bluuebunny/crossref_metadata_2025 huggingface dataset:
Rumour and Myth in the labour camps of Qatar (Respond to this article at http://www.therai.org.uk/at/debate)
Authors: Gardner Andrew
Published: December 2012

The petroleum‐rich states of the Arabian Peninsula comprise one of the principal transnational destinations for the global movement of labour. In the Gulf States, much of that labour force comes from South Asia. Legions of unskilled male labourers are typically housed in labor camps, a nomenclature that masks a wide variety of both formal and informal accommodation that, in spatial terms, is a fundamental mechanism for the social segregation of this foreign labor force from the citizenry. Building upon recent fieldwork in Doha, Qatar, this paper examines the myths and narratives that proliferate amongst the South Asian men in these labor camps – men who, often despite years of experience in the Gulf States, typically have little or no interaction with the native citizenry. This paper suggests that these myths and stories can be understood as instruments of governance in that they portray the collectively‐established boundaries of appropriate behavior in a culture foreign to these unskilled laborers. A close analysis of the content of these myths and rumors, however, also helps us grapple with the connections and contradictions between power, race, class, ethnicity, nationality, religion, gender and sexuality in the extraordinarily heterogeneous context of the contemporary Gulf State. As such, the analysis not only sheds light on the experiences of these foreign men and women, but also their collective understanding of that experience and of the society that hosts them.
Habitat specifity, endemism and the neotropical distribution of Amazonian white‐water floodplain trees
Authors: Wittmann Florian , Householder Ethan , Piedade Maria T. F. , de Assis Rafael L. , Schöngart Jochen , Parolin Pia , Junk Wolfgang J.
Published: December 2012

.The Amazon basin is covered by the most species‐rich forests in the world and is considered to house many endemic tree species. Yet, most Amazonian ecosystems lack reliable estimates of their degree of endemism, and causes of tree diversity and endemism are intense matters of debate. We reviewed the spatial distribution of 658 of the most important flood‐tolerant Amazonian white‐water (várzea) tree species across the entire Neotropics by using data from herbaria, floras, inventories and checklists. Our results show that 90% of the várzea tree species are partially or widely distributed across neotropical macro‐regions and biomes. Chi‐square analyses indicated that várzea species richness in non‐várzea macro‐regions was dependent on the flooding gradient and the longitudinal position. Cluster analysis combined with association tests indicated four significant patterns of várzea species distributions depending on species flood‐tolerance (low vs high) and spatial distribution (restricted vs widespread). We predict that the predominance of Andean substrates is the most important factor that determines the distribution of várzea tree species within and beyond the Amazon basin and explains the high floristic similarity to the Orinoco floodplains. Distribution patterns in other extra‐Amazonian macro‐regions are more likely linked to climatic factors, with rainforest climates housing more várzea species than savanna climates. 130 tree species were restricted to South‐American freshwater floodplains, and 68 (> 10%) were endemic to Amazonian várzea. We detected two centers of endemism, one in the western Amazon characterized by low and brief floods, and one in the central Amazon, characterized by high and prolonged floods. Differences in taxonomic composition of endemic centers in the western and central Amazon are the result of different abiotic factors (i.e. flood regimes), as well as the regional species pools from where the species are recruited from.

We hypothesize that numerous morphological, physiological and biochemical adaptations permit survival of trees in flooded environments. Furthermore, these adaptations are independently derived across many taxa and result in a highly specialized flora. We attribute higher than expected levels of endemism to the great spatial extent and age of floodplain ecosystems in the Amazon basin, and highlight the role of Amazonian várzea as an potential driver in speciation and diversification processes.
Therapy with compression stockings in Germany – results from the Bonn Vein Studies
Authors: Rabe Eberhard , Hertel Sabine , Bock Eva , Hoffmann Barbara , Jöckel Karl‐Heinz , Pannier Felizitas
Published: December 2012

Background: Despite the frequent use of medical compression stockings (MCS), reliable data are lacking on the frequency of MCS use and experience of patients with the treatment.

Patients and methods: The Bonn Vein Study included 3,072 participants from the general population aged 18 to 79 years (1,350 men/1,722 women). Between 2007 and 2008 (Bonn Vein Study 2) 1,978 participants from the Bonn Vein Study 1 were reinvestigated. This paper combines the results of both investigations.

Results: 14.6% (7.5% men, 20.3% women) reported having previously undergone treatment with compression stockings. A mean of 71.3% reported an improvement in their venous disease as a result of MCS treatment. During the 6.6 years of follow‐up (Bonn Vein Study 2), significantly more prescriptions of MCS were given to patients in higher CEAP clinical stages. 12.2% of the population in C2 was treated with MCS as were 19.1% in C3 and 27.0% in C4–C6. Among participants with chronic venous insufficiency (CVI) (skin changes up to venous ulcers), about 60% were not treated by MCS or bandages in the past years.

Conclusions: These results show that MCS is the most common treatment of venous disorders in the German population. At the same time, these figures also demonstrate severely lacking treatment with MCS in CVI.
Optimization of the sex pheromone of the rice leaffolder moth Cnaphalocrocis medinalis as a monitoring tool in China
Authors: Wu J. , Wu X. , Chen H. , Xu L. , Liu G. , Mao B. , Quo R. , Du Y.
Published: December 2012

The crude extract from Cnaphalocrocis medinalis (Lepidoptera, Pyralidae) has been identified to be (Z)‐11‐octadecenal (Z11‐18:Ald), (Z)‐13‐octadecenal (Z13‐18:Ald), (Z)‐11‐octadecen‐1‐ol (Z11‐18:OH) and (Z)‐13‐octadecen‐1‐ol (Z13‐18:OH) in the GC‐MS, confirming the results reported previously in Japan. Field evaluation in China showed that the optimal blend is Z11‐18:Ald, Z13‐18:Ald, Z11‐18:OH and Z13‐18:OH at a ratio of 3 : 25 : 3 : 3. The optimal dosage is 500 μg Z13‐18:Ald per PVC tubing lure. In August, trap catches were highest between 3:00 and 4:00 a.m., and no moths were caught before 12:00 a.m. or after 6:00 a.m. The impact of trap design and trap height placement was also evaluated in the paddy field. The sticky wing trap was better than the water pan trap. The number of moths captured by the electric grid trap was 1.7 times greater than caught by the sticky wing trap. The optimal trap height was 20 cm below the top of the rice plants (80 cm high). Pheromone lure formulated from 60 μg Z11‐18:Ald, 500 μg Z13‐18:Ald, 60 μg Z11‐18:OH and 60 μg Z13‐18:OH was effective for population monitoring in trial sites in Zhejiang, Shanghai, Jiangxi, Hunan, Hubei, Guangxi, Guizhou, Chongqing and Hainan Provinces, encompassing both subtropical and temperate regions. Use of this synthetic pheromone blend provides a promising alternative to the currently used disturb and count method (DCM) for monitoring the population of C. medinalis in China.
Differential effects of methylphenidate and cocaine on GABA transmission in sensory thalamic nuclei
Authors: Goitia Belén , Raineri Mariana , González Laura E. , Rozas José L. , Garcia‐Rill Edgar , Bisagno Verónica , Urbano Francisco J.
Published: December 2012

Methylphenidate (MPH) is widely used to treat children and adolescents diagnosed with attention deficit/hyperactivity disorder. Although MPH shares mechanistic similarities to cocaine, its effects on GABAergic transmission in sensory thalamic nuclei are unknown. Our objective was to compare cocaine and MPH effects on GABAergic projections between thalamic reticular and ventrobasal (VB) nuclei. Mice (P18‐30) were subjected to binge‐like cocaine and MPH acute and sub‐chronic administrations. Cocaine and MPH enhanced hyperlocomotion, although sub‐chronic cocaine‐mediated effects were stronger than MPH effects. Cocaine and MPH sub‐chronic administration altered paired‐pulse and spontaneous GABAergic input differently. The effects of cocaine on evoked paired‐pulse GABA‐mediated currents changed from depression to facilitation with the duration of the protocols used, while MPH induced a constant increase throughout the administration protocols. Thalamic reticular nucleus GAD67 and VB CaV3.1 protein levels were measured using western blot to better understand their link to increased GABA release. Both proteins were increased by sub‐chronic administration of cocaine. MPH showed effects on GABAergic transmission that seems less disruptive than cocaine. Unique effects of cocaine on postsynaptic VB calcium currents might explain deleterious cocaine effects on sensory thalamic nuclei. These results suggest that cocaine and MPH produced distinct presynaptic alterations on GABAergic transmission.
Mephedrone does not damage dopamine nerve endings of the striatum, but enhances the neurotoxicity of methamphetamine, amphetamine, and MDMA
Authors: Angoa‐Pérez Mariana , Kane Michael J. , Briggs Denise I. , Francescutti Dina M. , Sykes Catherine E. , Shah Mrudang M. , Thomas David M. , Kuhn Donald M.
Published: December 2012

Mephedrone (4‐methylmethcathinone) is a β‐ketoamphetamine stimulant drug of abuse with close structural and mechanistic similarities to methamphetamine. One of the most powerful actions associated with mephedrone is the ability to stimulate dopamine (DA) release and block its re‐uptake through its interaction with the dopamine transporter (DAT). Although mephedrone does not cause toxicity to DA nerve endings, its ability to serve as a DAT blocker could provide protection against methamphetamine‐induced neurotoxicity like other DAT inhibitors. To test this possibility, mice were treated with mephedrone (10, 20, or 40 mg/kg) prior to each injection of a neurotoxic regimen of methamphetamine (four injections of 2.5 or 5.0 mg/kg at 2 h intervals). The integrity of DA nerve endings of the striatum was assessed through measures of DA, DAT, and tyrosine hydroxylase levels. The moderate to severe DA toxicity associated with the different doses of methamphetamine was not prevented by any dose of mephedrone but was, in fact, significantly enhanced. The hyperthermia caused by combined treatment with mephedrone and methamphetamine was the same as seen after either drug alone. Mephedrone also enhanced the neurotoxic effects of amphetamine and 3,4‐methylenedioxymethamphetamine on DA nerve endings. In contrast, nomifensine protected against methamphetamine‐induced neurotoxicity. As mephedrone increases methamphetamine neurotoxicity, the present results suggest that it interacts with the DAT in a manner unlike that of other typical DAT inhibitors. The relatively innocuous effects of mephedrone alone on DA nerve endings mask a potentially dangerous interaction with drugs that are often co‐abused with it, leading to heightened neurotoxicity.
DOES EMPLOYING UNDOCUMENTED WORKERS GIVE FIRMS A COMPETITIVE ADVANTAGE?*
Authors: Brown J. David , Hotchkiss Julie L. , Quispe‐Agnoli Myriam
Published: December 2012

ABSTRACT Using administrative data from the state of Georgia, this paper finds that, on average, across all firms, employing undocumented workers reduces a firm's hazard of exit by 19 percent. The advantage to firms from employing undocumented workers increases as more firms in the industry do so, decreases with the skill level of the firm's workers, increases with the breadth of a firm's market, and increases with the labor intensity of the firm's production process.
Baseline measures for a school‐based obesity control programme: Project Energize: Differences by ethnicity, rurality, age and school socio‐economic status
Authors: Rush Elaine , Reed Peter W , Simmons David , Coppinger Tara , McLennan Stephanie , Graham David
Published: December 2012

Aim

School‐based interventions to tackle the rise in childhood overweight and obesity remain inconclusive and are often limited in their application to diverse populations. To inform and measure the effect of the implementation of a primary school‐based longitudinal randomised controlled nutrition and activity intervention, Project Energize, baseline measures of body size and blood pressure were required.

Methods

This cross‐sectional study stratified by age, sex, ethnicity, rurality and school socio‐economic‐status (school‐SES) measured body mass index (BMI), percentage body fat (%BF), waist and resting blood pressure from 2752 5‐ and 10‐year‐old children (62% European, 31% Māori) representative of the Waikato region of New Zealand.

Result

Waikato children have a high prevalence of overweight and obesity that is linked with hypertension. Cardiovascular risk factors including raised blood pressure and hypertension, waist and arm circumference and percentage body fat (%BF) were more prevalent in 10‐year‐olds, lower school‐SES and to some extent, urban living. In European children, BMI and waist circumference were similarly predictive of %BF, but for Māori children, waist circumference predicted %BF better than BMI.

Conclusions

A variety of stratified, baseline measurements is important when designing school‐based interventions. In particular, waist circumference measures may be a more accurate predictor of %BF than BMI when determining measurement protocols that consider different ethnic groups and environments among children. The effect of targeted improvements of the school physical activity and nutrition environment on the rate of increase of weight, fatness and blood pressure in children should be examined.
Effect of a multifaceted intervention on documentation of vital signs and staff communication regarding deteriorating paediatric patients
Authors: McKay Heather , Mitchell Imogen A , Sinn Kam , Mugridge Heather , Lafferty Tony , Van Leuvan Chris , Mamootil Sarah , Abdel‐Latif Mohamed E
Published: December 2012

Aim

To evaluate the impact of newly designed Paediatric Early Warning Scores and an accompanying education package, COMPASS, on the frequency of documentation of vital signs and communication between health professionals and associated medical review in deteriorating paediatric patients.

Methods

One thousand fifty‐nine patients in the pre‐intervention phase and 899 in the post‐intervention phase were studied. The daily frequency of documentation of vital sign measurement, incidence of health professional communication and related medical reviews following clinical deterioration of a random subgroup of 262 pre‐intervention and 221 post‐intervention patients were studied in detail.

Results

There were no significant differences in hospital mortality, medical emergency team reviews or unplanned admissions to critical care areas between the pre‐intervention and post‐intervention groups. There were significant increases in the post‐intervention group for the median daily frequency of documentation of respiratory effort (0.0 (0–0) to 7.8 (5.8–12.6), P < 0.001), capillary refill (0 (0–0) to 1.1 (0–3.1), P < 0.001), blood pressure (0 (0–1.1) to 0 (0–1.6), P = 0.007) and level of consciousness (0 (0–0) to 7.8 (5.8–12.0), P < 0.001) and appropriate communication concerning patient deterioration 63 (8.5%) to 216 (40.9%), P < 0.001). There was a significant reduction in the number of children fulfilling the medical emergency team criteria (102 (38.9%) to 45 (20.4), P < 0.001).

Conclusions

A multifaceted intervention for the early recognition and response to clinical deterioration in children significantly improved documentation of vital signs, communication and time to medical review.
Why families choose not to participate in research: Feedback from non‐responders
Authors: Levickis Penny , Naughton Geraldine , Gerner Bibi , Gibbons Kay
Published: December 2012

Aim

Subjects who did not respond to an invitation to participate in a community‐based randomised controlled trial for childhood obesity in Melbourne, Australia were approached to investigate reasons for non‐participation.

Methods

Between January and September 2007, 305 families were sent a brief questionnaire and invited to take part in the current study. Thirty‐seven questionnaires were returned and 12 parents agreed to a follow‐up interview. Questionnaire data were quantitatively analysed. The interviews were conducted via the telephone and provided detailed qualitative information on non‐participation.

Results

Lack of time was cited as a main reason for non‐participation. Different aspects of time were discussed including lack of time to dedicate to a topic seen as low priority, overestimated perception of time for study commitments and the inappropriate timing of the request. Other major reasons for non‐participation included risk of negative experiences and the impact of the initial contact with the study.

Conclusions

This study illustrates the experiences of potential participants during the recruitment process, their perceptions of study commitments and how their previous experiences impact on their decision to participate in research. These findings provide insight into the decision not to participate in health research and could be used to modify recruitment procedures for future health research as a way of improving the recruitment experience for potential participants as well as enhancing recruitment rates.
The influence of the aridAndean high plateau on the phylogeography and population genetics of guanaco (Lama guanicoe) inSouthAmerica
Authors: Marin Juan C. , González Benito A. , Poulin Elie , Casey Ciara S. , Johnson Warren E.
Published: December 2012

A comprehensive study of the phylogeography and population genetics of the largest wild artiodactyl in the arid and cold‐temperateSouthAmerican environments, the guanaco (Lama guanicoe) was conducted. Patterns of molecular genetic structure were described using 514 bp of mtDNAsequence and 14 biparentally inherited microsatellite markers from 314 samples. These individuals originated from 17 localities throughout the current distribution acrossPeru,Bolivia,Argentina andChile. This confirmed well‐defined genetic differentiation and subspecies designation of populations geographically separated to the northwest (L. g. cacsilensis) and southeast (L. g. guanicoe) of the centralAndes plateau. However, these populations are not completely isolated, as shown by admixture prevalent throughout a limited contact zone, and a strong signal of expansion from north to south in the beginning of theHolocene. Microsatellite analyses differentiated three northwestern and 4–5 southeastern populations, suggesting patterns of genetic contact among these populations. Possible genetic refuges were identified, as were source‐sink patterns of gene flow at historical and recent time scales. Conservation and management of guanaco should be implemented with an understanding of these local population dynamics while also considering the preservation of broader adaptive variation and evolutionary processes.
Slc45a2 and V‐ATPase are regulators of melanosomal pH homeostasis in zebrafish, providing a mechanism for human pigment evolution and disease
Authors: Dooley Christopher M. , Schwarz Heinz , Mueller Kaspar P. , Mongera Alessandro , Konantz Martina , Neuhauss Stephan C. F. , Nüsslein‐Volhard Christiane , Geisler Robert
Published: December 2012

We present here the positional cloning of the Danio rerio albino mutant and show that the affected gene encodes Slc45a2. The human orthologous gene has previously been shown to be involved in human skin color variation, and mutations therein have been implicated in the disease OCA4. Through ultrastructural analysis of the melanosomes in albino alleles as well as the tyrosinase‐deficient mutant sandy, we add new insights into the role of Slc45a2 in the production of melanin. To gain further understanding of the role of Slc45a2 and its possible interactions with other proteins involved in melanization, we further analyzed the role of the V‐ATPase as a melanosomal acidifier. We show that it is possible to rescue the melanization potential of the albino melanosomes through genetic and chemical inhibition of V‐ATPase, thereby increasing internal melanosome pH.
Morality in Groups: On the Social‐Regulatory Functions of Right and Wrong
Authors: Ellemers Naomi , van den Bos Kees
Published: December 2012

Applying what we know about group‐based identities and concerns allows us to improve our understanding of the ways in which morality is relevant to social judgments of right and wrong. We distinguish between three different social functions of moral standards and moral judgments. The identity defining function of morality indicates where people want to belong, and how they are regarded by others. The group dynamic function indicates consensual definitions of what is right and wrong that guide individual behavioral choices. The intergroup relations function of group morality, speaks to the way people tend to communicate with and behave towards members of other groups that have different moral standards.
Emotion Regulation: The Interplay of Culture and Genes
Authors: Kim Heejung S. , Sasaki Joni Y.
Published: December 2012

Given the mounting empirical evidence to support both the cultural and biological shaping of emotional processes, there is a clear need to integrate these determinants of emotional processes. Much in the same vein as these efforts, in our research on gene‐culture interactions, we have examined how cultural and biological factors jointly influence emotion regulation. The present paper specifically aims to present research considering both cultural and genetic factors as two interacting influences that shape emotion regulation. A series of studies conducted to test the gene‐culture interaction involving OXTRrs53576 consistently show that individuals with the variant that is associated with socio‐emotional sensitivity tend to utilize culturally normative forms of emotion regulation more than those without it. These findings underscore the importance of considering the interplay between socio‐cultural and genetic factors that shape social behaviors.
Survival of human islets in microbeads containing high guluronic acid alginate crosslinked with Ca2+ and Ba2+
Authors: Qi Meirigeng , Mørch Yrr , Lacík Igor , Formo Kjetil , Marchese Enza , Wang Yong , Danielson Kirstie K. , Kinzer Katie , Wang Shusen , Barbaro Barbara , Kolláriková Gabriela , Chorvát Dušan , Hunkeler David , Skjåk‐Bræk Gudmund , Oberholzer José , Strand Berit L.
Published: December 2012

Qi M, Mørch Y, Lacík I, Formo K, Marchese E, Wang Y, Danielson KK, Kinzer K, Wang S, Barbaro B, Kolláriková G, Chorvát D Jr, Hunkeler D, Skjåk‐Bræk G, Oberholzer J, Strand BL. Survival of human islets in microbeads containing high guluronic acid alginate crosslinked with Ca2+ and Ba2+. Xenotransplantation 2012; 19: 355–364. © 2012 John Wiley & Sons A/S.

Abstract:  Background:  The main hurdles to the widespread use of islet transplantation for the treatment of type 1 diabetes continue to be the insufficient number of appropriate donors and the need for immunosuppression. Microencapsulation has been proposed as a means to protect transplanted islets from the host’s immune system.

Methods:  This study investigated the function of human pancreatic islets encapsulated in Ca2+/Ba2+–alginate microbeads intraperitoneally transplanted in diabetic Balb/c mice.

Results:  All mice transplanted with encapsulated human islets (n = 29), at a quantity of 3000 islet equivalent (IEQ), achieved normoglycemia 1 day after transplantation and retained normoglycemia for extended periods of time (mean graft survival 134 ± 17 days). In comparison, diabetic Balb/c mice transplanted with an equal amount of non‐encapsulated human islets rejected the islets within 2 to 7 days after transplantation (n = 5). Microbeads retrieved after 232 days (n = 3) were found with little to no fibrotic overgrowth and contained viable insulin‐positive islets. Immunofluorescent staining on the retrieved microbeads showed F4/80‐positive macrophages and alpha smooth muscle actin–positive fibroblasts but no CD3‐positive T lymphocytes.

Conclusions:  The Ca2+/Ba2+–alginate microbeads can protect human islets from xenogeneic rejection in immunocompetent mice without immunosuppression. However, grafts ultimately failed likely secondary to a macrophage‐mediated foreign body reaction.
Draft Genome Sequence of a Novel Bacterial Strain, LSJC7, Belonging to the Family Enterobacteriaceae with Dual Resistance to Arsenic and Tetracycline
Authors: Su JianQiang , Ye Jun , Zhu YongGuan
Published: December 2012

Strain LSJC7, with dual resistance to arsenic and tetracycline, was isolated from an antimony tailing in China. Its 16S rRNA gene sequence has the highest similarity to that of
Enterobacter cloacae
subsp.
dissolvens
LMG 2683
T
(97.02%). Here we present the approximately 4.6-Mbp draft genome sequence of strain LSJC7.
Draft Genome Sequence of the Biocontrol Strain Serratia plymuthica A30, Isolated from Rotting Potato Tuber Tissue
Authors: Czajkowski Robert , van der Wolf Jan M.
Published: December 2012

Serratia plymuthica
A30 is a Gram-negative bacterium expressing antagonistic activity toward blackleg- and soft rot-causing
Dickeya
sp. biovar 3 (“
Dickeya solani
”). Here, we present the draft genome sequence of strain A30, which has been isolated from rotten potato tuber tissue.
Genome Sequences of Burkholderia sp. Strains CCGE1002 and H160, Isolated from Legume Nodules in Mexico and Brazil
Authors: Ormeño-Orrillo Ernesto , Rogel Marco A. , Chueire Ligia Maria Oliveira , Tiedje James M. , Martínez-Romero Esperanza , Hungria Mariangela
Published: December 2012

The genome sequences of
Burkholderia
sp. strains CCGE1002 from Mexico and H160 from Brazil, isolated from legume nodules, are reported. Their gene contents in relation to plant-microbe interactions and xenobiotic degradation are discussed.
Draft Genome Sequence of Enterobacter cloacae subsp. cloacae Strain 08XA1, a Fecal Bacterium of Giant Pandas
Authors: Yan Yue , Zhao Chuan-Wu , Zhang Yi-Zheng , Zhang Zhi-He , Pan Guang-Lin , Liu Wen-Wang , Ma Qing-Yi , Hou Rong , Tan Xue-Mei
Published: December 2012

Enterobacter cloacae
, a common pathogenic bacterium, is a Gram-negative bacillus. We analyzed the draft genome of
Enterobacter cloacae
subsp.
cloacae
strain 08XA1 from the feces of a giant panda in China. Genes encoding a β-lactamase and efflux pumps, as well as other factors, have been found in the genome.
Complete Sequence of the First Chimera Genome Constructed by Cloning the Whole Genome of Synechocystis Strain PCC6803 into the Bacillus subtilis 168 Genome
Authors: Watanabe Satoru , Shiwa Yuh , Itaya Mitsuhiro , Yoshikawa Hirofumi
Published: December 2012

Genome synthesis of existing or designed genomes is made feasible by the first successful cloning of a cyanobacterium,
Synechocystis
PCC6803, in Gram-positive, endospore-forming
Bacillus subtilis
. Whole-genome sequence analysis of the isolate and parental
B. subtilis
strains provides clues for identifying single nucleotide polymorphisms (SNPs) in the 2 complete bacterial genomes in one cell.
Genome Sequence of the Alkane-Degrading Bacterium Alcanivorax hongdengensis Type Strain A-11-3
Authors: Lai Qiliang , Shao Zongze
Published: December 2012

Alcanivorax hongdengensis
A-11-3
T
was isolated from an oil-enriched consortium enriched from the surface seawater of Hong-Deng dock in the Straits of Malacca and Singapore. Strain A-11-3
T
can degrade
n
-alkane and produce a lipopeptide biosurfactant. Here we report the genome of A-11-3
T
and the genes associated with alkane degradation.
Genome Sequence of Galbibacter marinum Type Strain ck-I2-15
Authors: Lai Qiliang , Li Chongping , Shao Zongze
Published: December 2012

Galbibacter marinum
strain ck-I2-15
T
was isolated from an arsenite-resistant consortium enriched from the deep sea sediment of a hydrothermal vent field on the Southwest Indian Ocean Ridge. Here, we present the draft genome of strain ck-I2-15
T
, which contains 3,572,447 bp with a G+C content of 37.04% and contains 3,099 protein-coding genes and 38 tRNA genes.
Genome Sequence of Coxiella burnetii 109, a Doxycycline-Resistant Clinical Isolate
Authors: Rouli Laetitia , Rolain Jean-Marc , El Filali Adil , Robert Catherine , Raoult Didier
Published: December 2012

Coxiella burnetii
109, with a 2.03-Mb genome, is a doxycycline-resistant human isolate that was isolated from the cardiac valve of a German male patient with Q fever endocarditis who died during the course of the treatment due to the bacterium's resistance to doxycycline. This new genome can be useful for future comparative genomic or Q fever studies.
Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, “Candidatus Nitrosopumilus koreensis” AR1, from Marine Sediment
Authors: Park Soo-Je , Kim Jong-Geol , Jung Man-Young , Kim So-Jeong , Cha In-Tae , Kwon KaeKyoung , Lee Jung-Hyun , Rhee Sung-Keun
Published: December 2012

Ammonia-oxidizing archaea (AOA) are ubiquitous in various marine environments and play important roles in the global nitrogen and carbon cycles. We here present a high-quality draft genome sequence of an ammonia-oxidizing archaeon, “
Candidatus
Nitrosopumilus koreensis” AR1, which was found to dominate an ammonia-oxidizing enrichment culture in marine sediment off Svalbard, the Arctic Circle. Despite a significant number of nonoverlapping genes (ca. 30%), similarities of this strain to “
Candidatus
Nitrosopumilus maritimus” were revealed by core genes for archaeal ammonia oxidation and carbon fixation, G+C content, and extensive synteny conservation.
Genome Sequence of Acinetobacter baumannii TYTH-1
Authors: Liou Ming-Li , Liu Chih-Chin , Lu Chia-Wei , Hsieh Ming-Feng , Chang Kai-Chih , Kuo Han-Yueh , Lee Chi-Ching , Chang Chun-Tien , Yang Cheng-Yao , Tang Chuan Yi
Published: December 2012

Acinetobacter baumannii
has emerged recently as a major cause of health care-associated infections due to the extent of its antimicrobial resistance and its propensity to cause large nosocomial outbreaks. Here we report the genome sequence of
Acinetobacter baumannii
TYTH-1 isolated in Taiwan during 2008.
Complete Genome Sequence of Brucella abortus Strain BCB034, a Strain of Biovar 2 Isolated from Human
Authors: Zhong Zhijun , Wang Lulu , Chen Yanfen , Wang Zhoujia , Wang Yufei , Cui Mingquan , Li Tiefeng , Ke Yuehua , Yuan Xitong , Wang Dali , Chen Zeliang , Peng Guangneng
Published: December 2012

Brucella abortus
is divided into eight biovars, of which biovars 1 to 3 are the most frequently represented biovars in strains isolated from humans. Here, we report the genome sequence of
B. abortus
strain BCB034, a strain isolated from a human patient and that belongs to biovar 2.
Genome Sequence of “Candidatus Methanomethylophilus alvus” Mx1201, a Methanogenic Archaeon from the Human Gut Belonging to a Seventh Order of Methanogens
Authors: Borrel Guillaume , Harris Hugh M. B. , Tottey William , Mihajlovski Agnès , Parisot Nicolas , Peyretaillade Eric , Peyret Pierre , Gribaldo Simonetta , O'Toole Paul W. , Brugère Jean-François
Published: December 2012

We report the draft genome sequence of “
Candidatus
Methanomethylophilus alvus” Mx1201, a methanogen present in the human gut. It was enriched from human feces under anaerobic conditions with methanol as the substrate. Its circular genome, of around 1.7 Mb, contains genes needed for methylotrophic methanogenesis from methanol and tri-, di-, and monomethylamine.
Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, “Candidatus Nitrosopumilus sediminis” AR2, from Svalbard in the Arctic Circle
Authors: Park Soo-Je , Kim Jong-Geol , Jung Man-Young , Kim So-Jeong , Cha In-Tae , Ghai Rohit , Martín-Cuadrado Ana-Belén , Rodríguez-Valera Francisco , Rhee Sung-Keun
Published: December 2012

Ammonia-oxidizing archaea (AOA) typically predominate over ammonia-oxidizing bacteria in marine sediments. We herein present the draft genome sequence of an ammonia-oxidizing archaeon, “
Candidatus
Nitrosopumilus sediminis” AR2, which was enriched in culture from a marine sediment obtained off Svalbard, within the Arctic Circle. The typical genes involved in archaeal ammonia oxidation and carbon fixation necessary for chemolithoautotrophic growth were observed. Interestingly, the AR2 genome sequence was revealed to possess, uniquely among cultivated AOA from marine environments, a capability for urea utilization.
Genome Sequence of Thalassospira xiamenensis Type Strain M-5
Authors: Lai Qiliang , Shao Zongze
Published: December 2012

Thalassospira xiamenensis
M-5
T
was isolated from the surface water of a waste oil pool at the oil storage dock in the city of Xiamen, Fujian Province, China. Here, we present the draft genome of strain M-5
T
, which contains 4,705,237 bp with a G+C content of 54.65% and contains 4,343 protein-coding genes and 46 tRNA genes.
Draft Genome Sequence of Staphylococcus massiliensis Strain 5402776
T
Authors: Roux Véronique , Robert Catherine , Gimenez Grégory , Raoult Didier
Published: December 2012

A draft genome sequence of
Staphylococcus massiliensis
, Gram-positive cocci isolated from a human brain abscess sample, is described here. One clustered regularly interspaced short palindromic repeat, three transposases, six putative transposases, and one potential provirus were characterized.
Draft Genome Sequence of Agrobacterium albertimagni Strain AOL15
Authors: Trimble William L. , Phung Le T. , Meyer Folker , Gilbert Jack A. , Silver Simon
Published: December 2012

Agrobacterium albertimagni
strain AOL15 is an alphaproteobacterium isolated from arsenite-oxidizing biofilms whose draft genome contains 5.1 Mb in 55 contigs with 61.2% GC content and includes a 21-gene arsenic gene island. This is the first available genome for this species and the second
Agrobacterium
arsenic gene island.
Genome Sequence of Afipia birgiae, a Rare Bacterium Associated with Amoebae
Authors: Pagnier Isabelle , Croce Olivier , Robert Catherine , Raoult Didier , La Scola Bernard
Published: December 2012

Afipia birgiae
is an alphaproteobacterium from the family
Bradyrhizobiaceae
, growing in amoebae, and a potential human pathogen. We sequenced the genome of type strain 34632
T
. It is composed of 5,325,467 bp and contains 5,160 protein-coding genes and 53 RNA genes, including 3 rRNA genes.
Genome Sequence of Bartonella rattimassiliensis, a Bacterium Isolated from European Rattus norvegicus
Authors: Merhej Vicky , Croce Olivier , Robert Catherine , Rolain Jean-Marc , Raoult Didier
Published: December 2012

Bartonella rattimassiliensis
is a facultative intracellular bacterium isolated from the blood of
Rattus norvegicus
in Marseille. The present study reports the draft genome of
B. rattimassiliensis
strain 15908 (CIP 107705
T
).
Genome Sequence of the Pathogenic Herbaspirillum seropedicae Strain Os45, Isolated from Rice Roots
Authors: Zhu Bo , Ye Shuting , Chang Siping , Chen Mingyue , Sun Li , An Qianli
Published: December 2012

Most
Herbaspirillum seropedicae
strains are beneficial to plants. In contrast,
H. seropedicae
strain Os45, isolated from rice roots, is pathogenic. The draft genome sequence of strain Os45 presented here allows an in-depth comparative genome analysis to understand the subtle mechanisms of beneficial and pathogenic
Herbaspirillum
-plant interactions.
Draft Genome Sequencing of Bacillus sp. Strain M2-6, Isolated from the Roots of Korean Ginseng, Panax ginseng C. A. Meyer, after High-Hydrostatic-Pressure Processing
Authors: Kim Chong-Tai , Kim Bong-Soo , Kim Min-Ji , Park Bang Heon , Kwon Sujin , Maeng Hack Young , Kwak Jangyul , Chun Jongsik , Cho Yong-Jin , Kim Namsoo , Kim Chul-Jin , Maeng Jin-Soo
Published: December 2012

A bacterium, designated M2-6, was isolated from Korean ginseng,
Panax ginseng
C. A. Meyer, roots after high-hydrostatic-pressure processing. On the basis of 16 rRNA gene phylogeny, the isolate was presumptively identified as a
Bacillus
sp. Here we report the draft genome sequence of
Bacillus
sp. strain M2-6 (= KACC 16563).
Genome Sequence of the Immunomodulatory Strain Bifidobacterium bifidum LMG 13195
Authors: Gueimonde Miguel , Ventura Marco , Margolles Abelardo , Sánchez Borja
Published: December 2012

In this work, we report the genome sequences of
Bifidobacterium bifidum
strain LMG13195. Results from our research group show that this strain is able to interact with human immune cells, generating functional regulatory T cells.
Structure determination ofStreptococcus suisserotype 14 capsular polysaccharide
Authors: Van Calsteren Marie-Rose , Gagnon Fleur , Calzas Cynthia , Goyette-Desjardins Guillaume , Okura Masatoshi , Takamatsu Daisuke , Gottschalk Marcelo , Segura Mariela
Published: December 2012

The capsular polysaccharide (CPS) of Streptococcus suis serotype 14 was purified, chemically modified, and characterized. Sugar and absolute configuration analyses gave the following CPS composition: d-Gal, 3; d-Glc, 1; d-GlcNAc, 1; d-Neu5Ac, 1. The Sambucus nigra lectin, which recognizes the Neu5Ac(α2–6)Gal/GalNAc sequence, showed binding to the native CPS. Sialic acid was found to be terminal, and the CPS was quantitatively desialylated by mild acid hydrolysis. It was also submitted to periodate oxidation followed by borohydride reduction and Smith degradation. Sugar and methylation analyses,1H and13C nuclear magnetic resonance, and mass spectrometry of the native CPS or of its specifically modified products allowed to determine the repeating unit sequence: [6)[Neu5Ac(α2–6)Gal(β1–4)GlcNAc(β1–3)]Gal(β1–3)Gal(β1–4)Glc(β1–]n. S. suis serotype 14 CPS has an identical sialic acid-containing side chain as serotype 2 CPS, but differs by the absence of rhamnose in its composition. The same side chain is also present in group B Streptococcus type Ia CPS, except that in the latter sialic acid is 2,3- rather than 2,6-linked to the following galactose. A correlation between the S. suis CPS sequence and genes of the serotype 14 cps locus encoding putative glycosyltransferases and polymerase responsible for the biosynthesis of the repeating unit is proposed.
A Sault-outlet-referenced mid- to late-Holocene paleohydrograph for Lake Superior constructed from strandplains of beach ridges
Authors: Johnston John W. , Argyilan Erin P. , Thompson Todd A. , Baedke Steve J. , Lepper Kenneth , Wilcox Douglas A. , Forman Steven L.
Published: December 2012

The most detailed Lake Superior paleohydrograph relative to the current outlet near Sault Ste. Marie, Ontario–Michigan, was constructed from four strandplains of beach ridges. This provides a history of water-level, glacial isostatic adjustment (GIA), and the active outlet prior to monitoring and regulation. Four relative paleohydrographs that are offset and subparallel owing to differences in GIA were produced from 321 basal foreshore elevations and 56 optically stimulated luminescence ages. Subtracting modeled elevations in defined millennial lake phases between relative paleohydrographs and similarity between an inferred Sault Ste. Marie (hereinafter, Sault) paleohydrograph and data near the zero isobase corroborates rates of GIA derived from water-level gauges. A change in trend in the Sault paleohydrograph is related to the final separation of Lake Superior from Lakes Michigan and Huron and is the youngest age reported at 1060 ± 100 years. A near-horizontal trend in the Sault paleohydrograph for the past millennium has an intercept that is close to the historical average for Lake Superior. A consistently linear trend from about 2 to 1 ka suggests a relatively stable outlet similar to the past millennium, but a decreasing trend from 3 to 1 ka suggests an outlet other than the Sault. Although intercept data beyond the last millennium are similar in elevation to the reported bedrock sill near Chicago (Hansel et al. 1985), we argue that the Port–Huron outlet was the active outlet during this time and the inferred paleohydrograph of Baedke and Thompson (2000) requires reevaluation.
A transcriptomic study reveals differentially expressed genes and pathways respond to simulated acid rain in Arabidopsis thaliana
Authors: Liu Ting-Wu , Niu Li , Fu Bin , Chen Juan , Wu Fei-Hua , Chen Juan , Wang Wen-Hua , Hu Wen-Jun , He Jun-Xian , Zheng Hai-Lei
Published: December 2012

Acid rain, as a worldwide environmental issue, can cause serious damage to plants. In this study, we provided the first case study on the systematic responses of arabidopsis (Arabidopsis thaliana (L.) Heynh.) to simulated acid rain (SiAR) by transcriptome approach. Transcriptomic analysis revealed that the expression of a set of genes related to primary metabolisms, including nitrogen, sulfur, amino acid, photosynthesis, and reactive oxygen species metabolism, were altered under SiAR. In addition, transport and signal transduction related pathways, especially calcium-related signaling pathways, were found to play important roles in the response of arabidopsis to SiAR stress. Further, we compared our data set with previously published data sets on arabidopsis transcriptome subjected to various stresses, including wound, salt, light, heavy metal, karrikin, temperature, osmosis, etc. The results showed that many genes were overlapped in several stresses, suggesting that plant response to SiAR is a complex process, which may require the participation of multiple defense-signaling pathways. The results of this study will help us gain further insights into the response mechanisms of plants to acid rain stress.
CMS, CMS SPREADS AND SIMILAR OPTIONS IN THE MULTI-FACTOR HJM FRAMEWORK
Authors: HANTON PIERRE , HENRARD MARC
Published: December 2012

Constant maturity swaps (CMS) and CMS spread options are analysed in the multi-factor HJM framework. For Gaussian models, which include a version of the Libor Market Models and the G2++ model, explicit approximated pricing formulae are provided. Two approximating approaches are proposed: an exact solution to an approximated equation and an approximated solution to the exact equation. The first approach borrows from previous literature on other models; the second approach is new. For the latter, the price approximation errors are smaller than in the previous literature and negligible in practice. These approaches are being used here to price standard CMS and CMS spreads and can be used for other European exotic products.
AN IMPLIED VOLATILITY MODEL DETERMINED BY CREDIT DEFAULT SWAPS
Authors: HEIDER PASCAL
Published: December 2012

In this paper we propose a diffusion model relating the stock price dynamics to the CDS spread dynamics of a company by assuming a linear relationship between instantaneous stock volatility and CDS spread. To value contingent claims under this model we apply a finite elements discretization to the associated pricing partial differential equation. A robust calibration strategy is presented and numerical examples are studied to validate the model assumptions. Besides option pricing, we discuss further applications which are e.g. the identification of market situations allowing volatility and capital structure arbitrage.
WORST-OF OPTIONS AND CORRELATION SKEW UNDER A STOCHASTIC CORRELATION FRAMEWORK
Authors: MARABEL ROMO JACINTO
Published: December 2012

This article considers a multi-asset model based on Wishart processes that accounts for stochastic volatility and for stochastic correlations between the underlying assets, as well as between their volatilities. The model accounts for the existence of correlation term structure and correlation skew. The article shows that the Wishart specification can generate different patterns corresponding to the correlation skew for a wide range of correlation term structures.

Another advantage of the model is that it is analytically tractable and, hence, it is possible to obtain semi-closed-form solutions for the prices of plain vanilla options, as well as for the price of exotic derivatives. In this sense, this article develops semi-closed-form formulas for the price of European worst-of options with barriers and/or forward-start features. To motivate the introduction of the Wishart volatility model, the article compares the prices obtained under this model and under a multi-asset stochastic volatility model with constant instantaneous correlations. The results reveal the existence of a stochastic correlation premium and show that the consideration of stochastic correlation is a key element for the valuation of these structures.
WHOLE GENOME IDENTITY-BY-DESCENT DETERMINATION
Authors: SABAA HADI , CAI ZHIPENG , WANG YINING , GOEBEL RANDY , MOORE STEPHEN , LIN GUOHUI
Published: December 2012

High-throughput single nucleotide polymorphism genotyping assays conveniently produce genotype data for genome-wide genetic linkage and association studies. For pedigree datasets, the unphased genotype data is used to infer the haplotypes for individuals, according to Mendelian inheritance rules. Linkage studies can then locate putative chromosomal regions based on the haplotype allele sharing among the pedigree members and their disease status. Most existing haplotyping programs require rather strict pedigree structures and return a single inferred solution for downstream analysis. In this research, we relax the pedigree structure to contain ungenotyped founders and present a cubic time whole genome haplotyping algorithm to minimize the number of zero-recombination haplotype blocks. With or without explicitly enumerating all the haplotyping solutions, the algorithm determines all distinct haplotype allele identity-by-descent (IBD) sharings among the pedigree members, in linear time in the total number of haplotyping solutions. Our algorithm is implemented as a computer program iBDD. Extensive simulation experiments using 2 sets of 16 pedigree structures from previous studies showed that, in general, there are trillions of haplotyping solutions, but only up to a few thousand distinct haplotype allele IBD sharings. iBDD is able to return all these sharings for downstream genome-wide linkage and association studies.
THE VARIATIONS OF WATER IN HUMAN TISSUE UNDER CERTAIN COMPRESSION: STUDIED WITH DIFFUSE REFLECTANCE SPECTROSCOPY
Authors: LI CHENXI , JIANG JINGYING , XU KEXIN
Published: December 2012

The reflectance spectrum has been widely adopted to extract diagnosis information of human tissue because it possesses the advantages of noninvasive and rapidity. The external pressure brought by fiber optic probe may influence the accuracy of measurement. In this paper, a systematic study is focused on the effects of probe pressure on intrinsic changes of water and scattering particles in tissue. According to the biphasic nonlinear mixture model, the pressure modulated reflectance spectrum of both in vitro and in vivo tissue is measured and processed with second-derivation. The results indicate that the variations of bulk and bonded water in tissue have a nonlinear relationship with the pressure. Differences in tissue structure and morphology contribute to site-specific probe pressure effects. Then the finite element (FEM) and Monte Carlo (MC) method is employed to simulate the deformation and reflectance spectrum variations of tissue before and after compression. The simulation results show that as the pressure of fiber optic probe applied to the detected skin increased to 80 kPa, the effective photon proportion form dermis decreases significantly from 86% to 76%. Future designs might benefit from the research of change of water volume inside the tissue to mitigate the pressure applied to skin.