bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pharmacometric Approaches to Guide Dose Selection of the Novel GPR40 Agonist TAK‐875 in Subjects With Type 2 Diabetes Mellitus
Authors: Naik H , Lu J , Cao C , Pfister M , Vakilynejad M , Leifke E 
Published: January 2013

The G‐protein‐coupled receptor 40 agonist (GPR40) TAK‐875 is being developed as an adjunct to diet and exercise to improve glycemic control in patients with type 2 diabetes mellitus. Pharmacometric approaches such as model‐based exposure‐response and meta‐analyses were applied to (i) characterize exposure/dose–efficacy responses of TAK‐875, (ii) characterize the time course of glycosylated hemoglobin A1c (HbA1c) response with TAK‐875 6.25 to 200 mg q.d. doses for 12 weeks, (iii) project and compare HbA1c response with dipeptidyl peptidase 4 (DPP‐4) inhibitors and TAK‐875 up to 24 weeks, and (iv) provide a quantitative rationale for dose selection in phase 3. On the basis of phase 2 data, relationships between TAK‐875 concentrations and HbA1c were well characterized by exposure–response models. EC50 and Emax of TAK‐875 were estimated to be 3.16 µg/ml and 0.366, respectively. Model‐based simulations over 24 weeks indicated that the 25‐ and 50‐mg q.d. doses of TAK‐875 achieve efficacy as comparable with or better than that of commonly used antidiabetic agents.CPT: Pharmacometrics & Systems Pharmacology (2013) 2, e22; doi:10.1038/psp.2012.23; advance online publication 9 January 2013
MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data
Authors: Ramachandran Parameswaran , Palidwor Gareth A. , Porter Christopher J. , Perkins Theodore J. 
Published: January 2013

Abstract
Motivation: Reliable estimation of the mean fragment length for next-generation short-read sequencing data is an important step in next-generation sequencing analysis pipelines, most notably because of its impact on the accuracy of the enriched regions identified by peak-calling algorithms. Although many peak-calling algorithms include a fragment-length estimation subroutine, the problem has not been adequately solved, as demonstrated by the variability of the estimates returned by different algorithms.
Results: In this article, we investigate the use of strand cross-correlation to estimate mean fragment length of single-end data and show that traditional estimation approaches have mixed reliability. We observe that the mappability of different parts of the genome can introduce an artificial bias into cross-correlation computations, resulting in incorrect fragment-length estimates. We propose a new approach, called mappability-sensitive cross-correlation (MaSC), which removes this bias and allows for accurate and reliable fragment-length estimation. We analyze the computational complexity of this approach, and evaluate its performance on a test suite of NGS datasets, demonstrating its superiority to traditional cross-correlation analysis.
Availability: An open-source Perl implementation of our approach is available at http://www.perkinslab.ca/Software.html.
Contact: tperkins@ohri.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Modelling the impacts of environmental variation on the habitat suitability of swordfish, Xiphias gladius, in the equatorial Atlantic Ocean
Authors: Chang Yi-Jay , Sun Chi-Lu , Chen Yong , Yeh Su-Zan , DiNardo Gerard , Su Nan-Jay 
Published: January 2013

Abstract
Chang, Y.-J., Sun, C.-L., Chen, Y., Yeh, S.-Z., DiNardo, G., and Su, N.-J. 2013. Modelling the impacts of environmental variation on the habitat suitability of swordfish, Xiphias gladius, in the equatorial Atlantic Ocean. – ICES Journal of Marine Science, 70: 1000–1012. We developed a habitat suitability index (HSI) model to identify the optimal habitats of swordfish (Xiphias gladius) in the equatorial Atlantic Ocean. Environmental variables, including sea surface temperature (SST), mixed layer depth (MLD), chlorophyll-a concentrations, and sea surface height anomaly, as well as catch and effort data from Taiwanese longline fisheries, were used. The geometric mean model including all the above environmental variables was identified as the most parsimonious model for yielding HSI predictions coinciding with productive fishing grounds with high fishing effort. Swordfish mainly aggregated in the northwest region during March–May and spread southeast thereafter in response to seasonal shifts in oceanographic conditions. There was annual variation in the distribution of habitat patches, and the habitat quality was reduced in the northwest region of the equatorial Atlantic Ocean during 2005. The apparent spatial shifts in optimal habitats might be linked to reduced MLD and elevation in sea surface height, which might be related to climate variability (e.g. Niño-Southern Oscillation and/or Northern Atlantic Oscillation). Because environmental data regarding climate change scenarios are becoming readily available, we can utilize the proposed HSI models to evaluate possible changes in habitat suitability resulting from climate change and provide scientific advice for the development of management regulations.
Short time-scale AGN X-ray variability with EXOSAT: black hole mass and normalized variability amplitude
Authors: McHardy I. M. 
Published: January 2013

Abstract
The old EXOSAT medium energy measurements of high-frequency (HF) active galactic nuclei (AGN) power spectral normalization are re-examined in the light of accurate black hole mass determinations which were not available when these data were first published by Green et al. It is found that the normalized variability amplitude (NVA), measured directly from the power spectrum, is proportional to Mβ, where β ∼ −0.54 ± 0.08. As NVA is the square root of the power, these observations show that the normalization of the HF power spectrum for this sample of AGN varies very close to inversely with black hole mass. Almost the same value of β is obtained whether the quasar 3C 273 is included in the sample or not, suggesting that the same process that drives X-ray variability in Seyfert galaxies applies also to 3C 273. These observations support the work of Gierliński et al. who show that an almost exactly linear anticorrelation is required if the normalizations of the HF power spectra of AGN and X-ray binary systems are to scale similarly. These observations are also consistent with a number of studies showing that the short time-scale variance of AGN X-ray light curves varies approximately inversely with mass.
First Report of the Parasitic Plant Phelipanche aegyptiaca Infecting Kenaf in Israel
Authors: Lati R. , Aly R. , Eizenberg H. , Lande T. 
Published: January 2013

Kenaf (Hibiscus cannabinus L.; Malvaceae) is an annual fiber crop that has recently been introduced as a niche crop in Israel, and grown mainly at areas with high summer temperatures. It is advantageous in crop rotation in these areas since it can rapidly accumulate biomass under high temperatures when other crops (e.g., tomato, sunflower, corn, and sorghum) cannot be cultivated. Additionally, the fact that it can be irrigated with waste water makes it attractive under these climatic conditions. Broomrapes (Phelipanche and Orobanche spp.) are chlorophyll-lacking obligatory root-parasitic plants that parasitize the root system of many field crops and vegetables (1). Parasitism by P. aegyptiaca has economic impacts on various crops belonging to several botanical families (e.g., Solanaceae, Apiaceae, Fabaceae, and Asteraceae). This parasitic weed is common in most agricultural areas in Israel including the coastal plain, Yisre'el Valley, the Jordan Valley, and the Negev Desert. High infection levels by P. aegyptiaca have result in a severe yield losses and quality reduction in these crops. Parasitism of P. aegyptiaca on kenaf was observed in September 2012 in a field located in Bet-Shean Valley (Latitude 32° 30' N; Longitude 35° 30' E; 105 m), with an average density of 0.7 plant/m2, in a total area of 0.3 ha. This crop was planted on May 2012 in plots that were previously affected. Infection did not lead to visible symptoms or damage to kenaf, but allowed seed production by the parasite. In order to verify that kenaf was a host of P. aegyptiaca, 10 samples of kenaf plants infected with P. aegyptiaca were taken to the lab and the root systems of the plant and the parasite were carefully washed. Cross-sections of the connection between kenaf and the parasite were taken and inspected for xylem connections under a compound microscope (BX61, Olympus) equipped with high-resolution digital camera (DP-70, Olympus), under 40× magnification. A clear xylem connection between the weed's tubercles and kenaf roots was observed, confirming the development of functional Phelipanche haustoria. To our knowledge, this is the first report of kenaf as a host for P. aegyptiaca. Kenaf has been reported to induce the germination of O. cernua in India (3). Cotton, another member of the Malvaceae, has also been reported to stimulate seed germination of O. minor (4) and P. aegyptiaca (2). However, to the best of our knowledge, this finding reports the first occurrence of a Malvaceae crop as a host for P. aegyptiaca. References: (1) H. Eizenberg et al. Weed Sci. 55:152, 2007. (2) M. Ghotbi et al. Int. J. Agri. Sci. 2:62, 2012. (3) G. V. G. Krishnamurthy et al. Indian J. Weed Sci. 9:95, 1977. (4) Y. Ma et al. Agron. J. 104:569, 2012.
First Report of Banana mild mosaic virus Infecting Plantain in Ivory Coast
Authors: Kouadio K. T. , Agneroh T. A. , De Clerck C. , Lepoivre P. , Jijakli M. H. 
Published: January 2013

Plantain (Musa sp., genomic group AAB) is an important crop for millions of the world's poorest people. In Ivory Coast, it is the second most consumed food and an important source of income for farmers. Between 2010 and 2011, a survey for viruses infecting plantain (AAB) was conducted in 10 major plantain-growing regions located in eastern (Abengourou), middle-western (Bouaflé, Daloa, Issia, Oumé, Sinfra, Zuenoula), central (Yamoussoukro), and southern (Aboisso, Gagnoa) Ivory Coast. Leaf samples showing yellow streaks or mild chlorotic streaks were collected and dried on CaCl2 for storage. A representative sample from each location was selected and tested for the presence of Cucumber mosaic virus (CMV, genus Cucumovirus), Banana streak virus (BSV, genus Badnavirus), Banana mild mosaic virus (BanMMV, family Flexiviridae), and Banana bract mosaic virus (BBrMV, genus Potyvirus). Immunocapture (IC)-PCR was used for the detection of BSV while reverse transcription (RT)-PCR was used for the detection of CMV, BanMMV, and BBrMV. The following primers sets were used: BSV cl1 and BSV cl2 (1), CMV 3′ and CMV 5′ (3), BanMMV BanCP1 and BanCP2 (4), BBrMV Bract N2 and Bract NR (2). BanMMV was detected as mixed infections with BSV in the 10 tested samples, one of which also contained CMV. To confirm the identity of the amplification products from the BanMMV primers, one cDNA fragment was directly sequenced in the forward direction (Macrogen Inc., Seoul, South Korea). BLAST search in GenBank revealed that the partial coat protein (CP) sequence of the Ivorian isolate shared 80 to 88% nucleotides and 81 to 92% deduced amino acid similarities with BanMMV isolates. In contrast, partial CP sequence of the Ivorian isolate had less than 40% deduced amino acid sequence identity with other Flexiviridae CP sequence. The partial CP sequence of the Ivorian BanMMV isolate was deposited in GenBank under Accession No. JX014304. To further confirm the identification, all the samples were tested by plate trapped antigen (PTA)-ELISA with rabbit polyclonal antiserum specific to BanMMV (obtained from B. E. Lockhart, University of Minnesota, U.S.A.) and anti-rabbit IgG (Sigma-Aldrich, Belgium/A3687). The 10 samples reacted positive for BanMMV by ELISA. CMV and BSV have been reported in Ivory Coast, but to our knowledge, this is the first report of BanMMV in the country. The detection of BanMMV in association with BSV or CMV in mixed infection in 10 locations which are important plantain growing areas is a first step in the evaluation of the impact of virus diseases on plantain production in this country. References: (1) S. Dallot et al. Arch. Virol. 146:2182, 2001. (2) M.-L. Iskra-Caruana et al. J. Virol. Methods 153:224, 2008. (3) M. Sharman et al. J. Virol. Methods 89:77, 2000. (4) P.-Y. Teycheney et al. J. Gen. Virol. 86:3181, 2005.
First Report of the Occurrence and Resistance to Mefenoxam of Peronospora belbahrii, Causal Agent of Downy Mildew of Basil (Ocimum basilicum) in Israel
Authors: Cohen Y. , Vaknin M. , Ben-Naim Y. , Rubin A. E. , Galperin M. , Silverman D. , Bitton S. , Adler U. 
Published: January 2013

Downy mildew in basil was first reported from Uganda in 1933 (4). In 2004, it was reported from Italy (3) and, thereafter, from other countries around the world. In Israel, the disease was first observed in November 2011 in two greenhouses located in the northern part of the Jordan Valley. Within a month, second and third outbreaks of the disease occurred simultaneously near the southwest and southeast borders of Israel, 250 km from the initial disease outbreak. By the summer of 2012, the disease had appeared throughout the country, causing major economic damage. The causal agent, identified as Peronospora belbahrii (see below), produced chlorotic lesions on leaf blades with sporangia developing on the lower leaf surfaces. Lesions gradually turn necrotic, and infected leaves abscised. Sporangia were dark purple, oval, 30.4 ± 2.9 μm long × 21.4 ± 1.7 μm wide. Sporangiophores emerged from stomatal openings in a saturated atmosphere, were hyaline, 400 to 600 μm long, dichotomously branched, with three to five branches per sporangiophore, and bore a single sporangium on each branchlet tip. Oospores, seldom seen, were brown, round, and 46.2 ± 2.8 μm in diameter. Sporangia germinated directly, each producing a single germ tube that penetrated the periclinal wall of epidermal cells. PCR assays using sporangia and infected leaves as the template, and specific BAZ primers (1), produced a 134-bp band typical of P. belbahrii (1,2). Twenty isolates, collected from 12 locations in Israel from December 2011 to September 2012, were all sensitive to mefenoxam as the isolates did not cause symptoms on 15-leaf, potted basil plants (cv. Peri, Volcani Center, Israel) that were sprayed with 10 μg mefenoxam/ml (Ridomil Gold 48%, Syngenta, Basel, Switzerland) prior to inoculation. However, one isolate collected in early October 2012 from a severely infected plant in a greenhouse at Rehov in Bet-Shaan Valley, in which the plants had been treated with mefenoxam, was resistant to mefenoxan, showing abundant sporulation on leaves of potted basil plants that had been sprayed with 1,000 μg of mefenoxam/ml prior to inoculation. To our knowledge, this is the first report of the occurrence of downy mildew in basil in Israel. This is also the first global report of resistance to mefenoxam in P. belbahrii. References: (1) L. Belbahri et al. Mycol. Res. 109:1276, 2005. (2) R. Djalali et al. Mycol. Progress 11:961, 2012. (3) A. Garibaldi et al., Plant Dis. 89:683, 2004. (4) C. G. Hansford. Rev. Appl. Mycol. 12:421, 1933.
Comparison of Equivolume, Equiosmolar Solutions of Mannitol and Hypertonic Saline with or without Furosemide on Brain Water Content in Normal Rats
Authors: Wang Liang Chao , Papangelou Alexander , Lin Christopher , Mirski Marek A. , Gottschalk Allan , Toung Thomas J. K. 
Published: January 2013

Abstract

Background:
Mannitol and hypertonic saline (HS) are used by clinicians to reduce brain water and intracranial pressure and have been evaluated in a variety of experimental and clinical protocols. Administering equivolume, equiosmolar solutions in healthy animals could help produce fundamental data on water translocation in uninjured tissue. Furthermore, the role of furosemide as an adjunct to osmotherapy remains unclear.

Methods:
Two hundred twenty isoflurane-anesthetized rats were assigned randomly to receive equivolume normal saline, 4.2% HS (1,368 mOsm/L 25% mannitol (1,375 mOsm/L), normal saline plus furosemide (8 mg/kg), or 4.2% HS plus furosemide (8 mg/kg) over 45 min. Rats were killed at 1, 2, 3, and 5 h after completion of the primary infusion. Outcome measurements included body weight; urinary output; serum and urinary osmolarity and electrolytes; and brain, lung, skeletal muscle, and small bowel water content.

Results:
In the mannitol group, the mean water content of brain tissue during the experiment was 78.0% (99.3% CI, 77.9–78.2%), compared to results from the normal saline (79.3% [99.3% CI, 79.1–79.5%]) and HS (78.8% [99.3% CI, 78.6–78.9%]) groups (P < 0.001), whereas HS plus furosemide yielded 78.0% (99.3% CI, 77.8–78.2%) (P = 0.917). After reaching a nadir at 1 h, brain water content increased at similar rates for mannitol (0.27%/h [99.3% CI, 0.14–0.40%/h]) and HS (0.27%/h [99.3% CI, 0.17–0.37%/h]) groups (P = 0.968).

Conclusions:
When compared to equivolume, equiosmolar administration of HS, mannitol reduced brain water content to a greater extent over the entire course of the 5-h experiment. When furosemide was added to HS, the brain-dehydrating effect could not be distinguished from that of mannitol.
A new Seismic Wave Attenuation Module to experimentally measure low‐frequency attenuation in extensional mode
Authors: Madonna Claudio , Tisato Nicola 
Published: January 2013

ABSTRACTA Seismic Wave Attenuation Module is developed to experimentally measure the attenuation in extensional‐mode QE−1 and the Young's modulus of copper jacketed, 60 mm long and 25.4 mm in diameter samples in a gas medium (Paterson) rig. The new module is suitable for natural rock samples and was tested under confining pressure up to 50 MPa and room temperature. The module is designed to operate at a strain < 10−6, for which rocks behave linearly. To calculate attenuation, both the applied force and the bulk shortening of the sample are measured employing linear variable differential transformers. This technique allows measuring samples with a high degree of heterogeneity. Attenuation at low‐seismic frequencies (10−2–102 Hz) is obtained for rocks at dry and various saturation conditions. We present a series of measurements on Berea sandstone in a room‐dry condition and saturated with different fluids: water and glycerine solutions with viscosities of 10 cP and 22 cP, respectively, at a confining pressure of 10 MPa and with a pore pressure of 1 MPa. The accuracy of the attenuation data expressed as a phase shift is 0.0019 rad.
Sensitivity and specificity of PS/AA‐modified nanoparticles used in malaria detection
Authors: Thiramanas Raweewan , Jangpatarapongsa Kulachart , Asawapirom Udom , Tangboriboonrat Pramuan , Polpanich Duangporn 
Published: January 2013

SummaryPolystyrene (PS) nanoparticle (NP) copolymerized with acrylic acid (AA) and coloured monomer, i.e. 2,3,6,7‐tetra(2,2′‐bithiophene)‐1,4,5,8‐naphthalenetetracarboxylic‐N,N′‐di(2‐methylallyl)‐bisimide (ALN8T), was synthesized via the miniemulsion polymerization. Before applying for malaria antigen detection, the blue NP was conjugated with human polyclonal malaria IgG antibody (Ab) specific to Plasmodium falciparum. For the conjugation, three methods, i.e. physical adsorption, covalent coupling and affinity binding via streptavidin (SA) and biotin interaction, were employed. The optimum ratio of Ab to NPs used in each immobilization procedure and the latex agglutination test based on the reaction between Ab conjugated NPs and malaria patient plasma were investigated. All Ab–latex conjugates provided the high sensitivity for the detection of P. falciparum malaria plasma. The highest specificity to P. falciparum was obtained from using Ab–NPs conjugated via the SA–biotin interaction.
Transcriptional control of the F0F1‐ATP synthase operon of Corynebacterium glutamicum: SigmaH factor binds to its promoter and regulates its expression at different pH values
Authors: Barriuso‐Iglesias Mónica , Barreiro Carlos , Sola‐Landa Alberto , Martín Juan F. 
Published: January 2013

SummaryCorynebacterium glutamicum used in the amino acid fermentation industries is an alkaliphilic microorganism. Its F0F1‐ATPase operon (atpBEFHAGDC) is expressed optimally at pH 9.0 forming a polycistronic (7.5 kb) and a monocistronic (1.2 kb) transcripts both starting upstream of the atpB gene. Expression of this operon is controlled by the SigmaH factor. The sigmaH gene (sigH) was cloned and shown to be co‐transcribed with a small gene, cg0877, encoding a putative anti‐sigma factor. A mutant deleted in the sigH gene expressed the atpBEFHAGDC operon optimally at pH 7.0 at difference of the wild‐type strain (optimal expression at pH 9.0). These results suggested that the SigmaH factor is involved in pH control of expression of the F0F1 ATPase operon. The SigmaH protein was expressed in Escherichia coli fused to the GST (glutathione‐S‐transferase) and purified to homogeneity by affinity chromatography on a GSTrap HP column. The fused protein was identified by immunodetection with anti‐GST antibodies. DNA‐binding studies by electrophoretic mobility shift assays showed that the SigH protein binds to a region of the atpB promoter containing the sigmaH recognition sequence (−35)TTGGAT…18nt…GTTA(−10). SigmaH plays an important role in the cascade of control of pH stress in Corynebacterium.
Acute Ethanol Reduces Reversal Cost in Discrimination Learning by Reducing Perseverance in Adolescent Rhesus Macaques
Authors: Wright Jr M. Jerry , Glavis‐Bloom Courtney , Taffe Michael A. 
Published: January 2013

BackgroundAcute alcohol exposure produces cognitive deficits in adults but less is known about the acute cognitive effects of alcohol in adolescents. The cognitive impact of acute alcohol exposure includes deficits in discrimination and reversal learning, but traditional experimental approaches make it difficult to distinguish the effect of alcohol on discrimination learning from the effect of alcohol on reversal learning. Young rhesus macaques can be used to model some aspects of human adolescence because of their anatomical, neurophysiological, and cognitive similarities with humans.MethodsAdolescent male rhesus monkeys (n = 10) were trained to respond to visual stimuli on touch‐sensitive LCD panels controlled by the nonhuman primate version of CANTAB software. Discrimination and reversal learning tasks were subsequently assessed after monkeys were allowed to consume varying amounts of ethanol (EtOH) in a flavored vehicle (vehicle only, up to 0.5 g/kg EtOH, up to 1.0 g/kg EtOH, and up to 1.5 g/kg EtOH).ResultsAcute exposure to EtOH reduced perseverance, increased response accuracy, and reduced errors during reversal learning when the task was completed within 90 minutes of EtOH consumption. No reduction in reversal errors was observed when EtOH was consumed 3 or 24 hours prior to reversal learning. EtOH only impaired discrimination learning when monkeys had very little previous EtOH exposure.ConclusionsThe temporal relationship between EtOH consumption and reversal learning was consistent with selective EtOH‐induced impairment of retrieval, but not storage, processes. This was evidenced by diminished perseverance on the previously correct stimulus leading to decreased errors to criterion.