bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inverting proteomics analysis provides powerful insight into the peptide/protein conundrum
Authors: Bin Goh Wilson Wen , Wong Limsoon 
Published: August 2015

AbstractIn proteomics, a large proportion of mass spectrometry (MS) data is ignored due to the lack of, or insufficient statistical evidence for mappable peptides. In reality, only a small fraction of features are expected to be differentially relevant anyway. Mapping spectra to peptides and subsequently, proteins, produces uncertainty at several levels. We propose it is better to analyze proteomic profiling data directly at MS level, and then relate these features to peptides/proteins. In a renal cancer data comprising 12 normal and 12 cancer subjects, we demonstrate that a simple rule-based binning approach can give rise to informative features. We note that the peptides associated with significant spectral bins gave rise to better class separation than the corresponding proteins, suggesting a loss of signal in the peptide-to-protein transition. Additionally, the binning approach sharpens focus on relevant protein splice forms rather than just canonical sequences. Taken together, the inverted raw spectra analysis paradigm, which is realised by the MZ-Bin method described in this article, provides new possibilities and insights, in how MS-data can be interpreted.
Estimating directed connectivity from cortical recordings and reconstructed sources
Authors: Papadopoulou Margarita , Friston Karl , Marinazzo Daniele 
Published: August 2015

AbstractIn cognitive neuroscience, electrical brain activity is most commonly recorded at the scalp. In order to infer the contributions and connectivity of underlying neuronal sources within the brain, it is necessary to reconstruct sensor data at the source level. Several approaches to this reconstruction have been developed, thereby solving the so-called implicit inverse problem (Michel et al. 2004). However, a unifying premise against which to validate these source reconstructions is seldom available. The dataset provided in this work, in which brain activity is simultaneously recorded on the scalp (non-invasively) by electroencephalography (EEG) and on the cortex (invasively) by electrocorticography (ECoG), can be of a great help in this direction. These multimodal recordings were obtained from a macaque monkey under wakefulness and sedation. Our primary goal was to establish the connectivity architecture between two sources of interest (frontal and parietal), and to assess how their coupling changes over the conditions. We chose these sources because previous studies have shown that the connections between them are modified by anaesthesia (Boly et al. 2012). Our secondary goal was to evaluate the consistency of the connectivity results when analyzing sources recorded from invasive data (128 implanted ECoG sources) and source activity reconstructed from scalp recordings (19 EEG sensors) at the same locations as the ECoG sources. We conclude that the directed connectivity in the frequency domain between cortical sources reconstructed from scalp EEG is qualitatively similar to the connectivity inferred directly from cortical recordings, using both data-driven (directed transfer function; DTF) and biologically grounded (dynamic causal modelling; DCM) methods. Furthermore, the connectivity changes identified were consistent with previous findings (Boly et al. 2012). Our findings suggest that inferences about directed connectivity based upon non-invasive electrophysiological data have construct validity in relation to invasive recordings.
INSULIN GROWTH FACTOR I AND ITS RECEPTOR ARE ANTAGONISTIC MODULATORS OF GLUCOSE HANDLING BY ASTROCYTES
Authors: Hernandez-Garzón E. , Fernandez A.M. , Perez-Alvarez A. , Mederos S. , Perez-Domper P. , Bascuñana P. , de la Rosa R.F. , Delgado M. , Pozo M.A. , Miranda-Vizuete A. , Guerrero-Gomez D. , Moreno E. , McCormick P.J. , Santi A. , Genis L. , Trueba A. , Garcia-Caceres C. , Tschöp M.H. , Araque A. , Perea G. , Martin E.D. , Torres Aleman I. 
Published: August 2015

AbstractReducing insulin-like growth factor I receptor (IGF-IR) levels or administration of IGF-I show beneficial effects in the brain. We now provide evidence to help resolve this paradox. The unliganded IGF-IR inhibits glucose uptake by astrocytes while its stimulation with IGF-I, in concert with insulin activation of the insulin receptor, produces the opposite effect. In vivo imaging showed that shRNA interference of brain IGF-IR increased glucose uptake by astrocytes while pharmacological blockade of IGF-IR reduced it. Brain18FGlucose-PET of IGF-IR shRNA injected mice confirmed an inhibitory role of unliganded IGF-IR on glucose uptake, whereas glucose-dependent recovery of neuronal activity in brain slices was blunted by pharmacological blockade of IGF-IR. Mechanistically, we found that the unliganded IGF-IR retains glucose transporter 1 (GLUT1), the main glucose transporter in astrocytes, inside the cell while IGF-I, in cooperation with insulin, synergistically stimulates MAPK/PKD to promote association of IGF-IR with GLUT 1 via Rac1/GIPC1 and increases GLUT1 availability at the cell membrane. These findings identify IGF-I and its receptor as antagonistic modulators of brain glucose uptake.
Comparison of biochemical, histological and morphological response of muscle-based condition indices to varying food levels in pre-flexionDicentrarchus labrax(L.) larvae
Authors: Catalán Ignacio A. , Pilar Olivar M. , Berdalet Elisa 
Published: August 2015

AbstractThe time-response, dynamics, classification power and relationship with survival of three muscle-based condition indices were analysed in pre-flexion sea bass (Dicentrarchus labraxL.) larvae in response to three feeding treatments: fed, non-fed and late-feeding. Larvae were reared at 19 ± 0.8°C and analysed from the second day of feeding (6 days after hatching (DAH)) to just prior the flexion stage (21 DAH). The indices were analysed in trunk muscle at biochemical (RNA/DNA, R/D), histological (percentage of muscle fibre separation, MFS) and morphometric (size-standardised body depth at the anus level, DAZ) level. No index was correlated with muscle length in the fed treatment regardless the period analysed (before or after full external feeding). The R/D was the only index that could detect past feeding differences in larvae ≤ 13 DAH. For larvae > 13 DAH, MFS, R/D andDAZin that order, yielded the best discrimination among treatments. For late-feeding larvae, latency was two days (R/D) and two-four days (MFS). Dynamics of recovery after food addition was also similar for R/D and MFS. Significant relationships between muscle growth and R/D or MFS were only found in larvae > 13 DAH. Both R/D and MFS encompassed the mass mortality event observed in non-fed larvae at 17 DAH. TheDAZlargely failed to give information on the feeding status.
Phylogenetic relationships of the Helmeted Woodpecker (Dryocopus galeatus): A case of interspecific mimicry?
Authors: Benz Brett W. , Robbins Mark B. , Zimmer Kevin J. 
Published: August 2015

ABSTRACTExamples of phenotypic convergence in plumage coloration have been reported in a wide diversity of avian taxonomic groups, yet the underlying evolutionary mechanisms driving this phenomenon have received little scientific inquiry. Herein, we document a striking new case of plumage convergence in the Helmeted Woodpecker (Dryocopus galeatus) and explore the possibility of visual mimicry among Atlantic Forest woodpeckers. Our multi-locus phylogenetic analyses unequivocally placeD.galeatuswithinCeleus, indicating the former has subsequently converged in appearance upon the distantly related and syntopicDryocopus lineatus, to which it bears a remarkable resemblance in plumage coloration and pattern. Although details of the Helmeted Woodpecker’s ecology and natural history are only now beginning to emerge, its smaller size and submissive behavior are consistent with predictions derived from evolutionary game theory models and the interspecific social dominance mimicry hypothesis (ISDM). Moreover, estimates of avian visual acuity suggest that size-related mimetic deception is plausible at distances ecologically relevant toCeleusandDryocopusforaging behavior. In light of our results, we recommend taxonomic transfer ofD.galeatustoCeleusand emphasize the need for detailed behavioral studies that examine the social costs and benefits of plumage convergence to explicitly test for ISDM and other forms of mimicry in these Atlantic Forest woodpecker communities. Future field studies examining potential cases of competitive mimicry should also take into account the mimic’s acoustic behavior, particularly in the presence of putative model species and other heterospecific competitors, as any discontinuity between morphological and behavioral mimicry would likely preclude the possibility of deception.
Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression
Authors: Wiedenhoeft John , Brugel Eric , Schliep Alexander 
Published: August 2015

AbstractBy combining Haar wavelets with Bayesian Hidden Markov Models, we improve detection of genomic copy number variants (CNV) in array CGH experiments compared to the state-of-the-art, including standard Gibbs sampling. At the same time, we achieve drastically reduced running times, as the method concentrates computational effort on chromosomal segments which are difficult to call, by dynamically and adaptively recomputing consecutive blocks of observations likely to share a copy number. This makes routine diagnostic use and re-analysis of legacy data collections feasible; to this end, we also propose an effective automatic prior. An open source software implementation of our method is available athttp://bioinformatics.rutgers.edu/Software/HaMMLET/. The web supplement is athttp://bioinformatics.rutgers.edu/Supplements/HaMMLET/.Author SummaryIdentifying large-scale genome deletions and duplications, or copy number variants (CNV), accurately in populations or individual patients is a crucial step in indicating disease factors or diagnosing an individual patient's disease type. Hidden Markov Models (HMM) are a type of statistical model widely used for CNV detection, as well as other biological applications such as the analysis of gene expression time course data or the analysis of discrete-valued DNA and protein sequences.As with many statistical models, there are two fundamentally different inference approaches. In the frequentist framework, a single estimate of the model parameters would be used as a basis for subsequent inference, making the identification of CNV dependent on the quality of that estimate. This is an acute problem for HMM as methods for finding globally optimal parameters are not known. Alternatively, one can use a Bayesian approach and integrate over all possible parameter choices. While the latter is known to lead to significantly better results, the much—up to hundreds of times—larger computational effort prevents wide adaptation so far.Our proposed method addresses this by combining Haar wavelets and HMM. We greatly accelerate fully Bayesian HMMs, while simultaneously increasing convergence and thus the accuracy of the Gibbs sampler used for Bayesian computations, leading to substantial improvements over the state-of-the-art.
Editor and reviewer gender influence the peer review process but not peer review outcomes at an ecology journal
Authors: Fox Charles W. , Burns C. Sean , Meyer Jennifer A. 
Published: August 2015

Summary

Lack of diversity on editorial boards might generate disparities in editorial and peer review that contribute to gender and geographic disparities in scholarly publishing.

We use a comprehensive data set of the peer review process for all papers submitted to the journal Functional Ecology from January 2004 to June 2014 to examine how gender, seniority and geographic location of editors and reviewers influence reviewer recruitment and scores given to papers by reviewers.

The gender ratio of editors for Functional Ecology was majority male, but the proportion of female editors increased over time. The gender ratio of selected reviewers was also highly majority male, but the proportion of women selected as reviewers increased over the 10 years largely because the number of women on the editorial board increased and female editors invited more female reviewers than did male editors. Male editors selected <25% female reviewers even in the year they selected the most women, but female editors consistently selected ˜30–35% female reviewers. Editors also over‐selected reviewers from their own geographic locality.

Women invited to review were less likely to respond to review invitations, but more likely to accept if they responded. Women invited to review responded to the invitation similarly regardless of whether the editor inviting them was male or female, but men invited to review were both less likely to respond and more likely to decline if the editor was female.

Review scores given to papers did not differ between male and female reviewers, and final decisions (proportion of papers rejected) did not differ between male and female editors.

The proportion of women among selected reviewers decreased with editor seniority when the editor was male but increased with editor seniority when the editor was female. Thus, the gender ratio of selected reviewers differed little between early‐career male and female editors but differed a lot between late‐career (more senior) male and female editors. Individuals invited to review were less likely to agree to review if the editor was more senior.

Editor gender, seniority and geographic location affect who is invited to review for Functional Ecology, and how invitees respond to review invitations, but not the final outcome of the peer review process. To increase diversity of reviewer populations, journals should increase gender, age and geographic diversity of their editorial boards.
Functional assessment of animal interactions with shrub‐facilitation complexes: a formal synthesis and conceptual framework
Authors: Lortie Christopher J. , Filazzola Alessandro , Sotomayor Diego A. 
Published: August 2015

Summary

Facilitation studies focus primarily on plants often neglecting the extended effects that cascade through ecological networks. Plants interact with other organisms through consumptive effects and a myriad of non‐trophic effects such as habitat amelioration or pollination.

Shrubs are a dominant benefactor species frequent in plant‐facilitation studies but can also have direct and indirect interactions with animals. Herein, we use a systematic review to address the following two objectives: (i) to propose a conceptual framework that explores these interactions including the functional roles of the interacting species, and (ii) to quantitatively summarize the current state of this field examining effects beyond plant–plant interactions.

To date, a relatively limited number of studies have examined the importance of coupled benefactor‐subordinate plant positive interactions with animals (79 studies in total). From this set of studies, 36 studies documented positive plant interactions generating a total of 53 independent instances of either shrub–plant–animal or shrub–animal–plant interactions.

These interaction pathways were evenly split between direct (49%) and indirect (51%) interactions of shrubs with animals. Hypotheses frequently tested included seed trapping, herbivore protection, magnet pollination and facilitation‐mediated secondary seed dispersal. The most common functional role of shrubs was protection from herbivory, and the most common animal role associated with plant‐facilitation complexes was that of a consumer.

None of these studies explored bidirectional plant–animal interactions, used a network approach to describe the interaction sets, nor contrasted interaction strengths. Multitrophic, integrated sets of experiments incorporating plant facilitation into community dynamics are thus critical in advancing management of high‐stress ecosystems wherein positive interactions are commonly reported.
The length‐dependent activation of contraction is equally impaired in impuberal male and female rats in monocrotaline‐induced right ventricular failure
Authors: Lookin Oleg , Balakin Alexander , Kuznetsov Daniil , Protsenko Yuri 
Published: August 2015

SummaryThe length‐dependent activation of contraction is attenuated in the failing myocardium of adult male rats. This pathological change is not seen in adult female rats, possibly because of a protective effect of sex hormones. The present study evaluated length‐dependent changes in isometric twitch, Ca2+ transient (CaT) and action potential (AP) in the right ventricular myocardium of impuberal healthy male and female rats (control) and in rats treated with a single injection of 50 mg/kg monocrotaline (MCT). Compared with sex‐matched control rats, MCT‐treated male and female rats exhibited increased right ventricular weight (134% and 142% of control, respectively), decreased left ventricular weight (72% and 79%), twitch attenuation (48.8 ± 2.7% and 57.5 ± 1.2%) and prolongation (125 ± 3% and 127 ± 2%), CaT attenuation (37.8 ± 0.4% and 39.1 ± 1.1%) and prolongation (114 ± 1% and 116 ± 1%) and AP prolongation at 90% repolarization (195 ± 2% and 203 ± 1%). The MCT‐treated male rats exhibited a 50% lower integral magnitude and an approximately 25% larger time‐to‐peak ‘bump’ compared with control male rats. These parameters in MCT‐treated female rats tended to show similar changes to those seen in the control female rats, with no significant difference between the two groups. In all groups, integral magnitude and time‐to‐peak ‘bump’ increased with length. In conclusion, the length‐dependent activation of contraction was equally blunted in the failing right ventricular myocardium of impuberal male and female rats. This was related to changes in CaT and AP, which were similar between male and female rats. Therefore, puberty is necessary for manifestation of the protective effects of sex hormones on this remodelling.
Asiatic acid alleviates cardiovascular remodelling in rats with L‐NAME‐induced hypertension
Authors: Bunbupha Sarawoot , Prachaney Parichat , Kukongviriyapan Upa , Kukongviriyapan Veerapol , Welbat Jariya Umka , Pakdeechote Poungrat 
Published: August 2015

SummaryA previous study demonstrated the antihypertensive effect of asiatic acid. The current study investigates the effect of asiatic acid on cardiovascular remodelling and possible mechanisms involved in Nω‐nitro‐L‐arginine methyl ester hydrochloride (L‐NAME)‐induced hypertensive rats. Male Sprague–Dawley rats were treated with L‐NAME (40 mg/kg per day) for 3 weeks in order to induce hypertension. Hypertensive rats were administered asiatic acid (20 mg/kg per day) or vehicle for a further 2 weeks. It was found that hypertensive rats showed high systolic blood pressure, left ventricular (LV) hypertrophy, increases in LV fibrosis, aortic wall thickness and aortic collagen deposition (P < 0.05). Moreover, decreased plasma nitrate and nitrite (NOx) and increased plasma tumor necrosis factor alpha (TNF‐α) were observed in hypertensive rats (P < 0.05). This was consistent with downregulation of endothelial nitric oxide synthase (eNOS) expression and upregulation of inducible nitric oxide synthase (iNOS) expression in heart and aortic tissues (P < 0.05). Levels of malondialdehyde (MDA) in plasma, aortic and heart tissues were significantly increased in hypertensive rats (P < 0.05). Asiatic acid markedly reduced blood pressure, alleviated cardiovascular remodelling, and restored plasma NOx and TNF‐α as well as eNOS/iNOS expression in heart and aortic tissues (P < 0.05). Additionally, there was a significant reduction of MDA levels in the tissues of treated hypertensive rats. In conclusion, this study demonstrates the therapeutic effects of asiatic acid on blood pressure and cardiovascular remodelling, which is possibly related to the restoration of eNOS/iNOS expression, and the resulting anti‐inflammatory and antioxidant activities.
Angiotensin and mineralocorticoid receptor antagonism attenuates cardiac oxidative stress in angiotensin II‐infused rats
Authors: Minas Jacqueline N , Thorwald Max A , Conte Debra , Vázquez‐Medina Jose‐Pablo , Nishiyama Akira , Ortiz Rudy M 
Published: August 2015

SummaryAngiotensin II (Ang II) and aldosterone contribute to hypertension, oxidative stress and cardiovascular damage, but the contributions of aldosterone during Ang II‐dependent hypertension are not well defined because of the difficulty to assess each independently. To test the hypothesis that during Ang II infusion, oxidative and nitrosative damage is mediated through both the mineralocorticoid receptor (MR) and angiotensin type 1 receptor (AT1), five groups of Sprague–Dawley rats were studied: (i) control; (ii) Ang II infused (80 ng/min × 28 days); (iii) Ang II + AT1 receptor blocker (ARB; 10 mg losartan/kg per day × 21 days); (iv) Ang II + mineralocorticoid receptor (MR) antagonist (Epl; 100 mg eplerenone/day × 21 days); and (v) Ang II + ARB + Epl (Combo; × 21 days). Both ARB and combination treatments completely alleviated the Ang II‐induced hypertension, whereas eplerenone treatment only prolonged the onset of the hypertension. Eplerenone treatment exacerbated the Ang II‐mediated increase in plasma and heart aldosterone 2.3‐ and 1.8‐fold, respectively, while ARB treatment reduced both. Chronic MR blockade was sufficient to ameliorate the AT1‐mediated increase in oxidative damage. All treatments normalized protein oxidation (nitrotyrosine) levels; however, only ARB and Combo treatments completely reduced lipid peroxidation (4‐hydroxynonenal) to control levels. Collectively, these data suggest that receptor signalling, and not the elevated arterial blood pressure, is the principal culprit in the oxidative stress‐associated cardiovascular damage in Ang II‐dependent hypertension.
Parasitic myoma after laparoscopic morcellation: a systematic review of the literature
Authors: Van der Meulen JF , Pijnenborg JMA , Boomsma CM , Verberg MFG , Geomini PMAJ , Bongers MY 
Published: August 2015

BackgroundLaparoscopic morcellation is frequently used for tissue removal after laparoscopic hysterectomy or myomectomy and may result in parasitic myomas, due to seeding of remained tissue fragments in the abdominal cavity. However, little is known about the incidence and risk factors of this phenomenon.ObjectivesTo identify the incidence and risk factors for the development of parasitic myoma after laparoscopic morcellation.Search strategyA systematic review of the literature in Pubmed (MEDLINE) and Embase was conducted. Reference lists of identified relevant articles were checked for missing case reports.Selection criteriaStudies reporting on incidence or cases of parasitic myoma diagnosed after laparoscopic morcellation were selected. Studies were excluded when history of laparoscopic morcellation was lacking or final pathology demonstrated a malignancy or endometriosis.Data collection and analysisData were extracted and analysed on incidence of parasitic myomas and characteristics of case reports.Main resultsFourty‐four studies were included. Sixty‐nine women diagnosed with parasitic myomas after laparoscopic morcellation were identified. Mean age was 40.8 (± 7.5) years (range 24–57), median time between surgery and diagnosis was 48.0 months (range 1–192) and mean number of parasitic myomas was 2.9 (± 3.3) (range 1–16). The overall incidence of parasitic myomas after laparoscopic morcellation was 0.12–0.95%.ConclusionAlthough the incidence is relatively low, it is important to discuss the risk of parasitic myoma after laparoscopic morcellation with women and balance towards alternative treatment options. The duration of steroid exposure after laparoscopic morcellation might be a risk factor for development of parasitic myomas.Tweetable abstractSystematic review on the incidence and risk factors for parasitic myoma after laparoscopic morcellation.