bluuebunny/crossref_metadata_2025 huggingface dataset:
Individualised dietary strategies for Olympic combat sports: Acute weight loss, recovery and competition nutrition
Authors: Reale Reid , Slater Gary , Burke Louise M.
Published: March 2017

Olympic combat sports separate athletes into weight divisions, in an attempt to reduce size, strength, range and/or leverage disparities between competitors. Official weigh‐ins are conducted anywhere from 3 and up to 24 h prior to competition ensuring athletes meet weight requirements (i.e. have ‘made weight’). Fighters commonly aim to compete in weight divisions lower than their day‐to‐day weight, achieved via chronic and acute manipulations of body mass (BM). Although these manipulations may impair health and absolute performance, their strategic use can improve competitive success. Key considerations are the acute manipulations around weigh‐in, which differ in importance, magnitude and methods depending on the requirements of the individual combat sport and the weigh‐in regulations. In particular, the time available for recovery following weigh‐in/before competition will determine what degree of acute BM loss can be implemented and reversed. Increased exercise and restricted food and fluid intake are undertaken to decrease body water and gut contents reducing BM. When taken to the extreme, severe weight‐making practices can be hazardous, and efforts have been made to reduce their prevalence. Indeed some have called for the abolition of these practices altogether. In lieu of adequate strategies to achieve this, and the pragmatic recognition of the likely continuation of these practices as long as regulations allow, this review summarises guidelines for athletes and coaches for manipulating BM and optimising post weigh‐in recovery, to achieve better health and performance outcomes across the different Olympic combat sports.
Acute kinematic and kinetic adaptations to wearable resistance during vertical jumping
Authors: Macadam Paul , Simperingham Kim D. , Cronin John B. , Couture Grace , Evison Chloe
Published: March 2017

One variation of vertical jump (VJ) training is resisted or weighted jump training, where wearable resistance (WR) enables jumping to be overloaded in a movement specific manner. A two‐way analysis of variance with Bonferroni post hoc contrasts was used to determine the acute changes in VJ performance with differing load magnitudes and load placements. Kinematic and kinetic data were quantified using a force plate and contact mat. Twenty sport active subjects (age: 27.8 ± 3.8 years; body mass (BM): 70.2 ± 12.2 kg; height: 1.74 ± 0.78 m) volunteered to participate in the study. Subjects performed the counter movement jump (CMJ), drop jump (DJ) and pogo jump (PJ) wearing no resistance, 3% or 6% BM affixed to the upper or lower body. The main finding in terms of the landing phase was that the effect of WR was non‐significant (P > .05) on peak ground reaction force. With regard to the propulsive phase the main findings were that for both the CMJ and DJ, WR resulted in a significant (P < .05) decrease in jump height (CMJ: −12% to −17%, DJ: −10% to −14%); relative peak power (CMJ: −8% to −17%, DJ: −7% to −10%); and peak velocity (CMJ: −4% to −7%, DJ: −3% to −8%); while PJ reactive strength index was significantly reduced (−15% to −21%) with all WR conditions. Consideration should be given to the inclusion of WR in sports where VJ's are important components as it may provide a novel movement specific training stimulus.

Highlights

WR of 3 or 6 % BM provided a means to overload the subjects in this study resulting in decreased propulsive power and velocity that lead to a reduced jump height and landing force.

Specific strength exercises that closely mimic sporting performance are more likely to optimise transference, therefore WR with light loads of 3–6% body mass (BM)appear a suitable tool for movement specific overload training and maximising transference to sporting performance.

Practitioners can safely load their athletes with upper or lower body WR of 3–6% BM without fear of overloading the athletesover and above the landing forces they are typically accustomed too.

As a training stimulus it would seem the WR loading provides adequate overload and athletes should focus on velocity of movement to improve power output and jump height i.e. take‐off velocity.
The effects of an increased calorie breakfast consumed prior to simulated match‐play in Academy soccer players
Authors: Briggs Marc A. , Harper Liam D. , McNamee Ged , Cockburn Emma , Rumbold Penny L.S. , Stevenson Emma J. , Russell Mark
Published: March 2017

Dietary analysis of Academy soccer players highlights that total energy and carbohydrate intakes are less than optimal, especially, on match‐days. As UK Academy matches predominantly kick‐off at ∼11:00 h, breakfast is likely the last pre‐exercise meal and thus may provide an intervention opportunity on match‐day. Accordingly, the physiological and performance effects of an increased calorie breakfast consumed ∼135‐min before soccer‐specific exercise was investigated. English Premier League Academy soccer players (n = 7) repeated a 90‐min soccer match simulation on two occasions after consumption of habitual (Bhab; ∼1100 kJ) or increased (Binc; ∼2100 kJ) energy breakfasts standardised for macronutrient contributions (∼60% carbohydrates, ∼15% proteins and ∼25% fats). Countermovement jump height, sprint velocities (15‐m and 30‐m), 30‐m repeated sprint maintenance, gut fullness, abdominal discomfort and soccer dribbling performances were measured. Blood samples were taken at rest, pre‐exercise, half‐time and every 15‐min during exercise. Although dribbling precision (P = .522; 29.9 ± 5.5 cm) and success (P = .505; 94 ± 8%) were unchanged throughout all time‐points, mean dribbling speed was faster (4.3 ± 5.7%) in Binc relative to Bhab (P = .023; 2.84 vs 2.75 m s−1). Greater feelings of gut fullness (67 ± 17%, P = .001) were observed in Binc without changes in abdominal discomfort (P = .595). All other physical performance measures and blood lactate and glucose concentrations were comparable between trials (all P > .05). Findings demonstrate that Academy soccer players were able to increase pre‐match energy intake without experiencing abdominal discomfort; thus, likely contributing to the amelioration of energy deficits on match‐days. Furthermore, whilst Binc produced limited benefits to physical performance, increased dribbling speed was identified, which may be of benefit to match‐play.
Open public data (OPD) and the Gulf Cooperation Council (GCC): challenges and prospects
Authors: Saxena Stuti
Published: March 2017

This paper seeks to assess the nature and scope of open data in government (OPD/open public data) in the Gulf Cooperation Council (GCC) countries of Bahrain, Kuwait, Qatar, Oman, Saudi Arabia and the United Arab Emirates (UAE). Following a qualitative approach, OPD portals of GCC countries are being studied besides seeking inputs from secondary data sources which are relevant in providing theoretical understanding of OPD. The paper shows that OPD in the GCC countries is in its nascent stage and little academic interest has been shown in this area. Future research should highlight the prospects of OPD implementation in the GCC countries given their strategic importance for many reasons. To ascertain that the OPD implementation gathers pace in the GCC countries, governments need to make more robust strategies in terms of physical and research infrastructure for better data analytics and utility. Hitherto, there has been no study covering the significance and implications of OPD in a GCC context; this is the first study to undertake this as its research theme. Furthermore, academic research on OPD in the GCC countries is lacking; the present study seeks to fill this gap.
Chlamydia preserves the mitochondrial network necessary for replication via microRNA-dependent inhibition of fission
Authors: Chowdhury Suvagata Roy , Reimer Anastasija , Sharan Malvika , Kozjak-Pavlovic Vera , Eulalio Ana , Prusty Bhupesh K. , Fraunholz Martin , Karunakaran Karthika , Rudel Thomas
Published: March 2017

Obligate intracellular bacteria such as Chlamydia trachomatis depend on metabolites of the host cell and thus protect their sole replication niche by interfering with the host cells’ stress response. Here, we investigated the involvement of host microRNAs (miRNAs) in maintaining the viability of C. trachomatis–infected primary human cells. We identified miR-30c-5p as a prominently up-regulated miRNA required for the stable down-regulation of p53, a major suppressor of metabolite supply in C. trachomatis–infected cells. Loss of miR-30c-5p led to the up-regulation of Drp1, a mitochondrial fission regulator and a target gene of p53, which, in turn, severely affected chlamydial growth and had a marked effect on the mitochondrial network. Drp1-induced mitochondrial fragmentation prevented replication of C. trachomatis even in p53-deficient cells. Additionally, Chlamydia maintain mitochondrial integrity during reactive oxygen species–induced stress that occurs naturally during infection. We show that C. trachomatis require mitochondrial ATP for normal development and hence postulate that they preserve mitochondrial integrity through a miR-30c-5p–dependent inhibition of Drp1-mediated mitochondrial fission.
Fluorescein-Guided Neuroendoscopy for Intraventricular Lesions: A Case Series
Authors: Fiorindi Alessandro , Boaro Alessandro , Del Moro Giulia , Longatti Pierluigi
Published: March 2017

BACKGROUND: The benefits of neuroendoscopy in the pathological diagnosis of intra- and paraventricular tumors have already been shown in many neurosurgical studies. However, most authors agree that neuroendoscopic biopsies are not infrequently inconclusive due to small or inadequate samples, prompting the need for new diagnostic strategies.

OBJECTIVE: To describe a technique not previously reported in the literature, combining neuroendoscopy with angiofluorescein guidance for the pathological diagnosis of intra- and paraventricular tumors.

METHODS: The 4-mm steerable fiberscope used was equipped with dual observation modes for white light and fluorescein. Access was by the classical precoronal burr hole. After inspecting the ventricular system in white light, a 10-mg/kg dose of fluorescein sodium (FS) was administered intravenously to the patient. The endoscope was then switched to the blue light fluorescent mode to better localize the pathological tissue. The protocol had been submitted to the local ethics committee.

RESULTS: From September 2011 to March 2015, 9 consecutive patients (aged 1-56 yr) harboring intra- and paraventricular lesions prospectively underwent angiofluorescein-guided endoscopy. In all cases, a pathological diagnosis was obtained without complications. In 5 patients, an endoscopic third ventriculostomy, and, in 1 patient, a septostomy was performed during the same procedure. Fluorescein guidance definitely modified our site of biopsy in 4 cases.

CONCLUSION: In our experience, FS has proven to be a strong enhancer of all ventricular lesions presenting with a disrupted blood–brain barrier, including inflammatory processes. Fluorescein-guided neuroendoscopy appears to be a safe, economic method to improve diagnostic potential in ventricular lesions.
First Report of Tomato chlorotic spot virus in the Non-Solanaceous Weeds Erect Spiderling (Boerhavia erecta), Asian Spiderflower (Cleome viscosa), and Sweet Chili Pepper (Capsicum chinense) in Puerto Rico
Authors: Estévez de Jensen Consuelo , Badillo-Vargas Ismael E. , Frantz Galen , Mellinger H. Charles , Turechek William W. , Hutton Samuel F. , Funderburk Joseph E. , Naidu Rayapati A. , Adkins Scott
Published: March 2017

Tomato chlorotic spot virus (TCSV) has recently been detected in tomato, bell pepper, jimsonweed, and lettuce in Puerto Rico. Observations of weeds and additional crops in 2015 and 2016 revealed TCSV-like symptoms. Testing of these symptomatic plants identified three new hosts of TCSV in Puerto Rico: erect spiderling (Boerhavia erecta); Asian spiderflower (Cleome viscosa); and sweet chili pepper (Capsicum chinense).
Patient Use of the Electronic Communication Portal in Management of Type 2 Diabetes
Authors: Peremislov Diana
Published: March 2017

High incidence and prevalence of type 2 diabetes require urgent attention to the management of this chronic disease. The purpose of this study was to explore electronic communication (e-communication) between patients with type 2 diabetes and their providers within the patient portal. Qualitative design with conventional content analysis techniques was used. A purposive random sample of 90 electronic medical record charts of patient-portal users with type 2 diabetes was subjected to a retrospective review. The sample mainly consisted of patients between the ages of 50 and 70 years, who were white, non-Hispanic, and English-speaking. The three major themes that emerged in e-communication via patient portal were inform theme, which was the most frequently identified theme; instruct/request theme, which was mainly used in initiation of e-communication; and the question theme. The patient portal was used primarily for requests by patients and instruction by providers, showing relatively short e-message encounters with a high number of partially completed encounters, frequent lack of resolution, and a low level of involvement of diabetes specialists in e-communication. There is a need to revise healthcare system guidelines on initiation and use of e-communication via patient portal and develop standardized templates to promote diabetes education in type 2 diabetes.
MSH6, Past and Present and Muir–Torre Syndrome—Connecting the Dots
Authors: Mahalingam Meera
Published: March 2017

Sebaceous neoplasms such as adenoma, sebaceoma, and carcinoma, although sporadic in their occurrence, are clinically significant because of their association with Muir–Torre syndrome (MTS). MTS is a rare autosomal dominant genodermatosis characterized by the occurrence of sebaceous neoplasms and/or keratoacanthomas and visceral malignancies. MTS is usually the result of germline mutations in the DNA mismatch repair genes MSH2 and, albeit less commonly, MLH1. Although less know, MSH6 is yet another key player. Evidence from Lynch syndrome indicates that pathogenic germline mutations in MSH6 are typically microsatellite stable and have a clinical presentation that differs from that associated with germline mutations in MSH2 and/or MLH1. Given this unique mutator phenotype of MSH6, the primary aim of this review was to underscore the clinical manifestations associated with pathogenic mutations in MSH6 in patients with MTS. As the current clinical and laboratory work-up of MTS is geared toward patients harboring a germline mutation in MSH2 and/or MLH1, an additional aim was to provide a scaffolding for the work-up of a patient presenting with an isolated germline mutation in MSH6.
Squared-Off Nuclei and “Appliqué” Pattern as a Histopathological Clue to Periocular Sebaceous Carcinoma: A Clinicopathological Study of 50 Neoplasms From 46 Patients
Authors: Broekaert Sigrid M. C. , Flux Katharina , Kyrpychova Liubov , Kacerovska Denisa , Ivan Doina , Schön Michael P. , Ströbel Philipp , Michal Michal , Denisjuk Natalja , Kerl Katrin , Kazakov Dmitry V.
Published: March 2017

The histopathological diagnosis of periocular sebaceous carcinoma can be difficult in poorly differentiated cases showing few mature sebocytes. The authors examined 50 periocular sebaceous carcinomas from 46 patients to determine the frequency of 2 features seen in this neoplasm, namely cells with squared-off nuclei and so-called “appliqué” pattern (peritumoral subnecrosis of peripherally located neoplastic cells). Neoplastic cells with squared-off nuclei were found in varying numbers in both the intraepithelial and dermal (invasive) components in all neoplasms, whereas the appliqué pattern was observed in a third of the cases. It is concluded that these features, taken together, may serve as a clue for the diagnosis of periocular sebaceous carcinoma.
Supporting a Youth with Cerebellar Ataxia into Adolescence
Authors: Meneses Veronica , Gonzalez-Castillo Zurisadai , Edgar Veronica B. , Augustyn Marilyn
Published: March 2017

CASE:

Zoe, a 13-year-old white girl, presents as a new patient to your pediatric clinic with complaints of frequent emesis, anxiety, and learning problems, and previous diagnosis of cerebellar ataxia. Parents accompany Zoe and state, “it is really hard for her to go out, she gets sick and falls easily.” She was born full term by vaginal delivery without complications. Given globally delayed milestones, she received early intervention services. Feeding problems began at infancy, including gastroesophageal reflux and aspiration pneumonia.

At age 2, Zoe saw a neurologist and brain MRI revealed cerebellar atrophy. She recently saw a geneticist and genetic studies are pending. Parents report receiving “little” information regarding prognosis; through their own research, they read about individuals having similar symptoms in adulthood, with a degenerative pattern. They worry that Zoe is “still very young and we do not know what her future will be like.”

Despite ongoing speech and feeding challenges, the parents report difficulty finding a speech and language therapist in their area. Zoe does see an otolaryngologist for frequent otitis media and hearing loss and an ophthalmologist for vision problems. Still, she continues to fall further behind in school. Furthermore, she is intensely afraid of falling at school and has few friends, resulting in the family being at a loss regarding “what to do about school.”

She lives with both parents and 2 healthy older sisters. Her mother has Crohn's disease and has been unable to work. Her maternal aunt is close to Zoe and has hypothyroidism. Her father works as an insurance agent and resources have been “tight.” Zoe's mother describes “making” Zoe go out to the movies, “otherwise she just stays home.” Zoe usually needs assistance to walk in public, to keep from stumbling. Parents share that simply being in a public place or meeting a new physician may trigger emesis. Zoe does enjoy interacting with neighborhood children and says she wants to be “normal,” wear nail polish, and date. She seeks independence, often refusing to use her wheelchair. Parents feel she requires more intensive occupational and physical therapy.

On examination, she is very slender with hypertelorism and nystagmus. Holding an emesis bag, she gags intermittently, producing clear secretions. She has a notable tremor and walks slightly stooped with wide-based gait. Her few words demonstrate articulation differences and cognitive expression characteristic of a younger child. She wears light make-up and age-appropriate clothes. She asks, “When can I go home?”

At the end of the visit, parents share their worry that Zoe is “so young and we do not know anything, what to expect, or what to tell her.” As the family's new medical home, they ask you to weigh in on what to do next to best support her? Where do you begin?
Cross-Talk Between Insulin Signaling and G Protein–Coupled Receptors
Authors: Fu Qin , Shi Qian , West Toni M. , Xiang Yang K.
Published: March 2017

Diabetes is a major risk factor for the development of heart failure. One of the hallmarks of diabetes is insulin resistance associated with hyperinsulinemia. The literature shows that insulin and adrenergic signaling is intimately linked to each other; however, whether and how insulin may modulate cardiac adrenergic signaling and cardiac function remains unknown. Notably, recent studies have revealed that insulin receptor and β2 adrenergic receptor (β2AR) forms a membrane complex in animal hearts, bringing together the direct contact between 2 receptor signaling systems, and forming an integrated and dynamic network. Moreover, insulin can drive cardiac adrenergic desensitization via protein kinase A and G protein-receptor kinases phosphorylation of the β2AR, which compromises adrenergic regulation of cardiac contractile function. In this review, we will explore the current state of knowledge linking insulin and G protein–coupled receptor signaling, especially β-adrenergic receptor signaling in the heart, with emphasis on molecular insights regarding its role in diabetic cardiomyopathy.
Activity rhythms and clinical correlates in fibromyalgia
Authors: Neikrug Ariel B. , Donaldson Gary , Iacob Eli , Williams Sam L. , Hamilton Christopher A. , Okifuji Akiko
Published: March 2017

The primary aim of this study was to evaluate activity rhythms in fibromyalgia syndrome (FMS) and their association with FMS-related symptoms. We hypothesized that stronger and more consistent activity rhythms would be associated with reduced symptom severity and presentation in FMS. Two hundred ninety-two patients with FMS (mean age = 45.1 ± 11.1; 272 women) provided a 7-day actigraphy recording and responses to questionnaires addressing degree of pain, fatigue, mood, and physical impairment. Using a simple cosine model, we extracted Amplitude (activity range), Phi (time at maximum), Mesor (mean activity), and their variabilities (across days) from each participant's actigraphy. The clinical and actigraphic measures were operationally independent. There was a significant canonical relationship between activity rhythm parameters and clinical FMS measures (r = 0.376, R
2 = 0.14, P < 0.001). The set of Mesor, Amplitude, and Phi activity parameters remained associated with clinical measures when controlled statistically for both demographics and activity variability (P < 0.001). Each activity parameter provided unique discrimination of the clinical set by multivariate test (P = 0.003, 0.018, and 0.007 for Amplitude, Phi, and Mesor, respectively). These results revealed that better pain, fatigue, mood, physical impairment, and sleep outcomes were associated with higher activity range and more rhythmicity (Amplitude), increased mean activity (Mesor), and with earlier timing of peak activity (Phi). Exploratory analyses revealed significantly worse sleep for individuals with low Amplitude and more delayed Phi.
Breast Tumors Classification Using Adaptive Neuro-Fuzzy Inference System
Authors: Mohammed Sahar Haj Ali A. , Mustafa Zeinab Adam
Published: March 2017

Breast cancer is one of the world's leading causes of cancer-related deaths and ranks second in the cancer fact sheets. In Sudan, the increasing incidence, detection at late stages, and early onset of the disease make early detection and diagnosis of breast cancer an overbearing task. The objective of this study was to create a computer interfacing system for the localization, detection, and classification of breast masses using adaptive neuro-fuzzy inference system (ANFIS). The ANFIS classifier was used to detect the breast cancer when 5 features defining breast cancer indications were used as inputs. The proposed ANFIS model combined the neural network adaptive capabilities and the fuzzy-logic qualitative approach. Results demonstrated that the proposed methodologies have high potential in enhancing breast images and localizing, detecting, and classifying the breast tumor. The system was able to achieve an accuracy of 94.4% sensitivity, 100% specificity, 97.1% positive predictive value, 100% negative predictive value, an Az value of .972, and an overall classification accuracy of 98%.
Safety and Quality Concern of In-Home Suction Equipment Failure Over Time
Authors: Ng Yeow Chye , O’Neal Pamela V. , Frith Karen H. , Riley Linda P.
Published: March 2017

Portable suction machines are widely implemented in both clinical and home care settings. Two identical new machines were tested at 3 different levels of pressure settings operating at intermittent intervals. The study uncovered that noncalibrated portable suction triggers an additional 17% higher suction pressure than the actual most efficient and desired pressure setting. There are statistically significant differences between the calibrated suction machine and noncalibrated suction machine at 3 levels of settings: 80, 100, and 120 mm Hg. This emphasizes the need for fundamental safety redesign of clinical calibration measures for clinical engineering.
The geometry of structural equilibrium
Authors: McRobie Allan
Published: March 2017

Building on a long tradition from Maxwell, Rankine, Klein and others, this paper puts forward a geometrical description of structural equilibrium which contains a procedure for the graphic analysis of stress resultants within general three-dimensional frames. The method is a natural generalization of Rankine’s reciprocal diagrams for three-dimensional trusses. The vertices and edges of dual abstract 4-polytopes are embedded within dual four-dimensional vector spaces, wherein the oriented area of generalized polygons give all six components (axial and shear forces with torsion and bending moments) of the stress resultants. The relevant quantities may be readily calculated using four-dimensional Clifford algebra. As well as giving access to frame analysis and design, the description resolves a number of long-standing problems with the incompleteness of Rankine’s description of three-dimensional trusses. Examples are given of how the procedure may be applied to structures of engineering interest, including an outline of a two-stage procedure for addressing the equilibrium of loaded gridshell rooves.
A model of urban scaling laws based on distance dependent interactions
Authors: Ribeiro Fabiano L. , Meirelles Joao , Ferreira Fernando F. , Neto Camilo Rodrigues
Published: March 2017

Socio-economic related properties of a city grow faster than a linear relationship with the population, in a log–log plot, the so-called
superlinear scaling
. Conversely, the larger a city, the more efficient it is in the use of its infrastructure, leading to a
sublinear scaling
on these variables. In this work, we addressed a simple explanation for those scaling laws in cities based on the interaction range between the citizens and on the fractal properties of the cities. To this purpose, we introduced a measure of social potential which captured the influence of social interaction on the economic performance and the benefits of amenities in the case of infrastructure offered by the city. We assumed that the population density depends on the fractal dimension and on the distance-dependent interactions between individuals. The model suggests that when the city interacts as a whole, and not just as a set of isolated parts, there is improvement of the socio-economic indicators. Moreover, the bigger the interaction range between citizens and amenities, the bigger the improvement of the socio-economic indicators and the lower the infrastructure costs of the city. We addressed how public policies could take advantage of these properties to improve cities development, minimizing negative effects. Furthermore, the model predicts that the sum of the scaling exponents of social-economic and infrastructure variables are 2, as observed in the literature. Simulations with an agent-based model are confronted with the theoretical approach and they are compatible with the empirical evidences.
Strain identification and quorum sensing inhibition characterization of marine-derived
Rhizobium
sp. NAO1
Authors: Chang Hong , Zhou Jin , Zhu Xiaoshan , Yu Shenchen , Chen Lu , Jin Hui , Cai Zhonghua
Published: March 2017

A novel strategy for combating pathogens is through the ongoing development and use of anti-quorum sensing (QS) treatments such as therapeutic bacteria or their anti-QS substances. Relatively little is known about the bacteria that inhabit the open ocean and of their potential anti-pathogenic attributes; thus, in an initiative to identify these types of therapeutic bacteria, planktonic microbes from the North Atlantic Ocean were collected, isolated, cultured and screened for anti-QS activity. Screening analysis identified one such strain,
Rhizobium
sp. NAO1. Extracts of
Rhizobium
sp. NAO1 were identified via ultra-performance liquid chromatography (UPLC) analysis. They were shown to contain
N
-acyl homoserine lactone (AHL)-based QS analogues (in particular, the
N
-butyryl homoserine lactone (C4-AHL) analogue) and could disrupt biofilm formation by
Pseudomonas aeruginosa
PAO1. QS inhibition was confirmed using confocal scanning laser microscopy and growth curves, and it was shown to occur in a dose-dependent manner without affecting bacterial growth. Secondary metabolites of
Rhizobium
sp. NAO1 inhibited PAO1 pathogenicity by downregulating AHL-mediated virulence factors such as elastase activity and siderophore production. Furthermore, as a result of biofilm structure damage, the secondary metabolite products of
Rhizobium
sp. NAO1 significantly increased the sensitivity of PAO1 to aminoglycoside antibiotics. Our results demonstrated that
Rhizobium
sp. strain NAO1 has the ability to disrupt
P. aeruginosa
PAO1 biofilm architecture, in addition to attenuating
P. aeruginosa
PAO1 virulence factor production and pathogenicity. Therefore, the newly identified ocean-derived
Rhizobium
sp. NAO1 has the potential to serve as a QS inhibitor and may be a new microbial resource for drug development.
Landslides and tsunamis predicted by incompressible smoothed particle hydrodynamics (SPH) with application to the 1958 Lituya Bay event and idealized experiment
Authors: Xenakis A. M. , Lind S. J. , Stansby P. K. , Rogers B. D.
Published: March 2017

Tsunamis caused by landslides may result in significant destruction of the surroundings with both societal and industrial impact. The 1958 Lituya Bay landslide and tsunami is a recent and well-documented terrestrial landslide generating a tsunami with a run-up of 524 m. Although recent computational techniques have shown good performance in the estimation of the run-up height, they fail to capture all the physical processes, in particular, the landslide-entry profile and interaction with the water. Smoothed particle hydrodynamics (SPH) is a versatile numerical technique for describing free-surface and multi-phase flows, particularly those that exhibit highly nonlinear deformation in landslide-generated tsunamis. In the current work, the novel multi-phase incompressible SPH method with shifting is applied to the Lituya Bay tsunami and landslide and is the first methodology able to reproduce realistically both the run-up and landslide-entry as documented in a benchmark experiment. The method is the first paper to develop a realistic implementation of the physics that in addition to the non-Newtonian rheology of the landslide includes turbulence in the water phase and soil saturation. Sensitivity to the experimental initial conditions is also considered. This work demonstrates the ability of the proposed method in modelling challenging environmental multi-phase, non-Newtonian and turbulent flows.
SPARSE—A subgrid particle averaged Reynolds stress equivalent model: testing witha prioriclosure
Authors: Davis Sean L. , Jacobs Gustaaf B. , Sen Oishik , Udaykumar H. S.
Published: March 2017

A Lagrangian particle cloud model is proposed that accounts for the effects of Reynolds-averaged particle and turbulent stresses and the averaged carrier-phase velocity of the subparticle cloud scale on the averaged motion and velocity of the cloud. The SPARSE (subgrid particle averaged Reynolds stress equivalent) model is based on a combination of a truncated Taylor expansion of a drag correction function and Reynolds averaging. It reduces the required number of computational parcels to trace a cloud of particles in Eulerian–Lagrangian methods for the simulation of particle-laden flow. Closure is performed in ana priorimanner using a reference simulation where all particles in the cloud are traced individually with a point-particle model. Comparison of a first-order model and SPARSE with the reference simulation in one dimension shows that both the stress and the averaging of the carrier-phase velocity on the cloud subscale affect the averaged motion of the particle. A three-dimensional isotropic turbulence computation shows that only one computational parcel is sufficient to accurately trace a cloud of tens of thousands of particles.
Screened Coulomb interactions with non-uniform surface charge
Authors: Ghosal Sandip , Sherwood John D.
Published: March 2017

The screened Coulomb interaction between a pair of infinite parallel planes with spatially varying surface charge is considered in the limit of small electrical potentials for arbitrary Debye lengths. A simple expression for the disjoining pressure is derived in terms of a two-dimensional integral in Fourier space. The integral is evaluated for periodic and random charge distributions and the disjoining pressure is expressed as a sum over Fourier–Bloch reciprocal lattice vectors or in terms of an integral involving the autocorrelation function, respectively. The force between planes with a finite area of uniform charge, a model for the DLVO interaction between finite surfaces, is also calculated. It is shown that the overspill of the charge cloud beyond the region immediately between the charged areas results in a reduction of the disjoining pressure, as reported by us recently in the long Debye length limit for planes of finite width.
Evolution of male and female choice in polyandrous systems
Authors: Puurtinen Mikael , Fromhage Lutz
Published: March 2017

We study the evolution of male and female mating strategies and mate choice for female fecundity and male fertilization ability in a system where both sexes can mate with multiple partners, and where there is variation in individual quality (i.e. in the availability of resources individuals can allocate to matings, mate choice and production of gametes). We find that when the cost of mating differs between sexes, the sex with higher cost of mating is reluctant to accept matings and is often also choosy, while the other sex accepts all matings. With equal mating costs, the evolution of mating strategies depends on the strength of female sperm limitation, so that when sperm limitation is strong, males are often reluctant and choosy, whereas females tend to accept available matings. Male reluctance evolves because a male's benefit per mating diminishes rapidly as he mates too often, hence losing out in the process of sperm competition as he spends much of his resources on mating costs rather than ejaculate production. When sperm limitation is weaker, females become more reluctant and males are more eager to mate. The model thus suggests that reversed sex roles are plausible outcomes of polyandry and limited sperm production. Implications for empirical studies of mate choice are discussed.
Climate warming and humans played different roles in triggering Late Quaternary extinctions in east and west Eurasia
Authors: Wan Xinru , Zhang Zhibin
Published: March 2017

Climate change and humans are proposed as the two key drivers of total extinction of many large mammals in the Late Pleistocene and Early Holocene, but disentangling their relative roles remains challenging owing to a lack of quantitative evaluation of human impact and climate-driven distribution changes on the extinctions of these large mammals in a continuous temporal–spatial dimension. Here, our analyses showed that temperature change had significant effects on mammoth (genus
Mammuthus
), rhinoceros (Rhinocerotidae), horse (Equidae) and deer (Cervidae). Rapid global warming was the predominant factor driving the total extinction of mammoths and rhinos in frigid zones from the Late Pleistocene and Early Holocene. Humans showed significant, negative effects on extirpations of the four mammalian taxa, and were the predominant factor causing the extinction or major extirpations of rhinos and horses. Deer survived both rapid climate warming and extensive human impacts. Our study indicates that both the current rates of warming and range shifts of species are much faster than those from the Late Pleistocene to Holocene. Our results provide new insight into the extinction of Late Quaternary megafauna by demonstrating taxon-, period- and region-specific differences in extinction drivers of climate change and human disturbances, and some implications about the extinction risk of animals by recent and ongoing climate warming.
Natal dispersers pay a lifetime cost to increased reproductive effort in a wild bird population
Authors: Germain Marion , Pärt Tomas , Gustafsson Lars , Doligez Blandine
Published: March 2017

Natal dispersal is assumed to be costly. Such costs can be difficult to detect, and fitness consequences of dispersal are therefore poorly known. Because of lower phenotypic quality and/or familiarity with the environment, natal dispersers may be less buffered against a sudden increase in reproductive effort. Consequently, reproductive costs associated with natal dispersal may mostly be detected in harsh breeding conditions. We tested this prediction by comparing lifetime reproductive success between natal dispersers and non-dispersers in a patchy population of collared flycatchers (Ficedula albicollis) when they reared either a non-manipulated brood or an experimentally increased or decreased brood. Natal dispersers achieved lower lifetime reproductive success than non-dispersers only under more stressful breeding conditions (i.e. when brood size was experimentally increased). This was mostly due to a lower number of recruits produced in the year of the increase. Our results suggest a cost associated with natal dispersal paid immediately after an increase in reproductive effort and not subsequently compensated for through increased survival or future offspring recruitment. Natal dispersers adjusted their breeding investment when reproductive effort is as predicted but seemed unable to efficiently face a sudden increase in effort, which could affect the influence of environmental predictability on dispersal evolution.
Moving beyond linear food chains: trait-mediated indirect interactions in a rocky intertidal food web
Authors: Trussell Geoffrey C. , Matassa Catherine M. , Ewanchuk Patrick J.
Published: March 2017

In simple, linear food chains, top predators can have positive indirect effects on basal resources by causing changes in the traits (e.g. behaviour, feeding rates) of intermediate consumers. Although less is known about trait-mediated indirect interactions (TMIIs) in more complex food webs, it has been suggested that such complexity dampens trophic cascades. We examined TMIIs between a predatory crab (Carcinus maenas) and two ecologically important basal resources, fucoid algae (Ascophyllum nodosum) and barnacles (Semibalanus balanoides), which are consumed by herbivorous (Littorina littorea) and carnivorous (Nucella lapillus) snails, respectively. Because crab predation risk suppresses snail feeding rates, we hypothesized that crabs would also shape direct and indirect interactions among the multiple consumers and resources. We found that the magnitude of TMIIs between the crab and each resource depended on the suite of intermediate consumers present in the food web. Carnivorous snails (Nucella) transmitted TMIIs between crabs and barnacles. However, crab–algae TMIIs were transmitted by both herbivorous (Littorina) and carnivorous (Nucella) snails, and these TMIIs were additive. By causingNucellato consume fewer barnacles, crab predation risk allowed fucoids that had settled on or between barnacles to remain in the community. Hence, positive interactions between barnacles and algae caused crab–algae TMIIs to be strongest when both consumers were present. Studies of TMIIs in more realistic, reticulate food webs will be necessary for a more complete understanding of how predation risk shapes community dynamics.
Immanent conditions determine imminent collapses: nutrient regimes define the resilience of macroalgal communities
Authors: Boada Jordi , Arthur Rohan , Alonso David , Pagès Jordi F. , Pessarrodona Albert , Oliva Silvia , Ceccherelli Giulia , Piazzi Luigi , Romero Javier , Alcoverro Teresa
Published: March 2017

Predicting where state-changing thresholds lie can be inherently complex in ecosystems characterized by nonlinear dynamics. Unpacking the mechanisms underlying these transitions can help considerably reduce this unpredictability. We used empirical observations, field and laboratory experiments, and mathematical models to examine how differences in nutrient regimes mediate the capacity of macrophyte communities to sustain sea urchin grazing. In relatively nutrient-rich conditions, macrophyte systems were more resilient to grazing, shifting to barrens beyond 1 800 g m
−2
(urchin biomass), more than twice the threshold of nutrient-poor conditions. The mechanisms driving these differences are linked to how nutrients mediate urchin foraging and algal growth: controlled experiments showed that low-nutrient regimes trigger compensatory feeding and reduce plant growth, mechanisms supported by our consumer–resource model. These mechanisms act together to halve macrophyte community resilience. Our study demonstrates that by mediating the underlying drivers, inherent conditions can strongly influence the buffer capacity of nonlinear systems.
Allometric growth in reef-building corals
Authors: Dornelas Maria , Madin Joshua S. , Baird Andrew H. , Connolly Sean R.
Published: March 2017

Predicting demographic rates is a critical part of forecasting the future of ecosystems under global change. Here, we test if growth rates can be predicted from morphological traits for a highly diverse group of colonial symbiotic organisms: scleractinian corals. We ask whether growth is isometric or allometric among corals, and whether most variation in coral growth rates occurs at the level of the species or morphological group. We estimate growth as change in planar area for 11 species, across five morphological groups and over 5 years. We show that coral growth rates are best predicted from colony size and morphology rather than species. Coral size follows a power scaling law with a constant exponent of 0.91. Despite being colonial organisms, corals have consistent allometric scaling in growth. This consistency simplifies the task of projecting community responses to disturbance and climate change.
A new crustacean from the Herefordshire (Silurian) Lagerstätte, UK, and its significance in malacostracan evolution
Authors: Siveter David J. , Briggs Derek E. G. , Siveter Derek J. , Sutton Mark D. , Legg David
Published: March 2017

Cascolus ravitisgen. et sp. nov. is a three-dimensionally preserved fossil crustacean with soft parts from the Herefordshire (Silurian) Lagerstätte, UK. It is characterized by a head with a head shield and five limb pairs, and a thorax (pereon) with nine appendage-bearing segments followed by an apodous abdomen (pleon). All the appendages except the first are biramous and have a gnathobase. The post-mandibular appendages are similar one to another, and bear petal-shaped epipods that probably functioned as a part of the respiratory–circulatory system. Cladistic analysis resolves the new taxon as a stem-group leptostracan (Malacostraca). This well-preserved arthropod provides novel insights into the evolution of appendage morphology, tagmosis and the possible respiratory–circulatory physiology of a basal malacostracan.
deStruct: Accurate Rearrangement Detection using Breakpoint Specific Realignment
Authors: McPherson Andrew , Shah Sohrab , Sahinalp S. Cenk
Published: March 2017

We propose that a breakpoint specific alignment procedure would improve breakpoint prediction. Our method, deStruct, uses multiple stages of realignment and clustering to progressively refine breakpoint prediction quality and accuracy. We show using simulated data that deStruct predicts breakpoints with higher sensitivity and specificity than existing breakpoint prediction tools.
Bacterial physiological adaptations to contrasting edaphic conditions identified using landscape scale metagenomics
Authors: Malik Ashish A. , Thomson Bruce C. , Whiteley Andrew S. , Bailey Mark , Griffiths Robert I.
Published: March 2017

Environmental factors relating to soil pH are widely known to be important in structuring soil bacterial communities, yet the relationship between taxonomic community composition and functional diversity remains to be determined. Here, we analyze geographically distributed soils spanning a wide pH gradient and assess the functional gene capacity within those communities using whole genome metagenomics. Low pH soils consistently had fewer taxa (lower alpha and gamma diversity), but only marginal reductions in functional alpha diversity and equivalent functional gamma diversity. However, coherent changes in the relative abundances of annotated genes between pH classes were identified; with functional profiles clustering according to pH independent of geography. Differences in gene abundances were found to reflect survival and nutrient acquisition strategies, with organic-rich acidic soils harboring a greater abundance of cation efflux pumps, C and N direct fixation systems and fermentation pathways indicative of anaerobiosis. Conversely, high pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings show that bacterial functional versatility may not be constrained by taxonomy, and we further identify the range of physiological adaptations required to exist in soils of varying nutrient availability and edaphic conditions.
Brain connectivity-informed regularization methods for regression
Authors: Karas Marta , Brzyski Damian , Dzemidzic Mario , Goni Joaquin , Kareken David A. , Randolph Timothy W. , Harezlak Jaroslaw
Published: March 2017

A challenging problem arising in brain imaging research is principled incorporation of information from different imaging modalities. Frequently each modality is analyzed separately using, for instance, dimensionality reduction techniques which result in a loss of mutual information. We propose a novel regularization method to estimate the association between the brain structure features and a scalar outcome within the linear regression framework. Our regularization technique provides a principled approach to utilizing external information arising from the structural brain connectivity to inform the estimation of the regression coefficients. Our proposal extends the classical Tikhonov regularization framework by defining a penalty term based on the structural connectivity-derived Laplacian matrix. In the work presented, we address both theoretical and computational issues. The approach is illustrated using simulated data and compared with other penalized regression methods. Finally, we apply our regularization method to study the associations between the alcoholism phenotypes and brain cortical thickness using a diffusion tensor imaging (DTI) derived measure of structural connectivity.
ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
Authors: Hunt Martin , Mather Alison E. , Sánchez-Busó Leonor , Page Andrew J. , Parkhill Julian , Keane Jacqueline A. , Harris Simon R.
Published: March 2017

Antimicrobial resistance (AMR) is one of the major threats to human and animal health worldwide, yet few high-throughput tools exist to analyse and predict the resistance of a bacterial isolate from sequencing data. Here we present a new tool, ARIBA, that identifies AMR-associated genes and single nucleotide polymorphisms directly from short reads, and generates detailed and customisable output. The accuracy and advantages of ARIBA over other tools are demonstrated on three datasets from Gram-positive and Gram-negative bacteria, with ARIBA outperforming existing methods. ARIBA is available athttps://github.com/sanger-pathogens/ariba.