bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amino acid sequence variations of signaling lymphocyte activation molecule and mortality caused by morbillivirus infection in cetaceans
Authors: Shimizu Yui , Ohishi Kazue , Suzuki Rintaro , Tajima Yuko , Yamada Tadasu , Kakizoe Yuka , Bando Takeharu , Fujise Yoshihiro , Taru Hajime , Murayama Tsukasa , Maruyama Tadashi 
Published: July 2013

ABSTRACTMorbillivirus infection is a severe threat to marine mammals. Mass die‐offs caused by this infection have repeatedly occurred in bottlenose dolphins (Turiops truncatus) and striped dolphins (Stenella coeruleoalba), both of which belong to the family Delphinidae, but not in other cetaceans. However, it is unknown whether sensitivity to the virus varies among cetacean species. The signaling lymphocyte activation molecule (SLAM) is a receptor on host cells that allows morbillivirus invasion and propagation. Its immunoguloblin variable domain‐like (V) region provides an interface for the virus hemagglutinin (H) protein. In this study, variations in the amino acid residues of the V region of 26 cetacean species, covering almost all cetacean genera, were examined. Three‐dimensional (3D) models of them were generated in a homology model using the crystal structure of the marmoset SLAM and measles virus H protein complex as a template. The 3D models showed 32 amino acid residues on the interface that possibly bind the morbillivirus. Among the cetacean species studied, variations were found at six of the residues. Bottlenose and striped dolphins have substitutions at five positions (E68G, I74V, R90H, V126I, and Q130H) compared with those of baleen whales. Three residues (at positions 68, 90 and 130) were found to alternate electric charges, possibly causing changes in affinity for the virus. This study shows a new approach based on receptor structure for assessing potential vulnerability to viral infection. This method may be useful for assessing the risk of morbillivirus infection in wildlife.
Multiscale, presence‐only habitat suitability models: fine‐resolution maps for eight bat species
Authors: Bellamy Chloe , Scott Christopher , Altringham John 
Published: July 2013

Summary

To manage anthropogenic environmental change for the benefit of biodiversity, we must improve our understanding of the complex relationships between organisms and their environment. We have developed multiscale habitat suitability models (HSMs) for bats, a mobile group of mammals, for a geographically varied region of the UK. We ask whether the models have sufficient accuracy to contribute to informed decision‐making in habitat management and in minimizing the impact of climate change and human infrastructural development.

We used acoustic surveys supplemented by catching to gather presence data for eight species from 30 sites across the south of the Lake District National Park in NW England. Species were identified by manual and automated extraction and analysis of echolocation calls. Fine‐resolution (50 and 100 m) habitat maps were generated at twelve spatial scales by calculating the variables across squares of increasing size, from 100 to 6000 m, around each focal 50 or 100 m square. Presence‐only HSM software, MaxEnt, was used to determine the predictive power of each habitat variable at each scale. Multiscale models included data for each variable at the scale at which it had the strongest relationship with the presence of each species.

The best multiscale models were selected using fivefold cross‐validation, with backwards, stepwise variable removal, whilst minimizing residual spatial autocorrelation and sampling bias. Further tests with independent field data indicated good model transferability across the entire National Park.

Foraging bats were generally most strongly associated with variables measured at small spatial scales and distance measures. However, each species responded differently across the range of scales, and strong associations were also found at the largest scale of analysis (6000 m).

Synthesis and applications. The best models for determining habitat suitability had few variables, making them easy to interpret and use in practical conservation planning. The approach is applicable to any taxa for which reliable presence records are available, providing insight into the potential impacts of land‐use and environmental change. Maps identify areas of conservation concern, such as hot spots for diversity, rare or vulnerable species and potential or threatened network corridors, making them useful for ecological impact assessment of proposed developments, and to conservation managers planning habitat creation or improvement.
Inferring extinctions from sighting records of variable reliability
Authors: Lee Tamsin E. , McCarthy Michael A. , Wintle Brendan A. , Bode Michael , Roberts David L. , Burgman Mark A. 
Published: July 2013

Summary

A range of mathematical models has been developed to infer whether a species is extinct based on a sighting record. Although observations have variable reliability, current methods for detecting extinction do not differentiate observation qualities.

A more suitable approach would consider certain and uncertain sightings throughout the sighting period. We consider a small population system, meaning we assume sighting rates are constant and the population is not declining. Based on such an assumption, we develop a Bayesian method that assumes that certain and uncertain sightings occur independently and at uniform rates. These two types of sightings are connected by a common extinction date. Several rates of false sightings can be calculated to differentiate between observation types. Prior rates of false and true sightings, as well as a prior probability that the species is extant, are included. The model is implemented in OpenBugs, which uses Markov chain Monte Carlo (MCMC).

Based on records of variable reliability, we estimate the probability that the following species are extinct: Caribbean seal Monachus tropicalis, grey, black‐footed ferret Mustela nigripes, Audubon & Bachman, greater stick‐nest rat Leporillus conditor, Sturt, and lesser stick‐nest rat Leporillus apicalis, Gould. As further examples, Birdlife International provided the sighting records for the Alaotra grebe Tachybaptus rufolavatus, Delacour, Jamaica petrel Pterodroma caribbaea, Carte, and Pohnpei mountain starling Aplonis pelzelni, Finsch, with prior probabilities for extinction. The results are compared with existing methods, which ignore uncertain sightings. We find that including uncertain sightings can considerably change the probability that the species is extant, in either direction. However, in our examples, including the quality of the uncertain sighting made little difference. When we ignore uncertain sightings, our results agree with existing methods, especially when the last sighting was near the end of the sighting period.

Synthesis and applications. Estimating the probability that a species is extinct based on sighting records is important when determining conservation priorities and allocating available resources into management activities. Having a model that allows for certain and uncertain observations throughout the sighting period better accommodates the realities of sighting quality, providing a more reliable basis for decision‐making.
Supplementation of the maternal diet during pregnancy with chocolate and fructose interacts with the high‐fat diet of the young to facilitate the onset of metabolic disorders in rat offspring
Authors: Zhang Zhi‐Yun , Dai Yun‐Bin , Wang Hao‐Nan , Wang Ming‐Wei 
Published: July 2013

Summary

Obesity and non‐alcoholic fatty liver disease are the most common metabolic disorders in society today. Previously, we found that supplementing the maternal diet during pregnancy with chocolate and fructose has negative effects on the well‐being of the offspring that were ameliorated if the offspring were fed a normal diet during postnatal life. In the present study, we investigated whether feeding offspring a high‐fat diet would augment the maternal programming effects and whether extra protein supply can correct the low birth weight resulting from the chocolate‐supplemented maternal diet.

Pregnant Sprague‐Dawley rats were divided into three groups and fed either standard chow (normal nutrition; NN), chocolate‐ and fructose‐supplemented standard chow with casein sodium (overnutrition; ON) or the supplemented standard chow without casein sodium (malnutrition; MN) throughout pregnancy. Male offspring were weaned on either standard or high‐fat chow.

Dams in the MN group exhibited moderate weight gain, consumed 50% less protein (P < 0.001) but more carbohydrates during gestation and delivered pups with a 12% lower birth weight (P < 0.05) than pups in the NN group, results that are consistent with previous findings. When fed on a high‐fat diet after birth, pups from dams in the MN group (MNHD) had 30% more body fat (P = 0.023) and liver triglyceride (TG) levels that were double (P < 0.01) those in offspring in the other groups, leading to fatty livers in these offspring at 14 weeks of age. Hepatic expression of the PPARα, ApoB100, MTTP, CPT1 and SREBP1c genes was significantly downregulated in the MNHD group (P < 0.05 for all), indicating changes in lipid metabolism. Although dams in the ON group exhibited marked gestational weight gain (P < 0.01), they gave birth to normal weight pups that only manifested mild increases in body fat and liver TG content (P < 0.05), without significant changes in the expression of most genes when fed with the high‐fat diet.

The results suggest that the extra protein supply in the form of casein sodium was able to correct some negative programming effects of the chocolate and fructose supplementation of the maternal diet, which, in conjunction with a high‐fat diet in the offspring, may facilitate the onset of metabolic disorders, with impaired liver gene expression possibly a key contributor.
Circuits of Knowledge and Techniques: The Transnational Flow of Planning Ideas and Practices
Authors: Healey Patsy 
Published: July 2013

AbstractThis article considers the conceptual and methodological tools which may help to focus the critical analysis of transnational flows of planning ideas and practices in the present period. The discussion starts from the rejection of the ‘modernization myth’ with its linear concept of a single development trajectory and reviews the philosophical background to the array of alternative conceptions which have displaced it. It then examines three, often overlapping, fields of intellectual development which offer promising concepts for exploring contemporary transnational flows of planning ideas and practices: actor‐network theory (especially with respect to the way ideas and technologies get to ‘travel’ and get ‘translated’), institutionalist versions of policy ‘discourse analysis’ (discourse structuration and institutionalization, in particular), and discussions about circuits of knowledge and hegemonic projects in the globalization and international development literatures. Drawing on these, I suggest that critical analysis of such flows should give special attention to the ‘origin stories’ of such ideas, their ‘travelling histories’ and the ‘translation experiences’ through which exogenous planning ideas and practices become ‘localized’. I conclude by commenting on what may be distinctive about transnational flows in the present period, why undertaking critical analysis of such flows is valuable, and key methodological attitudes to keep in mind in conducting such analyses.
Prediction of retinal pigment epithelial tear in serous vascularized pigment epithelium detachment
Authors: Clemens Christoph R. , Bastian Nina , Alten Florian , Milojcic Carolin , Heiduschka Peter , Eter Nicole 
Published: July 2013

Abstract.Purpose:  The aim of the study was to identify predictive factors for detection of impending retinal pigment epithelium (RPE) tears in patients under anti‐VEGF therapy for treatment of retinal pigment epithelial detachment (PED) due to exudative age‐related macular degeneration (AMD) using near‐infrared reflectance imaging (NIR), spectral‐domain optical coherence tomography (SD‐OCT) and fluorescein angiography (FLA).Methods:  We retrospectively evaluated NIR, SD‐OCT and FLA images, number of intravitreal injections as well as demographical data of 103 eyes of 98 patients with vascularized PED [48.5% fibrovascular PED (fPED), 51.5% serous vascularized PED (svPED)] secondary to AMD.Results:  Fifteen eyes with svPED of 103 included eyes (14.6%) developed an RPE tear under anti‐VEGF therapy. Prior to RPE tear formation, we could identify radial hyperreflective lines spreading in a funnel‐like pattern across the PED lesion in NIR images in 11 eyes correlating with folds in the RPE on corresponding SD‐OCT scans (mean observation period: 115.4 ± 66.6 days; mean number of injections: 3.2 ± 1.5; mean PED height 828.2 ± 356.5 μm). In nine RPE tears (81.8%), the edge of the tear could be clearly localized on the opposite side of the PED lesion in relation to the origin of hyperreflective lines. None of the fPED patients showed the described signal.Conclusions:  Patients under anti‐VEGF therapy for treatment of svPED due to AMD frequently show radial hyperreflective lines in NIR images prior to RPE tear development that correspond to wrinkled changes in the RPE. Hyperreflective lines may serve as an indicator for an impending RPE tear in svPED patients.
Hyaluronan‐mediated motility receptor (RHAMM) immunohistochemical expression and androgen deprivation in normal peritumoral, hyperplasic and neoplastic prostate tissue
Authors: Korkes Fernando , de Castro Marilia Germanos , de Cassio Zequi Stenio , Nardi Lívia , Del Giglio Auro , de Lima Pompeo Antonio Carlos 
Published: July 2013

Objectives
To evaluate hyaluronan‐mediated motility receptor (RHAMM) expression in normal, hyperplasic and neoplastic prostate tissue after various types and durations of androgen‐deprivation therapy (ADT). Clinical and oncological data from men with localised prostate adenocarcinoma were also assessed and compared with RHAMM expression data.
Patients and Methods
Data from 367 men who underwent histological evaluation of the prostate were retrospectively evaluated under six conditions: (i) benign prostatic hyperplasia (BPH), (ii) BPH treated with finasteride, (iii) prostate cancer without ADT, (iv) prostate cancer treated with neoadjuvant ADT before prostatectomy (cyproterone 200 mg/day), (v) castration‐resistant prostate cancer (CRPC), and (vi) normal peritumoral prostate tissue.
Tissue microarrays were constructed and 1354 cores were evaluated for immunohistochemical RHAMM expression.
Results
There was no RHAMM expression in any tissue from normal patients or those with BPH or prostate cancer without ADT.
There was RHAMM expression in 39.4% of prostate cancer tissues treated with ADT and in 46.2% of CRPC samples (P = 0.001).
There was a significant increase in RHAMM expression with increased ADT duration in group 4, with a marked increase in RHAMM expression after 6–12 months of ADT (P = 0.04).
No prognostic or clinical factors related to prostate cancer were associated with RHAMM expression.
Conclusions
RHAMM expression in prostate cancer is directly associated with ADT. Significant RHAMM expression occurs as early as after 1 month of ADT and progressively increases with ADT duration.
When prostate cancer becomes CRPC, RHAMM expression is higher. RHAMM expression was not associated with prostate cancer prognostic factors.
RHAMM overexpression may contribute to the development of hormonal resistance in prostate cancer.
Prognosis of patients with pelvic lymph node (LN) metastasis after radical prostatectomy: Value of extranodal extension and size of the largest LN metastasis
Authors: Passoni Niccolo M. , Fajkovic Harun , Xylinas Evanguelos , Kluth Luis , Seitz Christian , Robinson Brian D. , Rouprêt Morgan , Chun Felix K. , Lotan Yair , Roehrborn Claus G. , Crivelli Joseph J. , Karakiewicz Pierre I. , Scherr Douglas S. , Rink Michael , Graefen Markus , Schramek Paul , Briganti Alberto , Montorsi Francesco , Tewari Ashutosh , Shariat Shahrokh F. 
Published: July 2013

Objective
To assess the prognostic role of extranodal extension (ENE) and the size of the largest lymph node (LN) metastasis in predicting early biochemical relapse (eBCR) in patients with LN metastasis after radical prostatectomy (RP).
Patients and Methods
We evaluated BCR‐free survival in men with LN metastases after RP and pelvic LN dissection performed in six high‐volume centres.
Multivariable Cox regression tested the role of ENE and diameter of largest LN metastasis in predicting eBCR after adjusting for clinicopathological variables.
We compared the discrimination of multivariable models including ENE, the size of largest LN metastasis and the number of positive LNs.
Results
Overall, 484 patients were included. The median (interquartile range, IQR) follow‐up was 16.1 (6–27.5) months. The median (IQR) number of removed LNs was 10 (4–14), and the median (IQR) number of positive LNs was 1 (1–2). ENE was present in 280 (58%) patients, and 211 (44%) had their largest metastasis >10 mm. Patients with ENE and/or largest metastasis of >10 mm had significantly worse eBCR‐free survival (all P < 0.01).
On multivariable analysis, number of positive LNs (≤2 vs >2) and the diameter of LN metastasis (≤10 vs >10 mm), but not ENE, were significant predictors of eBCR (all P < 0.003).
ENE and diameter of LN metastasis increased the area under the curve of a baseline multivariable model (0.663) by 0.016 points.
Conclusions
The diameter of the largest LN metastasis and the number of positive LNs are independent predictors of eBCR.
Considered together, ENE and the diameter of the largest LN metastasis have less discrimination than the number of positive LNs.
Prospective evaluation of a preoperative biomarker panel for prediction of upstaging at radical cystectomy
Authors: Shariat Shahrokh F. , Passoni Niccolo , Bagrodia Aditya , Rachakonda Varun , Xylinas Evanguelos , Robinson Brian , Kapur Payal , Sagalowsky Arthur I. , Lotan Yair 
Published: July 2013

Objectives
To prospectively test whether a panel of biomarkers could identify patients with organ‐confined disease likely to be upstaged at radical cystectomy (RC), as retrospective studies have found that cell‐cycle‐ and proliferation‐related biomarkers can help improve prognostic accuracy after RC.
Patients and Methods
We prospectively performed p53, p21, p27, Ki67, and cyclin E1 immunohistochemical staining on transurethral resection of the bladder (TURB) specimens from 87 patients treated with RC for organ‐confined urothelial carcinoma of the bladder (UCB).
The number of altered biomarkers was categorised as ‘favourable’ (≤2 altered markers) or ‘unfavourable’ (>2).
Results
Expression of p53, p21, p27, cyclin E1, and Ki67 were altered in 61 (70%), 19 (22%), 26 (30%), four (5%), and 70 (80%) patients, respectively.
The median number of positive markers was two. In all, 47 (54%) patients were upstaged when T‐stage was considered alone and 49 (56%) when T‐ and/or N‐stage were considered both as upstaging. In multivariable analyses that adjusted for the effects of age, clinical stage, concomitant carcinoma in situ, and time from TURB to RC, an ‘unfavourable’ biomarker score was independently associated with T‐stage upstaging (hazard ratio [HR] 3.3, P = 0.024) but not T‐ and/or N‐stage upstaging (HR 2.76, P = 0.06).
Addition of p27, number of positive markers, and biomarker score each increased the discrimination of a base model for prediction of T‐stage upstaging (5%, 6%, and 5%, respectively) and T‐ and/or N‐stage upstaging (4%, 6%, and 3%, respectively).
Conclusions
Cell‐cycle‐ and proliferation‐related markers in the TURB specimen improve the prediction of upstaging at RC.
Such a marker panel may help identify patients with non‐muscle‐invasive UCB who are clinically under‐staged needing RC and patients with muscle‐invasive UCB who are likely to be non‐organ‐confined thereby potentially benefiting from neoadjuvant chemotherapy.
Synthesis of 1,4‐Anthracene‐9,10‐dione Derivatives and Their Regulation of Nitric Oxide, IL‐1β and TNF‐α in Activated RAW264.7 Cells
Authors: Corrêa Taís Arthur , Alves Caio C. S. , Castro Sandra B. R. , Oliveira Erick E. , Franco Lucas S. , Ferreira Ana P. , de Almeida Mauro V. 
Published: July 2013

Mitoxantrone is an anthracenedione antineoplastic and immunosuppressive agent approved for multiple sclerosis treatment. Novel mono‐ and disubstituted anthraquinone derivatives, analogues of mitoxantrone, were synthesized through the addition of lipophilic amino alcohols and evaluated for their effect on IL‐1β, TNF‐α and nitric oxide production by LPS/IFN‐γ‐stimulated RAW264.7 cells. The disubstituted 1,4‐anthracene‐9,10‐dione 10 showed significant inhibition of nitric oxide, TNF‐α and IL‐1β production at the concentration of 5 μg/mL, with a much lower cytotoxicity than mitoxantrone. The monosubstituted 3, 4, 11, 12 and 13 also displayed a moderate to good inhibitory capacity on IL‐1β production. However, the methylated compounds 11, 12 and 13 failed to inhibit the TNF‐α production, and compound 13 was the only one to decrease the production of nitric oxide. None of these derivatives was toxic at the tested concentrations. Compounds 10 and 13 had better inhibitory capacity of the inflammatory mediators analyzed, with reliable viability of the cells.
Activity and expression of histone acetylases and deacetylases in inflammatory phenotypes of asthma
Authors: Gunawardhana L. P. , Gibson P. G. , Simpson J. L. , Powell H. , Baines K. J. 
Published: July 2013

SummaryBackgroundHistone acetyltransferases (HATs) and histone deacetylases (HDACs) regulate gene expression, yet differences in the activity of these enzymes in the inflammatory phenotypes of asthma are unknown. We hypothesized that neutrophilic asthma (NA) would be associated with increased HAT and decreased HDAC activity.ObjectiveTo investigate total HAT/HDAC activity and gene expression in isolated blood monocytes and sputum macrophages from healthy and patients with asthma.MethodsPeripheral blood and induced sputum were collected from adults with asthma (n = 52) and healthy controls (n = 9). Sputum inflammatory cell counts were performed and asthma inflammatory phenotypes were classified according to sputum eosinophil and neutrophil cut‐off's of > 3% and > 61% respectively. Peripheral blood monocytes were isolated (n = 61) and sputum macrophages were isolated from a subgroup of patients with asthma (n = 14), using immunomagnetic cell separation. RNA and nuclear proteins were extracted and quantified. Enzyme activity was assessed using fluorescent assays and gene expression of EP300, KAT2B, CREBBP, and HDACs 1, 2 and 3 were measured by qPCR.ResultsThere was a significant inverse association between blood monocyte HAT and HDAC activity (r = −0.58, P < 0.001). NA was associated with increased blood monocyte HAT enzyme activity (P = 0.02), decreased HDAC activity (P = 0.03), and increased HAT: HDAC ratio (P < 0.01) compared with eosinophilic asthma. There were no differences in gene expression of EP300, KAT2B, CREBBP, or HDACs 1, 2 and 3 in blood monocytes from subjects with asthma or inflammatory phenotypes of asthma. There was no effect of inhaled corticosteroid use, poor asthma control, or asthma severity on HAT/HDAC activities. Sputum macrophages had increased expression of KAT2B in eosinophilic compared with paucigranulocytic asthma.Conclusions and Clinical RelevanceNeutrophilic airway inflammation is associated with increased HAT and reduced HDAC activity in blood monocytes, demonstrating further systemic manifestations relating to the altered inflammatory gene transcription profile of neutrophilic asthma.