bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probabilities of Fitness Consequences for Point Mutations Across the Human Genome
Authors: Gulko Brad , Hubisz Melissa J. , Gronau Ilan , Siepel Adam 
Published: July 2014

AbstractWe describe a novel computational method for estimating the probability that a point mutation at each position in a genome will influence fitness. Thesefitness consequence(fit-Cons) scores serve as evolution-based measures of potential genomic function. Our approach is to cluster genomic positions into groups exhibiting distinct “fingerprints” based on high-throughput functional genomic data, then to estimate a probability of fitness consequences for each group from associated patterns of genetic polymorphism and divergence. We have generated fitCons scores for three human cell types based on public data from EN-CODE. Compared with conventional conservation scores, fitCons scores show considerably improved prediction power forcis-regulatory elements. In addition, fitCons scores indicate that 4.2–7.5% of nucleotides in the human genome have influenced fitness since the human-chimpanzee divergence, and, in contrast to several recent studies, they suggest that recent evolutionary turnover has had limited impact on the functional content of the genome.
Combined Increases in Mitochondrial Cooperation and Oxygen Photoreduction Compensate for Deficiency in Cyclic Electron Flow in Chlamydomonas reinhardtii
Authors: Dang Kieu-Van , Plet Julie , Tolleter Dimitri , Jokel Martina , Cuiné Stéphan , Carrier Patrick , Auroy Pascaline , Richaud Pierre , Johnson Xenie , Alric Jean , Allahverdiyeva Yagut , Peltier Gilles 
Published: July 2014

Abstract
During oxygenic photosynthesis, metabolic reactions of CO2 fixation require more ATP than is supplied by the linear electron flow operating from photosystem II to photosystem I (PSI). Different mechanisms, such as cyclic electron flow (CEF) around PSI, have been proposed to participate in reequilibrating the ATP/NADPH balance. To determine the contribution of CEF to microalgal biomass productivity, here, we studied photosynthesis and growth performances of a knockout Chlamydomonas reinhardtii mutant (pgrl1) deficient in PROTON GRADIENT REGULATION LIKE1 (PGRL1)–mediated CEF. Steady state biomass productivity of the pgrl1 mutant, measured in photobioreactors operated as turbidostats, was similar to its wild-type progenitor under a wide range of illumination and CO2 concentrations. Several changes were observed in pgrl1, including higher sensitivity of photosynthesis to mitochondrial inhibitors, increased light-dependent O2 uptake, and increased amounts of flavodiiron (FLV) proteins. We conclude that a combination of mitochondrial cooperation and oxygen photoreduction downstream of PSI (Mehler reactions) supplies extra ATP for photosynthesis in the pgrl1 mutant, resulting in normal biomass productivity under steady state conditions. The lower biomass productivity observed in the pgrl1 mutant in fluctuating light is attributed to an inability of compensation mechanisms to respond to a rapid increase in ATP demand.
Psoriasis and bone mineral density: Implications for long‐term patients
Authors: D'Epiro Sara , Marocco Chiara , Salvi Monica , Mattozzi Carlo , Luci Cecilia , Macaluso Laura , Giancristoforo Simona , Campoli Marco , Scarnò Marco , Migliaccio Silvia , Calvieri Stefano , Richetta Antonio 
Published: July 2014

AbstractPsoriasis is a chronic inflammatory disease associated with several comorbidities. Osteoporosis is defined as a reduction in bone mineral density with impaired bone microarchitecture. Several mechanisms may be implicated as a possible cause for the association between psoriasis and osteoporosis, such as systemic inflammation, anti‐psoriatic drug intake and joint dysfunction for psoriatic arthritis (PsA). The aim of the present study was to assess bone mineral density (BMD) in patients with psoriasis, correlating the prevalence of osteopenia/osteoporosis with Psoriasis Area and Severity Index (PASI) score, mean duration of psoriatic disease, PsA and previous treatments for psoriasis. Forty‐three consecutive patients with psoriasis, 19 of whom were affected by the arthropathic form, were enrolled. We evaluated the severity of psoriasis as measured by PASI score, the CASPAR criteria and ultrasounds of the joints to verify the diagnosis of PsA and the age of psoriasis onset to estimate mean disease duration. Patients underwent a bone density scan of the lumbar spine and femoral neck by dual‐energy X‐ray absorptiometry to measure BMD. Patients with osteopenia/osteoporosis showed a statistically significant longer average duration of psoriatic disease (17 years), compared to patients affected by psoriasis with normal T‐score (8.8 years) (P = 0.04). The linear logistic regression confirms a significant relation between mean psoriatic disease duration and BMD alterations (P = 0.04). Our results suggest the necessity of an early diagnostic evaluation of bone metabolism in patients with psoriasis, especially if characterized by longer disease duration.
Maternal effects influence phenotypes and survival during early life stages in an aquatic turtle
Authors: Mitchell Timothy S. , Maciel Jessica A. , Janzen Fredric J. 
Published: July 2014

SummaryOffspring phenotypic variation can be substantially influenced by non‐genetic factors such as maternal effects, which ultimately can influence organismal fitness. For oviparous organisms that lack parental care, oviposition‐site choice and egg size are maternal effects that can greatly affect offspring traits. Yet, few studies examine the consequences of these traits in the wild.We manipulated the contents of natural painted turtle nests such that offspring spent two life stages (incubation and hibernation) in either maternally selected nest sites or randomly selected nest sites and quantified treatment differences in environmental parameters and offspring phenotypes. Additionally, we tracked the fates of individual eggs and hatchlings, which allowed us to quantify the strength and form of selection acting on egg size during incubation and, for the first time, body size during hibernation.Maternally selected nest sites were warmer and produced offspring that were longer and hatched earlier than their siblings emerging from cooler, randomly selected nests. Treatments did not affect any measured traits during hibernation.We detected no selection on egg size during the incubation stage, but significant linear selection favouring larger hatchlings during hibernation.Our results suggest that nest‐site choice allows mothers to partially control the environment of their incubating eggs, but is less effective at controlling hatchling environments during hibernation. Additionally, we provide novel support for the ‘bigger‐is‐better’ hypothesis in turtles by showing a positive relationship between size and survival during the hibernation stage.
Experimental evaluation shows limited influence of pine plantations on the connectivity of highly fragmented bird populations
Authors: Mortelliti Alessio , Westgate Martin J. , Lindenmayer David B. 
Published: July 2014

SummaryConversion of natural and agricultural areas to conifer plantations is an important element of global change. Despite their widespread distribution and global importance, it is still unclear whether conifer plantations hinder or enhance movement by biota.Population connectivity is difficult to quantify without detailed studies such as those using capture–mark–recapture methods. A novel solution is to quantify the synchrony in abundance between populations over time. Using this approach, more connected populations are expected to display synchrony, whereas disconnected populations are expected to fluctuate asynchronously. Here, we compared the relative effects of spatial proximity and matrix type on the population synchrony of a suite of forest‐dependent birds in a long‐term, fully controlled, and replicated landscape‐scale experiment in south‐eastern Australia.Our experiment consisted of comparing bird populations inhabiting remnant eucalypt patches surrounded by Radiata pinePinus radiataplantations (50 patches) with bird populations inhabiting remnant eucalypt patches where the surrounding landscapes are grazing fields (55 patches). Our data set encompassed 10 years and included 52 bird species characterized by different life history traits. After controlling for the effects of rainfall and patch characteristics on population dynamics, we found that spatial proximity, not matrix type, was the main driver of population synchrony for 16 species. The effect of the pine plantation matrix was negative (it reduced synchrony). However, the magnitude of its effect was particularly low (being significant only in four species).Synthesis and applications. Our results show that pine plantations do not increase connectivity. In fact, they have little effect, with the exception of a few species, for which they may constitute a barrier. The implications of our findings for landscape management are that the conversion of agricultural areas to plantation forestry does not promote substantial movement of individuals (to the extent that would synchronize populations). Therefore, plantation expansion should not be promoted on the belief that it increases connectivity relative to an agricultural matrix.
Assessing trends in biodiversity over space and time using the example ofBritish breeding birds
Authors: Harrison Philip J. , Buckland Stephen T. , Yuan Yuan , Elston David A. , Brewer Mark J. , Johnston Alison , Pearce‐Higgins James W. 
Published: July 2014

SummaryPartitioning biodiversity change spatially and temporally is required for effective management, both to determine whether action is required and whether it should be applied at a regional level or targeted more locally. As biodiversity is a multifaceted concept, comparative analyses of different indices, focussing on different components of biodiversity change (evenness vs. abundance), give better information than a single headline index.We model changes in the spatial and temporal distribution ofBritish breeding birds using generalized additive models applied to count data collected between 1994 and 2011. Abundance estimates, accounting for differences in detectability, are then used in community‐specific (farmland and woodland) biodiversity indices. Temporal trends in biodiversity, and change points in those trends, are assessed at different spatial scales. The geometric mean of relative abundance, a headline indicator of biodiversity change, is assessed together with a goodness‐of‐fit evenness measure focussing separately on the rare and common species in the communities.Our analysis reveals predominantly declining trends in biodiversity indices for farmland and woodland bird communities in southern and easternEngland, perhaps signalling environmental deterioration in this part of the country. Conversely, our results also show generally more positive trends in the north ofBritain, consistent with north–south gradient expectations from the effects of climate change. We also reveal predominantly positive changes in evenness for the common species and negative changes in evenness for the rarer species in the communities, consistent with previously documented homogenization in bird communities.Synthesis and applications. Bird populations are seen as good indicators of ecosystem health, and trends for different communities can be indicative of wider biodiversity changes within their respective habitats. However, temporal trends in biodiversity at the national level may miss opposing trends occurring at different locations within the nation. We develop methods that allow assessment of how temporal trends vary spatially and whether these trends differ for the rare and common species in the respective communities. Our methods may be used to test hypotheses about the processes that generate the trends.
The Effects of Uncertainty and Disclosure on Auditors' Fair Value Materiality Decisions
Authors: GRIFFIN JEREMY B. 
Published: July 2014

ABSTRACTFinancial accounting standards increasingly require fair value measurements. I experimentally examine how uncertainty affects auditors’ adjustment decisions when evaluating fair values. I manipulate two types of uncertainty, input subjectivity and outcome imprecision, and one reporting choice, supplemental disclosure. I find that auditors are most likely to require adjustments when fair values contain both more input subjectivity and more outcome imprecision, but that this likelihood diminishes when clients supplement recognized fair values with additional disclosure. Thus, consistent with moral licensing, I find that auditors tolerate greater potential misstatement in the financial statements when clients provide disclosure, suggesting that the SEC's preference for supplemental disclosure may have the unintended consequence of affecting fair values recognized in the body of the financial statements. I also provide evidence that auditors determine adjustment size by comparing recorded fair value to the nearest bound, rather than the midpoint, of the auditors’ own range estimate, consistent with strict application of auditing standards.
The Difficult Task of Assessing Perimortem and Postmortem Fractures on the Skeleton: A Blind Text on 210 Fractures of Known Origin
Authors: Cappella Annalisa , Amadasi Alberto , Castoldi Elisa , Mazzarelli Debora , Gaudio Daniel , Cattaneo Cristina 
Published: July 2014

AbstractThe distinction between perimortem and postmortem fractures is an important challenge for forensic anthropology. Such a crucial task is presently based on macro‐morphological criteria widely accepted in the scientific community. However, several limits affect these parameters which have not yet been investigated thoroughly. This study aims at highlighting the pitfalls and errors in evaluating perimortem or postmortem fractures. Two trained forensic anthropologists were asked to classify 210 fractures of known origin in four skeletons (three victims of blunt force trauma and one natural death) as perimortem, postmortem, or dubious, twice in 6 months in order to assess intraobserver error also. Results show large errors, ranging from 14.8 to 37% for perimortem fractures and from 5.5 to 14.8% for postmortem ones; more than 80% of errors concerned trabecular bone. This supports the need for more objective and reliable criteria for a correct assessment of peri‐ and postmortem bone fractures.
Vertical stratification of ichneumonid wasp communities: the effects of forest structure and life‐history traits
Authors: Di Giovanni Filippo , Cerretti Pierfilippo , Mason Franco , Minari Emma , Marini Lorenzo 
Published: July 2014

AbstractParasitoid wasp communities of the canopy of temperate forests are still largely unexplored. Very little is known about the community composition of parasitoids between canopy and understory and how much of this difference is related to forest structure or parasitoid biological strategies. In this study we investigated upon the difference in the community composition of the parasitic wasps Ichneumonidae between canopy and understory in a lowland temperate forest in northern Italy. We used general linear models to test whether parasitic strategy modifies species vertical stratification and the effect of forest structure. We also tested differences in β‐diversity between canopy and understory traps and over time within single forest layers. We found that stand basal area was positively related to species richness, suggesting that the presence of mature trees can influence local wasp diversity, providing a higher number of microhabitats and hosts. The ichneumonid community of the canopy was different from that of the understory, and the β‐diversity analysis showed higher values for the canopy, due to a higher degree of species turnover between traps. In our analyses, the vertical stratification was different between groups of ichneumonids sharing different parasitic strategies. Idiobiont parasitoids of weakly or deeply concealed hosts were more diverse in the understory than in the canopy while parasitoids of spiders were equally distributed between the two layers. Even though the ichneumonid community was not particularly species‐rich in the canopy of the temperate forests, the extension of sampling to that habitat significantly increased the number of species recorded.
Effects of 4‐hexylresorcinol on the phenoloxidase from Hyphantria cunea (Lepidoptera: Arctiidae): In vivo and in vitro studies
Authors: Sharifi Mahboobeh , Ghadamyari Mohammad , Sajedi Reza H. , Mahmoodi Nosrat O. 
Published: July 2014

AbstractInsecticidal effects of 4‐hexylresorcinol, a phenoloxidase (PO) inhibitor, were determined on Hyphantria cunea (Drury) under laboratory conditions. The LC50 for the 15‐d‐old larvae was estimated to be 2.95 g/L after 96 h exposure. The activities of glutathione S‐transferase (GST) and PO showed a decrease in larvae treated with 4‐hexylresorcinol, and the IC50 of GST and PO were estimated to be 0.8 and 0.43 g/L, respectively, 24 h after treatment. The PO from the hemolymph of fall webworm was purified by ammonium sulfate precipitation, gel‐filtration, and ion‐exchange chromatography, and then enzymatic characteristics and the mechanism of inhibition were determined using L‐dihydroxyphenylalanine (L‐DOPA) as the substrate. The purified PO showed a single band on SDS‐PAGE with a molecular weight of about 70 kDa. The optimum pH for PO activity was observed at pH 7.0, optimum temperature was found to be 45 °C, and PO activity was strongly inhibited by Zn2+. IC50 values were estimated to be 8.2, 19.14, and 24.04 μmol/L for 4‐hexylresorsinol, kojic acid, and quercetin, respectively. The inhibitory potencies (i.e., I50 of each compound/I50 of 4‐hexylresorcinol) of kojic acid and quercetin on H. cunea PO were estimated to be 1.87 and 2.89, respectively. 4‐hexylresorcinol was determined to be a competitive inhibitor, and kojic acid and quercetin were determined to be mixed inhibitors. PO is one of the most important enzymes in an insect's immune system, and the use of PO inhibitors seems to be a promising approach for pest control due to their potential safety for humans.
Waterlogging responses of Schoenoplectus scirpoides (Schrad) Browning (Cyperaceae)
Authors: Naidoo Gonasageran , Naidoo Yougasphree 
Published: July 2014

AbstractWaterlogging responses of an emergent freshwater macrophyte, Schoenoplectus scirpoides, were investigated by carrying out laboratory and field experiments. Soil cores containing uniform plants of S. scirpoides were subjected to drained, 1/3 flooded, alternately flooded and drained at weekly intervals, and continuously flooded treatments for 6 months. Mean soil redox potential of the drained soil was 225 ± 29 mV and was significantly lower in the other treatments. Total dry biomass, above‐ground biomass and number of culms in the flooded/drained and flooded treatments were significantly higher than those in the drained and 1/3 flooded treatments. Below‐ground/above‐ground biomass ratios were highest in the drained treatment and significantly lower in the waterlogged treatments. Plant height and the growth rate of culms were least in the drained treatment and significantly higher in the other treatments. Culm specific gravity decreased significantly with increase in soil moisture. In the field study, soil redox potentials were moderately reduced in the inland and streamside sites, while culm elongation rate was significantly higher by 94% in the streamside compared with the inland site. Optimum growth occurred under flooded conditions, suggesting that the species could flourish with increasing water intrusion in estuarine areas, as predicted by global climate change.
Long‐term follow‐up of patients with thyroid eye disease treated with endoscopic orbital decompression
Authors: Gulati Shashi , Ueland Hans Olav , Haugen Olav H. , Danielsen Arild , Rødahl Eyvind 
Published: July 2014

AbstractPurposeTo evaluate the outcome of endoscopic decompression in a series of patients with thyroid eye disease.MethodsAll 46 patients operated at our institution in the period 2001 to 2011 were invited for re‐examination. Thirty‐seven patients were included in the study and underwent a general otorhinolaryngological and ophthalmological examination. Nasal endoscopy, autoperimetry and a CT scan of the orbits and paranasal sinuses were performed. Preoperative and early postoperative data were obtained from hospital records. Re‐examination was performed from 12 months to 9 years postoperatively. Paired t‐test was used to evaluate the change in pre‐ and postoperative data. Image‐guided surgery was used in two patients.ResultsVisual acuity improved from a median value (range) of 0.8 (0.05–1.25) to 1.0 (0.4–1.25) (p = 0.006). Intra‐ocular pressure (IOP) was reduced from a median value (range) of 18 mmHg (10–27 mmHg) to 14 mmHg (8–24 mmHg) (p < 0.001). Median (range) Hertel values were 22.5 mm (14–29 mm) preoperatively and 19 mm (11–26 mm) postoperatively (p < 0.001). Mean reduction in proptosis was 4.0 mm. At follow‐up, visual fields were normal in 16/37 patients (43%) and with small defects in 12/37 patients (32%). Seventeen patients (46%) had diplopia preoperatively in one or more directions of gaze while 9 (24%) suffered from constant diplopia. After endoscopic decompression, new onset diplopia was seen in seven (19%) individuals, while worsening of diplopia occurred in eight (22%). Impaired motility in abduction and/or elevation was seen in 20 (54%) individuals before decompression and in 23 (62%) after.Strabismus surgery was performed in 22 patients. On final examination 85% of the study population were totally free of diplopia or experienced diplopia only in the peripheral field of gaze. Three patients developed sinusitis. Of these, endoscopic sinus surgery was performed in two patients, and one patient was conservatively treated. Symptoms resolved in all three patients.ConclusionEndoscopic medial orbital decompression including removal of the medial floor of the orbit is a safe and effective procedure for treatment of thyroid eye disease. Navigation can be of valuable help to ensure complete resection of the bony walls. However, the majority of patients will need subsequent strabismus surgery, mainly due to significant increase of esotropia.
Addressing the burden of neonatal hyperbilirubinaemia in countries with significant glucose‐6‐phosphate dehydrogenase deficiency
Authors: Olusanya Bolajoko O. , Emokpae Abieyuwa A. , Zamora Tara G. , Slusher Tina M. 
Published: July 2014

AbstractGlucose‐6‐phosphate dehydrogenase (G6PD) deficiency is an established worldwide risk factor for severe hyperbilirubinaemia. This literature review examined the pattern and management of severe hyperbilirubinaemia in low‐ and middle‐income countries (LMICs) where G6PD deficiency was 10% or more and found that it was frequently associated with neonatal mortality and, or, neurodevelopmental disorders.ConclusionLow‐ and middle‐income countries need to pay urgent attention to G6PD deficiency to curtail the preventable burden of jaundice‐related morbidity, mortality and disability.