bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeny meets ecotoxicology: evolutionary patterns of sensitivity to a common insecticide
Authors: Hammond John I. , Jones Devin K. , Stephens Patrick R. , Relyea Rick A. 
Published: January 2012

AbstractPesticides commonly occur in aquatic systems and pose a substantial challenge to the conservation of many taxa. Ecotoxicology has traditionally met this challenge by focusing on short‐term, single‐species tests and conducting risk assessments based on the most sensitive species tested. Rarely have ecotoxicology data been examined from an evolutionary perspective, and to our knowledge, there has never been a phylogenetic analysis of sensitivity, despite the fact that doing so would provide insights into patterns of sensitivity among species and identify which clades are the most sensitive to a particular pesticide. We examined phylogenetic patterns of pesticide sensitivity in amphibians, a group of conservation concern owing to global population declines. Using the insecticide endosulfan, we combined previously published results across seven species of tadpoles and added eight additional species from the families Bufonidae, Hylidae, and Ranidae. We found significant phylogenetic signal in the sensitivity to the insecticide and in the existence of time lag effects on tadpole mortality. Bufonids were less sensitive than hylids, which were less sensitive than the ranids. Moreover, mortality time lags were common in ranids, occasional in hylids, and rare in bufonids. These results highlight the importance of an evolutionary perspective and offer important insights for conservation.
The genetics of uveal melanoma: an emerging framework for targeted therapy
Authors: Harbour J. William 
Published: January 2012

SummaryUveal melanoma is the second most common form of melanoma and the most common primary intraocular malignancy. Until recently, very little was known about the genetics of this aggressive cancer. Mutations in oncogenes and tumor suppressors that are common in other cancers are conspicuously absent in uveal melanoma. In recent years, however, uveal melanoma has begun to yield its secrets, and a fascinating picture is emerging of how it develops and progresses. Mutations in the Gq alpha subunits, encoded by GNAQ and GNA11, appear to be early or perhaps initiating events that require further mutations for malignant transformation. On the other hand, mutations in the BRCA1‐associated protein‐1 (BAP1) appear to occur later and demarcate a molecular brink beyond which metastasis becomes highly likely. BAP1 mutations can also occur in the germline, leading to a distinctive cancer predisposition syndrome. These mutations appear to be key events that provide the potential for targeted therapy. This article will review the genetic findings in uveal melanoma over the past two decades and suggest important areas for future work.
Multimodal imaging of dry age‐related macular degeneration
Authors: Forte Raimondo , Querques Giuseppe , Querques Lea , Massamba Nathalie , Le Tien Valerie , Souied Eric H. 
Published: January 2012

Abstract.Purpose:  The purpose of this study was to understand clinical significance of near‐infrared reflectance (NIR), blue fundus autofluorescence (FAF) and near‐infrared autofluorescence (NIA) in dry age‐related macular degeneration (AMD), by correlation with fluorescein angiography (FA) and cross‐sectional spectral domain optical coherence tomography (SD OCT).Methods:  We evaluated 110 eyes (62 patients, mean age: 64 ± 8 years) diagnosed with dry AMD between January 2010 and December 2010, which underwent NIR (λ = 830 nm), FAF and FA (excitation λ = 488 nm; emission λ > 500 nm), NIA (excitation λ = 787 nm; emission λ > 800 nm), and simultaneous SD OCT scanning using a combined confocal scanning laser ophthalmoscope/SD OCT device (Spectralis HRA + OCT; Heidelberg Engineering, Heidelberg, Germany).Results:  Drusen showed variable increased/decreased NIR, FAF, NIA and FA, which corresponded to variable increased/decreased thickness of the retinal pigment epithelium (RPE) and possible presence of subretinal deposits on SD OCT. Geographic atrophy (GA) was present in 43/110 eyes (39.0%) and showed increased NIR and fluorescence (FA), absent FAF and NIA, and loss of RPE on SD OCT. The hyperautofluorescence of the GA margin was never larger in FAF than that in NIA, while in 16.2% of cases, it was larger in NIA than that in FAF and corresponded to mild choroidal hyperreflectivity on SD OCT.Conclusions:  Simultaneous recording of SD OCT scans provided ultrastructural data for the evaluation of NIR, FAF, NIA and FA in dry AMD. Near‐infrared autofluorescence might detect earlier than FAF areas of RPE cell loss at the GA margin.
Twelve‐year Incidence of Exfoliation Syndrome in the Reykjavik Eye Study
Authors: Arnarsson Arsaell , Sasaki Hiroshi , Jonasson Fridbert 
Published: January 2012

Abstract.Purpose: To examine the 12‐year incidence of exfoliation syndrome (XFS) in persons aged 50–79 years at baseline and also to monitor changes in related ophthalmologic variables, to identify possible risk factors for incidence and to estimate the reliability of our diagnostic criteria.Methods: Baseline examination was performed in 1996 on a random sample of 1045 participants from the population of Reykjavik, 50 years and older. Five years later, in 2001, 88.2% of survivors returned for a follow‐up. In 2008, 12 years after the baseline examination, a total of 573 participants returned for the third examination (71.5% of survivors). On all three occasions, the participants underwent a thorough eye examination including slitlamp examination specifically looking for XFS and answered a comprehensive questionnaire.Results: A total of 8.0% of participants developed XFS during the follow‐up period in at least one eye, with women being more commonly affected than men, 9.2% versus 6.6%. The overall 12‐year incidence for either eye increased with increasing age, from 6.5% in those participants aged 50–59 years at baseline to 10.6% in those that were 70–79 years at baseline; 71% of clinically unilateral cases had converted to bilateral over 12 years.Conclusions: Twelve‐year incidence of XFS is higher in women than in men and higher in older age groups than in younger ones. Most persons deemed on the slitlamp to be unilaterally affected have converted to bilateral over 12 years. Eyes with XFS at baseline were 3–4 times more likely to have cataract surgery during the 12 years. Our definition of definite XFS generally holds, while our definition of probable XFS is of no prognostic value over 12 years.
Subfoveal choroidal blood flow and central retinal function in early glaucoma
Authors: Marangoni Dario , Falsini Benedetto , Colotto Alberto , Salgarello Tommaso , Anselmi Gianmario , Fadda Antonello , Di Renzo Antonio , Campos Emilio C. , Riva Charles E. 
Published: January 2012

Abstract.Purpose:  To assess subfoveal choroidal blood flow (ChBF) in patients with early manifest glaucoma (EMG) and to compare blood flow with functional measures of central retinal integrity, standard automated perimetry (SAP) and pattern electroretinogram (PERG).Methods:  Subfoveal ChBF was determined by confocal, real‐time laser Doppler flowmetry in 24 patients with EMG [>−6 dB mean deviation (MD), age range: 29–77 years, visual acuity: 20/25–20/20] and 23 age‐matched control subjects. All patients had a therapeutically (topical beta‐blockers with or without prostaglandin analogues) controlled intraocular pressure (IOP < 20 mmHg). Subfoveal choroidal blood volume (ChBVol), velocity (ChBVel) and ChBF were determined as the average of three 60 second recordings. In all patients and controls, the PERG and SAP (Humphrey 30‐2), following standardized protocols, were also recorded.Results:  In patients with EMG, reductions in average ChBVel and ChBF were roughly equal, respectively, by 30% and 33.4% (p < 0.01), when compared to control subjects, so that there was no significant difference in ChBVol between the two groups. Pattern electroretinogram amplitudes were reduced by 46% (p < 0.01) in patients compared to controls. No correlation was found between any of the ChBF parameters and PERG amplitude, or Humphrey 30‐2 MD and pattern standard deviation.Conclusion:  The results suggest a significant alteration of both ChBVel and ChBF in EMG, which does not appear to be associated with the severity of central retinal dysfunction. These findings may contribute to a better understanding of the pathophysiology of early glaucomatous damage in EMG and have implications for the treatment of this pathologic condition.
Time to consider a new treatment protocol for aggressive posterior retinopathy of prematurity?
Authors: Spandau Ulrich , Tomic Zoran , Ewald Uwe , Larsson Eva , Åkerblom Hanna , Holmström Gerd 
Published: January 2012

Abstract.Purpose:  To discuss treatment modalities for aggressive posterior retinopathy of prematurity (AP‐ROP).Methods:  The medical charts of all infants with AP‐ROP at Uppsala University Hospital, Sweden, during a 2‐year period (2009 and 2010) were reviewed. Eight infants (16 eyes) with a mean gestational age of 23.8 weeks and a mean birth weight of 592 g were treated with laser and/or intravitreal injections of bevacizumab (0.4 and 0.625 mg). RetCam photography was used to document the retinal appearance before and after treatment.Results:  All infants (16 eyes) had AP‐ROP in zone I. Mean time at initial treatment was 34 weeks postmenstrual age. Two eyes (one infant) were only treated with laser, and six eyes (three infants) were treated with laser therapy or cryopexy and, because of lack of regression, with bevacizumab as salvage therapy. Eight eyes (four infants) were treated with a first‐line bevacizumab injection and four of these eyes (two infants) with additional laser ablation for continued disease progression in zone II. Macular dragging occurred in one eye of one infant primarily treated with laser.Conclusions:  Given the high complication rate of the extensive laser treatment for zone I ROP, it is worth considering anti‐vascular endothelial growth factor treatment as an alternative therapy. Further knowledge concerning side effects and long‐term ocular and systemic outcome is warranted before this drug becomes general clinical practice.
Renal Disease in Cats Infected with Feline Immunodeficiency Virus
Authors: Baxter K.J. , Levy J.K. , Edinboro C.H. , Vaden S.L. , Tompkins M.B. 
Published: January 2012

BackgroundFeline immunodeficiency virus (FIV) and human immunodeficiency virus (HIV) infection cause similar clinical syndromes of immune dysregulation, opportunistic infections, inflammatory diseases, and neoplasia. Renal disease is the 4th most common cause of death associated with HIV infection.ObjectiveTo investigate the association between FIV infection and renal disease in cats.AnimalsClient‐owned cats (153 FIV‐infected, 306 FIV‐noninfected) and specific‐pathogen‐free (SPF) research colony cats (95 FIV‐infected, 98 FIV‐noninfected).MethodsA mixed retrospective/prospective cross‐sectional study. Blood urea nitrogen (BUN), serum creatinine, urine specific gravity (USG), and urine protein:creatinine ratio (UPC) data were compared between FIV‐infected and FIV‐noninfected cats. In FIV‐infected cats, total CD4+ and CD8+ T lymphocytes were measured using flow cytometry, and CD4+:CD8+ T lymphocyte ratio was calculated. Renal azotemia was defined as a serum creatinine ≥ 1.9 mg/dL with USG ≤ 1.035. Proteinuria was defined as a UPC > 0.4 with an inactive urine sediment.ResultsAmong the client‐owned cats, no association was detected between FIV infection and renal azotemia (P = .24); however, a greater proportion of FIV‐infected cats were proteinuric (25.0%, 16 of 64 cats) compared to FIV‐noninfected cats (10.3%, 20 of 195 cats) (P < .01). Neither neuter status nor health status were risk factors for proteinuria in FIV‐infected cats, but UPC was positively correlated with the CD4+:CD8+ T lymphocyte ratio (Spearman's rho = 0.37, P = .01). Among the SPF research colony cats, no association was detected between FIV infection and renal azotemia (P = .21) or proteinuria (P = .25).Conclusions and Clinical ImportanceProteinuria but not azotemia was associated with natural FIV infection.
Assessing individual heterogeneity using model selection criteria: how many mixture components in capture–recapture models?
Authors: Cubaynes Sarah , Lavergne Christian , Marboutin Eric , Gimenez Olivier 
Published: January 2012

Summary1. Capture–recapture mixture models are important tools in evolution and ecology to estimate demographic parameters and abundance while accounting for individual heterogeneity. A key step is to select the correct number of mixture components i) to provide unbiased estimates that can be used as reliable proxies of fitness or ingredients in management strategies and ii) classify individuals into biologically meaningful classes. However, there is no consensus method in the statistical literature for selecting the number of components.2. In ecology, most studies rely on the Akaike Information Criterion (AIC) and the Bayesian Information Criterion (BIC) that has recently gained attention in ecology. The Integrated Completed Likelihood criterion (ICL; IEEE Transactions on Pattern Analysis and Machine Intelligence, 2000, 22, 719) was specifically developed to favour well‐separated components, but its use has never been investigated in ecology.3. We compared the performance of AIC, BIC and ICL for selecting the number of components with regard to a) bias and accuracy of survival and detection estimates and b) success in selecting the true number of components using extensive simulations and data on wolf (Canis lupus) that were used for management through survival and abundance estimation.4. Bias in survival and detection estimates was <0.02 for both AIC and BIC, and more than 0.09 for ICL, while mean square error was <0.05 for all criteria. As expected, bias increased as heterogeneity increased. Success rates of AIC and BIC in selecting the ‘true’ number of components were better than ICL (68% for AIC, 58% for BIC, and 16% for ICL). As the degree of heterogeneity increased, AIC (and BIC in a lesser extent) overestimated the number of components, while ICL often underestimated this number. For the wolf study, the 2‐class model was selected by BIC and ICL, while AIC could not decide between the 2‐ and 3‐class models.5. We recommend using AIC or BIC when the aim is to estimate parameters. Regarding classification, we suggest taking the classification quality into account by using ICL in conjunction with BIC, pending further work to adapt its penalty term for capture–recapture data.
Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification
Authors: Collins Rupert A. , Boykin Laura M. , Cruickshank Robert H. , Armstrong Karen F. 
Published: January 2012

Summary1. DNA barcoding studies use Kimura's two‐parameter substitution model (K2P) as thede factostandard for constructing genetic distance matrices. Distances generated under this model then provide the basis for most downstream analyses, but uncertainty in model choice is rarely explored and could potentially affect how reliably DNA barcodes discriminate species.2. Using information‐theoretic approaches for a data set comprising 14 472 DNA barcodes from 14 published studies, we tested whether the K2P model was a good fit at the species level and whether applying a better fitting model biased error rates or changed overall identification success.3. We report that the K2P was a poorly fitting model at the species level; it was never selected as the best model and very rarely selected as a credible alternative model. Despite the lack of support for the K2P model, differences in distance between best model and K2P model estimates were usually minimal, and importantly, identification success rates were largely unaffected by model choice even when interspecific threshold values were reassessed.4. Although these conclusions may justify using the K2P model for specimen identification purposes, we found simpler metrics such aspdistance performed equally well, perhaps obviating the requirement for model correction in DNA barcoding. Conversely, when incorporating genetic distance data into taxonomic studies, we advocate a more thorough examination of model uncertainty.
Roles of
fkbN
in Positive Regulation and
tcs7
in Negative Regulation of FK506 Biosynthesis in Streptomyces sp. Strain KCTC 11604BP
Authors: Mo SangJoon , Yoo Young Ji , Ban Yeon Hee , Lee Sung-Kwon , Kim Eunji , Suh Joo-Won , Yoon Yeo Joon 
Published: January 2012

ABSTRACT

FK506 is an important 23-member polyketide macrolide with immunosuppressant activity. Its entire biosynthetic gene cluster was previously cloned from
Streptomyces
sp. strain KCTC 11604BP, and sequence analysis identified three putative regulatory genes,
tcs2
,
tcs7
, and
fkbN
, which encode proteins with high similarity to the AsnC family transcriptional regulators, LysR-type transcriptional regulators, and LAL family transcriptional regulators, respectively. Overexpression and in-frame deletion of
tcs2
did not affect the production of FK506 or co-occurring FK520 compared to results for the wild-type strain, suggesting that
tcs2
is not involved in their biosynthesis.
fkbN
overexpression improved the levels of FK506 and FK520 production by approximately 2.0-fold, and a deletion of
fkbN
caused the complete loss of FK506 and FK520 production. Although the overexpression of
tcs7
decreased the levels of FK506 and FK520 production slightly, a deletion of
tcs7
caused 1.9-fold and 1.5-fold increases in FK506 and FK520 production, respectively. Finally,
fkbN
overexpression in the
tcs7
deletion strain resulted in a 4.0-fold (21 mg liter
−1
) increase in FK506 production compared to that by the wild-type strain. This suggests that
fkbN
encodes a positive regulatory protein essential for FK506/FK520 biosynthesis and that the gene product of
tcs7
negatively regulates their biosynthesis, demonstrating the potential of exploiting this information for strain improvement. Semiquantitative reverse transcription-PCR (RT-PCR) analyses of the transcription levels of the FK506 biosynthetic genes in the wild-type and mutant strains proved that most of the FK506 biosynthetic genes are regulated by
fkbN
in a positive manner and negatively by
tcs7
.
Microbial Community Succession during Lactate Amendment and Electron Acceptor Limitation Reveals a Predominance of Metal-Reducing Pelosinus spp
Authors: Mosher Jennifer J. , Phelps Tommy J. , Podar Mircea , Hurt Richard A. , Campbell James H. , Drake Meghan M. , Moberly James G. , Schadt Christopher W. , Brown Steven D. , Hazen Terry C. , Arkin Adam P. , Palumbo Anthony V. , Faybishenko Boris A. , Elias Dwayne A. 
Published: January 2012

ABSTRACT

The determination of the success of
in situ
bioremediation strategies is complex. By using controlled laboratory conditions, the influence of individual variables, such as U(VI), Cr(VI), and electron donors and acceptors on community structure, dynamics, and the metal-reducing potential can be studied. Triplicate anaerobic, continuous-flow reactors were inoculated with Cr(VI)-contaminated groundwater from the Hanford, WA, 100-H area, amended with lactate, and incubated for 95 days to obtain stable, enriched communities. The reactors were kept anaerobic with N
2
gas (9 ml/min) flushing the headspace and were fed a defined medium amended with 30 mM lactate and 0.05 mM sulfate with a 48-h generation time. The resultant diversity decreased from 63 genera within 12 phyla to 11 bacterial genera (from 3 phyla) and 2 archaeal genera (from 1 phylum). Final communities were dominated by
Pelosinus
spp. and to a lesser degree,
Acetobacterium
spp., with low levels of other organisms, including methanogens. Four new strains of
Pelosinus
were isolated, with 3 strains being capable of Cr(VI) reduction while one also reduced U(VI). Under limited sulfate, it appeared that the sulfate reducers, including
Desulfovibrio
spp., were outcompeted. These results suggest that during times of electron acceptor limitation
in situ
, organisms such as
Pelosinus
spp. may outcompete the more-well-studied organisms while maintaining overall metal reduction rates and extents. Finally, lab-scale simulations can test new strategies on a smaller scale while facilitating community member isolation, so that a deeper understanding of community metabolism can be revealed.
Correlation between Composition of the Bacterial Community and Concentration of Volatile Fatty Acids in the Rumen during the Transition Period and Ketosis in Dairy Cows
Authors: Wang Xiaoxu , Li Xiaobing , Zhao Chenxu , Hu Pan , Chen Hui , Liu Zhaoxi , Liu Guowen , Wang Zhe 
Published: January 2012

ABSTRACT

The transition period is a severe challenge to dairy cows. Glucose supply cannot meet demand and body fat is mobilized, potentially leading to negative energy balance (NEB), ketosis, or fatty liver. Propionate produces glucose by gluconeogenesis, which depends heavily on the number and species of microbes. In the present study, we analyzed the rumen microbiome composition of cows in the transition period, cows with ketosis, and nonperinatal cows by terminal restriction fragment length polymorphism (TRFLP) analysis of 16S rRNA genes and quantitative PCR. TRFLP analysis indicated that the quantity of
Veillonellaceae
organisms was reduced and that of
Streptococcaceae
organisms was increased in rumen samples from the transition period and ketosis groups, with the number of
Lactobacillaceae
organisms increased after calving. Quantitative PCR data suggested that the numbers of the main propionate-producing microbes,
Megasphaera elsdenii
and
Selenomonas ruminantium
, were decreased, while numbers of the main lactate-producing bacterium,
Streptococcus bovis
, were increased in the rumen of cows from the transition period and ketosis groups, with the number of
Lactobacillus
sp. organisms increased after calving. Volatile fatty acid (VFA) and glucose concentrations were decreased, but the lactic acid concentration was increased, in rumen samples from the transition period and ketosis groups. Our results indicate that the VFA concentration is significantly related to the numbers of
Selenomonas ruminantium
and
Megasphaera elsdenii
organisms in the rumen.
Heterogeneity in Mitochondrial Morphology and Membrane Potential Is Independent of the Nuclear Division Cycle in Multinucleate Fungal Cells
Authors: Gerstenberger John P. , Occhipinti Patricia , Gladfelter Amy S. 
Published: January 2012

ABSTRACT

In the multinucleate filamentous fungus
Ashbya gossypii
, nuclei divide asynchronously in a common cytoplasm. We hypothesize that the division cycle machinery has a limited zone of influence in the cytoplasm to promote nuclear autonomy. Mitochondria in cultured mammalian cells undergo cell cycle-specific changes in morphology and membrane potential and therefore can serve as a reporter of the cell cycle state of the cytoplasm. To evaluate if the cell cycle state of nuclei in
A. gossypii
can influence the adjacent cytoplasm, we tested whether local mitochondrial morphology and membrane potential in
A. gossypii
are associated with the division state of a nearby nucleus. We found that mitochondria exhibit substantial heterogeneity in both morphology and membrane potential within a single multinucleated cell. Notably, differences in mitochondrial morphology or potential are not associated with a specific nuclear division state. Heterokaryon mutants with a mixture of nuclei with deletions of and wild type for the mitochondrial fusion/fission genes
DNM1
and
FZO1
exhibit altered mitochondrial morphology and severe growth and sporulation defects. This dominant effect suggests that the gene products may be required locally near their expression site rather than diffusing widely in the cell. Our results demonstrate that mitochondrial dynamics are essential in these large syncytial cells, yet morphology and membrane potential are independent of nuclear cycle state.