bluuebunny/crossref_metadata_2025 huggingface dataset:
SolupHred: a server to predict the pH-dependent aggregation of intrinsically disordered proteins
Authors: Pintado Carlos , Santos Jaime , Iglesias Valentín , Ventura Salvador
Published: October 2020

Polypeptides are exposed to changing environmental conditions that modulate their intrinsic aggregation propensities. Intrinsically disordered proteins (IDPs) constitutively expose their aggregation determinants to the solvent, thus being especially sensitive to its fluctuations. However, solvent conditions are often disregarded in computational aggregation predictors. We recently developed a phenomenological model to predict IDPs' solubility as a function of the solution pH, which is based on the assumption that both protein lipophilicity and charge depend on this parameter. The model anticipated solubility changes in different IDPs accurately. In this application note, we present SolupHred, a web-based interface that implements the aforementioned theoretical framework into a predictive tool able to compute IDPs aggregation propensities as a function of pH. SolupHred is the first dedicated software for the prediction of pH-dependent protein aggregation.

Availability and implementation

The SolupHred web server is freely available for academic users at: https://ppmclab.pythonanywhere.com/SolupHred. It is platform-independent and does not require previous registration.

Supplementary information

Supplementary data are available at Bioinformatics online.
Lipopolysaccharide-induced epididymitis modifies the transcriptional profile ofWfdcgenes in mice†
Authors: Andrade Alexandre D , Almeida Priscila G C , Mariani Noemia A P , Freitas Geanne A , Kushima Hélio , Filadelpho André L , Spadella Maria Angélica , Avellar Maria Christina W , Silva Erick J R
Published: October 2020

Whey-acidic protein four-disulfide core domain (WFDC) genes display putative roles in innate immunity and fertility. In mice, a locus on chromosome 2 contains 5 and 11 Wfdc genes in its centromeric and telomeric subloci, respectively. Although Wfdc genes are highly expressed in the epididymis, their contributions to epididymal function remain elusive. Here, we investigated whether Wfdc genes are regulated in response to lipopolysaccharide (LPS)-induced epididymitis, an inflammatory condition that impairs male fertility. We induced epididymitis in mice via (i) interstitial LPS injection into epididymal initial segment and (ii) intravasal LPS injection into the vas deferens towards cauda epididymis. Interstitial and intravasal LPS induced a differential upregulation of inflammatory mediators (interleukin 1 beta, interleukin 6, tumor necrosis factor, interferon gamma, and interleukin 10) in the initial segment and cauda epididymis within 72 h post-treatment. These changes were accompanied by a time-dependent endotoxin clearance from the epididymis. In the initial segment, interstitial LPS upregulated all centromeric (Slpi, Wfdc5, Wfdc12, Wfdc15a, and Wfdc15b) and five telomeric (Wfdc2, Wfdc3, Wfdc6b, Wfdc10, and Wfdc13) Wfdc transcripts at 24 and 72 h. In the cauda epididymis, intravasal LPS upregulated Wfdc5 and Wfdc2 transcripts at 24 h, followed by a downregulation of Wfdc15b and three telomeric (Wfdc6a, Wfdc11, and Wfdc16) gene transcripts at 72 h. Pharmacological inhibition of nuclear factor kappa B activation prevented LPS-induced upregulation of centromeric and telomeric Wfdc genes depending on the epididymal region. We show that LPS-induced inflammation differentially regulated the Wfdc locus in the proximal and distal epididymis, indicating region-specific roles for the Wfdc family in innate immune responses during epididymitis.
Basis expansions for functional snippets
Authors: Lin Zhenhua , Wang Jane-Ling , Zhong Qixian
Published: October 2020

Estimation of mean and covariance functions is fundamental for functional data analysis. While this topic has been studied extensively in the literature, a key assumption is that there are enough data in the domain of interest to estimate both the mean and covariance functions. We investigate mean and covariance estimation for functional snippets in which observations from a subject are available only in an interval of length strictly, and often much, shorter than the length of the whole interval of interest. For such a sampling plan, no data is available for direct estimation of the off-diagonal region of the covariance function. We tackle this challenge via a basis representation of the covariance function. The proposed estimator enjoys a convergence rate that is adaptive to the smoothness of the underlying covariance function, and has superior finite-sample performance in simulation studies.
Glioblastoma surgery related emotion recognition deficits are associated with right cerebral hemisphere tract changes
Authors: Sinha Rohitashwa , Dijkshoorn Aicha B C , Li Chao , Manly Tom , Price Stephen J
Published: October 2020

Patients with glioblastoma face abysmal overall survival, cognitive deficits, poor quality of life and limitations to social participation; partly attributable to surgery. Emotion recognition deficits mediated by pathophysiological mechanisms in the right inferior fronto-occipital fasciculus and right inferior longitudinal fasciculus have been demonstrated in traumatic brain injury and dementia, with negative associations for social participation. We hypothesise similar mechanisms occur in patients undergoing resection surgery for glioblastoma. Here, we apply tract-based spatial statistics using a combination of automated image registration methods alongside cognitive testing before and after surgery. In this prospective, longitudinal, observational study of 15 patients, surgery is associated with an increase of emotion recognition deficits (p = 0.009) and this is correlated with decreases in fractional anisotropy in the Inferior Longitudinal Fasciculus, Inferior Fronto-Occipital Fasciculus, Anterior Thalamic Radiation and Uncinate Fasciculus; all in the right hemisphere (p = 0.014). Methodologically, the combination of registration steps used demonstrate that tract-based spatial statistics can be applied in the context of large, scan distorting lesions such as glioblastoma. These results can inform clinical consultations with patients undergoing surgery, support consideration for social cognition rehabilitation and are consistent with theoretical mechanisms that implicate these tracts in emotion recognition deficits across different diseases.
Impacts of nitrogen addition on switchgrass root-associated diazotrophic community structure and function
Authors: Smercina Darian N , Evans Sarah E , Friesen Maren L , Tiemann Lisa K
Published: October 2020

Cellulosic bioenergy crops, like switchgrass (Panicum virgatum), have potential for growth on lands unsuitable for food production coupled with potential for climate mitigation. Sustainability of these systems lies in identifying conditions that promote high biomass yields on marginal lands under low-input agricultural practices. Associative nitrogen fixation (ANF) is a potentially important nitrogen (N) source for these crops, yet ANF contributions to plant N, especially under fertilizer N addition are unclear. In this study, we assess structure (nifH) and function (ANF) of switchgrass root-associated diazotrophic communities to long-term and short-term N additions using soil from three marginal land sites. ANF rates were variable and often unexpectedly high, sometimes 10× greater than reported in the literature, and did not respond in repeatable ways to long-term or short-term N. We found few impacts of N addition on root-associated diazotrophic community structure or membership. Instead, we found a very consistent root-associated diazotrophic community even though switchgrass seeds were germinated in soil from field sites with distinct diazotrophic communities. Ultimately, this work demonstrates that root-associated diazotrophic communities have the potential to contribute to switchgrass N demands, independent of N addition, and this may be driven by selection of the diazotrophic community by switchgrass roots.
Climate sensitive growth models for predicting diameter growth of western Canadian boreal tree species
Authors: Oboite Felix O , Comeau Philip G
Published: October 2020

In the face of anticipated climate change, growth models require modifications to effectively model likely future growth and survival of trees and stands. To support incorporation of climate effects in the Mixedwood Growth Model (MGM), we developed climate-sensitive mixed effects models for lodgepole pine (Pinus contorta Douglas ex Loudon), jack pine (Pinus banksiana Lamb.), trembling aspen (Populus tremuloides Michx.), balsam poplar (Populus balsamifera L.) and white spruce (Picea glauca (Moench) Voss), and examined how tree size, intra- and interspecific competition and climate will influence individual-tree diameter growth. Remeasurement data from permanent growth and yield sample plots from across the western Canadian boreal forest were used for this study. Based on the model that we developed, tree size, competition and climate had varying effects on growth, among tree species. Although intraspecific competition had a stronger negative effect on growth for deciduous and white spruce trees, interspecific competition had a stronger negative effect on the growth of pine. Deciduous trees growing in stands having longer frost-free period experienced an increase in growth but a negative effect of frost-free period was observed for conifers. In addition, higher moisture was found to increase tree growth, but the influence of available moisture on growth was dependent on competition. Overall, these results suggest that, under climate warming, between-species differences in growth responses will contribute to our understanding of the stand dynamics in the western boreal region of Canada. Climate sensitive growth models developed in this study will be useful in the recalibration of MGM and other individual-tree models, and predictions will contribute to better-informed decisions about silvicultural treatments for these economically important boreal tree species.
Single-Cell Transcriptomics of Abedinium Reveals a New Early-Branching Dinoflagellate Lineage
Authors: Cooney Elizabeth C , Okamoto Noriko , Cho Anna , Hehenberger Elisabeth , Richards Thomas A , Santoro Alyson E , Worden Alexandra Z , Leander Brian S , Keeling Patrick J
Published: October 2020

Dinoflagellates possess many cellular characteristics with unresolved evolutionary histories. These include nuclei with greatly expanded genomes and chromatin packaged using histone-like proteins and dinoflagellate-viral nucleoproteins instead of histones, highly reduced mitochondrial genomes with extensive RNA editing, a mix of photosynthetic and cryptic secondary plastids, and tertiary plastids. Resolving the evolutionary origin of these traits requires understanding their ancestral states and early intermediates. Several early-branching dinoflagellate lineages are good candidates for such reconstruction, however these cells tend to be delicate and environmentally sparse, complicating such analyses. Here, we employ transcriptome sequencing from manually isolated and microscopically documented cells to resolve the placement of two cells of one such genus, Abedinium, collected by remotely operated vehicle in deep waters off the coast of Monterey Bay, CA. One cell corresponds to the only described species, Abedinium dasypus, whereas the second cell is distinct and formally described as Abedinium folium, sp. nov. Abedinium has classically been assigned to the early-branching dinoflagellate subgroup Noctilucales, which is weakly supported by phylogenetic analyses of small subunit ribosomal RNA, the single characterized gene from any member of the order. However, an analysis based on 221 proteins from the transcriptome places Abedinium as a distinct lineage, separate from and basal to Noctilucales and the rest of the core dinoflagellates. The transcriptome also contains evidence of a cryptic plastid functioning in the biosynthesis of isoprenoids, iron–sulfur clusters, and heme, a mitochondrial genome with all three expected protein-coding genes (cob, cox1, and cox3), and the presence of some but not all dinoflagellate-specific chromatin packaging proteins.
A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data
Authors: Han Bangxing , Jing Yi , Dai Jun , Zheng Tao , Gu Fangli , Zhao Qun , Zhu Fucheng , Song Xiangwen , Deng Hui , Wei Peipei , Song Cheng , Liu Dong , Jiang Xueping , Wang Fang , Chen Yanjun , Sun Chuanbo , Yao Houjun , Zhang Li , Chen Naidong , Chen Shaotong , Li Xiaoli , Wei Yuan , Ouyang Zhen , Yan Hui , Lu Jiangjie , Wang Huizhong , Guo Lanping , Kong Lingdong , Zhao Jing , Li Shaoping , Luo Lifen , Kristiansen Karsten , Feng Zhan , Sun Silong , Chen Cunwu , Yue Zhen , Chen Naifu
Published: October 2020

Dendrobium huoshanense is used to treat various diseases in traditional Chinese medicine. Recent studies have identified active components. However, the lack of genomic data limits research on the biosynthesis and application of these therapeutic ingredients. To address this issue, we generated the first chromosome-level genome assembly and annotation of D. huoshanense. We integrated PacBio sequencing data, Illumina paired-end sequencing data, and Hi-C sequencing data to assemble a 1.285 Gb genome, with contig and scaffold N50 lengths of 598 kb and 71.79 Mb, respectively. We annotated 21,070 protein-coding genes and 0.96 Gb transposable elements, constituting 74.92% of the whole assembly. In addition, we identified 252 genes responsible for polysaccharide biosynthesis by Kyoto Encyclopedia of Genes and Genomes functional annotation. Our data provide a basis for further functional studies, particularly those focused on genes related to glycan biosynthesis and metabolism, and have implications for both conservation and medicine.
Assessing the performance of beneficiary targeting in Brazil’s More Doctors Programme
Authors: Özçelik Ece A , Massuda Adriano , McConnell Margaret , Castro Marcia C
Published: October 2020

Many countries employ strategies that rest on the use of an explicitly defined set of criteria to identify underserved communities. Yet, we know relatively little about the performance of community-level targeting in large-scale health programmes. To address this gap, we examine the performance of community targeting in the More Doctors Programme (MDP). Our analysis covers all 5570 municipalities in the period between 2013 and 2017 using publicly available data. We first calculate the rate at which vulnerable municipalities enrolled in the MDP. Next, we consider two types of mistargeting: (1) proportion of vulnerable municipalities that did not have any MDP physicians (i.e. under-coverage municipalities) and (2) proportion of MDP enrolees that did not fit the vulnerability criteria (i.e. non-target municipalities). We found that almost 70% of vulnerable municipalities received at least one MDP physician between 2013 and 2017; whereas non-target municipalities constituted 33% of beneficiaries. Targeting performance improved over time. Non-target municipalities had the highest levels of socioeconomic development and greater physician availability. The poverty rate among under-coverage municipalities was almost six times that in non-target municipalities. Under-coverage municipalities had the lowest primary care physician availability. They were also smaller and more sparsely populated. We also found small differences in the political party alignments of mayors and the President between under-coverage and non-target municipalities. Our results suggest that using community-level targeting approaches in large-scale health programmes is a complex process. Programmes using these approaches may face substantial challenges in beneficiary targeting. Our results highlight that policymakers who consider using these approaches should carefully study various municipal characteristics that may influence the implementation process, including the level of socioeconomic development, health supply factors, population characteristics and political party alignments.
Use of directed acyclic graphs (DAGs) to identify confounders in applied health research: review and recommendations
Authors: Tennant Peter W G , Murray Eleanor J , Arnold Kellyn F , Berrie Laurie , Fox Matthew P , Gadd Sarah C , Harrison Wendy J , Keeble Claire , Ranker Lynsie R , Textor Johannes , Tomova Georgia D , Gilthorpe Mark S , Ellison George T H
Published: October 2020

Background

Directed acyclic graphs (DAGs) are an increasingly popular approach for identifying confounding variables that require conditioning when estimating causal effects. This review examined the use of DAGs in applied health research to inform recommendations for improving their transparency and utility in future research.

Methods

Original health research articles published during 1999–2017 mentioning ‘directed acyclic graphs’ (or similar) or citing DAGitty were identified from Scopus, Web of Science, Medline and Embase. Data were extracted on the reporting of: estimands, DAGs and adjustment sets, alongside the characteristics of each article’s largest DAG.

Results

A total of 234 articles were identified that reported using DAGs. A fifth (n = 48, 21%) reported their target estimand(s) and half (n = 115, 48%) reported the adjustment set(s) implied by their DAG(s). Two-thirds of the articles (n = 144, 62%) made at least one DAG available. DAGs varied in size but averaged 12 nodes [interquartile range (IQR): 9–16, range: 3–28] and 29 arcs (IQR: 19–42, range: 3–99). The median saturation (i.e. percentage of total possible arcs) was 46% (IQR: 31–67, range: 12–100). 37% (n = 53) of the DAGs included unobserved variables, 17% (n = 25) included ‘super-nodes’ (i.e. nodes containing more than one variable) and 34% (n = 49) were visually arranged so that the constituent arcs flowed in the same direction (e.g. top-to-bottom).

Conclusion

There is substantial variation in the use and reporting of DAGs in applied health research. Although this partly reflects their flexibility, it also highlights some potential areas for improvement. This review hence offers several recommendations to improve the reporting and use of DAGs in future research.
The effect of the Mediterranean Diet on lifespan: a treatment-effect survival analysis of a population-based prospective cohort study in Southern Italy
Authors: Campanella Angelo , Misciagna Giovanni , Mirizzi Antonella , Caruso Maria Gabriella , Bonfiglio Caterina , Aballay Laura R , Vas de Arruda Silveira Liciana , Bianco Antonella , Franco Isabella , Sorino Paolo , Buongiorno Claudia , Cisternino Anna Maria , Notarnicola Maria , Guerra Vito M B , Osella Alberto R
Published: October 2020

Background

The Mediterranean diet (MedDiet) is associated with good health. We aimed to estimate the effect of levels of adherence to the MedDiet on lifespan by performing treatment effects survival analysis.

Methods

A sample of 5250 subjects aged ≥18 years were randomly selected from the electoral list of Castellana Grotte and Putignano (Apulian Region, Italy). Cohorts were enrolled in 2005–06 and followed-up until December 2018. The adherence to the MedDiet was measured by the relative Mediterranean score (rMED) and categorized as high, medium and low. Time-to-death (all-causes) as estimated by average treatment effect on the treated (ATET), potential outcome mean (POM) and relative efficiency of exposure were the outcomes.

Results

A total of 4896 subjects were included. The median follow-up time was 12.82 (inter quartile range (IQR) 12.22–13.05), 12.91 (IQR 12.21–13.27) and 12.84 (IQR 12.19–13.03) years for high, medium and low rMED subjects respectively. By December 2018, 453 (9.25%) had died. There was a strong effect of medium and low rMED {ATET, −5.10 [95% confidence interval (CI) −9.39, −0.80] and −8.91 (95%CI −13.37, −4.45), respectively}. High rMED has an important effect on mean age at death [POM 90.16 (95% CI 86.06, 94.25)]. The relative effect size for medium and low rMED subjects was a lower lifespan of 5.62% (95% CI 1.01, 10.3) and 9.90% (95% CI 5.30, 5.30), respectively.

Conclusions

We observed an important benefit in additional years of survival from adherence to MedDiet in this southern Italian cohort. Further investigation corroborating our findings in other population groups in other geographic regions will be an important contribution to promoting health and longevity.
Toward AGT for Parabolic Sheaves
Authors: Neguţ Andrei
Published: October 2020

We construct explicit elements $W_{ij}^k$ in (a completion of) the shifted quantum toroidal algebra of type $A$ and show that these elements act by 0 on the $K$-theory of moduli spaces of parabolic sheaves. We expect that the quotient of the shifted quantum toroidal algebra by the ideal generated by the elements $W_{ij}^k$ will be related to $q$-deformed $W$-algebras of type $A$ for arbitrary nilpotent, which would imply a $q$-deformed version of the Alday-Gaiotto-Tachikawa (AGT) correspondence between gauge theory with surface operators and conformal field theory.
Genes associated with somatic cell count index in Brown Swiss cattle
Authors: Jeretina Janez , Jevšinek Skok Daša
Published: October 2020

Subclinical mastitis (SM) is one of the most common diseases of cows in milk production herds caused by contagious and/or environmental pathogens. Since there are no visible abnormalities in the milk or udder, the detection of SM requires special diagnostic tests. Somatic cell count (SCC) is the most common test used to detect changes in milk due to the inflammatory process. Previously, we developed somatic cell count index (SCCI), a new method for the accurate prediction of milk yield losses caused by elevated SCC. The aim of this study was to identify new candidate genetic markers for SCCI in the Slovenian population of Brown Swiss (BS) cattle. For that purpose, we analyzed samples of BS cows, which were genotyped using single-nucleotide polymorphism (SNP) microarray ICBF International Dairy and Beef v3 (ICBF, Ireland) for a total of 53,262 SNP markers. After quality control, the set of 18,136 SNPs was used in association analysis. Our association analysis revealed that 130 SNPs were associated with SCCI, which were used for haplotype and overlap analysis. Haplotypes generated from the genotyped data for those 130 SNPs revealed 10 haplotype blocks among 22 SNPs. Additionally, all 130 SNPs, mastitis-related quantitative trait loci, and protein-coding genes are shown on the bovine genome. Overlap analysis shows that the majority of significantly associated SNPs (70) are intergenic, while 60 SNPs are mapped within, upstream, or downstream of the protein-coding genes. However, those genes can serve as strong candidate genes for the marker-assisted selection programs in our and possibly other populations of cattle.
Discovery of a Novel Flavivirus (Flaviviridae) From the Horse Fly, Tabanus rufidens (Diptera: Tabanidae): The Possible Coevolutionary Relationships Between the Classical Insect-Specific Flaviviruses and Host Dipteran Insects
Authors: Kobayashi Daisuke , Watanabe Mamoru , Faizah Astri Nur , Amoa-Bosompem Michael , Higa Yukiko , Tsuda Yoshio , Sawabe Kyoko , Isawa Haruhiko
Published: October 2020

Tabanid flies (Tabanidae: Diptera) are common hematophagous insects known to transmit some pathogens mechanically or biologically to animals; they are widely distributed throughout the world. However, no tabanid-borne viruses, except mechanically transmitted viruses, have been reported to date. In this study, we conducted RNA virome analysis of several human-biting tabanid species in Japan, to discover and characterize viruses associated with tabanids. A novel flavivirus was encountered during the study in the Japanese horse fly, Tabanus rufidens (Bigot, 1887). The virus was detected only in T. rufidens, but not in other tabanid species, and as such was designated Tabanus rufidens flavivirus (TrFV). TrFV could not be isolated using a mammalian cell line and showed a closer phylogenetic relationship to the classical insect-specific flaviviruses (cISFs) rather than the vertebrate-infecting flaviviruses (VIFs), suggesting that it is a novel member of the cISFs. The first discovery of a cISF from Brachycera provides new insight into the evolutionary history and dynamics of flaviviruses.
Acute midgut volvulus in a septuagenarian with secondary jejunoileal diverticulitis and undiagnosed congenital malrotation: an unusual presentation
Authors: Sigler Gregory , Baker Laura , Tadros Shaheer , Rekman Janelle , Apte Sameer S
Published: October 2020

A 79-year-old male presented with abdominal pain, incidental umbilical hernia and acute midgut volvulus that was not detected until surgical exploration. When he presented to hospital, computed tomography (CT) findings indicated perforated jejunoileal diverticulitis; however, in the operating room clockwise volvulization of the jejunum and ileum, secondarily inflamed jejunoileal diverticula, incomplete malrotation (right-sided duodenojejunal flexure), right retroperitoneal adhesions (Ladd’s bands) and numerous other congenital adhesive bands were found. A modified Ladd’s procedure and umbilical hernia repair were completed including detorsion, division of Ladd’s bands with medialization of the cecum and lysis of other congenital adhesions without appendectomy. The patient recovered to baseline function by 3 weeks postoperatively. Acute midgut volvulus is a life-threatening surgical emergency that is exceptionally rare in the elderly. CT is relatively insensitive, so misdiagnosis is common. A high index of suspicion is required, especially in patients with a history of congenital gastrointestinal abnormalities. Prompt surgical exploration for correction and prevention is crucial.
Capacity remuneration mechanisms on European electricity markets—legal basis and actual implementation status
Authors: Pugl-Pichler Christian , Tyma Franz , Süßenbacher Wilhelm , Blume-Werry Eike , Todem Christian
Published: October 2020

In recent years a range of different capacity remuneration mechanisms have been discussed and implemented on European electricity markets. This article gives an overview of different designs, classifying and exploring central and decentral capacity markets, strategic reserves and different capacity payments. To illustrate the particular designs, examples in Germany, Italy, France and Switzerland are discussed in detail. Given that all capacity remuneration mechanisms in the European Union (EU) are subject to EU state aid and electricity regulations, the article examines the legal framework of capacity remuneration mechanisms.
Marker-based crop model-assisted ideotype design to improve avoidance of abiotic stress in bread wheat
Authors: Bogard Matthieu , Hourcade Delphine , Piquemal Benoit , Gouache David , Deswartes Jean-Charles , Throude Mickael , Cohan Jean-Pierre
Published: October 2020

Wheat phenology allows escape from seasonal abiotic stresses including frosts and high temperatures, the latter being forecast to increase with climate change. The use of marker-based crop models to identify ideotypes has been proposed to select genotypes adapted to specific weather and management conditions and anticipate climate change. In this study, a marker-based crop model for wheat phenology was calibrated and tested. Climate analysis of 30 years of historical weather data in 72 locations representing the main wheat production areas in France was performed. We carried out marker-based crop model simulations for 1019 wheat cultivars and three sowing dates, which allowed calculation of genotypic stress avoidance frequencies of frost and heat stress and identification of ideotypes. The phenology marker-based crop model allowed prediction of large genotypic variations for the beginning of stem elongation (GS30) and heading date (GS55). Prediction accuracy was assessed using untested genotypes and environments, and showed median genotype prediction errors of 8.5 and 4.2 days for GS30 and GS55, respectively. Climate analysis allowed the definition of a low risk period for each location based on the distribution of the last frost and first heat days. Clustering of locations showed three groups with contrasting levels of frost and heat risks. Marker-based crop model simulations showed the need to optimize the genotype depending on sowing date, particularly in high risk environments. An empirical validation of the approach showed that it holds good promises to improve frost and heat stress avoidance.
A Historical Overview of the Palestinian Refugee Question
Authors: Albanese Francesca P , Takkenberg Lex
Published: October 2020

This chapter traces the history of the Palestinian refugee question and discusses the main events that created the conditions that enabled the mass displacement of most of the Arab population of Mandate Palestine. The events that befell Palestine between 1947 and 1948, i.e. the decision of the United Nations to partition Palestine and the resultant war, are defining moments of the Palestinian refugee question. Its roots, however, are to be found in the events that preceded and enabled it–starting with the socio-political and economic transformation that occurred in Palestine during the Ottoman Empire (1808–1917) and intensified during the thirty years of the British control over Palestine (1918–1948). It can also be found in the way the League of Nations first, and the United Nations after, attempted to resolve the dispute over Palestine. This historical account is crucial to understanding how international law was central to early attempts at resolving the refugee issue, and how it subsequently became effectively side-lined. The chapter also identifies some elements of continuity between the original displacement (in 1948 and 1967) and the current situation of Palestinians in the occupied Palestinian territory (oPt) and beyond.
Palestinian Refugees
Authors: Albanese Francesca P , Takkenberg Lex
Published: October 2020

This chapter examines the foundation of Palestinian refugees’ status in international law, as well as the characteristics of their distinctive institutional and normative regime compared to other refugees around the world. This distinctiveness stems from special arrangements the United Nations (UN) has made for them. This includes ad hoc UN agencies mandated to protect and assist Palestinian refugees, namely the United Nations Conciliation Commission for Palestine (UNCCP) and the United Nations Relief and Works Agency for Palestine Refugees in the Near East (UNRWA) as well as, under certain circumstances, the United Nations High Commissioner for Refugees (UNHCR). The chapter then considers both the genesis and meaning of Article 1D of the 1951 Refugee Convention, the provision specifically included with the Palestinian refugees in mind, including its recent interpretation and application, and various defintions of Palestine/Palestinian refugee offered for various purposes (i.e. assistance and relief, protection and durable solutions). It shows how the special arrangements for this group of refugees, put in place due to the circumstances of their displacement, were meant to ensure continuity of protection and how, the lack of durable solutions has made the arrangements set up for them, inclreasingly looking as an anomaly.
Defining Treaties
Authors: Hollis Duncan B
Published: October 2020

This chapter provides a comprehensive and robust overview of the treaty than the Vienna Convention on the Law of Treaties’ (VCLT) standard treatment. Part I elaborates three contexts beyond the VCLT where the ‘treaty’ acquires a different definition, and what purposes that definition serves in each setting. Part II unpacks the treaty’s meaning in a specific context — international law — along constitutive, differential, and functional lines. It explains how to constitute a treaty using Article 2(1)(a) as a baseline, and differentiates the treaty from other concepts of commitment and agreement while acknowledging questions about the mutual exclusivity of these concepts. Finally, the chapter adopts a functional perspective to explain the evolution in what treaties do across several distinct dimensions. It concludes by asking if the treaty concept might benefit from further clarification or disaggregation as these treaty functions continue to evolve.
Current
Theorizations about the Treaty in International Law
Authors: d'Aspremont Jean
Published: October 2020

This chapter has two primary aims. First, it sketches out the existing theorizations about treaties, elaborating the various dualist modes of thinking currently dominating international legal thought and practice. Second, it seeks to supplement current theorizations with some new perspectives. Specifically, it identifies three overlooked uses of the idea of the treaty in contemporary legal thought and practice that may further current theorizations about treaties. In particular, the second part shows the extent to which the idea of the treaty allows (i) the creation of conceptual anachronisms in the making of historical narratives about international law, (ii) the simplification of the processes of its interpretation, and (iii) the construction of a magic descendance that shield those invoking the treaty from any responsibility for anything that is made in the name of the treaty.
Making the Treaty
Authors: Fuentes Carlos Iván , Villalpando Santiago
Published: October 2020

This chapter surveys the often-complicated process of treaty-making. The process may be divided into four phases: (i) the drawing up and negotiation of the treaty; (ii) the adoption and authentication of the text; (iii) the expression of consent to be bound by the treaty; and (iv) the entry into force of the treaty. A universal quality of treaty-making is the absolute freedom of the negotiators, who remain masters of their own procedure. Negotiators have wide discretion in deciding the process to be followed for their discussions, the form of the final agreement, the means of consenting to be bound, and the ways in which the treaty enters into force. This explains why the Vienna Convention on the Law of Treaties’ codification renounced governing the negotiation phase, and restricted itself to reaffirming the discretion of negotiators while establishing a limited number of residual rules that will assist when specific issues remain undecided.
The
Validity and Invalidity of Treaties
Authors: Klabbers Jan
Published: October 2020

The validity or invalidity of treaties is a topic with no practical significance. And yet, the 1969 Vienna Convention on the Law of Treaties (VCLT) would have had a gaping hole in its middle if it had not paid any attention to the validity or invalidity of treaties: no legal system can do without rules on the validity of legal instruments, be it legislation, contracts, or treaties. This chapter discusses the rules on validity of treaties as laid down in the VCLT, paying attention to the corresponding position under the 1986 Vienna Convention as well as the presence (or lack) of relevant State practice. It addresses a few peculiarities about the function of validity that underlies the Vienna Convention(s), starting with some general reflections on validity, inspired by the curious circumstance that each and every lawyer will have some intuitive understanding of what validity refers to, yet scholarly exposés on validity are few and far between.
Terminating Treaties
Authors: Helfer Laurence R
Published: October 2020

This chapter reviews the research on treaty exit and draws upon a variety of recent examples and illustrations from a range of subject areas to discuss its practical, theoretical, and normative implications. Part I provides an overview of the international rules governing exit from multilateral and bilateral agreements, including key provisions of the Vienna Convention on the Law of Treaties. Part II highlights the wide variations in the design and invocation of treaty termination, denunciation, and withdrawal clauses. Part III sets forth a theory of treaty exit. It argues that termination, denunciation, and withdrawal clauses are tools for managing risk — a pervasive feature of international affairs. A concluding section identifies avenues for future research for scholars and practitioners alike.
History and Sources
Authors: Henckaerts Jean-Marie
Published: October 2020

This introductory chapter provides an overview of international humanitarian law (IHL), which is also known as the international law of armed conflict, or simply law of armed conflict (LOAC) or law of war. The rules and principles of IHL seek to limit the effects of armed conflict and at its core, IHL aims to preserve a sense of humanity in time of war. At the same time, IHL has been developed to regulate the social reality that is armed conflict. As such, in order to provide a realistic, and hence useful, legal framework, IHL must also take into account the military needs of parties to an armed conflict in their pursuit of defeating the adversary. The development of particular treaties and specific rules of IHL over time reflects the exercise of finding the correct balance between these humanitarian and military considerations. As a branch of international law, IHL is subject to the general rules of international law, such as those related to sources, treaty interpretation, and state responsibility. The sources of international law are set out in article 38 of the Statute of the International Court of Justice. This provision lists international conventions, international custom, and general principles of law as the main sources of international law in accordance with which the Court is to decide disputes submitted to it.
Implementation of International Humanitarian Law
Authors: Turns David
Published: October 2020

This chapter provides a holistic view of the implementation of international humanitarian law (IHL) as including all the various tools which may be used to render IHL effective in practice, whether they are used primarily before a situation of armed conflict arises, or during or after such a situation; whether they invoke the civil responsibility of the state or the criminal responsibility of individuals; and whether they fall to be implemented in a national or international context. Early attempts at the enforcement of the laws of war appeared through the prism of punishing those who were judged guilty of violating that body of rules. However, it was not until the advent of mass citizen-armies organized by nation-states as a public activity in the course of the seventeenth century that something resembling systematic national implementation of the laws of war began to take place. The chapter then sets out the contemporary legal framework provided by treaty instruments and recognized as customary international law, before examining specific state obligations relating to pre-conflict preventive measures; the supervision of conduct and repression of violations during conflict; and the subsequent enforcement of IHL by judicial, quasi-judicial, and non-judicial means. It also considers the increasingly important role played by non-state actors (NSAs)—such as non-governmental organizations (NGOs), civil society, and the media—in monitoring and advocacy on IHL issues.
Unexpected mould diversity in clinical isolates from French Guiana and associated identification difficulties
Authors: Nabet C , Imbert S , Normand A C , Blanchet D , Chanlin R , Becker P , Demar M , Piarroux R
Published: October 2020

New mold species are increasingly reported in invasive fungal infections. However, these fungi are often misdiagnosed or undiagnosed due to the use of inappropriate laboratory diagnostic tools. Tropical countries, such as French Guiana, harbor a vast diversity of environmental fungi representing a potential source of emerging pathogens. To assess the impact of this diversity on the accuracy of mold-infection diagnoses, we identified mold clinical isolates in French Guiana during a five-month follow-up using both microscopy and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. In total, 38.8% of the 98 obtained molds isolates could not be identified and required a DNA-based identification. Fungal diversity was high, including 46 species, 26 genera, and 13 orders. Fungal ecology was unusual, as Aspergillus species accounted for only 27% of all isolates, and the Nigri section was the most abundant out of the six detected Aspergillus sections. Macromycetes (orders Agaricales, Polyporales, and Russulales) and endophytic fungi accounted for respectively 11% and 14% of all isolates. Thus, in tropical areas with high fungal diversity, such as French Guiana, routine mold identification tools are inadequate. Molecular identifications, as well as morphological descriptions, are necessary for the construction of region-specific mass spectrum databases. These advances will improve the diagnosis and clinical management of new fungal infections.
Properties of flares and CMEs on EV Lac: possible erupting filament
Authors: Muheki Priscilla , Guenther E W , Mutabazi T , Jurua E
Published: October 2020

Flares and coronal mass ejections (CMEs) are very powerful events in which energetic radiation and particles are ejected within a short time. These events thus can strongly affect planets that orbit these stars. This is particularly relevant for planets of M-stars, because these stars stay active for a long time during their evolution and yet potentially habitable planets orbit at short distance. Unfortunately, not much is known about the relation between flares and CMEs in M-stars as only very few CMEs have so far been observed in M-stars. In order to learn more about flares and CMEs on M-stars, we monitored the active M-star EV Lac spectroscopically at high resolution. We find 27 flares with energies between 1.6 × 1031 and 1.4 × 1032 erg in $\rm H\alpha$ during 127 h of spectroscopic monitoring and 49 flares with energies between 6.3 × 1031 and 1.1 × 1033 erg during the 457 h of Transiting Exoplanet Survey Satellite (TESS) observation. Statistical analysis shows that the ratio of the continuum flux in the TESS band to the energy emitted in $\rm H\alpha$ is 10.408 ± 0.026. Analysis of the spectra shows an increase in the flux of the He ii 4686 Å line during the impulsive phase of some flares. In three large flares, we detect a continuum source with a temperature between 6900 and 23 000 K. In none of the flares we find a clear CME event indicating that these must be very rare in active M-stars. However, in one relatively weak event, we found an asymmetry in the Balmer lines of ${\sim}220\, \rm km\, s^{-1}$, which we interpret as a signature of an erupting filament.
The impact of disturbed galaxy clusters on the kinematics of active galactic nuclei
Authors: Bilton Lawrence E , Pimbblet Kevin A , Gordon Yjan A
Published: October 2020

We produce a kinematic analysis of AGN-hosting cluster galaxies from a sample of 33 galaxy clusters selected using the X-ray Clusters Database (BAX) and populated with galaxies from the Sloan Digital Sky Survey Data Release 8. The 33 galaxy clusters are delimited by their relative intensity of member galaxy substructuring as a proxy to core merging to derive two smaller sub-samples of 8 dynamically active (merging) and 25 dynamically relaxed (non-merging) states. The AGN were selected for each cluster sub-sample by employing the WHAN diagram to the strict criteria of log10([N ii]/Hα) ≥ −0.32 and EWHα ≥ 6 Å, providing pools of 70 mergings and 225 non-merging AGN sub-populations. By co-adding the clusters to their respective dynamical states to improve the signal-to-noise ratio of our AGN sub-populations we find that merging galaxy clusters on average host kinematically active AGN between 0–1.5r200 as r200 → 0, where their velocity dispersion profile (VDP) presents a significant deviation from the non-AGN sub-population VDP by ≳3σ. This result is indicative that the AGN-hosting cluster galaxies have recently coalesced on to a common potential. Further analysis of the composite distributions illustrates non-merging AGN-hosting sub-populations have, on average, already been accreted and predominantly lie within backsplash regions of the projected phase-space. This suggests merging cluster dynamical states hold relatively younger AGN sub-populations kinematically compared with those found in non-merging cluster dynamical states.
Missing [C ii] emission from early galaxies
Authors: Carniani S , Ferrara A , Maiolino R , Castellano M , Gallerani S , Fontana A , Kohandel M , Lupi A , Pallottini A , Pentericci L , Vallini L , Vanzella E
Published: October 2020

ALMA observations have revealed that [C ii] 158 μm line emission in high-z galaxies is ≈2–3 × more extended than the UV continuum emission. Here we explore whether surface brightness dimming (SBD) of the [C ii] line is responsible for the reported [C ii] deficit, and the large $L_{\rm [O\, \small {III}]}/L_{\rm [C\, \small {II}]}$ luminosity ratio measured in early galaxies. We first analyse archival ALMA images of nine z > 6 galaxies observed in both [C ii] and [O iii]. After performing several uv-tapering experiments to optimize the identification of extended line emission, we detect [C ii] emission in the whole sample, with an extent systematically larger than the [O iii] emission. Next, we use interferometric simulations to study the effect of SBD on the line luminosity estimate. About 40 per cent of the extended [C ii] component might be missed at an angular resolution of 0.8 arcsec, implying that $L_{\rm [C\, \small {II}]}$ is underestimated by a factor ≈2 in data at low (<7) signal-to-noise ratio. By combining these results, we conclude that $L_{\rm [C\, \small {II}]}$ of z > 6 galaxies lies, on average, slightly below the local $L_{\rm [C\, \small {II}]}-\mathrm{ SFR}$ relation (Δz =  6–9 = −0.07 ± 0.3), but within the intrinsic dispersion of the relation. SBD correction also yields $L_{\rm [O\, \small {III}]}/L_{\rm [C\, \small {II}]}\lt 10$, i.e. more in line with current hydrodynamical simulations.
The Mode of Action of Endosidin20 Differs from That of Other Cellulose Biosynthesis Inhibitors
Authors: Huang Lei , Zhang Chunhua
Published: October 2020

Endosidin20 (ES20) was recently identified as a cellulose biosynthesis inhibitor (CBI) that targets the catalytic domain of CELLULOSE SYNTHASE 6 (CESA6) and thus inhibits the growth of Arabidopsis thaliana. Here, we characterized the effects of ES20 on the growth of other plant species and found that ES20 is a broad-spectrum plant growth inhibitor. We tested the inhibitory effects of previously characterized CBIs (isoxaben, indaziflam and C17) on the growth of Arabidopsis cesa6 mutants that have reduced sensitivity to ES20. We found that most of these mutants are sensitive to isoxaben, indaziflam and C17, indicating that these tested CBIs have a different mode of action than ES20. ES20 also has a synergistic inhibitory effect on plant growth when jointly applied with other CBIs, further confirming that ES20 has a different mode of action than isoxaben, indaziflam and C17. We demonstrated that plants carrying two missense mutations conferring resistance to ES20 and isoxaben can tolerate the dual inhibitory effects of these CBIs when combined. ES20 inhibits Arabidopsis growth in growth medium and in soil following direct spraying. Therefore, our results pave the way for using ES20 as a broad-spectrum herbicide, and for the use of gene-editing technologies to produce ES20-resistant crop plants.