bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrafast critical ground state preparation via bang–bang protocols
Authors: Innocenti Luca , De Chiara Gabriele , Paternostro Mauro , Puebla Ricardo 
Published: August 2020

Abstract
The fast and faithful preparation of the ground state of quantum systems is a challenging but crucial task for several applications in the realm of quantum-based technologies. Decoherence limits the maximum time-window allowed to an experiment to faithfully achieve such desired states. This is of particular significance in systems featuring a quantum phase transition, where the vanishing energy gap challenges an adiabatic ground state preparation. We show that a bang–bang protocol, consisting of a time evolution under two different values of an externally tunable parameter, allows for a high-fidelity ground state preparation in evolution times no longer than those required by the application of standard optimal control techniques, such as the chopped-random basis quantum optimization. In addition, owing to their reduced number of variables, such bang–bang protocols are very well suited to optimization tasks, reducing the high computational cost of other optimal control protocols. We benchmark the performance of such approach through two paradigmatic models, namely the Landau–Zener and the Lipkin–Meshkov–Glick model. Remarkably, we find that the critical ground state of the latter model, i.e. its ground state at the critical point, can be prepared with a high fidelity in a total evolution time that scales slower than the inverse of the vanishing energy gap.
Probability of compound climate extremes in a changing climate: A copula-based study of hot, dry, and windy events in the central United States
Authors: Tavakol Ameneh , Rahmani Vahid , Harrington Jr. John 
Published: August 2020

Abstract
Climate extreme events exert disproportionate impacts on ecosystems and humankind. Focusing on univariate statistics to estimate the harm from compound extreme events usually falls short in communicating the real risk. Here, the co-occurrence of hot, dry, and windy events (HDWs) in the central United States was analyzed over the period 1949–2018. Results demonstrate south-west Kansas and north Texas as locations where HDWs are more frequent. The combination of drought and a heatwave in 1980 and 2011, increased the likelihood of HDWs. Use of copula enables the study of the co-occurrence of multiple extremes. The copula approach identified a greater risk of HDWs compared with traditional empirical analysis. The dependence structure between the temperature, humidity, and wind variables showed no effect on the co-occurrence frequency of HDWs in the warm-season (May through September). Results suggest an increase in the risk of HDWs in spite of the historical wind speed drop across the majority of Great Plains. Multivariate perspectives are necessary for a more informed assessment of compound extremes risk and for improved design of adaption strategies.
Accurate phase analysis of interferometric fringes by the spatiotemporal phase-shifting method
Authors: Ri Shien , Takimoto Taiki , Xia Peng , Wang Qinghua , Tsuda Hiroshi , Ogihara Shinji 
Published: August 2020

Abstract
Phase-shifting interferometry (PSI) has been widely applied in the field of accurate optical methodology. However, the fluctuation of background and amplitude intensities due to the instability of laser source, and phase-shifting error or vibration are significant problems for the PSI. In this study, the spatiotemporal phase-shifting method (ST-PSM) (Ri S et al 2019 J. Opt.
21 095702), which is a highly accurate and robust phase analysis method using spatial and temporal intensities information simultaneously, is first applied to laser interferometry to achieve a stable measurement. Through several simulations, three effects of fluctuations in background and amplitude intensities, phase-shifting error were investigated. As a result, we clarified that the periodic phase error with fundamental or second harmonic frequencies occurs in the conventional PSM method, whereas no periodic error occurs in the ST-PSM. Besides, the ST-PSM is also robust to the noise either for uniform or distorted interference fringe images. In the Michelson laser interferometer experiment, the ST-PSM realizes a much more stable measurement of phase and phase gradient distributions than the PSM. We have revealed the excellent performance and the striking advantage that ST-PSM is entirely free of periodic errors in a similar manner to the simulations. Therefore, laser interferometry using the ST-PSM can be expected to apply to various applications, including the extremely accurate non-contact shape and deformation measurement, as well as thickness measurement of transparent materials in life and material sciences.
Size and phenology control plant reproduction and agricultural production. A commentary on: ‘How plant allometry influences bud phenology and fruit yield in two Vaccinium species’
Authors: Bonser Stephen P 
Published: August 2020

This article comments on:
Marie-Pier Fournier, Maxime C. Paré, Valentina Buttò, Sylvain Delagrange, Jean Lafond and Annie Deslauriers, How plant allometry influences bud phenology and fruit yield in two Vaccinium species, Annals of Botany, Volume 126, Issue 5, 9 October 2020, Pages 825–835, https://doi.org/10.1093/aob/mcaa083
LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files
Authors: Dong Shan-Shan , He Wei-Ming , Ji Jing-Jing , Zhang Chi , Guo Yan , Yang Tie-Lin 
Published: August 2020

Abstract
The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD) pattern and haplotype block structure of SNPs is ubiquitous component of population-based genetic studies. However, current tools suffered from the problem of time and memory consuming. Here, we developed LDBlockShow, an open source software, for visualizing LD and haplotype blocks from variant call format files. It is time and memory saving. In a test dataset with 100 SNPs from 60 000 subjects, it was at least 10.60 times faster and used only 0.03–13.33% of physical memory as compared with other tools. In addition, it could generate figures that simultaneously display additional statistical context (e.g. association P-values) and genomic region annotations. It can also compress the SVG files with a large number of SNPs and support subgroup analysis. This fast and convenient tool will facilitate the visualization of LD and haplotype blocks for geneticists.
Adverse Childhood Experiences and Social Work: Relationship-based Practice Responses
Authors: Frederick John , Spratt Trevor , Devaney John 
Published: August 2020

Abstract
Individuals with higher numbers of adverse childhood experiences (ACEs) have been found to be overrepresented amongst users of social services. This poses challenges for service providers in seeking ways to incorporate knowledge about ACEs in the calibration of service provision, and for social workers as to how they might use such knowledge in their day-to-day practice. The key contribution of this article is as a position piece that aims to map out a possible response to the ACEs evidence from social work. Practice needs to be informed by an understanding of the causes and consequences of trauma in the lives of individuals and groups. Short-term interventions based on proximal causes have resulted in a fundamental misunderstanding as to the aetiology of the problems experienced and to the types of interventions required to facilitate their amelioration. ACEs research offers a new understanding of how connecting trajectories are formed and maintained in ways that integrate biological, psychological and sociological concepts. In this article, we have made selective use of key texts and studies in the social work literature to illustrate how relationship-based social work may be appropriated and repurposed to align with interventions to mitigate the effects of ACEs.
Intrapulmonary Pharmacokinetics of First-line Anti-tuberculosis Drugs in Malawian Patients With Tuberculosis
Authors: McCallum Andrew D , Pertinez Henry E , Else Laura J , Dilly-Penchala Sujan , Chirambo Aaron P , Sheha Irene , Chasweka Madalitso , Chitani Alex , Malamba Rose D , Meghji Jamilah Z , Gordon Stephen B , Davies Geraint R , Khoo Saye H , Sloan Derek J , Mwandumba Henry C 
Published: August 2020

Abstract

Background
Further work is required to understand the intrapulmonary pharmacokinetics of first-line anti-tuberculosis drugs. This study aimed to describe the plasma and intrapulmonary pharmacokinetics of rifampicin, isoniazid, pyrazinamide, and ethambutol, and explore relationships with clinical treatment outcomes in patients with pulmonary tuberculosis.

Methods
Malawian adults with a first presentation of microbiologically confirmed pulmonary tuberculosis received standard 6-month first-line therapy. Plasma and intrapulmonary samples were collected 8 and 16 weeks into treatment and drug concentrations measured in plasma, lung/airway epithelial lining fluid (ELF), and alveolar cells. Population pharmacokinetic modeling generated estimates of drug exposure (Cmax and AUC) from individual-level post hoc Bayesian estimates of plasma and intrapulmonary pharmacokinetics.

Results
One-hundred fifty-seven patients (58% HIV coinfected) participated. Despite standard weight-based dosing, peak plasma concentrations of first-line drugs were below therapeutic drug-monitoring targets. Rifampicin concentrations were low in all 3 compartments. Isoniazid, pyrazinamide, and ethambutol achieved higher concentrations in ELF and alveolar cells than plasma. Isoniazid and pyrazinamide concentrations were 14.6-fold (95% CI, 11.2–18.0-fold) and 49.8-fold (95% CI, 34.2–65.3-fold) higher in ELF than plasma, respectively. Ethambutol concentrations were highest in alveolar cells (alveolar cell–plasma ratio, 15.0; 95% CI, 11.4–18.6). Plasma or intrapulmonary pharmacokinetics did not predict clinical treatment response.

Conclusions
We report differential drug concentrations between plasma and the lung. While plasma concentrations were below therapeutic monitoring targets, accumulation of drugs at the site of disease may explain the success of the first-line regimen. The low rifampicin concentrations observed in all compartments lend strong support for ongoing clinical trials of high-dose rifampicin regimens.
Coronavirus Disease 2019 (COVID-19) Re-infection by a Phylogenetically Distinct Severe Acute Respiratory Syndrome Coronavirus 2 Strain Confirmed by Whole Genome Sequencing
Authors: To Kelvin Kai-Wang , Hung Ivan Fan-Ngai , Ip Jonathan Daniel , Chu Allen Wing-Ho , Chan Wan-Mui , Tam Anthony Raymond , Fong Carol Ho-Yan , Yuan Shuofeng , Tsoi Hoi-Wah , Ng Anthony Chin-Ki , Lee Larry Lap-Yip , Wan Polk , Tso Eugene Yuk-Keung , To Wing-Kin , Tsang Dominic Ngai-Chong , Chan Kwok-Hung , Huang Jian-Dong , Kok Kin-Hang , Cheng Vincent Chi-Chung , Yuen Kwok-Yung 
Published: August 2020

Abstract

Background
Waning immunity occurs in patients who have recovered from Coronavirus Disease 2019 (COVID-19). However, it remains unclear whether true re-infection occurs.

Methods
Whole genome sequencing was performed directly on respiratory specimens collected during 2 episodes of COVID-19 in a patient. Comparative genome analysis was conducted to differentiate re-infection from persistent viral shedding. Laboratory results, including RT-PCR Ct values and serum Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) IgG, were analyzed.

Results
The second episode of asymptomatic infection occurred 142 days after the first symptomatic episode in an apparently immunocompetent patient. During the second episode, there was evidence of acute infection including elevated C-reactive protein and SARS-CoV-2 IgG seroconversion. Viral genomes from first and second episodes belong to different clades/lineages. The virus genome from the first episode contained a a stop codon at position 64 of ORF8, leading to a truncation of 58 amino acids. Another 23 nucleotide and 13 amino acid differences located in 9 different proteins, including positions of B and T cell epitopes, were found between viruses from the first and second episodes. Compared to viral genomes in GISAID, the first virus genome was phylogenetically closely related to strains collected in March/April 2020, while the second virus genome was closely related to strains collected in July/August 2020.

Conclusions
Epidemiological, clinical, serological, and genomic analyses confirmed that the patient had re-infection instead of persistent viral shedding from first infection. Our results suggest SARS-CoV-2 may continue to circulate among humans despite herd immunity due to natural infection. Further studies of patients with re-infection will shed light on protective immunological correlates for guiding vaccine design.
The inflammation-resolution promoting molecule resolvin-D1 prevents atrial proarrhythmic remodelling in experimental right heart disease
Authors: Hiram Roddy , Xiong Feng , Naud Patrice , Xiao Jiening , Sirois Martin , Tanguay Jean-François , Tardif Jean-Claude , Nattel Stanley 
Published: August 2020

Abstract

Aims
Inflammation plays a role in atrial fibrillation (AF), but classical anti-inflammatory molecules are ineffective. Recent evidence suggests that failure of inflammation-resolution causes persistent inflammatory signalling and that a novel drug-family called resolvins promotes inflammation-resolution. Right heart disease (RHD) is associated with AF; experimental RHD shows signs of atrial inflammatory-pathway activation. Here, we evaluated resolvin-therapy effects on atrial arrhythmogenic remodelling in experimental RHD.

Methods and results
Pulmonary hypertension and RHD were induced in rats with an intraperitoneal injection of 60 mg/kg monocrotaline (MCT). An intervention group received daily resolvin-D1 (RvD1), starting 1 day before MCT administration. Right atrial (RA) conduction and gene-expression were analysed respectively by optical mapping and qPCR/gene-microarray. RvD1 had no or minimal effects on MCT-induced pulmonary artery or right ventricular remodelling. Nevertheless, in vivo transoesophageal pacing induced atrial tachyarrhythmias in no CTRL rats vs. 100% MCT-only rats, and only 33% RvD1-treated MCT rats (P &lt; 0.001 vs. MCT-only). Conduction velocity was significantly decreased by MCT, an effect prevented by RvD1. RHD caused RA dilation and fibrosis. RvD1 strongly attenuated RA fibrosis but had no effect on RA dilation. MCT increased RA expression of inflammation- and fibrosis-related gene-expression pathways on gene-microarray transcriptomic analysis, effects significantly attenuated by RvD1 (334 pathways enriched in MCT-rats vs. control; only 177 dysregulated by MCT with RvD1 treatment). MCT significantly increased RA content of type 1 (proinflammatory) CD68-positive M1 macrophages without affecting type 2 (anti-inflammatory) M2 macrophages. RvD1-treated MCT-rat RA showed significant reductions in proinflammatory M1 macrophages and increases in anti-inflammatory M2 macrophages vs. MCT-only. MCT caused statistically significant increases in protein-expression (western blot) of COL3A1, ASC, CASP1, CASP8, IL1β, TGFβ3, CXCL1, and CXCL2, and decreases in MMP2, vs. control. RvD1-treatment suppressed all these MCT-induced protein-expression changes.

Conclusion
The inflammation-resolution enhancing molecule RvD1 prevents AF-promoting RA remodelling, while suppressing inflammatory changes and fibrotic/electrical remodelling, in RHD. Resolvins show potential promise in combating atrial arrhythmogenic remodelling by suppressing ongoing inflammatory signalling.
Conducting Translational Gastrointestinal Research in the Era of COVID-19
Authors: Nayeri Shadi , Walshe Margaret , Lee Sun-Ho , Filice Melissa , Rho Stella , Jeyakumar Ajani , Stempak Joanne , Smith Michelle I , Silverberg Mark S 
Published: August 2020

Abstract
Spread of the novel coronavirus SARS-CoV-2 has resulted in a global pandemic that is affecting the health and economy of all World Health Organization [WHO] regions. Clinical and translational research activities have been affected drastically by this global catastrophe. In this document we provide a suggested roadmap for resuming gastrointestinal translational research activities, emphasising physical distancing and use of personal protective equipment. We discuss modes of virus transmission in enclosed environments [including clinical workplaces and laboratories] and potential risks of exposure in the endoscopy environment for research staff. The proposed guidelines should be considered in conjunction with local institutional and government guidelines so that translational research can be resumed as safely as possible.
Temporal Dimensions of Unemployment and Relationship Happiness in the United Kingdom
Authors: Blom Niels , Perelli-Harris Brienna 
Published: August 2020

Abstract
Here we study how unemployment is related to partner relationship happiness in the United Kingdom. We investigate multiple dimensions of unemployment—current unemployment, changes in unemployment, duration of unemployment, and past unemployment—each of which provides unique insights into how economic uncertainty can strain relationships. Not including these aspects potentially leads to an underestimation of the long-term effect of unemployment and times when couples are especially affected. Using British longitudinal data (UK Household Longitudinal Study), we employ random and fixed regression analyses. The results highlight the gendered nature of relationships and employment within British couples. As found in previous studies, unemployment, particularly men’s unemployment, is associated with unhappier relationships. However, we find that over the long-run, relationship happiness declined and did not always recover. In addition, men’s re-employment did not solve problems rising from unemployment, especially for women, who continued to be less happy with the relationship when their male partner was unemployed in the recent past. Overall, the research showed that unemployment is not only related to relationship happiness at the time of unemployment, but had a scarring effect on relationship happiness.
Catheter ablation of atrial fibrillation: cardiac imaging guidance as an adjunct to the electrophysiological guided approach
Authors: Markman Timothy M , Khoshknab Mirmilad , Nazarian Saman 
Published: August 2020

AbstractCatheter ablation is increasingly utilized to treat patients with atrial fibrillation (AF). Despite progress in technology and procedural strategy, there remain significant limitations with suboptimal outcomes. The role of imaging has continued to evolve, and multimodality imaging now presents an important opportunity to make substantial progress in the safety and efficacy of ablation. In this review, we discuss the history of imaging in the ablation of AF with a specific focus on the ability of cardiac computed tomography and magnetic resonance imaging to characterize anatomy, arrhythmogenic substrate, and guide ablation strategy. We will review the progress that has been made and highlight many of the limitations as well as future directions for the field.
Tree-Related Microhabitats: A Comparison of Managed and Unmanaged Oriental Beech–Dominated Forests in Northern Iran
Authors: Sefidi Kiomars , Copenheaver Carolyn A 
Published: August 2020

AbstractTree-related microhabitats (TreMs) provide ecological niches in features for a variety of species in forests and are suitable indicators of biodiversity for certain taxa. The study objective was to compare the abundance and occurrence of TreMs in managed versus unmanaged Oriental beech (Fagus orientalis Lipsky) forests of northern Iran to quantify the effect of forest management on biodiversity indicators. We inventoried 3,954 trees to identify the number of trees with TreMs and quantify the occurrence of different types of TreMs. Managed forests averaged 25 trees with TreMs per hectare, and unmanaged forests averaged 41 trees with TreMs per hectare. In both forests, larger-diameter trees (≥50 centimeters diameter at breast height [dbh]) had more TreMs than smaller-diameter trees. TreMs were found on trees larger than a minimum size (32 centimeters dbh) and were more common on trees in poor health, as indicated by vitality class. According to our findings, managed forests have a lower diversity of TreMs than unmanaged forests. However, if management plans in deciduous forests include the retention of large-diameter trees during harvesting events, it is possible to balance providing TreMs within the forest while maintaining growth of economically valuable timber.Study ImplicationsForest biodiversity is time and labor intensive to quantify, and researchers have begun using tree-related microhabitats (TreMs) as a proxy for biodiversity. This study found TreMs occurred at lower abundances but had a similar occurrence of TreM groupings (cavities, injuries and wounds, deformation/growth form, and epiphytes) in managed Oriental beech (Fagus orientalis Lipsky) forests compared with unmanaged Oriental beech forests. Managed hardwood stands provided 25 TreMs per hectare, which is similar to numbers recommended for managing for biodiversity, and thus it may be possible to promote TreM creation and retention as an opportunity to increase forest biodiversity while also managing forests for timber production. Abundance of TreMs was associated with large-diameter trees and low-vitality trees (poor health). In deciduous forests managed for timber production, the retention of large-diameter trees is likely to align more closely with other management objectives than the retention of trees in poor health.
Burn Severity Effects on Sediment and Nutrient Exports from Southeastern Forests Using Simulated Rainfall
Authors: Klimas Kipling , Hiesl Patrick , Hagan Donald , Park Dara 
Published: August 2020

Abstract

Burn severity, commonly assessed as the amount of fuel consumed during fire, is an indicator of postfire sediment yield and erosion. This study examined the effect of burn severity on sediment and nutrient response in three different fire-adapted forest types of the Southeast. Soil and litter samples were experimentally burned to achieve increasing levels of fuel consumption. Simulated rainfall was applied to burned litter samples collected from pine, hardwood, and mixed hardwood-pine forests in the Clemson Experimental Forest. Runoff and leachate samples were collected and analyzed for sediment yield (kilograms per hectare) and total suspended solids (grams per liter); both runoff and leachate samples were analyzed for ammonium (NH4–), nitrate (NO3–), and orthophosphate (PO43–). Sediment yield and total suspended solids increased at only the highest burn severity treatment in all three forest types, with pine litter samples yielding significantly greater sediment in surface runoff than both mixed and hardwood samples. Burn treatment did not readily affect soluble nutrient concentrations in either runoff or leachate, but the data suggest that high-severity burning increases the availability of PO43– bound to sediment. This study suggests that high-severity burn patches function as sediment sources, but overall sediment and nutrient response to burning was minimal.

Study Implications
This study suggests that low-to-moderate burn severity, in terms of litter removal, is not an important indicator of sediment and nutrient exports from southeastern forests; precipitation in the immediate aftermath of fire (&lt;48 hours) is not an effective transport mechanism for biologically available macronutrients; and that even at the highest burn severity treatment, sediment yield was relatively low.