bluuebunny/crossref_metadata_2025_split huggingface dataset:
13CO2 labeling kinetics in maize reveal impaired efficiency of C4 photosynthesis under low irradiance
Authors: Medeiros David B , Ishihara Hirofumi , Guenther Manuela , Rosado de Souza Laise , Fernie Alisdair R , Stitt Mark , Arrivault Stéphanie 
Published: June 2022

Abstract
C4 photosynthesis allows faster photosynthetic rates and higher water and nitrogen use efficiency than C3 photosynthesis, but at the cost of lower quantum yield due to the energy requirement of its biochemical carbon concentration mechanism. It has also been suspected that its operation may be impaired in low irradiance. To investigate fluxes under moderate and low irradiance, maize (Zea mays) was grown at 550 µmol photons m−2 s−l and 13CO2 pulse-labeling was performed at growth irradiance or several hours after transfer to 160 µmol photons m−2 s−1. Analysis by liquid chromatography/tandem mass spectrometry or gas chromatography/mass spectrometry provided information about pool size and labeling kinetics for 32 metabolites and allowed estimation of flux at many steps in C4 photosynthesis. The results highlighted several sources of inefficiency in low light. These included excess flux at phosphoenolpyruvate carboxylase, restriction of decarboxylation by NADP-malic enzyme, and a shift to increased CO2 incorporation into aspartate, less effective use of metabolite pools to drive intercellular shuttles, and higher relative and absolute rates of photorespiration. The latter provides evidence for a lower bundle sheath CO2 concentration in low irradiance, implying that operation of the CO2 concentration mechanism is impaired in this condition. The analyses also revealed rapid exchange of carbon between the Calvin–Benson cycle and the CO2-concentration shuttle, which allows rapid adjustment of the balance between CO2 concentration and assimilation, and accumulation of large amounts of photorespiratory intermediates in low light that provides a major carbon reservoir to build up C4 metabolite pools when irradiance increases.
A genomic meta-analysis of clinical variables and their association with intrinsic molecular subsets in systemic sclerosis
Authors: Franks Jennifer M , Toledo Diana M , Martyanov Viktor , Wang Yue , Huang Suiyuan , Wood Tammara A , Spino Cathie , Chung Lorinda , Denton Christopher P , Derrett-Smith Emma , Gordon Jessica K , Spiera Robert , Domsic Robyn , Hinchcliff Monique , Khanna Dinesh , Whitfield Michael L 
Published: June 2022

Abstract

Objectives
Four intrinsic molecular subsets (inflammatory, fibroproliferative, limited, normal-like) have previously been identified in SSc and are characterized by unique gene expression signatures and pathways. The intrinsic subsets have been linked to improvement with specific therapies. Here, we investigated associations between baseline demographics and intrinsic molecular subsets in a meta-analysis of published datasets.

Methods
Publicly available gene expression data from skin biopsies of 311 SSc patients measured by DNA microarray were classified into the intrinsic molecular subsets. RNA-sequencing data from 84 participants from the ASSET trial were used as a validation cohort. Baseline clinical demographics and intrinsic molecular subsets were tested for statistically significant associations.

Results
Males were more likely to be classified in the fibroproliferative subset (P = 0.0046). SSc patients who identified as African American/Black were 2.5 times more likely to be classified as fibroproliferative compared with White/Caucasian patients (P = 0.0378). ASSET participants sera positive for anti-RNA pol I and RNA pol III autoantibodies were enriched in the inflammatory subset (P = 5.8 × 10−5, P = 9.3 × 10−5, respectively), while anti-Scl-70 was enriched in the fibroproliferative subset. Mean modified Rodnan Skin Score (mRSS) was statistically higher in the inflammatory and fibroproliferative subsets compared with normal-like (P = 0.0027). The average disease duration for inflammatory subset was less than fibroproliferative and normal-like intrinsic subsets (P = 8.8 × 10−4).

Conclusions
We identified multiple statistically significant differences in baseline demographics between the intrinsic subsets that may represent underlying features of disease pathogenesis (e.g. chronological stages of fibrosis) and have implications for treatments that are more likely to work in certain SSc populations.
Preserved Unconscious Processing in Schizophrenia: The Case of Motivation
Authors: Berkovitch Lucie , Gaillard Raphaël , Abdel-Ahad Pierre , Smadja Sarah , Gauthier Claire , Attali David , Beaucamps Hadrien , Plaze Marion , Pessiglione Mathias , Vinckier Fabien 
Published: June 2022

Abstract

Background and Hypothesis
Motivation deficit is a hallmark of schizophrenia that has a strong impact on their daily life. An alteration of reward processing has been repeatedly highlighted in schizophrenia, but to what extent it involves a deficient amplification of reward representation through conscious processing remains unclear. Indeed, patients with schizophrenia exhibit a disruption of conscious processing, whereas unconscious processing appears to be largely preserved.

Study Design
To further explore the nature of motivational deficit in schizophrenia and the implication of consciousness disruption in this symptom, we used a masking paradigm testing motivation both under conscious and unconscious conditions in patients with schizophrenia (n = 31) and healthy controls (n = 32). Participants were exposed to conscious or subliminal coin pictures representing money at stake and were subsequently asked to perform an effort-task by squeezing a handgrip as hard as possible to win this reward.

Study Results
We observed a preserved effect of unconscious monetary rewards on force production in both groups, without any significant difference between them. By contrast, in the conscious condition, patients with schizophrenia were less sensitive to rewards than controls. Our results confirm that unconscious incentives have effects on exerted forces in the general population, and demonstrate that patients with schizophrenia exhibit a dissociation between an impaired conscious motivation and a preserved unconscious motivation.

Conclusions
These findings suggest the existence of several steps in motivational processes that can be differentially affected and might have implication for patient care.
Charity trustees: governance duties and conflicts of interest
Authors: Langford Rosemary Teele , Anderson Malcolm 
Published: June 2022

Abstract
This article reports the results of an extensive survey of charity trustees in England and Wales in relation to governance duties and conflicts of interest. The results help discern trustees’ understanding of, and confidence with, their governance duties, their enthusiasm for practical assistance with these duties, the strength of their conflict management procedures, as well as compliance motivations and perceived barriers to enhanced governance and compliance. This in turn assists in critical evaluation of the effectiveness of the governance and regulatory system of charities in England and Wales.
In which department should forages be taught?
Authors: Redmon Larry , Wickersham Tryon , Rouquette Monte 
Published: June 2022

Abstract
Forages as a discipline and forage workers in general are declining nationwide. Why is this? Could it be the department in which forage courses are taught? This paper will take a brief look at the history of forage/livestock grazing research, who currently teaches a forage course and where forages are currently taught at various land grant institutions. Finally, the question and a potential answer is provided regarding where might the forage discipline be taught to increase their exposure to undergraduate students.
Is socioeconomic status associated with risk of childhood type 1 diabetes? A comprehensive review
Authors: Ruiz Paz Lopez-Doriga , Stene Lars C. 
Published: June 2022

AimsStudies of social inequality in risk of type 1 diabetes seems inconsistent. The present review aimed to comprehensively review relevant literature and describe what has been reported on socioeconomic status or parental occupation and risk of type 1 diabetes in children.MethodsWe searched for publications between January 1, 1970, and November 30, 2021. We focused on the most recent and/or informative publication in case of multiple publications from the same data source and referred to these as primary studies.ResultsOur search identified 69 publications with relevant data. We identified eight primary cohort studies with individual-level data, which we considered the highest quality of evidence. Furthermore, we identified 13 primary case-control studies and 14 semi-ecological studies with area-level socioeconomic status variables which provide weaker quality of evidence. Four of eight primary cohort studies contained data on maternal education, showing non-linear associations with type 1 diabetes that were not consistent across studies. There were no consistent patterns on the association of parental occupation and childhood-onset type 1 diabetes.ConclusionsThere is a need for more high-quality studies, but the existing literature does not suggest a major and consistent role of socioeconomic status in the risk of type 1 diabetes.Novelty statement“What is already known?”- Socioeconomic status has been associated with a variety of exposures, but the influence on type 1 diabetes risk is unclear.“What this study has found?”- Our searches identified eight high-quality and several lower quality studies, mostly using socioeconomic status as a confounder. There was no consistent association between socioeconomic status and risk of childhood type 1 diabetes. No conclusions could be drawn for specific parental occupations.“What are the implications of the study?”-While there is a need for more high-quality studies, the existing literature does not suggest a major and consistent role of socioeconomic status in the risk of type 1 diabetes.
A novel widespread MITE element in the repeat-rich genome of theCardiniumendosymbiont of the spiderOedothorax gibbosus
Authors: Halter Tamara , Hendrickx Frederik , Horn Matthias , Manzano-Marín Alejandro 
Published: June 2022

ABSTRACTFree-living bacteria have evolved multiple times to become host-restricted endosymbionts. The transition from a free-living to a host-restricted lifestyle comes with a number of different genomic changes, including a massive loss of genes. In host-restricted endosymbionts, gene inactivation and genome reduction is facilitated by mobile genetic elements, mainly insertion sequences (ISs). ISs are small autonomous mobile elements, and one of, if not the most, abundant transposable elements in bacteria. Proliferation of ISs is common in some facultative endosymbionts, and is likely driven by the transmission bottlenecks, which increase the level of genetic drift. In the current study we present a manually curated genome annotation for aCardiniumendosymbiont of the dwarf spiderOedothorax gibbosus. Cardiniumspecies are host-restricted endosymbionts that, similarly toWolbachiaspp., include strains capable of manipulating host reproduction. Through the focus on mobile elements, the annotation revealed a rampant spread of ISs, extending earlier observations in otherCardiniumgenomes. We found that a large proportion of IS elements are actually pseudogenised, with many displaying evidence of recent inactivation. Most notably, we describe the lineage-specific emergence and spread of a novel IS-derivedMiniatureInverted repeatTransposableElement (MITE), likely being actively maintained by intact copies of its parental IS982-family element. This work highlights the relevance of manual curation of these repeat-rich endosymbiont genomes for the discovery of novel MITEs, as well as the possible role these understudied elements might play in genome streamlining.
Dynamic interplay of protrusive microtubule and contractile actomyosin forces drives tissue extension
Authors: Singh Amrita , Thale Sameedha , Leibner Tobias , Ricker Andrea , Nüsse Harald , Klingauf Jürgen , Ohlberger Mario , Matis Maja 
Published: June 2022

AbstractIn order to shape a tissue, cell-based mechanical forces have to be integrated into global force patterns. Over the last decades, the importance of actomyosin contractile arrays, which are the key constituents of various morphogenetic processes, has been established for many tissues. Intriguingly, recent studies demonstrate that the microtubule cytoskeleton mediates folding and elongation of the epithelial sheet during Drosophila morphogenesis, placing microtubule mechanics en par with actin-based processes. While these studies establish the importance of both cytoskeletal systems during cell and tissue rearrangements, a mechanistic explanation of their functional hierarchy is currently missing. Here, we dissect the individual roles of these two key generators of mechanical forces during epithelium elongation. We demonstrate that microtubules dictate cell shape changes and actomyosin refines them. Combining experimental and numerical approaches, we find that altering the microtubule and actomyosin functions results in predictable changes in tissue shape. We further show that planar polarized microtubule patterning is independent of cell geometry and actomyosin-based mechanics. These results support a hierarchical mechanism, whereby microtubule-based forces in some epithelial systems prime actomyosin-generated forces.
Antagonistic action of Siah2 and Pard3/JamC to promote germinal zone exit of differentiated cerebellar granule neurons by modulating Ntn1 signaling via Dcc
Authors: Laumonnerie Christophe , Shamambo Maleelo , Stabley Daniel R. , Lewis Tommy L. , Trivedi Niraj , Howell Danielle , Solecki David J 
Published: June 2022

SummaryGerminal zone (GZ) exit is at the top of a cascade of events promoting the maturation of neurons and their assembly into neuronal circuits. Developing neurons and their progenitors must interpret varied niche signals like morphogens, guidance molecules, extracellular matrix, or adhesive cues to navigate GZ occupancy. How newborn neurons integrate multiple cell-extrinsic niche cues with their cell-intrinsic machinery in exiting a GZ is unknown. We establish cooperation between cell polarity-regulated adhesion and Netrin-1 signaling comprises a coincidence detection circuit repelling maturing neurons from their GZ. In this circuit, the Partitioning defective 3 (Pard3) polarity protein and Junctional adhesion molecule-C (JAM-C) adhesion protein promote, while the Seven in absentia 2 (Siah2) ubiquitin ligase inhibits, Deleted in colorectal cancer (DCC) receptor surface recruitment to gate differentiation linked repulsion to GZ Netrin-1. These results demonstrate cell polarity as a central integrator of adhesive- and guidance cues cooperating to spur GZ exit.Highlights-Netrin1 expressed in the cerebellar GZ ranges from an attractive to repulsive cue depending on differentiation status or extracellular matrix context.-Modulation of DCC expression levels impacts the nature of the Netrin1 response and GZ occupancy status.-Siah2, Pard3, and JamC function to modulate responsiveness to purified Netrin1 and cooperate with Dcc to regulate GZ exit.-Pard3 and JamC promote both basal and Netrin1 stimulated DCC surface recruitment to control GZ exit and Netrin1 repulsion
Deep haplotype analyses of target-site resistance locusACCasein blackgrass enabled by pool-based amplicon sequencing
Authors: Kersten Sonja , Rabanal Fernando A. , Herrmann Johannes , Hess Martin , Kronenberg Zev N. , Schmid Karl , Weigel Detlef 
Published: June 2022

AbstractRapid adaptation of weeds to herbicide applications in agriculture through resistance development is a widespread phenomenon. In particular, the grassAlopecurus myosuroidesis an extremely problematic weed in cereal crops with the potential to manifest resistance in the course of only a few generations. Target-site resistances (TSRs), with their strong phenotypic response, play an important role in this rapid adaptive response. Recently, using PacBio’s long-read amplicon sequencing technology in hundreds of individuals, we were able to decipher the genomic context in which TSR mutations occur. However, sequencing individual amplicons is both costly and time consuming, thus impractical to implement for other resistance loci or applications. Alternatively, pool-based approaches overcome these limitations and provide reliable allele frequencies, albeit at the expense of not preserving haplotype information. In this proof-of-concept study, we sequenced with PacBio High Fidelity (HiFi) reads long-range amplicons (13.2 kb) encompassing the entireACCasegene in pools of over hundred individuals, and resolved them into haplotypes using the clustering algorithm PacBio amplicon analysis (pbaa), a new application for pools and for plants. From these amplicon pools, we were able to recover most haplotypes from previously sequenced individuals of the same population. In addition, we analyzed new pools from a Germany-wide collection ofA. myosuroidespopulations and found that TSR mutations originating from soft sweeps of independent origin were common. Forward-in-time simulations indicate that TSR haplotypes will persist for decades even at relatively low frequencies and without selection, pointing to the importance of accurate measurement of TSR haplotype prevalence for weed management.
Auxin-dependent acceleration of cell division rates regulates root growth at elevated temperature
Authors: Ai Haiyue , Bellstaedt Julia , Bartusch Kai Steffen , Eschen-Lippold Lennart , Babben Steve , Balcke Gerd Ulrich , Tissier Alain , Hause Bettina , Andersen Tonni Grube , Delker Carolin , Quint Marcel 
Published: June 2022

ABSTRACTRoots are highly plastic organs enabling plants to acclimate to a changing below-ground environment. In addition to abiotic factors like nutrients or mechanical resistance, plant roots also respond to temperature variation. Below the heat stress threshold,Arabidopsis thalianaseedlings react to elevated temperature by promoting primary root growth, possibly to reach deeper soil regions with potentially better water saturation. While above-ground thermomorphogenesis is enabled by thermo-sensitive cell elongation, it was unknown how temperature modulates root growth. We here show that roots are able to sense and respond to elevated temperature independent of shoot-derived signals. A yet unknown root thermosensor seems to employ auxin as a messenger to promote primary root growth. Growth is primarily achieved by accelerating cell division rates in the root apical meristem, likely maintained via temperature-sensitive organization of the polar auxin transport system. Hence, the primary cellular target of elevated ambient temperature differs fundamentally between root and shoot tissues, while the messenger auxin that relays temperature information to elongating or dividing cells, respectively, remains the same.
Rab7/Retromer-based endolysosomal trafficking facilitates effector secretion and host invasion in rice blast
Authors: Chen Xin , Selvaraj Poonguzhali , Lin Lili , Fang Wenqin , Wu Congxian , Yang Piao , Zhang Jing , Abubakar Yakubu Saddeeq , Yang Fan , Lu Guodong , Liu Wende , Wang Zonghua , Naqvi Naweed I. , Zheng Wenhui 
Published: June 2022

AbstractSecretion is a fundamental process in all living organisms. Using conventional secretion pathways, many plant pathogens release effectors into the host plants to downregulate immunity and promote infection. However, this does not always constitute the only way that effectors are sorted and tracked to their final destination such as the biotrophic interfacial complex-associated effectors produced by the blast fungus Magnaporthe oryzae. Here, we uncover a novel unconventional route originating from fungal vacuolar membrane to the host interface and plasma membrane. We found that a GFP-MoRab7 labeled vacuole is closely associated with the interface structure throughout M. oryzae invasive growth. Conditional inactivation of MoRab7 impaired the establishment of the biotrophy interface and secretion of Pwl2 effector. To perform the vacuolar trafficking pathway, MoRab7 first recruits the retromer complex to the vacuole membrane, enabling it recognizes a batch of SNARE proteins, including the v-SNARE MoSnc1. Live-cell imaging supports both retromer complex component and MoSnc1 protein labeled vesicles showing the trafficking dynamics toward the interface or plasma membrane, and then fusion with target membranes. Lastly, disruption of the MoRab7/Retromer/MoSnc1-based endolysosomal cascade affects effector secretion and fungal pathogenicity. Taken together, we discovered an unconventional protein and membrane trafficking route starting from the fungal endolysosomes to the M. oryzae-rice interaction interface, and dissect the role of MoRab7/Retromer/MoSnc1 constituent sorting machinery in effector secretion during invasive growth in M. oryzae.
Impact of daily octenidine skin washing on antiseptic tolerance of coagulase-negative staphylococci in two neonatal intensive care units with different bathing practices
Authors: Felgate Heather , Quinn Charlotte , Richardson Ben , Hudson Carol , Sethi Dheeraj , Oddie Sam , Clarke Paul , Webber Mark 
Published: June 2022

SummaryBackgroundCoagulase Negative Staphylococci (CoNS) are responsible for 80-90 % of catheter related sepsis in neonates which can cause life threatening and damaging effects. NICUs within the UK use various practices to decolonise neonates to prevent infection ranging from regular full body bathing to localised skin decontamination before insertion of indwelling devices. There is a disparity in bathing practices for infants admitted onto neonatal units, with some choosing to regularly bathe infants and others not, and some routinely washing with skin antiseptics, and others not.AimTo compare the abundance of CoNS within two UK NICUs with different approaches to skin bathing and to test their tolerances to antiseptics.MethodsA collection of CoNS from two UK based NICUs with differing bathing routines for neonates were collated and tested for susceptibility to the antiseptics in use, octenidine and chlorhexidine.FindingsRegular bathing of neonates in octenidine did not decrease the abundance of organisms on neonatal skin. Isolates from the unit where octenidine was in frequent use did not show any increased antiseptic tolerance. Isolates from the unit where regular bathing was not routine practice were less susceptible to both antiseptics.ConclusionFrequent whole-body skin washing with octenidine does not appear to result in a lasting reduction in numbers of organisms found on the skin but also does not appear to select for antiseptic tolerant CoNS.