bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of environmental changes on vegetable and legume yields and nutritional quality
Authors: Scheelbeek Pauline F. D. , Bird Frances A. , Tuomisto Hanna L. , Green Rosemary , Harris Francesca B. , Joy Edward J. M. , Chalabi Zaid , Allen Elizabeth , Haines Andy , Dangour Alan D. 
Published: June 2018

Significance
Environmental changes, including climate change, air pollution, and water scarcity and salinization, threaten global agricultural production, food security, and health. There is evidence that environmental change will reduce the yields of starchy staple crops, but impacts on (nonstaple) vegetables and legumes—important constituents of healthy diets—remain largely unknown. We systematically reviewed the available published evidence from experimental studies on the impact of environmental changes on yields and nutritional quality of (nonstaple) vegetables and legumes and found that environmental change would have a negative impact on yields without suitable responses from the agricultural sector. An enhanced understanding of the scale of environmental impacts on agricultural production is essential for the development of effective strategies to protect global population health.
Thallium isotopes reveal protracted anoxia during the Toarcian (Early Jurassic) associated with volcanism, carbon burial, and mass extinction
Authors: Them Theodore R. , Gill Benjamin C. , Caruthers Andrew H. , Gerhardt Angela M. , Gröcke Darren R. , Lyons Timothy W. , Marroquín Selva M. , Nielsen Sune G. , Trabucho Alexandre João P. , Owens Jeremy D. 
Published: June 2018

Significance
Declining oxygen contents in today’s oceans highlight the need to better understand ancient, natural marine deoxygenation and associated extinctions. In the Early Jurassic, the Toarcian Oceanic Anoxic Event (T-OAE; ∼183 Ma) is associated with significant perturbations to the Earth system, historically defined by carbon isotopes. We reconstructed global oceanic (de)oxygenation using thallium isotopes from two ocean basins that suggest a stepwise decline of oxygen that initiated before and extended well after the classically defined T-OAE interval. This initial deoxygenation occurs with the start of massive volcanism and marine extinctions, while a later shift corresponds to the traditional T-OAE. This emphasizes the need for more nuanced records of ancient environmental and biogeochemical feedbacks that lead to and maintain widespread marine anoxia.
Suppression of connexin 43 phosphorylation promotes astrocyte survival and vascular regeneration in proliferative retinopathy
Authors: Slavi Nefeli , Toychiev Abduqodir H. , Kosmidis Stylianos , Ackert Jessica , Bloomfield Stewart A. , Wulff Heike , Viswanathan Suresh , Lampe Paul D. , Srinivas Miduturu 
Published: June 2018

Significance
Vascular regeneration during retinal ischemia is critical for curtailing hypoxia-driven aberrant neovascularization and neuronal damage. Apoptotic cell death of astrocytes is a key initiating factor for improper vascular growth. Here we report that astrocytic connexin (Cx43) gap junction (GJ) channels are major contributors to astrocyte degeneration and vascular remodeling that follow tissue ischemia. Astrocyte apoptosis is due to phosphorylation of Cx43 by casein kinase 1δ (CK1δ), which in turn leads to an increase in GJ coupling and amplification of injury. Deletion of Cx43 or inhibition of its phosphorylation by CK1δ rescues astrocytes and leads to restoration of a functional vasculature in the retina, while reducing neovascularization and improving neuroretinal function, thereby providing viable options for the treatment of ischemic retinopathies.
Roles of Gag-RNA interactions in HIV-1 virus assembly deciphered by single-molecule localization microscopy
Authors: Yang Yantao , Qu Na , Tan Jie , Rushdi Muaz N. , Krueger Christopher J. , Chen Antony K. 
Published: June 2018

Significance
Single-molecule localization microscopy (SMLM) is useful for deciphering dynamic organizations of structures densely labeled by specific proteins in the cellular context with nanoscopic resolution not attainable by conventional imaging tools. Here we employed SMLM to investigate the mechanism by which the HIV-1 viral RNA (vRNA) mediates the assembly of thousands of Gag proteins into a virus particle at the plasma membrane. In contrast to the general notion that vRNA only triggers Gag assembly and is dispensable for subsequent assembly, we found that vRNA is indispensable throughout assembly, scaffolding the formation of assembly intermediates and maintaining their architectures via balancing of external forces acting on the assembly environment. These previously unidentified features may facilitate understanding of HIV-1 and, potentially, other retroviruses.
Random critical point separates brittle and ductile yielding transitions in amorphous materials
Authors: Ozawa Misaki , Berthier Ludovic , Biroli Giulio , Rosso Alberto , Tarjus Gilles 
Published: June 2018

Significance
Understanding how amorphous solids yield in response to external deformations is crucial both for practical applications and for theoretical reasons. Here we show that despite large differences in the materials’ microscopic interactions, a degree of universality emerges as there are only two ways in which amorphous solids respond to a deformation: One, typical of well-annealed materials, is characterized by an abrupt failure with a macroscopic stress drop and the sudden emergence of sharp shear bands; the other, typical of poorly annealed materials, shows merely a smooth crossover. By varying the preparation protocol, one can change the response of a given material from one to the other, and this change is controlled by a random critical point.
Differentiated human airway organoids to assess infectivity of emerging influenza virus
Authors: Zhou Jie , Li Cun , Sachs Norman , Chiu Man Chun , Wong Bosco Ho-Yin , Chu Hin , Poon Vincent Kwok-Man , Wang Dong , Zhao Xiaoyu , Wen Lei , Song Wenjun , Yuan Shuofeng , Wong Kenneth Kak-Yuen , Chan Jasper Fuk-Woo , To Kelvin Kai-Wang , Chen Honglin , Clevers Hans , Yuen Kwok-Yung 
Published: June 2018

Significance
Influenza virus infection represents a major threat to public health worldwide. There is no biologically relevant, reproducible, and readily available in vitro model for predicting the infectivity of influenza viruses in humans. Based on the long-term expanding 3D human airway organoids, we developed proximal differentiation and further established a 2D monolayer culture of airway organoids. The resultant 3D and 2D proximal differentiated airway organoids can morphologically and functionally simulate human airway epithelium and as a proof of concept can discriminate human-infective influenza viruses from poorly human-infective viruses. Thus, the proximal differentiated airway organoids can be utilized to predict the infectivity of influenza viruses and, more broadly, provide a universal platform for studying the biology and pathology of the human airway.
An archaeal primase functions as a nanoscale caliper to define primer length
Authors: Yan Jiangyu , Holzer Sandro , Pellegrini Luca , Bell Stephen D. 
Published: June 2018

Significance
The first phosphodiester linkage made during DNA replication is in the context of a short RNA primer synthesized by the dedicated RNA polymerase, primase. Primase, after synthesizing a defined short oligoribonucleotide, then transfers this primer to a DNA polymerase for extension. The mechanisms by which primer length is constrained remain elusive. Here, we dissect the basis of “counting” by an archaeal primase and propose a caliper-like mechanism to account for length determination.
Comparing the Commercial Theaters of Early Modern London and Madrid
Authors: Amelang David J. 
Published: June 2018

AbstractComparative studies have revealed uncanny similarities between the theatrical cultures of Shakespearean England and Golden Age Spain, and in particular between the Elizabethan amphitheaters and the Spanishcorrales de comedia(courtyard playhouses). Contrary to conventional wisdom, however, Spain’s (and, in particular, Madrid’s) courtyard theaters may have resembled the English indoor public playhouses, especially London’s Blackfriars, more than the Globe-like amphitheaters with which they are so often matched. That thecorralescould simultaneously play the part of both Globe and Blackfriars also helps account for the absence of indoor public playhouses in Habsburg Spain.
Oxidative stress-induced TGF-beta/TAB1-mediated p38MAPK activation in human amnion epithelial cells†
Authors: Richardson Lauren , Dixon Christopher Luke , Aguilera-Aguirre Leopoldo , Menon Ramkumar 
Published: June 2018

Abstract
Term and preterm parturition are associated with oxidative stress (OS)-induced p38 mitogen-activated protein kinase (p38MAPK)-mediated fetal tissue (amniochorion) senescence. p38MAPK activation is a complex cell- and stimulant-dependent process. Two independent pathways of OS-induced p38MAPK activation were investigated in amnion epithelial cells (AECs) in response to cigarette smoke extract (CSE: a validated OS inducer in fetal cells): (1) the OS-mediated oxidation of apoptosis signal-regulating kinase (ASK)-1 bound Thioredoxin (Trx[SH]2) dissociates this complex, creating free and activated ASK1-signalosome and (2) transforming growth factor-mediated activation of (TGF)-beta-activated kinase (TAK)1 and TGF-beta-activated kinase 1-binding protein (TAB)1. AECs isolated from normal term, not-in-labor fetal membranes increased p38MAPK in response to CSE and downregulated it in response to antioxidant N-acetylcysteine. In AECs, both Trx and ASK1 were localized; however, they remained dissociated and not complexed, regardless of conditions. Silencing either ASK1 or its downstream effectors (MKK3/6) did not affect OS-induced p38MAPK activation. Conversely, OS increased TGF-beta's release from AECs and increased phosphorylation of both p38MAPK and TAB1. Silencing of TAB1, but not TAK1, prevented p38MAPK activation, which is indicative of TAB1-mediated autophosphorylation of p38MAPK, an activation mechanism seldom seen. OS-induced p38MAPK activation in AECs is ASK1-Trx signalosome-independent and is mediated by the TGF-beta pathway. This knowledge will help to design strategies to reduce p38MAPK activation-associated pregnancy risks.
Theta Oscillations Index Frontal Decision-Making and Mediate Reciprocal Frontal–Parietal Interactions in Willed Attention
Authors: Rajan Abhijit , Siegel Scott N , Liu Yuelu , Bengson Jesse , Mangun George R , Ding Mingzhou 
Published: June 2018

Abstract
Attention can be attracted reflexively by sensory signals, biased by learning or reward, or focused voluntarily based on momentary goals. When voluntary attention is focused by purely internal decision processes (will), rather than instructions via external cues, we call this “willed attention.” In prior work, we reported ERP and fMRI correlates of willed spatial attention in trial-by-trial cuing tasks. Here we further investigated the oscillatory mechanisms of willed attention by contrasting the event-related EEG spectrogram between instructional and choice cues. Two experiments were conducted at 2 different sites using the same visuospatial attention paradigm. Consistent between the 2 experiments, we found increases in frontal theta power (starting at ~500 ms post cue) for willed attention relative to instructed attention. This frontal theta increase was accompanied by increased frontal–parietal theta-band coherence and bidirectional Granger causality. Additionally, the onset of attention-related posterior alpha power lateralization was delayed in willed attention relative to instructed attention, and the amount of delay was related to the timing of frontal theta increase. These results, replicated across 2 experiments, suggest that theta oscillations are the neuronal signals indexing decision-making in the frontal cortex, and mediating reciprocal communications between the frontal executive and parietal attentional control regions during willed attention.
A transform method for the biharmonic equation in multiply connected circular domains
Authors: Luca Elena , Crowdy Darren G 
Published: June 2018

AbstractA new transform approach for solving mixed boundary value problems for the biharmonic equation in simply and multiply connected circular domains is presented. This work is a sequel to Crowdy (2015, IMA J. Appl. Math., 80, 1902–1931) where new transform techniques were developed for boundary value problems for Laplace’s equation in circular domains. A circular domain is defined to be a domain, which can be simply or multiply connected, having boundaries that are a union of circular arc segments. The method provides a flexible approach to finding quasi-analytical solutions to a wide range of problems in fluid dynamics and plane elasticity. Three example problems involving slow viscous flows are solved in detail to illustrate how to apply the method; these concern flow towards a semicircular ridge, a translating and rotating cylinder near a wall as well as in a channel geometry.
Management of inflammatory rheumatic conditions in the elderly
Authors: Lahaye Clément , Tatar Zuzana , Dubost Jean-Jacques , Tournadre Anne , Soubrier Martin 
Published: June 2018

AbstractThe number of elderly people with chronic inflammatory rheumatic diseases is increasing. This heterogeneous and comorbid population is at particular risk of cardiovascular, neoplastic, infectious and iatrogenic complications. The development of biotherapies has paved the way for innovative therapeutic strategies, which are associated with toxicities. In this review, we have focused on the scientific and therapeutic changes impacting the management of elderly patients affected by RA, SpA or PsA. A multidimensional health assessment resulting in an integrated therapeutic strategy was identified as a major research direction for improving the management of elderly patients.
Generalization of the minimum covariance determinant algorithm for categorical and mixed data types
Authors: Beaton Derek , Sunderland Kelly M. ,   ADNI, Levine Brian , Mandzia Jennifer , Masellis Mario , Swartz Richard H. , Troyer Angela K. ,   ONDRI, Binns Malcolm A. , Abdi Hervé , Strother Stephen C. 
Published: June 2018

AbstractThe minimum covariance determinant (MCD) algorithm is one of the most common techniques to detect anomalous or outlying observations. The MCD algorithm depends on two features of multivariate data: the determinant of a matrix (i.e., geometric mean of the eigenvalues) and Mahalanobis distances (MD). While the MCD algorithm is commonly used, and has many extensions, the MCD is limited to analyses of quantitative data and more specifically data assumed to be continuous. One reason why the MCD does not extend to other data types such as categorical or ordinal data is because there is not a well-defined MD for data types other than continuous data. To address the lack of MCD-like techniques for categorical or mixed data we present a generalization of the MCD. To do so, we rely on a multivariate technique called correspondence analysis (CA). Through CA we can define MD via singular vectors and also compute the determinant from CA’s eigenvalues. Here we define and illustrate a generalized MCD on categorical data and then show how our generalized MCD extends beyond categorical data to accommodate mixed data types (e.g., categorical, ordinal, and continuous). We illustrate this generalized MCD on data from two large scale projects: the Ontario Neurodegenerative Disease Research Initiative (ONDRI) and the Alzheimer’s Disease Neuroimaging Initiative (ADNI), with genetics (categorical), clinical instruments and surveys (categorical or ordinal), and neuroimaging (continuous) data. We also make R code and toy data available in order to illustrate our generalized MCD.
Modeling large fluctuations of thousands of clones during hematopoiesis: the role of stem cell self-renewal and bursty progenitor dynamics in rhesus macaque
Authors: Xu Song , Kim Sanggu , Chen Irvin S. Y. , Chou Tom 
Published: June 2018

AbstractIn a recent clone-tracking experiment, millions of uniquely tagged hematopoietic stem cells (HSCs) were autologously transplanted into rhesus macaques and peripheral blood containing thousands of tags were sampled and sequenced over 14 years to quantify the abundance of hundreds to thousands of tags or “clones.” Two major puzzles of the data have been observed: consistent differences and massive temporal fluctuations of clone populations. The large sample-to-sample variability can lead clones to occasionally go “extinct” but “resurrect” themselves in subsequent samples. Although heterogeneity in HSC differentiation rates, potentially due to tagging, and random sampling of the animals’ blood and cellular demographic stochasticity might be invoked to explain these features, we show that random sampling cannot explain the magnitude of the temporal fluctuations. Moreover, we show through simplerneutralmechanistic and statistical models of hematopoiesis of tagged cells that a broad distribution in clone sizes can arise from stochastic HSC self-renewal instead of tag-induced heterogeneity. The very large clone population fluctuations that often lead to extinctions and resurrections can be naturally explained by a generation-limited proliferation constraint on the progenitor cells. This constraint leads to bursty cell population dynamics underlying the large temporal fluctuations. We analyzed experimental clone abundance data using a new statistic that counts clonal disappearances and provide least-squares estimates of two key model parameters in our model, the total HSC differentiation rate and the maximum number of progenitor-cell divisions.Author summaryHematopoiesis of virally tagged cells in rhesus macaques is analyzed in the context of a mechanistic and statistical model. We find that the clone size distribution and the temporal variability in the abundance of each clone (viral tag) in peripheral blood are consistent with (i) stochastic HSC self-renewal during bone marrow repair, (ii) clonal aging that restricts the number of generations of progenitor cells, and (iii) infrequent and small-size samples. By fitting data, we infer two key parameters that control the level of fluctuations of clone sizes in our model: the total HSC differentiation rate and the maximum proliferation capacity of progenitor cells. Our analysis provides insight into the mechanisms of hematopoiesis and a framework to guide future multiclone barcoding/lineage tracking measurements.
Synchrotron FTIR and Raman spectroscopy 1 ectroscopy provide unique spectral fingerprints for Arabidopsis floral stem vascular tissues
Authors: Dinant S , Wolff N , De Marco F , Vilaine F , Gissot L , Aubry E , Sandt C , Bellini C , Le Hir R 
Published: June 2018

AbstractCell walls are highly complex structures that are modified during plant growth and development. For example, the development of phloem and xylem vascular cells, which participate in the transport of sugars and water as well as support, can be influenced by cell-specific cell wall composition. Here, we used synchrotron radiation-based infrared (SR-FTIR) and Raman spectroscopy to analyze the cell wall composition of wild-type and double mutant sweet11-1sweet12-1, which impairs sugar transport, Arabidopsis floral stem vascular tissue. The SR-FTIR spectra showed that in addition to modified xylem cell wall composition, phloem cell walls in the double mutant line were characterized by modified hemicellulose composition. Moreover, combining Raman spectroscopy with a Classification and Regression Tree (CART) method identified combinations of Raman shifts that could distinguish xylem vessels and fibers. Additionally, the disruption of SWEET11 and SWEET12 genes impacts xylem cell wall composition in a cell-specific manner, with changes in hemicelluloses and cellulose observed at the xylem vessel interface. These results suggest that the facilitated transport of sugars by transporters that exist between vascular parenchyma cells and conducting cells is important to ensuring correct phloem and xylem cell wall composition.HighlightCombining vibrational spectroscopy techniques and multivariate analysis shows that the disruption of SWEET genes impacts phloem cell wall composition and that the effect on xylem cell wall composition is cell-specific.
Diffusible Signal Factor signaling regulates multiple functions in the opportunistic pathogen Stenotrophomonas maltophilia
Authors: An Shi-qi , Tang Ji-liang 
Published: June 2018

AbstractStenotrophomonas maltophilia is a Gram-negative bacterium commonly isolated from nosocomial infections. Analysis of the genome of the clinical Stenotrophomonas maltophilia isolate K279a indicates that it encodes a diffusible signal factor (DSF)-dependent cell-cell signaling mechanism that is highly similar to the system previously described in phytopathogens from the genera Xanthomonas and Xylella. Here we demonstrate that in S. maltophilia strain K279a, DSF signaling regulates factors contributing to virulence, biofilm formation and motility of this important opportunistic pathogen.
Culturing the ubiquitous freshwater actinobacterial acI lineage by supplying a biochemical ‘helper’ catalase
Authors: Kim Suhyun , Kang Ilnam , Seo Ji-Hui , Cho Jang-Cheon 
Published: June 2018

AbstractUnlike the ocean from which abundant microorganisms with streamlined genomes such as Prochlorococcus, Pelagibacter, and Nitrosopumilus have been isolated, no stable axenic bacterial cultures are available for the ubiquitous freshwater actinobacterial acI lineage. The acI lineage is among the most successful limnic bacterioplankton found on all continents, often representing more than half of all microbial cells in the lacustrine environment and constituting multiple ecotypes. Dilution-to-extinction culturing followed by whole-genome amplification recently yielded 20 complete acI genomes from lakes in Asia and Europe. However, stably growing pure cultures have not been established despite various efforts at cultivation using growth factors predicted from genome information. Here, we report two pure cultures of the acI lineage successfully maintained by supplementing the growth media with catalase. Catalase was critical for stabilizing growth by degrading hydrogen peroxide, irrespective of the genomic presence of the catalase-peroxidase (katG) gene, making the acI strains the first example of the Black Queen hypothesis reported for freshwater bacteria. The two strains, representing two novel species, displayed differential phenotypes and distinct preferences for reduced sulfurs and carbohydrates, some of which were difficult to predict based on genomic information. Our results suggest that culture of previously uncultured freshwater bacteria can be facilitated by a simple catalase-supplement method and indicate that genome-based metabolic prediction can be complemented by physiological analyses.