bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutations associated with neuropsychiatric conditions delineate functional brain connectivity dimensions contributing to autism and schizophrenia
Authors: Moreau Clara A. , Urchs Sebastian G. W. , Kuldeep Kumar , Orban Pierre , Schramm Catherine , Dumas Guillaume , Labbe Aurélie , Huguet Guillaume , Douard Elise , Quirion Pierre-Olivier , Lin Amy , Kushan Leila , Grot Stephanie , Luck David , Mendrek Adrianna , Potvin Stephane , Stip Emmanuel , Bourgeron Thomas , Evans Alan C. , Bearden Carrie E. , Bellec Pierre , Jacquemont Sebastien 
Published: October 2020

Abstract16p11.2 and 22q11.2 Copy Number Variants (CNVs) confer high risk for Autism Spectrum Disorder (ASD), schizophrenia (SZ), and Attention-Deficit-Hyperactivity-Disorder (ADHD), but their impact on functional connectivity (FC) remains unclear. Here we report an analysis of resting-state FC using magnetic resonance imaging data from 101 CNV carriers, 755 individuals with idiopathic ASD, SZ, or ADHD and 1,072 controls. We characterize CNV FC-signatures and use them to identify dimensions contributing to complex idiopathic conditions. CNVs have large mirror effects on FC at the global and regional level. Thalamus, somatomotor, and posterior insula regions play a critical role in dysconnectivity shared across deletions, duplications, idiopathic ASD, SZ but not ADHD. Individuals with higher similarity to deletion FC-signatures exhibit worse cognitive and behavioral symptoms. Deletion similarities identified at the connectivity level could be related to the redundant associations observed genome-wide between gene expression spatial patterns and FC-signatures. Results may explain why many CNVs affect a similar range of neuropsychiatric symptoms.
Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance
Authors: Herold Malte , Martínez Arbas Susana , Narayanasamy Shaman , Sheik Abdul R. , Kleine-Borgmann Luise A. K. , Lebrun Laura A. , Kunath Benoît J. , Roume Hugo , Bessarab Irina , Williams Rohan B. H. , Gillece John D. , Schupp James M. , Keim Paul S. , Jäger Christian , Hoopmann Michael R. , Moritz Robert L. , Ye Yuzhen , Li Sujun , Tang Haixu , Heintz-Buschart Anna , May Patrick , Muller Emilie E. L. , Laczny Cedric C. , Wilmes Paul 
Published: October 2020

AbstractThe development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts.
Single-cell transcriptomics identifies divergent developmental lineage trajectories during human pituitary development
Authors: Zhang Shu , Cui Yueli , Ma Xinyi , Yong Jun , Yan Liying , Yang Ming , Ren Jie , Tang Fuchou , Wen Lu , Qiao Jie 
Published: October 2020

AbstractThe anterior pituitary gland plays a central role in regulating various physiological processes, including body growth, reproduction, metabolism and stress response. Here, we perform single-cell RNA-sequencing (scRNA-seq) of 4113 individual cells from human fetal pituitaries. We characterize divergent developmental trajectories with distinct transitional intermediate states in five hormone-producing cell lineages. Corticotropes exhibit an early intermediate state prior to full differentiation. Three cell types of the PIT-1 lineage (somatotropes, lactotropes and thyrotropes) segregate from a common progenitor coexpressing lineage-specific transcription factors of different sublineages. Gonadotropes experience two multistep developmental trajectories. Furthermore, we identify a fetal gonadotrope cell subtype expressing the primate-specific hormone chorionic gonadotropin. We also characterize the cellular heterogeneity of pituitary stem cells and identify a hybrid epithelial/mesenchymal state and an early-to-late state transition. Here, our results provide insights into the transcriptional landscape of human pituitary development, defining distinct cell substates and subtypes and illustrating transcription factor dynamics during cell fate commitment.
A streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics
Authors: Fang Pan , Ji Yanlong , Silbern Ivan , Doebele Carmen , Ninov Momchil , Lenz Christof , Oellerich Thomas , Pan Kuan-Ting , Urlaub Henning 
Published: October 2020

AbstractRegulation of protein N-glycosylation is essential in human cells. However, large-scale, accurate, and site-specific quantification of glycosylation is still technically challenging. We here introduce SugarQuant, an integrated mass spectrometry-based pipeline comprising protein aggregation capture (PAC)-based sample preparation, multi-notch MS3 acquisition (Glyco-SPS-MS3) and a data-processing tool (GlycoBinder) that enables confident identification and quantification of intact glycopeptides in complex biological samples. PAC significantly reduces sample-handling time without compromising sensitivity. Glyco-SPS-MS3 combines high-resolution MS2 and MS3 scans, resulting in enhanced reporter signals of isobaric mass tags, improved detection of N-glycopeptide fragments, and lowered interference in multiplexed quantification. GlycoBinder enables streamlined processing of Glyco-SPS-MS3 data, followed by a two-step database search, which increases the identification rates of glycopeptides by 22% compared with conventional strategies. We apply SugarQuant to identify and quantify more than 5,000 unique glycoforms in Burkitt’s lymphoma cells, and determine site-specific glycosylation changes that occurred upon inhibition of fucosylation at high confidence.
Pearl millet genomic vulnerability to climate change in West Africa highlights the need for regional collaboration
Authors: Rhoné Bénédicte , Defrance Dimitri , Berthouly-Salazar Cécile , Mariac Cédric , Cubry Philippe , Couderc Marie , Dequincey Anaïs , Assoumanne Aichatou , Kane Ndjido Ardo , Sultan Benjamin , Barnaud Adeline , Vigouroux Yves 
Published: October 2020

AbstractClimate change is already affecting agro-ecosystems and threatening food security by reducing crop productivity and increasing harvest uncertainty. Mobilizing crop diversity could be an efficient way to mitigate its impact. We test this hypothesis in pearl millet, a nutritious staple cereal cultivated in arid and low-fertility soils in sub-Saharan Africa. We analyze the genomic diversity of 173 landraces collected in West Africa together with an extensive climate dataset composed of metrics of agronomic importance. Mapping the pearl millet genomic vulnerability at the 2050 horizon based on the current genomic-climate relationships, we identify the northern edge of the current areas of cultivation of both early and late flowering varieties as being the most vulnerable to climate change. We predict that the most vulnerable areas will benefit from using landraces that already grow in equivalent climate conditions today. However, such seed-exchange scenarios will require long distance and trans-frontier assisted migrations. Leveraging genetic diversity as a climate mitigation strategy in West Africa will thus require regional collaboration.
A role for tectorial membrane mechanics in activating the cochlear amplifier
Authors: Nankali Amir , Wang Yi , Strimbu Clark Elliott , Olson Elizabeth S. , Grosh Karl 
Published: October 2020

AbstractThe mechanical and electrical responses of the mammalian cochlea to acoustic stimuli are nonlinear and highly tuned in frequency. This is due to the electromechanical properties of cochlear outer hair cells (OHCs). At each location along the cochlear spiral, the OHCs mediate an active process in which the sensory tissue motion is enhanced at frequencies close to the most sensitive frequency (called the characteristic frequency, CF). Previous experimental results showed an approximate 0.3 cycle phase shift in the OHC-generated extracellular voltage relative the basilar membrane displacement, which was initiated at a frequency approximately one-half octave lower than the CF. Findings in the present paper reinforce that result. This shift is significant because it brings the phase of the OHC-derived electromotile force near to that of the basilar membrane velocity at frequencies above the shift, thereby enabling the transfer of electrical to mechanical power at the basilar membrane. In order to seek a candidate physical mechanism for this phenomenon, we used a comprehensive electromechanical mathematical model of the cochlear response to sound. The model predicts the phase shift in the extracellular voltage referenced to the basilar membrane at a frequency approximately one-half octave below CF, in accordance with the experimental data. In the model, this feature arises from a minimum in the radial impedance of the tectorial membrane and its limbal attachment. These experimental and theoretical results are consistent with the hypothesis that a tectorial membrane resonance introduces the correct phasing between mechanical and electrical responses for power generation, effectively turning on the cochlear amplifier.
Codon optimization with deep learning to enhance protein expression
Authors: Fu Hongguang , Liang Yanbing , Zhong Xiuqin , Pan ZhiLing , Huang Lei , Zhang HaiLin , Xu Yang , Zhou Wei , Liu Zhong 
Published: October 2020

AbstractHeterologous expression is the main approach for recombinant protein production ingenetic synthesis, for which codon optimization is necessary. The existing optimization methods are based on biological indexes. In this paper, we propose a novel codon optimization method based on deep learning. First, we introduce the concept of codon boxes, via which DNA sequences can be recoded into codon box sequences while ignoring the order of bases. Then, the problem of codon optimization can be converted to sequence annotation of corresponding amino acids with codon boxes. The codon optimization models for Escherichia Coli were trained by the Bidirectional Long-Short-Term Memory Conditional Random Field. Theoretically, deep learning is a good method to obtain the distribution characteristics of DNA. In addition to the comparison of the codon adaptation index, protein expression experiments for plasmodium falciparum candidate vaccine and polymerase acidic protein were implemented for comparison with the original sequences and the optimized sequences from Genewiz and ThermoFisher. The results show that our method for enhancing protein expression is efficient and competitive.
Cardiovascular adaptation to simulated microgravity and countermeasure efficacy assessed by ballistocardiography and seismocardiography
Authors: Rabineau Jeremy , Hossein Amin , Landreani Federica , Haut Benoit , Mulder Edwin , Luchitskaya Elena , Tank Jens , Caiani Enrico G. , van de Borne Philippe , Migeotte Pierre-François 
Published: October 2020

AbstractHead-down bed rest (HDBR) reproduces the cardiovascular effects of microgravity. We tested the hypothesis that regular high-intensity physical exercise (JUMP) could prevent this cardiovascular deconditioning, which could be detected using seismocardiography (SCG) and ballistocardiography (BCG). 23 healthy males were exposed to 60-day HDBR: 12 in a physical exercise group (JUMP), the others in a control group (CTRL). SCG and BCG were measured during supine controlled breathing protocols. From the linear and rotational SCG/BCG signals, the integral of kinetic energy ($$iK$$

iK

) was computed on each dimension over the cardiac cycle. At the end of HDBR, BCG rotational $$iK$$

iK

and SCG transversal $$iK$$

iK

decreased similarly for all participants (− 40% and − 44%, respectively, p < 0.05), and so did orthostatic tolerance (− 58%, p < 0.01). Resting heart rate decreased in JUMP (− 10%, p < 0.01), but not in CTRL. BCG linear $$iK$$

iK

decreased in CTRL (− 50%, p < 0.05), but not in JUMP. The changes in the systolic component of BCG linear iK were correlated to those in stroke volume and VO2 max (R = 0.44 and 0.47, respectively, p < 0.05). JUMP was less affected by cardiovascular deconditioning, which could be detected by BCG in agreement with standard markers of the cardiovascular condition. This shows the potential of BCG to easily monitor cardiac deconditioning.
High-field superconductivity in C-doped MgB2 bulk samples prepared by a rapid synthesis route
Authors: Matera D. , Bonura M. , Černý R. , McKeown Walker S. , Buta F. , LeBoeuf D. , Chaud X. , Giannini E. , Senatore C. 
Published: October 2020

AbstractThe upper critical field sets the thermodynamic limit to superconductivity. A big gap is present between the upper-critical-field values measured in MgB2 polycrystalline bulk superconductors and those of thin films, where values as high as ~ 50 T have been achieved at 4.2 K. Filling this gap would unlock the potential of MgB2 for magnet applications. This work presents the results of an extensive experimental campaign on MgB2 bulk samples, which has been guided by a Design of Experiment. We modeled the dependence of the upper critical field on the main synthesis parameters and established a new record (~ 35 T at 4.2 K) preparing C-doped bulk samples by a non-conventional rapid-synthesis route. This value appears to be an upper boundary for the upper critical field in bulk samples. Structural disorder in films seems to act selectively on one of the two bands where superconductivity in MgB2 takes place: this enhances the upper critical field while reducing the critical temperature only by few Kelvins. On the other hand, the critical temperature in bulk samples decreases monotonically when structural disorder increases, and this imposes a limit to the maximum achievable upper critical field.
Riparian and in-channel habitat properties linked to dragonfly emergence
Authors: O’Malley Zoë G. , Compson Zacchaeus G. , Orlofske Jessica M. , Baird Donald J. , Curry R. Allen , Monk Wendy A. 
Published: October 2020

AbstractIn freshwater ecosystems, habitat alteration contributes directly to biodiversity loss. Dragonflies are sentinel species that are key invertebrate predators in both aquatic (as larvae) and terrestrial ecosystems (as adults). Understanding the habitat factors affecting dragonfly emergence can inform management practices to conserve habitats supporting these species and the functions they perform. Transitioning from larvae to adults, dragonflies leave behind larval exoskeletons (exuviae), which reveal information about the emergent population without the need for sacrificing living organisms. Capitalizing on Atlantic Canada’s largest freshwater wetland, the Grand Lake Meadows (GLM) and the associated Saint John/Wolastoq River (SJWR), we studied the spatial (i.e., across the mainstem, tributary, and wetland sites) and temporal (across 3 years) variation in assemblages of emergent dragonflies (Anisoptera) and assessed the relative contribution of aquatic and terrestrial factors structuring these assemblages. The GLM complex, including the lotic SJWR and its tributaries and associated lentic wetlands, provided a range of riparian and aquatic habitat variability ideal for studying dragonfly emergence patterns across a relatively homogenous climatic region. Emergent dragonfly responses were associated with spatial, but not temporal, variation. Additionally, dragonfly communities were associated with both aquatic and terrestrial factors, while diversity was primarily associated with terrestrial factors. Specific terrestrial factors associated with the emergence of the dragonfly community included canopy cover and slope, while aquatic factors included water temperature, dissolved oxygen, and baseflow. Our results indicate that management of river habitats for dragonfly conservation should incorporate riparian habitat protection while maintaining aquatic habitat and habitat quality.
Multiple mutations in the EPSPS and ALS genes of Amaranthus hybridus underlie resistance to glyphosate and ALS inhibitors
Authors: García Maria J. , Palma-Bautista Candelario , Vazquez-Garcia José G. , Rojano-Delgado Antonia M. , Osuna María D. , Torra Joel , De Prado Rafael 
Published: October 2020

AbstractAmaranthus hybridus is one of the main weed species in Córdoba, Argentina. Until recently, this weed was effectively controlled with recurrent use of glyphosate. However, a population exhibiting multiple resistance (MR2) to glyphosate and imazamox appeared in a glyphosate resistant (GR) soybean field, with levels of resistance up to 93 and 38-fold higher to glyphosate and imazamox, respectively compared to the susceptible (S) population. In addition to imidazolinones, MR2 plants showed high resistance levels to sulfonylamino-carbonyl (thio) benzoates and moderate resistance to sulfonylureas and triazolopyrimidines. Multiple amino acid substitutions were found in both target genes, acetolactate synthase (ALS) and 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), responsible for conferring high herbicides resistance levels in this A. hybridus population. In the case of EPSPS, the triple amino acid substitution TAP-IVS was found. In addition, MR2 plants also showed increased EPSPS gene expression compared to susceptible plants. A Ser653Asn substitution was found in the ALS sequence of MR2, explaining the pattern of cross-resistance to the ALS-inhibitor herbicide families found at the ALS enzyme activity level. No other mutations were found in other conserved domains of the ALS gene. This is the first report worldwide of the target site resistance mechanisms to glyphosate and ALS inhibitors in multiple herbicide resistance Amaranthus hybridus.
Health system utilization before age 1 among children later diagnosed with autism or ADHD
Authors: Engelhard Matthew M. , Berchuck Samuel I. , Garg Jyotsna , Henao Ricardo , Olson Andrew , Rusincovitch Shelley , Dawson Geraldine , Kollins Scott H. 
Published: October 2020

AbstractChildren with autism spectrum disorder (ASD) or attention deficit hyperactivity disorder (ADHD) have 2–3 times increased healthcare utilization and annual costs once diagnosed, but little is known about their utilization patterns early in life. Quantifying their early health system utilization could uncover condition-specific health trajectories to facilitate earlier detection and intervention. Patients born 10/1/2006–10/1/2016 with ≥ 2 well-child visits within the Duke University Health System before age 1 were grouped as ASD, ADHD, ASD + ADHD, or No Diagnosis using retrospective billing codes. An additional comparison group was defined by later upper respiratory infection diagnosis. Adjusted odds ratios (AOR) for hospital admissions, procedures, emergency department (ED) visits, and outpatient clinic encounters before age 1 were compared between groups via logistic regression models. Length of hospital encounters were compared between groups via Mann–Whitney U test. In total, 29,929 patients met study criteria (ASD N = 343; ADHD N = 1175; ASD + ADHD N = 140). ASD was associated with increased procedures (AOR = 1.5, p < 0.001), including intubation and ventilation (AOR = 2.4, p < 0.001); and outpatient specialty care, including physical therapy (AOR = 3.5, p < 0.001) and ophthalmology (AOR = 3.1, p < 0.001). ADHD was associated with increased procedures (AOR = 1.41, p < 0.001), including blood transfusion (AOR = 4.7, p < 0.001); hospital admission (AOR = 1.60, p < 0.001); and ED visits (AOR = 1.58, p < 0.001). Median length of stay was increased after birth in ASD (+ 6.5 h, p < 0.001) and ADHD (+ 3.8 h, p < 0.001), and after non-birth admission in ADHD (+ 1.1 d, p < 0.001) and ASD + ADHD (+ 2.4 d, p = 0.003). Each condition was associated with increased health system utilization and distinctive patterns of utilization before age 1. Recognizing these patterns may contribute to earlier detection and intervention.
New fossil from mid-Cretaceous Burmese amber confirms monophyly of Liadopsyllidae (Hemiptera: Psylloidea)
Authors: Drohojowska Jowita , Szwedo Jacek , Müller Patrick , Burckhardt Daniel 
Published: October 2020

AbstractAmecephala pusillagen. et sp. nov. is described and illustrated on the basis of a well-preserved female psyllid (Liadopsyllidae) in a piece of Cretaceous Myanmar amber. The new genus differs from other members of Liadopsyllidae in details of the antennae and forewings. For the first time, the presence of a circumanal ring is documented for Mesozoic psyllids. Based on differences in the length of female terminalia, it is suggested that Liadopsyllidae may have displayed a diversified oviposition biology. As far as known, Liadopsyllidae lack a pulvillus, a putative autapomorphy supporting the monophyly of Liadopsyllidae. An identification key to genera and an annotated checklist of known Liadopsyllidae species are provided. New synonyms and combinations are proposed and the status of the subfamily Miralinae is discussed.
Propagation of optically tunable coherent radiation in a gas of polar molecules
Authors: Gładysz Piotr , Wcisło Piotr , Słowik Karolina 
Published: October 2020

AbstractCoherent, optically dressed media composed of two-level molecular systems without inversion symmetry are considered as all-optically tunable sources of coherent radiation in the microwave domain. A theoretical model and a numerical toolbox are developed to confirm the main finding: the generation of low-frequency radiation, and the buildup and propagation dynamics of such low-frequency signals in a medium of polar molecules in a gas phase. The physical mechanism of the signal generation relies on the permanent dipole moment characterizing systems without inversion symmetry. The molecules are polarized with a DC electric field yielding a permanent electric dipole moment in the laboratory frame; the direction and magnitude of the moment depend on the molecular state. As the system is resonantly driven, the dipole moment oscillates at the Rabi frequency and, hence, generates microwave radiation. We demonstrate the tuning capability of the output signal frequency with the drive amplitude and detuning. We find that even though decoherence mechanisms such as spontaneous emission may damp the output field, a scenario based on pulsed illumination yields a coherent, pulsed output of tunable temporal width. Finally, we discuss experimental scenarios exploiting rotational levels of gaseous ensembles of heteronuclear diatomic molecules.