bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stem rust resistance in wheat is suppressed by a subunit of the mediator complex
Authors: Hiebert Colin W. , Moscou Matthew J. , Hewitt Tim , Steuernagel Burkhard , Hernández-Pinzón Inma , Green Phon , Pujol Vincent , Zhang Peng , Rouse Matthew N. , Jin Yue , McIntosh Robert A. , Upadhyaya Narayana , Zhang Jianping , Bhavani Sridhar , Vrána Jan , Karafiátová Miroslava , Huang Li , Fetch Tom , Doležel Jaroslav , Wulff Brande B. H. , Lagudah Evans , Spielmeyer Wolfgang 
Published: February 2020

AbstractStem rust is an important disease of wheat that can be controlled using resistance genes. The geneSuSr-D1identified in cultivar ‘Canthatch’ suppresses stem rust resistance.SuSr-D1mutants are resistant to several races of stem rust that are virulent on wild-type plants. Here we identifySuSr-D1by sequencing flow-sorted chromosomes, mutagenesis, and map-based cloning. The gene encodes Med15, a subunit of the Mediator Complex, a conserved protein complex in eukaryotes that regulates expression of protein-coding genes. Nonsense mutations in Med15b.D result in expression of stem rust resistance. Time-course RNAseq analysis show a significant reduction or complete loss of differential gene expression at 24 h post inoculation inmed15b.Dmutants, suggesting that transcriptional reprogramming at this time point is not required for immunity to stem rust. Suppression is a common phenomenon and this study provides novel insight into suppression of rust resistance in wheat.
Vertical eddy iron fluxes support primary production in the open Southern Ocean
Authors: Uchida Takaya , Balwada Dhruv , P. Abernathey Ryan , A. McKinley Galen , K. Smith Shafer , Lévy Marina 
Published: February 2020

AbstractThe primary productivity of the Southern Ocean ecosystem is limited by iron availability. Away from benthic and aeolian sources, iron reaches phytoplankton primarily when iron-rich subsurface waters enter the euphotic zone. Here, eddy-resolving physical/biogeochemical simulations of a seasonally-forced, open-Southern-Ocean ecosystem reveal that mesoscale and submesoscale isopycnal stirring effects a cross-mixed-layer-base transport of iron that sustains primary productivity. The eddy-driven iron supply and consequently productivity increase with model resolution. We show the eddy flux can be represented by specific well-tuned eddy parametrizations. Since eddy mixing rates are sensitive to wind forcing and large-scale hydrographic changes, these findings suggest a new mechanism for modulating the Southern Ocean biological pump on climate timescales.
A 3D printing approach toward targeted intervention in telerehabilitation
Authors: Barak Ventura Roni , Rizzo Alessandro , Nov Oded , Porfiri Maurizio 
Published: February 2020

AbstractNeuromuscular impairment requires adherence to a rehabilitation regimen for maximum recovery of motor function. Consumer-grade game controllers have emerged as a viable means to relay supervised physical therapy to patients’ homes, thereby increasing their accessibility to healthcare. These controllers allow patients to perform exercise frequently and improve their rehabilitation outcomes. However, the non-universal design of game controllers targets healthy people and does not always accommodate people with disability. Consequently, many patients experience considerable difficulty assuming certain hand postures and performing the prescribed exercise correctly. Here, we explore the feasibility of improving rehabilitation outcomes through a 3D printing approach that enhances off-the-shelf game controllers in home therapy. Specifically, a custom attachment was 3D printed for a commercial haptic device that mediates fine motor rehabilitation. In an experimental study, 25 healthy subjects performed a navigation task, with the retrofit attachment and without it, while simulating disability of the upper limb. When using the attachment, subjects extended their wrist range of motion, yet maintained their level of compensation. The subjects also showed higher motivation to repeat the exercise with the enhanced device. The results bring forward evidence for the potential of this approach in transforming game controllers toward targeted interventions in home therapy.
Enrichment and characterisation of ethanol chain elongating communities from natural and engineered environments
Authors: Candry Pieter , Huang Shengle , Carvajal-Arroyo José Maria , Rabaey Korneel , Ganigue Ramon 
Published: February 2020

AbstractChain elongation is a microbial process in which an electron donor, such as ethanol, is used to elongate short chain carboxylic acids, such as acetic acid, to medium chain carboxylic acids. This metabolism has been extensively investigated, but the spread and differentiation of chain elongators in the environment remains unexplored. Here, chain elongating communities were enriched from several inocula (3 anaerobic digesters, 2 animal faeces and 1 caproic acid producing environment) using ethanol and acetic acid as substrates at pH 7 and 5.5. This approach showed that (i) the inoculum’s origin determines the pH where native chain elongators can grow; (ii) pH affects caproic acid production, with average caproic acid concentrations of 6.4 ± 1.6  g·L−1 at pH 7, versus 2.3 ± 1.8  g·L−1 at pH 5.5; however (iii) pH does not affect growth rates significantly; (iv) all communities contained a close relative of the known chain elongator Clostridium kluyveri; and (v) low pH selects for communities more enriched in this Clostridium kluyveri-relative (57.6 ± 23.2% at pH 7, 96.9 ± 1.2% at pH 5.5). These observations show that ethanol-consuming chain elongators can be found in several natural and engineered environments, but are not the same everywhere, emphasising the need for careful inoculum selection during process development.
T-cell subset abnormalities predict progression along the Inflammatory Arthritis disease continuum: implications for management
Authors: Ponchel Frederique , Burska Agata N. , Hunt Laura , Gul Hanna , Rabin Thibault , Parmar Rekha , Buch Maya H. , Conaghan Philip G. , Emery Paul 
Published: February 2020

AbstractThe presence of a disease continuum in inflammatory arthritis (IA) is a recognised concept, with distinct stages from at-risk stage (presence of anti citrullinated-peptide autoantibody) to diagnosis of rheumatoid arthritis (RA), including therapy-induced remission. Despite T-cell dysregulation being a key feature of RA, there are few reports of T-cell phenotyping along the IA-continuum. We investigated the disturbances of naïve, regulatory and inflammation related cell (IRC) CD4+ T-cell subsets in 705 individuals across the IA-continuum, developing a simple risk-score (summing presence/absence of a risk-associated with a subset) to predict progression from one stage to the next. In 158 at-risk individuals, the 3 subsets had individual association with progression to IA and the risk-score was highly predictive (p < 0.0001). In evolving IA patients, 219/294 developed RA; the risk-score included naïve and/or Treg and predicted progression (p < 0.0001). In 120 untreated RA patients, the risk-score for predicting treatment-induced remission using naïve T-cells had an odds ratio of 15.4 (p < 0.0001). In RA patients in treatment-induced remission, a score using naïve T-cells predicted disease flare (p < 0.0001). Evaluating the risk of progression using naïve CD4+ T-cells was predictive of progression along the whole IA-continuum. This should allow identification of individuals at high-risk of progression, permitting targeted therapy for improved outcomes.
Artificial shaking signals in honey bee colonies elicit natural responses
Authors: Koenig Phoebe A. , Smith Michael L. , Horowitz Logan H. , Palmer Daniel M. , Petersen Kirstin H. 
Published: February 2020

AbstractHoney bee signals are primarily studied through natural observation combined with manipulations of the colony or environment, not direct manipulation of the signal stimulus or receivers. Consequently, we know little about which signal aspects are necessary to reproduce behavioral responses. Here, we focus on the shaking signal, wherein a worker grabs onto another bee and vibrates. All castes receive shaking signals, but individual responses depend on context, and the signal may be multi-modal (mechanical, odor, sound, etc.). We designed a tool to mimic the shaking signal. We tested whether a purely mechanical stimulus elicited the same behavioral response as a natural shaking signal, teasing apart the effects of signal and receiver characteristics. We found that both workers and drones increased their movement after being artificially shaken, and that shaken drones were more likely to engage in feeding and grooming than a sham control. These behavioral changes support the idea that the shaking signal serves to generally increase worker activity, but also serves to activate male reproductives (drones). With this tool, we show that vibration itself is responsible for eliciting much of the shaking signal’s behavioral response, in one of the few examples of direct playback in social insects.
Antibody transcytosis across brain endothelial-like cells occurs nonspecifically and independent of FcRn
Authors: Ruano-Salguero John S. , Lee Kelvin H. 
Published: February 2020

AbstractThe blood-brain barrier (BBB) hinders the brain delivery of therapeutic immunoglobulin γ (IgG) antibodies. Evidence suggests that IgG-specific processing occurs within the endothelium of the BBB, but any influence on transcytosis remains unclear. Here, involvement of the neonatal Fc receptor (FcRn), which mediates IgG recycling and transcytosis in peripheral endothelium, was investigated by evaluating the transcytosis of IgGs with native or reduced FcRn engagement across human induced pluripotent stem cell-derived brain endothelial-like cells. Despite differential trafficking, the permeability of all tested IgGs were comparable and remained constant irrespective of concentration or competition with excess IgG, suggesting IgG transcytosis occurs nonspecifically and originates from fluid-phase endocytosis. Comparison with the receptor-enhanced permeability of transferrin indicates that the phenomena observed for IgG is ubiquitous for most macromolecules. However, increased permeability was observed for macromolecules with biophysical properties known to engage alternative endocytosis mechanisms, highlighting the importance of biophysical characterizations in assessing transcytosis mechanisms.
No association of complement mannose-binding lectin deficiency with cardiovascular disease in patients with Systemic Lupus Erythematosus
Authors: Kieninger-Gräfitsch A. , Vogt S. , Ribi C. , Dubler D. , Chizzolini C. , Huynh-Do U. , Osthoff M. , Trendelenburg M. 
Published: February 2020

AbstractCardiovascular (CV) morbidity is the major cause of death in patients with Systemic Lupus Erythematosus (SLE). Previous studies on mannose-binding lectin (MBL) gene polymorphisms in SLE patients suggest that low levels of complement MBL are associated with cardiovascular disease (CVD). However, as large studies on MBL deficiency based on resulting MBL plasma concentrations are lacking, the aim of our study was to analyze the association of MBL concentrations with CVD in SLE patients. Plasma MBL levels SLE patients included in the Swiss SLE Cohort Study were quantified by ELISA. Five different CV organ manifestations were documented. Of 373 included patients (85.5% female) 62 patients had at least one CV manifestation. Patients with MBL deficiency (levels below 500 ng/ml or 1000 ng/ml) had no significantly increased frequency of CVD (19.4% vs. 15.2%, P = 0.3 or 17.7% vs. 15.7%, P = 0.7). After adjustment for traditional CV risk factors, MBL levels and positive antiphospholipid serology (APL+) a significant association of CVD with age, hypertension, disease duration and APL+ was demonstrated. In our study of a large cohort of patients with SLE, we could not confirm previous studies suggesting MBL deficiency to be associated with an increased risk for CVD.
Genetic assignment of illegally trafficked neotropical primates and implications for reintroduction programs
Authors: Oklander Luciana Inés , Caputo Mariela , Solari Agustín , Corach Daniel 
Published: February 2020

AbstractThe black and gold howler monkey (Alouatta caraya) is a neotropical primate threatened by habitat loss and capture for illegal trade in Argentina. Using multilocus microsatellite genotypes from 178 A. carayaindividuals sampled from 15 localities in Argentina, we built a genotype reference database (GRDB). Bayesian assignment methods applied to the GRDB allowed us to correctly re-assign 73% of individuals to their true location of origin and 93.3% to their cluster of origin. We used the GRDB to assign 22 confiscated individuals (17 of which were reintroduced), and 3 corpses to both localities and clusters of origin. We assigned with a probability >70% the locality of origin of 14 individuals and the cluster of origin of 21. We found that most of the confiscated individuals were assigned to one cluster (F-Ch-C) and two localities included in the GRDB, suggesting that traffickedA. carayaprimarily originated in this area. Our results reveal that only 4 of 17 reintroduced individuals were released in sites corresponding to their cluster of origin. Our findings illustrate the applicability of genotype databases for inferring hotspots of illegal capture and for guiding future reintroduction efforts, both of which are essential elements of species protection and recovery programs.
The genetics of situs inversus without primary ciliary dyskinesia
Authors: Postema Merel C. , Carrion-Castillo Amaia , Fisher Simon E. , Vingerhoets Guy , Francks Clyde 
Published: February 2020

AbstractSitus inversus (SI), a left-right mirror reversal of the visceral organs, can occur with recessive Primary Ciliary Dyskinesia (PCD). However, most people with SI do not have PCD, and the etiology of their condition remains poorly studied. We sequenced the genomes of 15 people with SI, of which six had PCD, as well as 15 controls. Subjects with non-PCD SI in this sample had an elevated rate of left-handedness (five out of nine), which suggested possible developmental mechanisms linking brain and body laterality. The six SI subjects with PCD all had likely recessive mutations in genes already known to cause PCD. Two non-PCD SI cases also had recessive mutations in known PCD genes, suggesting reduced penetrance for PCD in some SI cases. One non-PCD SI case had recessive mutations in PKD1L1, and another in CFAP52 (also known as WDR16). Both of these genes have previously been linked to SI without PCD. However, five of the nine non-PCD SI cases, including three of the left-handers in this dataset, had no obvious monogenic basis for their condition. Environmental influences, or possible random effects in early development, must be considered.
A xylan glucuronosyltransferase gene exhibits pleiotropic effects on cellular composition and leaf development in rice
Authors: Gao Dawei , Sun Wenqiang , Wang Dianwen , Dong Hualin , Zhang Ran , Yu Sibin 
Published: February 2020

AbstractLeaf chlorophyll content is an important physiological indicator of plant growth, metabolism and nutritional status, and it is highly correlated with leaf nitrogen content and photosynthesis. In this study, we report the cloning and identification of a xylan glucuronosyltransferase gene (OsGUX1) that affects relative chlorophyll content in rice leaf. Using a set of chromosomal segment substitution lines derived from a cross of wild rice accession ACC10 and indica variety Zhenshan 97 (ZS97), we identified numerous quantitative trait loci for relative chlorophyll content. One major locus of them for relative chlorophyll content was mapped to a 10.3-kb region that contains OsGUX1. The allele OsGUX1AC from ACC10 significantly decreases nitrogen content and chlorophyll content of leaf compared with OsGUX1ZS from ZS97. The overexpression of OsGUX1 reduced chlorophyll content, and the suppression of this gene increased chlorophyll content of rice leaf. OsGUX1 is located in Golgi apparatus, and highly expressed in seedling leaf and the tissues in which primary cell wall synthesis occurring. Our experimental data indicate that OsGUX1 is responsible for addition of glucuronic acid residues onto xylan and participates in accumulation of cellulose and hemicellulose in the cell wall deposition, thus thickening the primary cell wall of mesophyll cells, which might lead to reduced chlorophyll content in rice leaf. These findings provide insights into the association of cell wall components with leaf nitrogen content in rice.
Genomic alterations and abnormal expression of APE2 in multiple cancers
Authors: Jensen Katherine A. , Shi Xinghua , Yan Shan 
Published: February 2020

AbstractAlthough APE2 plays essential roles in base excision repair and ATR-Chk1 DNA damage response (DDR) pathways, it remains unknown how the APE2 gene is altered in the human genome and whether APE2 is differentially expressed in cancer patients. Here, we report multiple-cancer analyses of APE2 genomic alterations and mRNA expression from cancer patients using available data from The Cancer Genome Atlas (TCGA). We observe that APE2 genomic alterations occur at ~17% frequency in 14 cancer types (n = 21,769). Most frequent somatic mutations of APE2 appear in uterus (2.89%) and skin (2.47%) tumor samples. Furthermore, APE2 expression is upregulated in tumor tissue compared with matched non-malignant tissue across 5 cancer types including kidney, breast, lung, liver, and uterine cancers, but not in prostate cancer. We also examine the mRNA expression of 13 other DNA repair and DDR genes from matched samples for 6 cancer types. We show that APE2 mRNA expression is positively correlated with PCNA, APE1, XRCC1, PARP1, Chk1, and Chk2 across these 6 tumor tissue types; however, groupings of other DNA repair and DDR genes are correlated with APE2 with different patterns in different cancer types. Taken together, this study demonstrates alterations and abnormal expression of APE2 from multiple cancers.
Layer-specific sensory processing impairment in the primary somatosensory cortex after motor cortex infarction
Authors: Fukui Atsushi , Osaki Hironobu , Ueta Yoshifumi , Kobayashi Kenta , Muragaki Yoshihiro , Kawamata Takakazu , Miyata Mariko 
Published: February 2020

AbstractPrimary motor cortex (M1) infarctions sometimes cause sensory impairment. Because sensory signals play a vital role in motor control, sensory impairment compromises the recovery and rehabilitation of motor disability. However, the neural mechanism of the sensory impairment is poorly understood. We show that sensory processing in mouse primary somatosensory cortex (S1) was impaired in the acute phase of M1 infarctions and recovered in a layer-specific manner in the subacute phase. This layer-dependent recovery process and the anatomical connection pattern from M1 to S1 suggested that functional connectivity from M1 to S1 plays a key role in the sensory processing impairment. A simulation study demonstrated that the loss of inhibition from M1 to S1 in the acute phase of M1 infarctions could impair sensory processing in S1, and compensation for the inhibition could recover the temporal coding. Consistently, the optogenetic activation of M1 suppressed the sustained response in S1. Taken together, we revealed how focal stroke in M1 alters the cortical network activity of sensory processing, in which inhibitory input from M1 to S1 may be involved.
Imaging active faulting in the western Taiwan Strait
Authors: Zhang Yifeng , Kuo-Chen Hao , Alvarez-Marron Joaquina , Brown Dennis , Lin Andrew Tien-Shun , Xie Zhizhao , Jin Xing 
Published: February 2020

AbstractLarge, destructive historical earthquakes off the coast of China’s Fujian Province point to important tectonic activity in the western Taiwan Strait that, until recently, has received little attention. We present newly acquired reflection seismic data that is used to study the shallow crustal structure of the western Taiwan Strait. With these data we map the location of the Benhai fault for the first time, describe its upper crustal geometry and, in combination with seismicity and earthquake focal mechanisms, interpret its kinematics. These new data demonstrate that there is wide spread evidence of faulting that reaches the sea floor in the western Taiwan Strait, clearly indicating that the Benhai fault is active. Faults that cut up section from steep basin sidewalls to form flower structures or terraced sidewall fault zones, together with the fault and basin map pattern, are consistent with this fault zone being in the early developmental stages of a dextral strike-slip system. Earthquake focal mechanisms, although not definitive, support the model of an active dextral strike-slip fault system in the western Taiwan Strait.
Identification of significant gene biomarkers of low back pain caused by changes in the osmotic pressure of nucleus pulposus cells
Authors: Zhao Changsong , Quan Xuemin , He Jie , Zhao Rugang , Zhang Yao , Li Xin , Sun Sheng , Ma Rui , Zhang Qiang 
Published: February 2020

AbstractThe incidence of intervertebral disc (IVD) degeneration disease, caused by changes in the osmotic pressure of nucleus pulposus (NP) cells, increases with age. In general, low back pain is associated with IVD degeneration. However, the mechanism and molecular target of low back pain have not been elucidated, and there are no data suggesting specific biomarkers of low back pain. Therefore, the research aims to identify and verify the significant gene biomarkers of low back pain. The differentially expressed genes (DEGs) were screened in the Gene Expression Omnibus (GEO) database, and the identification and analysis of significant gene biomarkers were also performed with various bioinformatics programs. A total of 120 patients with low back pain were recruited. Before surgery, the degree of pain was measured by the numeric rating scale (NRS), which enables comparison of the pain scores from individuals. After surgery, IVD tissues were obtained, and NP cells were isolated. The NP cells were cultured in two various osmotic media, including iso-osmotic media (293 mOsm/kg H2O) to account for the morbid environment of NP cells in IVD degeneration disease and hyper-osmotic media (450 mOsm/kg H2O) to account for the normal condition of NP cells in healthy individuals. The relative mRNA expression levels of CCL5, OPRL1, CXCL13, and SST were measured by quantitative real-time PCR in thein vitroanalysis of the osmotic pressure experiments. Finally, correlation analysis and a neural network module were employed to explore the linkage between significant gene biomarkers and pain. A total of 371 DEGs were identified, including 128 downregulated genes and 243 upregulated genes. Furthermore, the four genes (CCL5, OPRL1, SST, and CXCL13) were identified as significant gene biomarkers of low back pain (P < 0.001) based on univariate linear regression, and CCL5 (odds ratio, 34.667; P = 0.003) and OPRL1 (odds ratio, 19.875; P < 0.001) were significantly related to low back pain through multivariate logistic regression. The expression of CCL5 and OPRL1 might be correlated with low back pain in patients with IVD degeneration disease caused by changes in the osmotic pressure of NP cells.