bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular epidemiology of tuberculosis in Havana, Cuba, 2009
Authors: González Díaz Alexander , Battaglioli Tullia , Díaz Rodríguez Raúl , Goza Valdés Roxana , González Ochoa Edilberto , Van der Stuyft Patrick
Published: July 2015

Objectives

To estimate the proportion of tuberculosis cases attributable to recent transmission and the risk factors possibly associated with tuberculosis clustering.

Methods

Population‐based study combining information from epidemiological investigation of tuberculosis cases notified to the National Tuberculosis Control Program in Havana, Cuba, in 2009 with the results of genotyping of Mycobacterium tuberculosis isolates with variable number tandem repeat of mycobacterial interspersed repetitive units (MIRU‐VNTR) typing.

Results

Of 186 cases, 61 were genotyped: 33 patterns and five clusters with 19, 7, 3, 2 and 2 cases were found. The proportion of cases due to recent transmission was 45% (95% confidence interval 33–58%). Routine contact investigation failed to identify a substantial number of epidemiological links. A history of living in a closed setting was strongly associated with clustering.

Conclusions

The proportion of cases due to recent transmission in Havana in 2009 is high. The existing control measures in closed settings should be strengthened. A study on a larger number of cases and for a longer time period should be carried out to obtain more precise estimates. Further studies on the utility and cost‐effectiveness of the addition of molecular epidemiology techniques to support the progress towards tuberculosis elimination in Cuba, a low‐incidence resource‐limited setting, are also needed.
Influence of microwave annealing on optical and electrical properties of plasma-induced defect structures in Si substrate
Authors: Iwai Takaaki , Eriguchi Koji , Yamauchi Shohei , Noro Naotaka , Kitagawa Junichi , Ono Kouichi
Published: July 2015

The authors investigate the effects of microwave annealing (MWA) on the recovery of plasma process-induced ion-bombardment damage in Si substrates. For damage creation, Ar discharges by a capacitively coupled plasma etcher are used. For damage repairing, the MWA or a rapid thermal annealing (RTA) are conducted. The authors employ spectroscopic ellipsometry (SE), photoreflectance spectroscopy (PRS), and capacitance–voltage (C–V) measurement to analyze the damaged structures. Recovery of the damage is discussed by comparing the obtained parameters before and after the annealing processes. In the SE analysis, the change in the real part of dielectric constant (Δεr) is investigated. The Δεr spectral peak around 3.4 eV decreases with an increase in the annealing temperature (Ta) for both MWA and RTA, indicating the decrease in the density of defects created in the Si substrate. In the PRS analysis, the spectral peak intensity is found to decrease by the plasma exposure, and then to increase with Ta, which implies the recovery of the Si crystalline structure by MWA as well as by RTA. In the C–V measurement, the voltage shift (ΔVb) in the respective C–V curves is used as a measure of the number of defects present in the surface and interface damaged regions. The ΔVb in the negative bias direction is observed after the plasma exposure for all damaged structures, while after annealing the ΔVb in the positive bias direction is confirmed, suggesting the recovery of the damage in the surface and interface regions. Moreover, it is experimentally found that MWA induces larger |ΔVb| than RTA. These findings indicate the decrease in carrier trap sites in the surface and interface regions of damaged structures, and that MWA is more effective in repairing such damage than RTA. The authors propose a model explaining these mechanisms where defect-induced dipole moments that interact with the incident microwave are considered. The present results draw a new damage-recovery picture by MWA, in particular, for plasma-induced damage in surface and interface regions of Si substrates.
Improving the extraction of characteristic field enhancement factors from nonlinear Fowler–Nordheim plots: Call for experimental tests
Authors: de Assis Thiago A.
Published: July 2015

The author shows that the dependence between the effective emission area and the macroscopic electric field allow for the introduction of a new correction, ω, in the elementary slope characterization parameter (SCP) for extracting the characteristic field enhancement factor, γC, from (precise) orthodox cold-field electron emission measurements. The authors assume that the local macroscopic enhancement factors, γ, are Gaussian-distributed, as has been experimentally determined for the potential candidates of cold-field electron emission applications. Using the recent developments in cold-field electron emission theory, the authors found that for the typical experimental range of 1 V/μm ≤ FM ≤ 10 V/μm, the nonlinearities that are often observed in cold-field electron emission experiments may appear in JM-FM-type Fowler–Nordheim plots. Finally, our results show that depending on the dispersion in the distribution of γ, Δγ/γ0, where γ0 is the average value, the error in estimating the γC using the elementary SCP (a common practice for experimentalists) may be relevant.
Review of SPECT collimator selection, optimization, and fabrication for clinical and preclinical imaging
Authors: Van Audenhaege Karen , Van Holen Roel , Vandenberghe Stefaan , Vanhove Christian , Metzler Scott D. , Moore Stephen C.
Published: July 2015

In single photon emission computed tomography, the choice of the collimator has a major impact on the sensitivity and resolution of the system. Traditional parallel‐hole and fan‐beam collimators used in clinical practice, for example, have a relatively poor sensitivity and subcentimeter spatial resolution, while in small‐animal imaging, pinhole collimators are used to obtain submillimeter resolution and multiple pinholes are often combined to increase sensitivity. This paper reviews methods for production, sensitivity maximization, and task‐based optimization of collimation for both clinical and preclinical imaging applications. New opportunities for improved collimation are now arising primarily because of (i) new collimator‐production techniques and (ii) detectors with improved intrinsic spatial resolution that have recently become available. These new technologies are expected to impact the design of collimators in the future. The authors also discuss concepts like septal penetration, high‐resolution applications, multiplexing, sampling completeness, and adaptive systems, and the authors conclude with an example of an optimization study for a parallel‐hole, fan‐beam, cone‐beam, and multiple‐pinhole collimator for different applications.
Liver 4DMRI: A retrospective image‐based sorting method
Authors: Paganelli Chiara , Summers Paul , Bellomi Massimo , Baroni Guido , Riboldi Marco
Published: July 2015

Purpose:

Four‐dimensional magnetic resonance imaging (4DMRI) is an emerging technique in radiotherapy treatment planning for organ motion quantification. In this paper, the authors present a novel 4DMRI retrospective image‐based sorting method, providing reduced motion artifacts than using a standard monodimensional external respiratory surrogate.

Methods:

Serial interleaved 2D multislice MRI data were acquired from 24 liver cases (6 volunteers + 18 patients) to test the proposed 4DMRI sorting. Image similarity based on mutual information was applied to automatically identify a stable reference phase and sort the image sequence retrospectively, without the use of additional image or surrogate data to describe breathing motion.

Results:

The image‐based 4DMRI provided a smoother liver profile than that obtained from standard resorting based on an external surrogate. Reduced motion artifacts were observed in image‐based 4DMRI datasets with a fitting error of the liver profile measuring 1.2 ± 0.9 mm (median ± interquartile range) vs 2.1 ± 1.7 mm of the standard method.

Conclusions:

The authors present a novel methodology to derive a patient‐specific 4DMRI model to describe organ motion due to breathing, with improved image quality in 4D reconstruction.
Handle Shape Affects the Grip Force Distribution and the Muscle Loadings During Power Grip Tasks
Authors: Rossi Jérémy , De Monsabert Benjamin Goislard , Berton Eric , Vigouroux Laurent
Published: July 2015

The objectives of this study were to investigate the effect of handle shape on the grip force distribution in the hand and on the muscle forces during maximal power grip tasks. Eleven subjects maximally grasped 3 handles with different external shapes (circular, elliptic, and double-frustum). A handle dynamometer, equipped with both a force sensor and a pressure map, was used to record the forces exerted at the hand/handle interface. The finger and wrist joint postures were also computed from synchronized kinematic measurement. These processed data were then used as input of a biomechanical hand model to estimate muscle forces. The results showed that handle shape influences the maximal grip force, the grip force distribution, and the finger joint postures. Particularly, we observed that the elliptical shape resulted in a 6.6% lower maximal grip force compared with the circular and double-frustum handle. Concomitantly, the estimated muscle forces also varied significantly according to the handle shape, with up to 48% differences for the flexor digitorum superficialis muscle for example. Interestingly, different muscle coordination strategies were observed depending on the handle shape, therefore suggesting a potential influence of these geometrical characteristics on pathological risks such as tendonitis.
Effects of Fatigue on Running Mechanics: Spring-Mass Behavior in Recreational Runners After 60 Seconds of Countermovement Jumps
Authors: Fischer Gabriela , Storniolo Jorge L.L. , Peyré-Tartaruga Leonardo A.
Published: July 2015

The purpose of this study was to investigate the effects of acute fatigue on spring-mass model (SMM) parameters among recreational runners at different speeds. Eleven participants (5 males and 6 females) performed running trials at slower, self-selected, and faster speeds on an indoor track before and after performing a fatigue protocol (60 s of countermovement jumps). Maximal vertical force (Fmax), impact peak force (Fpeak), loading rate (LR), contact time (Tc), aerial time (Ta), step frequency (SF), step length (SL), maximal vertical displacement of the center of mass (ΔZ), vertical stiffness (Kvert), and leg work (Wleg) were measured using a force plate integrated into the track. A significant reduction (–43.1 ± 8.6%; P < .05) in mechanical power during jumps indicated that the subjects became fatigued. The results showed that under fatigue conditions, the runners adjusted their running mechanics at slower (≈2.7 ms–1; ΔZ –12% and SF +3.9%; P < .05), self-selected (≈3.3 ms–1; SF +3%, SL –6.8%, Ta –16%, and Fmax –3.3%; P < .05), and faster (≈3.6 ms–1 SL –6.9%, Ta –14% and Fpeak –9.8%; P < .05) speeds without significantly altering Kvert (P > .05). During constant running, the previous 60 s of maximal vertical jumps induced mechanical adjustments in the spatiotemporal parameters without altering Kvert.
Abrupt warming events drove Late Pleistocene Holarctic megafaunal turnover
Authors: Cooper Alan , Turney Chris , Hughen Konrad A. , Brook Barry W. , McDonald H. Gregory , Bradshaw Corey J. A.
Published: July 2015

Climate killed off the megafauna

The causes of the Pleistocene extinctions of large numbers of megafaunal species in the Northern Hemisphere remain unclear. A range of evidence points to human hunting, climate change, or a combination of both. Using ancient DNA and detailed paleoclimate data, Cooper
et al.
report a close relationship between Pleistocene megafaunal extinction events and rapid warming events at the start of interstadial periods. Their analysis strengthens the case for climate change as the key driver of megafaunal extinctions, with human impacts playing a secondary role.

Science
, this issue p.
602
Voltage-tunable circular photogalvanic effect in silicon nanowires
Authors: Dhara Sajal , Mele Eugene J. , Agarwal Ritesh
Published: July 2015

Chirality from achiral structures

The most common materials used in electronics produce only a simple optical response. Dhara
et al.
observed a complex circular photogalvanic effect in silicon nanowires, with the magnitude and direction of the induced photocurrent dependent on the polarization of the light. The specifics of the structure and geometry of the component materials are responsible for the effect. It should therefore be possible to engineer the same effect in other achiral materials and thus expand the box of enhanced functional materials for optical applications.

Science
, this issue p.
726
RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself
Authors: Liddicoat Brian J. , Piskol Robert , Chalk Alistair M. , Ramaswami Gokul , Higuchi Miyoko , Hartner Jochen C. , Li Jin Billy , Seeburg Peter H. , Walkley Carl R.
Published: July 2015

RNA editing helps identify cellular RNAs

Adenosine bases in messenger RNA (mRNAs) can be enzymatically modified and changed into inosine bases. This RNA “editing” is mediated by adenosine deaminase acting on RNA (ADAR) enzymes. Liddicoat
et al.
show that the in vivo targets of the principal editing enzyme, ADAR1, are long double-stranded RNA (dsRNA) structures in noncoding portions of cellular mRNAs. ADAR1-directed editing of these cellular targets is critical to avoid activation of an immune response to dsRNA in the cytoplasm, because dsRNA is also a marker of viral infection.

Science
, this issue p.
1115
Genome Sequence of Torulaspora delbrueckii NRRL Y-50541, Isolated from Mezcal Fermentation
Authors: Gomez-Angulo Jorge , Vega-Alvarado Leticia , Escalante-García Zazil , Grande Ricardo , Gschaedler-Mathis Anne , Amaya-Delgado Lorena , Arrizon Javier , Sanchez-Flores Alejandro
Published: July 2015

Torulaspora delbrueckii
presents metabolic features interesting for biotechnological applications (in the dairy and wine industries). Recently, the
T. delbrueckii
CBS 1146 genome, which has been maintained under laboratory conditions since 1970, was published. Thus, a genome of a new mezcal yeast was sequenced and characterized and showed genetic differences and a higher genome assembly quality, offering a better reference genome.
Draft Genome Sequence of Escherichia coli O157:H7 ATCC 35150 and a Nalidixic Acid-Resistant Mutant Derivative
Authors: Markell James A. , Koziol Adam G. , Lambert Dominic
Published: July 2015

Shiga toxin-producing
Escherichia coli
strains, occasionally isolated from food, are of public health importance. Here, we report on the 5.30-Mbp draft genome sequence of
E. coli
O157:H7 EDL931 (strain ATCC 35150) and the 5.32-Mbp draft genome sequence of a nalidixic acid-resistant mutant derivative used as a distinguishable control strain in food-testing laboratories.
Genome Sequence of Brevibacillus formosus F12
T
for a Genome-Sequencing Project for Genomic Taxonomy and Phylogenomics of
Bacillus
-Like Bacteria
Authors: Wang Jie-Ping , Liu Bo , Liu Guo-Hong , Chen Qian-qian , Zhu Yu-jing , Chen Zheng , Che Jian-mei
Published: July 2015

Brevibacillus formosus
F12
T
is a Gram-positive, spore-forming, and strictly aerobic bacterium. Here, we report the draft 6.215-Mb genome sequence of
B. formosus
F12
T
, which will provide useful information for genomic taxonomy and phylogenomics of
Bacillus
-like bacteria, as well as for the functional gene mining and application of
B. formosus
.
Draft Genome Sequence of Environmental Bacterium Vibrio vulnificus CladeA-yb158
Authors: Danin-Poleg Yael , Raz Nili , Roig Francisco J. , Amaro Carmen , Kashi Yechezkel
Published: July 2015

We report the genome sequence of the environmental
Vibrio vulnificus
biotype 1_cladeA. This draft genome of the CladeA-yb158 strain, isolated in Israel, represents this newly emerged clonal group that contains both clinical and environmental strains.
Draft Genome Sequence of the Cellulolytic and Xylanolytic Thermophile Clostridium clariflavum Strain 4-2a
Authors: Rooney Elise A. , Rowe Kenneth T. , Guseva Anna , Huntemann Marcel , Han James K. , Chen Amy , Kyrpides Nikos C. , Mavromatis Konstantinos , Markowitz Victor M. , Palaniappan Krishna , Ivanova Natalia , Pati Amrita , Liolios Konstantinos , Nordberg Henrik P. , Cantor Michael N. , Hua Susan X. , Shapiro Nicole , Woyke Tanja , Lynd Lee R. , Izquierdo Javier A.
Published: July 2015

Clostridium clariflavum
strain 4-2a, a novel strain isolated from a thermophilic biocompost pile, has demonstrated an extensive capability to utilize both cellulose and hemicellulose under thermophilic anaerobic conditions. Here, we report the draft genome of this strain.
Draft Genome Sequence of
Burkholderia
sp. Strain PML1(12), an Ectomycorrhizosphere-Inhabiting Bacterium with Effective Mineral-Weathering Ability
Authors: Uroz Stéphane , Oger Phil
Published: July 2015

We report the draft genome sequence of
Burkholderia
sp. PML1(12), a soil bacterium isolated from the Oak-
Scleroderma citrinum
ectomycorrhizosphere in the experimental forest site of Breuil-Chenue (France).
Genome Sequence of
Geobacillus
sp. Strain ZGt-1, an Antibacterial Peptide-Producing Bacterium from Hot Springs in Jordan
Authors: Alkhalili Rawana N. , Hatti-Kaul Rajni , Canbäck Björn
Published: July 2015

This paper reports the draft genome sequence of the firmicute
Geobacillus
sp. strain ZGt-1, an antibacterial peptide producer isolated from the Zara hot spring in Jordan. This study is the first report on genomic data from a thermophilic bacterial strain isolated in Jordan.
Genome Sequence of Klebsiella pneumoniae CICC10011, a Promising Strain for High 2,3-Butanediol Production
Authors: Tong Ying-Jia , Ji Xiao-Jun , Liu Lu-Gang , Shen Meng-Qiu , Huang He
Published: July 2015

Klebsiella pneumoniae
CICC10011, a promising 2,3-butanediol producer, has received much attention because of its high productivity. Here, the first draft genome sequence of this efficient strain may provide the genetic basis for further insights into the metabolic and regulatory mechanisms underlying the production of 2,3-butanediol at a high titer.
Draft Genome Sequences of Klebsiella oxytoca Isolates Originating from a Highly Contaminated Liquid Hand Soap Product
Authors: Hammerl J. A. , Lasch P. , Nitsche A. , Dabrowski P. W. , Hahmann H. , Wicke A. , Kleta S. , Dahouk S. Al , Dieckmann R.
Published: July 2015

In 2013, contaminated liquid soap was detected by routine microbiological monitoring of consumer products through state health authorities. Because of its high load of
Klebsiella oxytoca
, the liquid soap was notified via the European Union Rapid Alert System for Dangerous Non-Food Products (EU-RAPEX) and recalled. Here, we present two draft genome sequences and a summary of their general features.
Draft Genome Sequence of the Biofilm-Hyperproducing Acinetobacter baumannii Clinical Strain MAR002
Authors: Álvarez-Fraga Laura , López María , Merino María , Rumbo-Feal Soraya , Tomás María , Bou Germán , Poza Margarita
Published: July 2015

We report the draft genome sequence of
Acinetobacter baumannii
strain MAR002, a biofilm-hyperproducing clinical strain isolated during the study CP/09/0033 (GEIH/REIPI-Ab2010, Spain). The genome of
A. baumannii
MAR002 has an approximate length of 3,717,929 bp and 3,300 protein-coding sequences, with a C+G content of 39.09%.
An innovative approach to strengthening health professionals’ infection control and limiting hospital-acquired infection: video-reflexive ethnography
Authors: Iedema Rick , Hor Su-Yin , Wyer Mary , Gilbert Gwendolyn L , Jorm Christine , Hooker Claire , O'Sullivan Matthew Vincent Neil
Published: July 2015

Objective

To strengthen clinicians’ infection control awareness and risk realisation by engaging them in scrutinising footage of their own infection control practices and enabling them to articulate challenges and design improvements.

Design and participants

Clinicians and patients from selected wards of 2 hospitals in western Sydney.

Main outcome measures

Evidence of risk realisation and new insights into infection control as articulated during video-reflexive feedback meetings.

Results

Frontline clinicians identified previously unrecognised infection risks in their own practices and in their team's practices. They also formulated safer ways of dealing with, for example, charts and patient transfers.

Conclusions

Video-reflexive ethnography enables frontline clinicians to identify infection risks and to design locally tailored solutions for existing risks and emerging ones.
Socioeconomic determinants of risk of harmful alcohol drinking among people aged 50 or over in England
Authors: Iparraguirre José
Published: July 2015

Objectives

This paper looks into the socioeconomic determinants of risk of harmful alcohol drinking and of the transitions between risk categories over time among the population aged 50 or over in England.

Setting

Community-dwellers across England.

Participants

Respondents to the English Longitudinal Survey of Ageing, waves 4 and 5.

Results

(Confidence level at 95% or higher, except when stated):

▸ Higher risk drinking falls with age and there is a non-linear association between age and risk for men, peaking in their mid-60s.

▸ Retirement and income are positively associated with a higher risk for women but not for men.

▸ Education and smoking are positively associated for both sexes.

▸ Loneliness and depression are not associated.

▸ Caring responsibilities reduce risk among women.

▸ Single, separated or divorced men show a greater risk of harmful drinking (at 10% confidence level).

▸ For women, being younger and having a higher income at baseline increase the probability of becoming a higher risk alcohol drinker over time.

▸ For men, not eating healthily, being younger and having a higher income increase the probability of becoming a higher risk alcohol drinker. Furthermore, the presence of children living in the household, being lonely, being older and having a lower income are associated with ceasing to be a higher risk alcohol drinker over time.

Conclusions

Several socioeconomic factors found to be associated with high-risk alcohol consumption behaviour among older people would align with those promoted by the ‘successful ageing’ policy framework.
‘Including health in systems responsible for urban planning’: a realist policy analysis research programme
Authors: Harris Patrick , Friel Sharon , Wilson Andrew
Published: July 2015

Introduction

Realist methods are increasingly being used to investigate complex public health problems. Despite the extensive evidence base clarifying the built environment as a determinant of health, there is limited knowledge about how and why land-use planning systems take on health concerns. Further, the body of research related to the wider determinants of health suffers from not using political science knowledge to understand how to influence health policy development and systems. This 4-year funded programme of research investigates how the land-use planning system in New South Wales, Australia, incorporates health and health equity at multiple levels.

Methods and analysis

The programme uses multiple qualitative methods to develop up to 15 case studies of different activities of the New South Wales land-use planning system. Comparison cases from other jurisdictions will be included where possible and useful.Data collectionincludes publicly available documentation and purposively sampled stakeholder interviews and focus groups of up to 100 participants across the cases. The units of analysis in each case are institutional structures (rules and mandates constraining and enabling actors), actors (the stakeholders, organisations and networks involved, including health-focused agencies), and ideas (policy content, information, and framing).Data analysiswill focus on and develop propositions concerning the mechanisms and conditions within and across each case leading to inclusion or non-inclusion of health. Data will be refined using additional political science and sociological theory. Qualitative comparative analysis will compare cases to develop policy-relevant propositions about the necessary and sufficient conditions needed to include health issues.

Ethics and dissemination

Ethics has been approved by Sydney University Human Research Ethics Committee (2014/802 and 2015/178). Given the nature of this research we will incorporate stakeholders, often as collaborators, throughout. We outline our research translation strategies following best practice approaches.
Republished: Treatment of wide-necked basilar tip aneurysm not amenable to Y-stenting using the PulseRider device
Authors: Sheth Sunil A , Patel Nirav S , Ismail Ameera F , Freeman Dena , Duckwiler Gary , Tateshima Satoshi
Published: July 2015

Endovascular treatment of broad-necked bifurcation aneurysms remains challenging. Stent-assisted coiling has been successful but requires catheterization of the branches off the parent vessel. We present the case of a patient who failed primary and stent-assisted coiling of a large basilar tip aneurysm because the morphology of the aneurysm precluded successful distal catheterization of the posterior cerebral artery (PCA) branches. Using the PulseRider device, which does not require catheterization of bifurcation branches, we were able to treat the aneurysm successfully.
Environmental survival of Mycoplasma bovis on a white veal farm
Authors: Piccinini Renata , Gosney Faye , Snel Gustavo G M , Luini Mario Vittorio , Nicholas Robin A J
Published: July 2015

Mycoplasma bovis is an emerging cause of bovine respiratory disease (BRD), particularly in intensive feedlots where disease is mainly spread by aerosol route over close distances. The present study aimed to investigate the occurrence of mycoplasmas in the environment of barns housing white veal calves presenting BRD. The majority of calves seroconverted to M bovis three weeks after arrival; there was little evidence of respiratory virus activity, but Mannheimia haemolytica and Pasteurella multocida were isolated from clinically affected calves. M bovis was detected in nasal swabs of sick animals and also on cages and mangers. The isolates were mostly of the same molecular type, suggesting the possibility of infection from the environment. Environmental resistance conferred by biofilm formation might play a significant role in the continuous circulation of M bovis within the white veal herd, indicating the need for all‐in, all‐out replacement systems and effective disinfection.
Supplementation with a proprietary blend of ancient peat and apple extract may improve body composition without affecting hematology in resistance-trained men
Authors: Joy Jordan M. , Falcone Paul H. , Vogel Roxanne M. , Mosman Matt M. , Kim Michael P. , Moon Jordan R.
Published: July 2015

Adenosine-5′-triphosphate (ATP) is primarily known as a cellular source of energy. Increased ATP levels may have the potential to enhance body composition. A novel, proprietary blend of ancient peat and apple extracts has been reported to increase ATP levels, potentially by enhancing mitochondrial ATP production. Therefore, the purpose of this investigation was to determine the supplement’s effects on body composition when consumed during 12 weeks of resistance training. Twenty-five healthy, resistance-trained, male subjects (age, 27.7 ± 4.8 years; height, 176.0 ± 6.5 cm; body mass, 83.2 ± 12.1 kg) completed this study. Subjects supplemented once daily with either 1 serving (150 mg) of a proprietary blend of ancient peat and apple extracts (TRT) or placebo (PLA). Supervised resistance training consisted of 8 weeks of daily undulating periodized training followed by a 2-week overreach and a 2-week taper phase. Body composition was assessed using dual-energy X-ray absorptiometry and ultrasound at weeks 0, 4, 8, 10, and 12. Vital signs and blood markers were assessed at weeks 0, 8, and 12. Significant group × time (p < 0.05) interactions were present for ultrasound-determined cross-sectional area, which increased in TRT (+0.91 cm2) versus PLA (–0.08 cm2), as well as muscle thickness (TRT: +0.46; PLA: +0.04 cm). A significant group × time (p < 0.05) interaction existed for creatinine (TRT: +0.06; PLA: +0.15 mg/dL), triglycerides (TRT: +24.1; PLA: –20.2 mg/dL), and very-low-density lipoprotein (TRT: +4.9; PLA: –3.9 mg/dL), which remained within clinical ranges. Supplementation with a proprietary blend of ancient peat and apple extracts may enhance resistance training-induced skeletal muscle hypertrophy without affecting fat mass or blood chemistry in healthy males.
Acanthocorticium brueggemannii, a new corticioid genus and species related to cyphelloid fungi in the euagarics clade (Agaricales, Basidiomycota)
Authors: Baltazar Juliano M. , Gorjón Sergio P. , Pildain María Belén , Rajchenberg Mario , da Silveira Rosa Mara B.
Published: July 2015

Acanthocorticium brueggemannii gen. et sp. nov. is introduced based on specimens from Southern Brazil. This corticioid fungus is characterized by resupinate basidiomes with smooth to tuberculate hymenophore, a monomitic hyphal system with simple-septate hyphae, finely echinulate halocystidia, cylindrical to clavate, dextrinoid acanthophyses, and globose, hyaline, smooth, and thin-walled IKI– basidiospores. Phylogenetic analyses of a LSU data set and a combined data set of ITS and LSU were carried out and the new taxon was found to be related to cyphelloid fungi within the Agaricales. Descriptions and drawings of the microscopic features of A. brueggemannii are provided.
Dynamical equations for the period vectors in a periodic system under constant external stress
Authors: Liu Gang
Published: July 2015

The purpose of this paper is to derive the dynamical equations for the period vectors of a periodic system under constant external stress. The explicit starting point is Newton’s second law applied to halves of the system. Later statistics over indistinguishable translated states and forces associated with transport of momentum are applied to the resulting dynamical equations. In the final expressions, the period vectors are driven by the imbalance between internal and external stresses. The internal stress is shown to have both full interaction and kinetic energy terms.
Second Born fully differential cross sections for direct ionization of H(1s) by proton and antiproton collisions
Authors: Tantawi Reda S.
Published: July 2015

Fully differential cross sections for ionization of H(1s) atoms by collision with protons and antiprotons are calculated within the second-order Born closure approximation. The calculations are performed for emission of electrons with different energies into planes, moving from the scattering to the perpendicular planes at different impact energies and small scattering angles from which a significant contribution to the total cross section comes. The influence of the projectile’s charge and the second Born term on the calculations varies according to the incident energy, emission energy, and the scattering angle.
Resurrecting phenotypes from ancient DNA sequences: promises and perspectives
Authors: Campbell K.L. , Hofreiter M.
Published: July 2015

Anatomical changes in extinct mammalian lineages over evolutionary time, such as the loss of fingers and teeth and the rapid increase in body size that accompanied the late Miocene dispersal of the progenitors of Steller’s sea cows (Hydrodamalis gigas (Zimmermann, 1780)) into North Pacific waters and the convergent development of a thick pelage and accompanying reductions in ear and tail surface area of woolly mammoths (Mammuthus primigenius (Blumenbach, 1799)) and woolly rhinoceros (Coelodonta antiquitatis (Blumenbach, 1799)), are prime examples of adaptive evolution underlying the exploitation of new habitats. It is likely, however, that biochemical specializations adopted during these evolutionary transitions were of similar or even greater biological importance. As these “living” processes do not fossilize, direct information regarding the physiological attributes of extinct species has largely remained beyond the range of scientific inquiry. However, the ability to retrieve genomic sequences from ancient DNA samples, combined with ectopic expression systems, now permit the evolutionary origins and structural and functional properties of authentic prehistoric proteins to be examined in great detail. Exponential technical advances in ancient DNA retrieval, enrichment, and sequencing will soon permit targeted generation of complete genomes from hundreds of extinct species across the last one million years that, in combination with emerging in vitro expression, genome engineering, and cell differentiation techniques, promises to herald an exciting new trajectory of evolutionary research at the interface of biochemistry, genomics, palaeontology, and cell biology.
Involvement of p38 MAPK in the Anticancer Activity of Cultivated Cordyceps militaris
Authors: Chou Shang-Min , Lai Wan-Jung , Hong Tzuwen , Tsai Sheng-Hong , Chen Yen-Hsun , Kao Cheng-Hsiang , Chu Richard , Shen Tang-Long , Li Tsai-Kun
Published: July 2015

Cordyceps militaris is a traditional Chinese medicine frequently used for tonic and therapeutic purposes. Reports from our laboratory and others have demonstrated that extracts of the cultivated fruiting bodies of C. militaris (CM) exhibit a potent cytotoxic effect against many cancer cell lines, especially human leukemia cells. Here, we further investigated the underlying mechanism through which CM is cytotoxic to cancer cells. The CM-mediated induction of PARP cleavage and its related DNA damage signal (γH2AX) was diminished by caspase inhibitor I. In contrast, a ROS scavenger failed to prevent CM-mediated leukemia cell death. Moreover, two signaling molecules, AKT and p38 MAPK, were activated during the course of apoptosis induction. Employing MTT analysis, we found that a p38 MAPK inhibitor but not an AKT inhibitor could rescue cells from CM-mediated cell death, as well as inhibit the cleavage of PARP, formation of apoptotic bodies and up-regulation of the γH2AX signal. These results suggest that CM-mediated leukemia cell death occurs through the activation of the p38 MAPK pathway, indicating its potential therapeutic effects against human leukemia.
Recurrence relation for the 6j-symbol of suq(2) as a symmetric eigenvalue problem
Authors: Khavkine Igor
Published: July 2015

A well-known recurrence relation for the 6j-symbol of the quantum group su q(2) is realized as a tridiagonal, symmetric eigenvalue problem. This formulation can be used to implement an efficient numerical evaluation algorithm, taking advantage of existing specialized numerical packages. For convenience, all formulas relevant for such an implementation are collected in Appendix A. This realization is a byproduct of an alternative proof of the recurrence relation, which generalizes a classical (q = 1) result of Schulten and Gordon and uses the diagrammatic spin network formalism of Temperley–Lieb recoupling theory to simplify intermediate calculations.
Optical properties and electronic structures of axially-ligated group 9 porphyrins
Authors: Wang Bei-Bei , Zuo Huiping , Mack John , Majumdar Poulomi , Nyokong Tebello , Chan Kin Shing , Shen Zhen
Published: July 2015

A series of group 9 metal tetra-(p-tolyl)-porphyrin ( M(ttp) , M = Co(II) , Rh(III) , Ir(III)) complexes with axial phenyl substituents have been synthesized and characterized. An aryl bromide cleavage reaction of transition metal complexes was used to prepare the complexes from Co(ttp) , Rh(ttp) Cl and Ir(ttp)COCl , respectively. Magnetic circular dichroism (MCD) spectroscopy and TD-DFT calculations have been used to study trends in the optical spectra and electronic structures. The effect of introducing different para-substituents on the phenyl substituents was examined. During fluorescence emission studies, phosphorescence was observed for the Ir(III) complexes in the near infrared (NIR) region.
RAPID DIAGNOSIS OF BLUETONGUE VIRUS SEROTYPES 2 AND 12 INFECTION BY REVERSE TRANSCRIPTION LOOP-MEDIATED ISOTHERMAL AMPLIFICATION
Authors: Yang Jia-Ling , Li Yi-Chia , Hu Shu-Chia , Lee Fan , Wang Fun-In
Published: July 2015

Bluetongue (BT), an arthropod-borne viral disease, is caused by the bluetongue virus (BTV), belonging to the genus Orbivirus of the family Reoviridae. Most species of ruminants are susceptible to BTV, but most infections go subclinical. These 'reservoir hosts' may potentially further increase the viral transmission and expansion of the disease; thus, detection of subclinical infection is important. To detect the BTV, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed using primers targeted to six regions of the segment 5 (NS1) gene of the BTV2/KM/2003. The assay was completed in 1 h at a temperature 65°C, and the products were specifically digested with MboII enzyme presented in the target region. The in vitro sensitivity of the RT-LAMP was 100 copies, characterized by a qRT-PCR. The RT-LAMP did not cross-react with four tested common ruminant infectious agents, namely foot and mouth disease virus, goat pox virus, bovine herpesvirus 1, and Clostridium perfrigens. The RT-LAMP was applied to whole blood samples from 15 clinically healthy dairy cattle, and was able to detect BTV from 3/15 animals, and in particular 1 of the 3 animals was seronegative by cELISA. Positive RT-LAMP samples were reproducible. This RT-LAMP provides a simple, efficient, and sensitive method to specifically detect BTV and is suitable for the screening of field samples with a potential to pick up subclinical infection. The alignments of the outer primer region indicated matches of > 85% with 18 out of 26 BTV serotypes, implying its potential as universal primers.
Enlarged major arcs in the Waring–Goldbach problem
Authors: Li Taiyu
Published: July 2015

In this short note, we treat the enlarged major arcs of circle method in the Waring–Goldbach problem.
Extensive parity analysis of broken 5-diamond partitions
Authors: Lin Bernard L. S. , Malik Amita , Wang Andrew Y. Z.
Published: July 2015

In this paper, we investigate congruences for [Formula: see text] modulo 2 and characterize the parity of [Formula: see text] and [Formula: see text] according to the arithmetic property of [Formula: see text]. As a consequence, we obtain various Ramanujan type congruences for [Formula: see text]. We also extend these results to several infinite families of congruences.
Local factors valued in normal domains
Authors: Česnavičius Kęstutis
Published: July 2015

We give an exposition of Deligne’s theory of local [Formula: see text]-factors over fields and discrete valuation rings under the assumption that the theory over the complex numbers is known. We then employ standard techniques from algebraic geometry to deduce the theory of local [Formula: see text]-factors over arbitrary normal integral schemes.
Finite element modeling and analysis of planetary gear transmission based on transient meshing properties
Authors: Zeng Qingliang , Jiang Shoubo , Wan Lirong , Li Xueyi
Published: July 2015

Planetary gear trains are widely applied in various transmission units. Whether strengths of all gears are accurately calculated or not can affect reliability of the entire system significantly. Strength calculation method for planetary gear trains usually follows the method for cylindrical gears, in which the worst meshing positions for both contact stress and bending stress cannot be determined precisely, and calculation results tend to be conservative. To overcome these shortcomings, a kinematics analysis for a planetary gear train is firstly performed, in which the influence of relative speed is investigated. Then the finite element strength analysis of a planetary gear train based on its transient meshing properties is carried out in ANSYS. Time–history curves of contact and bending stresses of sun gear, planetary gears and ring gear are respectively obtained. Also the accurate moment and its corresponding position of the maximum stress are precisely determined. Finally, calculation results of finite element method (FEM) and traditional method are compared in order to verify the effectiveness. Simulation and comparison show the stability of the proposed method in this paper. Researches in this paper establish the foundations for fatigue analysis and optimization for a planetary gear train.
Switchgrass as a bioenergy feedstock: advances in breeding and genomics research
Authors: Bhandari H.S. , Missaoui A.M. , Bouton J.H. , Saha M.C.
Published: July 2015

Switchgrass (Panicum virgatum L), a native perennial of the North American prairie, possesses high biomass yield potential in marginal environments with limited input. It is an outcrossing tetraploid (2n = 4x = 36) with disomic inheritance. Previous research on cultivar improvement was focused primarily on herbage yield and forage digestibility. The decision of the U.S. Department of Energy Biomass Feedstock Development Program (NFDP) to develop switchgrass as a lignocellulosic bioenergy feedstock in the USA in the 1990s prompted a growing motivation for breeding and genomics research. The species is in early stages of domestication and current cultivars include mostly early releases for forage use that were selected directly from collected strains. Recent releases specifically for biomass feedstock have undergone one or two cycles of selection. As an outcrossing self-incompatible species, switchgrass possesses ample genetic diversity both between and within native populations. Conventional population improvement approaches such as recurrent restricted phenotypic selection (RRPS) are effective in improving forage yield and digestibility. Hybrids between different populations also demonstrated heterosis for key feedstock traits. However, genetic gains per year from selection using conventional approaches are low due to perennial growth habit and low heritability of important traits. Genomic approaches could be helpful in improving selection gain. Significant efforts have been placed in developing genomics resources. Genetic linkage maps were published and a large number of DNA-based markers were developed. Whole-genome sequencing is near completion, and the genetic bases of inheritance of key feedstock traits are being investigated. New insights into the molecular mechanisms will enable tailoring more efficient cultivar breeding approaches in the future.
An economic analysis of bioethanol production from the marine macroalga Ulva (Chlorophyta)
Authors: Korzen Leor , Peled Yoav , Shamir Shiri Zemah , Shechter Mordechai , Gedanken Aharon , Abelson Avigdor , Israel Alvaro
Published: July 2015

We performed a cost-benefit analysis for bioethanol production using biomass of Ulva rigida, a marine macroalga (seaweed), co-cultured with fish in an intensive offshore aquaculture unit. This is the first report for such analysis that takes into consideration offshore seaweed cultivation and uses a recently developed, novel and simplified ethanol production technology that is devoid of costly pre-treatments imposed to the seaweed biomass. By simultaneously producing ethanol with valuable Dried Distillers Grains with Solubles (DDGS) by-products such as animal feed, the economic viability of this system is plausible over a production range of 77–240 dry tons of seaweed per day. As such, applying the model to suggested future scenarios for the Israeli Mediterranean shorelines, which limits aquaculture to ca. 600 ha, results in unprofitability. Further, sensitivity analyses place profitability as mainly dependent on DDGS prices and on the daily growth rate (biomass yield) of the macroalga. These two are key factors to achieve profitability at the 600-ha scenario.
Neuropeptide S inhibits gastrointestinal motility and increases mucosal permeability through nitric oxide
Authors: Wan Saudi Wan Salman , Halim Md. Abdul , Rudholm-Feldreich Tobias , Gillberg Linda , Rosenqvist Evelina , Tengholm Anders , Sundbom Magnus , Karlbom Urban , Näslund Erik , Webb Dominic-Luc , Sjöblom Markus , Hellström Per M.
Published: July 2015

Neuropeptide S (NPS) receptor (NPSR1) polymorphisms are associated with enteral dysmotility and inflammatory bowel disease (IBD). This study investigated the role of NPS in conjunction with nitrergic mechanisms in the regulation of intestinal motility and mucosal permeability. In rats, small intestinal myoelectric activity and luminal pressure changes in small intestine and colon, along with duodenal permeability, were studied. In human intestine, NPS and NPSR1 were localized by immunostaining. Pre- and postprandial plasma NPS was measured by ELISA in healthy and active IBD humans. Effects and mechanisms of NPS were studied in human intestinal muscle strips. In rats, NPS 100-4,000 pmol·kg−1·min−1had effects on the small intestine and colon. Low doses of NPS increased myoelectric spiking ( P < 0.05). Higher doses reduced spiking and prolonged the cycle length of the migrating myoelectric complex, reduced intraluminal pressures ( P < 0.05-0.01), and increased permeability ( P < 0.01) through NO-dependent mechanisms. In human intestine, NPS localized at myenteric nerve cell bodies and fibers. NPSR1 was confined to nerve cell bodies. Circulating NPS in humans was tenfold below the ∼0.3 nmol/l dissociation constant ( Kd) of NPSR1, with no difference between healthy and IBD subjects. In human intestinal muscle strips precontracted by bethanechol, NPS 1–1,000 nmol/l induced NO-dependent muscle relaxation ( P < 0.05) that was sensitive also to tetrodotoxin ( P < 0.01). In conclusion, NPS inhibits motility and increases permeability in neurocrine fashion acting through NO in the myenteric plexus in rats and humans. Aberrant signaling and upregulation of NPSR1 could potentially exacerbate dysmotility and hyperpermeability by local mechanisms in gastrointestinal functional and inflammatory reactions.
Protocadherin-1 binds to SMAD3 and suppresses TGF-β1-induced gene transcription
Authors: Faura Tellez Grissel , Vandepoele Karl , Brouwer Uilke , Koning Henk , Elderman Robin M. , Hackett Tillie-Louise , Willemse Brigitte W. M. , Holloway John , Van Roy Frans , Koppelman Gerard H. , Nawijn Martijn C.
Published: July 2015

Genetic studies have identified Protocadherin-1 ( PCDH1) and Mothers against decapentaplegic homolog-3 ( SMAD3) as susceptibility genes for asthma. PCDH1 is expressed in bronchial epithelial cells and has been found to interact with SMAD3 in yeast two-hybrid (Y2H) overexpression assays. Here, we test whether PCDH1 and SMAD3 interact at endogenous protein levels in bronchial epithelial cells and evaluate the consequences thereof for transforming growth factor-β1 (TGF-β1)-induced gene transcription. We performed Y2H screens and coimmunoprecipitation (co-IP) experiments of PCDH1 and SMAD3 in HEK293T and 16HBE14o− (16HBE) cell lines. Activity of a SMAD3-driven luciferase reporter gene in response to TGF-β1 was measured in BEAS-2B cells transfected with PCDH1 and in 16HBE cells transfected with PCDH1-small-interfering RNA (siRNA). TGF-β1-induced gene expression was quantified in BEAS-2B clones overexpressing PCDH1 and in human primary bronchial epithelial cells (PBECs) transfected with PCDH1-siRNA. We confirm PCDH1 and SMAD3 interactions by Y2H and by co-IP in HEK293T cells overexpressing both proteins, and at endogenous protein levels in 16HBE cells. TGF-β-induced activation of a SMAD3-driven reporter was reduced by exogenous PCDH1 in BEAS2B cells, whereas it was increased by siRNA-mediated knockdown of endogenous PCDH1 in 16HBE cells. Overexpression of PCDH1 suppressed expression of TGF-β target genes in BEAS-2B cells, whereas knockdown of PCDH1 in human PBECs increased TGF-β-induced gene expression. In conclusion, we demonstrate that PCDH1 binds to SMAD3 and regulates its activation by TGF-β signaling in bronchial epithelial cells. We propose that PCDH1 and SMAD3 act in a single pathway in asthma susceptibility that affects sensitivity of the airway epithelium to TGF-β.