bluuebunny/crossref_metadata_2025 huggingface dataset:
GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation forSaccharomyces cerevisiae
Authors: Mondeel Thierry D G A , Crémazy Frédéric , Barberis Matteo
Published: January 2018

Motivation

Multi-scale modeling of biological systems requires integration of various information about genes and proteins that are connected together in networks. Spatial, temporal and functional information is available; however, it is still a challenge to retrieve and explore this knowledge in an integrated, quick and user-friendly manner.

Results

We present GEMMER (GEnome-wide tool for Multi-scale Modeling data Extraction and Representation), a web-based data-integration tool that facilitates high quality visualization of physical, regulatory and genetic interactions between proteins/genes in Saccharomyces cerevisiae. GEMMER creates network visualizations that integrate information on function, temporal expression, localization and abundance from various existing databases. GEMMER supports modeling efforts by effortlessly gathering this information and providing convenient export options for images and their underlying data.

Availability and implementation

GEMMER is freely available at http://gemmer.barberislab.com. Source code, written in Python, JavaScript library D3js, PHP and JSON, is freely available at https://github.com/barberislab/GEMMER.

Supplementary information

Supplementary data are available at Bioinformatics online.
Verra Four-Folds, Twisted Sheaves, and the Last Involution
Authors: Camere Chiara , Kapustka Grzegorz , Kapustka Michał , Mongardi Giovanni
Published: January 2018

We study the geometry of some moduli spaces of twisted sheaves on K3 surfaces. In particular we introduce induced automorphisms from a K3 surface on moduli spaces of twisted sheaves on this K3 surface. As an application we prove the unirationality of moduli spaces of irreducible holomorphic symplectic manifolds of K3[2]-type admitting non-symplectic involutions with invariant lattices U(2) ⊕ D4(−1) or U(2) ⊕ E8(−2). This complements the results obtained in [43], [13], and the results from [29] about the geometry of irreducible holomorphic symplectic (IHS) four-folds constructed using the Hilbert scheme of (1, 1) conics on Verra four-folds. As a byproduct we find that IHS four-folds of K3[2]-type with Picard lattice U(2) ⊕ E8(−2) naturally contain non-nodal Enriques surfaces.
Smooth and Topological Almost Concordance
Authors: Nagel Matthias , Orson Patrick , Park JungHwan , Powell Mark
Published: January 2018

We investigate the disparity between smooth and topological almost concordance of knots in general 3-manifolds Y. Almost concordance is defined by considering knots in Y modulo concordance in Y × [0, 1] and the action of the concordance group of knots in S3 that ties in local knots. We prove that the trivial free homotopy class in every 3-manifold other than the 3-sphere contains an infinite family of knots, all topologically concordant, but not smoothly almost concordant to one another. Then, in every lens space and for every free homotopy class, we find a pair of topologically concordant but not smoothly almost concordant knots. Finally, as a topological counterpoint to these results, we show that in every lens space every free homotopy class contains infinitely many topological almost concordance classes.
Surgery for Glioblastoma in Light of Molecular Markers: Impact of Resection and MGMT Promoter Methylation in Newly Diagnosed IDH-1 Wild-Type Glioblastomas
Authors: Gessler Florian , Bernstock Joshua D , Braczynski Anne , Lescher Stephanie , Baumgarten Peter , Harter Patrick N , Mittelbronn Michel , Wu Tianxia , Seifert Volker , Senft Christian
Published: January 2018

BACKGROUND

Previous studies addressing the influence of surgery on the outcome of patients with glioblastomas (GBM) have not addressed molecular markers. The value of surgery versus the tumor's major biological markers remains unclear.

OBJECTIVE

We investigate the extent of resection as a prognosticator for patients with newly diagnosed primary GBM with the incorporation of molecular diagnostics as per the updated WHO 2016 diagnostic criteria for GBM.

METHODS

Patients with newly diagnosed GBM who underwent resection were prospectively included within a database. We analyzed patients with newly diagnosed GBM and excluded patients who presented with IDH1 R132H mutations. Gross total resection (GTR) was defined as complete removal of enhancing disease.

RESULTS

One hundred seventy-five patients were included within the analysis. One hundred four patients (59.4%) had GTR, 71 patients (40.6%) had subtotal or partial resection. Eighty patients (45.7%) displayed O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation, 95 patients (54.3%) showed no MGMT promoter methylation. In Cox regression analysis, MGMT promoter methylation (hazard ratio [HR] 1.55; 95% confidence interval [CI], 1.01-2.19; P = .0133) and GTR (HR 1.48; 95% CI, 1.06-2.07; P = .0206) were significantly associated with favorable progression-free survival. MGMT promoter methylation (HR 2.13; 95% CI, 1.45-3.12; P = .0001) and GTR (HR 1.81; 95% CI, 1.24-2.63; P = .002) were associated with favorable overall survival (OS). Of other risk factors analyzed, age (>60 vs ≤ 60 yr) was significantly associated with progression-free survival (HR 1.60; 95% CI, 1.14-2.24; P = .006) and OS (HR 2.19; 95% CI, 1.51-3.19; P < .0001).

CONCLUSION

GTR and MGMT promoter methylation are independent prognosticators for improved overall and progression-free survival in a homogeneous cohort of newly diagnosed patients with IDH wild-type glioblastoma.
Adalimumab for Corticosteroid and Infliximab-Resistant Immune Reconstitution Inflammatory Syndrome in the Setting of TB/HIV Coinfection
Authors: Lwin Nilar , Boyle Michael , Davis Joshua S
Published: January 2018

Corticosteroids are the mainstay of therapy for immune reconstitution inflammatory syndrome (IRIS). However, little is known about how to treat IRIS unresponsive to steroids. We report a patient with HIV-TB coinfection who was unresponsive to first prednisolone and then infliximab but whose IRIS resolved with adalimumab.
Energy-dependent intensity variation of the persistent X-ray emission of magnetars observed with Suzaku
Authors: Nakagawa Yujin , Ebisawa Ken , Enoto Teruaki
Published: January 2018

The emission mechanism of magnetars is still controversial even though various observational and theoretical studies have been made. In order to investigate mechanisms of both the persistent X-ray emission and the burst emission of the magnetars, we propose a model in which the persistent X-ray emission consists of numerous micro-bursts of various sizes. If this model is correct, root mean square (rms) intensity variations of the persistent emission would exceed the values expected from the Poisson distribution. Using Suzaku archive data of 11 magnetars (22 observations), the rms intensity variations were calculated from 0.2 keV to 70 keV. As a result, we found significant excess rms intensity variations from all 11 magnetars. We suppose that numerous micro-bursts constituting the persistent X-ray emission cause the observed variations, suggesting that the persistent X-ray emission and the burst emission have identical emission mechanisms. In addition, we found that the rms intensity variations clearly increase toward higher energy bands for four magnetars (six observations). The energy-dependent rms intensity variations imply that the soft thermal component and the hard X-ray component are emitted from different regions far apart from each other.
Pregnancy-Related Coronary Artery Dissection
Authors: Robinson Julie R.
Published: January 2018

Pregnancy-related spontaneous coronary artery dissection (P-SCAD) is a rare but life-threatening condition of the peripartum and postpartum mother. The gold standard of diagnosing P-SCAD is a left cardiac catheterization; however, this diagnostic tool may not be used early because myocardial infarction is not typically a top differential diagnosis for women and especially young pregnant women presenting with acute chest pain. Providers and registered nurses, particularly those in the prehospital setting, the emergency department, and labor and delivery units, should be aware of signs, symptoms, potential risk factors, and diagnostic results that could indicate P-SCAD and initiate early and appropriate treatment to improve maternal outcomes.
Persistent Symptoms and Objectively Measured Balance Performance Among OEF/OIF Veterans With Remote Mild Traumatic Brain Injury
Authors: Hebert Jeffrey R. , Forster Jeri E. , Stearns-Yoder Kelly A. , Penzenik Molly E. , Brenner Lisa A.
Published: January 2018

Objective:

To investigate linear relationships between dizziness, fatigue, and depression and posttraumatic stress disorder (PTSD) and objectively measured balance performance in Veterans with remote mild traumatic brain injury (mTBI).

Setting:

Academic laboratory; Veterans Affairs Medical Center.

Participants:

Thirty Veterans (28 men) who served in Iraq/Afghanistan and whose most recent mTBI was sustained more than 6 months prior to enrollment.

Design:

Cross-sectional, observational trial.

Main Measures:

The Computerized Dynamic Posturography-Sensory Organization Test (CDP-SOT) and the Community Balance and Mobility (CB&M) scale measured balance. Dizziness (Dizziness Handicap Inventory), fatigue (Modified Fatigue Impact Scale), depression-related symptoms (Beck Depression Inventory-II), and PTSD-related symptoms (PTSD Checklist 5) were also measured.

Results:

Objectively measured balance, CDP-SOT composite, was impaired (mean score of 67.9). CDP-SOT scores correlated with dizziness (r = −0.53; P = .002), fatigue (r = −0.38; P = .03), depression (r = −0.55; P = .001), and PTSD symptoms (r = −0.53; P = .002). Dizziness, time since most recent mTBI, and PTSD symptoms and depression combined explained significant variability in CDP-SOT scores (R
2 = 0.46; P = .003), as did fatigue depression and PTSD symptoms (R
2 = 0.33; P = .01).

Conclusions:

Impaired balance was identified among the cohort. Findings suggest that dizziness, fatigue, depression and PTSD, and time since most recent mTBI may influence balance performance. Additional research is needed to identify the potentially interrelated natural histories of these co-occurring symptoms.
The Interaction of Genetic Predisposition and Socioeconomic Position With Type 2 Diabetes Mellitus: Cross-Sectional and Longitudinal Analyses From the Lifelines Cohort and Biobank Study
Authors: van Zon Sander K.R. , Reijneveld Sijmen A. , van der Most Peter J. , Swertz Morris A. , Bültmann Ute , Snieder Harold
Published: January 2018

Objective

A strong genetic predisposition for type 2 diabetes mellitus (T2DM) may aggravate the negative effects of low socioeconomic position (SEP) in the etiology of the disorder. This study aimed to examine cross-sectional and longitudinal associations and interactions of a genetic risk score (GRS) and SEP with T2DM and to investigate whether clinical and behavioral risk factors can explain these associations and interactions.

Methods

We used data from 13,027 genotyped participants from the Lifelines study. The GRS was based on single-nucleotide polymorphisms genome-wide associated with T2DM and was categorized into tertiles. SEP was measured as educational level. T2DM was based on biological markers, recorded medication use, and self-reports. Cross-sectional and longitudinal associations and interactions between the GRS and SEP on T2DM were examined.

Results

The combination of a high GRS and low SEP had the strongest association with T2DM in cross-sectional (odds ratio = 3.84, 95% confidence interval = 2.28–6.46) and longitudinal analyses (hazard ratio = 2.71, 1.39–5.27), compared with a low GRS and high SEP. Interaction between a high GRS and a low SEP was observed in cross-sectional (relative excess risk due to interaction = 1.85, 0.65–3.05) but not in longitudinal analyses. Clinical and behavioral risk factors mostly explained the observed associations and interactions.

Conclusions

A high GRS combined with a low SEP provides the highest risk for T2DM. These factors also exacerbated each other's impact cross-sectionally but not longitudinally. Preventive measures should target individual and contextual factors of this high-risk group to reduce the risk of T2DM.
Cochlear Implantation in Postmeningitic Deafness
Authors: Tokat Taskin , Catli Tolgahan , Bayrak Feda , Bozkurt Ergul Basaran , Olgun Levent
Published: January 2018

Purpose:

The aim of this study is to evaluate long-term outcomes of cochlear implantation (CI) in patients with postmeningitic deafness.

Methods:

Twenty-seven patients with severe to profound hearing loss due to bacterial meningitis and received CI were the subjects of this study. Surgical findings and long-term audiological performances were evaluated. Speech perception and speech intelligibility of the implanted patients were evaluated with the categories of auditory performance–II (CAP-II) test and speech intelligibility rating (SIR) test, respectively.

Results:

Eighteen of the 27 patients had received full electrode insertion through the patent cochlear lumen. Remaining 9 patients had varying degrees of ossification throughout the cochlea and needed to be drilled to achieve partial electrode insertion. None of the patients exhibited surgical complication. Scores in both test batteries (CAP-II and SIR) were comparable between patients who received full or partial electrode insertion (P > 0.05).

Conclusion:

Cochlear implantation after postmeningitic deafness has favorable outcomes especially in long term. Although this type of inner ear pathology may require special considerations during surgery, it is a relatively safe procedure.
Three-Dimensional Printed Pediatric Airway Model Improves Novice Learners' Flexible Bronchoscopy Skills With Minimal Direct Teaching From Faculty
Authors: DeBoer Emily M. , Wagner Jennifer , Kroehl Miranda E. , Albietz Joseph , Shandas Robin , Deterding Robin R. , Rustici Matthew J.
Published: January 2018

Introduction

Training in pediatric flexible bronchoscopy (FB) is predominantly completed on patients. Early trainees are less accurate and slower than experienced bronchoscopists. This report describes the development of a three-dimensional printed airway model and describes how the model was used to teach learners basic FB skills.

Methods

Postgraduate year two (PGY2) pediatric residents completing a 1-month pediatric pulmonology rotation with minimal previous exposure to FB were randomized into a simulation trainee group (n = 18) or a control resident group (n = 9). The simulation group received four 15-minute practice sessions (3 self-directed, 1 with feedback). Participants completed a bronchoscopy assessment on the model at prestudy, poststudy, and delayed (at least 2 months after the rotation) time points. Outcomes were identification of markers located in the six lung areas and completion time.

Results

There was no difference in prestudy scores between groups. In the poststudy assessment, the simulation participants correctly identified more lung area markers (median = 6 vs 1.5, P < 0.001) and were faster (median = 102 vs 600 seconds, P < 0.001). In the delayed assessment, correct marker identification trended toward improvement in the simulation group compared with controls (median = 4 vs 2, P = 0.077).

Conclusions

With 1 hour of practice time, requiring 15 minutes of direct teaching, novice resident bronchoscopists are able to more accurately identify and visualize the five lung lobes and lingula via FB and are able to do so in less time than control residents. This anatomically accurate model could be used to train basic FB skills at a low cost compared with other models.
Targeting the SUMO pathway primes all-trans-retinoic acid-induced differentiation of non promyelocytic Acute Myeloid Leukemias
Authors: Baik Hayeon , Boulanger Mathias , Hosseini Mohsen , Kowalczyk Julie , Zaghdoudi Sonia , Salem Tamara , Sarry Jean-Emmanuel , Hicheri Yosr , Cartron Guillaume , Piechaczyk Marc , Bossis Guillaume
Published: January 2018

Differentiation therapies using All-trans-retinoic acid (ATRA) are highly efficient at treating Acute Promyelocytic Leukemia (APL), a minor subtype of Acute Myeloid Leukemias (AML). However, their efficacy, if any, is very limited in the case of non-APL AMLs. We report here that the inhibition of SUMOylation, a post-translational modification related to ubiquitinylation, restores the pro-differentiation and anti-proliferative activities of retinoids in non-APL AMLs. Controlled inhibition of SUMOylation with pharmacological inhibitors (2-D08 or anacardic acid), orviaoverexpression of SENP desumoylases, strongly enhances the ATRA-induced expression of key genes involved in differentiation, proliferation and apoptosis in non-APL AML cells. This activates ATRA-induced terminal myeloid differentiation and reduces cell proliferation and viability, including in AML cells resistant to chemotherapeutic drugs. Conversely, enhancement of SUMOylation by overexpressing the SUMO-conjugating enzyme Ubc9 dampens the expression of ATRA-responsive genes and prevents differentiation. Thus, inhibition of the SUMO pathway is a promising strategy to sensitize non-APL AML patients to retinoids and improve the treatment of this poor prognosis cancer, which has not significantly changed over the past 40 years.
Identification and comparison of individual chromosomes of threeHordeum chilenseaccessions,Hordeum vulgareandTriticum aestivumby FISH
Authors: Rey María-Dolores , Moore Graham , Martín Azahara C.
Published: January 2018

Karyotypes of three accessions ofHordeum chilense(H1, H16 and H7),Hordeum vulgareandTriticum aestivumwere characterized by physical mapping of several repetitive sequences. A total of fourteen repetitive sequences were used as probes for fluorescence in situ hybridization (FISH) with the aim of identifying inter‐ and intra-species polymorphisms. The (AG)12and 4P6 probes only produced hybridization signals in wheat, the BAC7 probe only hybridized to the centromeric region ofH. vulgare, and the pSc119.2 probe hybridized to both wheat andH. chilense, but not toH. vulgare. The remaining repetitive sequences used in this study produced a hybridization signal in all the genotypes. Probes pAs1, pTa535, pTa71, CCS1 and CRW were much conserved, showing no significant polymorphism among the genotypes studied. Probes GAA, (AAC)5, (CTA)5, HvT01 and pTa794 produced the most different hybridization pattern. We identified large polymorphisms in the three accessions ofH. chilensestudied, supporting the proposal of the existence of different groups insideH. chilensespecies. The set of probes described in this work allowed the identification of every single chromosome in all three species, providing a complete cytogenetic karyotype ofH. chilense, H. vulgareandT. aestivumchromosomes, useful in wheat and tritordeum breeding programs.
Help thine enemy: the evolution of short ranging signals
Authors: Számadó Szabolcs
Published: January 2018

The proximity risk model offers one possible explanation of honest signalling of aggressive intent in biology. This model assumes that the probability of successful attack is a function of the distance between the contestants and that this distance can be correctly estimated. This later assumption may not hold in nature where contestants have to estimate this distance under noisy conditions. Here I investigate with the help of a game theoretical model whether short-range ranging signals can be evolutionarily stable under such conditions. These signals can help the opponent to estimate the correct distance, thus they can promote honest signalling of intentions. Here I show that ranging signals that help the estimation of distance between opponents can be evolutionarily stable. However, such help only benefits those individuals who are able and willing to attack. As a result, ranging signals in themselves are an honest cue of proximity and in turn they are honest cues of aggressive intent. I give an example: “soft-song” in birds, and I discuss the predictions of the model.
When metabolism meets physiology: Harvey and Harvetta
Authors: Thiele Ines , Sahoo Swagatika , Heinken Almut , Heirendt Laurent , Aurich Maike K. , Noronha Alberto , Fleming Ronan M.T.
Published: January 2018

Precision medicine is an emerging paradigm that requires realistic, mechanistic models capturing the complexity of the human body. We present two comprehensive molecular to physiological-level, gender-specific whole-body metabolism (WBM) reconstructions, named Harvey, in recognition of William Harvey, and Harvetta. These validated, knowledge-based WBM reconstructions capture the metabolism of 20 organs, six sex organs, six blood cells, the gastrointestinal lumen, systemic blood circulation, and the blood-brain barrier. They represent 99% of the human body weight, when excluding the weight of the skeleton. Harvey and Harvetta can be parameterized based on physiological, dietary, and omics data. They correctly predict inter-organ metabolic cycles, basal metabolic rates, and energy use. We demonstrate the integration of microbiome data thereby allowing the assessment of individual-specific, organ-level modulation of host metabolism by the gut microbiota. The WBM reconstructions and the individual organ reconstructions are available underhttp://vmh.life. Harvey and Harvetta represent a pivotal step towards virtual physiological humans.
Kinetics of winter deacclimation in response to temperature determines dormancy status and explains budbreak in differentVitisspecies
Authors: Kovaleski Alisson P. , Reisch Bruce I. , Londo Jason P.
Published: January 2018

2.

Bud dormancy and cold hardiness are critical adaptations for surviving winter cold stress for temperate perennial plant species, with shifting temperature-based responses during the winter. The objective of this study was to uncover the relationship between dormancy transition (chilling requirement) and temperature on the loss of cold hardiness and budbreak. Dormant cuttings ofVitis vinifera,V. aestivalis,V. amurensis, andV. ripariawere examined to determine the relationship between chilling requirement and temperature on rate of deacclimation (kdeacc). Differential thermal analysis was used to determinekdeaccusing mean low temperature exotherms. Effect of chill was evaluated as the deacclimation potential (ψdeacc), which was the change inkdeaccdue to chill accumulation. Budbreak was also evaluated in fully chilled buds at different temperatures. Results indicate that ψdeaccvaries dependent on dormancy state, following a logarithmic response to chill accumulation. The effect of temperature onkdeaccwas exponential at low and logarithmic at high temperatures. The combination of ψdeaccandkdeaccresulted in good prediction of deacclimation. Budbreak phenology was also explained by differences inkdeacc. Deacclimation rates can be used as a quantitative determinant of dormancy transition and budbreak, and to refine models predicting effects of climate change.
Social rewards: the basis for collaboration in honor cultures
Authors: Ramirez-Marin Jimena Yolanda , Shafa Saïd
Published: January 2018

Purpose

The purpose of this paper is twofold: first, to define social rewards, as acts and expressions which specifically signal respect, courtesy and benevolence to the other party, based on cultural scripts found in honor cultures. Second, to explore whether social rewards mitigate competitive aspirations and foster collaboration in competitive settings, with honor values being a culturally relevant mechanism for this effect.

Design/methodology/approach

This paper reports on two experiments assessing high-honor and low-honor culture participants’ aspirations and behavioral decisions. In study 1, participants described a personal situation where they were praised by close others (social reward) or praised themselves (control condition), before responding to a buyer/seller negotiation scenario. In study 2, participants were either complimented (social reward) or not complimented (control condition), before engaging in live competition with a confederate for monetary outcomes.

Findings

Both studies indicate that social rewards diminish competitive aspirations and offers among high-honor culture participants, but not among low-honor culture participants. Results of study 1 indicate that endorsement of honor values mediates this effect. In conclusion, social rewards can improve interactions with members of honor cultures.

Research limitations/implications

These studies advance our understanding of cultural differences in negotiations and provide insight into social rewards as one of the mechanisms necessary to successfully manage intercultural negotiations and collaboration. Future research should address the effect of social rewards on self-worth and empowerment.

Originality/value

This research is the first to shed light on the relevance and importance of social rewards as a device to facilitate social interactions in honor cultures.
A novel bearing-assisted TDOA-GROA approach for passive source localization
Authors: Luo Ji-An , Tan Zhi-Wen , Peng Dong-Liang
Published: January 2018

Purpose

The passive source localization (PSL) problem using angles of arrival (AOA), time differences of arrival (TDOA) or gain ratios of arrival (GROA) is generally nonlinear and nontrival. In this research, the purpose of this paper is to design an accurate hybrid source localization approach to solve the PSL problem. The inspiration is drawn from the fact that the bearings, TDOAs and GROAs are complementary in terms of their geometry properties.

Design/methodology/approach

The maximum-likelihood (ML) method is reexamined by using hybrid measurements. Being assisted by the bearings, a new hybrid weighted least-squares (WLS) method is then proposed by jointly utilizing the bearing, TDOA and GROA measurements.

Findings

Theoretical performance analysis illustrates that the mean-square error of the ML or WLS method can attain the Cramér-Rao lower bound for Gaussian noise over small error region. However, the WLS method has much lower computational complexity than the ML algorithm. Compared with the AOA-only, TDOA-only, AOA-TDOA, TDOA-GROA methods, the localization accuracy can be greatly improved by combining the AOAs, TDOAs and GROAs, especially for some specific geometries.

Originality/value

A novel bearing-assisted TDOA-GROA method is proposed for source localization, and a new hybrid WLS estimator is presented inspired from the fact that the bearings, TDOAs and GROAs are complementary in terms of their geometry properties.
Value-at-risk and related measures for the Bitcoin
Authors: Stavroyiannis Stavros
Published: January 2018

Purpose

The purpose of this paper is to examine the value-at-risk and related measures for the Bitcoin and to compare the findings with Standard and Poor’s SP500 Index, and the gold spot price time series.

Design/methodology/approach

A GJR-GARCH model has been implemented, in which the residuals follow the standardized Pearson type-IV distribution. A large variety of value-at-risk measures and backtesting criteria are implemented.

Findings

Bitcoin is a highly volatile currency violating the value-at-risk measures more than the other assets. With respect to the Basel Committee on Banking Supervision Accords, a Bitcoin investor is subjected to higher capital requirements and capital allocation ratio.

Practical implications

The risk of an investor holding Bitcoins is measured and quantified via the regulatory framework practices.

Originality/value

This paper is the first comprehensive approach to the risk properties of Bitcoin.
Prolonging network lifetime and optimizing energy consumption using swarm optimization in mobile wireless sensor networks
Authors: M. Sangeetha , A. Sabari
Published: January 2018

Purpose

This paper aims to provide prolonging network lifetime and optimizing energy consumption in mobile wireless sensor networks (MWSNs). Forming clusters of mobile nodes is a great task owing to their dynamic nature. Such clustering has to be performed with a higher consumption of energy. Perhaps sensor nodes might be supplied with batteries that cannot be recharged or replaced while in the field of operation. One optimistic approach to handle the issue of energy consumption is an efficient way of cluster organization using the particle swarm optimization (PSO) technique.

Design/methodology/approach

In this paper two improved versions of centralized PSO, namely, unequal clustering PSO (UC-PSO) and hybrid K-means clustering PSO (KC-PSO), are proposed, with a focus of achieving various aspects of clustering parameters such as energy consumption, network lifetime and packet delivery ratio to achieve energy-efficient and reliable communication in MWSNs.

Findings

Theoretical analysis and simulation results show that improved PSO algorithms provide a balanced energy consumption among the cluster heads and increase the network lifetime effectively.

Research limitations/implications

In this work, each sensor node transmits and receives packets at same energy level only. In this work, focus was on centralized clustering only.

Practical implications

To validate the proposed swarm optimization algorithm, a simulation-based performance analysis has been carried out using NS-2. In each scenario, a given number of sensors are randomly deployed and performed in a monitored area. In this work, simulations were carried out in a 100 × 100 m2 network consisting 200 nodes by using a network simulator under various parameters. The coordinate of base station is assumed to be 50 × 175. The energy consumption due to communication is calculated using the first-order radio model. It is considered that all nodes have batteries with initial energy of 2 J, and the sensing range is fixed at 20 m. The transmission range of each node is up to 25 m and node mobility is set to 10 m/s.

Practical implications

This proposed work utilizes the swarm behaviors and targets the improvement of mobile nodes’ lifetime and energy consumption.

Originality/value

PSO algorithms have been implemented for dynamic sensor nodes, which optimize the clustering and CH selection in MWSNs. A new fitness function is evaluated to improve the network lifetime, energy consumption, cluster formation, packet transmissions and cluster head selection.
Density regulation in Northeast Atlantic fish populations: Density dependence is stronger in recruitment than in somatic growth
Authors: Zimmermann Fabian , Ricard Daniel , Heino Mikko
Published: January 2018

Population regulation is a central concept in ecology, yet in many cases its presence and the underlying mechanisms are difficult to demonstrate. The current paradigm maintains that marine fish populations are predominantly regulated by density‐dependent recruitment.

While it is known that density‐dependent somatic growth can be present too, its general importance remains unknown and most practical applications neglect it. This study aimed to close this gap by for the first time quantifying and comparing density dependence in growth and recruitment over a large set of fish populations.

We fitted density‐dependent models to time‐series data on population size, recruitment and age‐specific weight from commercially exploited fish populations in the Northeast Atlantic Ocean and the Baltic Sea. Data were standardized to enable a direct comparison within and among populations, and estimated parameters were used to quantify the impact of density regulation on population biomass.

Statistically significant density dependence in recruitment was detected in a large proportion of populations (70%), whereas for density dependence in somatic growth the prevalence of density dependence depended heavily on the method (26% and 69%). Despite age‐dependent variability, the density dependence in recruitment was consistently stronger among age groups and between alternative approaches that use weight‐at‐age or weight increments to assess growth. Estimates of density‐dependent reduction in biomass underlined these results: 97% of populations with statistically significant parameters for growth and recruitment showed a larger impact of density‐dependent recruitment on population biomass.

The results reaffirm the importance of density‐dependent recruitment in marine fishes, yet they also show that density dependence in somatic growth is not uncommon. Furthermore, the results are important from an applied perspective because density dependence in somatic growth affects productivity and catch composition, and therefore the benefits of maintaining fish populations at specific densities.
Use of atropine in four‐dimensional hysterosalpingo‐contrast sonography: Does it suppress pain during infertility examination?
Authors: Ma Yunfei , Du Lianfang , Li Fan , Zhu Zhengqiu
Published: January 2018

This study aimed to ascertain if atropine is useful for suppressing the pain suffered during four‐dimensional hysterosalpingo‐contrast sonography (4D‐HyCoSy) when assessing infertility in women. A total of 252 patients were divided into 2 groups to receive or not receive atropine (0.5 mg) injection 30 minutes before 4D‐HyCoSy. Pain was evaluated using a numerical rating scale (NRS): during 4D‐HyCoSy; upon 2‐dimensional transvaginal sonography; before catheter insertion; upon insertion and fixation of the catheter into the uterine cavity; 30 minutes after 4D‐HyCoSy. According to the degree of patency of Fallopian tubes, the 6 patterns observed were integrated further into 3 patient groups: all‐negative (both Fallopian tubes were negative), positive‐and‐negative (one Fallopian tube showed patency and the other showed stenosis or non‐patency), and all‐positive (both Fallopian tubes showed stenosis or non‐patency). We compared the NRS scores and prevalence of side‐effects other than pain between the atropine‐injection and non‐atropine‐injection groups within the three groups mentioned above. The NRS score showed no significant differences among the groups at any time point (all P > .05). The different prevalence of side‐effects other than pain was significant between the atropine‐injection and atropine‐non‐injection groups (P = .012). These data suggest that atropine does not reduce pain in patients during 4D‐HyCoSy. However, atropine may reduce the prevalence of other side‐effects during 4D‐HyCoSy, which needs a further, large, prospective, multi‐cohort study to verify.
A Comparison of Care Delivered in Hospital‐based and Freestanding Emergency Departments
Authors: Pines Jesse M. , Zocchi Mark S. , Black Bernard S.
Published: January 2018

Objective

We compare case mix, hospitalization rates, length of stay (LOS), and resource use in independent freestanding emergency departments (FSEDs) and hospital‐based emergency departments (H‐EDs).

Methods

Data from 74 FSEDs (2013–2015) in Texas and Colorado were compared to H‐ED data from the 2013–2014 National Hospital Ambulatory Medical Care Survey. In the unrestricted sample, large differences in visit characteristics (e.g., payer and case mix) were found between patients that use FSEDs compared to H‐EDs. Therefore, we restricted our analysis to patients commonly treated in both settings (<65 years, privately insured, nonambulance) and used inverse propensity score weighting (IPW) to balance the two settings on observable patient characteristics. We then compared ED LOS and as well as hospital admission rates and resource utilization rates in the IPW‐weighted samples.

Results

Before balancing, FSEDs saw more young adults (age 25–44) and fewer older adults (age 45–64) than H‐EDs. FSED patients had fewer comorbidities, more injuries and respiratory infections, and fewer diagnoses of chest or abdominal pain. In balanced samples, LOS for FSED visits was 46% shorter (60 minutes) than H‐ED patients. Hospital admission rates were 37% lower overall (95% confidence interval = –51% to –23%) in FSEDs and varied considerably by primary discharge diagnosis. X‐ray and electrocardiogram use was significantly lower at FSEDs while others measures of resource utilization were similar (ultrasound, computed tomography scans, and laboratory tests).

Conclusion

In this sample of FSEDs, a greater proportion of younger patients with fewer comorbidities and more injuries and respiratory system diseases were evaluated, and almost all patients had private health insurance. When restricted to < 65 years, privately insured, and nonambulance patients in both samples, LOS was considerably shorter and hospital admission rates lower at FSEDs, as well as the use of some diagnostic testing. This study is limited as diagnoses codes may not fully capture severity and patients who perceived greater need of hospital admission may have chosen a H‐ED over FSEDs.
Impaired sperm function in infertile men relies on the membrane sterol pattern
Authors: Garolla A. , Šabović I. , Tescari S. , De Toni L. , Menegazzo M. , Cosci I. , De Filippis V. , Giarola M. , Foresta C.
Published: January 2018

Membrane cholesterol removal appears a key step for the gain of fertility potential during sperm maturation. However, the membrane sterol pattern in sperm cells from infertile patients, with impaired sperm parameters, has been poorly investigated. To elucidate a causative link between sperm membrane composition in male fertility, here we have investigated the levels of cholesterol and its oxidized derivatives 7β‐hydroxycholesterol and 7‐keto‐cholesterol in sixteen infertile patients with oligo‐asthenozoospermia and 16 normozoospermic (N) fertile subjects. Furthermore, ten of 16 N fertile subjects agreed to receive a defined testicular thermal challenge by adhering to a programme of sauna sessions for 1 month. Semen samples were obtained from each of the participants, and sperm parameters were assessed according to the World Health Organization criteria. Sperm levels of cholesterol, 7β‐hydroxycholesterol and 7‐keto‐cholesterol were quantified by ultra‐pressure liquid chromatography mass spectrometry. The results showed that oligo‐asthenozoospermia patients had a huge amount of cholesterol content compared with fertile subjects (12.40 ± 6.05 μg/106 cells vs. 0.45 ± 0.28 μg/106 cells, p < 0.001, N and oligo‐asthenozoospermia, respectively). Also, oxidized derivatives were significantly higher in oligo‐asthenozoospermia patients (7β‐hydroxycholesterol: 1.96 ± 1.03 ng/106 cells vs. 0.075 ± 0.05 ng/106 cells, p < 0.001 and 7‐keto‐cholesterol: 1.11 ± 0.72 ng/106 cells vs. 0.005 ± 0.003 ng/106 cells, p < 0.001). Moreover, sauna exposure, in parallel with a progressive worsening of sperm motility parameters, was associated with a reversible increase in sperm cholesterol after the third and fourth week of treatment, whilst 7β‐hydroxycholesterol and 7‐keto‐cholesterol levels showed an earlier enhancement starting from the second week. Our data show for the first time in humans a strong difference in the cholesterol and its oxidized derivatives of infertile and fertile subjects. These findings suggest a strict biochemical link relating testis function, sperm membrane status and male fertility potential.
Deregulation of microRNA‐155 and its transcription factor NF‐kB by polychlorinated biphenyls during viral infections
Authors: Waugh Courtney A. , Arukwe Augustine , Jaspers Veerle L. B.
Published: January 2018

Polychlorinated biphenyls (PCBs), and similar environmental contaminants, have been linked to virus outbreaks and increased viral induced mortality since the 1970s. Yet the mechanisms behind this increased susceptibility remain elusive. It has recently been illustrated that the innate immune viral detection system is tightly regulated by small non‐coding RNAs, including microRNAs (miRNAs). For virus infections miRNA‐155 expression is an important host response against infection, and deregulation of this miRNA is closely associated with adverse outcomes. Thus, we designed a targeted in vitro study using primary chicken fibroblasts, first exposed to a mixture of PCBs (Arochlor‐1250) before being stimulated with a synthetic RNA virus (poly I:C), to determine if PCBs have the potential to deregulate miRNA‐155. In this paper, we provide the first data for the deregulation of miRNA‐155 when a host is exposed to a mixture of PCBs before a virus infection. Thus, we provide important evidence that PCBs can be involved in the deregulation of important miRNA pathways involved in the immune system; thereby demonstrating novel insights into the mechanism of PCB toxicity on the immune system.
Categorization of fetal external findings in developmental toxicology studies by the Terminology Committee of the Japanese Teratology Society
Authors: Izumi Yuko , Ooshima Yojiro , Chihara Kazuhiro , Fujiwara Michio , Katsumata Yoshihiro , Shiota Kohei
Published: January 2018

Categorization of fetal external findings in common laboratory animals, intended to make the agreement at Berlin Workshop in 2014 more practical, was proposed by the Terminology Committee of the Japanese Teratology Society at the Workshop in the 55th Japanese Teratology Society Annual Meeting in 2015. In the Workshop, 73 external findings, which had been categorized as “Gray zone” anomalies but not as “Malformation” or “Variation” in the 2014 Berlin Workshop, were discussed and classified as Malformation, “Non‐structural abnormality,” Variation, and “Not applicable.” The proposal was based on the results of a survey conducted in 2014, where 20 facilities (including pharmaceutical, chemical, and pesticide companies and contract laboratories) and 2 selected expert teratologists in Japan were asked for their opinions on the categorization of these findings. Based on the discussion, Japanese Teratology Society members have agreed that 42 out of the 73 findings can be classified as Malformations (38), Non‐structural abnormalities (3), Malformations/Non‐structural abnormalities (1), and Variations (0), while the remaining 31 findings were recommended to be categorized as Not applicable for fetuses. The details of the classification are shown on the website of the Japanese Teratology Society (http://www.umin.ac.jp/cadb/External.pdf).
Evaluation of primary stability in modified implants: Analysis by resonance frequency and insertion torque
Authors: Sciasci Plínio , Casalle Nicole , Vaz Luís Geraldo
Published: January 2018

Background

Changes in the macrogeometry of dental implants are known to influence primary stability and the osseointegration process.

Purpose

The purpose of the present in vitro study was to evaluate the mechanical behavior of geometric changes in the apex region of dental implants.

Methods

Thirty‐five cylindrical dental implants (Titamax Ti; Neodent) were machined at the apical third to reproduce the experimental groups: without apical cut (Wc), apical bi‐split cut, apical tri‐split cut, apical quadri‐split cut (Qs). One (control group) (Titamax Ti Ex) (n = 7) without any modifications was added. The implants had the same final dimensions (4.1 x 11 mm2). All implants were inserted into artificial bone blocks and were evaluated by insertion torque and resonance frequency by ISQ values (Osstell). Two‐tailed analysis of variance (One‐way ANOVA) and Tukey's post‐test (P < .05).

Results

Control and Qs implants showed a significant increase of the insertion torque (P < .001). For the resonance frequency, Wc and (control) implants had the greatest ISQ values. However, there's no significant difference between (control) and Qs for the ISQ values (P < .001).

Conclusion

Within the limitations of the present study, the proposed geometries at the apical third of dental implants greatly influenced its insertion torque and primary stability in vitro.
When conservation goes viral: The diffusion of innovative biodiversity conservation policies and practices
Authors: Mascia Michael B. , Mills Morena
Published: January 2018

Despite billions of dollars invested, “getting to scale” remains a fundamental challenge for conservation donors and practitioners. Occasionally, however, a conservation intervention will “go viral,” with rapid, widespread adoption that transforms the relationship between people and nature across large areas. The factors that shape rates and patterns of conservation interventions remain unclear, puzzling scientists and hindering evidence‐based policymaking. Diffusion of innovation theory—the study of the how and why innovations are adopted, and the rates and patterns of adoption—provides a novel lens for examining rates and patterns in the establishment of conservation interventions. Case studies from Tanzania and the Pacific illustrate that characteristics of the innovation, of the adopters, and of the social‐ecological context shape spatial and temporal dynamics in the diffusion of community‐centered conservation interventions. Differential trends in adoption mirrored the relative advantage of interventions to local villagers and villager access to external technical assistance. Theories of innovation diffusion highlight new arenas for conservation research and provide critical insights for conservation policy and practice, suggesting the potential to empower donors and practitioners with the ability to catalyze conservation at scale—and to do so at less cost and with longer‐lasting impacts.
Kidney allograft subclinical rejection modulates systemic inflammation measured by C‐reactive protein at 1 year after transplantation
Authors: García‐Carro Clara , Dörje Christina , Åsberg Anders , Midtvedt Karsten , Scott Helge , Reinholt Finn P. , Holdaas Hallvard , Reisæter Anna V. , Seron Daniel
Published: January 2018

Kidney allograft inflammation is associated with proinflammatory modifications of peripheral blood mononuclear cells, suggesting that renal inflammation contributes to systemic inflammation. Thus, the aim of this study was to evaluate the relationship between subclinical inflammation in surveillance biopsies performed at 1 year and systemic inflammation assessed by C‐reactive protein (CRP) levels at the time of biopsy. We analyzed 544 surveillance biopsies performed at 1 year that were classified as normal (n = 368), borderline (n = 148), or subclinical rejection (SCR) (n = 28). CRP levels were divided into quartiles. Patients in 1st, 2nd, and 3rd quartile were classified as low CRP (n = 408) and patients in the 4th quartile as high CRP (n = 136). Univariate analysis showed that the proportion of patients with SCR was higher in the high CRP group (10.3% vs 3.4%, P = 0.0067). Multivariate analysis showed that independent predictors of high CRP were body mass index (odds ratio [OR] 1.072 and 95% confidence interval [CI] 1.027‐1.119), a positive urine culture at the day of the biopsy (OR 2.760 and 95% CI 1.205‐6.323), and the presence of SCR at 1‐year surveillance biopsy (OR 7.260 and 95% CI 3.530‐14.935). In summary, we describe that subclinical acute rejection constitutes an independent predictor of systemic inflammation as measured by CRP.