bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leaf traits from stomata to morphology are associated with climatic and edaphic variables for dominant tropical forest evergreen oaks
Authors: Lin Yutong , Kuang Luhui , Tang Songbo , Mou Zhijian , Phillips Oliver L , Lambers Hans , Liu Zhanfeng , Sardans Jordi , Peñuelas Josep , Lai Yuan , Lin Mingxian , Chen Dexiang , Kuang Yuanwen 
Published: June 2021

AbstractAimsUnderstanding variation and coordination of leaf traits at multiscales along elevational gradients can help predict the likely responses of dominant species to climate change. We seek to determine the extent to which variation in leaf stomatal, anatomical and morphological traits is associated with environmental factors, and whether ecological strategies of Cyclobalanopsis species shift with elevations.MethodsIn a tropical forest landscape in Jianfengling, South China, we determined leaf traits related to stomata, anatomy and morphology of six evergreen oak species (Cyclobalanopsis bambusaefolia, C. hui, C. patelliformis, C. fleuryi, C. tiaoloshanica and C. phanera) along a long elevational gradient (400–1400 m above sea level).Important FindingsWe found that stomatal density and stomatal pore index increased, whereas spongy mesophyll thickness to leaf thickness ratios decreased, significantly with elevation. The leaf area and leaf dry matter content increased and decreased, respectively, with elevation. Variations in stomatal, anatomical and morphological traits were mainly correlated to the mean annual temperature, mean annual sum precipitation and soil pH. At low and high elevations, the oak species exhibited strong stress tolerance combined with competition strategy, while they shifted toward more clearly the competitive strategy at intermediate elevations. And the changes in soil phosphorus concentration and soil pH along the elevation may drive the shift of ecological strategy. The results showed that the dominant oak species in tropical forests respond to environmental change by modulating traits at multiple levels, from that of the individual cell, through tissue and up to the whole leaf scale.
Unique Pathogen Peptidomes Facilitate Pathogen-Specific Selection and Specialization of MHC Alleles
Authors: Özer Onur , Lenz Tobias L 
Published: June 2021

Abstract
A key component of pathogen-specific adaptive immunity in vertebrates is the presentation of pathogen-derived antigenic peptides by major histocompatibility complex (MHC) molecules. The excessive polymorphism observed at MHC genes is widely presumed to result from the need to recognize diverse pathogens, a process called pathogen-driven balancing selection. This process assumes that pathogens differ in their peptidomes—the pool of short peptides derived from the pathogen’s proteome—so that different pathogens select for different MHC variants with distinct peptide-binding properties. Here, we tested this assumption in a comprehensive data set of 51.9 Mio peptides, derived from the peptidomes of 36 representative human pathogens. Strikingly, we found that 39.7% of the 630 pairwise comparisons among pathogens yielded not a single shared peptide and only 1.8% of pathogen pairs shared more than 1% of their peptides. Indeed, 98.8% of all peptides were unique to a single pathogen species. Using computational binding prediction to characterize the binding specificities of 321 common human MHC class-I variants, we investigated quantitative differences among MHC variants with regard to binding peptides from distinct pathogens. Our analysis showed signatures of specialization toward specific pathogens especially by MHC variants with narrow peptide-binding repertoires. This supports the hypothesis that such fastidious MHC variants might be maintained in the population because they provide an advantage against particular pathogens. Overall, our results establish a key selection factor for the excessive allelic diversity at MHC genes observed in natural populations and illuminate the evolution of variable peptide-binding repertoires among MHC variants.
Functional interplay of histone lysine 2-hydroxyisobutyrylation and acetylation in Arabidopsis under dark-induced starvation
Authors: Zheng Lanlan , Li Chen , Ma Xueping , Zhou Hanlin , Liu Yuan , Wang Ping , Yang Huilan , Tamada Yosuke , Huang Ji , Wang Chunfei , Hu Zhubing , Wang Xuening , Wang Guodong , Li Haihong , Hu Juntao , Liu Xiaoyun , Zhou Chao , Zhang Yonghong 
Published: June 2021

AbstractLysine 2-hydroxyisobutyrylation (Khib) is a novel type of histone acylation whose prevalence and function in plants remain unclear. Here, we identified 41 Khib sites on histones in Arabidopsis thaliana, which did not overlap with frequently modified N-tail lysines (e.g. H3K4, H3K9 and H4K8). Chromatin immunoprecipitation-sequencing (ChIP-seq) assays revealed histone Khib in 35% of protein-coding genes. Most Khib peaks were located in genic regions, and they were highly enriched at the transcription start sites. Histone Khib is highly correlated with acetylation (ac), particularly H3K23ac, which it largely resembles in its genomic and genic distribution. Notably, co-enrichment of histone Khib and H3K23ac correlates with high gene expression levels. Metabolic profiling, transcriptome analyses, and ChIP-qPCR revealed that histone Khib and H3K23ac are co-enriched on genes involved in starch and sucrose metabolism, pentose and glucuronate interconversions, and phenylpropanoid biosynthesis, and help fine-tune plant response to dark-induced starvation. These findings suggest that Khib and H3K23ac may act in concert to promote high levels of gene transcription and regulate cellular metabolism to facilitate plant adaption to stress. Finally, HDA6 and HDA9 are involved in removing histone Khib. Our findings reveal Khib as a conserved yet unique plant histone mark acting with lysine acetylation in transcription-associated epigenomic processes.
Characteristics of patients ≥10 years of age with diffuse intrinsic pontine glioma: a report from the International DIPG/DMG Registry
Authors: Erker Craig , Lane Adam , Chaney Brooklyn , Leary Sarah , Minturn Jane E , Bartels Ute , Packer Roger J , Dorris Kathleen , Gottardo Nicholas G , Warren Katherine E , Broniscer Alberto , Kieran Mark W , Zhu Xiaoting , White Peter , Dexheimer Phillip J , Black Katie , Asher Anthony , DeWire Mariko , Hansford Jordan R , Gururangan Sridharan , Nazarian Javad , Ziegler David S , Sandler Eric , Bartlett Allison , Goldman Stewart , Shih Chie-Schin , Hassall Tim , Dholaria Hetal , Bandopadhayay Pratiti , Samson Yvan , Monje Michelle , Fisher Paul G , Dodgshun Andrew , Parkin Sarah , Chintagumpala Murali , Tsui Karen , Gass David , Larouche Valerie , Broxson Emmett , Garcia Lombardi Mercedes , Wang Stacie Shiqi , Ma Jie , Hawkins Cynthia , Hamideh Dima , Wagner Lars , Koschmann Carl , Fuller Christine , Drissi Rachid , Jones Blaise V , Leach James , Fouladi Maryam 
Published: June 2021

AbstractBackgroundDiffuse intrinsic pontine gliomas (DIPG) generally occur in young school-age children, although can occur in adolescents and young adults. The purpose of this study was to describe clinical, radiological, pathologic, and molecular characteristics in patients ≥10 years of age with DIPG enrolled in the International DIPG Registry (IDIPGR).MethodsPatients ≥10 years of age at diagnosis enrolled in the IDIPGR with imaging confirmed DIPG diagnosis were included. The primary outcome was overall survival (OS) categorized as long-term survivors (LTS) (≥24 months) or short-term survivors (STS) (&lt;24 months).ResultsAmong 1010 patients, 208 (21%) were ≥10 years of age at diagnosis; 152 were eligible with a median age of 12 years (range 10-26.8). Median OS was 13 (2-82) months. The 1-, 3-, and 5-year OS was 59.2%, 5.3%, and 3.3%, respectively. The 18/152 (11.8%) LTS were more likely to be older (P &lt; .01) and present with longer symptom duration (P &lt; .01). Biopsy and/or autopsy were performed in 50 (33%) patients; 77%, 61%, 33%, and 6% of patients tested had H3K27M (H3F3A or HIST1H3B), TP53, ATRX, and ACVR1 mutations/genome alterations, respectively. Two of 18 patients with IDH1 testing were IDH1-mutant and 1 was a LTS. The presence or absence of H3 alterations did not affect survival.ConclusionPatients ≥10 years old with DIPG have a median survival of 13 months. LTS present with longer symptom duration and are likely to be older at presentation compared to STS. ATRX mutation rates were higher in this population than the general DIPG population.
Redo craniotomy or bevacizumab for symptomatic steroid-refractory true or pseudoprogression following IMRT for glioblastoma
Authors: Cook Theresa A , Jayamanne Dasantha T , Wheeler Helen R , Wong Matthew H F , Parkinson Jonathon F , Cook Raymond J , Kastelan Marina A , Cove Nicola J , Brown Christopher , Back Michael F 
Published: June 2021

Abstract

Background
There is minimal evidence to support decision making for symptomatic steroid-refractory pseudoprogression or true progression occurring after intensity-modulated radiation therapy (IMRT) for glioblastoma (GBM). This study audited the survival outcome of patients managed with redo craniotomy (RedoSx) or bevacizumab (BEV) for steroid-refractory mass effect after IMRT for GBM.

Methods
Patients with GBM managed between 2008 and 2019 with the EORTC-NCIC Protocol were entered into a prospective database. Patients with symptomatic steroid-refractory mass effect within 6 months of IMRT managed with either RedoSx or BEV were identified for analysis. For the primary endpoint of median overall survival (OS) postintervention, outcome was analyzed in regards to potential prognostic factors, and differences between groups were assessed by log-rank analyses.

Results
Of the 399 patients managed with the EORTC-NCIC Protocol, 78 required an intervention within 6 months of IMRT completion for either true or pseudoprogression (49 with RedoSx and 29 with BEV). Subsequently, 20 of the 43 patients managed with RedoSx when BEV was clinically available, required salvage with BEV within 6 months after RedoSx. Median OS postintervention was 8.7 months (95% CI: 7.84-11.61) for the total group; and 8.7 months (95% CI: 6.8-13.1) for RedoSx and 9.4 months (95% CI: 7.8-13.6) for BEV (P = .38). Subsequent use of BEV in RedoSx patients was not associated with improved survival compared with RedoSx alone (P = .10). Age, time from IMRT, and ECOG performance status were not associated with OS. In the RedoSx patients, immunohistochemical features such as Ki-67% reduction correlated with survival. The presence of pure necrosis and residual tumor cells only had improved survival compared with the presence of gross tumor (P &lt; .001).

Conclusions
At time of symptomatic steroid-refractory true or pseudoprogression following IMRT for GBM, BEV was equivalent to RedoSx in terms of OS. Pseudoprogression with residual cells at RedoSx was not associated with worse outcome compared to pure necrosis.
X-ray observations of accretion disks
Authors: Inoue Hajime 
Published: June 2021

Abstract
Present understandings of accretion disks based on X-ray observations are reviewed. The main focus is on observational properties of accretion disks around black holes in X-ray binaries and their phenomenological interpretations. Since there are several excellent reviews on black hole binaries already, we here pick up a limited number of important works which introduced key observational clues which widen and/or deepen the understanding of the accretion disks, recalling histories of X-ray observations of binary X-ray sources with a number of X-ray astronomy satellites successively launched from the United States, European countries, and Japan. We at certain points compare some observational evidence from black hole binaries with similar phenomena observed from binaries with a weakly magnetized neutron star, to clarify the basic nature of accretion disks. We also try to understand accretion environments in active galactic nuclei by applying what we have learned from the black hole binaries to them.
The bare necessities of plant K+ channel regulation
Authors: Lefoulon Cécile 
Published: June 2021

Abstract
Potassium (K+) channels serve a wide range of functions in plants from mineral nutrition and osmotic balance to turgor generation for cell expansion and guard cell aperture control. Plant K+ channels are members of the superfamily of voltage-dependent K+ channels, or Kv channels, that include the Shaker channels first identified in fruit flies (Drosophila melanogaster). Kv channels have been studied in depth over the past half century and are the best-known of the voltage-dependent channels in plants. Like the Kv channels of animals, the plant Kv channels are regulated over timescales of milliseconds by conformational mechanisms that are commonly referred to as gating. Many aspects of gating are now well established, but these channels still hold some secrets, especially when it comes to the control of gating. How this control is achieved is especially important, as it holds substantial prospects for solutions to plant breeding with improved growth and water use efficiencies. Resolution of the structure for the KAT1 K+ channel, the first channel from plants to be crystallized, shows that many previous assumptions about how the channels function need now to be revisited. Here, I strip the plant Kv channels bare to understand how they work, how they are gated by voltage and, in some cases, by K+ itself, and how the gating of these channels can be regulated by the binding with other protein partners. Each of these features of plant Kv channels has important implications for plant physiology.
Fractional Parts of Non-Integer Powers of Primes. II
Authors: Shubin Andrei 
Published: June 2021

Abstract
We continue to study the distribution of prime numbers p, satisfying the condition $\{p^{\alpha} \} \in I \subset [0; 1)$, in arithmetic progressions. In this paper, we prove an analogue of Bombieri–Vinogradov theorem for 0 &lt; α &lt; 1/9 with the level of distribution $\theta = 2/5 - (3/5) \alpha$, which improves the previous result corresponding to $\theta \leqslant 1/3$.
Persistent thrombocytopenia predicts poor long-term survival in patients with antiphospholipid syndrome: a 38-year follow-up study
Authors: Pardos-Gea José , Marques-Soares Joana R , Buján Segundo , Ordi-Ros José , Alijotas-Reig Jaume 
Published: June 2021

Abstract

Objectives
To investigate the impact of thrombocytopenia on survival in patients with APS.

Methods
Thrombocytopenia and other predictors of outcome were retrospectively evaluated in an aPL-positive and APS cohort with 38-year follow-up (1980–2018). Thrombocytopenia was defined as &lt;150 × 109 platelets/l. Hazard ratios (HR) of mortality were calculated using Cox-regression models.

Results
Among 114 patients, 64% had primary APS, 25% secondary APS and 10% asymptomatic aPL. Mean follow-up was 19 (range 5–38) years. ANA [hazard ratio (HR) 1.8, 95% CI 0.8, 3.6, P = 0.10], arterial thrombotic events (HR 7.0, 95% CI 1.4, 3.5, P = 0.016), myocardial infarction (HR 8.3, 95% CI 1.1, 59, P = 0.03), intracardiac thrombosis (HR 17, 95% CI 1, 279, P = 0.04) and thrombocytopenia (HR 2.9, 95% CI 1.4, 6.1, P = 0.004) were risk factors for all-cause mortality, but in multivariate analysis only thrombocytopenia (HR 2.7, 95% CI 1.3, 6.0, P = 0.01) remained significant. Persistent (HR 4.4, 95% CI 2.1, 9.2, P = 0.001) and low–moderate thrombocytopenia (HR 2.8, 95% CI 1.2, 6.4, P = 0.01) were associated with a significant increase in mortality compared with acute (HR 1.6, 95% CI 0.5, 5.3, P = 0.40) and severe (HR 2.1, 95% CI 0.5, 9.2, P = 0.30) forms. APS patients with vs without thrombocytopenia were more frequently male (58 vs 24%, P = 0.001) with arterial thrombosis (55 vs 32%, P = 0.04), LA positivity (100 vs 87%, P = 0.04), type I aPL profile (89% vs 71%, P = 0.05) and anticoagulant treatment (89 vs 63%, P = 0.01). Thrombosis caused 13% of deaths in thrombocytopenic patients and 1% in those without (P = 0.01).

Conclusion
Thrombocytopenia is an aPL-related manifestation that identifies patients with severe disease phenotype and high thrombotic risk. Persistent low–moderate thrombocytopenia is associated with a reduced long-term survival.
SKY PLC v SKYKICK UK LTD
Authors:   Court of Justice of the European Union (Fourth Chamber)
Published: June 2021

Abstract
H1 Trade Marks – European trade marks – SKY – Validity – Specification of goods and services – Broad specifications – “Computer software” – Requirement of clarity and precision – Whether a ground of invalidity – Whether amounting to failure to satisfy requirement of graphical representability – Whether contrary to the public interest – Bad faith – Effect of lack of intention to use in whole or in part – Vires of s. 32(3) of the Trade Marks Act 1994 – Reference to Court of Justice
Empirical and Methodological Challenges to the Model-Based Inference of Diversification Rates in Extinct Clades
Authors: Černý David , Madzia Daniel , Slater Graham J 
Published: June 2021

AbstractChanges in speciation and extinction rates are key to the dynamics of clade diversification, but attempts to infer them from phylogenies of extant species face challenges. Methods capable of synthesizing information from extant and fossil species have yielded novel insights into diversification rate variation through time, but little is known about their behavior when analyzing entirely extinct clades. Here, we use empirical and simulated data to assess how two popular methods, PyRate and Fossil BAMM, perform in this setting. We inferred the first tip-dated trees for ornithischian dinosaurs and combined them with fossil occurrence data to test whether the clade underwent an end-Cretaceous decline. We then simulated phylogenies and fossil records under empirical constraints to determine whether macroevolutionary and preservation rates can be teased apart under paleobiologically realistic conditions. We obtained discordant inferences about ornithischian macroevolution including a long-term speciation rate decline (BAMM), mostly flat rates with a steep diversification drop (PyRate) or without one (BAMM), and episodes of implausibly accelerated speciation and extinction (PyRate). Simulations revealed little to no conflation between speciation and preservation, but yielded spuriously correlated speciation and extinction estimates while time-smearing tree-wide shifts (BAMM) or overestimating their number (PyRate). Our results indicate that the small phylogenetic data sets available to vertebrate paleontologists and the assumptions made by current model-based methods combine to yield potentially unreliable inferences about the diversification of extinct clades. We provide guidelines for interpreting the results of the existing approaches in light of their limitations and suggest how the latter may be mitigated. [BAMM; diversification; fossils; macroevolutionary rates; Ornithischia; PyRate.]
Commercial beef farms excelling in terminal and maternal genetic merit generate more gross profit
Authors: Kelly David N , Connolly K , Kelly P , Cromie A R , Murphy C P , Sleator R D , Berry D P 
Published: June 2021

Abstract
Validation of beef total merit breeding indexes for improving performance and profitability has previously been undertaken at the individual animal level; however, no herd-level validation of beef genetic merit and profit has been previously investigated. The objective of the present study was to quantify the relationship between herd profitability and both herd-average terminal and maternal genetic merit across 1,311 commercial Irish beef herds. Herd-level physical and financial performance data were available from a financial benchmarking tool used by Irish farmers and their extension advisors. Animal genetic merit data originated from the Irish Cattle Breeding Federation who undertake the national beef and dairy genetic evaluations. Herd-average genetic merit variables included the terminal index of young animals, the maternal index of dams, and the terminal index of service sires. The herds represented three production systems: 1) cow-calf to beef, 2) cow-calf to weanling/yearling, and 3) weanling/yearling to beef. Associations between herd financial performance metrics and herd average genetic merit variables were quantified using a series of linear mixed models with year, production system, herd size, stocking rate, concentrate input, and the two-way interactions between production system and herd size, stocking rate, and concentrate input included as nuisance factors. Herd nested within the county of Ireland (n = 26) was included as a repeated effect. Herds with young cattle excelling in terminal index enjoyed greater gross and net profit per hectare (ha), per livestock unit (LU), and per kg net live-weight output. The change in gross profit per LU per unit change in the terminal index of young animals was €1.41 (SE = 0.23), while the respective regression coefficient for net profit per LU was €1.37 (SE = 0.30); the standard deviation of the terminal index is €37. Herd-average dam maternal index and sire terminal index were both independently positively associated with gross profit per ha and gross profit per LU. Each one unit increase in dam maternal index (standard deviation of €38) was associated with a €1.40 (SE = 0.48) and €0.76 (SE = 0.29) greater gross profit per ha and per LU, respectively. Results from the present study at the herd-level concur with previous validation studies at the individual animal level thus instilling further confidence among stakeholders as to the expected improvement in herd profitability with improving genetic merit.
Risk factors, outcomes and time to detect positive blood culture among cases with acute brucellosis
Authors: Gaifer Zied , Ali Mohammed E Mohammed , AlJehani Basmah H , Shaikh Hawazin A , Hussein Sheikheldin B 
Published: June 2021

Abstract

Background
Brucellosis causes a disabling human disease and loss of animals' lives. The clinical significance of Brucella bacteremia is still unclear and Brucella identification in blood culture is suboptimal.

Methods
This was a retrospective study conducted in Medina in Saudi Arabia from August 2016 to May 2019. We included cases with brucellosis symptoms and a positive culture or serological evidence for brucellosis, comparing bacteremic with non-bacteremic brucellosis cases for the rates of complications, infection relapses and brucellosis development. Also, we estimated blood culture positivity rates and the time to detect Brucella in an automatic blood culture instrument.

Results
Of the total number of 147 cases, 62 (42%) had a positive blood culture for Brucella, and the blood culture instrument (BACT/ALERT 3D) detected all positive blood cultures within 3 d of incubation. We found higher rates of chronic brucellosis in bacteremia than non-bacteremia cases (OR 7.25, 95% CI 1.41 to 37.23; p=0.018). Patients aged &lt;15 y developed a higher rate of bacteremia than those aged ≥15 yr (OR 11.93 95% CI 1.37 to 103.75; p=0.025).

Conclusion
Brucella bacteremia is an independent predictor for the development of chronic infection. Brucella bacteremia cases may need long follow-up periods and a more thorough evaluation to exclude deep-seated infection.
Difficult Conversations in Palliative Care: Innovations in Learning
Authors: Halliday Deborah A. , Dorney Paulette , Landis Jennifer 
Published: June 2021

Abstract
Accelerated nursing students have a short time frame in which to assimilate knowledge as postbaccalaureate nursing programs are approximately 16 months in length. Research has demonstrated limited innovative evidence-based teaching strategies when developing palliative care curricula in accelerated nursing programs. The authors addressed this gap by using student-centered learning activities and simulation within the context of an end-of-life course. This novel approach allowed students the opportunity to practice important therapeutic communication skills while enhancing their knowledge of palliative nursing care.