bluuebunny/crossref_metadata_2025 huggingface dataset:
A modified time-of-flight method for precise determination of high speed ratios in molecular beams
Authors: Salvador Palau A. , Eder S. D. , Kaltenbacher T. , Samelin B. , Bracco G. , Holst B.
Published: February 2016

Time-of-flight (TOF) is a standard experimental technique for determining, among others, the speed ratio S (velocity spread) of a molecular beam. The speed ratio is a measure for the monochromaticity of the beam and an accurate determination of S is crucial for various applications, for example, for characterising chromatic aberrations in focussing experiments related to helium microscopy or for precise measurements of surface phonons and surface structures in molecular beam scattering experiments. For both of these applications, it is desirable to have as high a speed ratio as possible. Molecular beam TOF measurements are typically performed by chopping the beam using a rotating chopper with one or more slit openings. The TOF spectra are evaluated using a standard deconvolution method. However, for higher speed ratios, this method is very sensitive to errors related to the determination of the slit width and the beam diameter. The exact sensitivity depends on the beam diameter, the number of slits, the chopper radius, and the chopper rotation frequency. We present a modified method suitable for the evaluation of TOF measurements of high speed ratio beams. The modified method is based on a systematic variation of the chopper convolution parameters so that a set of independent measurements that can be fitted with an appropriate function are obtained. We show that with this modified method, it is possible to reduce the error by typically one order of magnitude compared to the standard method.
Comment on “Approximate solutions of the Dirac equation for the Rosen-Morse potential including the spin-orbit centrifugal term” [J. Math. Phys. 51, 023525 (2010)]
Authors: Ghoumaid A. , Benamira F. , Guechi L.
Published: February 2016

It is shown that the application of the Nikiforov-Uvarov method by Ikhdair for solving the Dirac equation with the radial Rosen-Morse potential plus the spin-orbit centrifugal term is inadequate because the required conditions are not satisfied. The energy spectra given is incorrect and the wave functions are not physically acceptable. We clarify the problem and prove that the spinor wave functions are expressed in terms of the generalized hypergeometric functions 2F1(a, b, c; z). The energy eigenvalues for the bound states are given by the solution of a transcendental equation involving the hypergeometric function.
BV-BFV approach to general relativity: Einstein-Hilbert action
Authors: Cattaneo Alberto S. , Schiavina Michele
Published: February 2016

The present paper shows that general relativity in the Arnowitt-Deser-Misner formalism admits a BV-BFV formulation. More precisely, for any d + 1 ≠ 2 (pseudo-) Riemannian manifold M with space-like or time-like boundary components, the BV data on the bulk induces compatible BFV data on the boundary. As a byproduct, the usual canonical formulation of general relativity is recovered in a straightforward way.
Barrier height inhomogeneity and its impact on (Al,In,Ga)N Schottky diodes
Authors: Laurent Matthew A. , Gupta Geetak , Suntrup Donald J. , DenBaars Steven P. , Mishra Umesh K.
Published: February 2016

III-N materials, especially ternary and quaternary alloys, are profoundly affected by barrier height inhomogeneity as evidenced by great variability in reported barrier height and Richardson constant values for Schottky diode samples involving epilayers with identical material composition. Research into AlInGaN-based devices is gaining traction due to its usefulness for strain engineering, polarization engineering, and vertical device design. Thus it is important to characterize the Schottky barrier height between AlInGaN and technologically relevant metals like nickel. It is proposed that alloy composition fluctuations inherent to low-temperature III-N alloys result in a Schottky barrier height inhomogeneity, and that the Schottky barrier height follows a Gaussian distribution. Current vs voltage data as a function of temperature was measured for three AlInGaN samples of varying composition. Utilizing a model tailored to thermionic emission over a Gaussian distribution of barriers, both the average barrier height and the standard deviation in the distribution were extracted from experimental data via multiple linear regression. Average barrier height was found to correlate with the AlInGaN band gap, while the standard deviation in barrier height increased with aluminum and indium concentration on the group-III sublattice.
Zooplankton generation following inundation of floodplain soils: effects of vegetation type and riverine connectivity
Authors: Catlin Alicia K. , Collier Kevin J. , Duggan Ian C.
Published: February 2016

We investigated the potential for zooplankton to emerge following inundation of dry soils on the lower Waikato River floodplain, North Island, New Zealand. Soil cores were collected from native forest remnants, scrub (predominantly Salix spp.) and pasture, and from sites inside or outside of stopbanks, to examine the effects of vegetation type and hydrological disconnection. We hypothesised that more larger-bodied zooplankton would emerge from forested floodplain areas, and that areas with high connectivity with the river would produce more zooplankton. Zooplankton appeared from soil cores within 3 days of wetting and no new taxa arose after 12 days. Community composition differed between vegetation types, with larger bodied cladocerans and copepods dominating forested and scrub sites, and rotifers dominating pastoral sites. Connectivity did not play a statistically significant role in determining community composition. Soil conditions were implicated as important in affecting emergent zooplankton community composition, with copepods and cladocerans characteristic of sites with wetter soils and bdelloid rotifers abundant in open sites with higher soil temperatures. Our findings indicate scrub and forested floodplains can be important areas for large-bodied zooplankton production, and that maintaining vegetative heterogeneity on floodplains may promote trophic subsidies for migrating juvenile fish as floodwaters subside.
MicroRNA indicators of follicular steroidogenesis
Authors: Donadeu F. X. , Sontakke S. D. , Ioannidis J.
Published: February 2016

MicroRNAs (miRNAs) can provide useful biomarkers of tissue function. The aim of the present study was to determine, in bovine follicles (n = 66; diameter 4–22 mm), the relationship among several indices of steroidogenesis and levels of 15 miRNAs previously identified to be associated with follicle development. Oestradiol levels, the oestradiol : progesterone (E : P) ratio and cytochrome P450 family 19 subfamily A member 1 (CYP19A1) expression were strongly correlated with each other (ρ > 0.8) and with LH/choriogonadotropin receptor (LHCGR) expression (ρ ≥ 0.6; P < 0.01). Levels of nine different miRNAs in the follicular wall were correlated (P < 0.01) with oestradiol, the E : P ratio and CYP19A1, with miR-873 showing the strongest correlation in each case (ρ > 0.7). Analyses of follicular fluid miRNAs identified miR-202 as correlated with oestradiol, the E : P ratio and CYP19A1 (ρ > 0.5; P < 0.01). When considering all follicle end-points together, we found that using a cut-off value of E : P = 1 overestimated the number of oestrogen-inactive follicles, whereas using CYP19A1 as a classifier provided a clearer separation of follicle samples based on oestrogen activity, in agreement with the E : P ratio, LHCGR expression and levels of miR-873 and miR-202. In conclusion, we identified miR-873 and miR-202 as miRNAs whose levels in follicular tissues can be used as indicators of steroidogenic capacity in bovine. We showed that these or other gene expression parameters, in addition or alternatively to the E : P ratio, should be used to accurately classify follicles based on steroidogenic capacity.
T cell-intrinsic S1PR1 regulates endogenous effector T-cell egress dynamics from lymph nodes during infection
Authors: Benechet Alexandre P. , Menon Manisha , Xu Daqi , Samji Tasleem , Maher Leigh , Murooka Thomas T. , Mempel Thorsten R. , Sheridan Brian S. , Lemoine Francois M. , Khanna Kamal M.
Published: February 2016

Significance

The control of a microbial infection by effector T cells is intrinsically linked to their migration. However, little is known about the mechanisms that control effector T-cell egress after infection. Sphingosine-1-phosphate receptor-1 (S1PR1) is a G-coupled protein receptor that plays an important role in naive T-cell egress from lymph nodes. However, less is known about its role in regulating effector T-cell trafficking during infection. Here, we used an inducible mouse model with temporally disrupted S1PR1 signaling exclusively in endogenous effector CD8 T cells to demonstrate that, after infection, even in the absence of retention signals such as CC chemokine receptor 7 (CCR7), intrinsic S1PR1 signaling is the overriding factor that regulates effector T-cell egress kinetics from the draining lymph node.
Anoctamin 2 identified as an autoimmune target in multiple sclerosis
Authors: Ayoglu Burcu , Mitsios Nicholas , Kockum Ingrid , Khademi Mohsen , Zandian Arash , Sjöberg Ronald , Forsström Björn , Bredenberg Johan , Lima Bomfim Izaura , Holmgren Erik , Grönlund Hans , Guerreiro-Cacais André Ortlieb , Abdelmagid Nada , Uhlén Mathias , Waterboer Tim , Alfredsson Lars , Mulder Jan , Schwenk Jochen M. , Olsson Tomas , Nilsson Peter
Published: February 2016

Significance

Despite the growing evidence that autoantibodies are team players in the pathogenesis of multiple sclerosis (MS), the target autoantigens are yet to be identified. In this work, we mined the autoantibody repertoire within MS by screening more than 2,000 plasma samples from patients with MS and controls and identified increased autoantibody reactivity against an ion-channel protein called “anoctamin 2” (ANO2). This finding points toward an ANO2 autoimmune sub-phenotype in MS and might contribute to the development of clinical algorithms to characterize a subgroup of MS patients.
Circadian control of oscillations in mitochondrial rate-limiting enzymes and nutrient utilization by PERIOD proteins
Authors: Neufeld-Cohen Adi , Robles Maria S. , Aviram Rona , Manella Gal , Adamovich Yaarit , Ladeuix Benjamin , Nir Dana , Rousso-Noori Liat , Kuperman Yael , Golik Marina , Mann Matthias , Asher Gad
Published: February 2016

Significance

Mitochondria are major cellular energy suppliers and have to cope with changes in nutrient supply and energy demand that naturally occur throughout the day. We obtained the first, to our knowledge, comprehensive mitochondrial proteome around the clock and identified extensive oscillations in mitochondrial protein abundance that predominantly peak during the early light phase. Remarkably, several rate-limiting mitochondrial enzymes that process different nutrients accumulate in a diurnal manner and are dependent on the clock proteins PER1/2. Concurrently, we uncovered daily oscillations in mitochondrial respiration that are substrate-specific and peak during different times of the day. We propose that the circadian clock PERIOD proteins regulate the diurnal utilization of different nutrients by the mitochondria and thus, optimize mitochondrial function to daily changes in energy supply/demand.
Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation
Authors: Hattori Takamitsu , Lai Darson , Dementieva Irina S. , Montaño Sherwin P. , Kurosawa Kohei , Zheng Yupeng , Akin Louesa R. , Świst-Rosowska Kalina M. , Grzybowski Adrian T. , Koide Akiko , Krajewski Krzysztof , Strahl Brian D. , Kelleher Neil L. , Ruthenburg Alexander J. , Koide Shohei
Published: February 2016

Significance

Extensive studies of the structure–function relationship of antibodies have established that conventional immunoglobulins contain two copies of the antigen-binding fragment (Fab), each of which serves as an autonomous and complete unit for recognizing an antigen. In this paper, we report a previously unidentified mode of antibody–antigen recognition, dubbed “antigen clasping,” where two antigen-binding sites cooperatively clasp one antigen, and the design of a long-neck antibody format that facilitates antigen clasping. Antigen clasping led to recombinant antibodies for histone posttranslational modifications with extraordinarily high specificity, valuable tools for epigenetic research. This study substantially broadens the long-standing paradigm for antibody–antigen recognition.
Assessment of Provider Attitudes toward #Naloxone on Twitter
Authors: Haug Nancy A. , Bielenberg Jennifer , Linder Steven H. , Lembke Anna
Published: February 2016

Background

As opioid overdose rates continue to pose a major public health crisis, the need for naloxone treatment by emergency first responders is critical. Little is known about the views of those who administer naloxone. The current study examines attitudes of health professionals on the social media platform Twitter to better understand their perceptions of opioid users, the role of naloxone, and potential training needs.

Methods

Public comments on Twitter regarding naloxone were collected for a period of 3 consecutive months. The occupations of individuals who posted tweets were identified through Twitter profiles or hashtags. Categories of emergency service first responders and medical personnel were created. Qualitative analysis using a grounded theory approach was used to produce thematic content. The relationships between occupation and each theme were analyzed using Pearson chi-square statistics and post hoc analyses.

Results

A total of 368 individuals posted 467 naloxone-related tweets. Occupations consisted of professional first responders such as emergency medical technicians (EMTs), firefighters, and paramedics ( n = 122); law enforcement officers ( n = 70); nurses ( n = 62); physicians ( n = 48); other health professionals including pharmacists, pharmacy technicians, counselors, and social workers ( n = 31); naloxone-trained individuals ( n = 12); and students ( n = 23). Primary themes included burnout, education and training, information seeking, news updates, optimism, policy and economics, stigma, and treatment. The highest levels of burnout, fatigue, and stigma regarding naloxone and opioid overdose were among nurses, EMTs, other health care providers, and physicians. In contrast, individuals who self-identified as “naloxone-trained” had the highest optimism and the lowest amount of burnout and stigma.

Conclusions

Provider training and refinement of naloxone administration procedures are needed to improve treatment outcomes and reduce provider stigma. Social networking sites such as Twitter may have potential for offering psychoeducation to health care providers.
Quotient stacks and equivariant étale cohomology algebras: Quillen’s theory revisited
Authors: Illusie Luc , Zheng Weizhe
Published: February 2016

Let

k
k

be an algebraically closed field. Let

Λ
\Lambda

be a noetherian commutative ring annihilated by an integer invertible in

k
k

and let

ℓ
\ell

be a prime number different from the characteristic of 

k
k

. We prove that if

X
X

is a separated algebraic space of finite type over 

k
k

endowed with an action of a

k
k

-algebraic group

G
G

, the equivariant étale cohomology algebra

H
∗

(
[
X

/

G
]
,
Λ
)

H^*([X/G],\Lambda )

, where

[
X

/

G
]

[X/G]

is the quotient stack of

X
X

by

G
G

, is finitely generated over

Λ
\Lambda

. Moreover, for coefficients

K
∈

D
c
+

(
[
X

/

G
]
,

F

ℓ

)

K \in D^+_c([X/G],\mathbb {F}_{\ell })

endowed with a commutative multiplicative structure, we establish a structure theorem for

H
∗

(
[
X

/

G
]
,
K
)

H^*([X/G],K)

, involving fixed points of elementary abelian

ℓ
\ell

-subgroups of

G
G

, which is similar to Quillen’s theorem in the case

K
=

F

ℓ

K = \mathbb {F}_{\ell }

. One key ingredient in our proof of the structure theorem is an analysis of specialization of points of the quotient stack. We also discuss variants and generalizations for certain Artin stacks.
Clinician Attitudes, Screening Practices, and Interventions to Reduce Firearm-Related Injury
Authors: Roszko Paul J. D. , Ameli Jonathan , Carter Patrick M. , Cunningham Rebecca M. , Ranney Megan L.
Published: February 2016

Firearm injury is a leading cause of injury-related morbidity and mortality in the United States. We sought to systematically identify and summarize existing literature on clinical firearm injury prevention screening and interventions. We conducted a systematic search of PubMed, Web of Science, Cumulative Index of Nursing and Allied Health Literature (CINAHL), PsycInfo, and ClinicalTrials.gov for English-language original research (published 1992–2014) on clinical screening methods, patient-level firearm interventions, or patient/provider attitudes on the same. Unrelated studies were excluded through title, abstract, and full-text review, and the remaining articles underwent data abstraction and quality scoring. Of a total of 3,260 unique titles identified, 72 were included in the final review. Fifty-three articles examined clinician attitudes/practice patterns; prior training, experience, and expectations correlated with clinicians' regularity of firearm screening. Twelve articles assessed patient interventions, of which 6 were randomized controlled trials. Seven articles described patient attitudes; all were of low methodological quality. According to these articles, providers rarely screen or counsel their patients—even high-risk patients—about firearm safety. Health-care–based interventions may increase rates of safe storage of firearms for pediatric patients, suicidal patients, and other high-risk groups. Some studies show that training clinicians can increase rates of effective firearm safety screening and counseling. Patients and families are, for the most part, accepting of such screening and counseling. However, the current literature is, by and large, not high quality. Rigorous, large-scale, adequately funded studies are needed.
Juvenile northern rock sole (Lepidopsetta polyxystra) spatial distribution and abundance patterns in the eastern Bering Sea: spatially dependent production linked to temperature
Authors: Cooper Daniel W. , Nichol Daniel G.
Published: February 2016

Annual spatial distribution and relative abundance of age-2 and age-3 northern rock sole (Lepidopsetta polyxystra) and summer bottom temperatures were analysed using data from eastern Bering Sea summer trawl surveys from 1982 through 2012. Previously observed differences in age-0 northern rock sole distribution persisted until age-2 and age-3. Latitudinal distributions of age-2 and age-3 fish were correlated most strongly with summer bottom temperatures 2 and 3 years prior to the survey year, during the time that the fish would have been age-0. Thus, temperature during the age-0 year may affect spatial distribution for the first few years of life. Distribution of age-2 and age-3 fish shifted northwards 2 years after the beginning of a warming trend from 1999 to 2003, and shifted southwards 2 years after a cooling trend from 2004 through 2010. Northerly distributions were correlated with high abundances. Density dependence was ruled out as a reason for northward shifts in distribution given a lack of correlation between latitudinal distributions and the annual abundances within the southern part of the distribution. We propose that the large northern nursery area produces large cohorts of northern rock sole, and that bottom temperatures in the age-0 year affect use of the northern nursery area.
START or SMART? Timing of Antiretroviral Therapy Initiation and Cardiovascular Risk for People With Human Immunodeficiency Virus Infection
Authors: Siedner Mark J.
Published: February 2016

The Initiation of Antiretroviral Therapy in Early Asymptomatic HIV Infection (START) study has reinforced the benefits of early initiation of antiretroviral therapy (ART). However, a notable secondary finding from that study was that immediate initiation of ART did not prevent cardiovascular disease (CVD) events (0.17 vs 0.20 events/1000 person-years, P = .65). This result appears to contradict a body of evidence, most notably from the Strategies for Management of Antiretroviral Therapy (SMART) study, which reported a 70% increased hazard of cardiovascular events for those deferring or interrupting treatment. Thus, an important unresolved question is whether the timing of ART impacts CVD risk. In this review, published data on relationships between timing of ART and CVD risk are reviewed. The data support a role for ART in mitigating CVD risk at lower CD4 counts, but data also suggests that, among those initiating therapy early, ART alone appears to suboptimally mitigate CVD risk. Additional interventions to address CVD risk among human immunodeficiency virus-infected populations are likely to be needed.
Microbial Communities in Globodera pallida Females Raised in Potato Monoculture Soil
Authors: Eberlein Caroline , Heuer Holger , Vidal Stefan , Westphal Andreas
Published: February 2016

Globodera spp. are under strict quarantine in many countries. Suppressiveness to cyst nematodes can evolve under monoculture of susceptible hosts. Females developing in potato monoculture soil infested with G. pallida populations Chavornay or Delmsen were examined for inherent microbial communities. In the greenhouse, nonheated and heat-treated (134°C for 10 min) portions of this soil were placed in root observation chambers, planted with Solanum tuberosum ‘Selma’, and inoculated with G. pallida Pa3 Chavornay. At harvest in Delmsen soil, cysts had fewer eggs in nonheated than heat-treated soil. In denaturing gradient gel electrophoresis analysis, bacterial and fungal fingerprints were characterized by a high variability between replicates; nonheated soils displayed more dominant bands than heated soils, indicating more bacterial and fungal populations. In amplicon pyrosequencing, females from nonheated portions frequently contained internal transcribed spacer sequences of the fungus Malassezia. Specific for the Chavornay and Delmsen population, ribosomal sequences of the bacteria Burkolderia and Ralstonia were abundant on eggs. In this first report of microbial communities in G. pallida raised in potato monoculture, candidate microorganisms perhaps associated with the health status of the eggs of G. pallida were identified. If pathologies on cyst nematodes can be ascertained, these organisms could improve the sustainability of production systems.
Lamina Cribrosa Depth is Associated With the Cup-to-Disc Ratio in Eyes With Large Optic Disc Cupping and Cup-to-Disc Ratio Asymmetry
Authors: Jung Kyoung In , Jeon Sooji , Park Chan Kee
Published: February 2016

Purpose:

To investigate the lamina cribrosa (LC) depth and its relationship with the cup-to-disc ratio (CDR) in the eyes with generalized increased optic disc cupping and CDR asymmetry.

Methods:

Glaucoma suspect subjects with a CDR≥0.7, CDR asymmetry ≥0.2 in the absence of visual field (VF) loss, and normal control subjects were enrolled. The optic nerve head was imaged using the enhanced depth imaging modes of Spectralis optical coherence tomography. The LC depth was determined at the mid-horizontal, and the superior and inferior mid-peripheral regions of the optic nerve head.

Results:

Disc area and CDRs were larger in the glaucoma suspect group compared with the control group (P<0.001). The mean LC depth was significantly greater in the disc area–matched glaucoma suspect group compared with the normal control group (P<0.001). The mean LC depth was positively correlated with the average and vertical CDRs (r=0.755 and 0.664, respectively; both P<0.001), which was maintained after controlling for the disc area (r=0.756 and 0.645, respectively; both P<0.001). In eyes with CDR asymmetry, the LC was located more posteriorly in eyes with a higher CDR compared with fellow eyes with a lower CDR (P<0.001).

Conclusions:

The LC depth was greater in eyes with generalized increased cupping, as well as in eyes with a higher CDR than fellow eyes, and was significantly related to the CDR. These results suggest that the clinical appearance of cup enlargement or cupping has LC displacement components.
Accuracy of Measurements With the iCare HOME Rebound Tonometer
Authors: Termühlen Julia , Mihailovic Natasa , Alnawaiseh Maged , Dietlein Thomas S. , Rosentreter André
Published: February 2016

Purpose:

To evaluate the accuracy of intraocular pressure (IOP) measurements obtained with the newly available iCare HOME (RTHOME) rebound tonometer compared with the iCare ONE (RTONE) tonometer and Goldmann applanation tonometry (GAT), and possible correlation with central corneal thickness (CCT).

Materials and Methods:

IOP measurements were obtained from 154 patients by an ophthalmologist (doc) using each of the above-mentioned tonometers. In addition, patients (pat) measured their own IOP with the RTHOME and RTONE. The means and SD of results obtained with the different tonometers were compared. Agreement between the tonometers was calculated using the Bland-Altman method.

Results:

Mean IOPs for the right eyes only were 15.9±6.4 mm Hg (RTONEdoc), 15.8±6.4 mm Hg (RTONEpat), 15.0±5.9 mm Hg (RTHOMEdoc), 14.9±6.3 mm Hg (RTHOMEpat), and 15.8±4.4 mm Hg (GAT). Bland-Altman analysis revealed mean differences (bias) between RTONEdoc and RTHOMEdoc, between RTHOMEdoc and RTHOMEpat, and between RTHOMEdoc and GAT of 0.8, 0.1, and −0.8 mm Hg, respectively, with 95% limits of agreement of −3.5 to 5.2, −4.9 to 5.1, and −7.2 to 5.6 mm Hg, respectively. Linear regression of the comparisons revealed a proportional error over the range of pressures examined in the case of RTHOMEdoc versus GAT (slope=0.32, P<0.001). Considering the data from all eyes, the difference between RTHOMEdoc and GAT correlated significantly with the CCT (P=0.01).

Conclusion:

RTHOME readings correlate well with the GAT results although some limitations such as dependency of readings on CCT and increasing differences at lower and higher IOP levels need to be taken into account.
Species-dependent hydrodynamics of flagellum-tethered bacteria in early biofilm development
Authors: Bennett Rachel R. , Lee Calvin K. , De Anda Jaime , Nealson Kenneth H. , Yildiz Fitnat H. , O'Toole George A. , Wong Gerard C. L. , Golestanian Ramin
Published: February 2016

Monotrichous bacteria on surfaces exhibit complex spinning movements. Such spinning motility is often a part of the surface detachment launch sequence of these cells. To understand the impact of spinning motility on bacterial surface interactions, we develop a hydrodynamic model of a surface-bound bacterium, which reproduces behaviours that we observe in
Pseudomonas aeruginosa
,
Shewanella oneidensis
and
Vibrio cholerae
, and provides a detailed dictionary for connecting observed spinning behaviour to bacteria–surface interactions. Our findings indicate that the fraction of the flagellar filament adhered to the surface, the rotation torque of this appendage, the flexibility of the flagellar hook and the shape of the bacterial cell dictate the likelihood that a microbe will detach and the optimum orientation that it should have during detachment. These findings are important for understanding species-specific reversible attachment, the key transition event between the planktonic and biofilm lifestyle for motile, rod-shaped organisms.
From the primordial soup to self-driving cars: standards and their role in natural and technological innovation
Authors: Wagner Andreas , Ortman Scott , Maxfield Robert
Published: February 2016

Standards are specifications to which the elements of a technology must conform. Here, we apply this notion to the biochemical ‘technologies' of nature, where objects like DNA and proteins, as well as processes like the regulation of gene activity are highly standardized. We introduce the concept of standards with multiple examples, ranging from the ancient genetic material RNA, to Palaeolithic stone axes, and digital electronics, and we discuss common ways in which standards emerge in nature and technology. We then focus on the question of how standards can facilitate technological and biological innovation. Innovation-enhancing standards include those of proteins and digital electronics. They share common features, such as that few standardized building blocks can be combined through standard interfaces to create myriad useful objects or processes. We argue that such features will also characterize the most innovation-enhancing standards of future technologies.
Big data integration shows Australian bush-fire frequency is increasing significantly
Authors: Dutta Ritaban , Das Aruneema , Aryal Jagannath
Published: February 2016

Increasing Australian bush-fire frequencies over the last decade has indicated a major climatic change in coming future. Understanding such climatic change for Australian bush-fire is limited and there is an urgent need of scientific research, which is capable enough to contribute to Australian society. Frequency of bush-fire carries information on spatial, temporal and climatic aspects of bush-fire events and provides contextual information to model various climate data for accurately predicting future bush-fire hot spots. In this study, we develop an ensemble method based on a two-layered machine learning model to establish relationship between fire incidence and climatic data. In a 336 week data trial, we demonstrate that the model provides highly accurate bush-fire incidence hot-spot estimation (91% global accuracy) from the weekly climatic surfaces. Our analysis also indicates that Australian weekly bush-fire frequencies increased by 40% over the last 5 years, particularly during summer months, implicating a serious climatic shift.
A model of muscle atrophy based on live microscopy of muscle remodelling inDrosophilametamorphosis
Authors: Kuleesha Yadav , Puah Wee Choo , Wasser Martin
Published: February 2016

Genes controlling muscle size and survival play important roles in muscle wasting diseases. InDrosophila melanogastermetamorphosis, larval abdominal muscles undergo two developmental fates. While a doomed population is eliminated by cell death, another persistent group is remodelled and survives into adulthood. To identify and characterize genes involved in the development of remodelled muscles, we devised a workflow consisting ofin vivoimaging, targeted gene perturbation and quantitative image analysis. We show that inhibition ofTORsignalling and activation of autophagy promote developmental muscle atrophy in early, whileTORandyorkieactivation are required for muscle growth in late pupation. We discovered changes in the localization of myonuclei during remodelling that involve anti-polar migration leading to central clustering followed by polar migration resulting in localization along the midline. We demonstrate that the Cathepsin L orthologueCp1is required for myonuclear clustering in mid, while autophagy contributes to central positioning of nuclei in late metamorphosis. In conclusion, studying muscle remodelling in metamorphosis can provide new insights into the cell biology of muscle wasting.
Predator olfactory cues generate a foraging–predation trade-off through prey apprehension
Authors: Siepielski Adam M. , Fallon Eric , Boersma Kate
Published: February 2016

Most animals are faced with the challenge of securing food under the risk of predation. This frequently generates a trade-off whereby animals respond to predator cues with reduced movement to avoid predation at the direct cost of reduced foraging success. However, predators may also cause prey to be apprehensive in their foraging activities, which would generate an indirect ‘apprehension cost’. Apprehension arises when a forager redirects attention from foraging tasks to predator detection and incurs a cost from such multi-tasking, because the forager ends up making more mistakes in its foraging tasks as a result. Here, we test this apprehension cost hypothesis and show that damselflies miss a greater proportion of their prey during foraging bouts in response to both olfactory cues produced by conspecifics that have only viewed a fish predator and olfactory cues produced directly by fish. This reduced feeding efficiency is in addition to the stereotypical anti-predator response of reduced activity, which we also observed. These results show that costs associated with anti-predator responses not only arise through behavioural alterations that reduce the risk of predation, but also from the indirect costs of apprehension and multi-tasking that can reduce feeding efficiency under the threat of predation.
Random noise can help to improve synchronization of excimer laser pulses
Authors: Mingesz Róbert , Barna Angéla , Gingl Zoltán , Mellár János
Published: February 2016

Recently, we have reported on a compact microcontroller-based unit developed to accurately synchronize excimer laser pulses (Mingesz
et al.
2012
Fluct. Noise Lett.
11, 1240007 (
doi:10.1142/S021947751240007X
)). We have shown that dithering based on random jitter noise plus pseudorandom numbers can be used in the digital control system to radically reduce the long-term drift of the laser pulse from the trigger and to improve the accuracy of the synchronization. In this update paper, we present our new experimental results obtained by the use of the delay-controller unit to tune the timing of a KrF excimer laser as an addition to our previous numerical simulation results. The hardware was interfaced to the laser using optical signal paths in order to reduce sensitivity to electromagnetic interference and the control algorithm tested by simulations was applied in the experiments. We have found that the system is able to reduce the delay uncertainty very close to the theoretical limit and performs well in real applications. The simple, compact and flexible system is universal enough to also be used in various multidisciplinary applications.
Dopamine regulates termite soldier differentiation through trophallactic behaviours
Authors: Yaguchi Hajime , Inoue Takaya , Sasaki Ken , Maekawa Kiyoto
Published: February 2016

Caste polyphenism in social insects is regulated by social interactions among colony members. Trophallaxis is one of the most frequently observed interactions, but no studies have been conducted identifying the intrinsic factors involved in this behaviour and caste differentiation. Dopamine (DA) has multiple roles in the modulation of behaviours and physiology, and it produces species-specific behaviours in animals. Here, to verify the role of DA in termite soldier differentiation, we focused on the first soldier in an incipient colony ofZootermopsis nevadensis, which always differentiates from the oldest 3rd instar (No. 1 larva) via a presoldier. First, brain DA levels of the No. 1 larva at day 3 after its appearance were significantly higher than day 0. Second, DA synthesis gene expression levels were extraordinarily high in the No. 1 larva at day 0–1 after appearance. Finally, injection of a DA receptor antagonist into the No. 1 larva resulted in the inhibition of presoldier differentiation. Behavioural observations of the antagonist or control-injected larvae suggested that brain DA and signalling activity regulate the frequencies of trophallaxis from reproductives and presoldier differentiation. Because trophallaxis is a social behaviour frequently observed in natural conditions, the role of DA should be investigated in other social insects with frequent trophallactic and allogrooming behaviour.
Migration of sodium chloride in dry porous materials
Authors: Hird Robert , Bolton Malcolm D.
Published: February 2016

Groundwater can saturate soil above the water table within the capillary fringe associated with the pore size of the parent soil. External evaporation has been viewed as a mechanism for enhancing upward flow, potentially creating problems of salt heave beneath roads and foundations if the groundwater is saline, analogous to concerns with efflorescence in masonry. The role of internal evaporation in promoting crystallization, and especially in altering the transport process of the pore fluid, has been recognized but is only partially understood. The purpose of this paper is to examine evidence for the upward percolation of brine accompanying salt crystallization inside a porous granular material. A series of experiments are described using vertical flow columns packed with dry sand above a reservoir of saline fluid, to explore whether salt transport could take place by autogenous wicking above the initial capillary fringe. The conditions inside the columns were monitored at specific elevations with sensors measuring bulk electrical conductivity, dielectric constant and relative humidity. Dendritic salt crystallization was observed inside the sand, accompanying surface heave. Ultimately, efflorescence on the surface led to the formation of a salt crust. Some implications for the potential damage to roads and foundations in arid regions, and to masonry subject to rising damp, are discussed.
Post-liquefaction reconsolidation of sand
Authors: Adamidis O. , Madabhushi G. S. P.
Published: February 2016

Loosely packed sand that is saturated with water can liquefy during an earthquake, potentially causing significant damage. Once the shaking is over, the excess pore water pressures that developed during the earthquake gradually dissipate, while the surface of the soil settles, in a process called post-liquefaction reconsolidation. When examining reconsolidation, the soil is typically divided in liquefied and solidified parts, which are modelled separately. The aim of this paper is to show that this fragmentation is not necessary. By assuming that the hydraulic conductivity and the one-dimensional stiffness of liquefied sand have real, positive values, the equation of consolidation can be numerically solved throughout a reconsolidating layer. Predictions made in this manner show good agreement with geotechnical centrifuge experiments. It is shown that the variation of one-dimensional stiffness with effective stress and void ratio is the most crucial parameter in accurately capturing reconsolidation.
Effects of weak nonlinearity on the dispersion relation and frequency band-gaps of a periodic Bernoulli–Euler beam
Authors: Sorokin Vladislav S. , Thomsen Jon Juel
Published: February 2016

The paper deals with analytically predicting the effects of weak nonlinearity on the dispersion relation and frequency band-gaps of a periodic Bernoulli–Euler beam performing bending oscillations. Two cases are considered: (i) large transverse deflections, where nonlinear (true) curvature, nonlinear material and nonlinear inertia owing to longitudinal motions of the beam are taken into account, and (ii) mid-plane stretching nonlinearity. A novel approach is employed, the method of varying amplitudes. As a result, the isolated as well as combined effects of the considered sources of nonlinearities are revealed. It is shown that nonlinear inertia has the most substantial impact on the dispersion relation of a non-uniform beam by removing all frequency band-gaps. Explanations of the revealed effects are suggested, and validated by experiments and numerical simulation.
Spinor Lie derivatives and Fermion stress–energies
Authors: Helfer A. D.
Published: February 2016

Stress–energies for Fermi fields are derived from the principle of general covariance. This is done by developing a notion of Lie derivatives of spinors along arbitrary vector fields. A substantial theory of such derivatives was first introduced by Kosmann; here, I show how an apparent conflict in the literature on this is due to a difference in the definitions of spinors, and that tracking the Lie derivative of the Infeld–van der Waerden symbol, as well as the spinor fields under consideration, gives a fuller picture of the geometry and leads to the Fermion stress–energy. The differences in the definitions of spinors do not affect the results here, but could matter in certain quantum-gravity programs and for spinor transformations under discrete symmetries.
Transcontinental latitudinal variation in song performance and complexity in house wrens (Troglodytes aedon)
Authors: Kaluthota Chinthaka , Brinkman Benjamin E. , dos Santos Ednei B. , Rendall Drew
Published: February 2016

There is growing interest in latitudinal effects on animal behaviour and life history. One recent focus is on birdsong, which is hypothesized to be more elaborated or complex in the north temperate zone compared with the tropics. Current evidence is mixed and based on cross-species comparisons, or single species with restricted distributions. We circumvent these limitations using a transcontinental sample of 358 songs from house wrens (Troglodytes aedon) at 281 locations spanning more than 100° of latitude (52° N–55° S) across the Americas. We found a significant latitudinal gradient in several basic elements of song performance and complexity between north temperate and tropical populations. Furthermore, we document convergence in song patterns between populations at higher latitudes in the Northern and Southern Hemispheres. Effects were strongest for the number of elements in a song, and the rate of element production, both increasing towards the poles, with similar but weaker effects for other song dimensions (e.g. number of unique elements, trills and trill rate). We consider possible causes related to variable habitats and morphology, concluding that the shorter breeding seasons at higher latitudes in both hemispheres may favour greater song elaboration to mediate territory competition and mate choice.
Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation, and homozygous truncating mutations
Authors: Doran Anthony G. , Wong Kim , Flint Jonathan , Adams David J. , Hunter Kent W. , Keane Thomas M.
Published: February 2016

Background

The Mouse Genomes Project is an ongoing collaborative effort to sequence the genomes of the common laboratory mouse strains. In 2011, the initial analysis of sequence variation across 17 strains found 56.7M unique SNPs and 8.8M indels. We carry out deep sequencing of 13 additional inbred strains (BUB/BnJ, C57BL/10J, C57BR/cdJ, C58/J, DBA/1J, I/LnJ, KK/HiJ, MOLF/EiJ, NZB/B1NJ, NZW/LacJ, RF/J, SEA/GnJ and ST/bJ), cataloging molecular variation within and across the strains. These strains include important models for immune response, leukemia, age-related hearing loss and rheumatoid arthritis. We now have several examples of fully sequenced closely related strains that are divergent for several disease phenotypes.

Results

Approximately, 27.4M unique SNPs and 5M indels are identified across these strains compared to the C57BL/6J reference genome (GRCm38). The amount of variation found in the inbred laboratory mouse genome has increased to 71M SNPs and 12M indels. We investigate the genetic basis of highly penetrant cancer susceptibility in RF/J finding private novel missense mutations in DNA damage repair and highly cancer associated genes. We use two highly related strains (DBA/1J and DBA/2J) to investigate the genetic basis of collagen induced arthritis susceptibility.

Conclusion

This paper significantly expands the catalog of fully sequenced laboratory mouse strains and now contains several examples of highly genetically similar strains with divergent phenotypes. We show how studying private missense mutations can lead to insights into the genetic mechanism for a highly penetrant phenotype.
AAV-mediated CRISPR/Cas gene editing of retinal cellsin vivo
Authors: Hung Sandy SC , Chrysostomou Vicki , Li Fan , Lim Jeremiah KH , Wang Jiang-Hui , Powell Joseph E , Tu Leilei , Daniszewski Maciej , Lo Camden , Wong Raymond C , Crowston Jonathan G , Pébay Alice , King Anna E , Bui Bang V , Liu Guei-Sheung , Hewitt Alex W
Published: February 2016

PURPOSE

CRISPR/Cas has recently been adapted to enable efficient editing of the mammalian genome, opening novel avenues for therapeutic intervention of inherited diseases. In seeking to disrupt Yellow Fluorescent Protein (YFP) in a Thy1-YFP transgenic mouse, we assessed the feasibility of utilising the adeno-associated virus 2 (AAV2) to deliver CRISPR/Cas for gene modification of retinal cellsin vivo.

METHODS

sgRNA plasmids were designed to targetYFPand afterin vitrovalidation, selected guides were cloned into a dual AAV system. One AAV2 construct was used to deliver SpCas9 and the other delivered sgRNA againstYFPorLacZ(control) in the presence of mCherry. Five weeks after intravitreal injection, retinal function was determined using electroretinography and CRISPR/Casmediated gene modifications were quantified in retinal flat mounts.

RESULTS

AAV2-mediatedin vivodelivery of SpCas9 with sgRNA targetingYFP, significantly reduced the number of YFP fluorescent cells of the inner retina of our transgenic mouse model. Overall, we found an 84.0% (95% CI: 81.8-86.9) reduction of YFP-positive cells inYFP-sgRNA infected retinal cells compared to eyes treated withLacZ-sgRNA. Electroretinography profiling found no significant alteration in retinal function following AAV2-mediated delivery of CRISPR/Cas components compared to contralateral untreated eyes.

CONCLUSIONS

Thy1-YFP transgenic mice were used as a rapid quantifiable means to assess the efficacy of CRISPR/Cas-based retinal gene modificationin vivo. We demonstrate that genomic modification of cells in the adult retina can be readily achieved by viral mediated delivery of CRISPR/Cas.
Predicting symptom severity in autism spectrum disorder based on cortical thickness measures in agglomerative data
Authors: Moradi Elaheh , Khundrakpam Budhachandra , Lewis John D. , Evans Alan C. , Tohka Jussi
Published: February 2016

Machine learning approaches have been widely used for the identification of neuropathology from neuroimaging data. However, these approaches require large samples and suffer from the challenges associated with multi-site, multi-protocol data. We propose a novel approach to address these challenges, and demonstrate its usefulness with the Autism Brain Imaging Data Exchange (ABIDE) database. We predict symptom severity based on cortical thickness measurements from 156 individuals with autism spectrum disorder (ASD) from four different sites. The proposed approach consists of two main stages: a domain adaptation stage using partial least squares regression to maximize the consistency of imaging data across sites; and a learning stage combining support vector regression for regional prediction of severity with elastic-net penalized linear regression for integrating regional predictions into a whole-brain severity prediction. The proposed method performed markedly better than simpler alternatives, better with multi-site than single-site data, and resulted in a considerably higher cross-validated correlation score than has previously been reported in the literature for multi-site data. This demonstration of the utility of the proposed approach for detecting structural brain abnormalities in ASD from the multi-site, multi-protocol ABIDE dataset indicates the potential of designing machine learning methods to meet the challenges of agglomerative data.