bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of GOUNDRY, a cryptic subgroup of Anopheles gambiae s.l., and its impact on susceptibility to Plasmodium infection
Authors: Crawford Jacob E. , Riehle Michelle M. , Markianos Kyriacos , Bischoff Emmanuel , Guelbeogo Wamdaogo M. , Gneme Awa , Sagnon N'Fale , Vernick Kenneth D. , Nielsen Rasmus , Lazzaro Brian P.
Published: February 2016

The recent discovery of a previously unknown genetic subgroup of Anopheles gambiae sensu lato underscores our incomplete understanding of complexities of vector population demographics in Anopheles. This subgroup, named GOUNDRY, does not rest indoors as adults and is highly susceptible to Plasmodium infection in the laboratory. Initial description of GOUNDRY suggested it differed from other known Anopheles taxa in surprising and sometimes contradictory ways, raising a number of questions about its age, population size and relationship to known subgroups. To address these questions, we sequenced the complete genomes of 12 wild‐caught GOUNDRY specimens and compared these genomes to a panel of Anopheles genomes. We show that GOUNDRY is most closely related to Anopheles coluzzii, and the timing of cladogenesis is not recent, substantially predating the advent of agriculture. We find a large region of the X chromosome that has swept to fixation in GOUNDRY within the last 100 years, which may be an inversion that serves as a partial barrier to contemporary gene flow. Interestingly, we show that GOUNDRY has a history of inbreeding that is significantly associated with susceptibility to Plasmodium infection in the laboratory. Our results illuminate the genomic evolution of one of probably several cryptic, ecologically specialized subgroups of Anopheles and provide a potent example of how vector population dynamics may complicate efforts to control or eradicate malaria.
Too early and too northerly: evidence of temperate trees in northern Central Europe during the Younger Dryas
Authors: Robin Vincent , Nadeau Marie‐Josée , Grootes Pieter M. , Bork Hans‐Rudolf , Nelle Oliver
Published: February 2016

This paper presents highly unexpected paleobotanical data.

Eight 14C‐accelerator mass spectrometry (AMS) dates of soil macrocharcoal pieces, identified taxonomically, indicate the presence of oak and beech in the Younger Dryas, and pine in the Allerød, in the northernmost low mountain range of Central Europe, the Harz Mountains, in Germany. If the presence of pine at such latitude and periods is not surprising, the presence of temperate‐adapted trees is highly improbable, because they are assumed to have reached the area from a southern location several thousand years later.

Two hypotheses are postulated to explain this record. Both are related to the warm periods of the Bølling and Allerød: the classically ‘short’ duration of this warm period makes the migration of the temperate trees from the identified refuge areas in the southern location implausible, and so the presence of intermediary microrefugia at a medium latitude in Central Europe is postulated; recent data reveal that the warm period of the Late Glacial phase was much longer than considered in the classical view and, thus, would be long enough for a northward migration of temperate‐adapted trees.

Although our dataset does not permit disentanglement of these hypotheses, it provides significant innovative insights for the biogeography of Central Europe.
Atherogenesis: hyperhomocysteinemia interactions with LDL, macrophage function, paraoxonase 1, and exercise
Authors: Chernyavskiy Ilya , Veeranki Sudhakar , Sen Utpal , Tyagi Suresh C.
Published: February 2016

Despite great strides in understanding the atherogenesis process, the mechanisms are not entirely known. In addition to diet, cigarette smoking, genetic predisposition, and hypertension, hyperhomocysteinemia (HHcy), an accumulation of the noncoding sulfur‐containing amino acid homocysteine (Hcy), is a significant contributor to atherogenesis. Although exercise decreases HHcy and increases longevity, the complete mechanism is unclear. In light of recent evidence, in this review, we focus on the effects of HHcy on macrophage function, differentiation, and polarization. Though there is need for further evidence, it is most likely that HHcy‐mediated alterations in macrophage function are important contributors to atherogenesis, and HHcy‐countering strategies, such as nutrition and exercise, should be included in the combinatorial regimens for effective prevention and regression of atherosclerotic plaques. Therefore, we also included a discussion on the effects of exercise on the HHcy‐mediated atherogenic process.
Late Manifestation of Coronary Sinus and Left Atrial Perforation of a Left Ventricular Pacemaker Lead at Extraction
Authors: OESTERLE ADAM , BALKHY HUSAM H. , GREEN JOHN , BURKE MARTIN C.
Published: February 2016

A 56‐year‐old man presented for lead extraction of a left ventricular (LV) lead that had been deactivated due to hiccups and of a right ventricular (RV) lead with a high threshold. Pus was noted upon entering the pocket. The right atrial and RV leads were extracted, but traction on the LV lead caused ischemia and was not performed. An echocardiogram demonstrated the lead in the left atrium and a robotic‐assisted thoracotomy was used to remove the lead that had unroofed the coronary sinus, gone into the left atrium, and perforated through the free wall into the pericardium.
Attentional gain and processing capacity limits predict the propensity to neglect unexpected visual stimuli
Authors: Papera Massimiliano , Richards Anne
Published: February 2016

Exogenous allocation of attentional resources allows the visual system to encode and maintain representations of stimuli in visual working memory (VWM). However, limits in the processing capacity to allocate resources can prevent unexpected visual stimuli from gaining access to VWM and thereby to consciousness. Using a novel approach to create unbiased stimuli of increasing saliency, we investigated visual processing during a visual search task in individuals who show a high or low propensity to neglect unexpected stimuli. When propensity to inattention is high, ERP recordings show a diminished amplification concomitantly with a decrease in theta band power during the N1 latency, followed by a poor target enhancement during the N2 latency. Furthermore, a later modulation in the P3 latency was also found in individuals showing propensity to visual neglect, suggesting that more effort is required for conscious maintenance of visual information in VWM. Effects during early stages of processing (N80 and P1) were also observed suggesting that sensitivity to contrasts and medium‐to‐high spatial frequencies may be modulated by low‐level saliency (albeit no statistical group differences were found). In accordance with the Global Workplace Model, our data indicate that a lack of resources in low‐level processors and visual attention may be responsible for the failure to “ignite” a state of high‐level activity spread across several brain areas that is necessary for stimuli to access awareness. These findings may aid in the development of diagnostic tests and intervention to detect/reduce inattention propensity to visual neglect of unexpected stimuli.
Surveillance of maternal antibodies against West Nile virus in chicken eggs in South‐West Germany
Authors: Börstler Jessica , Engel Dimitri , Petersen Mathis , Poggensee Claudia , Jansen Stephanie , Schmidt‐Chanasit Jonas , Lühken Renke
Published: February 2016

Objective

The emergence of West Nile virus (WNV) in several European countries increases the risk of its introduction to Germany. This study evaluated a new method for WNV surveillance by testing for maternal antibodies in chicken eggs.

Methods

A total of 1,990 eggs were collected in 35 sampling sites in the south‐west of Germany and tested for WNV‐specific antibodies.

Results

The results did not indicate evidence for WNV circulation in the study area.

Conclusion

This work serves as a proof‐of‐concept that such a method is useful and a potential alternative to use of sentinel chicken for regular WNV surveillance.
Proteomic analysis reveals the differential histone programs between male germline cells and vegetative cells in Lilium davidii
Authors: Yang Hao , Yang Ning , Wang Tai
Published: February 2016

In flowering plants, male germline fate is determined after asymmetric division of the haploid microspore. Daughter cells have distinct fates: the generative cell (GC) undergoes further mitosis to generate sperm cells (SCs), and the vegetative cell (VC) terminally differentiates. However, our understanding of the mechanisms underlying germline development remains limited. Histone variants and modifications define chromatin states, and contribute to establishing and maintaining cell identities by affecting gene expression. Here, we constructed a lily protein database, then extracted and detailed histone entries into a comprehensive lily histone database. We isolated large amounts of nuclei from VCs, GCs and SCs from lily, and profiled histone variants of all five histone families in all three cell types using proteomics approaches. We revealed 92 identities representing 32 histone variants: six for H1, 11 for H2A, eight for H2B, five for H3 and two for H4. Nine variants, including five H1, two H2B, one H3 and one H4 variant, specifically accumulated in GCs and SCs. We also detected H3 modification patterns in the three cell types. GCs and SCs had almost identical histone profiles and similar H3 modification patterns, which were significantly different from those of VCs. Our study also revealed the presence of multiple isoforms, and differential expression patterns between isoforms of a variant. The results suggest that differential histone programs between the germline and companion VCs may be established following the asymmetric division, and are important for identity establishment and differentiation of the male germline as well as the VC.
Dynamin‐Actin Cross Talk Contributes to Phagosome Formation and Closure
Authors: Marie‐Anaïs Florence , Mazzolini Julie , Herit Floriane , Niedergang Florence
Published: February 2016

Phagocytosis is a mechanism used by macrophages to internalize and eliminate microorganisms or cellular debris. It relies on profound rearrangements of the actin cytoskeleton that is the driving force allowing plasma membrane extension around the particle. The closure step of phagocytosis, however, remains poorly defined. We used a dedicated experimental setup with Total Internal Reflection Fluorescence Microscopy (TIRFM) to monitor phagosome formation and closure in three dimensions in living cells. We show that dynamin‐2, which mediates the scission of endocytic vesicles, was recruited early and concomitantly with actin during phagosome formation. Dynamin‐2 accumulated at the site of phagosome closure in living macrophages. Inhibition of its activity with dominant negative mutants or drugs demonstrated that dynamin‐2 is implicated in actin dynamics and pseudopod extension. Depolymerization of actin led to impaired dynamin‐2 recruitment or activity. Finally, we show that dynamin‐2 plays a critical role in the effective scission of the phagosome from the plasma membrane. Thus, we establish that a cross talk between actin and dynamin takes place for phagosome formation and closure before dynamin functions for scission.
Endothelin‐1 modulates methacholine‐induced cutaneous vasodilatation but not sweating in young human skin
Authors: Halili Lyra , Singh Maya Sarah , Fujii Naoto , Alexander Lacy M. , Kenny Glen P.
Published: February 2016

Key points

Endothelin‐1 (ET‐1) is a potent endothelial‐derived vasoconstrictor that may modulate cholinergic cutaneous vascular regulation. Endothelin receptors are also expressed on the human eccrine sweat gland, although it remains unclear whether ET‐1 modulates cholinergic sweating.

We investigated whether ET‐1 attenuates cholinergic cutaneous vasodilatation and sweating through a nitric oxide synthase (NOS)‐dependent mechanism. Our findings show that ET‐1 attenuates methacholine‐induced cutaneous vasodilatation through a NOS‐independent mechanism.

We also demonstrate that ET‐1 attenuates cutaneous vasodilatation in response to sodium nitroprusside, suggesting that ET‐1 diminishes the dilatation capacity of vascular smooth muscle cells.

We show that ET‐1 does not modulate methacholine‐induced sweating at any of the administered concentrations.

Our findings advance our knowledge pertaining to the peripheral control underpinning the regulation of cutaneous blood flow and sweating and infer that ET‐1 may attenuate the heat loss responses of cutaneous blood flow, but not sweating.

The present study investigated the effect of endothelin‐1 (ET‐1) on cholinergic mechanisms of end‐organs (i.e. skin blood vessels and sweat glands) for heat dissipation. We evaluated the hypothesis that ET‐1 attenuates cholinergic cutaneous vasodilatation and sweating through a nitric oxide synthase (NOS)‐dependent mechanism. Cutaneous vascular conductance (CVC) and sweat rate were assessed in three protocols: in Protocol 1 (n = 8), microdialysis sites were perfused with lactated Ringer solution (Control), 40 pm, 4 nm or 400 nm ET‐1; in Protocol 2 (n = 11) sites were perfused with lactated Ringer solution (Control), 400 nm ET‐1, 10 mm NG‐nitro‐l‐arginine (l‐NNA; a NOS inhibitor) or a combination of 400 nm ET‐1 and 10 mm l‐NNA; in Protocol 3 (n = 8), only two sites (Control and 400 nm ET‐1) were utilized to assess the influence of ET‐1 on the dilatation capacity of vascular smooth muscle cells (sodium nitroprusside; SNP). Methacholine (MCh) was co‐administered in a dose‐dependent manner (0.0125, 0.25, 5, 100, 2000 mm, each for 25 min) at all skin sites. ET‐1 at 400 nm (P < 0.05) compared to lower doses (40 pm and 4 nm) (all P > 0.05) significantly attenuated increases in CVC in response to 0.25 and 5 mm MCh. A high dose of ET‐1 (400 nm) co‐infused with l‐NNA further attenuated CVC during 0.25, 5 and 100 mm MCh administration relative to the ET‐1 site (all P < 0.05). Cutaneous vasodilatation in response to SNP was significantly blunted after administration of 400 nm ET‐1 (P < 0.05). We show that ET‐1 attenuates cutaneous vasodilatation through a NOS‐independent mechanism, possibly through a vascular smooth muscle cell‐dependent mechanism, and methacholine‐induced sweating is not altered by ET‐1.
Turbine Blade Tip Film Cooling With Blade Rotation—Part I: Tip and Pressure Side Coolant Injection
Authors: Tamunobere Onieluan , Acharya Sumanta
Published: February 2016

An experimental study of film cooling is conducted on the tip of a turbine blade with a blade rotation speed of 1200 rpm. The coolant is injected from the blade tip and pressure side (PS) holes, and the effect of the blowing ratio on the heat transfer coefficient and film cooling effectiveness of the blade tip is investigated. The blade has a tip clearance of 1.7% of the blade span and consists of a cut back squealer rim, two cylindrical tip holes, and six shaped PS holes. The stator–rotor–stator test section is housed in a closed loop wind tunnel that allows for the performance of transient heat transfer tests. Measurements of the heat transfer coefficient and film cooling effectiveness are done on the blade tip using liquid crystal thermography. These measurements are reported for the no coolant case and for blowing ratios of 1.0, 1.5, 2.0, 3.0, and 4.0. The heat transfer result for the no coolant injection shows a region of high heat transfer on the blade tip near the blade leading edge region as the incident flow impinges on that region. This region of high heat transfer extends and stretches on the tip as more coolant is introduced through the tip holes at higher blowing ratios. The cooling results show that increasing the blowing ratio increases the film cooling effectiveness. The cooling effectiveness signatures indicate that the tip coolant is pushed toward the blade suction side thereby providing better coverage in that region. This shift in coolant flow toward the blade suction side, as opposed to the PS in stationary studies, can primarily be attributed to the effects of the blade relative motion.
Ion energy distribution function measurements by laser-induced fluorescence in a dual radio frequency sheath
Authors: Moore Nathaniel B. , Gekelman Walter , Pribyl Patrick
Published: February 2016

Ion dynamics are investigated in a dual frequency radio frequency sheath as a function of radius above a 30 cm diameter biased silicon wafer in an industrial inductively coupled (440 kHz, 500 W) plasma etch tool. Ion velocity distribution (IVD) function measurements in the argon plasma are taken using laser induced fluorescence. Planar sheets of laser light enter the chamber both parallel and perpendicular to the surface of the wafer in order to measure both parallel and perpendicular IVDs at thousands of spatial positions. A fast (30 ns exposure) charge coupled device camera measures the resulting fluorescence with a spatial resolution of 0.4 mm. The dual-frequency bias on the wafer is comprised of a 2 MHz low frequency (LF) bias and a 19 MHz high frequency bias. The laser is phase locked to the LF bias and IVD measurements are taken at several different LF phases. Ion energy distribution (IED) function measurements and calculated moments are compared for several cases. IEDs were measured at two disparate phases of the phase-locked LF bias. IEDs were found to be multipeaked and were well-approximated by a sum of Maxwellian distributions. The calculated fluxes in the dual frequency case were found to be substantially more radially uniform than the single frequency bias case. For industrial applications, this radially uniform ion flux is evidently a trade off with the undesirable multipeaked structure in the IEDs.
Growth of Bi2Se3 topological insulator films using a selenium cracker source
Authors: Ginley Theresa P. , Law Stephanie
Published: February 2016

In this article, the authors describe growth of high-quality Bi2Se3 topological insulator films using a selenium cracking source on c-plane sapphire substrates. Films are grown using molecular beam epitaxy and characterized by Hall effect measurements and atomic force microscopy. The use of a cracker sources results in films with low carrier density and reduced aging effects. Growth conditions giving the best electrical properties correspond with the best surface structure as determined by atomic force microscopy. This improved film quality opens the door to the creation of real electronic or spintronic devices based on these unique materials.
Scatter radiation intensities around a clinical digital breast tomosynthesis unit and the impact on radiation shielding considerations
Authors: Yang Kai , Li Xinhua , Liu Bob
Published: February 2016

Purpose:

To measure the scattered radiation intensity around a clinical digital breast tomosynthesis (DBT) unit and to provide updated data for radiation shielding design for DBT systems with tungsten‐anode x‐ray tubes.

Methods:

The continuous distribution of scattered x‐rays from a clinical DBT system (Hologic Selenia Dimensions) was measured within an angular range of 0°–180° using a linear‐array x‐ray detector (X‐Scan 0.8f3‐512, Detection Technology, Inc., Finland), which was calibrated for the x‐ray spectrum range of the DBT unit. The effects of x‐ray field size, phantom size, and x‐ray kVp/filter combination were investigated. Following a previously developed methodology by Simpkin, scatter fraction was determined for the DBT system as a function of angle around the phantom center. Detailed calculations of the scatter intensity from a DBT system were demonstrated using the measured scatter fraction data.

Results:

For the 30 and 35 kVp acquisition, the scatter‐to‐primary‐ratio and scatter fraction data closely matched with data previously measured by Simpkin. However, the measured data from this study demonstrated the nonisotropic distribution of the scattered radiation around a DBT system, with two strong peaks around 25° and 160°. The majority scatter radiation (>70%) originated from the imaging detector assembly, instead of the phantom. With a workload from a previous survey performed at MGH, the scatter air kerma at 1 m from the phantom center for wall/door is 1.76 × 10−2 mGy patient−1, for floor is 1.64 × 10−1 mGy patient−1, and for ceiling is 3.66 × 10−2 mGy patient−1.

Conclusions:

Comparing to previously measured data for mammographic systems, the scatter air kerma from Holgoic DBT is at least two times higher. The main reasons include the harder primary beam with higher workload (measured with total mAs/week), added tomosynthesis acquisition, and strong small angle forward scattering. Due to the highly conservative initial assumptions, the shielding recommendation from NCRP Report 147 is still sufficient for the Hologic DBT system given the workload from a previous survey at MGH. With the data provided from this study, accurate shielding calculation can be performed for Hologic DBT systems with specific workload and barrier distance.
Automated fluence map optimization based on fuzzy inference systems
Authors: Dias Joana , Rocha Humberto , Ventura Tiago , Ferreira Brígida , Lopes Maria do Carmo
Published: February 2016

Purpose:

The planning of an intensity modulated radiation therapy treatment requires the optimization of the fluence intensities. The fluence map optimization (FMO) is many times based on a nonlinear continuous programming problem, being necessary for the planner to define a priori weights and/or lower bounds that are iteratively changed within a trial‐and‐error procedure until an acceptable plan is reached. In this work, the authors describe an alternative approach for FMO that releases the human planner from trial‐and‐error procedures, contributing for the automation of the planning process.

Methods:

The FMO is represented by a voxel‐based convex penalty continuous nonlinear model. This model makes use of both weights and lower/upper bounds to guide the optimization process toward interesting solutions that are able to satisfy all the constraints defined for the treatment. All the model's parameters are iteratively changed by resorting to a fuzzy inference system. This system analyzes how far the current solution is from a desirable solution, changing in a completely automated way both weights and lower/upper bounds. The fuzzy inference system is based on fuzzy reasoning that enables the use of common‐sense rules within an iterative optimization process. The method is built in two stages: in a first stage, an admissible solution is calculated, trying to guarantee that all the treatment planning constraints are being satisfied. In this first stage, the algorithm tries to improve as much as possible the irradiation of the planning target volumes. In a second stage, the algorithm tries to improve organ sparing, without jeopardizing tumor coverage.

Results:

The proposed methodology was applied to ten head‐and‐neck cancer cases already treated in the Portuguese Oncology Institute of Coimbra (IPOCFG) and signalized as complex cases. IMRT treatment was considered, with 7, 9, and 11 equidistant beam angles. It was possible to obtain admissible solutions for all the patients considered and with no human planner intervention. The results obtained were compared with the optimized solution using a similar optimization model but with human planner intervention. For the vast majority of cases, it was possible to improve organ sparing and at the same time to assure better tumor coverage.

Conclusions:

Embedding a fuzzy inference system into FMO allows human planner reasoning to be used in the guidance of the optimization process toward interesting regions in a truly automated way. The proposed methodology is capable of calculating high quality plans within reasonable computational times and can be an important contribution toward fully automated radiation therapy treatment planning.
Risky reactor fuel to linger
Authors: Cho Adrian
Published: February 2016

Getting highly enriched uranium out of research reactors will stretch to at least 2035, U.S. study concludes.
Calling all failed replication experiments
Authors: Kaiser Jocelyn
Published: February 2016

New journal will publish methods, data, and results.
What makes DARPA tick?
Authors: Mervis Jeffrey
Published: February 2016

The stellar reputation of this small but mighty defense agency rests on the unparalleled clout of its program managers.
Biology came late, and arrived with a bang
Authors: Mervis Jeffrey
Published: February 2016

New global threats made expertise in the life sciences essential.
Holocene deceleration of the Greenland Ice Sheet
Authors: MacGregor Joseph A. , Colgan William T. , Fahnestock Mark A. , Morlighem Mathieu , Catania Ginny A. , Paden John D. , Gogineni S. Prasad
Published: February 2016

Keeping a stiff upper layer

The interior of the Greenland Ice Sheet is growing thicker, in contrast to the thinning that is occurring at its edges. Why? MacGregor
et al.
conclude that more snow is accumulating and that the ice in the interior is flowing more slowly than it did thousands of years ago (see the Perspective by Hvidberg). During the last glacial period, higher rates of atmospheric dust deposition produced softer ice, which flowed more readily than cleaner ice. During most of the Holocene, though, atmospheric dust concentrations were lower, and the less-dusty ice that formed was stiffer, meaning it did not flow or thin so rapidly. Thus, the thickening seen today in the central regions of Greenland is partly a response to changes in ice rheology that occurred thousands of years ago.

Science
, this issue p.
590
; see also p.
562
Transmutable nanoparticles with reconfigurable surface ligands
Authors: Kim Youngeun , Macfarlane Robert J. , Jones Matthew R. , Mirkin Chad A.
Published: February 2016

Controlled colloid bonding using DNA

Colloidal particles can act as analogs of atoms for studying crystallization and packing behavior, but they don't naturally bond together the way atoms do. Short strands of DNA are one versatile way to link together colloidal particles (see the Perspective by Tao). Kim
et al.
designed a series of gold colloids with DNA ligands that reversibly bound to or released neighboring particles via DNA strands that opened or closed hairpin loops. Liu
et al.
devised a set of DNA strands that pack into origami structures. Inside each structure were strands that cage a gold nanoparticle. These were further linked to other uncaged nanoparticles to assemble a diamond-like structure. Changing the strand design yielded a wide range of sparsely packed colloidal crystals.

Science
, this issue p.
561
, p.
579
; see also p.
582
A small-molecule inhibitor of sarcomere contractility suppresses hypertrophic cardiomyopathy in mice
Authors: Green Eric M. , Wakimoto Hiroko , Anderson Robert L. , Evanchik Marc J. , Gorham Joshua M. , Harrison Brooke C. , Henze Marcus , Kawas Raja , Oslob Johan D. , Rodriguez Hector M. , Song Yonghong , Wan William , Leinwand Leslie A. , Spudich James A. , McDowell Robert S. , Seidman J. G. , Seidman Christine E.
Published: February 2016

Powering down yields a healthier heart

In hypertrophic cardiomyopathy (HCM), the heart muscle enlarges and becomes progressively less efficient at pumping blood. HCM can be caused by mutations in components of the sarcomere (the heart's contractile unit), most notably myosin. Hypercontractility is among the earliest heart disturbances seen in mice carrying these myosin mutations, implying that the mutations inflict their damage by increasing myosin's power production. Green
et al.
identified a small molecule that binds to myosin and inhibits its activity (see the Perspective by Warshaw). When orally administered to young mice, the molecule prevented the development of several hallmark features of HCM without adversely affecting skeletal muscle.

Science
, this issue p.
617
; see also p.
556
Addressing an antiferromagnetic memory
Authors: Marrows Christopher
Published: February 2016

Antiferromagnets could form a stable and robust platform for future spintronic technology

[Also see Report by

Wadley
et al.

]
Draft Genome Sequence of Mycobacterium tuberculosis KT-0204, Isolated in South Korea
Authors: Yun Mi-ran , Han Seung Jung , Yoo Won Gi , Kwon Taesoo , Lee Sanghyun , Lee Jong Seok , Kim Dae-Won
Published: February 2016

Here, we describe the draft genome sequence of
Mycobacterium tuberculosis
KT-0204, non-Beijing family. This sequence will reveal genes related to the evolution and adaptation of
M. tuberculosis
KT-0204 in human hosts.
Draft Genome Sequence of Caloramator mitchellensis, a Thermoanaerobe Isolated from the Waters of the Great Artesian Basin
Authors: Patel Bharat K. C. , Te'o Valentino Setoa Junior
Published: February 2016

The genome sequence of
Caloramator mitchellensis
strain VF08, a rod-shaped, heterotrophic, strictly anaerobic bacterium isolated from the free-flowing waters of a Great Artesian Basin (GAB) bore well located in Mitchell, an outback Queensland town in Australia, is reported here. The analysis of the 2.42-Mb genome sequence indicates that the attributes of the genome are consistent with its physiological and phenotypic traits.
Complete Genome Sequence of the WHO International Standard for HIV-2 RNA Determined by Deep Sequencing
Authors: Ham Claire , Morris Clare , Berry Neil
Published: February 2016

The World Health Organization (WHO) International Standard for HIV-2 RNA nucleic acid assays was characterized by complete genome deep sequencing. The entire coding sequence and flanking long terminal repeats (LTRs), including minority species, were assigned subtype A. This information will aid design, development, and evaluation of HIV-2 RNA amplification assays.
Complete Genome Sequence of Streptococcus salivarius HSISS4, a Human Commensal Bacterium Highly Prevalent in the Digestive Tract
Authors: Mignolet Johann , Fontaine Laetitia , Kleerebezem Michiel , Hols Pascal
Published: February 2016

The human commensal bacterium
Streptococcus salivarius
plays a major role in the equilibrium of microbial communities of the digestive tract. Here, we report the first complete genome sequence of a
Streptococcus salivarius
strain isolated from the small intestine, namely, HSISS4. Its circular chromosome comprises 1,903 coding sequences and 2,100,988 nucleotides.
Draft Whole-Genome Sequence of Haemophilus ducreyi Strain AUSPNG1, Isolated from a Cutaneous Ulcer of a Child from Papua New Guinea
Authors: Gangaiah Dharanesh , Marinov Georgi K. , Roberts Sally A. , Robson Jenny , Spinola Stanley M.
Published: February 2016

Haemophilus ducreyi
has recently emerged as a leading cause of cutaneous ulcers in the yaws-endemic areas of Papua New Guinea and other South Pacific islands. Here, we report the draft genome sequence of the
H. ducreyi
strain AUSPNG1, isolated from a cutaneous ulcer of a child from Papua New Guinea.
Draft Genome Sequence of Coccoid Lactobacillus equigenerosi NRIC 0697
T
Isolated from the Gastrointestinal Tracts of Healthy Thoroughbreds
Authors: Toh Hidehiro , Nakano Akiyo , Nguyen Co Thi Kim , Mimura Iyo , Arakawa Kensuke , Tashiro Kosuke , Kikusui Takefumi , Morita Hidetoshi
Published: February 2016

Lactobacillus equi
generosi NRIC 0697
T
was isolated from the gastrointestinal tracts of healthy thoroughbreds. This strain produced unique spherical or oval cells, which is rare in the genus
Lactobacillus
. Here, we report the draft genome sequence of this strain.
Complete Closed Genome Sequences of Salmonella enterica subsp.
enterica
Serotypes Anatum, Montevideo, Typhimurium, and Newport, Isolated from Beef, Cattle, and Humans
Authors: Harhay Dayna M. , Bono James L. , Smith Timothy P. L. , Fields Patricia I. , Dinsmore Blake A. , Santovenia Monica , Kelley Christy M. , Wang Rong , Harhay Gregory P.
Published: February 2016

Salmonella enterica
spp. are a diverse group of bacteria with a wide range of virulence potential. To facilitate genome comparisons across this virulence spectrum, we present eight complete closed genome sequences of four
S. enterica
serotypes (Anatum, Montevideo, Typhimurium, and Newport), isolated from various cattle samples and from humans.
Draft Genome Sequence of Actinomyces odontolyticus subsp.
actinosynbacter
Strain XH001, the Basibiont of an Oral TM7 Epibiont
Authors: McLean Jeffrey S. , Liu Quanhui , Bor Batbileg , Bedree Joseph K. , Cen Lujia , Watling Michael , To Thao T. , Bumgarner Roger E. , He Xuesong , Shi Wenyuan
Published: February 2016

Here, we present the draft genome sequence of
Actinomyces odontolyticus
subsp.
actinosynbacter
strain XH001, isolated from the human oral cavity. Uniquely, it was discovered as a host bacterium to the ultrasmall epibiont TM7x, which is the first cultivated member of “
Candidatus
Saccharibacteria” (formerly candidate phylum TM7).
Draft Genome Sequences of Sarcina ventriculi Strains Isolated from Wild Japanese Macaques in Yakushima Island
Authors: Ushida Kazunari , Tsuchida Sayaka , Ogura Yoshitoshi , Hayashi Tetsuya , Sawada Akiko , Hanya Goro
Published: February 2016

We report the draft genome sequences ofSarcina ventriculistrains 14 and 17, both isolated from feces of wild Yakushima macaques (Macaca fuscatayakui). These genomic sequences will be helpful for the phylogenetic consideration of the familyClostridiaceaeand understanding of the contribution of intestinal microbiota to the survival of Yakushima macaques.
Infant Gut Microbiota Development Is Driven by Transition to Family Foods Independent of Maternal Obesity
Authors: Laursen Martin Frederik , Andersen Louise B. B. , Michaelsen Kim F. , Mølgaard Christian , Trolle Ellen , Bahl Martin Iain , Licht Tine Rask
Published: February 2016

The potential influence of maternal obesity on infant gut microbiota may occur either through vertically transmitted microbes or through the dietary habits of the family. Recent studies have suggested that the heritability of obesity may partly be caused by the transmission of “obesogenic” gut microbes. However, the findings presented here suggest that maternal obesityper sedoes not affect the overall composition of the gut microbiota and its development after introduction of complementary foods. Rather, progression in complementary feeding is found to be the major determinant for gut microbiota establishment. Expanding our understanding of the influence of complementary diet on the development and establishment of the gut microbiota will provide us with the knowledge to tailor a beneficial progression of our intestinal microbial community.
The genetic assessment of looked after children: common reasons for referral and recent advances
Authors: Parker Michael J , Teasdale Katherine , Parker Michael J
Published: February 2016

Looked after children are recognised as generally having greater health needs than their peers. There are numerous potential causes, environmental and genetic, and the aetiology is often multifactorial. Assessments, especially clinical genetic ones, may be limited if the information available is incomplete or not shared. There have been some exciting recent advances in diagnostic genetic testing and more are on the horizon. However, we are currently only able to make a genetic diagnosis in less than half of patients, even when both parents are available for comparative testing. There may, therefore, remain an inevitable degree of residual uncertainty about the genetic contribution to a particular child's problems. There are increasing societal pressures for genetic information to be made available to individuals in general. However, there are significant considerations in carrier/predictive testing in children and we would maintain that looked after children should not be treated differently to other children in this regard, unless there is a compelling ‘best interest’ justification for so doing. Diagnostic criteria exist for fetal alcohol syndrome and other embryopathies and should be applied. Such should be considered as diagnoses of exclusion, so a child should not be prematurely labelled with these conditions, without fully assessing for the contribution of other factors, genetic or otherwise.
State of diagnostic quandary solved by modern technology: a rare case of Madelung's disease
Authors: Kyaw Htoo , Grillo Michael , Lin Aung Naing , Kapp David A
Published: February 2016

Madelung's disease is a neglected metabolic disease characterised by generalised multiple fatty tissue deposits. A 64-year-old Caucasian woman presented with generalised weakness and symptomatic hypoglycaemia with altered mental status. Physical examination showed very distinct physical characteristics with multiple lumps distributed over the upper body. Her neurological symptoms were solved by giving intravenous glucose and optimisation of medical treatment. Even though she had unique characteristics of Madelung's disease, many physicians, on several occasions, failed to recognise her ‘hidden diagnosis’. This diagnostic uncertainty was able to be solved by searching the Internet for similar clinical features and images. This case demonstrates characteristics and unique features of a rare disease that can be seen in a female patient even though it is mostly found in males.
Dietary sources and sodium intake in a sample of Australian preschool children
Authors: O'Halloran Siobhan A , Grimes Carley A , Lacy Kathleen E , Nowson Caryl A , Campbell Karen J
Published: February 2016

Objectives

To assess dietary sodium intake and the food sources of sodium in a sample of Australian preschool children.

Design

Cross-sectional.

Setting

Mothers were followed up when children were approximately 3.5 years of age after participating in a cluster randomised controlled trial: the Melbourne Infant Feeding Activity and Nutrition Trial Program.

Participants

251 Australian children aged 3.5±0.19 (SD) years.

Primary and secondary outcome measures

The average daily sodium intake was determined using three unscheduled 24 h dietary recalls. The contributions of food groups, core, discretionary and processed foods to daily sodium intake were assessed.

Results

The average sodium intake was 1508±495 (SD) mg/day, (salt equivalent 3.9±1.3 (SD) g/day) and 87% of children exceeded the Australian Upper Level of Intake (UL) for sodium of 1000 mg/day (salt equivalent 2.6 g/day). Main food sources of sodium were cereal/cereal products (25%), milk products (19%), meat, poultry/game (17%) and cereal-based products (15%). Core foods contributed 65%, and discretionary foods 35% of total daily sodium intake, and within the total diet, minimally processed, processed, processed culinary ingredient and ultraprocessed foods contributed 16%, 35%, 1% and 48% of sodium, respectively.

Conclusions

Within this sample, most children exceeded the recommended UL for sodium. Core and ultraprocessed foods were key sources of sodium which suggests that reductions in the sodium content of these foods are required to reduce sodium intake in young children. These data also provide further support for public health campaigns that seek to reduce consumption of energy-dense, nutrient-poor foods.
HIV testing among men who have sex with men in Tijuana, Mexico: a cross-sectional study
Authors: Pines Heather A , Goodman-Meza David , Pitpitan Eileen V , Torres Karla , Semple Shirley J , Patterson Thomas L
Published: February 2016

Objectives

HIV testing is critical to the delivery of comprehensive HIV prevention and care services, yet coverage of sexual minorities by HIV testing programmes remains insufficient in many low- and middle-income countries, including Mexico. The objective of this study was to identify the prevalence and correlates of HIV testing among men who have sex with men (MSM) in Tijuana, Mexico.

Methods

We conducted a cross-sectional study (2012–2013) among 189 MSM recruited via respondent-driven sampling (RDS). RDS-weighted logistic regression was used to identify correlates of prior HIV testing.

Results

RDS-adjusted prevalence of prior and recent (≤12 months) HIV testing was 63.5% (95% CI 51.9% to 73.5%) and 36.8% (95% CI 25.4% to 46.4%), respectively. Prior HIV testing was positively associated with older age (adjusted OR (AOR)=1.09, 95% CI 1.04 to 1.15), being born in Tijuana (AOR=2.68, 95% CI 1.05 to 6.86), higher levels of education (AOR=2.65, 95% CI 1.08 to 6.53), identifying as homosexual or gay (AOR=3.73, 95% CI 1.48 to 9.42), being more ‘out’ about having sex with men (AOR=1.28, 95% CI:1.02 to 1.62), and a history of sexual abuse (AOR=3.24, 95% CI 1.06 to 9.86). Prior HIV testing was negatively associated with reporting more condomless anal intercourse acts (past 2 months) (AOR=0.95, 95% CI 0.92 to 0.98) and greater internalised homophobia (AOR=0.92, 95% CI 0.86 to 0.99).

Conclusions

Our findings indicate an urgent need for expanded HIV testing services for MSM in Tijuana. Innovative, non-stigmatising, confidential HIV testing interventions targeted at young, less educated, migrant and non-gay identifying MSM may facilitate HIV testing and timely linkage to HIV care and treatment within this population.
Galactic entropy in extended Kaluza–Klein cosmology
Authors: Yanar Hilmi , Salti Mustafa , Aydogdu Oktay , Acikgoz Irfan , Yasar Erol
Published: February 2016

We use a Kaluza–Klein model with variable cosmological and gravitational terms to discuss the nature of galactic entropy function. For this purpose, we assume a universe filled with dark fluid and consider five-dimensional (5D) field equations using the Gamma law equation. We mainly discuss the validity of the first and generalized second laws of galactic thermodynamics for viable Kaluza–Klein models.
Cosmological model with fermion and tachyon fields interacting via Yukawa-type potential
Authors: Ribas Marlos O. , Devecchi Fernando P. , Kremer Gilberto M.
Published: February 2016

A model for the universe with tachyonic and fermionic fields interacting through a Yukawa-type potential is investigated. It is shown that the tachyonic field answers for the initial accelerated regime and for the subsequent decelerated regime so that it behaves as an inflaton at early times and as a matter field at intermediate times, while the fermionic field has the role of a dark energy constituent, since it leads to an accelerated regime at later times. The interaction between the fields via a Yukawa-type potential controls the duration of the decelerated era, since a stronger coupling makes a shorter decelerated period.
Vanishing effective Majorana neutrino mass and light sterile neutrinos
Authors: Verma Surender
Published: February 2016

We examine the possibility of vanishing effective Majorana mass [Formula: see text] in the presence of one or two sterile neutrinos taking into account the recent data on neutrino masses and mixings, particularly, on [Formula: see text]. Also, within the framework of standard three active neutrinos, we find that effective Majorana mass [Formula: see text] can be vanishingly small if neutrino masses observe normal hierarchy. However, the same is not valid for inverted hierarchical neutrino masses. The predictions for Majorana phases [Formula: see text] and [Formula: see text] have also been obtained and shown as scatter plots. We also examine the condition [Formula: see text] within the framework wherein fermion sector has been extended by the addition of either one or two sterile neutrinos. The condition of vanishing effective Majorana mass is found to be inconsistent with the recent measurement of [Formula: see text] in these classes of models except for [Formula: see text], [Formula: see text] neutrino mass scheme for small values of the lightest neutrino mass, [Formula: see text].
The decay τ → K−π0ντ in the Nambu–Jona-Lasinio model
Authors: Volkov M. K. , Pivovarov A. A.
Published: February 2016

In this paper, the width of the decay [Formula: see text] is calculated in the framework of the Nambu–Jona-Lasinio (NJL) model. The contributions of the intermediate vector [Formula: see text] and scalar [Formula: see text] mesons are taken into account. It is shown that the main contribution to the width of this decay is given by the subprocesses with the intermediate [Formula: see text]-boson and vector [Formula: see text] meson. The scalar channel with the intermediate [Formula: see text] meson gives an insignificant contribution. In Appendix A, it is shown that the contribution of the subprocess with the intermediate [Formula: see text] meson is negligible as well. The obtained results are in satisfactory agreement with the experimental data.
Link community detection based on line graphs with a novel link similarity measure
Authors: Wang Guishen , Huang Lan , Wang Yan , Pang Wei , Ma Qin
Published: February 2016

Link community gradually unfolds its capacity in complex network research. In this paper, a novel link similarity measure on line graphs is proposed. This measure can be adapted to different types of networks with an adjustable parameter. We prove its value converges to a limit on line graphs with the relationship of the nonneighbor links taken into account. Based on this similarity measure, we propose a novel link community detection algorithm for link clustering on line graphs. The detection algorithm combines the novel link similarity measure with the classic Markov Cluster (MCL) Algorithm and determines the link community partitions by calculating an extended modularity measure. Extensive experiments on two types of complex networks demonstrate the effectiveness, reliability and rationality of our solution in contrast to the other two classical algorithms.
Transient Calculation of Electric Power Circuits with Special Reference to Magnetizing Nonlinearity
Authors: Zhang Xiaoqin
Published: February 2016

This paper proposes a realistic model of magnetizing branches for transient calculation of electric power circuits. The model represents the nonlinear relationship between flux linkage and exciting current of magnetizing branches with a major loop and a family of minor loop trajectories, which has the capability of simulating the multi-valued hysteresis behavior. By applying the proposed model to transient calculation, an efficient algorithm is developed for obtaining the transient responses in electric power circuits. In the algorithm, the electric power circuit is divided into the magnetizing branches and the remaining linear part. The nonlinear differential equations are set up for the magnetizing branches and solved by the semi-explicit Runge–Kutta method. The transient calculation for the remaining linear part is performed on the basis of the solution to the magnetizing branches. Then, a laboratory measurement is made with a reduced-scale experimental arrangement. The measured results are compared with the calculated ones and a reasonable agreement is shown between them.
A 1.1V 12μW 86dB DR Sigma-Delta Modulator for Health Monitoring System
Authors: Zhao Long , Deng Chenxi , Wang Guan , Chen Hongming , Cheng Yuhua
Published: February 2016

A low-voltage low-power Sigma-Delta modulator for health monitoring system is designed using a standard 0.18[Formula: see text][Formula: see text]m CMOS technology. To achieve high accuracy with low power consumption in low supply voltage environment, the designed modulator is implemented with a one-bit third-order topology, in which the input-feedforward structure and switched-opamp (SO) technique are combined. Using the proposed design method, the SO meets the system requirements with the minimal power consumption and good stability in a feedback loop. The modulator achieves 86[Formula: see text]dB dynamic range (DR) over a 300[Formula: see text]Hz bandwidth with an oversampling ratio (OSR) of 128, while it occupies 0.16[Formula: see text]mm2 and consumes 12[Formula: see text][Formula: see text]W under a 1.1[Formula: see text]V supply.