bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of the menopausal transition and physical activity energy expenditure on inflammatory markers: a MONET group study
Authors: Razmjou Sahar , Bastard Jean-Philippe , Doucet Eric , Rabasa-Lhoret Remi , Fellahi Soraya , Lavoie Jean-Marc , Prud’homme Denis 
Published: August 2016

Abstract

Objective:
Menopausal transition is usually associated with changes in body composition and a decrease in physical activity energy expenditure. Adipose tissue, especially visceral fat, is an important source of inflammatory markers, which contributes to the development of a proinflammatory state. Conversely, high levels of physical activity and exercise have an anti-inflammatory effect. This study aimed to investigate the impact of menopausal transition and physical activity on inflammatory makers.

Methods:
One hundred two healthy premenopausal women participated in a 5-year longitudinal study. The present secondary analyses were performed on 58 participants with a full set of data (age: 49.6 ± 1.7 y; body mass index: 23.3 ± 2.4 kg/m2). Measures included body composition, waist circumference, fasting glucose and insulin levels, insulin sensitivity, plasma lipid levels, cardiorespiratory fitness, physical activity energy expenditure, and inflammatory markers.

Results:
Repeated measure analyses revealed, after the 5-year follow-up, significant increases in ferritin, interleukin-8 (IL-8), and soluble tumor necrosis factor-α receptor 1 and 2 (sTNFR1 and sTNFR2) (P < 0.001), and a significant decrease in serum high-sensitive C-reactive protein (P < 0.05). Positive correlations were observed between change (year 5 to baseline) in waist circumference and changes in high-sensitive C-reactive protein, orosomucoid (ORM), haptoglobin, and apolipoprotein B (ApoB) levels (0.26 ≤ r ≤ 0.34; P < 0.05), and between change in peripheral fat and changes in ORM, ApoB, sTNFR2 (0.28 ≤ r ≤ 0.39; P < 0.05). On the contrary, negative correlations were found between change in physical activity energy expenditure and changes in ORM as well as ApoB (r = −0.35 and r = −0.36, respectively; P < 0.05). No significant correlations were found between change in cardiorespiratory fitness, glucose, insulin, insulin sensitivity and changes in inflammatory markers. Multiple regression analyses showed that changes in physical activity energy expenditure and waist circumference together explained 23% of the individual variance of change in ORM (P < 0.05). Also, change in physical activity energy expenditure explained 15% (P < 0.05) of the variance of change in ApoB. Fat mass change explained 15% (P < 0.05) of the variance of change in IL-8, and finally change in peripheral fat explained 15% of variance of change in sTNFR2 (P < 0.05).

Conclusions:
The present study indicates that the menopausal transition is accompanied by an increase in inflammatory markers, namely ferritin, IL-8, sTNFR1, and sTNFR2. The increase in IL-8 and sTNFR2 with menopause could be explained, in part, by changes in fat mass and peripheral fat, respectively.
INTRAVITREAL METHOTREXATE FOR MANTLE CELL LYMPHOMA INFILTRATION OF THE OPTIC NERVES: A CASE REPORT
Authors: Singer James R. , Nigalye Archana K. , Champion Mary T. , Welch Matthew J. 
Published: August 2016

Purpose:
To report the successful treatment of a 78-year-old woman with bilateral mantle cell lymphoma involving the optic nerves. Chemotherapy initially was administered in the form of intravitreal methotrexate (MTX) monotherapy and was subsequently combined with systemic ibrutinib.

Methods:
Retrospective case report. The diagnosis of CD5-negative mantle cell lymphoma was confirmed via immunohistopathological analysis of an axillary lymph node. Serial ophthalmologic examinations in conjunction with fluorescein angiography, fundus photography, and spectral domain optical coherence tomography were used to assess the treatment response.

Results:
Prompt improvement in optic nerve infiltration, no significant side effects, and excellent tolerability were noted after two weekly injections of unilateral intravitreal MTX monotherapy. Combined systemic treatment with ibrutinib and bilateral weekly MTX intravitreal injections then resulted in continued regression of optic nerve infiltration bilaterally as confirmed by serial fundus photography and optical coherence tomography. After eight additional bilateral weekly injections, a mild MTX-associated keratopathy developed, which resolved promptly with cessation of injections and administration of topical lubrication. Six weeks after MTX cessation, but with continued ibrutinib treatment, the optic nerves revealed near-complete resolution of the lymphomatous infiltration and the visual acuity improved.

Conclusion:
Intravitreal MTX injections and systemic ibrutinib may represent effective treatment options for patients diagnosed with intraocular mantle cell lymphoma.
The Validity of the Different Versions of the Hamilton Depression Scale in Separating Remission Rates of Placebo and Antidepressants in Clinical Trials of Major Depression
Authors: Kyle Phillip Raphael , Lemming Ole Michael , Timmerby Nina , Søndergaard Susan , Andreasson Kate , Bech Per 
Published: August 2016

Abstract
Our objective was to validate the different versions of the Hamilton Depression Scale (HAM-D) both psychometrically (scalability) and clinically in discriminating antidepressants from placebo in terms of remission rates in an 8-week clinical trial in the acute treatment of major depression. The traditional HAM-D17 version was compared with the shorter HAM-D6 and the longer HAM-D21 or HAM-D24 in a fixed-dose placebo-controlled vortioxetine study. Clinical Global Impression of Severity scores were used to establish standardized cutoff scores for remission across each scale. Using these cutoff scores, we compared the ability of each scale to separate drug-placebo remission rates, evaluated by the number needed to treat for clinical evidence. The HAM-D6 was superior to HAM-D17 in separating drug-placebo remission rates at the end point, defined as number needed to treat of less than 10. More items in the longer HAM-D versions indicated smaller discriminating validity over placebo. The HAM-D6 indicated a dose effect on remission for vortioxetine in both moderate and severe major depression. The brief HAM-D6 was thus found superior to HAM-D17, HAM-D21, and HAM-D24 both in terms of scalability and in discriminating antidepressants from placebo.
Development and Validation of a Grading Scale for Custom Ocular Prosthesis
Authors: Dave Tarjani V. , Kumar Sathish , Vasanthalin Jaya , Kaliki Swathi , Ali Mohammad Javed , Naik Milind N. 
Published: August 2016

ABSTRACT

Purpose
To develop a standardized and universally reproducible grading scale for artistic outcome of a custom ocular prosthesis.

Methods
A retrospective review of photographs of patients with custom ocular prosthesis. From the ocularistry database of a tertiary eye care hospital, photographs of patients with custom ocular prosthesis (30 random photos with additional 18 repetitions, total n = 50) were selected. Two independent oculoplastic surgeons, on the basis of characteristics of limbus, vascularity, and pigmentation, graded these photos. The photos were adjusted for confounders like magnification and illumination, and both graders used the same display system. The surgeons were blinded to each other. The characteristics were graded on a scale of 0 to 2 and total score was calculated for each photo. Inter-observer and intra-observer agreement was calculated using the kappa statistic.

Results
The inter-observer kappa coefficient for the three characteristics (95% confidence interval) were as follows: limbus 0.7 (0.55–0.85), vascularity 0.76 (0.58–0.94), and pigmentation 0.6 (0.34–0.85). The intra-observer kappa coefficient for the first surgeon was as follows: limbus 0.88 (0.7–0.95), vascularity 0.88 (0.73–0.95), and pigmentation 0.82 (0.54–0.93). The intra-observer kappa coefficient for the second surgeon was as follows: limbus 0.8 (0.44–0.93), vascularity 0.55 (0.13–0.8), and pigmentation 0.76 (0.6–0.84).

Conclusions
A good intra- and inter-observer agreement was demonstrated. In view of no existing grading for prosthesis, this is a unique system to objectively grade the outcome of custom ocular prosthesis and can be incorporated in ocularistry teaching modules for standardization of outcomes.
Plasma n-6 Fatty Acid Levels Are Associated With CD4 Cell Counts, Hospitalization, and Mortality in HIV-Infected Patients
Authors: Kabagambe Edmond K. , Ezeamama Amara E. , Guwatudde David , Campos Hannia , Fawzi Wafaie W. 
Published: August 2016

Background:
Fatty acids, including n-6 series, modulate immune function, but their effect on CD4 cell counts, death, or hospitalization in HIV-infected patients on antiretroviral therapy is unknown.

Methods:
In a randomized trial for effects of multivitamins in HIV-infected patients in Uganda, we used gas chromatography to measure plasma n-6 fatty acids at baseline; determined CD4 counts at baseline, 3, 6, 12, and 18 months; and recorded hospitalization or death events. The associations of fatty acids with CD4 counts and events were analyzed using repeated-measures analysis of variance and Cox regression, respectively.

Results:
Among 297 patients with fatty acids measurements, 16 patients died and 69 were hospitalized within 18 months. Except for linoleic acid, n-6 fatty acids levels were positively associated with CD4 counts at baseline but not during follow-up. In models that included all 5 major n-6 fatty acids, age; sex; body mass index; anemia status; use of antiretroviral therapy, multivitamin supplements, and alcohol; and the risk of death or hospitalization decreased significantly with an increase in linoleic acid and gamma-linolenic acid levels, whereas associations for dihomo-gamma-linolenic acid, arachidonic acid, and aolrenic acid were null. The hazard ratios (95% confidence intervals) per 1 SD increase in linoleic acid and gamma-linolenic acid were 0.73 (0.56–0.94) and 0.51 (0.36–0.72), respectively. Gamma-linolenic acid remained significant (hazard ratio = 0.51; 95% confidence interval: 0.35 to 0.68) after further adjustment for other plasma fatty acids.

Conclusions:
Lower levels of gamma-linolenic acid are associated with lower CD4 counts and an increased risk of death or hospitalization. These results suggest a potential for using n-6 fatty acids to improve outcomes from antiretroviral therapy.
Figure-of-Eight Suspension Suture in Open Technique Septorhinoplasty
Authors: Celik Mehmet , Cayonu Melih , Comoglu Senol , Kanliada Deniz 
Published: August 2016

Abstract
The aim of this study was to describe a novel surgical suture technique for achieving ideal nasal tip rotation and projection with nasal supratip angle. The figure-of-eight suspension suture (FOESS) technique was used in 68 patients who underwent open technique septorhinoplasty operation between the years 2013 and 2015. Fifty-four of the patients were female and 14 were male. The mean age of the patients was 28.2. The mean follow-up time of the patients was between 6 and 18 months. No complications were observed due to the FOESS technique. Satisfactory results were obtained in the postoperative period after surgery. The FOESS technique generated power against the anterior-inferior tensile strength of the alar cartilages. Thus, it can be possible to shape the nasal tip rotation and projection in the desired dimensions. In addition, this technique helps us to create supratip break point and angle.
Odontogenic Sinusitis Resulting in Abscess Formation Within the Optic Chiasm and Tract: Case Report and Review
Authors: Ghobrial George M. , Pisculli Mary L. , Evans James J. , Bilyk Jurij R. , Farrell Christopher J. 
Published: August 2016

Abstract:
A 33-year-old immunocompetent man developed rapid visual loss and a third nerve palsy secondary to acute rhinosinusitis and intracranial abscess formation. Despite endoscopic drainage of the ethmoid and sphenoid sinuses and empiric broad-spectrum antibiotics, the patient experienced progressive visual and neurological decline and ultimately required craniotomy for drainage of an optic apparatus abscess. Although odontogenic sinusitis rarely results in abscess formation of the visual pathways, early recognition and immediate treatment is imperative to decrease the risk of profound and permanent visual impairment.
Stochastic competitive exclusion leads to a cascade of species extinctions
Authors: Capitán José A , Cuenda Sara , Alonso David 
Published: August 2016

AbstractCommunity ecology has traditionally relied on the competitive exclusion principle, a piece of common wisdom in conceptual frameworks developed to describe species assemblages. Key concepts in community ecology, such as limiting similarity and niche partitioning, are based on competitive exclusion. However, this classical paradigm in ecology relies on implications derived from simple, deterministic models. Here we show how the predictions of a symmetric, deterministic model about the way extinctions proceed can be utterly different from the results derived from the same model when ecological drift (demographic stochasticity) is explicitly considered. Using analytical approximations to the steady-state conditional probabilities for assemblages with two and three species, we demonstrate that stochastic competitive exclusion leads to a cascade of extinctions, whereas the symmetric, deterministic model predicts a multiple collapse of species. To test the robustness of our results, we have studied the effect of environmental stochasticity and relaxed the species symmetry assumption. Our conclusions highlight the crucial role of stochasticity when deriving reliable theoretical predictions for species community assembly.
Efficient randomization of biological networks while preserving functional characterization of individual nodes
Authors: iorio Francesco , Bernardo-Faura Marti , Gobbi Andrea , Cokelae Thomas , Jurman Giuseppe , Saez-Rodrigue Julio 
Published: August 2016

AbstractBackgroundNetworks are popular and powerful tools to describe and model biological processes. Many computational methods have been developed to infer biological networks from literature, high-throughput experiments, and combinations of both. Additionally, a wide range of tools has been developed to map experimental data onto reference biological networks, in order to extract meaningful modules. Many of these methods assess results’ significance against null distributions of randomized networks. However, these standard unconstrained randomizations do not preserve the functional characterization of the nodes in the reference networks (i.e. their degrees and connection signs), hence including potential biases in the assessment.ResultsBuilding on our previous work about rewiring bipartite networks, we propose a method for rewiring any type of unweighted networks. In particular we formally demonstrate that the problem of rewiring a signed and directed network preserving its functional connectivity (F-rewiring) reduces to the problem of rewiring two induced bipartite networks. Additionally, we reformulate the lower bound to the iterations’ number of the switching-algorithm to make it suitable for the F-rewiring of networks of any size. Finally, we presentBiRewire 3, an open-source Bioconductor software enabling the F-rewiring of any type of unweighted network. We illustrate its application to a case study about the identification of modules from gene expression data mapped on protein interaction networks, and a second one focused on building logic models from more complex signed-directed reference signaling networks and phosphoproteomic data.ConclusionsBiRewire3it is freely available athttps://www.bioconductor.org/packages/BiRewire/, and it should have a broad application as it allows an efficient and analytically derived statistical assessment of results from any network biology tool.
Recurrent promoter mutations in melanoma are defined by an extended context-specific mutational signature
Authors: Fredriksson Nils Johan , Elliot Kerryn , Filges Stefan , Ståhlberg Anders , Larsson Erik 
Published: August 2016

SummarySequencing of whole tumor genomes holds the promise of revealing functional somatic regulatory mutations, such as those described in theTERTpromoter. Recurrent promoter mutations have been identified in many additional genes and appear to be particularly common in melanoma, but convincing functional data such as influence on gene expression has been more elusive. Here, we show that frequently recurring promoter mutations in melanoma occur almost exclusively at cytosines flanked by a distinct sequence signature, TTCCG, withTERTas a notable exception. In active, but not inactive, promoters, mutation frequencies for cytosines at the 5’ end of this ETS-like motif were considerably higher than expected based on a UV trinucleotide mutational signature. Additional analyses solidify this pattern as an extended context-specific mutational signature that mediates an exceptional position-specific vulnerability to UV mutagenesis, arguing against positive selection. We further use ultra-sensitive amplicon sequencing to demonstrate that cell cultures exposed to UV light quickly develop subclonal mutations specifically in affected positions. Our findings have implications for the interpretation of somatic mutations in regulatory regions, and underscore the importance of genomic context and extended sequence patterns to accurately describe mutational signatures in cancer.
The field of view available to the ventral occipito-temporal reading circuitry
Authors: Le Rosemary , Witthoft Nathan , Ben-Shachar Michal , Wandell Brian 
Published: August 2016

AbstractSkilled reading requires rapidly recognizing letters and word forms; people learn this skill best for words presented in the central visual field. Measurements over the last decade have shown that when children learn to read, responses within ventral occipito-temporal cortex (VOT) become increasingly selective to word forms. We call these regions the VOT reading circuitry (VOTRC). The portion of the visual field that evokes a response in the VOTRC is called thefield of view (FOV). We measured the FOV of the VOTRC and found that it is a small subset of the entire field of view available to the human visual system. For the typical subject, the FOV of the VOTRC in each hemisphere is contralaterally and foveally biased. The FOV of the left VOTRC extends ~9° into the right visual field and ~4° into the left visual field along the horizontal meridian. The FOV of the right VOTRC is roughly mirror symmetric to that of the left VOTRC. The size and shape of the FOV covers the region of the visual field that contains relevant information for reading English. It may be that the size and shape of the FOV, which varies between subjects, will prove useful in predicting behavioral aspects of reading.
Loss of a doublecortin (DCX) domain containing protein causes structural defects in a tubulin-based organelle ofToxoplasma gondiiand impairs host cell invasion
Authors: Nagayasu Eiji , Hwang Yu-chen , Liu Jun , Murray John M. , Hu Ke 
Published: August 2016

AbstractThe ~6000 species in phylum Apicomplexa are single-celled obligate intracellular parasites. Their defining characteristic is the “apical complex”, membranous and cytoskeletal elements at the apical end of the cell that participate in host-cell invasion. The apical complex ofToxoplasma gondiiand some other apicomplexans includes a cone-shaped assembly, the “conoid”, which (inT. gondii) comprises 14 spirally arranged fibers that are non-tubular polymers of tubulin. The tubulin dimers used for the conoid fibers make canonical microtubules elsewhere in the same cell, suggesting that their special arrangement in the conoid fibers is dictated by non-tubulin proteins. One candidate for this role is TgDCX, which has a doublecortin (DCX) domain and a TPPP/P25-alpha domain, known modulators of tubulin polymer structure. Loss of TgDCX radically disrupts the structure of the conoid, severely impairs host cell invasion, and slows growth. The defects of TgDCX-null parasites are corrected by re-introduction of a TgDCX coding sequence.
Peptide partitions and protein identification: a computational analysis
Authors: Sampath G. 
Published: August 2016

AbstractPeptide sequences from a proteome can be partitioned into N mutually exclusive sets and used to identify their parent proteins in a sequence database. This is illustrated with the human proteome (http://www.uniprot.org; id UP000005640), which is partitioned into eight subsets KZ*R, KZ*D, KZ*E, KZ*, Z*R, Z*D, Z*E, and Z*, where Z ∈ {A, N, C, Q, G, H, I, L, M, F, P, S, T, W, Y, V} and Z* ≡ 0 or more occurrences of Z. If the full peptide sequence is known then over 98% of the proteins in the proteome can be identified from such sequences. The rate exceeds 78% if the positions of four internal residue types are known. When the standard set of 20 amino acids is replaced with an alphabet of size four based on residue volume the identification rate exceeds 96%. In an information-theoretic sense this last result suggests that protein sequences effectively carry nearly the same amount of information as the exon sequences in the genome that code for them using an alphabet of size four. An appendix discusses possible in vitro methods to create peptide partitions and potential ways to sequence partitioned peptides.
Why are the fat cats still purring?
Authors: Beal Brian 
Published: August 2016

Purpose
The paper examines two different approaches adopted in the UK to regulate directors’ remuneration. The aim is to explore the approaches to understand which one better regulates directors’ pay and why. It provides an account of the approaches’ evolution, effectiveness and challenges toward the regulation of directors’ remuneration.

Design/methodology/approach
The paper reviews various corporate governance codes, their recommendations on directors’ remuneration, their effectiveness and the challenges of regulating directors’ remuneration. The paper also reviews provisions of the Companies Act 2006.

Findings
The paper finds that corporate governance adopts a better approach to regulating directors’ pay than the Companies Act 2006, because it targets the pay-setting process. However, the existence of gray areas and lack of enforcement procedure poses a challenge to its effectiveness. The Companies Act 2006 is unable to regulate directors’ pay adequately, because it adopts a corrective approach and it considers directors’ remuneration as a management responsibility.

Originality/value
The paper offers an up-to-date assessment of the two approaches to regulating directors’ pay in the UK. It highlights the challenges faced by both approaches and considers which approach could regulate directors pay better and its challenges.