bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rare genetic susceptibility variants assessment in autism spectrum disorder: detection rate and practical use
Authors: Husson Thomas , Lecoquierre François , Cassinari Kevin , Charbonnier Camille , Quenez Olivier , Goldenberg Alice , Guerrot Anne-Marie , Richard Anne-Claire , Drouin-Garraud Valérie , Brehin Anne-Claire , Soleimani Maryam , Taton Romain , Rotharmel Maud , Rosier Antoine , Chambon Pascal , Le Meur Nathalie , Joly-Helas Géraldine , Saugier-Veber Pascale , Boland Anne , Deleuze Jean-François , Olaso Robert , Frebourg Thierry , Nicolas Gael , Guillin Olivier , Campion Dominique 
Published: February 2020

AbstractAutism spectrum disorder (ASD) is a neurodevelopmental disorder with a strong genetic component whose knowledge evolves quickly. Next-generation sequencing is the only effective technology to deal with the high genetic heterogeneity of ASD in a clinical setting. However, rigorous criteria to classify rare genetic variants conferring ASD susceptibility are currently lacking. We have performed whole-exome sequencing to identify both nucleotide variants and copy number variants (CNVs) in 253 ASD patients, including 68 patients with intellectual disability (ID) and 90 diagnosed as Asperger syndrome. Using explicit criteria to classify both susceptibility genes and susceptibility variants we prioritized 217 genes belonging to the following categories: syndromic genes, genes with an excess of de novo protein truncating variants and genes targeted by rare CNVs. We obtained a susceptibility variant detection rate of 19.7% (95% CI: [15–25.2%]). The rate for CNVs was 7.1% (95% CI: [4.3–11%]) and 12.6% (95% CI: [8.8–17.4%]) for nucleotide variants. The highest rate (30.1%, 95% CI: [20.2–43.2%]) was obtained in the ASD + ID subgroup. A strong contributor for at risk nucleotide variants was the recently identified set of genes (n = 81) harboring an excess of de novo protein truncating variants. Since there is currently no evidence that the genes targeted here are necessary and sufficient to cause ASD, we recommend to avoid the term “causative of ASD” when delivering the information about a variant to a family and to use instead the term “genetic susceptibility factor contributing to ASD”.
Fox Insight collects online, longitudinal patient-reported outcomes and genetic data on Parkinson’s disease
Authors: Smolensky Luba , Amondikar Ninad , Crawford Karen , Neu Scott , Kopil Catherine M. , Daeschler Margaret , Riley Lindsey ,   23andMe Research Team, Agee Michelle , Alipanahi Babak , Auton Adam , Bell Robert K. , Bryc Katarzyna , Cannon Paul , Clarke Sarah , Elson Sarah L. , Fonseca Peter , Fontanillas Pierre , Furlotte Nicholas A. , Hicks Barry , Hinds David A. , Heilbron Karl , Huber Karen E. , Jewett Ethan M. , Jiang Yunxuan , Kleinman Aaron , Lin Keng-Han , Litterman Nadia K. , Luff Marie , McIntyre Matthew H. , McManus Kimberly F. , Mountain Joanna L. , Noblin Elizabeth S. , Northover Carrie A. M. , Pitts Steven J. , Poznik G. David , Rowbotham Helen M. , Sathirapongsasuti J. Fah , Schloetter Madeleine , Shelton Janie F. , Shringarpure Suyash , Tian Chao , Tung Joyce Y. , Vacic Vladimir , Wang Xin , Wilson Catherine H. , Wojcicki Anne , Yu Linda P. C. , Brown Ethan , Toga Arthur W. , Tanner Caroline 
Published: February 2020

AbstractFox Insight is an online, longitudinal health study of people with and without Parkinson’s disease with targeted enrollment set to at least 125,000 individuals. Fox Insight data is a rich data set facilitating discovery, validation, and reproducibility in Parkinson’s disease research. The dataset is generated through routine longitudinal assessments (health and medical questionnaires evaluated at regular cycles), one-time questionnaires about environmental exposure and healthcare preferences, and genetic data collection. Qualified Researchers can explore, analyze, and download patient-reported outcomes (PROs) data and Parkinson’s disease- related genetic variants at https://foxden.michaeljfox.org. The full Fox Insight genetic data set, including approximately 600,000 single nucleotide polymorphisms (SNPs), can be requested separately with institutional review and are described outside of this data descriptor.
Impact of multisection and immunohistochemistry in lymph node staging of Gastric Carcinoma – Case series
Authors: Santos Fernando A. V. , Drummond-Lage Ana P. , Wainstein Alberto J. A. , Dias-Filho Marco A. , Savassi-Rocha Paulo R. , Navarro Tulio P. 
Published: February 2020

AbstractGastric carcinoma (GC) locoregional recurrence may occur even in cases where the tumor has been completely resected, possibly due to lymph node (LN) micrometastases. It is estimated that in 10% to 30% of cases, LN micrometastases are not detected by a conventional method for histological assessment of LN metastases with hematoxylin-eosin (HE). A cross-sectional study assessed 51 patients with GC by histological evaluation of the LN micrometastases through LN multi sectioning associated with immunohistochemistry analysis with monoclonal antibodies AE1 and AE3. Total gastrectomy was performed in 51% of patients. The total number of resected LN nodes was 1698, with a mean number of resected LN of 33.3 ± 13.2 per surgical specimen, of which 187 had metastasis. After the application of LN multisection and immunohistochemistry, LN micrometastases were found in 45.1% of the cases. LN staging changed in 29.4%, and tumor staging changed in 23.5% of the cases. In patients initially staged as pN0, LN staging and tumor staging changed, both in 19.2% of the cases. In patients initially staged as pN1 or more, LN staging changed in 40.0% of them, and tumor staging changed in 28.0% of the cases. The accuracy of HE for the histological staging of LN tumoral involvement was 76%, which was considered insufficient for CG patients staging. Investigation of LN micrometastasis through LN multisection and immunohistochemistry should be performed, particularly in cases where the presence of blood and lymphatic vessel invasion has been identified after conventional histological analysis, as well as in patients with advanced GC.
Biocarbon from peanut hulls and their green composites with biobased poly(trimethylene terephthalate) (PTT)
Authors: Picard Maisyn , Thakur Suman , Misra Manjusri , Mielewski Deborah F. , Mohanty Amar K. 
Published: February 2020

AbstractThere are millions of tons of post-food processing residues discarded annually. Currently, these waste materials are discarded to landfill, used as animal feed or incinerated. This suggests that there are potential uses for these materials in value-added applications. This work focuses on the characterization and valorization of peanut hulls through the generation of green composites. Peanut hulls were pyrolyzed at 500 °C and analyzed to discover their unique surface morphology and relatively low ash content. Raman spectral analysis determined ID/IG values of 0.74 for the samples, suggesting greater graphitic content than disordered carbon content. Such results were confirmed in X-ray diffraction analysis by the presence of (002) and (100) planes. Partially biobased engineering thermoplastic, poly(trimethylene terephthalate) (PTT), was combined with 20 wt.% biocarbon. The tensile and flexural moduli improved with the addition of biocarbon, and the bio-content increased from 35 to 48 wt.% as compared to neat PTT. The higher temperature biocarbon was found to have superior performance over the lower temperature sample. The enhanced sustainability of these materials suggested that peanut hulls can be valorized via thermochemical conversion to generate value-added products. Future works could focus on the optimization of these materials for non-structural automotive components or electrical housings.
Nitrogen supply modulates nitrogen remobilization and nitrogen use of wheat under supplemental irrigation in the North China Plain
Authors: Zheng Xuejiao , Yu Zhenwen , Zhang Yongli , Shi Yu 
Published: February 2020

AbstractExcessive nitrogen (N) input and irrigation exacerbate N leaching in winter wheat production in the North China Plain (NCP). To explore the optimal N for better N remobilization and higher N utilization of wheat under water-saving irrigation will be conductive to less environmental contamination. A field experiment was conducted at 300 (N300), 240 (N240), 180 (N180), and 0 (N0) kg N ha−1 of N application under supplemental irrigation (SI) that brought the relative soil water content (RSWC) to 70% at jointing and 65% at anthesis. Compared with N0, N180 improved the free amino acid content in the flag leaf and grain after anthesis, dry matter and plant N accumulation at maturity, N translocation amount of vegetable organs and its contribution to grain from anthesis to maturity. Compared to N240 and N300, N180 increased the N translocation efficiency of vegetable organs, and reduced the soil NO3-N residue in the 60–180 cm soil layer, which contributing to no significant reduction in grain yield and grain protein yield, but higher grain N recovery efficiency (GREN), N recovery efficiency (REN), and N partial factor productivity (PFPN). Positive relationships were found between leaf N translocation efficiency and grain yield, grain protein yield, PFPN, GREN, and REN. Therefore, N180 is appropriate to obtain a steady grain yield over 7.5 t ha−1 for at least 2 years under SI based on RSWC in the NCP.
Crows control working memory before and after stimulus encoding
Authors: Fongaro Erica , Rose Jonas 
Published: February 2020

AbstractThe capacity of working memory is limited and this limit is comparable in crows and primates. To maximize this resource, humans use attention to select only relevant information for maintenance. Interestingly, attention-cues are effective not only before but also after the presentation of to-be-remembered stimuli, highlighting control mechanisms beyond sensory selection. Here we explore if crows are also capable of these forms of control over working memory. Two crows (Corvus corone) were trained to memorize two, four or six visual stimuli. Comparable to our previous results, the crows showed a decrease in performance with increasing working memory load. Using attention cues, we indicated the critical stimulus on a given trial. These cues were either presented before (pre-cue) or after sample-presentation (retro-cue). On other trials no cue was given as to which stimulus was critical. We found that both pre- and retro-cues enhance the performance of the birds. These results show that crows, like humans, can utilize attention to select relevant stimuli for maintenance in working memory. Importantly, crows can also utilize cues to make the most of their working memory capacity even after the stimuli are already held in working memory. This strongly implies that crows can engage in efficient control over working memory.
SiGe nanocrystals in SiO2 with high photosensitivity from visible to short-wave infrared
Authors: Stavarache Ionel , Logofatu Constantin , Sultan Muhammad Taha , Manolescu Andrei , Svavarsson Halldor Gudfinnur , Teodorescu Valentin Serban , Ciurea Magdalena Lidia 
Published: February 2020

AbstractFilms of SiGe nanocrystals (NCs) in oxide have the advantage of tuning the energy band gap by adjusting SiGe NCs composition and size. In this study, SiGe-SiO2 amorphous films were deposited by magnetron sputtering on Si substrate followed by rapid thermal annealing at 700, 800 and 1000 °C. We investigated films with Si:Ge:SiO2 compositions of 25:25:50 vol.% and 5:45:50 vol.%. TEM investigations reveal the major changes in films morphology (SiGe NCs with different sizes and densities) produced by Si:Ge ratio and annealing temperature. XPS also show that the film depth profile of SiGe content is dependent on the annealing temperature. These changes strongly influence electrical and photoconduction properties. Depending on annealing temperature and Si:Ge ratio, photocurrents can be 103 times higher than dark currents. The photocurrent cutoff wavelength obtained on samples with 25:25 vol% SiGe ratio decreases with annealing temperature increase from 1260 nm in SWIR for 700 °C annealed films to 1210 nm for those at 1000 °C. By increasing Ge content in SiGe (5:45 vol%) the cutoff wavelength significantly shifts to 1345 nm (800 °C annealing). By performing measurements at 100 K, the cutoff wavelength extends in SWIR to 1630 nm having high photoresponsivity of 9.35 AW−1.
A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns
Authors: Marsland Robert , Cui Wenping , Mehta Pankaj 
Published: February 2020

AbstractSurveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these patterns to identify the ecological processes shaping microbial ecosystems. One promising approach is to use minimal models that can relate mechanistic assumptions at the microbe scale to community-level patterns. Here, we demonstrate the utility of this approach by showing that the Microbial Consumer Resource Model (MiCRM) – a minimal model for microbial communities with resource competition, metabolic crossfeeding and stochastic colonization – can qualitatively reproduce patterns found in survey data including compositional gradients, dissimilarity/overlap correlations, richness/harshness correlations, and nestedness of community composition. By using the MiCRM to generate synthetic data with different environmental and taxonomical structure, we show that large scale patterns in the EMP can be reproduced by considering the energetic cost of surviving in harsh environments and HMP patterns may reflect the importance of environmental filtering in shaping competition. We also show that recently discovered dissimilarity-overlap correlations in the HMP likely arise from communities that share similar environments rather than reflecting universal dynamics. We identify ecologically meaningful changes in parameters that alter or destroy each one of these patterns, suggesting new mechanistic hypotheses for further investigation. These findings highlight the promise of minimal models for microbial ecology.
A genome-wide association study in mice reveals a role for Rhbdf2 in skeletal homeostasis
Authors: Levy Roei , Levet Clemence , Cohen Keren , Freeman Matthew , Mott Richard , Iraqi Fuad , Gabet Yankel 
Published: February 2020

AbstractLow bone mass and an increased risk of fracture are predictors of osteoporosis. Individuals who share the same bone-mineral density (BMD) vary in their fracture risk, suggesting that microstructural architecture is an important determinant of skeletal strength. Here, we utilized the rich diversity of the Collaborative Cross mice to identify putative causal genes that contribute to the risk of fractures. Using microcomputed tomography, we examined key structural features that pertain to bone quality in the femoral cortical and trabecular compartments of male and female mice. We estimated the broad-sense heritability to be 50–60% for all examined traits, and we identified five quantitative trait loci (QTL) significantly associated with six traits. We refined each QTL by combining information inferred from the ancestry of the mice, ranging from RNA-Seq data and published literature to shortlist candidate genes. We found strong evidence for new candidate genes, particularly Rhbdf2, whose close association with the trabecular bone volume fraction and number was strongly suggested by our analyses. We confirmed our findings with mRNA expression assays of Rhbdf2 in extreme-phenotype mice, and by phenotyping bones of Rhbdf2 knockout mice. Our results indicate that Rhbdf2 plays a decisive role in bone mass accrual and microarchitecture.
Laterals take it better – Emerging and young lateral roots survive lethal salinity longer than the primary root in Arabidopsis
Authors: Ambastha Vivek , Friedmann Yael , Leshem Yehoram 
Published: February 2020

AbstractPlant responses to salinity have been extensively studied over the last decades. Despite the vast accumulated knowledge, the ways Arabidopsis lateral roots (LR) cope with lethal salinity has not been fully resolved. Here we compared the primary root (PR) and the LR responses during events leading to lethal salinity (NaCl 200 mM) in Arabidopsis. We found that the PR and young LR responded differently to lethal salinity: While the PR died, emerging and young LR’s remained strikingly viable. Moreover, “age acquired salt tolerance” (AAST) was observed in the PR. During the 2 days after germination (DAG) the PR was highly sensitive, but at 8 DAG there was a significant increase in the PR cell survival. Nevertheless, the young LR exhibited an opposite pattern and completely lost its salinity tolerance, as it elongated beyond 400 µm. Examination of several cell death signatures investigated in the young LR showed no signs of an active programmed cell death (PCD) during lethal salinity. However, Autophagic PCD (A-PCD) but not apoptosis-like PCD (AL-PCD) was found to be activated in the PR during the high salinity conditions. We further found that salinity induced NADPH oxidase activated ROS, which were more highly distributed in the young LR compared to the PR, is required for the improved viability of the LR during lethal salinity conditions. Our data demonstrated a position-dependent resistance of Arabidopsis young LR to high salinity. This response can lead to identification of novel salt stress coping mechanisms needed by agriculture during the soil salinization challenge.
A novelty-retrieval-extinction paradigm leads to persistent attenuation of remote fear memories
Authors: Huang Fulian , Zou Guangjing , Li Can , Meng Hui , Liu Xiaoyan , Yang Zehua 
Published: February 2020

AbstractExposure to a novel environment can enhance the extinction of recent contextual fear in mice. This has been explained by a tagging and capture hypothesis. Consistently, we show in mice that exposure to a novel environment before extinction training promoted the extinction of recent auditory fear. However, such a promoting effect of novelty was absent for remote memories. In the present study, we replaced the regular extinction training with a retrieval-extinction session which capitalized on a reconsolidation window. When novelty exposure was followed by a retrieval-extinction session, remote fear was distinguished more easily and permanently. We have termed it as a “novelty-retrieval-extinction” paradigm. This paradigm played a greater role in the extinction of remote fear when fear conditioning and retrieval-extinction occurred in two different contexts other than in one identical context. The mechanism underlying the facilitating effect of this paradigm might involve up-regulation of histone acetylation in the hippocampus, which has been reported to increase functional and structural neuroplasticity. The present work proposes an effective, drug-free paradigm for the extinction of remote fear, which could be easily adapted in humans with least side effects.
Transcriptome analyses reveal the synergistic effects of feeding and eyestalk ablation on ovarian maturation in black tiger shrimp
Authors: Sittikankaew Kanchana , Pootakham Wirulda , Sonthirod Chutima , Sangsrakru Duangjai , Yoocha Thippawan , Khudet Jutatip , Nookaew Intawat , Uawisetwathana Umaporn , Rungrassamee Wanilada , Karoonuthaisiri Nitsara 
Published: February 2020

AbstractUnilateral eyestalk ablation in the female black tiger shrimpPenaeus monodonis commonly employed to induce ovarian maturation. However, the importance of complementing this practice with the provision of live feed supplement (such as polychaetes) has not been emphasized in previous studies. Indeed, it has been less emphasized that female broodstock must be fed with live feeds such as polychaetes for this practice to be effective. While the effects of eyestalk ablation have been thoroughly studied in various aspects, the synergistic effects of feeding with live feeds and the ablation have never been elucidated at a transcriptome-wide level. With recent advances in the next-generation sequencing platforms, it is now possible to investigate the effects of eyestalk ablation and live feeds at the transcriptomic levels. This study employed both short-read Illumina RNA sequencing and long-read Pacific Biosciences (PacBio) isoform sequencing (Iso-seq) to generate the first high-quality ovarian reference transcriptome inP.monodon. This novel assembly allowed us to dissect the effects of feeds and eyestalk ablation and reveal their synergistic effects at the transcriptomic level through the regulation of important genes involved in fatty acid regulation, energy production, and hormone-mediated oocyte maturation pathways. The synergistic effects between the polychaete feeding and the eyestalk ablation in the process of ovarian maturation in black tiger shrimp suggest that without having proper nutrients from the polychaetes, female broodstock might not be ready to develop its ovary. However, even with proper nutrients, the eyestalk ablation is still necessary to perhaps manipulate the female endocrine of the black tiger shrimp. These findings shed the light on molecular mechanisms and key molecular pathways that lead to successful ovarian maturation.
Emergence of global synchronization in directed excitatory networks of type I neurons
Authors: Ziaeemehr Abolfazl , Zarei Mina , Sheshbolouki Aida 
Published: February 2020

AbstractThe collective behaviour of neural networks depends on the cellular and synaptic properties of the neurons. The phase-response curve (PRC) is an experimentally obtainable measure of cellular properties that quantifies the shift in the next spike time of a neuron as a function of the phase at which stimulus is delivered to that neuron. The neuronal PRCs can be classified as having either purely positive values (type I) or distinct positive and negative regions (type II). Networks of type 1 PRCs tend not to synchronize via mutual excitatory synaptic connections. We study the synchronization properties of identical type I and type II neurons, assuming unidirectional synapses. Performing the linear stability analysis and the numerical simulation of the extended Kuramoto model, we show that feedforward loop motifs favour synchronization of type I excitatory and inhibitory neurons, while feedback loop motifs destroy their synchronization tendency. Moreover, large directed networks, either without feedback motifs or with many of them, have been constructed from the same undirected backbones, and a high synchronization level is observed for directed acyclic graphs with type I neurons. It has been shown that, the synchronizability of type I neurons depends on both the directionality of the network connectivity and the topology of its undirected backbone. The abundance of feedforward motifs enhances the synchronizability of the directed acyclic graphs.