bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative evaluation of shape retrieval methods on macromolecular surfaces: an application of computer vision methods in structural bioinformatics
Authors: Machat Mohamed , Langenfeld Florent , Craciun Daniela , Sirugue Léa , Labib Taoufik , Lagarde Nathalie , Maria Maxime , Montes Matthieu 
Published: July 2021

Abstract

Motivation
The investigation of the structure of biological systems at the molecular level gives insights about their functions and dynamics. Shape and surface of biomolecules are fundamental to molecular recognition events. Characterizing their geometry can lead to more adequate predictions of their interactions. In the present work, we assess the performance of reference shape retrieval methods from the computer vision community on protein shapes.

Results
Shape retrieval methods are efficient in identifying orthologous proteins and tracking large conformational changes. This work illustrates the interest for the protein surface shape as a higher-level representation of the protein structure that (i) abstracts the underlying protein sequence, structure or fold, (ii) allows the use of shape retrieval methods to screen large databases of protein structures to identify surficial homologs and possible interacting partners and (iii) opens an extension of the protein structure–function paradigm toward a protein structure-surface(s)-function paradigm.

Availabilityand implementation
All data are available online at http://datasetmachat.drugdesign.fr.

Supplementary information
Supplementary data are available at Bioinformatics online.
Efficient gradient-based parameter estimation for dynamic models using qualitative data
Authors: Schmiester Leonard , Weindl Daniel , Hasenauer Jan 
Published: July 2021

Abstract

Motivation
Unknown parameters of dynamical models are commonly estimated from experimental data. However, while various efficient optimization and uncertainty analysis methods have been proposed for quantitative data, methods for qualitative data are rare and suffer from bad scaling and convergence.

Results
Here, we propose an efficient and reliable framework for estimating the parameters of ordinary differential equation models from qualitative data. In this framework, we derive a semi-analytical algorithm for gradient calculation of the optimal scaling method developed for qualitative data. This enables the use of efficient gradient-based optimization algorithms. We demonstrate that the use of gradient information improves performance of optimization and uncertainty quantification on several application examples. On average, we achieve a speedup of more than one order of magnitude compared to gradient-free optimization. In addition, in some examples, the gradient-based approach yields substantially improved objective function values and quality of the fits. Accordingly, the proposed framework substantially improves the parameterization of models from qualitative data.

Availability and implementation
The proposed approach is implemented in the open-source Python Parameter EStimation TOolbox (pyPESTO). pyPESTO is available at https://github.com/ICB-DCM/pyPESTO. All application examples and code to reproduce this study are available at https://doi.org/10.5281/zenodo.4507613.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Transformative Power of Trust: Exploring Tertiary Desistance in Reinventive Prisons
Authors: Ugelvik Thomas 
Published: July 2021

AbstractWhile prisons are often described as places of pain, despair and hopelessness, studies show that some prisoners under certain conditions report positive life changes happening in prison. This paper explores the connections between trust and desistance processes, specifically between the experience of being trusted and ‘tertiary desistance’. I argue that trust can be an engine of positive change in prison and that the experience of being trusted might even acquire additional value from the low-trust and risk-sensitive environment that most prisons normally offer prisoners. Finally, I discuss whether prisons that manage to get this balance right deserve to be called ‘reinventive prisons’.
Incidence of Respiratory Syncytial Virus Infection Among Hospitalized Adults, 2017–2020
Authors: Branche Angela R , Saiman Lisa , Walsh Edward E , Falsey Ann R , Sieling William D , Greendyke William , Peterson Derick R , Vargas Celibell Y , Phillips Matthew , Finelli Lyn 
Published: July 2021

Abstract

Background
Respiratory syncytial virus (RSV) causes acute respiratory illness (ARI) and triggers exacerbations of cardiopulmonary disease. Estimates of incidence in hospitalized adults range widely, with few data on incidence in adults with comorbidities that increase the risk of severity. We conducted a prospective, population-based, surveillance study to estimate incidence of RSV hospitalization among adults overall and those with specific comorbidities.

Methods
Hospitalized adults aged ≥18 years residing in the surveillance area with ≥2 ARI symptoms or exacerbation of underlying cardiopulmonary disease were screened during the 2017–2018, 2018–2019, and 2019–2020 RSV seasons in 3 hospitals in Rochester, New York and New York City. Respiratory specimens were tested for RSV using polymerase chain reaction assays. RSV incidence per 100 000 was adjusted by market share.

Results
Active and passive surveillance identified 1099 adults hospitalized with RSV. Annual incidence during 3 seasons ranged from 44.2 to 58.9/100 000. Age-group–specific incidence ranged from 7.7 to 11.9/100 000, 33.5 to 57.5/100 000, and 136.9 to 255.6/100 000 in patients ages 18–49, 50–64, and ≥65 years, respectively. Incidence rates in patients with chronic obstructive pulmonary disease, coronary artery disease, and congestive heart failure were 3–13, 4–7, and 4–33 times, respectively, the incidence in patients without these conditions.

Conclusions
We found a high burden of RSV hospitalization in this large prospective study. Notable was the high incidence among older patients and those with cardiac conditions. These data confirm the need for effective vaccines to prevent RSV infection in older and vulnerable adults.
Acute tubulointerstitial nephritis and COVID-19
Authors: Ng Jia H , Zaidan Mohamad , Jhaveri Kenar D , Izzedine Hassan 
Published: July 2021

Abstract
Coronavirus disease 2019 (COVID-19) is an ongoing pandemic that to date has spread to &gt;100 countries. Acute kidney injury is not uncommon with this disease. The most common kidney biopsy finding is acute tubular injury. Glomerular diseases such as collapsing glomerulopathy and vasculitis, and thrombotic microangiopathy have been reported. Viral inclusion particles with distinctive spikes in the tubular epithelium and podocytes, and endothelial cells of the glomerular capillary loops, have been visualized by electron microscopy by some but disputed by others as non-viral structures. Interstitial infiltrates have not commonly been described in the published kidney biopsy series from patients with COVID-19. Medications used to treat COVID-19 can lead to interstitial nephritis, but very few have been reported. In summary, interstitial kidney disease is a rare finding in COVID-19.
Interleukin-5-induced eosinophil population improves cardiac function after myocardial infarction
Authors: Xu Jun Yan , Xiong Yu Yan , Tang Rui Jie , Jiang Wen Yang , Ning Yu , Gong Zhao Ting , Huang Pei Sen , Chen Gui Hao , Xu Jun , Wu Chun Xiao , Hu Meng Jin , Xu Jing , Xu Yi , Huang Cun Rong , Jin Chen , Lu Xiao Tong , Qian Hai Yan , Li Xiang Dong , Yang Yue Jin 
Published: July 2021

Abstract

Aims
Interleukin (IL)-5 mediates the development of eosinophils (EOS) that are essential for tissue post-injury repair. It remains unknown whether IL-5 plays a role in heart repair after myocardial infarction (MI). This study aims to test whether IL-5-induced EOS population promotes the healing and repair process post-MI and to reveal the underlying mechanisms.

Methods and results
MI was induced by permanent ligation of the left anterior descending coronary artery in wild-type C57BL/6 mice. Western blot and real-time polymerase chain reaction revealed elevated expression of IL-5 in the heart at 5 days post-MI. Immunohistostaining indicated that IL-5 was secreted mainly from macrophages and CD127+ cells in the setting of experimental MI. External supply of recombinant mouse IL-5 (20 min, 1 day, and 2 days after MI surgery) reduced the infarct size and increased ejection fraction and angiogenesis in the border zone. A significant expansion of EOS was detected in both the peripheral blood and infarcted myocardium after IL-5 administration. Pharmacological depletion of EOS by TRFK5 pretreatment muted the beneficial effects of IL-5 in MI mice. Mechanistic studies demonstrated that IL-5 increased the accumulation of CD206+ macrophages in infarcted myocardium at 7 days post-MI. In vitro co-culture experiments showed that EOS shifted bone marrow-derived macrophage polarization towards the CD206+ phenotypes. This activity of EOS was abolished by IL-4 neutralizing antibody, but not IL-10 or IL-13 neutralization. Western blot analyses demonstrated that EOS promoted the macrophage downstream signal transducer and activator of transcription 6 (STAT6) phosphorylation.

Conclusion
IL-5 facilitates the recovery of cardiac dysfunction post-MI by promoting EOS accumulation and subsequent CD206+ macrophage polarization via the IL-4/STAT6 axis.
Deep-sea hydrothermal vent sediments reveal diverse fungi with antibacterial activities
Authors: Keeler Emma , Burgaud Gaëtan , Teske Andreas , Beaudoin David , Mehiri Mohamed , Dayras Marie , Cassand Jacquelin , Edgcomb Virginia 
Published: July 2021

ABSTRACTRelatively little is known about the diversity of fungi in deep-sea, hydrothermal sediments. Less thoroughly explored environments are likely untapped reservoirs of unique biodiversity with the potential to augment our current arsenal of microbial compounds with biomedical and/or industrial applications. In this study, we applied traditional culture-based methods to examine a subset of the morphological and phylogenetic diversity of filamentous fungi and yeasts present in 11 hydrothermally influenced sediment samples collected from eight sites on the seafloor of Guaymas Basin, Mexico. A total of 12 unique isolates affiliating with Ascomycota and Basidiomycota were obtained and taxonomically identified on the basis of morphological features and analyses of marker genes including actin, β-tubulin, small subunit ribosomal DNA (18S rRNA), internal transcribed spacer (ITS) and large subunit ribosomal DNA (26S rRNA) D1/D2 domain sequences (depending on taxon). A total of 11 isolates possess congeners previously detected in, or recovered from, deep-sea environments. A total of seven isolates exhibited antibacterial activity against human bacterial pathogens Staphylococcus aureus ATCC-35556 and/or Escherichia coli ATCC-25922. This first investigation suggests that hydrothermal environments may serve as promising reservoirs of much greater fungal diversity, some of which may produce biomedically useful metabolites.
Ultralong Oxford Nanopore Reads Enable the Development of a Reference-Grade Perennial Ryegrass Genome Assembly
Authors: Frei Daniel , Veekman Elisabeth , Grogg Daniel , Stoffel-Studer Ingrid , Morishima Aki , Shimizu-Inatsugi Rie , Yates Steven , Shimizu Kentaro K , Frey Jürg E , Studer Bruno , Copetti Dario 
Published: July 2021

AbstractDespite the progress made in DNA sequencing over the last decade, reconstructing telomere-to-telomere genome assemblies of large and repeat-rich eukaryotic genomes is still difficult. More accurate basecalls or longer reads could address this issue, but no current sequencing platform can provide both simultaneously. Perennial ryegrass (Lolium perenne L.) is an example of an important species for which the lack of a reference genome assembly hindered a swift adoption of genomics-based methods into breeding programs. To fill this gap, we optimized the Oxford Nanopore Technologies’ sequencing protocol, obtaining sequencing reads with an N50 of 62 kb—a very high value for a plant sample. The assembly of such reads produced a highly complete (2.3 of 2.7 Gb), correct (QV 45), and contiguous (contig N50 and N90 11.74 and 3.34 Mb, respectively) genome assembly. We show how read length was key in determining the assembly contiguity. Sequence annotation revealed the dominance of transposable elements and repeated sequences (81.6% of the assembly) and identified 38,868 protein coding genes. Almost 90% of the bases could be anchored to seven pseudomolecules, providing the first high-quality haploid reference assembly for perennial ryegrass. This protocol will enable producing longer Oxford Nanopore Technology reads for more plant samples and ushering forage grasses into modern genomics-assisted breeding programs.
Effects of urbanization on vulnerability to heat-related mortality in urban and rural areas in South Korea: a nationwide district-level time-series study
Authors: Lee Whanhee , Choi Munjeong , Bell Michelle L , Kang Cinoo , Jang Jeongju , Song Insung , Kim Yong-Ook , Ebi Kristie , Kim Ho 
Published: July 2021

Abstract

Background
Although urbanization is often an important topic in climate change studies, the complex effect of urbanization on heat vulnerability in urban and rural areas has rarely been studied. We investigated the disparate effects of urbanization on heat vulnerability in urban and rural areas, using nationwide data.

Methods
We collected daily weather data for all 229 administrative districts in South Korea (2011–17). Population density was applied as an urbanization indicator. We calculated the heat-mortality risk using a distributed lag nonlinear model and analysed the relationship with population density. We also examined district characteristics that can be related to the spatial heterogeneity in heat-mortality risk.

Results
We found a U-shaped association between population density and heat-mortality risk, with the highest risk for rural populations; in urban areas, risk increases with increasing population density. Higher heat-mortality risk was associated with a lower number of hospital beds per person and higher percentage of people requiring recuperation. The association between hospital beds and heat-mortality risk was prominent in high-density urban areas, whereas the association between the percentage of people requiring recuperation and heat-mortality risk was pronounced in rural areas.

Conclusions
Our findings indicate that the association between population density and heat-mortality risk is different in urban and rural areas, and that district characteristics related to heat-mortality risk also differ by urbanicity. These results can contribute to understanding the complex role of urbanization on heat vulnerability and can provide evidence to policy makers for prioritizing resources.
Occurrence and Distribution of Nonfalciparum Malaria Parasite Species Among Adolescents and Adults in Malawi
Authors: Gumbo Austin , Topazian Hillary M , Mwanza Alexis , Mitchell Cedar L , Puerto-Meredith Sydney , Njiko Ruth , Kayange Michael , Mwalilino David , Mvula Bernard , Tegha Gerald , Mvalo Tisungane , Hoffman Irving , Juliano Jonathan J 
Published: July 2021

Abstract

Background
Plasmodium falciparum malaria dominates throughout sub-Saharan Africa, but the prevalence of Plasmodium malariae, Plasmodium ovale spp., and Plasmodium vivax increasingly contribute to infection in countries that control malaria using P. falciparum-specific diagnostic and treatment strategies.

Methods
We performed quantitative polymerase chain reaction (qPCR) on 2987 dried blood spots from the 2015–2016 Malawi Demographic and Health Survey to identify presence and distribution of nonfalciparum infection. Bivariate models were used to determine species-specific associations with demographic and environmental risk factors.

Results
Nonfalciparum infections had broad spatial distributions. Weighted prevalence was 0.025 (SE, 0.004) for P. malariae, 0.097 (SE, 0.008) for P. ovale spp., and 0.001 (SE, 0.0005) for P. vivax. Most infections (85.6%) had low-density parasitemias ≤ 10 parasites/µL, and 66.7% of P. malariae, 34.6% of P. ovale spp., and 40.0% of P. vivax infections were coinfected with P. falciparum. Risk factors for P. malariae were like those known for P. falciparum; however, there were few risk factors recognized for P. ovale spp. and P. vivax, perhaps due to the potential for relapsing episodes.

Conclusions
The prevalence of any nonfalciparum infection was 11.7%, with infections distributed across Malawi. Continued monitoring of Plasmodium spp. becomes critical as nonfalciparum infections become important sources of ongoing transmission.
Sub-Lethal Effects of λ-Cyhalothrin on Behavior and Development of the ParasitoidAphidius colemani(Hymenoptera: Braconidae) onkdr-Resistant and Susceptible Green Peach Aphid,Myzus persicae(Hemiptera: Aphididae)
Authors: Alfaro-Tapia Armando , Alvarez-Baca Jeniffer K , Figueroa Christian C , Fuentes-Contreras Eduardo 
Published: July 2021

AbstractThe green peach aphid, Myzus persicae (Sulzer), is a pest mainly controlled with insecticides, and it can acquire resistance through different mechanisms. Pyrethroids can select the knock down resistance (kdr) mutation in M. persicae and can also produce lethal and sub-lethal effects on its main parasitoid, Aphidius colemani Viereck. However, kdr-resistant M. persicae exhibits a reduced response to alarm pheromone and increased vulnerability to natural enemies. To study the effects of sub-lethal concentrations of a pyrethroid on the aphid-parasitoid interaction, kdr-resistant and susceptible M. persicae were confronted with A. colemani with residual sub-lethal concentrations of λ-cyhalothrin. The behavior, survival, and development of parasitoids were evaluated after exposure to λ-cyhalothrin LC20 for adult parasitoids (0.52 mg/liter) for susceptible (Mp-SS, 0.56 mg/liter) and kdr-resistant M. persicae (Mp-RR, 12.15 mg/liter). The foraging and oviposition behaviors of the parasitoids were not affected by the lower parasitoid or Mp-SS LC20. Conversely, the higher Mp-RR LC20 significantly reduced parasitoid walking, the frequency of sting attempts, and successful stings, as well as aphid defensive behaviors, such as walking, kicking, and jerking. Therefore, the higher vulnerability of kdr-resistant M. persicae could not be capitalized by A. colemani parasitoids under a high concentration of λ-cyhalothrin. Similarly, the parasitism rate, survival of progeny, productivity, sex ratio (proportion of females), longevity, and adult body mass were reduced, and the development time increased with a higher Mp-RR LC20. Our results suggest that A. colemani could efficiently control kdr-resistant and susceptible M. persicae only at lower λ-cyhalothrin concentrations.
Local border reforms and economic activity
Authors: Egger Peter H , Koethenbuerger Marko , Loumeau Gabriel 
Published: July 2021

Abstract
In this article, we make use of large-scale municipal border changes in Germany to provide the first evidence on the effect of local border changes on the distribution of activity in space. To allow for a comparison of economic activity within unique geographical units over time, we use geo-coded light data as well as local land-use data. Applying a difference-in-differences approach, we find evidence that municipalities absorbing their merger partners and hosting the new administrative center experience a significant increase in local activity, while the municipalities that are being absorbed and are losing the administrative center experience a decrease in such activity. The difference between the gains in activity from absorbing municipalities and the losses from absorbed ones is positive. These previously undocumented results point to the importance of distance to the administrative center as a determinant of the spatial distribution of economic activity.
Improving Energy Efficiency: The Significance of Normativity
Authors: Kirk Elizabeth A , Besco Laurel 
Published: July 2021

Abstract
The failure of the global community to effectively address many large-scale environmental challenges calls into question the existing regulatory approaches. A large number of these challenges are diffuse issues which have, over the years been targeted by significant and sizable regulatory frameworks and yet the challenges persist—energy efficiency is one such issue and is the focus of this article. Increasing monitoring or enforcement to achieve improvements in regulatory compliance is too expensive in the context of diffuse problems due to the scale and costs such activities would entail. We suggest a focus on the fit between regulatory frameworks and norm creation may identify more fruitful routes to regulatory reform. Drawing on the ‘interactional account of law’ as a framework, this research uses new empirical data from a survey and a set of interviews to investigate the failure of energy efficiency regulatory frameworks at achieving energy efficient norms of behaviour in industry. We look at Canada and the UK as our case studies and our emphasis is on industry actors as they represent a significant and yet understudied area of society. We find that though existing regulatory structures seem adequate to generate general shared understandings around obligations to engage in energy efficiency actions, more specific shared practice around actually engaging in these actions remains elusive, resulting in a failure to engender norms of behaviour. These failures, we suggest, link directly to an inadequate fit between the regulatory tools and Fuller’s criteria for the internal morality of law.
Platycarya strobilacea Sieb. et Zucc.: a review of its traditional uses, botany, phytochemistry, pharmacology and toxicology
Authors: Zhao Peiyuan , Han Lizhu , Wang Yunlan , Qiu Jinqing , Zhang Xinbo , Tang Zhishu , Duan Xi , Song Xiao 
Published: July 2021

Abstract

Objectives
Platycarya strobilacea Sieb. et Zucc. is the dry infructescence of P. strobilacea, a Juglandaceae plant and is a traditional Chinese medicine with great development potential and utilization value. This study summarizes the research progress on the traditional uses, botany, phytochemistry, extraction methods, pharmacology and toxicology of Platycarya strobilacea Sieb. et Zucc., and provides potential therapeutic uses and drug development prospects for this plant.

Key findings
Phytochemical studies showed that this plant mainly contains volatile constituents, phenols, terpenoids and a carbohydrate. The pharmacological activity of Platycarya strobilacea Sieb. et Zucc. includes antibacterial and anti-inflammatory effects, anti-tumour effects and antioxidant effects. This plant is especially effective in the treatment of allergic rhinitis and chronic sinusitis.

Summary
In this review, the phytochemistry and pharmacological effects of Platycarya strobilacea Sieb. et Zucc. are described in detail, which will have guiding significance for the future development of this drug.