bluuebunny/crossref_metadata_2025_split huggingface dataset:
Truncated branch and bound achieves efficient constraint-based genetic design
Authors: Egen Dennis , Lun Desmond S. 
Published: April 2012

Abstract
Motivation: Computer-aided genetic design is a promising approach to a core problem of metabolic engineering—that of identifying genetic manipulation strategies that result in engineered strains with favorable product accumulation. This approach has proved to be effective for organisms including Escherichia coli and Saccharomyces cerevisiae, allowing for rapid, rational design of engineered strains. Finding optimal genetic manipulation strategies, however, is a complex computational problem in which running time grows exponentially with the number of manipulations (i.e. knockouts, knock-ins or regulation changes) in the strategy. Thus, computer-aided gene identification has to date been limited in the complexity or optimality of the strategies it finds or in the size and level of detail of the metabolic networks under consideration.
Results: Here, we present an efficient computational solution to the gene identification problem. Our approach significantly outperforms previous approaches—in seconds or minutes, we find strategies that previously required running times of days or more.
Availability and implementation: GDBB is implemented using MATLAB and is freely available for non-profit use at http://crab.rutgers.edu/~dslun/gdbb.
Contact: dslun@rutgers.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Potato virus Y in Potato in Tajikistan
Authors: Alabi O. J. , Crosslin J. M. , Saidov N. , Naidu R. A. 
Published: May 2012

Potato (Solanum tuberosum L.) is widely grown as a staple food and cash crop in Tajikistan and is an important food security crop in the country. In June 2011, we conducted a survey of potatoes in farmers' fields in the Buston and Dushanbe regions (about 200 miles apart) of Tajikistan. Potato plants with stunted growth and leaves showing chlorotic spots, curling, and necrotic spots and rings were observed with the disease incidence monitored in 10 fields each in Buston and Dushanbe areas varying between 10 and 60%. Representative samples from symptomatic plants tested positive for Potato virus Y (PVY) using virus-specific immunostrips (Agdia Inc., Elkhart, IN). Leaf samples from symptomatic plants were collected from Buston and Dushanbe areas, imprinted on FTA Classic Cards (Whatman International Ltd., Maidstone, UK), air dried, and shipped to the lab at Washington State University for confirmatory diagnostic tests. Total nucleic acids were eluted from FTA cards (1) and subjected to reverse transcription (RT)-PCR with primers (PVY/Y4A and PVY/Y3S) specific to the coat protein of PVY (3). Samples infected with PVY ordinary strain (PVYO), tuber necrosis strain (PVYNTN), tobacco veinal necrosis strains (PVYEU-N and PVYNA-N), and a recombinant strain (PVYN:O) were included as references to validate RT-PCR results. A single DNA product of approximately 480 bp was amplified from potato samples that tested positive with PVY-specific immunostrips. The amplified fragments from two samples from Dushanbe and six from Buston areas were cloned separately into pCR2.1 (Invitrogen Corp., Carlsbad, CA) and two independent clones per amplicon were sequenced from both orientations. Pairwise comparison of these sequences showed 90 to 100% identity among the cloned amplicons (GenBank Accession Nos. JQ743609 to JQ743616) and 90 to 100% with corresponding nucleotide sequence of reference PVY strains (GenBank Accession Nos. JQ743617 to JQ743621). A global phylogenetic analysis of sequences revealed the presence of PVYO in both samples from Dushanbe and one sample from Buston regions and presence of PVYNTN in the remaining five samples from the Buston region. Because of the possible occurrence of mixed infections of PVY strains (2), further studies are needed to determine the presence of mixed infections of two or more strains of PVY and their specificity to potato cultivars. To our knowledge, this study represents the first confirmed report of two distinct strains of PVY in potato in Tajikistan. The occurrence of PVYNTN, a quarantine pathogen in many countries (2), warrants additional investigations to improve sanitary status of potato fields and to facilitate the availability of virus-free seed in clean plant programs for significant yield increases in Tajikistan. References: (1) O. J. Alabi et al. J. Virol. Methods 154:111, 2008. (2) S. Gray et al. Plant Dis. 94:1384, 2010. (3) R. P. Singh et al. J. Virol. Methods 59:189, 1996.
Palmitoylation of virus proteins
Authors: Veit Michael 
Published: May 2012

AbstractThe article summarises the results of more than 30 years of research on palmitoylation (S‐acylation) of viral proteins, the post‐translational attachment of fatty acids to cysteine residues of integral and peripheral membrane proteins. Analysing viral proteins is not only important to characterise the cellular pathogens but also instrumental to decipher the palmitoylation machinery of cells. This comprehensive review describes methods to identify S‐acylated proteins and covers the fundamental biochemistry of palmitoylation: the location of palmitoylation sites in viral proteins, the fatty acid species found in S‐acylated proteins, the intracellular site of palmitoylation and the enzymology of the reaction. Finally, the functional consequences of palmitoylation are discussed regarding binding of proteins to membranes or membrane rafts, entry of enveloped viruses into target cells by spike‐mediated membrane fusion as well as assembly and release of virus particles from infected cells. The topics are described mainly for palmitoylated proteins of influenza virus, but proteins of other important pathogens, such as the causative agents of AIDS and severe acute respiratory syndrome, and of model viruses are discussed.
Carbon pools of an intact forest in Gabon
Authors: Gautam Sishir , Pietsch Stephan A. 
Published: May 2012

AbstractQuantitative and qualitative loss of tropical forests prompted international policy agendas to slow down forest loss through reducing emissions from deforestation and forest degradation (REDD)+, ensuring carbon offset payments to developing countries. So far, many African countries lack reliable forest carbon data and monitoring systems as required by REDD+. In this study, we estimate the carbon stocks of a naturally forested landscape unaffected by direct human impact. We used data collected from 34 plots randomly distributed across the Mount Birougou National Park (690 km2) in southern Gabon. We used tree‐level data on species, diameter, height, species‐specific wood density and carbon fraction as well as site‐level data on dead wood, soil and litter carbon to calculate carbon content in aboveground, belowground, dead wood, soil and litter as 146, 28, 14, 186 and 7 Mg ha−1, respectively. Results may serve as a benchmark to assess ecosystem carbon loss/gain for the Massif du Chaillu in Gabon and the Republic of Congo, provide field data for remote sensing and also may contribute to establish national monitoring systems.
Testing the stress‐gradient hypothesis with aquatic detritivorous invertebrates: insights for biodiversity‐ecosystem functioning research
Authors: Fugère V. , Andino P. , Espinosa R. , Anthelme F. , Jacobsen D. , Dangles O. 
Published: May 2012

Summary1. The stress‐gradient hypothesis (SGH) states that environmental stress modulates species interactions, causing a shift from negative interactions to net positive interactions with increasing stress.2. Potentially, this modulation of species interactions could in turn influence biodiversity‐ecosystem function (B‐EF) relationships along stress gradients. Although the SGH has been extensively discussed in plant community ecology in the past two decades, it has received little attention from animal ecologists.3. To explore whether the SGH could be applied to animal communities, we conducted a litter decomposition experiment with aquatic detritivorous invertebrates in which we manipulated litter quality and measured species interactions along this resource quality gradient. Litter quality was manipulated by presenting detritivores with leaves of plant species varying in specific leaf area and decomposition rate in streams.4. We found a switch from negative to neutral interactions with increasing resource quality stress, in line with the SGH. However, by re‐examining other published results with aquatic detritivores from the perspective of the SGH, we found that a diversity of patterns seem to characterize detritivore interactions along stress gradients.5. Although the basic pattern proposed by the SGH may not apply to animal systems in general, we show that aquatic detritivore interactions do change along stress gradients, which underlines the importance of incorporating environmental stressors more explicitly in B‐EF research.
Population genetic structure and long‐distance dispersal among seabird populations: Implications for colony persistence
Authors: BICKNELL A. W. J. , KNIGHT M. E. , BILTON D. , REID J. B. , BURKE T. , VOTIER S. C. 
Published: May 2012

AbstractDramatic local population decline brought about by anthropogenic‐driven change is an increasingly common threat to biodiversity. Seabird life history traits make them particularly vulnerable to such change; therefore, understanding population connectivity and dispersal dynamics is vital for successful management. Our study used a 357‐base pair mitochondrial control region locus sequenced for 103 individuals and 18 nuclear microsatellite loci genotyped for 245 individuals to investigate population structure in the Atlantic and Pacific populations of the pelagic seabird, Leach’s storm‐petrelOceanodroma leucorhoa leucorhoa. This species is under intense predation pressure at one regionally important colony on St Kilda, Scotland, where a disparity between population decline and predation rates hints at immigration from other large colonies.amova,FST,ΦSTand Bayesian cluster analyses revealed no genetic structure among Atlantic colonies (Global ΦST = −0.02P > 0.05, GlobalFST = 0.003,P > 0.05,structureK = 1), consistent with either contemporary gene flow or strong historical association within the ocean basin. The Pacific and Atlantic populations are genetically distinct (Global ΦST = 0.32P < 0.0001, GlobalFST = 0.04,P < 0.0001,structureK = 2), but evidence for interocean exchange was found with individual exclusion/assignment and population coalescent analyses. These findings highlight the importance of conserving multiple colonies at a number of different sites and suggest that management of this seabird may be best viewed at an oceanic scale. Moreover, our study provides an illustration of how long‐distance movement may ameliorate the potentially deleterious impacts of localized environmental change, although direct measures of dispersal are still required to better understand this process.
Measuring the stiffness of bacterial cells from growth rates in hydrogels of tunable elasticity
Authors: Tuson Hannah H. , Auer George K. , Renner Lars D. , Hasebe Mariko , Tropini Carolina , Salick Max , Crone Wendy C. , Gopinathan Ajay , Huang Kerwyn Casey , Weibel Douglas B. 
Published: May 2012

SummaryAlthough bacterial cells are known to experience large forces from osmotic pressure differences and their local microenvironment, quantitative measurements of the mechanical properties of growing bacterial cells have been limited. We provide an experimental approach and theoretical framework for measuring the mechanical properties of live bacteria. We encapsulated bacteria in agarose with a user‐defined stiffness, measured the growth rate of individual cells and fit data to a thin‐shell mechanical model to extract the effective longitudinal Young's modulus of the cell envelope of Escherichia coli (50–150 MPa), Bacillus subtilis (100–200 MPa) and Pseudomonas aeruginosa (100–200 MPa). Our data provide estimates of cell wall stiffness similar to values obtained via the more labour‐intensive technique of atomic force microscopy. To address physiological perturbations that produce changes in cellular mechanical properties, we tested the effect of A22‐induced MreB depolymerization on the stiffness of E. coli. The effective longitudinal Young's modulus was not significantly affected by A22 treatment at short time scales, supporting a model in which the interactions between MreB and the cell wall persist on the same time scale as growth. Our technique therefore enables the rapid determination of how changes in genotype and biochemistry affect the mechanical properties of the bacterial envelope.
Meta‐analysis of the association between cognitive abilities and everyday functioning in bipolar disorder
Authors: Depp Colin A , Mausbach Brent T , Harmell Alexandrea L , Savla Gauri N , Bowie Christopher R , Harvey Philip D , Patterson Thomas L 
Published: May 2012

Depp CA, Mausbach BT, Harmell AL, Savla GN, Bowie CR, Harvey PD, Patterson TL. Meta‐analysis of the association between cognitive abilities and everyday functioning in bipolar disorder. Bipolar Disord 2012: 14: 217–226. © 2012 The Authors. Journal compilation © 2012 John Wiley & Sons A/S.Objectives:  Neurocognitive deficits are common in bipolar disorder and contribute to functional disability. However, the degree to which general and specific cognitive deficits affect everyday functioning in bipolar disorder is unknown. The goal of this meta‐analysis was to examine the magnitude of the effect of specific neurocognitive abilities on everyday functioning in bipolar disorder.Methods:  We conducted a comprehensive meta‐analysis of studies that reported associations between performance on objective neuropsychological tasks and everyday functioning among individuals with bipolar disorder. From an initial pool of 486 papers, 22 studies met inclusion criteria, comprising a total of 1344 participants. Correlation coefficients were calculated for 11 cognitive domains and four measurement modalities for functioning. We also examined effect moderators, such as sample age, clinical state, and study design.Results:  The mean Pearson correlation between neurocognitive ability and functioning was 0.27, and was significant for all cognitive domains and varied little by cognitive domain. Correlations varied by methods of everyday functioning assessment, being lower for clinician and self‐report than performance‐based tasks and real‐world milestones such as employment. None of the moderator analyses were significant.Conclusions:  Overall, the strength of association between cognitive ability and everyday functioning in bipolar disorder is strikingly similar to that seen in schizophrenia, with little evidence for differences across cognitive domains. The strength of association differed to a greater extent according to functional measurement approach.
Impact of crimson clover dying mulch on two eggplant insect herbivores
Authors: Hooks C. R. R. , Hinds J. , Zobel E. , Patton T. 
Published: May 2012

AbstractEggplantSolanum melongenaL., is often colonized by two early season insect defoliators. The Colorado potato beetle (CPB),Leptinotarsa decemlineata(Say), and flea beetlesEpitrixspp., emerge from their overwintering sites in early spring and seek out emerging host plants such as eggplant. During the 2009 and 2010 growing season, field studies were conducted to investigate the impact of inter‐planting eggplant into a crimson clover (CC),Trifolium incarnatumL., winter cover crop on populations of flea beetles, CPB and their associated arthropod predators. The experiment consisted also of two levels of insecticide usage such as an application of azadirachtins plus pyrethrins followed by several applications of spinosad or no insecticide sprays as subplot treatments. During both study years, significantly fewer (adults, larvae and egg masses) were found on eggplant inter‐planted into CC than in bare‐ground (BG) eggplant plots. Although flea beetle abundance was greater in BG eggplant during 2010, they appeared to be less influenced by the presence of CC than were CPB. Additionally, there was no apparent impact of insecticide treatment on CPB populations on eggplant inter‐planted into CC. However, there was a decline in CPB following treatments with insecticides in BG eggplant plots. This suggests that a winter cover crop such as CC can be used to help manage CPB in eggplant, however, using this tactic in tandem with insecticide sprays may not result in greater CPB management.
Colorectal stenting for malignant obstruction: an 8‐year clinical experience
Authors: Chouhan Hanumant , Wong Christopher X. , Maharaj Preeya , Lawrence Mathew J. , Hunter Andrew , Moore James W. 
Published: May 2012

AbstractBackground:  A substantial percentage of patients with colorectal cancer present with obstructive symptoms. In such patients, surgery is often required and is associated with significant morbidity and mortality. Colorectal stenting is an increasingly commonplace alternative with potentially fewer risks than open surgery. We present our clinical experience over an 8‐year period with colorectal stenting in a major tertiary Australian hospital.Methods:  From 2000 to 2008, patients undergoing colorectal stenting were identified via medical records. Clinical data collected included patient demographics, tumour type, extent of metastatic disease, stent characteristics, technical and clinical success, acute and chronic complications, and long‐term follow‐up status.Results:  Thirty‐five patients (69 ± 13 years, 25 male) received a total of 39 stents. Technical success was achieved in 37 (95%), and clinical relief of obstruction was achieved in 34 (89%). One case was complicated by perforation at the time of procedure and three cases experienced delayed perforation. Reintervention was required in 17% of patients, all of whom had less than 50% hepatic volume replacement by metastatic disease.Conclusions:  Colorectal stenting is a feasible and safe alternative for patients presenting with obstructive symptoms but the benefit may be restricted to patients with a short expected survival.
Culture and the absurd: the means and meanings of Aboriginal identity in the time of cultural revivalism
Authors: COWLISHAW GILLIAN 
Published: May 2012

This essay proposes that a fundamental arbitrariness and absurdity at the heart of culture becomes visible in times of radical social change. As the Australian nation attempts to celebrate and revive Aboriginal Culture, and institutions call upon culture to remedy Aboriginal ills, Aboriginal traditions are also being held responsible for present distress and social disorder. However, some Aboriginal people are also developing new relationships with ‘their culture’, taking up opportunities to refashion or construct identities that are free of ancestral power, and encouraging new forms of subjective identification, social recognition, and self‐assertion. Equivalent processes are explored in remote and suburban Australia at semiotic, political, and social levels.RésuméLe présent essai postule que les périodes de changements sociaux radicaux dévoilent l'arbitraire et l'absurdité fondamentaux qui se nichent au cœur de la culture. À l'heure où la nation australienne tente de mettre en lumière et de ranimer la Culture Aborigène et où les institutions en appellent à la culture pour remédier aux maux des Aborigènes, les traditions aborigènes sont aussi tenues responsables de la détresse et des désordres sociaux actuels. Certains peuples aborigènes sont cependant en train de tisser de nouveaux liens avec « leur culture » en profitant des occasions de remodeler des identités dégagées du pouvoir des ancêtres et en favorisant de nouvelles formes d'identification collective, de reconnaissance sociale et d'affirmation de soi. L'auteure explore des processus équivalents, au niveau sémiotique, politique et social, dans les zones isolées et suburbaines d'Australie.
Regulation of the glucocorticoid response to stress‐related disorders by the Hsp90‐binding immunophilin FKBP51
Authors: Galigniana Natalia M. , Ballmer Luzia T. , Toneatto Judith , Erlejman Alejandra G. , Lagadari Mariana , Galigniana Mario D. 
Published: May 2012

J. Neurochem. (2012) 122, 4–18.AbstractImmunophilin is the collective name given to a family of proteins that bind immunosuppressive drugs: Some immunophilins are Hsp90‐binding cochaperones that affect steroid receptor function. Mood and anxiety disorders are stress‐related diseases characterized by an impaired function of the mineralocorticoid and glucocorticoid receptors, two of the major regulatory elements of the hypothalamus‐pituitary‐adrenocortical axis. Genetic variations of the FK506‐binding protein of 51‐kDa, FKBP51, one of the immunophilins bound to those steroid receptor complexes, were associated with the effectiveness of treatments against depression and with a major risk‐factor for the development of post‐traumatic stress disorders. Interestingly, immunophilins show polymorphisms and some polymorphic isoforms of FKBP51 correlate with a greater impairment of steroid receptor functions. In this review, we discuss different aspects of the role of FKBP51 in such steroid receptor function and the impact of genetic variants of the immunophilin on the dysregulation of the stress response.
Therapeutic effects of metabotropic glutamate receptor 5 positive allosteric modulator CDPPB on phencyclidine‐induced cognitive deficits in mice
Authors: Horio Mao , Fujita Yuko , Hashimoto Kenji 
Published: May 2012

AbstractThis study was undertaken to examine the effects of CDPPB (3‐cyano‐N‐(1,3‐diphenyl‐1H‐pyrazol‐5‐yl)benzamide), a positive allosteric modulator (PAM) of metabotropic glutamate receptor 5 (mGlu5), on cognitive deficits in mice after repeated administration of the N‐methyl‐D‐aspartate (NMDA) receptor antagonist phencyclidine (PCP). In the novel object recognition test, PCP (10 mg/kg/day for 10 days)‐induced cognitive deficits in mice were not improved by a single administration of CDPPB (10 mg/kg/day). However, PCP (10 mg/kg/day for 10 days)‐induced cognitive deficits in mice were significantly improved by subsequent subchronic (14 days) administration of CDPPB (10 mg/kg/day), but not of CDPPB (1.0 mg/kg/day). This study suggests that PCP‐induced cognitive deficits in mice are improved by subsequent subchronic administration of CDPPB. Therefore, mGlu5 PAMs would be potential therapeutic drugs for cognitive deficits in schizophrenia.