Kang Heeyoung , Kim Haneul , Lee Beom-Il , Joung Yochan , Joh Kiseong
Published: January 2014

A novel bacterial strain designated HME7863T was isolated from a freshwater reservoir in Goheung, Republic of Korea. Cells of strain HME7863T were Gram-staining-negative, strictly aerobic, orange-pigmented, rod-shaped and motile by gliding. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain HME7863T formed a lineage within the genus

Sediminibacterium

. Strain HME7863T was closely related to

Sediminibacterium ginsengisoli

DCY13T (96.9 % sequence similarity) and

Sediminibacterium salmoneum

NJ-44T (96.4 %). The major cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH and iso-C16 : 0 3-OH. Polar lipid analysis revealed the presence of phosphatidylethanolamine, five unidentified aminolipids, two unidentified aminophospholipids, one unidentified phospholipid and two unidentified polar lipids. The only respiratory quinone was MK-7. The DNA G+C content was 40.5 mol%. On the basis of the evidence presented in this study, strain HME7863T represents a novel species of the genus

Sediminibacterium

, for which the name Sediminibacterium goheungense sp. nov., is proposed. The type strain is HME7863T ( = KCTC 23945T = CECT 8100T).
Oceanobacillus pacificus sp. nov., isolated from a deep-sea sediment
Authors: Yu Cong , Yu Shaolan , Zhang Zenghu , Li Zhao , Zhang Xiao-Hua
Published: January 2014

A moderately halophilic bacterial strain, designated XH204T, was isolated from deep-sea sediment core (45° 58′ S 163° 11′ W) of the South Pacific Gyre during the Integrated Ocean Drilling Program Expedition 329. The strain was Gram-stain-positive, rod-shaped, motile by peritrichous flagella and produced ellipsoidal endospores subterminally positioned within swollen sporangia. Growth of strain XH204T occurred at 15–42 °C (optimum 37 °C), in the presence of 0–14 % (w/v) NaCl (optimum 4 %) and at pH 7.0–10.0 (optimum pH 8.0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH204T belonged to the genus

Oceanobacillus

and showed the highest sequence similarity to

Oceanobacillus profundus

CL-MP28T (95.6 %); strain XH204T exhibited 93.4 % 16S rRNA gene sequence similarity to the type strain of the type species of the genus

Oceanobacillus

,

Oceanobacillus iheyensis

HTE831T. The dominant fatty acids of strain XH204T were anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The cell wall of strain XH204T contained meso-diaminopimelic acid as the diagnostic diamino acid, and ribose, glucose and galactose as the major whole-cell sugars. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. Menaquinone-7 (MK-7) was the only isoprenoid quinone and the DNA G+C content was 38.8 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic analysis, strain XH204T represents a novel species of the genus

Oceanobacillus

, for which the name Oceanobacillus pacificus sp. nov. is proposed. The type strain is XH204T ( = DSM 25873T = JCM 18381T).
Oceanobacillus limi sp. nov., a moderately halophilic bacterium from a salt lake
Authors: Amoozegar Mohammad Ali , Bagheri Maryam , Makhdoumi-Kakhki Ali , Didari Maryam , Schumann Peter , Spröer Cathrin , Sánchez-Porro Cristina , Ventosa Antonio
Published: January 2014

A Gram-stain-positive, endospore-forming, rod-shaped, strictly aerobic, moderately halophilic bacterium, designated strain H9BT, was isolated from a mud sample of the hypersaline lake Aran-Bidgol in Iran. Cells of strain H9BT were motile and produced colonies with a yellowish-grey pigment. Growth occurred between 2.5 and 10 % (w/v) NaCl and the isolate grew optimally at 7.5 % (w/v) NaCl. The optimum pH and temperature for growth of the strain were pH 7.0 and 35 °C, respectively, while it was able to grow over pH and temperature ranges of pH 6–10 and 25–45 °C, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain H9BT is a member of the genus

Oceanobacillus

. The closest relative to this strain was

Oceanobacillus profundus

CL-MP28T with 97.1 % 16S rRNA gene sequences similarity. The level of DNA–DNA relatedness between the novel isolate and this phylogenetically related species was 17 %. The major cellular fatty acids of the isolate were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C16 : 0. The polar lipid pattern of strain H9BT consisted of phosphatidylglycerol, diphosphatidylglycerol, four phospholipids and an aminolipid. It contained MK-7 as the predominant menaquinone and meso-diaminopimelic acid in the cell-wall peptidoglycan. The G+C content of the genomic DNA of this strain was 37.1 mol%. Phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data suggest that this strain represents a novel species of the genus

Oceanobacillus

, for which the name Oceanobacillus limi sp. nov. is proposed. The type strain of Oceanobacillus limi is strain H9BT ( = IBRC-M 10780T = KCTC 13823T = CECT 7997T).
Oceanisphaera profunda sp. nov., a marine bacterium isolated from deep-sea sediment, and emended description of the genus Oceanisphaera
Authors: Xu Zhong , Zhang Xi-Ying , Su Hai-Nan , Yu Zi-Chao , Liu Chang , Li Hai , Chen Xiu-Lan , Song Xiao-Yan , Xie Bin-Bin , Qin Qi-Long , Zhou Bai-Cheng , Shi Mei , Huang Yong , Zhang Yu-Zhong
Published: January 2014

A Gram-stain-negative, aerobic, oxidase- and catalase-positive, flagellated, rod-shaped bacterial strain, designated SM1222T, was isolated from the deep-sea sediment of the South China Sea. The strain grew at 4–35 °C and with 0.5–8 % NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SM1222T was affiliated with the genus

Oceanisphaera

in the class

Gammaproteobacteria

. It shared the highest sequence similarity with the type strain of

Oceanisphaera ostreae

(96.8 %) and 95.4–96.6 % sequence similarities with type strains of other species of the genus

Oceanisphaera

with validly published names. Strain SM1222T contained summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C18 : 1ω7c, C16 : 0, C12 : 0 and summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I) as the major fatty acids and ubiquinone Q-8 as the predominant respiratory quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of strain SM1222T was 51.5 mol%. On the basis of the evidence presented in this study, strain SM1222T represents a novel species of the genus

Oceanisphaera

, for which the name Oceanisphaera profunda sp. nov. is proposed. The type strain of Oceanisphaera profunda is SM1222T ( = CCTCC AB 2013241T = KCTC 32510T). An emended description of the genus

Oceanisphaera

Romanenko et al. 2003 emend. Choi et al. 2011 is also proposed.
Ramlibacter solisilvae sp. nov., isolated from forest soil, and emended description of the genus Ramlibacter
Authors: Lee Hyo Jung , Lee Se Hee , Lee Sang-Suk , Lee Joon Seon , Kim Yongseong , Kim Seung-Chul , Jeon Che Ok
Published: January 2014

A Gram-staining-negative, strictly aerobic, white-colony-forming bacterium, designated strain 5-10T, was isolated from forest soil of Bac Kan Province in Vietnam. Cells were non-motile rods or coccoids, showing oxidase- and catalase-positive reactions. Growth was observed at 10–37 °C (optimum, 30 °C), at pH 5.0–9.0 (optimum, pH 7.0) and in the presence of 0–1.0 % (w/v) NaCl (optimum, 0–0.5 %). The major cellular fatty acids were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0, C10 : 0 3-OH and summed feature 8 (comprising C18 : 1ω6c and/or C18 : 1ω7c). The G+C content of the genomic DNA was 69.9 mol% and the only respiratory quinone detected was ubiquinone 8 (Q-8). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 5-10T formed a tight phyletic lineage with members of the genus

Ramlibacter

. Strain 5-10T was most closely related to

Ramlibacter tataouinensis

TTB310T (97.3 %), but the DNA–DNA relatedness level between the two strains was 38.2±1.8 %. Based on phenotypic, chemotaxonomic and molecular features, strain 5-10T was shown to represent a novel species of the genus

Ramlibacter

, for which the name Ramlibacter solisilvae sp. nov. is proposed. The type strain is 5-10T ( = KACC 17567T = JCM 19319T). An emended description of the genus

Ramlibacter

is also proposed.
Mucilaginibacter flavus sp. nov., isolated from wetland
Authors: Joung Yochan , Kim Haneul , Lee Beom-Il , Kang Heeyoung , Kim Tae-Su , Kim Seung Bum , Joh Kiseong
Published: January 2014

A non-motile, pale yellow, colony-forming strain, designated HME6839T, was isolated from the wetland of Jeju Island, Republic of Korea. The major fatty acids of strain HME6839T were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), iso-C15 : 0 and C16 : 1ω5c. The DNA G+C content was 41.2 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME6839T formed a lineage within the genus

Mucilaginibacter

. Strain HME6857T was closely related to

Mucilaginibacter dorajii

(96.7 %),

Mucilaginibacter polysacchareus

(96.5 %) and

Mucilaginibacter lappiensis

(96.3 %). On the basis of the chemotaxonomic and phylogenetic results presented in this study, strain HME6839T represents a novel species of the genus

Mucilaginibacter

, for which the name Mucilaginibacter flavus sp. nov., is proposed. The type strain is HME6839T ( = KCTC 23441T = CECT 7857T).
Description of Anaerobacterium chartisolvens gen. nov., sp. nov., an obligately anaerobic bacterium from Clostridium rRNA cluster III isolated from soil of a Japanese rice field, and reclassification of Bacteroides cellulosolvens Murray et al. 1984 as Pseudobacteroides cellulosolvens gen. nov., comb. nov.
Authors: Horino Haruka , Fujita Takashi , Tonouchi Akio
Published: January 2014

An obligately anaerobic bacterial strain designated T-1-35T was isolated as a dominant cultivable cellulose-degrading bacterium from soil of a Japanese rice field as an anaerobic filter-paper degrader. Cells of strain T-1-35T stained Gram-positive and were non-spore-forming rods with rounded ends, 0.8–1.0×3.5–15.0 µm, and motile by means of two to four polar flagella. Cells of strain T-1-35T exhibited pleomorphism: in aged cultures (over 90 days of incubation), almost all cells were irregularly shaped. Although no spore formation was observed, cells tolerated high temperatures, up to 90 °C for 10 min. The temperature range for growth was 15–40 °C, with an optimum at 35 °C. The pH range for growth was 5.5–9.0, with an optimum at pH 8.0–8.5 (slightly alkaliphilic). Strain T-1-35T fermented some carbohydrates to produce ethanol and lactate as the major products. Major cellular fatty acids were iso-C16 : 0 and iso-C13 : 0 3-OH. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain T-1-35T belonged to Clostridium rRNA cluster III. The closest relative of strain T-1-35T was

Bacteroides cellulosolvens

WM2T, with 16S rRNA gene sequence similarity of 93.4 %. Phenotypic, physiological and molecular genetic methods demonstrated that strain T-1-35T was distinct from its phylogenetic relatives (members of Clostridium rRNA cluster III) because it predominantly produced ethanol, iso-C13 : 0 3-OH was a major cellular fatty acid and it always exhibited pleomorphism. On the basis of the results of a polyphasic taxonomic study, strain T-1-35T is considered to represent a novel genus and species, Anaerobacterium chartisolvens gen. nov., sp. nov. The type strain of Anaerobacterium chartisolvens is T-1-35T ( = DSM 27016T = NBRC 109520T). In addition, from the results of our phylogenetic analysis and its phenotypic features, the species

Bacteroides cellulosolvens

Murray et al. 1984 is proposed to be reclassified in the new genus Pseudobacteroides as Pseudobacteroides cellulosolvens gen. nov., comb. nov., with the type strain WM2T ( = ATCC 35603T = DSM 2933T = NRCC 2944T).
Cribrihabitans marinus gen. nov., sp. nov., isolated from a biological filter in a marine recirculating aquaculture system
Authors: Chen Zhu , Liu Ying , Liu Liang-Zi , Zhong Zhi-Ping , Liu Zhi-Pei , Liu Ying
Published: January 2014

A Gram-negative bacterium, strain CZ-AM5T, was isolated from an aerated biological filter in a marine recirculating aquaculture system in Tianjin, China. Its taxonomic position was investigated by using a polyphasic approach. Cells of strain CZ-AM5T were non-spore-forming rods, 0.5–0.8 µm wide and 1.2–2.0 µm long, and motile by means of one or two polar or lateral flagella. Strain CZ-AM5T was strictly aerobic, heterotrophic, oxidase-negative and catalase-positive. Growth occurred at 15–40 °C (optimum, 30–35 °C), at pH 6.5–10.5 (optimum, pH 7.0–7.5) and in the presence of 0–12.0 % (w/v) NaCl (optimum, 4.0 %). The predominant fatty acid was C18 : 1ω7c (80.3 %). Ubiquinone 10 (Q-10) was the sole respiratory quinone. The polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unknown aminolipid, an unknown phospholipid and three unknown lipids. The DNA G+C content was 60.4 mol%. Strain CZ-AM5T showed the highest 16S rRNA gene sequence similarity (96.5 %) to

Phaeobacter caeruleus

LMG 24369T; it exhibited 16S rRNA gene sequence similarity of 95.0–96.5, 95.2–96.3, 96.2, 94.6–95.7 and 94.8–95.8 % to members of the genera

Phaeobacter

,

Ruegeria

,

Citreimonas

,

Leisingera

and

Donghicola

, respectively. However, phylogenetic trees based on 16S rRNA gene sequences showed that strain CZ-AM5T did not join any of the above genera, but formed a distinct lineage in the trees. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain CZ-AM5T is considered to represent a novel genus and species of the family

Rhodobacteraceae

, for which the name Cribrihabitans marinus gen. nov., sp. nov. is proposed. The type strain of Cribrihabitans marinus is CZ-AM5T ( = CGMCC 1.13219T = JCM 19401T).
Description of Thermogemmatispora carboxidivorans sp. nov., a carbon-monoxide-oxidizing member of the class Ktedonobacteria isolated from a geothermally heated biofilm, and analysis of carbon monoxide oxidation by members of the class Ktedonobacteria
Authors: King C. E. , King G. M.
Published: January 2014

A thermophilic, aerobic, Gram-stain-positive bacterium (strain PM5T), which formed mycelia of irregularly branched filaments and produced multiple exospores per cell, was isolated from a geothermally heated biofilm. Strain PM5T grew at 40–65 °C and pH 4.1–8.0, with optimal growth at 55 °C and pH 6.0. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain PM5T belonged to the class

Ktedonobacteria

, and was related most closely to

Thermogemmatispora onikobensis

ONI-1T (97.7 % similarity) and

Thermogemmatispora foliorum

ONI-5T (96.1 %). Morphological features and fatty acid profiles (major fatty acids: iso-C17 : 0, iso-C19 : 0 and 12,17-dimethyl C18 : 0) supported the affiliation of strain PM5T to the genus

Thermogemmatispora

. Strain PM5T oxidized carbon monoxide [CO; 10±1 nmol h−1 (mg protein)−1], but did not grow with CO as a sole carbon and energy source. Results from analyses of related strains indicated that the capacity for CO uptake occurred commonly among the members of the class

Ktedonobacteria

; 13 of 14 strains tested consumed CO or harboured coxL genes that potentially enabled CO oxidation. The results of DNA–DNA hybridization and physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain PM5T from the two recognized species of the genus

Thermogemmatispora

. Strain PM5T differed from

Thermogemmatispora onikobensis

ONI-1T in its production of orange pigment, lower temperature optimum, hydrolysis of casein and starch, inability to grow with mannitol, xylose or rhamnose as sole carbon sources, and utilization of organic acids and amino acids. Strain PM5T is therefore considered to represent a novel species, for which the name Thermogemmatispora carboxidivorans sp. nov. is proposed. The type strain is PM5T ( = DSM 45816T = ATCC BAA-2534T).
Relationship between O-antigen chain length and resistance to colicin E2 in Shigella flexneri
Authors: Tran Elizabeth Ngoc Hoa , Papadopoulos Magdalene , Morona Renato
Published: January 2014

The Shigella flexneri polysaccharide co-polymerase class 1a (PCP1a) protein, WzzBSF, regulates LPS O-antigen (Oag) chain length to confer short (S)-type Oag chains of ~10–17 Oag repeat units (RUs). The S-type Oag chains affect Shigella flexneri virulence as they influence IcsA-mediated actin-based motility. However, they do not confer resistance to complement; this is conferred by the very-long (VL)-type Oag chains determined by WzzBpHS2. Colicins are bacterial proteins produced by some Escherichia coli strains to kill related strains. While the presence of Oag chains has been shown to shield outer-membrane proteins from colicins, the impact of Oag chain length against colicins is unknown. In this study, initial testing indicated that a Shigella flexneri Y wzz : : kanr
mutant was more sensitive to colicin E2 compared with the WT strain. Plasmids encoding Wzz mutant and WT PCP1a proteins conferring different Oag modal chain lengths were then expressed in the mutant background, and tested against purified colicin E2. Analysis of swab and spot sensitivity assays showed that strains expressing either S-type or long (L)-type Oag chains (16–28 Oag RUs) conferred greater resistance to colicin E2 compared with strains having very-short-type (2–8 Oag RUs), intermediate-short-type (8–14 Oag RUs) or VL-type (>80 Oag RUs) Oag chains. These results suggest a novel role for LPS Oag chain length control that may have evolved due to selection pressure from colicins in the environment.
The Flavonoid Biosynthetic Enzyme Chalcone Isomerase Modulates Terpenoid Production in Glandular Trichomes of Tomato
Authors: Kang Jin-Ho , McRoberts John , Shi Feng , Moreno Javier E. , Jones A. Daniel , Howe Gregg A.
Published: January 2014

Flavonoids and terpenoids are derived from distinct metabolic pathways but nevertheless serve complementary roles in mediating plant interactions with the environment. Here, we show that glandular trichomes of the anthocyanin free (af) mutant of cultivated tomato (Solanum lycopersicum) fail to accumulate both flavonoids and terpenoids. This pleiotropic metabolic deficiency was associated with loss of resistance to native populations of coleopteran herbivores under field conditions. We demonstrate that Af encodes an isoform (SlCHI1) of the flavonoid biosynthetic enzyme chalcone isomerase (CHI), which catalyzes the conversion of naringenin chalcone to naringenin and is strictly required for flavonoid production in multiple tissues of tomato. Expression of the wild-type SlCHI1 gene from its native promoter complemented the anthocyanin deficiency in af. Unexpectedly, the SlCHI1 transgene also complemented the defect in terpenoid production in glandular trichomes. Our results establish a key role for SlCHI1 in flavonoid production in tomato and reveal a link between CHI1 and terpenoid production. Metabolic coordination of the flavonoid and terpenoid pathways may serve to optimize the function of trichome glands in dynamic environments.
Debaryomyces hansenii and Rhodotorula mucilaginosa comprised the yeast core gut microbiota of wild and reared carnivorous salmonids, croaker and yellowtail
Authors: Raggi Patricia , Lopez Paulina , Diaz Angélica , Carrasco Diana , Silva Alfonso , Velez Antonio , Opazo Rafael , Magne Fabien , Navarrete Paola A.
Published: January 2014

This is the first study using molecular and culture‐based methods aimed at investigating the composition of the intestinal yeast microbiota of wild and reared carnivorous salmonids, croaker and yellowtail, to characterize their cores and to evaluate the enzymatic activities of the cultivated yeast. Among 103 samples from salmonids, croaker and yellowtail, yeast were detected in 85.4%, with 43 species identified. The core of reared fish was composed of eight species, in contrast to the wild fish core, which consisted of two species: Debaryomyces hansenii and Rhodotorula mucilaginosa. Despite the smaller diversity of the wild fish core, similar enzymatic profiles were detected for the species from the wild and reared cores. For principal component analysis, samples grouped together independently of host species, domestication status and location. A high proportion of yeast produced aminopeptidases and lipases, which may be explained by the high proportion of protein and lipids in the carnivorous diet. This study reveals the presence of a yeast community in the fish gut that appears to be strongly shaped by a carnivorous diet. Yeast in the gut increases the repertoire of microorganisms interacting with the host intestine, which could influence health and disease.
A simple method for estimating species abundance from occurrence maps
Authors: Yin Deyi , He Fangliang
Published: January 2014

The issue of how to estimate species abundance from presence/absence maps has attracted much attention. Several methods have been developed to address this problem. However, those methods either overlook the structure of spatial autocorrelation of species distribution, thus leading to underestimation, or they demand extra information besides presence/absence maps.

This study first developed a new method that takes account of spatial autocorrelation and only requires occurrence maps, without any extra information. This method was further improved by incorporating a correction factor to it. We used an index defined by joint counts of occupied and unoccupied cells to measure spatial autocorrelation and to correct the underestimation of the random placement model.

The performance of our method was compared against four other major methods (random placement model, negative binomial model, Conlisk et al.'s method and Solow & Smith's method) using both simulated and empirical data. The results showed that the performance of our method is comparable with other methods but requires less and readily obtained input data, a property important for real applications.

We suggest this simple, data‐parsimonious method be a useful alternative to the currently available methods for estimating abundance from occurrence.
Burden of Disease Associated with Alcohol Use Disorders in the United States
Authors: Rehm Jürgen , Dawson Deborah , Frick Ulrich , Gmel Gerrit , Roerecke Michael , Shield Kevin D. , Grant Bridget
Published: January 2014

Background

Alcohol use disorders (AUD) have long been considered to be some of the most disabling mental disorders; however, empirical data on the burden of disease associated with AUD have been sparse. The objective of this article is to quantify the burden of disease (in disability‐adjusted life years [DALYs] lost), deaths, years of life lost due to premature mortality (YLL), and years of life lost due to disability (YLD) associated with AUD for the United States in 2005.

Methods

Statistical modeling was based on epidemiological indicators derived from the National Epidemiologic Survey on Alcohol and Related Conditions. Formal consistency analyses were applied. Risk relations were taken from recent meta‐analyses and the disability weights from the burden of disease study of the National Institutes of Health. Monte Carlo simulations were used to derive confidence intervals. All analyses were performed by sex and age. Sensitivity analyses were undertaken on key indicators.

Results

In the United States in 2005, 65,000 deaths, 1,152,000 YLL, 2,443,000 YLD, and 3,595,000 DALYs were associated with AUD. For individuals 18 years of age and older, AUD were associated with 3% of all deaths (5% for men and 1% for women), and 5% of all YLL (7% for men and 2% for women). The majority of the burden of disease associated with AUD stemmed from YLD, which accounted for 68% of DALYs associated with AUD (66% for men and 74% for women). The youngest age group had the largest proportion of DALYs associated with AUD stemming from YLD.

Conclusions

Using data from a large representative survey (checked for consistency) and by combining these data with the best available evidence, we found that AUD were associated with a larger burden of disease than previously estimated. To reduce this disease burden, implementation of prevention interventions and expansion of treatment are necessary.
Impact of Interventions Targeting Unhealthy Alcohol Use in Kenya on HIV Transmission and AIDS‐Related Deaths
Authors: Braithwaite R. Scott , Nucifora Kimberly A. , Kessler Jason , Toohey Christopher , Mentor Sherry M. , Uhler Lauren M. , Roberts Mark S. , Bryant Kendall
Published: January 2014

Background

HIV remains a major cause of preventable morbidity and mortality in Kenya. The effects of behaviors that accompany unhealthy alcohol consumption are a pervasive risk factor for HIV transmission and progression. Our objective was to estimate the portion of HIV infections attributable to unhealthy alcohol use and to evaluate the impact of hypothetical interventions directed at unhealthy alcohol use on HIV infections and deaths.

Methods

We estimated outcomes over a time horizon of 20 years using a computer simulation of the Kenyan population. This computer simulation integrates a compartmental model of HIV transmission with a mechanistic model of HIV progression that was previously validated in sub‐Saharan Africa. Integration of the transmission and progression models allows simultaneous consideration of alcohol's effects on HIV transmission and progression (e.g., lowering antiretroviral adherence may increase transmission risk by elevating viral load, and may simultaneously increase progression by increasing the likelihood of AIDS). The simulation considers important aspects of heterogeneous sexual mixing patterns, including assortativeness of partners by age and activity level, age‐discordant relationships, and high activity subgroups. Outcomes included number of new HIV infections, number of AIDS deaths, and infectivity (number of new infections per infected person per year).

Results

Our model estimated that the effects of behaviors accompanying unhealthy alcohol consumption are responsible for 13.0% of new HIV infections in Kenya. An alcohol intervention with effectiveness similar to that observed in a published randomized controlled trial of a cognitive‐behavioral therapy‐based intervention in Kenya (45% reduction in unhealthy alcohol consumption) could prevent nearly half of these infections, reducing their number by 69,858 and reducing AIDS deaths by 17,824 over 20 years. Estimates were sensitive to assumptions with respect to the magnitude of alcohol's underlying effects on condom use, antiretroviral therapy adherence, and sexually transmitted infection prevalence.

Conclusions

A substantial number of new HIV infections in Kenya are attributable to unhealthy alcohol use. An alcohol intervention with the effectiveness observed in a published randomized controlled trial has the potential to reduce infections over 20 years by nearly 5% and avert nearly 18,000 deaths related to HIV.
Alcohol‐Related Interpretation Bias in Alcohol‐Dependent Patients
Authors: Woud Marcella L. , Pawelczak Steffen , Rinck Mike , Lindenmeyer Johannes , Souren Pierre , Wiers Reinout W. , Becker Eni S.
Published: January 2014

Background

Models of addictive behaviors postulate that implicit alcohol‐related memory associations and biased interpretation processes contribute to the development and maintenance of alcohol misuse and abuse. The present study examined whether alcohol‐dependent patients (AP) show an alcohol‐related interpretation bias. Second, the relationship between the interpretation bias and levels of harmful drinking was investigated.

Methods

The sample included 125 clinically diagnosed AP and 69 clinically diagnosed control patients (CP) who had either a mood or an anxiety disorder. Participants completed a booklet containing 12 open‐ended ambiguous scenarios. Seven scenarios were alcohol‐relevant, and 5 were emotionally relevant, that is, panic‐ or depression‐relevant. Participants were asked to read each scenario and to generate a continuation. In addition, the Alcohol Use Disorder Identification Test (AUDIT) and Beck Depression Inventory were administered.

Results

Logistic multivariate multilevel analyses revealed that AP’ probability of generating an alcohol‐related continuation on all 3 scenario types was higher than that of CP. Moreover, alcohol‐related interpretation biases were positively associated with levels of harmful drinking (i.e., AUDIT scores).

Conclusions

These findings are the first to show that AP show an alcohol‐related interpretation bias, which generalizes to other ambiguous emotionally relevant contexts, and therefore advance our understanding of the role of implicit biased alcohol‐related memory associations and interpretation processes.
Peripherally Circulating Ghrelin Does Not Mediate Alcohol‐Induced Reward and Alcohol Intake in Rodents
Authors: Jerlhag Elisabet , Ivanoff Lisa , Vater Axel , Engel Jörgen A.
Published: January 2014

Background

Development of alcohol dependence, a chronic and relapsing disease, largely depends on the effects of alcohol on the brain reward systems. By elucidating the mechanisms involved in alcohol use disorder, novel treatment strategies may be developed. Ghrelin, the endogenous ligand for the growth hormone secretagogue receptor 1A, acts as an important regulator of energy balance. Recently ghrelin and its receptor were shown to mediate alcohol reward and to control alcohol consumption in rodents. However, the role of central versus peripheral ghrelin for alcohol reward needs to be elucidated.

Methods

Given that ghrelin mainly is produced by peripheral organs, the present study was designed to investigate the role of circulating endogenous ghelin for alcohol reward and for alcohol intake in rodents.

Results

We showed that the Spiegelmer NOX‐B11‐2, which binds and neutralizes acylated ghrelin in the periphery with high affinity and thus prevents its brain access, does not attenuate the alcohol‐induced locomotor activity, accumbal dopamine release and expression of conditioned place preference in mice. Moreover, NOX‐B11‐2 does not affect alcohol intake using the intermittent access 20% alcohol 2‐bottle‐choice drinking paradigm in rats, suggesting that circulating ghrelin does not regulate alcohol intake or the rewarding properties of alcohol. In the present study, we showed however, that NOX‐B11‐2 reduced food intake in rats supporting a role for circulating ghrelin as physiological regulators of food intake. Moreover, NOX‐B11‐2 did not affect the blood alcohol concentration in mice.

Conclusions

Collectively, the past and present studies suggest that central, rather than peripheral, ghrelin signaling may be a potential target for pharmacological treatment of alcohol dependence.
Live weight and relative faecal production of Hylamorpha elegans (Burm.) (Coleoptera: Scarabaeidae) larvae fed on soils with different particulate organic matter content
Authors: Millas Paz , Carrillo Roberto
Published: January 2014

Previous studies using white grub larvae have not found a relationship between scarabaeid larval growth and the quantity of total organic matter (OM) in the feeding soil. This is probably because it is the type or quality of the OM that is more important to larval nutritional requirements. The aim of this research was to study, under laboratory conditions, how the quality of OM, measured as the percentage of particulate OM (POM), affected the live weight and faecal production of Hylamorpha elegans (Coleoptera: Scarabaeidae) larvae. Results showed that live weight gain of second and third instar larvae increased with an increase in the amount of POM. The faecal production showed no differences. Therefore, the effect on second and third instar larvae was related to the quality of the resource and not to an increase in the quantity of soil ingested. Better understanding of the dynamics of POM and other labile fractions of the soil OM as microbial biomass could be fundamental to assessing and implementing out agricultural practices that can ameliorate the impact of this pest.
Androgen deprivation therapy improves pneumoperitoneum time during laparoscopic radical prostatectomy in Japanese patients with enlarged prostates
Authors: Takeda Toshikazu , Miyajima Akira , Kaneko Gou , Kikuchi Eiji , Nakagawa Ken , Oya Mototsugu
Published: January 2014

Introduction

The aim of this study was to investigate if neoadjuvant hormone therapy (NHT) is associated with surgical outcomes of laparoscopic radical prostatectomy.

Methods

A total of 286 patients with organ‐confined prostate cancer and a preoperative prostate volume that could be estimated by transrectal ultrasound underwent laparoscopic radical prostatectomy between 2006 and 2011 at our institution. We examined whether NHT was associated with pneumoperitoneum time (PT) or estimated blood loss during laparoscopic radical prostatectomy.

Results

NHT was performed in 80 patients; the mean duration of NHT was 5.2 ± 0.2 months. Multivariate analysis demonstrated that history of NHT and no NHT were not independent predictors of prolonged PT or higher estimated blood loss. Next, we evaluated 57 patients whose estimated preoperative baseline prostate volume was over 50 mL. Multivariate analysis demonstrated that no history of NHT (P = 0.011) was an independent predictor of prolonged PT. PT was significantly shorter in the NHT group (164.5 ± 39.0 min, n = 26) than in the non‐NHT group (184.0 ± 36.7 min, n = 31) (P = 0.048). In the NHT group, mean prostate volume was reduced from 63.7 ± 16.0 mL to 42.1 ± 18.6 mL (33.9% reduction) by NHT.

Conclusion

NHT shortened the PT of the patients whose preoperative baseline prostate volume was over 50 mL. This suggests NHT downsized prostate volume, resulting in greater working space and shorter PT.
Nutrient pulses after prescribed winter fires and preferential patterns of N uptake may contribute to the expansion of Brachypodium pinnatum (L.) P. Beauv. in highland grasslands
Authors: Canals Rosa‐Maria , Pedro Javier , Rupérez Esther , San‐Emeterio Leticia
Published: January 2014

Question

Do prescribed winter fires – authorized to prevent shrub encroachment and control necromass accumulation in protected grassland communities – promote significant changes in soils and in the pool of nutrients available to plants? Does Brachypodium pinnatum, an expanding native grass, take better advantage of the most dynamic nutrient pulse, that of N, than other dominant native grasses?

Location

Aezkoa commons, western Pyrenees.

Methods

We scheduled experimental winter burnings in three semi‐natural grasslands with incipient shrub encroachment and tracked the short‐term physical–chemical changes produced in the soil. During the peak biomass period, we performed a stable isotope field experiment in order to follow the fate of three different chemical forms of labelled N (15, 15 and 13C2‐15N‐glycine) in 48 undisturbed stands of B. pinnatum and Festuca gr. rubra.

Results

The soil pools of available phosphorus, potassium and ammonium significantly increased after the fire. Four months later, a pulse of nitrate was also recorded. The isotopic labelling experiment revealed that, although the three forms of N were absorbed by the grasses, significant differences in 15N tissue enrichment appeared after 48 h. Altogether, the results indicated a higher response of B. pinnatum to the pulse than F. rubra, although the latter was able to absorb intact glycine, unlike B. pinnatum.

Conclusions

Controlled winter burnings, despite being low intensity, cause a significant release of the main nutrients associated with plant growth. This makes the plant community more susceptible to floristic changes. The field experiment suggests that B. pinnatum may make better use of the post‐fire pulse than F. rubra. This preferential uptake, together with other competing mechanisms of the species, may trigger the expansion of B. pinnatum in burned areas.
On the Use of In Silico Tools for Prioritising Toxicity Testing of the Low‐Volume Industrial Chemicals in REACH
Authors: Rybacka Aleksandra , Rudén Christina , Andersson Patrik L.
Published: January 2014

This study was conducted to evaluate the utility of a selection of commercially and freely available non‐testing tools and to analyse how REACH registrants can apply these as prioritisation tool for low‐volume chemicals. The analysis was performed on a set of organic industrial chemicals and pesticides with extensive peer‐reviewed risk assessment data. Analysed in silico model systems included Derek Nexus, Toxtree, QSAR Toolbox, LAZAR, TEST and VEGA, and results from these were compared with expert‐judged risk classification according to the classifying, labelling and packaging (CLP) regulation. The most reliable results were obtained for carcinogenicity; however, less reliable predictions were derived for mutagenicity and reproductive toxicity. A group of compounds frequently predicted as false negatives was identified. These were relatively small molecules with low structural complexity, for example benzene derivatives with hydroxyl‐, amino‐ or aniline‐substituents. A rat liver S9 metabolite simulator was applied to illustrate the importance of considering metabolism in the risk assessment procedure. We also discuss outcome of combining predictions from multiple model systems and advise how to apply in silico tools. These models are proposed to be used to prioritise low‐volume chemicals for testing within the REACH legislation, and we conclude that further guidance is needed so that industry can select and apply models in a reliable, systematic and transparent way.
Preventative Effect of Zingiber officinale on Insulin Resistance in a High‐Fat High‐Carbohydrate Diet‐Fed Rat Model and its Mechanism of Action
Authors: Li Yiming , Tran Van H. , Kota Bhavani P. , Nammi Srinivas , Duke Colin C. , Roufogalis Basil D.
Published: January 2014

Insulin resistance is a core component of metabolic syndrome and usually precedes the development of type 2 diabetes mellitus. We have examined the preventative effect of an ethanol extract of ginger (Zingiber officinale, Zingiberaceae) on insulin resistance in a high‐fat high‐carbohydrate (HFHC) diet‐fed rat model of metabolic syndrome. The HFHC control rats displayed severe insulin resistance, whilst rats treated with ginger extract (200 mg/kg) during HFHC diet feeding showed a significant improvement of insulin sensitivity using the homeostatic model assessment of insulin resistance (HOMA‐IR) after 10 weeks (p < 0.01). An in vitro mechanistic study showed that (S)‐[6]‐gingerol, the major pungent phenolic principle in ginger, dose‐dependently (from 50 to 150 μM) increased AMPK α‐subunit phosphorylation in L6 skeletal muscle cells. This was accompanied by a time‐dependent marked increment of PGC‐1α mRNA expression and mitochondrial content in L6 skeletal muscle cells. These results suggest that the protection from HFHC diet‐induced insulin resistance by ginger is likely associated with the increased capacity of energy metabolism by its major active component (S)‐[6]‐gingerol.