bluuebunny/crossref_metadata_2025_split huggingface dataset:
Osteopontin expression in healing wounds of horses and in human keloids
Authors: Miragliotta V. , Pirone A. , Donadio E. , Abramo F. , Ricciardi M. P. , Theoret C. L. 
Published: October 2014

SummaryReasons for performing studyConvincing evidence shows that persistent or excessive expression of osteopontin (OPN) is linked to fibroproliferation of various organs in laboratory animals and in man, such that its downregulation is a logical therapeutic objective.ObjectivesTo investigate OPN expression in an equine model of wound healing and in clinical specimens of equine exuberant granulation tissue and human keloids in an effort to better understand the contribution of this protein to inflammation‐associated skin fibrosis.Study designDescription of gene and protein expression in an experimental equine model of wound healing and clinical specimens in horse and man.MethodsOsteopontin gene expression was evaluated by quantitative PCR, while protein expression was investigated by means of immunohistochemical staining.ResultsQuantitative PCR showed that the OPN gene is expressed in normal intact skin of horses and continues to be expressed during the wound‐healing process. An increase in gene expression was observed throughout the phases of wound healing, with a final decrease at wound closure. The protein was not detected in normal skin. Keratinocytes in wound‐edge samples did not express the protein, whereas dermal immunoreactivity was confined to inflammatory cells. Healed wounds were devoid of staining. Equine exuberant granulation tissue showed immunoreactivity of the surrounding epidermis, infiltrating neutrophils, mononuclear cells, endothelial cells and fibroblasts. Human keloids showed OPN immunoreactivity throughout the epidermis as well as in mononuclear cells and scattered fibroblasts.ConclusionsImmunohistochemical data show a different pattern of expression between normally healing and fibrotic wounds (exuberant granulation tissue and keloids), thus suggesting a role in fibroproliferation in horses and man.
Crystal structures and kinetics of Type III 3‐phosphoglycerate dehydrogenase reveal catalysis by lysine
Authors: Singh Rohit K. , Raj Isha , Pujari Rajesh , Gourinath Samudrala 
Published: October 2014

d‐Phosphoglycerate dehydrogenase (PGDH) catalyzes the first committed step of the phosphorylated serine biosynthesis pathway. Here, we report for the first time, the crystal structures of Type IIIK PGDH from Entamoeba histolytica in the apo form, as well as in complexes with substrate (3‐phosphoglyceric acid) and cofactor (NAD+) to 2.45, 1.8 and 2.2 Å resolution, respectively. Comparison of the apo structure with the substrate‐bound structure shows that the substrate‐binding domain is rotated by ~ 20° to close the active‐site cleft. The cofactor‐bound structure also shows a closed‐cleft conformation, in which NAD+ is bound to the nucleotide‐binding domain and a formate ion occupies the substrate‐binding site. Superposition of the substrate‐ and cofactor‐bound structures represents a snapshot of the enzyme in the active form, where C2 of the substrate and C4N of the cofactor are 2.2 Å apart, and the amino group of Lys263 is close enough to the substrate to remove the proton from the hydroxyl group of PGA, indicating the role of Lys in the catalysis. Mutation of Lys263 to Ala yields just 0.8% of the specific activity of the wild‐type enzyme, revealing that Lys263 indeed plays an integral role in the catalytic activity. The detectable activity of the mutant, however, indicates that after 20° rotation of the substrate‐binding domain, the resulting positions of the substrate and cofactor are sufficiently close to make a productive reaction.DatabaseThe atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.pdb.org (PDB ID code 4NFY, 4NJM and 4NJO)Structured digital abstract

EhPGDH and EhPGDH bind by x-ray crystallography (View interaction)

EhPGDH and EhPGDH bind by molecular sieving (View interaction)
Structural and functional analysis of the fibronectin‐binding protein FNE from Streptococcus equi spp. equi
Authors: Tiouajni Mounira , Durand Dominique , Blondeau Karine , Graille Marc , Urvoas Agathe , Valerio‐Lepiniec Marielle , Guellouz Asma , Aumont‐Nicaise Magali , Minard Philippe , van Tilbeurgh Herman 
Published: October 2014

Streptococcus equi is a horse pathogen belonging to Lancefield group C. Infection by S. equi ssp. equi causes strangles, a serious and highly contagious disease of the upper respiratory tract. S. equi ssp. equi secretes a fibronectin (Fn)‐binding protein, FNE, that does not contain cell wall‐anchoring motifs. FNE binds to the gelatin‐binding domain (GBD) of Fn, composed of the motifs 6FI12FII789FI. FNE lacks the canonical Fn‐binding peptide repeats observed in many microbial surface components recognizing adhesive matrix molecules. We found that the interaction between FNE and the human GBD is mediated by the binding of the disordered C‐terminal region (residues 208–262) of FNE to the 789FI GBD subfragment. The crystal structure of FNE showed that it is similar to the minor pilus protein Spy0125 of Streptococcus pyogenes, found at the end of pilus polymers and responsible for adhesion. FNE and Spy0125 both have a superimposable internal thioester bond between highly conserved Cys and Gln residues. Small‐angle X‐ray scattering of the FNE–789FI complex provided a model that aligns the C‐terminal peptide of FNE with the E‐strands of the FI domains, adopting the β‐zipper extension model observed in previous structures of microbial surface components recognizing adhesive matrix molecule adhesion peptides bound to FI domains.DatabaseThe coordinates of the FNE–αREP3 complex have been deposited at the Protein Data Bank under the code 4PFG.Structured digital abstract

GBD and FNE bind by isothermal titration calorimetry (View interaction)

GBD 789FI and FNE bind by isothermal titration calorimetry (View interaction)

FNE-CT and GBD 789FI bind by isothermal titration calorimetry (View interaction)

GBD and FNE-CT bind by isothermal titration calorimetry (View interaction)

FNE and GBD 789FI bind by molecular sieving (View interaction)

FNE-CT binds to GBD 789FI by pull down (View interaction)

FNE and GBD 789FI bind by x ray scattering (View interaction)

GBD and FNE physically interact by fluorescence polarization spectroscopy (View interaction)

collagen and GBD bind by fluorescence polarization spectroscopy (View interaction)
Identifying functionally important cis‐peptide containing segments in proteins and their utility in molecular function annotation
Authors: Das Sreetama , Ramakumar Suryanarayanarao , Pal Debnath 
Published: October 2014

Cis‐peptide embedded segments are rare in proteins but often highlight their important role in molecular function when they do occur. The high evolutionary conservation of these segments illustrates this observation almost universally, although no attempt has been made to systematically use this information for the purpose of function annotation. In the present study, we demonstrate how geometric clustering and level‐specific Gene Ontology molecular‐function terms (also known as annotations) can be used in a statistically significant manner to identify cis‐embedded segments in a protein linked to its molecular function. The present study identifies novel cis‐peptide fragments, which are subsequently used for fragment‐based function annotation. Annotation recall benchmarks interpreted using the receiver‐operator characteristic plot returned an area‐under‐curve > 0.9, corroborating the utility of the annotation method. In addition, we identified cis‐peptide fragments occurring in conjunction with functionally important trans‐peptide fragments, providing additional insights into molecular function. We further illustrate the applicability of our method in function annotation where homology‐based annotation transfer is not possible. The findings of the present study add to the repertoire of function annotation approaches and also facilitate engineering, design and allied studies around the cis‐peptide neighborhood of proteins.
Uncertainties in predicting rice yield by current crop models under a wide range of climatic conditions
Authors: Li Tao , Hasegawa Toshihiro , Yin Xinyou , Zhu Yan , Boote Kenneth , Adam Myriam , Bregaglio Simone , Buis Samuel , Confalonieri Roberto , Fumoto Tamon , Gaydon Donald , Marcaida Manuel , Nakagawa Hiroshi , Oriol Philippe , Ruane Alex C. , Ruget Françoise , Singh Balwinder‐ , Singh Upendra , Tang Liang , Tao Fulu , Wilkens Paul , Yoshida Hiroe , Zhang Zhao , Bouman Bas 
Published: October 2014

AbstractPredicting rice (Oryza sativa) productivity under future climates is important for global food security. Ecophysiological crop models in combination with climate model outputs are commonly used in yield prediction, but uncertainties associated with crop models remain largely unquantified. We evaluated 13 rice models against multi‐year experimental yield data at four sites with diverse climatic conditions in Asia and examined whether different modeling approaches on major physiological processes attribute to the uncertainties of prediction to field measured yields and to the uncertainties of sensitivity to changes in temperature and CO2 concentration [CO2]. We also examined whether a use of an ensemble of crop models can reduce the uncertainties. Individual models did not consistently reproduce both experimental and regional yields well, and uncertainty was larger at the warmest and coolest sites. The variation in yield projections was larger among crop models than variation resulting from 16 global climate model‐based scenarios. However, the mean of predictions of all crop models reproduced experimental data, with an uncertainty of less than 10% of measured yields. Using an ensemble of eight models calibrated only for phenology or five models calibrated in detail resulted in the uncertainty equivalent to that of the measured yield in well‐controlled agronomic field experiments. Sensitivity analysis indicates the necessity to improve the accuracy in predicting both biomass and harvest index in response to increasing [CO2] and temperature.
Purification and characterisation of antioxidant and nitric oxide inhibitory peptides from Tilapia (Oreochromis niloticus) protein hydrolysate
Authors: Kangsanant Sureeporn , Thongraung Chakree , Jansakul Chaweewan , Murkovic Michael , Seechamnanturakit Vatcharee 
Published: October 2014

SummaryNitric oxide (NO)‐inhibitory and antioxidative activities of tilapia hydrolysates were prepared using ultrasound pretreatment at 70 W for 30 and 45 min, respectively, followed by Flavourzyme hydrolysis for 1 h. Both hydrolysates were fractionated using size exclusion chromatography on Sephadex G‐25 column and purified by RP‐HPLC. The amino acid sequence of the most potent and purified fractions was determined using LC/MS/MS. The antioxidant peptide (KAFAVIDQDKSGFIEEDELKLFLQNFSAGARAGDSDGDGKIGVDEFAALVK, MW: 6334.49 KDa) and NO‐inhibitory peptide (AFAVIDQDKSGFIEEDELKLFLQNFSAGARAGDSDGDGKIGVDEFAALVK, MW: 6309.49 Da) produced no cytotoxicity in RAW264.7 macrophage cell lines at the concentration of 100 mg mL−1. The purified peptides at the concentration 100 μg mL−1 possessed antioxidative and NO‐inhibitory activities 83.0 ± 1.1% and 40.9 ± 0.2%, respectively, which were about 100 times those of their counterpart crude hydrolysates.
Between Control and Support. The Protection of Unaccompanied Minor Asylum Seekers at Risk: The Dutch Case
Authors: Galloway Moira , Smit Monika , Kromhout Mariska 
Published: October 2014

AbstractDrawing on research by the Research and Documentation Centre (WODC) of the Dutch Ministry of Security and Justice (Kromhout et al., 2010), this article describes how the Dutch government tried to protect Unaccompanied Minor Asylum Seekers (UMAs) who were (at risk of becoming) victims of human trafficking by implementing “Protected Reception”. It was concluded that the three objectives of this pilot programme were met to some extent: the influx of risk groups and the number of disappearances decreased, yet there was no (immediate) increase in return migration to the country of origin, after leaving Protected Reception. An important question that was raised was how far a state can go in protecting these vulnerable young people, by (partially) limiting their freedom of movement. It was concluded that placement and stay in Protected Reception had to be qualified as a deprivation of liberty for which Dutch legislation did not offer any ground.
Endoscopic, Transoral, Reduction of Epiglottic Entrapment Via Wire Snare Technique
Authors: Coleridge Matthew O.D. , DiGiovanni Daria L. , Rodgerson Dwayne H. , Spirito Michael A. 
Published: October 2014

ObjectiveTo describe the use of a wire snare technique for epiglottic entrapment.Study DesignCase series.AnimalsEight adult horses.MethodsUnder general anesthesia, a modified mouth gag was placed in the oropharynx. An endoscope was passed through the gag until there was adequate visualization of the entrapped epiglottis. The entrapping mucosa was grasped with bronchoesophageal forceps and pulled rostrally, releasing the epiglottis. A custom snare was passed down the bronchoesophageal forceps to encircle the redundant subepiglottic mucosa. Tension was applied to the entrapping mucosa via the forceps as the obstetric wire was tightened at the base and the redundant mucosa (aryepiglottic fold) was excised.ResultsThe procedure was performed on 8 adult thoroughbred horses. Re‐evaluation by endoscopy did not show entrapment in any horse and no horse developed complications or has had problems with performance.ConclusionsThis technique is a minimally invasive, competitively priced and straightforward method for resection of entrapping subepiglottic mucosa in adult horses.
The Potassium‐Argon Laser Experiment (KArLE):In SituGeochronology for Planetary Robotic Missions
Authors: Cohen Barbara A. , Miller J. Scott , Li Zheng‐Hua , Swindle Timothy D. , French Renee A. 
Published: October 2014

Geochronology is a fundamental measurement for planetary samples, providing global and solar system context for the conditions prevailing on the planet at the time of major geological events. The potassium (K)‐Argon (Ar) laser experiment (KArLE) will makein situnoble gas geochronology measurements aboard planetary robotic missions such as rovers and landers. Laser‐induced breakdown spectroscopy (LIBS) is used to measure the K abundance in a sample and to release its noble gases; the evolved Ar is measured by mass spectrometry, and relative K content is related to absolute Ar abundance by sample mass, determined by optical measurement of the ablated volume. This approach allows K and Ar to be measured on identical volumes multiple times to create an isochron, which improves the age determination and reveals irregularities in the rock if they exist. TheKArLEtechnique measures a whole‐rock K‐Ar age with 10% uncertainty or better for rocks 2 Ga or older, sufficient to resolve the absolute age of many planetary samples. TheLIBS–mass spectrometry approach is attractive because the analytical components have been flight‐proven, do not require further technical development and provide essential measurements (complete elemental abundance, evolved volatile analysis, micro‐imaging) as well asin situgeochronology.
The Federalist Perspective in Elections to the European Parliament
Authors: Clark Nicholas 
Published: October 2014

AbstractThe literature on elections to the European Parliament establishes that both national and EU‐relevant considerations influence the decision to participate in EP elections as well as the likelihood that EP voters will switch their support between different parties. However, there have been relatively few efforts to identify the conditions that prompt individuals to consider the EU when deciding to participate or when casting a ballot. This article theorizes that individuals from decentralized political systems are more keenly aware of the distribution of functional responsibilities within the EU and are thus more likely to vote on EU‐relevant concerns in EP elections. The results from analyses of survey data from the 2009 European Election Study, together with contextual measures of decentralization, suggest that individuals from decentralized systems are more likely to participate in EP elections and that vote‐switchers are more likely to be motivated by evaluations of the EU's performance.
Female mate choice predicts paternity success in the absence of additive genetic variance for other female paternity bias mechanisms in Drosophila serrata
Authors: Collet J. M. , Blows M. W. 
Published: October 2014

AbstractAfter choosing a first mate, polyandrous females have access to a range of opportunities to bias paternity, such as repeating matings with the preferred male, facilitating fertilization from the best sperm or differentially investing in offspring according to their sire. Female ability to bias paternity after a first mating has been demonstrated in a few species, but unambiguous evidence remains limited by the access to complex behaviours, sperm storage organs and fertilization processes within females. Even when found at the phenotypic level, the potential evolution of any mechanism allowing females to bias paternity other than mate choice remains little explored. Using a large population of pedigreed females, we developed a simple test to determine whether there is additive genetic variation in female ability to bias paternity after a first, chosen, mating. We applied this method in the highly polyandrous Drosophila serrata, giving females the opportunity to successively mate with two males ad libitum. We found that despite high levels of polyandry (females mated more than once per day), the first mate choice was a significant predictor of male total reproductive success. Importantly, there was no detectable genetic variance in female ability to bias paternity beyond mate choice. Therefore, whether or not females can bias paternity before or after copulation, their role on the evolution of sexual male traits is likely to be limited to their first mate choice in D. serrata.
Do aggressive signals evolve towards higher reliability or lower costs of assessment?
Authors: Ręk P. 
Published: October 2014

AbstractIt has been suggested that the evolution of signals must be a wasteful process for the signaller, aimed at the maximization of signal honesty. However, the reliability of communication depends not only on the costs paid by signallers but also on the costs paid by receivers during assessment, and less attention has been given to the interaction between these two types of costs during the evolution of signalling systems. A signaller and receiver may accept some level of signal dishonesty by choosing signals that are cheaper in terms of assessment but that are stabilized with less reliable mechanisms. I studied the potential trade‐off between signal reliability and the costs of signal assessment in the corncrake (Crex crex). I found that the birds prefer signals that are less costly regarding assessment rather than more reliable. Despite the fact that the fundamental frequency of calls was a strong predictor of male size, it was ignored by receivers unless they could directly compare signal variants. My data revealed a response advantage of costly signals when comparison between calls differing with fundamental frequencies is fast and straightforward, whereas cheap signalling is preferred in natural conditions. These data might improve our understanding of the influence of receivers on signal design because they support the hypothesis that fully honest signalling systems may be prone to dishonesty based on the effects of receiver costs and be replaced by signals that are cheaper in production and reception but more susceptible to cheating.
Evaluation of Probiotic Characteristics of Lactic Acid Bacteria Isolated from Artisan Cheese
Authors: Hermanns Gislaine , Funck Graciele Daiana , Schmidt Jéssica Tamiozzo , Pereira Jamile Queiroz , Brandelli Adriano , Richards Neila Silvia Pereira dos Santos 
Published: October 2014

AbstractThe objective of this study was to identify and to evaluate probiotic characteristics and possible virulence factors of lactic acid bacteria (LAB) isolated from artisan cheeses from the northwestern region of Rio Grande do Sul (RS) state, south of Brazil. Among the isolated LAB, six strains showing broader antimicrobial activity were identified by polymerase chain reaction amplification and sequencing of 16S rDNA and ribosomal 16S‐23S intergenic spacer region. The results showed most isolates were Enterococcus faecium (n = 4) and the other strains were Enterococcus faecalis and Lactobacillus plantarum. These isolates showed tolerance to acidic conditions and bile salts, and to simulated gastrointestinal juices. Isolates were also evaluated for susceptibility to antimicrobials and production of β‐hemolysin as indicators of virulence. Hemolysin was negative for all isolates, but only E. faecium strains were susceptible to all antibiotics tested.Practical ApplicationsArtisan cheeses can be an interesting source for autochthonous bacteria for food use. The selected lactic acid bacteria showing antimicrobial activity on pathogenic bacteria have potential health benefits to the dairy industry. Some Enterococcus species isolated in this study showed desirable properties as potential probiotic strains, which can contribute for their use in food and feed industry.
Predictive Models Based on Support Vector Machines: Whole‐Brain versus Regional Analysis of Structural MRI in the Alzheimer's Disease
Authors: Retico Alessandra , Bosco Paolo , Cerello Piergiorgio , Fiorina Elisa , Chincarini Andrea , Fantacci Maria Evelina 
Published: October 2014

ABSTRACTDecision‐making systems trained on structural magnetic resonance imaging data of subjects affected by the Alzheimer's disease (AD) and healthy controls (CTRL) are becoming widespread prognostic tools for subjects with mild cognitive impairment (MCI). This study compares the performances of three classification methods based on support vector machines (SVMs), using as initial sets of brain voxels (ie, features): (1) the segmented grey matter (GM); (2) regions of interest (ROIs) by voxel‐wise t‐test filtering; (3) parceled ROIs, according to prior knowledge. The recursive feature elimination (RFE) is applied in all cases to investigate whether feature reduction improves the classification accuracy. We analyzed more than 600 AD Neuroimaging Initiative (ADNI) subjects, training the SVMs on the AD/CTRL dataset, and evaluating them on a trial MCI dataset. The classification performance, evaluated as the area under the receiver operating characteristic curve (AUC), reaches AUC = (88.9 ± .5)% in 20‐fold cross‐validation on the AD/CTRL dataset, when the GM is classified as a whole. The highest discrimination accuracy between MCI converters and nonconverters is achieved when the SVM‐RFE is applied to the whole GM: with AUC reaching (70.7 ± .9)%, it outperforms both ROI‐based approaches in predicting the AD conversion.
Anomalous Origin of Left Vertebral Artery from Carotid Bulb Seen as “Trifurcation” of Left Common Carotid Artery with Acute Infarct in Ipsilateral Thalamus: A Case Report
Authors: Patil Parag V. , Patil Abhijit M. , Apte Abhang V. , Attarde Vinod Y. 
Published: October 2014

ABSTRACTAnomalous origin of vertebral arteries is not common and usually seen as an incidental finding on imaging. We report a case of anomalous origin of left vertebral artery from left carotid bulb (“trifurcation” of left common carotid artery) on magnetic resonance angiography in a 64‐year old male who also had ipsilateral thalamic acute infarct.