bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial ranking strategy and enhanced peripheral vision discrimination optimize performance and efficiency of visual sequential search
Authors: Veneri Giacomo , Pretegiani Elena , Fargnoli Francesco , Rosini Francesca , Vinciguerra Claudia , Federighi Pamela , Federico Antonio , Rufa Alessandra 
Published: June 2014

AbstractVisual sequential search might use a peripheral spatial ranking of the scene to put the next target of the sequence in the correct order. This strategy, indeed, might enhance the discriminative capacity of the human peripheral vision and spare neural resources associated with foveation. However, it is not known how exactly the peripheral vision sustains sequential search and whether the sparing of neural resources has a cost in terms of performance. To elucidate these issues, we compared strategy and performance during an alpha‐numeric sequential task where peripheral vision was modulated in three different conditions: normal, blurred, or obscured. If spatial ranking is applied to increase the peripheral discrimination, its use as a strategy in visual sequencing should differ according to the degree of discriminative information that can be obtained from the periphery. Moreover, if this strategy spares neural resources without impairing the performance, its use should be associated with better performance. We found that spatial ranking was applied when peripheral vision was fully available, reducing the number and time of explorative fixations. When the periphery was obscured, explorative fixations were numerous and sparse; when the periphery was blurred, explorative fixations were longer and often located close to the items. Performance was significantly improved by this strategy. Our results demonstrated that spatial ranking is an efficient strategy adopted by the brain in visual sequencing to highlight peripheral detection and discrimination; it reduces the neural cost by avoiding unnecessary foveations, and promotes sequential search by facilitating the onset of a new saccade.
Conformation‐dependent backbone geometry restraints set a new standard for protein crystallographic refinement
Authors: Moriarty Nigel W. , Tronrud Dale E. , Adams Paul D. , Karplus P. Andrew 
Published: May 2014

Ideal values of bond angles and lengths used as external restraints are crucial for the successful refinement of protein crystal structures at all but the highest of resolutions. The restraints in common use today have been designed on the assumption that each type of bond or angle has a single ideal value that is independent of context. However, recent work has shown that the ideal values are, in fact, sensitive to local conformation, and, as a first step towards using such information to build more accurate models, ultra‐high‐resolution protein crystal structures have been used to derive a conformation‐dependent library (CDL) of restraints for the protein backbone [Berkholz et al. (2009) Structure 17, 1316–1325]. Here, we report the introduction of this CDL into the phenix package and the results of test refinements of thousands of structures across a wide range of resolutions. These tests show that use of the CDL yields models that have substantially better agreement with ideal main‐chain bond angles and lengths and, on average, a slightly enhanced fit to the X‐ray data. No disadvantages of using the backbone CDL are apparent. In phenix, use of the CDL can be selected by simply specifying the cdl = True option. This successful implementation paves the way for further aspects of the context dependence of ideal geometry to be characterized and applied to improve experimental and predictive modeling accuracy.
Temperate extinction in squamate reptiles and the roots of latitudinal diversity gradients
Authors: Pyron R. Alexander 
Published: June 2014

AbstractAimMany ecological and evolutionary hypotheses have been proposed to explain latitudinal diversity gradients. However, any mechanistic explanation must include factors that change at least one of the three processes that can directly affect species richness: speciation, extinction and dispersal. I hypothesize that higher extinction in temperate areas, higher speciation in tropical areas and reduced dispersal into temperate regions drives latitudinal diversity gradients in squamates, and that these processes may be common in other groups.LocationWorld‐wide.MethodsI test for these processes using phylogenetic methods that can untangle speciation and extinction with respect to latitudinal position (GeoSSE), using a dated phylogeny containing c. 45% of all squamates (4161 species) with data on their geographic occurrence.ResultsI find that lineages in the tropics have high speciation and low extinction, but that temperate lineages have even higher speciation and extinction, leading to lower net diversification and higher turnover in temperate areas, with much higher rates of dispersal into the tropics from temperate areas than the reverse.Main conclusionsRecent empirical studies using dated molecular phylogenies appear to be consistent in supporting a similar set of simple and intuitive results for processes driving latitudinal gradients in species richness: higher net diversification rates in the tropics, higher relative extinction fractions in temperate regions and reduced dispersal out of the tropics. I suggest that higher temperate extinction represents a dominant force for the origin and maintenance of latitudinal gradients, particularly in groups with ancient temperate clades.
Asp68His mutation in the A1 domain of human factor V causes impaired secretion and ineffective translocation
Authors: Liu H.‐C. , Shen M.‐C. , Eng H.‐L. , Wang C.‐H. , Lin T.‐M. 
Published: June 2014

SummaryCongenital factor V (FV) deficiency is a rare inherited disorder. We determined the mechanism of a missense mutation, Asp68His, in the A1 domain of the FV protein, is associated with severe FV deficiency. We characterized the mutant FV‐Asp68His protein using in vitro expression studies by using specific secretion and degradation pathway inhibitors and analysed the intracellular translocation of the mutant protein by immunofluorescence staining. The Asp68His mutation caused very low levels of FV protein in the conditioned media, with normal specific FV activity. Similar mRNA degradation rates between FV‐wild‐type (wt) and FV‐Asp68His mRNA showed that the Asp68His mutation does not affect FV expression at the transcriptional level. A specific secretion pathway inhibitor, brefeldin A, was used to demonstrate that the lower efficiency of transport to the outside of the cell for FV‐Asp68His mutant protein compared with that of the FV‐wt protein. Furthermore, we showed that the Asp68His mutation resulted in increased intracellular degradation through a MG132‐mediated proteasomal degradation pathway. In the transfected cell lysates, FV‐wt protein had multiple posttranslational modified forms, but the FV‐Asp68His protein was not completely glycosylated. We further observed that the FV‐Asp68His protein was retrieved in the endoplasmic reticulum only and did not undergo transport to the Golgi apparatus, leading to impaired secretion. These results strongly suggest that the Asp68His mutation may result in intracellular defective trafficking and enhanced degradation, and impaired secretion of FV protein.
Erythropoietin‐stimulating agents in the management of anemia of end‐stage renal disease patients on regular hemodialysis: A prospective randomized comparative study from Qatar
Authors: Al‐Ali Fadwa Saqr , El‐Sayed Abdelfattah Mohamed , Fawzy Ashraf Ahmed , Hamdy Ahmed Farouk , Abdulla Aisha Elsayed 
Published: June 2014

AbstractDespite extensive use, to the best of our knowledge, no trial has simultaneously compared the three currently used erythropoietin‐stimulating agents (ESAs) in a prospective manner in the treatment of anemia of end‐stage renal disease patients. All hemodialysis patients in Qatar who were treated with short‐acting epoetin alfa or beta have been screened. Eligible patients had been prospectively randomized, either to continue on the previous regimen of epoetin or to receive darbepoetin alfa or continuous erythropoietin receptor activator (CERA) for a total period of 40 weeks. All groups were assessed at the end of the study for safety and efficacy parameters. A total of 327 eligible patients were randomized. Mean hemoglobin concentration remained constant within the recommended target range (11–12 g/dL) throughout the study in the three studied groups. The percentage of patients who reached the target range was constantly above 50% in the second half of the study among CERA group patients who also had significantly lower mean number of dose adjustments as compared with the other two groups (P = 0.001). Similarly, the number of discontinuations of ESA among epoetin, darbepoetin, and CERA groups was 17, 19, and 9, respectively (P = 0.042). The frequencies of adverse events were similar in all groups. This study has specifically compared the effect of ESA type on the variability of serum hemoglobin levels in hemodialysis patients. Furthermore, it confirmed the efficacy and safety of once monthly CERA for maintaining tight hemoglobin control within recommended target ranges.
Fibroblast growth factor receptor (FGFR) gene amplifications are rare events in bladder cancer
Authors: Fischbach Anna , Rogler Anja , Erber Ramona , Stoehr Robert , Poulsom Richard , Heidenreich Axel , Schneevoigt Birte‐Swantje , Hauke Sven , Hartmann Arndt , Knuechel Ruth , Veeck Jürgen , Gaisa Nadine T 
Published: June 2014

AimsActivating point mutations and protein overexpression of fibroblast growth factor receptors (FGFRs), especially FGFR3, are frequent events in bladder cancer. Little is known about gene amplifications, therefore we characterized amplification of FGFR1‐3 by fluorescence in‐situ hybridization (FISH).Methods and resultsTumours of 153 patients (n = 65 pTa low‐grade, n = 15 pTa high‐grade, n = 37 pT1, n = 20 pT2, n = 10 pT3, n = 6 pT4) were analysed by FISH for FGFR1‐3 copy numbers and screened for FGFR3 mutations and immunohistochemical protein expression. Amplifications of FGFR1 were found in 1.6% (two of 122), FGFR2 in 0.8% (one of 121) and FGFR3 in 3.4% (five of 145). All amplifications were high‐level amplifications, not overlapping with polysomy. Amplifications were found in papillary/papillary‐invasive tumour parts, and predominantly in tumours with enhanced Ki67 index (>10%), aberrant CK20 expression, and low p53 expression. All FGFR3‐amplified samples showed concomitant FGFR3 mutations and FGFR3 protein overexpression. FGFR amplifications were not associated significantly with gender, age, grade or stage in statistical analyses.ConclusionsFGFR amplifications are rare events in bladder cancer, with FGFR3 amplification being the most prevalent (3.4% of cases). Concomitant FGFR3 mutations and protein overexpression indicate that FGFR3‐mediated signalling in these tumours would probably be highly active. This patient subgroup may be particularly suited to FGFR‐targeted pharmacotherapy.
Etidronate causes minimal changes in the ability of sodium hypochlorite to dissolve organic matter
Authors: Tartari T. , Guimarães B. M. , Amoras L. S. , Duarte M. A. H. , Silva e Souza P. A. R. , Bramante C. M. 
Published: June 2014

AbstractAimTo evaluate the effect of individual and combined use of sodium hypochlorite (NaOCl), etidronate (HEDP) and ethylenediaminetetraacetic acid (EDTA) in tissue dissolution.MethodologySixty fragments of bovine muscle tissue were prepared and their weights determined on a precision scale. The samples were then distributed in the following groups (n = 10): G1 – saline solution (control); G2 – 17% EDTA; G3 – 18% HEDP; G4 – 2.5% NaOCl; G5 – mixture of 5% NaOCl + 17% EDTA; and G6 – mixture of 5% NaOCl + 18% HEDP. The specimens in each group were immersed in the solutions for 5, 10 and 15 min and reweighted at each time period. Analysis of variance (anova) and Tukey's multiple‐comparison tests (α<0.05) were applied to identify the intragroup and intergroup differences.ResultsG1, G2, G3 and G5 did not dissolve the organic matter. G4 and G6 significantly reduced the weights of specimens at all periods. Amongst the groups, the difference in ability to dissolve organic matter was greater and significant in the following order G4 = G6 > G5 = G3 = G2 = G1 after 5 min of immersion and G4 > G6 > G5 = G3 = G2 = G1 after 10 and 15 min of immersion.ConclusionThe only solution capable of dissolving organic matter was NaOCl. In the mixtures analysed, this ability was arrested by EDTA; however, it was minimally affected by the HEDP, proving that this combination, if used during the biomechanical preparation, is able to dissolve of organic matter.
Pilonidal sinus surgery: could we predict postoperative complications?
Authors: Milone Marco , Di Minno Matteo ND , Bianco Paolo , Coretti Guido , Musella Mario , Milone Francesco 
Published: June 2014

AbstractPilonidal sinus surgery could, as of now, be considered a surgery tailored more to the surgeon than to the patient. In an attempt to give to surgeons an objective instrument of decision, we have evaluated which variables could be considered predictive of postoperative complications after pilonidal sinus surgery. A prospective electronic database of all patients treated for sacrococcygeal pilonidal disease was analysed. Sex, age, obesity, smoking, recurrent disease, the presence of multiple orifices and the distance between the most lateral orifice and midline were recorded and correlated with the occurrence of postoperative complications (infection and recurrence); 1006 patients were evaluated. Excision with primary mid‐line closure was performed on all the patients. Mean follow‐up was 7·3 ± 3·6 years. A total of 158 patients with postoperative complications (infection and/or recurrence) were recorded during this period. A multivariate analysis showed that, after adjusting for major clinical and demographic characteristics, only a recurrent disease [odds ratio (OR): 3·41, 95% confidence interval (CI): 1·89–6·15, P < 0·001] and the distance of lateral orifice from midline (OR: 26·3, 95% CI: 12·2–56·7, P < 0·001) were independent predictors of overall postoperative complications. Focussing on the distance from midline, the receiver operative characteristic (ROC) analysis showed that the distance of lateral orifice from midline predicted 79·2% of complications and the Youden's test identified the best cut‐off as 2·0 cm for this variable. An evidence‐based tool for deciding on the type of surgical intervention could be developed and validated by further ad hoc prospective studies evaluating our results in comparison to other different types of surgical techniques. Our results support the use of these variables as an effective way to tailor pilonidal sinus surgery to the patient, so as to obtain the best results in patient care.
Evidence for sex‐specific selection in brain: a case study of the nine‐spined stickleback
Authors: Herczeg G. , Välimäki K. , Gonda A. , Merilä J. 
Published: June 2014

AbstractTheory predicts that the sex making greater investments into reproductive behaviours demands higher cognitive ability, and as a consequence, larger brains or brain parts. Further, the resulting sexual dimorphism can differ between populations adapted to different environments, or among individuals developing under different environmental conditions. In the nine‐spine stickleback (Pungitius pungitius), males perform nest building, courtship, territory defence and parental care, whereas females perform mate choice and produce eggs. Also, predation‐adapted marine and competition‐adapted pond populations have diverged in a series of ecologically relevant traits, including the level of phenotypic plasticity. Here, we studied sexual dimorphism in brain size and architecture in nine‐spined stickleback from marine and pond populations reared in a factorial experiment with predation and food treatments in a common garden experiment. Males had relatively larger brains, largertelencephala,cerebellaandhypothalami(6–16% divergence) than females, irrespective of habitat. Females tended to have largerbulbi olfactoriithan males (13%) in the high food treatment, whereas no such difference was found in the low food treatment. The strong sexual dimorphism in brain architecture implies that the different reproductive allocation strategies (behaviourvs. egg production) select for different investments into the costly brains between males and females. The lack of habitat dependence in brain sexual dimorphism suggests that the sex‐specific selection forces on brains differ only negligibly between habitats. Although significance of the observed sex‐specific brain plasticity in the size ofbulbus olfactoriusremains unclear, it demonstrates the potential for sex‐specific neural plasticity.
West versus East Mediterranean Sea: origin and genetic differentiation of the sea cucumber Holothuria polii
Authors: Valente Sara , Serrão Ester A. , González‐Wangüemert Mercedes 
Published: June 2014

AbstractWe studied the genetic structure of the sea cucumber Holothuria (Roweothuria) polii (Delle Chiaje 1823) by analysing the mitochondrial DNA variation in two fragments of cytochrome oxidase I (COI) and 16S genes. Individuals were collected in seven locations along the Mediterranean Sea, which cover a wide range of the species distribution. We found high haplotype diversity for COI and moderate diversity for 16S, and low nucleotide diversity for both genes. Our results for the COI gene showed many recent and exclusive haplotypes with few mutational changes, suggesting recent or ongoing population expansion. The Western and Eastern Mediterranean populations exhibited slight but significant genetic differentiation (COI gene) with higher genetic diversity in the East. The most ancient haplotype was not present in the westernmost sampling location (SE Spain). The oldest expansion time was observed in Turkey, corresponding to mid‐Pleistocene. Turkey had also the highest genetic diversity (number of total and exclusive haplotypes, polymorphisms, haplotype and nucleotide diversity). This suggests that this region could be the origin of the subsequent colonizations through the Mediterranean Sea, a hypothesis that should be assessed with nuclear markers in future research.
Spectrum of renal disease in diabetes
Authors: Teng Jessie , Dwyer Karen M , Hill Prue , See Emily , Ekinci Elif I , Jerums George , MacIsaac Richard J 
Published: June 2014

AbstractThe spectrum of renal disease in patients with diabetes encompasses both diabetic kidney disease (including albuminuric and non‐albuminuric phenotypes) and non‐diabetic kidney disease. Diabetic kidney disease can manifest as varying degrees of renal insufficiency and albuminuria, with heterogeneity in histology reported on renal biopsy. For patients with diabetes and proteinuria, the finding of non‐diabetic kidney disease alone or superimposed on the changes of diabetic nephropathy is increasingly reported. It is important to identify non‐diabetic kidney disease as some forms are treatable, sometimes leading to remission. Clinical indications for a heightened suspicion of non‐diabetic kidney disease and hence consideration for renal biopsy in patients with diabetes and nephropathy include absence of diabetic retinopathy, short duration of diabetes, atypical chronology, presence of haematuria or other systemic disease, and the nephrotic syndrome.
S‐acylation anchors remorin proteins to the plasma membrane but does not primarily determine their localization in membrane microdomains
Authors: Konrad Sebastian S. A. , Popp Claudia , Stratil Thomas F. , Jarsch Iris K. , Thallmair Veronika , Folgmann Jessica , Marín Macarena , Ott Thomas 
Published: June 2014

Summary

Remorins are well‐established marker proteins for plasma membrane microdomains. They specifically localize to the inner membrane leaflet despite an overall hydrophilic amino acid composition. Here, we determined amino acids and post‐translational lipidations that are required for membrane association of remorin proteins.

We used a combination of cell biological and biochemical approaches to localize remorin proteins and truncated variants of those in living cells and determined S‐acylation on defined residues in these proteins.

S‐acylation of cysteine residues in a C‐terminal hydrophobic core contributes to membrane association of most remorin proteins. While S‐acylation patterns differ between members of this multi‐gene family, initial membrane association is mediated by protein–protein or protein–lipid interactions. However, S‐acylation is not a key determinant for the localization of remorins in membrane microdomains.

Although remorins bind via a conserved mechanism to the plasma membrane, other membrane‐resident proteins may be involved in the recruitment of remorins into membrane domains. S‐acylation probably occurs after an initial targeting of the proteins to the plasma membrane and locks remorins in this compartment. As S‐acylation is a reversible post‐translational modification, stimulus‐dependent intracellular trafficking of these proteins can be envisioned.
Successful treatment of fulminant Wilson's disease without liver transplantation
Authors: Motobayashi Mitsuo , Fukuyama Tetsuhiro , Nakayama Yoshiko , Sano Kenji , Noda Shunsuke , Hidaka Yoshihiko , Amano Yoshiro , Ikeda Shu‐ichi , Koike Kenichi , Inaba Yuji 
Published: June 2014

AbstractFulminant Wilson's disease (WD) is life‐threatening. The revised WD prognostic index (RWPI) has been used to predict the severity of the disease, with a score ≥11 indicating fatal outcome without liver transplantation (LTx). We here report the case of a 10‐year‐old female patient with fulminant WD (RWPI, 16) who recovered fully after plasma exchange and continuous hemodiafiltration, followed by treatment with copper chelate agents. To the best of our knowledge, there have been five fulminant WD patients with RWPI ≥ 11 including the present patient, in whom LTx was not done. Based on the therapeutic modalities in these five cases, non‐surgical treatment (blood purification and copper chelate agents) may be able to avoid LTx in fulminant WD even with very high RWPI, although preparation for LTx is necessary.