bluuebunny/crossref_metadata_2025 huggingface dataset:
Spectral fingerprinting: microstate readout via remanence ferromagnetic resonance in artificial spin ice
Authors: Vanstone Alex , Gartside Jack C , Stenning Kilian D , Dion Troy , Arroo Daan M , Branford Will R
Published: March 2022

Artificial spin ices (ASIs) are magnetic metamaterials comprising geometrically tiled strongly-interacting nanomagnets. There is significant interest in these systems spanning the fundamental physics of many-body systems to potential applications in neuromorphic computation, logic, and recently reconfigurable magnonics. Magnonics focused studies on ASI have to date have focused on the in-field GHz spin-wave response, convoluting effects from applied field, nanofabrication imperfections (‘quenched disorder’) and microstate-dependent dipolar field landscapes. Here, we investigate zero-field measurements of the spin-wave response and demonstrate its ability to provide a ‘spectral fingerprint’ of the system microstate. Removing applied field allows deconvolution of distinct contributions to reversal dynamics from the spin-wave spectra, directly measuring dipolar field strength and quenched disorder as well as net magnetisation. We demonstrate the efficacy and sensitivity of this approach by measuring ASI in three microstates with identical (zero) magnetisation, indistinguishable via magnetometry. The zero-field spin-wave response provides distinct spectral fingerprints of each state, allowing rapid, scaleable microstate readout. As artificial spin systems progress toward device implementation, zero-field functionality is crucial to minimize the power consumption associated with electromagnets. Several proposed hardware neuromorphic computation schemes hinge on leveraging dynamic measurement of ASI microstates to perform computation for which spectral fingerprinting provides a potential solution.
Polychromatic drivers for inertial fusion energy
Authors: Zhao Yao , Sheng Zhengming , Cui Zijian , Ren Lei , Zhu Jianqiang
Published: March 2022

Although tremendous achievements have been made toward inertial confinement fusion, laser plasma instabilities (LPIs) remain to be an inevitable problem for current drive schemes. To mitigate these instabilities, significant efforts have been paid to produce high-power broadband ultraviolet lasers. However, no practical scheme has been demonstrated up to now for efficient triple-frequency conversion of broadband laser. Here we propose the design of polychromatic drivers for the generation of multicolor beams mainly based upon the optical parametric amplification, which can significantly enhance the third-harmonic conversion efficiency. Each polychromatic light has four colors of monochromatic beamlets with a full spectrum width of 3%, and the beamlet colors of any two adjacent flanges are different. The suppression effects of such polychromatic lights have been investigated via large scale particle-in-cell simulations, which indicate that more than 35% of the incident energy can be saved from the LPIs compared with monochromatic lasers for the direct-drive scheme, or high-density filled target for the indirect-drive scheme. The proposed polychromatic drivers are based on the matured technologies, and thus may pave the way towards realization of robust and high-efficiency fusion ignition.
A comprehensive study of the antibacterial and shielding properties of micro and nano-EPVC lead-free shields
Authors: Ghasemi-Nejad Mahdieh , Gholamzadeh Leila , Adeli Ruhollah , Shirmardi Seyed Pezhman
Published: March 2022

Lead-composites products are usable materials for the personal protection of the patient from x-ray during radiation operations. Nevertheless, lead has high toxicity and environmental disadvantages. This research aims at the preparation of flexible, lead-free, and antibacterial composites for protection against x-ray radiation. At first, nanoparticles of molybdenum trioxide (MoO3), copper oxide (CuO), and tin (IV) oxide (SnO2) were synthesized with hydrothermal and sol-gel methods. Six types of composites containing the 50% Wt of various mixtures of nano and micro particles of MoO3, CuO, and SnO2 in the emulsion of polyvinylchloride were prepared. Then, the morphological characteristics and size distribution of the samples were determined by the dynamic light scattering (DLS) analysis, and the bond between the matrix and the filler was investigated by Fourier Transform Infrared Spectroscopy (FTIR). Also, the antibacterial effect of the composites and X-ray diffraction (XRD) of nanoparticles were studied. Furthermore, the x-ray attenuation coefficient was measured in 40, 80, and 120 kVp. Indeed, the mass attenuation coefficients and 0.25 mm lead equivalent thickness were calculated for all samples. The results indicated that the nanocomposites show better attenuation than the other composites in all the energies. The composites containing MoO3 and CuO also proved to have better mass attenuation coefficients than the others. Considering the equivalent thickness for 0.25 mm of lead in high and low energy, the composites containing all the three metal oxides can be considered suitable for attenuation. Also, the composites containing CuO can provide antibacterial properties.
Co-expressing fast channelrhodopsin with step-function opsin overcomes spike failure due to photocurrent desensitization in optogenetics: a theoretical study
Authors: Bansal Himanshu , Pyari Gur , Roy Sukhdev
Published: March 2022

Objective. A fundamental challenge in optogenetics is to elicit long-term high-fidelity neuronal spiking with negligible heating. Fast channelrhodopsins (ChRs) require higher irradiances and cause spike failure due to photocurrent desensitization under sustained illumination, whereas, more light-sensitive step-function opsins (SFOs) exhibit prolonged depolarization with insufficient photocurrent and fast response for high-fidelity spiking. Approach. We present a novel method to overcome this fundamental limitation by co-expressing fast ChRs with SFOs. A detailed theoretical analysis of ChETA co-expressed with different SFOs, namely ChR2(C128A), ChR2(C128S), stabilized step-function opsin (SSFO) and step-function opsin with ultra-high light sensitivity (SOUL), expressing hippocampal neurons has been carried out by formulating their accurate theoretical models. Main results. ChETA-SFO-expressing hippocampal neurons shows more stable photocurrent that overcomes spike failure. Spiking fidelity in these neurons can be sustained even at lower irradiances of subsequent pulses (77% of initial pulse intensity in ChETA-ChR2(C128A)-expressing neurons) or by using red-shifted light pulses at appropriate intervals. High-fidelity spiking upto 60 Hz can be evoked in ChETA-ChR2(C128S), ChETA-SSFO and ChETA-SOUL-expressing neurons, which cannot be attained with only SFOs. Significance. The present study provides important insights about photostimulation protocols for bi-stable switching of neurons. This new approach provides a means for sustained low-power, high-frequency and high-fidelity optogenetic switching of neurons, necessary to study various neural functions and neurodegenerative disorders, and enhance the utility of optogenetics for biomedical applications.
Edge transport and fuelling studies via gas puff modulation in ASDEX Upgrade L-mode plasmas
Authors: Schuster C.U. , Wolfrum E. , Fable E. , Fischer R. , Griener M. , Tal B. , Angioni C. , Eich T. , Manz P. , Stroth U. , the ASDEX Upgrade Team
Published: March 2022

Gas puff modulation experiments are performed at ASDEX Upgrade in L-mode plasmas. We model the discharge with the ASTRA transport code in order to determine transport coefficients outside of a normalized radius of ρ
pol = 0.95. The experimental data is consistent with a range of particle diffusivities and pinch velocities of the order of D = (0.20 ± 0.13) m2 s−1 and v = (−1 ± 2) m s−1, respectively. The electron temperature response caused by the gas modulation permits to estimate also that heat diffusivity χ
e increases almost linearly when collisionality rises due to fuelling. The fuelling particle flux is amplified by recycling, overcompensating losses.
Phase shift in periodically driven non-equilibrium systems: its identification and a bound
Authors: Degünther Julius , Koyuk Timur , Seifert Udo
Published: March 2022

Time-dependently driven stochastic systems form a vast and manifold class of non-equilibrium systems used to model important applications on small length scales such as bit erasure protocols or microscopic heat engines. One property that unites all these quite different systems is some form of lag between the driving of the system and its response. For periodic steady states, we quantify this lag by introducing a generalized phase difference and prove a tight upper bound for it. In its most general version, this bound depends only on the relative speed of the driving.
A radiation tolerant clock generator for the CMS endcap timing layer readout chip
Authors: Sun H. , Sun Q. , Biereigel S. , Francisco R. , Gong D. , Huang G. , Huang X. , Kulis S. , Leroux P. , Liu C. , Liu T. , Liu T. , Moreira P. , Prinzie J. , Wu J. , Ye J. , Zhang L. , Zhang W.
Published: March 2022

We present the test results of a low jitter Phase Locked Loop (PLL) prototype chip for the CMS Endcap Timing Layer readout chip (ETROC). This chip is based on the improved version of a clock synthesis circuit named ljCDR from the Low Power Gigabit Transceiver (lpGBT) project. The ljCDR is tested in its PLL mode. An automatic frequency calibration (AFC) block with the Triple Modular Redundancy (TMR) register is developed for the LC-oscillator calibration. The chip was manufactured in a 65 nm CMOS process with 10 metal layers. The chip has been extensively tested, including Total Ionizing Dose (TID) testing up to 300 Mrad and Single Event Upset (SEU) testing with heavy ions possessing a Linear Energy Transfer (LET) from 1.3 to 62.5 MeV × cm2/mg.
Combining randomized field experiments with observational satellite data to assess the benefits of crop rotations on yields
Authors: Kluger Dan M , Owen Art B , Lobell David B
Published: March 2022

With climate change threatening agricultural productivity and global food demand increasing, it is important to better understand which farm management practices will maximize crop yields in various climatic conditions. To assess the effectiveness of agricultural practices, researchers often turn to randomized field experiments, which are reliable for identifying causal effects but are often limited in scope and therefore lack external validity. Recently, researchers have also leveraged large observational datasets from satellites and other sources, which can lead to conclusions biased by confounding variables or systematic measurement errors. Because experimental and observational datasets have complementary strengths, in this paper we propose a method that uses a combination of experimental and observational data in the same analysis. As a case study, we focus on the causal effect of crop rotation on corn (maize) and soybean yields in the Midwestern United States. We find that, in terms of root mean squared error, our hybrid method performs 13% better than using experimental data alone and 26% better than using the observational data alone in the task of predicting the effect of rotation on corn yield at held-out experimental sites. Further, the causal estimates based on our method suggest that benefits of crop rotations on corn yield are lower in years and locations with high temperatures whereas the benefits of crop rotations on soybean yield are higher in years and locations with high temperatures. In particular, we estimated that the benefit of rotation on corn yields (and soybean yields) was 0.85 t ha−1(0.24 t ha−1) on average for the top quintile of temperatures, 1.03 t ha−1(0.21 t ha−1) on average for the whole dataset, and 1.19 t ha−1(0.16 t ha−1) on average for the bottom quintile of temperatures. This association between temperatures and rotation benefits is consistent with the hypothesis that the benefit of the corn-soybean rotation on soybean yield is largely driven by pest pressure reductions while the benefit of the corn-soybean rotation on corn yields is largely driven by nitrogen availability.
Comparing sources of uncertainty in community greenhouse gas estimation techniques
Authors: Blackhurst Michael , Matthews H Scott
Published: March 2022

Independent methods for estimating local greenhouse gas emissions have been developed utilizing different instrumentation, sampling, and estimation techniques. Comparing independent estimates theoretically improves understanding of emission sources. However, each method estimates emissions with varying fidelity, complicating comparisons across methods, cities, and over time. It is thus difficult for decision-makers to judge how to use novel estimation methods, particularly when the literature implies a singular method is best. We review 650 articles to define the scope and contours of estimation methods, develop and apply an uncertainty typology, and describe the strengths and weaknesses of different approaches. We identify two prominent process-based estimation techniques (summing of utility bills and theoretical modeling), three techniques that attribute observed atmospheric CO2to source locations (eddy covariance footprinting, dispersion models, and regression), and methods that spatiotemporally distribute aggregate emissions using source proxies. We find that ‘ground truth’ observations for process-based method validation are available only at the aggregate scale and emphasize that validation at the aggregate scale does not imply a valid underlying spatiotemporal distribution. ‘Ground truth’ observations are also available post-combustion as atmospheric CO2concentrations. While dispersion models can spatially and temporally estimate upwind source locations, missing validation data by source introduces unknowable uncertainty. We find that many comparisons in the literature are made across methods with unknowable uncertainty, making it infeasible to rank methods empirically. We see promise in the use of regression for source attribution owing to its controlling for confounding emissions, flexibly accommodating different source proxies, explicitly quantifying uncertainty, and growing availability of CO2samples for modeling. We see developing cross-walks between land use and end-use sectors as an important step to comparing process-based methods with those attributing atmospheric CO2to sources. We suggest pooling data streams can produce better decision support resources for cities with proper attribution of empirical fidelity.
Large Turing independent sets
Authors: Kumar Ashutosh , Shelah Saharon
Published: March 2022

For a set of reals

X
X

and

1
≤
n
>
ω

1 \leq n > \omega

, define

X
X

to be

n
n

-Turing independent iff the Turing join of any

n
n

reals in

X
X

does not compute another real in

X
X

.

X
X

is Turing independent iff it is

n
n

-Turing independent for every

n
n

. We show the following: (1) There is a non-meager Turing independent set. (2) The statement “Every set of reals of size continuum has a Turing independent subset of size continuum” is independent of ZFC plus the negation of CH. (3) The statement “Every non-meager set of reals has a non-meager

n
n

-Turing independent subset” holds in ZFC for

n
=
1

n = 1

and is independent of ZFC for

n
≥
2

n \geq 2

(assuming the consistency of a measurable cardinal). We also show the measure analogue of (3).
Face numbers of high-dimensional Poisson zero cells
Authors: Kabluchko Zakhar
Published: March 2022

Let

Z

d

\mathcal Z_d

be the zero cell of a

d
d

-dimensional, isotropic and stationary Poisson hyperplane tessellation. We study the asymptotic behavior of the expected number of

k
k

-dimensional faces of

Z

d

\mathcal Z_d

, as

d
→
∞

d\to \infty

. For example, we show that the expected number of hyperfaces of

Z

d

\mathcal Z_d

is asymptotically equivalent to

2
π

/

3

d

3

/

2

\sqrt {2\pi /3}\, d^{3/2}

, as

d
→
∞

d\to \infty

. We also prove that the expected solid angle of a random cone spanned by

d
d

random vectors that are independent and uniformly distributed on the unit upper half-sphere in

R

d

\mathbb R^{d}

is asymptotic to

3

π

−
d

\sqrt 3 \pi ^{-d}

, as

d
→
∞

d\to \infty

.
HRM
Authors: Wilkinson Adrian
Published: March 2022

‘HRM’ examines the link between Human Resource Management (HRM) and strategy. Much of the interest in the contemporary HRM literature has been around the idea that the HR unit is now in charge of developing and utilizing the potential of human resources in pursuit of the organization’s strategic objectives. Integration, fit, and the notion of matching dominate the discussion. However, organizations are embedded in society and all that this entails in terms of laws, regulation, culture, and expectations. As such, HRM has to balance and integrate the needs of employers, employees, and the wider society and should be guided by a moral and professional base.
Who does HRM and how?
Authors: Wilkinson Adrian
Published: March 2022

‘Who does HRM and how?’ identifies who does Human Resource Management (HRM) and how. The practice of HRM is not something that resides solely in the hands of those who design HRM policies, namely senior managers and HR staff/departments. Whatever policies are designed by those at the top, others further down the ranks must implement them, even where there is an HR department to provide support and advice. Indeed, line managers implement HRM and the lived experience of HRM for most staff is provided by their line managers. It is also important to consider the gap between intended, actual, and perceived HR practices and not simply assume they are the same.
Managing performance and rewards
Authors: Wilkinson Adrian
Published: March 2022

‘Managing payment and rewards’ focuses on reward management and performance, which is a key component of Human Resource Management (HRM). Increasingly, pay and reward are now seen as key levers to elicit effort and performance, and it is not simply the amount of money but how that money is paid that is important. This perspective is the so-called ‘new pay’ approach. The New Pay model uses reward to link business strategy and the behaviours required to achieve it. Then there are the issues of performance evaluation; executive pay and associated packages such as bonuses and stock options; and the gender pay gap which relate to this topic.
8. Collective labour law 2: industrial action
Authors: Cabrelli David
Published: March 2022

‘Collective labour law 2: industrial action’ explores industrial action. The institution and practice of the strike is so endemic in the culture of industrial capitalism that it is often associated with particular economic, social, and political ideologies. Two limitations are commonly applied: pre-strike notice and balloting constraints. They require trade unions to give prior notice of the date of the strike to the employer and to ensure that they have held an official ballot and obtained a majority vote in favour of the strike. Other conditions on the lawfulness of a strike include those related to its purpose or objectives. Secondary or sympathy industrial action and mass picketing are both prohibited in many countries.
4. The sacred and the secular
Authors: Dwyer Philip
Published: March 2022

‘The sacred and the secular’ reviews the state monopolization of violence that gained momentum from the 16th century onwards, highlighting the willingness of societies to inflict death on those who deviate from the rules and the readiness of crowds to enjoy the spectacle of pain and humiliation applied to people they thought deserved it. This has been common to all cultures from the ancient world to the modern era. The relationship between power and violence is worth considering. The criminal justice system has evolved over time and with that, we have seen changing attitudes towards public executions and torture. What role does the state play in the use of public executions?
5. Collective and communal violence
Authors: Dwyer Philip
Published: March 2022

‘Collective and communal violence’ focuses on collective violence, which involves the mob or groups of people that are part of a specific organization. There are different kinds of collective violence which have existed throughout history, such as riots and large-scale revolts. We also see long traditions of food riots and tax revolts brought about by the fear of starvation in Europe, China, and India over the centuries. We can distinguish between spontaneous collective action from prolonged, large-scale collective action. A spontaneous collective action is an event where people react to what they see as an injustice, while a prolonged, large-scale collective action requires an organization to take the lead.
6. Violence and the state
Authors: Dwyer Philip
Published: March 2022

‘Violence and the state’ talks about how interpersonal violence declined as states gained a monopoly over violence. As the state assumed responsibility for the exercise of violence, it was able to reduce levels of violence among ordinary people. It is worth looking at the assumption that any reduction of violence must come from the state, and that those who are most directly touched by violence have little or no agency. The state’s monopolization of violence and state sponsored genocides around the world make it one of the key vectors of violence in the 19th and 20th centuries. The roles played by colonialism, state-sanctioned violence, extreme violence against civilians in warfare, and terrorism in the history of violence are also important.
2. Formal matters
Authors: Post Jonathan F. S.
Published: March 2022

‘Formal matters’ develops from a single, general formal observation about Bishop’s art: that her poems never repeat. Bishop wrote various kinds of lyrical poems, such as nursery rhymes, songs, ballads, and recursive forms, such as the sonnet and the villanelle. She had an unusual practices with stanzas, as can be seen in the case of ‘Roosters’. This can also be seen through her disagreements with Marianne Moore, and her adventurous use of free verse and the use her poetry makes of features typically associated with prose. Using ‘Questions of Travel’ as an example, we see the concept of the baroque in her poetry and the importance of using verse to represent not a thought but a mind thinking. In this preference, she both continues and differentiates herself from Wallace Stevens’s account of modern poetry.
6. Late travel poems
Authors: Post Jonathan F. S.
Published: March 2022

‘Late travel poems’ recognizes Elizabeth Bishop as one of the great travel poets of the modern era, and one reason why readers keep returning to her poetry. Despite her love of small things and out-of-the-way places, her travel poems are motivated by reflecting—and reflecting on—the experience of travel and not by focusing on a scene or setting for its own sake. The poems ‘Crusoe in England’, ‘The Moose’, and ‘The End of March’, all from GeographyIII, and ‘Santarém’, illustrate instances of her late style. What these poems have in common is an equation between lyric time and leisurely thinking. Topics include Crusoe’s unsparing solitude, the sudden epiphany in ‘The Moose’, the mysterious entangling of a kite in ‘The End of March’, and the Edenic comedy of river travel on the Amazon in ‘Santarém’.
2. Gothic rebellion
Authors: Gordon Charlotte
Published: March 2022

‘Gothic rebellion’ analyses the role that Gothic tales of horror and romance played in shaping Mary Shelley’s work. Mary’s life as a young girl was lonely. She saw herself as a Gothic heroine who was persecuted and wronged by a villain, which in her case was her stepmother, Mary Jane Clairmont. Mary’s conflicts with her stepmother helped shape her into an independent young woman, who rebelled against social conventions. She was then sent to live in Scotland, and later returned to London, where she met and fell in love with the poet Percy Shelley, although he was already married at the time. Together, they ran away to Paris; when they returned to London she was reviled by the English press as a ‘whore’ and excluded from London society.
5. Valperga, The Last Man, The Fortunes of Perkin Warbeck, and the new Frankenstein (1821‒1831)
Authors: Gordon Charlotte
Published: March 2022

‘Valperga, The Last Man, The Fortunes of Perkin Warbeck, and the new Frankenstein (1821‒1831)’ discusses Mary Shelley’s middle novels, Valperga, The Last Man, and The Fortunes of Perkin Warbeck, which were the first books she published under her own name—a courageous step for any 19th-century woman author. Mary Shelley depicted the evils of war and tyranny in all three novels, creating strong heroines who challenge the ambitions of the male characters, even though Castruccio Castracani, in particular, had been glorified by Machiavelli. Valperga and Perkin Warbeck were set in the past, enabling Mary Shelley to make her political points indirectly. The Last Man, set in a dystopian future, describes the catastrophic effect of a pandemic that wipes out the human race, offering trenchant criticisms of 19th-century politics, the British government, patriarchy, injustice, and the class system. All three novels were written while Mary Shelley grieved the tragic deaths of her two small children.
The effect of seed-dispersal timing on seedling recruitment is modulated by environmental conditions that vary across altitude in a threatened palm
Authors: de Souza Aline C , Donohue Kathleen , de Mattos Eduardo A
Published: March 2022

Background and Aims

The timing of seed dispersal determines the environmental conditions that plants face during early life stages. In seasonal environments, selection is expected to favour dispersal timing that is matched to environmental conditions suitable for successful recruitment. Our aim here was to test whether the timing of seed dispersal influences seedling establishment success in two populations of Euterpe edulis that are located at contrasting altitudes, have different seed-dispersal phenologies and are subjected to distinct climatic conditions.

Methods

We sowed E. edulis seeds in contrasting altitudes on different dates, and monitored seed germination, emergence and seedling establishment at each altitude over 4 years. At the high-altitude site, five seed-dispersal cohorts were established during the natural dispersal period. At the low-altitude site, three seed-dispersal cohorts were established during natural dispersal, and two were established either before or after natural dispersal.

Key Results

At the high-altitude site, seed-dispersal timing did not affect seed germination, seedling emergence or seedling establishment success. In contrast, at the low-altitude site, late seed dispersal near the end of the wet season resulted in a lower probability of seedling establishment, possibly due to the exposure of seeds, germinants and seedlings to unfavourable drought conditions. In addition, at the low-altitude site, the natural seed-dispersal period was poorly matched to favourable environmental conditions for seedling establishment.

Conclusions

The greater effect of seed-dispersal timing on seedling establishment at the low-altitude site is probably related to a more seasonal and drought-prone environment that favours a restricted period of seed dispersal. The magnitude of the effect of dispersal timing on seedling establishment success was modulated by environmental conditions that vary across altitude. Furthermore, reproductive phenology appears to be subject to more intense selection at the lower limit of the altitudinal range, due to a more restrictive window of opportunity for successful seedling establishment.
Survival and growth of a high-mountain daisy transplanted outside its local range, and implications for climate-induced distribution shifts
Authors: Sumner Emma E , Morgan John W , Venn Susanna E , Camac James S
Published: March 2022

Field transplant experiments can improve our understanding of the effects of climate on distributions of plants versus a milieu of biotic factors which may be mediated by climate. We use a transplant experiment to test how survival and growth of a mountain-top daisy (Podolepis robusta), when planted within and outside its current local range, varies as a function of individual plant size, elevation, aspect and the presence of other vegetation. We expected a home-site advantage for the species, with highest survival and growth within the species’ current elevational limits, and a decline in vital rates above (due to physiological limitations) and below (due to competition with near-neighbours) these limits. Transplant survival during the beginning of the census was high (89 %), though by the third growing season, 36 % of initial transplants were remaining. Elevation had a significant negative effect on individual mortality rates; plants growing at higher elevations had a lower estimated hazard rate and thus, higher survival relative to those planted at elevations below the current lower limit of the distribution. By contrast, we detected no significant effect of elevation on growth rates. Small vegetation gaps had no effect on growth rates, though we found a negative, but non-significant, effect on mortality rates. Aspect had a very strong impact on growth. Plants transplanted to cool aspects had a significantly lower growth rate relative to transplants growing on a warm aspect. Conversely, aspect was not a significant predictor of individual mortality rates. Restrictions on the local distribution of P. robusta appear to be governed by mortality drivers at lower elevation and by growth drivers associated with aspect. We highlight that our ability to understand the drivers of distributions in current and future climates will be limited if contextual- and individual-level plant responses remain understudied.
RegScaf: a regression approach to scaffolding
Authors: Li Mengtian , Li Lei M
Published: March 2022

Motivation

Crucial to the correctness of a genome assembly is the accuracy of the underlying scaffolds that specify the orders and orientations of contigs together with the gap distances between contigs. The current methods construct scaffolds based on the alignments of ‘linking’ reads against contigs. We found that some ‘optimal’ alignments are mistaken due to factors such as the contig boundary effect, particularly in the presence of repeats. Occasionally, the incorrect alignments can even overwhelm the correct ones. The detection of the incorrect linking information is challenging in any existing methods.

Results

In this study, we present a novel scaffolding method RegScaf. It first examines the distribution of distances between contigs from read alignment by the kernel density. When multiple modes are shown in a density, orientation-supported links are grouped into clusters, each of which defines a linking distance corresponding to a mode. The linear model parameterizes contigs by their positions on the genome; then each linking distance between a pair of contigs is taken as an observation on the difference of their positions. The parameters are estimated by minimizing a global loss function, which is a version of trimmed sum of squares. The least trimmed squares estimate has such a high breakdown value that it can automatically remove the mistaken linking distances. The results on both synthetic and real datasets demonstrate that RegScaf outperforms some popular scaffolders, especially in the accuracy of gap estimates by substantially reducing extremely abnormal errors. Its strength in resolving repeat regions is exemplified by a real case. Its adaptability to large genomes and TGS long reads is validated as well.

Availability and implementation

RegScaf is publicly available at https://github.com/lemontealala/RegScaf.git.

Supplementary information

Supplementary data are available at Bioinformatics online.
Towards understanding genetic risk in febrile seizures: innate immunity and neuronal excitability
Authors: Olson Heather E , Poduri Annapurna
Published: March 2022

This scientific commentary refers to ‘Genome-wide association study of febrile seizures implicates fever response and neuronal excitability genes’ by Skotte et al. (https://doi.org/10.1093/brain/awab260).
Wetland fishes avoid a carbon dioxide deterrent deployed in the field
Authors: Bzonek P A , Mandrak N E
Published: March 2022

Biological invasions are poorly controlled and contribute to the loss of ecosystem services and function. Altered watershed connectivity contributes to aquatic invasions, but such hydrologic connections have become important for human transport. Carbon dioxide (CO2) deterrents have been proposed to control the range expansion of invasive fishes, particularly through altered hydrologic connections, without impeding human transport. However, the effectiveness of CO2 deterrents needs to be further evaluated in the field, where fishes are situated in their natural environment and logistical challenges are present.

We deployed a proof-of-concept CO2 deterrent within a trap-and-sort fishway in Cootes Paradise, Ontario, Canada, to determine the avoidance responses of fishes attempting to disperse into a wetland. We aimed to describe deterrent efficiency for our target species, common carp, and for native fishes dispersing into the wetland. Our inexpensive inline CO2 deterrent was deployed quickly and rapidly produced a CO2 plume of 60 mg/l. Over 2000 fishes, representing 13 species, were captured between 23 May and 8 July 2019. A generalized linear model determined that the catch rates of our target species, common carp (n = 1662), decreased significantly during deterrent activation, with catch rates falling from 2.56 to 0.26 individuals per hour. Aggregated catch rates for low-abundance species (n < 150 individuals per species) also decreased, while catch rates for non-target brown bullhead (n = 294) increased. Species did not express a phylogenetic signal in avoidance responses. These results indicate that CO2 deterrents produce a robust common carp avoidance response in the field. This pilot study deployed an inexpensive and rapidly operating deterrent, but to be a reliable management tool, permanent deterrents would need to produce a more concentrated CO2 plume with greater infrastructural support.
RNF207 exacerbates pathological cardiac hypertrophy via post-translational modification of TAB1
Authors: Yuan Lin , Bu Shichen , Du Meng , Wang Yilong , Ju Chenhui , Huang Dandan , Xu Wenjing , Tan Xin , Liang Minglu , Deng Shan , Yang Liu , Huang Kai
Published: March 2022

Aims

The heart undergoes pathological remodelling, featured by the hypertrophic growth of cardiomyocytes and increased cardiac fibrosis, under biomechanical stress such as haemodynamic overload. Ring Finger Protein 207 (RNF207) is an E3 ubiquitin ligase that is predominantly expressed in the heart, but its function remains elusive. In this study, we aimed to explore the role of RNF207 in the development of pathological cardiac hypertrophy and dysfunction.

Methods and results

Transverse aortic constriction (TAC) surgery was performed on mice to induce cardiac hypertrophy. Cardiac function and remodelling were evaluated by echocardiography, histological assessment, and molecular analyses. Our data indicated that RNF207 overexpression (OE) exacerbated cardiac hypertrophy, fibrosis, and systolic dysfunction. In contrast, TAC-induced cardiac remodelling was profoundly blunted in RNF207 knockdown (KD) hearts. In line with the in vivo findings, RNF207 OE augmented, whereas RNF207 KD alleviated, phenylephrine-induced cardiomyocyte hypertrophy in vitro. Mechanistically, we demonstrated that RNF207 elicited detrimental effects by promoting K63-linked ubiquitination of TAK1-binding protein 1 (TAB1), which triggered the autophosphorylation of transforming growth factor-β activated kinase 1 (TAK1) and the activation of downstream p38 and c-Jun N-terminal kinase (JNK)1/2 signalling pathways. In the TAB1-KD cardiomyocytes, RNF207-OE-induced cell hypertrophy was significantly attenuated, indicating that RNF207-induced hypertrophy is, at least in part, TAB1-dependent.

Conclusions

This study demonstrates that RNF207 exacerbates pressure overload-induced cardiac hypertrophy and dysfunction via post-translational modification of TAB1.
Cannulation strategies for acute type A dissection—role of central cannulation
Authors: Ramaprabhu Krithika , Saran Nishant , Dearani Joseph , Lahr Brian , Schaff Hartzell , Greason Kevin , Yalamuri Suraj , Mangukia Chirantan , Stulak John , Bagameri Gabor , Crestanello Juan , Pochettino Alberto
Published: March 2022

OBJECTIVES

The purpose of this study was to assess the safety and efficacy of direct cannulation of the ascending aorta in comparison with cannulating peripheral arteries.

METHODS

We retrospectively analysed type A dissection patients [n = 107; median (interquartile range [IQR]) age, 64 [53–73] years] from January 2008 to March 2018. The cohort was divided into 2 groups: direct ascending aorta cannulation (group A, n = 47; median [IQR] age, 69 [54–74] years; 34% female) and non-aortic cannulation (group B, n = 60; median [IQR] age, 62 [52–72] years; 20% female). Postoperative outcomes and long-term survival were compared.

RESULTS

Baseline characteristics were not significantly different between the 2 groups, except for higher creatinine in group B (median 0.9 vs 1.1, P = 0.028) and higher prevalence of dyslipidaemia in group A (58.7% vs 38.3%, P = 0.037). Overall early mortality was 12.1% (n = 13); 12.8% (n = 6) in group A and 11.7% (n = 7) in group B (P = 0.863). The incidence of stroke was 10.6% (n = 5) in group A and 6.7% (n = 4) in group B (P = 0.463). After adjusting for CPB and circulatory arrest times, there was no group difference in the length of ICU (P = 0.257) or hospital stay (P = 0.118), all-cause reoperation (P = 0.709), peak postoperative creatinine (P = 0.426) and lactate values (n = 60; P = 0.862). Overall survival at 1, 3 and 5 years was 84%, 78% and 73%, respectively, with no difference between the 2 groups after adjustment (P = 0.629).

CONCLUSIONS

Direct cannulation of the ascending aorta is a safe cannulation strategy for type A dissection repair, offering the opportunity for rapid arterial cannulation and antegrade perfusion.
Matched comparison of 3 cerebral perfusion strategies in open zone-0 anastomosis for acute type A aortic dissection
Authors: Montagner Matteo , Kofler Markus , Pitts Leonard , Heck Roland , Buz Semih , Kurz Stephan , Falk Volkmar , Kempfert Jörg
Published: March 2022

OBJECTIVES

The present study aims to investigate outcomes after the surgical treatment of acute type A aortic dissection in regard to three available selective cerebral perfusion strategies.

METHODS

From 2000 to 2019, patients were selected based on the employment of either retrograde cerebral perfusion (RCP), unilateral antegrade cerebral perfusion (uACP) or bilateral antegrade cerebral perfusion (bACP) during open zone-0 anastomosis. Propensity score TriMatch analysis considering several preoperative and intraoperative variables was used to identify well-balanced triplets. The primary end point of the study was a new cerebral operation-related neurologic deficit.

RESULTS

Operative times (operation time, cardiopulmonary bypass time, reperfusion time) were significantly longer in the RCP group, in which deeper hypothermia was applied (27.5 [24–28], 28 [26–28] and 16 [16–17]°C for uACP, bACP and RCP, respectively, P-value <0.001). The RCP group showed higher red blood cell concentrates and fresh frozen plasma transfusion rates. No significant difference of new cerebral operation-related neurologic deficit was observed between the 3 groups (12.9% vs 12.9% vs 11.3% for RCP, uACP and bACP, P-value = 0.86). In addition, 30-day mortality showed similar distribution independently of the cerebral perfusion strategy adopted (17.7% vs 14.5% vs 17.7% for RCP, uACP and bACP, P-value = 0.86).

CONCLUSIONS

However, based on a small sample size, the comparison showed no relevant differences in terms of neurologic outcome and 30-day mortality, confirming RCP, uACP and bACP as safe and reproducible selective cerebral perfusion strategies in surgery for acute type A aortic dissection.
Surgical treatment of hypertrophic obstructive cardiomyopathy in relatively elderly patients: Short- and long-term outcomes
Authors: Lapenna Elisabetta , Nisi Teodora , Carino Davide , Del Forno Benedetto , Ruggeri Stefania , Schiavi Davide , Meneghin Roberta , Macrì Demartino Roberto , Castiglioni Alessandro , Maisano Francesco , Alfieri Ottavio , De Bonis Michele
Published: March 2022

OBJECTIVES

Our goal was to assess the short- and long-term outcomes of surgical treatment for hypertrophic obstructive cardiomyopathy in patients ≥65 years of age compared to patients < 65 years of age.

METHODS

Sixty-four patients aged ≥65 years, surgically treated for symptomatic hypertrophic obstructive cardiomyopathy, were compared to a control group of 125 patients <65 years.

RESULTS

Patients aged ≥65 years were less frequently male (36% vs 68%, P < 0.001) and had higher EuroSCORE II scores [1.4 (1.1–2.2) vs 0.8 (0.7–1.2), P < 0.001], lower risk of sudden death, higher pulmonary artery pressure [40 (30–50) vs 30 (30–43), P = 0.04) and more mitral annulus calcifications (44% vs 14%, P < 0.001) compared to younger patients.

Hospital death was 1%, with no difference between the 2 groups (1.5% vs 0.8%, P = 0.9).

Patients aged ≥65 years had more concomitant coronary bypass grafting (12% vs 5%, P = 0.05) and a higher incidence of blood transfusions (50% vs 17%, P < 0.001) and postoperative atrial fibrillation (19% vs 8%, P = 0.02).

Follow-up was 98% complete [median 8.3 (5.3–12.8) years]. The 13-year survival in the group aged ≥65 was 54 (SD: 9) % vs 83 (SD: 5) % in the control group (P < 0.001), but it was comparable to that expected in the age-sex matched general national population.

At 13 years, the cumulative incidence function of cardiac death in the elderly group was 19 (SD: 7)%, mostly unrelated to hypertrophic cardiomyopathy causes.

At the last follow-up, 90% of patients were in New York Heart Association functional class I-II and 68% were in sinus rhythm.

CONCLUSIONS

Selected elderly symptomatic patients with hypertrophic obstructive cardiomyopathy can benefit from surgery, with low hospital mortality and morbidity, relief of symptoms and late survival comparable to that expected in the age-sex matched general population.
The European Heart Journal: fulfilling the mission
Authors: Crea Filippo , Badimon Lina , Berry Colin , De Caterina Raffaele , Elliott Perry M , Hatala Robert , Libby Peter , Linde Cecilia , Tybjaerg-Hansen Anne
Published: March 2022

In September 2020, the new Editors of the European Heart Journal (EHJ) wrote the following in their inaugural editorial: “The fundamental mission of the Journal remains the reduction of the global burden of cardiovascular disease. We aspire to advance this aim by worldwide teamwork to communicate practice-changing research, inspire clinical cardiologists, and pursue rigour and transparency in the application of science at the service of human health. The Journal will strive to lead the field in its impact, influence, and reach”. After more than one year of experience the Editors hope the cardiological community will agree that they are fulfilling this mission. As stewards of the EHJ, the Editor's primary goal is not solely to achieve a high Impact Factor (which attests to the scientific quality and influence of our publications) but also to elevate the practice of cardiovascular medicine worldwide. Accordingly, various initiatives of the EHJ strive to strengthen further links among Editors, Authors, Reviewers and Readers through a series of coordinated and diverse activities, including webinars, active social media presence, and active participation at congresses worldwide. The Editors are proud to serve one of the most important scientific journals in cardiovascular medicine.
Healthcare professionals’ families’ perception of life during COVID-19 in Iran: a qualitative study
Authors: Mohammadi Fateme , Masoumi Seyedeh Zahra , Oshvandi Khodayar , Borzou Seyed Reza , Khodaveisi Masoud , Bashirian Saeid , Bijani Mostafa
Published: March 2022

Background

The families of healthcare professionals are one of the most vulnerable groups whose lives have been severely damaged by the COVID-19 pandemic. So far, the experiences and perceptions of these individuals have not been explored. The present study aims to investigate the experiences and perceptions of the family members of the healthcare professionals during COVID-19.

Methods

The present study is a qualitative research with a phenomenological design. The participants were 25 family members of healthcare professionals which were selected from the medical centres in Iran via purposeful sampling from August 2021 to October 2021. The sampling was kept on until the data became saturated. To collect data, individual semi-structured interviews were conducted online. The Colaizzi approach was used to analyse the data collected.

Results

The findings of the study emerged as two main themes: psychological tension with five categories (indescribable fear and worry, longing to see their loved ones, patient stone, bitter farewell, fear of the future) and dignity with four categories (acclamation, appreciation, feeling proud, spiritual growth).

Conclusion

During the COVID-19 pandemic, the family members of healthcare professionals have experienced dignity combined with the degrees of psychological tension which were beyond the experiences of the majority of people in the society, but similar to the psychological tension experienced by the families of COVID-19 victims. The families of healthcare workers are continuously anxious about the safety of their loved ones who are responsible to obtain the treatment of COVID-19 patients, which potentially jeopardizes their physical and psychological well-being. Therefore, the appreciation and support of people in the community of the family members of healthcare professionals have increased their tolerance. Healthcare providers can successfully promote the health of healthcare professionals’ families by providing comprehensive assistance to healthcare personnel and their families.
Conjugative transfer of naturally occurring plasmid in Mycolicibacterium sp
Authors: Morgado Sergio , Vicente Ana Carolina
Published: March 2022

Conjugation is considered the main horizontal gene transfer mechanism in bacterial adaptation and evolution. In the Mycobacteriaceae family, Mycolicibacterium smegmatis has been used as the model organism for the conjugative transfer of hybrid plasmids. However, the natural conjugation process in any bacteria would involve the transfer of naturally occurring plasmids. Currently, there is a gap in this regard about this abundant environmental genus of Mycobacteriaceae. Here, we performed conjugation experiments between wild Mycolicibacterium sp. strains involving naturally occurring plasmids, and interestingly, evidence of conjugative transfer was obtained. Thus, it is likely that conjugation occurs in Mycolicibacterium in the natural environment, representing a source of diversification and evolution in this genus of bacteria.