bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leaf density and chemical composition explain variation in leaf mass area with spectral composition among 11 widespread forbs in a common garden
Authors: Wang Qing‐Wei , Liu Chenggang , Robson Thomas Matthew , Hikosaka Kouki , Kurokawa Hiroko 
Published: July 2021

AbstractLeaf mass per area (LMA) is a key leaf functional trait correlated with plant strategies dictating morphology, physiology, and biochemistry. Although sunlight is generally accepted as a dominant factor driving LMA, the contribution of each spectral region of sunlight in shaping LMA is poorly understood. In the present study, we grew 11 widespread forb species in a common garden and dissected the traits underpinning differences in LMA, such as its morphological components (leaf density [LD] and leaf thickness [LT]), macroelement, and metabolite composition under five spectral‐attenuation treatments: (1) transmitting c. 95% of the whole solar spectrum (> 280 nm), (2) attenuating ultraviolet‐B radiation (UV‐B), (3) attenuating both UV‐A and UV‐B radiation, (4) attenuating UV radiation and blue light, (5) attenuating UV radiation, blue, and green light. We found that LMA, LD, and chemical traits varied significantly across species depending on spectral treatments. LMA was significantly increased by UV‐B radiation and green light, while LD was increased by UV‐A but decreased by blue light. LMA positively correlated with LD across treatments but was only weakly related to LT, suggesting that LD was a better determinate of LMA for this specific treatment. Regarding leaf elemental and metabolite composition, carbon, nitrogen, and total phenolics were all positively correlated with LMA, whereas lignin, non‐structural carbohydrates, and soluble sugars had negative relationships with LMA. These trends imply a tradeoff between biomass allocation to structural and metabolically functional components. In conclusion, sunlight can spectrally drive LMA mainly through modifying functional and structural support.
Sequential gains and losses during gambling feedback: Differential effects in time‐frequency delta and theta measures
Authors: Bachman Matthew D. , Watts Adreanna T. M. , Collins Paul , Bernat Edward M. 
Published: July 2021

AbstractOne critical aspect of reward‐feedback is the impact of local outcome history—how past experiences with choices and outcomes influences current behavior and neural activity. Yet, prior event‐related potential work in this area has been contentious. This study contributes to this field by using time‐frequency measures to better isolate constituent processes. Specifically, we identify how theta and delta are differentially sensitive to local outcome history. Participants completed a binary monetary choice task while we collected EEG data. Unbeknownst to them, trial outcomes were manipulated into pre‐determined sequences, ranging from one to eight gains or losses in a row. Analyses were arranged by sequence establishment (first 2 trials of a sequence) and continuation (prolonged sequences of 3–8 trials). During the establishment of a sequence, delta activity to gains and losses were virtually identical on the first (change) trial, demonstrating marked divergence only on the second trial. This difference grew throughout the continuation period, as delta activity was sustained with accruing gains but declined with multiple losses. Theta activity, conversely, demonstrated a maximal loss‐gain difference on the change trial but was insensitive to the establishment of a new sequence. Differential theta activity between outcomes decreased as sequences continued, with theta activity increasing over accruing gains and remaining stable over losses. Results indicate that delta‐gain and theta‐loss signals are relatively stable across sequential outcomes. Furthermore, theta is most sensitive to loss‐gain differences on the initial change trial, while delta is more sensitive to gain‐loss differences with the continuation of a sequence.
Policy for the public without the public: Net neutrality in Israel
Authors: Ginosar Avshalom 
Published: July 2021

AbstractThis study investigates the policy process through which net neutrality (NN) policy in Israel has been shaped. The analysis employs a framework based on the Internet Governance concept and the multi‐stakeholder approach. Based on the analysis of formal documents, debates in parliamentary committees and the Parliament plenum, and position papers of various actors, the findings show that NN policy in Israel is one more layer of the neo‐liberal policy in the telecommunication sector. It is demonstrated how experts and bureaucrats, influenced by industry interests, have been dominant during the policy process while civil society groups representing the public interests have been only marginal actors. The paper concludes with a call for a more proactive attitude of all stakeholder groups in order to enable a more balanced governance of central internet issues, such as NN.
Stratigraphy and sedimentary evolution of a modern macro‐tidal incised valley: An analogue for reservoir facies and architecture
Authors: McGhee Claire , Muhammed Dahiru , Simon Naboth , Acikalin Sanem , Utley James E. P. , Griffiths Joshua , Wooldridge Luke , Verhagen Iris T. E. , van der Land Cees , Worden Richard H. 
Published: July 2021

AbstractIncised valley fills are complex as they correspond to multiple sea‐level cycles which makes interpretation and correlation of stratigraphic surfaces fraught with uncertainty. Despite numerous studies of the stratigraphy of incised valley fills, few have focused on extensive core coverage linked to high fidelity dating in a macro‐tidal, tide‐dominated setting. For this study nineteen sediment cores were drilled through the Holocene succession of the macro‐tidal Ravenglass Estuary in north‐west England, UK. A facies and stratigraphic model of the Ravenglass incised valley complex was constructed, to understand the lateral and vertical stacking patterns relative to the sea‐level changes. The Ravenglass Estuary formed in five main stages. First, incision by rivers (ca 11 500 to ca 10 500 yrs bp) cutting through the shelf during lowstand, which was a period of fluvial dominance. Secondly, a rapid transgression and landward migration of the shoreline (10 500 to 6000 yrs bp). Wave action was dominant, promoting spit formation. The third stage was a highstand at ca 6000 to ca 5000 yrs bp, creating maximum accommodation and the majority of backfilling. The spits narrowed the inlet and dampened wave action. The fourth stage was caused by a minor fall of sea level (ca 5000 to ca 226 yrs bp), which forced the system to shift basinward. The fifth and final stage (226 yrs bp to present) involved the backfilling of the River Irt, southward migration of the northerly (Drigg) spit and merging of the River Irt with the Rivers Esk and Mite. The final stage was synchronous with the development of the central basin. As an analogue for ancient and deeply buried sandstones, most of the estuarine sedimentation occurred after transgression, of which the coarsest and cleanest sands are found in the tidal inlet, on the foreshore and within in‐channel tidal bars. The best‐connected (up to 1 km) reservoir‐equivalent sands belong to the more stable channels.
Radish concretions grown in mud during compaction
Authors: Wetzel Andreas , Bojanowski Maciej 
Published: July 2021

AbstractRadish concretions exhibit a typical columnar to pear‐shaped, stipe downward geometry. In Middle Jurassic mudrock in south‐west Germany, radish concretions started to form around an iron‐sulphide lined tube by pervasive cementation constituting an ellipsoidal parent domain in uncompacted sediment at burial depths of ≤5 to 8 m as recorded by 75 to 80% minus‐cement porosity. Thereafter, the concretions grew vertically in compacting sediment as evidenced by laminae within the concretions being increasingly inclined towards the tips, and concomitantly decreasing minus‐cement porosity. During early diagenesis, prior to septarian crack formation, bicarbonate generating the microbial cement originated within the sulphate reduction zone chiefly from anaerobic oxidation of methane and to a lesser degree of organoclastic material. Later, at 50 to 70 m burial depth, septarian cracks formed as evaluated by sedimentation–compaction analysis based on minus‐cement porosity data and compressibility of similarly composed sediments. The outward‐narrowing septarian cracks indicate that they formed when the concretions were still in a plastic state but already cemented sufficiently to be resistant against compaction. In this stage, up to one‐quarter of the pore volume of the concretions was still open as suggested by shrinkage experiments. This pore volume, and the septarian cracks, were filled with cement termed late diagenetic. In the study area, the decompacted net‐sedimentation rate was low, about 2 to 3 cm kyr−1, for ca 2.5 Myr, allowing the concretions to reside for a long time within the sulphate reduction zone and to grow. Radish concretions formed within the transition zone from thick, rapidly deposited to long‐term, slowly accumulating sediment.
Combining molecular datasets with strongly heterogeneous taxon coverage enlightens the peculiar biogeographic history of stoneflies (Insecta: Plecoptera)
Authors: Letsch Harald , Simon Sabrina , Frandsen Paul B. , Liu Shanlin , Machida Ryuichiro , Mayer Christoph , Misof Bernhard , Niehuis Oliver , Zhou Xin , Wipfler Benjamin 
Published: July 2021

AbstractExtant members of the ancient insect order of stoneflies exhibit a disjunct, antitropical distribution, with one major lineage exclusively occurring in the Southern Hemisphere and the other, with few exceptions, on the Northern continents. Here, we address the biogeographic distribution and phylogenetic relationships of stoneflies using a phylogenetic workflow that combines both transcriptomic and Sanger sequence datasets with heterogeneous taxon coverage. We used a dataset comprising 2997 genes derived from the transcriptomes of 30 species and Sanger sequences of seven genes for 498 species. The backbone phylogeny was mainly inferred from the transcriptomic data, whereas the Sanger nucleotide sequence data provided high species density for divergence time estimation and diversification analyses. Our results show that the biogeographic pattern we observe today is primarily more likely shaped by long‐distance over‐land dispersal than by vicariance. We inferred that the ancestors of extant stoneflies originated in the Northern Hemisphere approximately 265 Ma and were presumably restricted to this area due to climatic and geographic boundaries. Our analyses suggest that with the break‐up of Pangaea around 200 Ma and the associated climatic and geographical changes, two groups of stoneflies, the Anarctoperlaria and the Notonemouridae, dispersed to Gondwana and subsequently went extinct on the northern continents. Both groups likely dispersed across Gondwana before its break‐up into the modern continents. At least one member of another group of ‘northern’ stoneflies, the Acroneuriinae, seems to have migrated from North America to South America around 67 Ma. We found four major net diversification rate shifts, indicating rapid radiation patterns that hampered a robust phylogenetic placement of these stonefly groups. Our study provides the first conclusive evolutionary explanation for the unique distribution pattern of stoneflies.
Integrative phylogenomics reveals a Permian origin of Adephaga beetles
Authors: Baca Stephen M. , Gustafson Grey T. , Alexander Alana M. , Gough Harlan M. , Toussaint Emmanuel F. A. 
Published: July 2021

AbstractBeetles are arguably the most diverse group of animals on Earth with over 400 000 described species. Yet the timing of main diversification events among these insects remains debated. The use of phylogenomic data generated using next‐generation sequencing recently resolved most recalcitrant phylogenetic relationships across Coleoptera. However, limited taxon sampling for some major clades still prevents the use of important fossil calibrations that could provide more accurate estimates of the timing of lineage diversification events among beetles. Here, we present a new fossil‐based dated framework with a focus on the suborder Adephaga. We rely on an integrative phylogenomic approach using a combination of genomic, ultraconserved element and RNAseq transcriptomic datasets, further revealing the prevalent exonic nature of ultraconserved elements in Coleoptera. We infer a robust phylogenomic tree under various optimality criteria and analytical conditions. Our preferred phylogenetic reconstruction is consistent with those of previous phylogenomic studies in recovering the paraphyly of ‘Hydradephaga’, Gyrinidae as sister to all other Adephaga, the monophyly of Geadephaga and Haliplidae as sister to a monophyletic Dytiscoidea. We further recover strong support for paraphyly of Aspidytidae and the placement of Hygrobiidae as part of a clade comprising Aspidytes, Ribera, Beutel, Balke & Vogler, Sinaspidytes Balke, Beutel & Ribera and Amphizoidae. Using 23 carefully chosen fossil calibrations across Coleoptera, we infer the origin of modern beetles ca. 317 Ma in the mid‐Carboniferous, the divergence between Archostemata and Adephaga ca. 296 Ma in the early Permian, and the crown of Adephaga in the end‐Permian ca. 255 Ma. Importantly, our analyses provide more precise estimates of divergence times for internal splits within Adephaga, including ground beetles, tiger beetles and aquatic adephagan lineages. These results represent a major step forward in our understanding of beetle diversification and will serve as a fundamental framework to unravel the evolutionary history of many clades within Adephaga.
Review of diagnostic methods and results for HIV‐associated disseminated histoplasmosis: Pathologists are not sufficiently involved
Authors: Nacher Mathieu , Valdes Audrey , Adenis Antoine , Blaizot Romain , Ugo Françoise , Abboud Philippe , Demar Magalie , Djossou Félix , Epelboin Loïc , Misslin Caroline , Blanchet Denis , Couppié Pierre , Alsibai Kinan Drak 
Published: July 2021

AbstractObjectivesDisseminated histoplasmosis is a major killer of HIV‐infected persons in Latin America. Antigen detection, fungal culture and Polymerase Chain Reaction are often not available, but cytology and histology are present in most hospitals and may offer a diagnostic alternative. In this study, we review 34 years of clinical experience to describe the roles of cytology and histology in diagnosing disseminated histoplasmosis.MethodsRetrospective multicentric study of 349 patients between 1 January 1981 and 1 October 2014 with confirmed disseminated histoplasmosis.ResultsAround 32/214 (14.9%) of samples were screened using cytopathology, as were 10/101 (9.9%) bronchoalveolar lavage samples and 5/61 (8.2%) of spinal fluid samples. The samples most commonly sent to pathology were liver biopsies, lower digestive tract and lymphnode biopsies; the greatest proportion of positive results were found in lower digestive tract (43/59 (72.9%) positives), lymph node (39/63 (66.1%)), and liver (38/75 (50.7%)) samples. Overall, 97.2% of bone marrow and 97% of bronchoalveolar lavage samples were directly examined by a mycologist. Positive direct examination was independently associated with death (aHR = 1.5 (95%CI = 1–2.2)).ConclusionsOpportunities for a rapid diagnosis were regularly missed, notably for bone marrow samples, which could have been examined using staining methods complementary to those of the mycologist.
Studies in Ecological Rationality
Authors: Hertwig Ralph , Leuker Christina , Pachur Thorsten , Spiliopoulos Leonidas , Pleskac Timothy J. 
Published: July 2021

AbstractEcological rationality represents an alternative to classic frameworks of rationality. Extending on Herbert Simon's concept of bounded rationality, it holds that cognitive processes, including simple heuristics, are not per se rational or irrational, but that their success rests on their degree of fit to relevant environmental structures. The key is therefore to understand how cognitive and environmental structures slot together. In recent years, a growing set of analyses of heuristic–environment systems has deepened the understanding of the human mind and how boundedly rational heuristics can result in successful decision making. This article is concerned with three conceptual challenges in the study of ecological rationality. First, do heuristics also succeed in dynamic contexts involving competitive agents? Second, can the mind adapt to environmental structures via an unsupervised learning process? Third, how can research go beyond mere descriptions of environmental structures to develop theories of the mechanisms that give rise to those structures? In addressing these questions, we illustrate that a successful theory of rationality will focus on the adaptive aspects of the mind and will need to account for three components: the mind's information processing, the environment to which the mind adapts, and the intersection between the environment and the mind.
Whole‐genome assembly and annotation of northern wild rice, Zizania palustris L., supports a whole‐genome duplication in the Zizania genus
Authors: Haas Matthew , Kono Thomas , Macchietto Marissa , Millas Reneth , McGilp Lillian , Shao Mingqin , Duquette Jacques , Qiu Yinjie , Hirsch Candice N. , Kimball Jennifer 
Published: July 2021

SummaryZizania palustris L. (northern wild rice, NWR) is an aquatic grass native to North America that is notable for its nutritious grain. This is an important species with ecological, cultural and agricultural significance, specifically in the Great Lakes region of the USA. Using flow cytometry, we first estimated the NWR genome size to be 1.8 Gb. Using long‐ and short‐range sequencing, Hi‐C scaffolding and RNA‐seq data from eight tissues, we generated an annotated whole‐genome de novo assembly of NWR. The assembly was 1.29 Gb in length, highly repetitive (approx. 76.0%) and contained 46 421 putative protein‐coding genes. The expansion of retrotransposons within the genome and a whole‐genome duplication (WGD) after the Zizania–Oryza speciation event have both led to an increase in the genome size of NWR in comparison with Oryza sativa L. and Zizania latifolia. Both events depict a genome rapidly undergoing change over a short evolutionary time. Comparative analyses revealed the conservation of large syntenic blocks between NWR and O. sativa, which were used to identify putative seed‐shattering genes. Estimates of divergence times revealed that the Zizania genus diverged from Oryza approximately 26–30 million years ago (26–30 MYA), whereas NWR and Z. latifolia diverged from one another approximately 6–8 MYA. Comparative genomics confirmed evidence of a WGD in the Zizania genus and provided support that the event occurred prior to the NWR–Z. latifolia speciation event. This genome assembly and annotation provides a valuable resource for comparative genomics in the Oryzeae tribe and provides an important resource for future conservation and breeding efforts of NWR.
New high‐quality peach (Prunus persica L. Batsch) genome assembly to analyze the molecular evolutionary mechanism of volatile compounds in peach fruits
Authors: Cao Ke , Yang Xuanwen , Li Yong , Zhu Gengrui , Fang Weichao , Chen Changwen , Wang Xinwei , Wu Jinlong , Wang Lirong 
Published: July 2021

SUMMARYPeach (Prunus persica L. Batsch) is an economically important fruit crop worldwide. Although a high‐quality peach genome has previously been published, Sanger sequencing was used for its assembly, which generated short contigs. Here, we report a chromosome‐level genome assembly and sequence analysis of Chinese Cling, an important founder cultivar for peach breeding programs worldwide. The assembled genome contained 247.33 Mb with a contig N50 of 4.13 Mb and a scaffold N50 of 29.68 Mb, representing 99.8% of the estimated genome. Comparisons between this genome and the recently published one (Lovell peach) uncovered 685 407 single nucleotide polymorphisms, 162 655 insertions and deletions, and 16 248 structural variants. Gene family analysis highlighted the contraction of the gene families involved in flavone, flavonol, flavonoid, and monoterpenoid biosynthesis. Subsequently, the volatile compounds of 256 peach varieties were quantitated in mature fruits in 2015 and 2016 to perform a genome‐wide association analysis. A comparison with the identified domestication genomic regions allowed us to identify 25 quantitative trait loci, associated with seven volatile compounds, in the domestication region, which is consistent with the differences in volatile compounds between wild and cultivated peaches. Finally, a gene encoding terpene synthase, located within a previously reported quantitative trait loci region, was identified to be associated with linalool synthesis. Such findings highlight the importance of this new assembly for the analysis of evolutionary mechanisms and gene identification in peach species. Furthermore, this high‐quality peach genome provides valuable information for future fruit improvement.
Increased incidence of gastrointestinal toxicity in canine cancer patients treated with concurrent abdominal radiation therapy and toceranib phosphate
Authors: Prebble Amber R. , Weishaar Kristen M. , Thamm Douglas H. , Leary Del , LaRue Susan M. , Martin Tiffany , Boss Mary‐Keara 
Published: July 2021

AbstractReceptor tyrosine kinase inhibitors (TKIs) are used to treat human and canine cancers and may be combined with radiation therapy (RT) to enhance tumor control due their anticancer and antiangiogenic effects; however, recent case reports have emerged describing incidences of gastrointestinal toxicity when antiangiogenic therapies are combined with hypofractionated radiotherapy in human cancer patients. We evaluated the incidence of gastrointestinal (GI) toxicity in dogs receiving concurrent hypofractionated abdominal RT and the TKI toceranib (TOC) compared to those receiving abdominal RT alone, TOC alone, or concurrent non‐abdominal RT and TOC. Medical records of canine cancer patients were retrospectively reviewed and identified dogs were included in the following treatment categories: dogs which received RT to a portion of the abdomen and concurrent TOC (n = 19), abdominal RT alone (n‐29), TOC alone (n = 20), or non‐abdominal RT plus TOC (n = 9). Toxicities were graded using the Veterinary Cooperative Oncology Group ‐ Common Terminology Criteria for Adverse Events criteria and compared to published data on TOC‐associated GI toxicity. Patients receiving TOC while undergoing abdominal RT had significantly increased rates of any grade of diarrhea (p = 0.002), hyporexia (p = 0.0045), and vomiting (p = 0.003), as well as severe hyporexia (p = 0.003) when compared across the treatment groups. This retrospective study reveals significantly increased incidences of GI toxicity when abdominal RT is combined with TOC in canine patients. These findings are in‐line with the clinical concerns reported for increased normal tissue toxicity in human patients when antiangiogenics are combined with RT.