bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits
Authors: Lu Jiangjie , Luo Meifang , Wang Li , Li Kunpeng , Yu Yongyi , Yang Weifei , Gong Pichang , Gao Huihui , Li Qiaoru , Zhao Jing , Wu Lanfeng , Zhang Mingshu , Liu Xueyang , Zhang Xuemei , Zhang Xian , Kang Jieyu , Yu Tongyuan , Li Zhimin , Jiao Yuannian , Wang Huizhong , He Chaoying 
Published: November 2021

AbstractThe fruits of Physalis (Solanaceae) have a unique structure, a lantern-like fruiting calyx known as inflated calyx syndrome (ICS) or the Chinese lantern, and are rich in steroid-related compounds. However, the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown. Here, we present a high-quality chromosome-level reference genome assembly of Physalis floridana (~1.40 Gb in size) with a contig N50 of ~4.87 Mb. Through evolutionary genomics and experimental approaches, we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that, together with the previously revealed mutation affecting floral MPF2 expression, might have contributed to the origination of ICS in Physaleae, suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation. Moreover, the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits. The results reveal the importance of gene gains (duplication) and/or subsequent losses as genetic bases of the evolution of distinct fruit traits, and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.
An infant case of pseudohypoaldosteronism type1A caused by a novel NR3C2 variant
Authors: Noda Saki , Aoyama Kohei , Kondo Yuto , Okamura Jun , Suzuki Atsushi , Yamaguchi Naoya , Yoshida Aya , Miyake Yoshishige 
Published: November 2021

AbstractPseudohypoaldosteronism type1A (PHA1A) is the renal form of pseudohypoaldosteronism with autosomal dominant inheritance. PHA1A is caused by haploinsufficiency of the mineralocorticoid receptor, which is encoded by NR3C2. We encountered an infant who was diagnosed with PHA1A due to hyponatremia, hyperkalemia, and poor weight gain in the neonatal period. She carried a novel heterozygous mutation (NM_000901.5: c.1757 + 1 G > C) in the splice donor site of IVS-2 in NR3C2.
Orbital torque in magnetic bilayers
Authors: Lee Dongjoon , Go Dongwook , Park Hyeon-Jong , Jeong Wonmin , Ko Hye-Won , Yun Deokhyun , Jo Daegeun , Lee Soogil , Go Gyungchoon , Oh Jung Hyun , Kim Kab-Jin , Park Byong-Guk , Min Byoung-Chul , Koo Hyun Cheol , Lee Hyun-Woo , Lee OukJae , Lee Kyung-Jin 
Published: November 2021

AbstractThe orbital Hall effect describes the generation of the orbital current flowing in a perpendicular direction to an external electric field, analogous to the spin Hall effect. As the orbital current carries the angular momentum as the spin current does, injection of the orbital current into a ferromagnet can result in torque on the magnetization, which provides a way to detect the orbital Hall effect. With this motivation, we examine the current-induced spin-orbit torques in various ferromagnet/heavy metal bilayers by theory and experiment. Analysis of the magnetic torque reveals the presence of the contribution from the orbital Hall effect in the heavy metal, which competes with the contribution from the spin Hall effect. In particular, we find that the net torque in Ni/Ta bilayers is opposite in sign to the spin Hall theory prediction but instead consistent with the orbital Hall theory, which unambiguously confirms the orbital torque generated by the orbital Hall effect. Our finding opens a possibility of utilizing the orbital current for spintronic device applications, and it will invigorate researches on spin-orbit-coupled phenomena based on orbital engineering.
Model-based assessment of Chikungunya and O’nyong-nyong virus circulation in Mali in a serological cross-reactivity context
Authors: Hozé Nathanaël , Diarra Issa , Sangaré Abdoul Karim , Pastorino Boris , Pezzi Laura , Kouriba Bourèma , Sagara Issaka , Dabo Abdoulaye , Djimdé Abdoulaye , Thera Mahamadou Ali , Doumbo Ogobara K. , de Lamballerie Xavier , Cauchemez Simon 
Published: November 2021

AbstractSerological surveys are essential to quantify immunity in a population but serological cross-reactivity often impairs estimates of the seroprevalence. Here, we show that modeling helps addressing this key challenge by considering the important cross-reactivity between Chikungunya (CHIKV) and O’nyong-nyong virus (ONNV) as a case study. We develop a statistical model to assess the epidemiology of these viruses in Mali. We additionally calibrate the model with paired virus neutralization titers in the French West Indies, a region with known CHIKV circulation but no ONNV. In Mali, the model estimate of ONNV and CHIKV prevalence is 30% and 13%, respectively, versus 27% and 2% in non-adjusted estimates. While a CHIKV infection induces an ONNV response in 80% of cases, an ONNV infection leads to a cross-reactive CHIKV response in only 22% of cases. Our study shows the importance of conducting serological assays on multiple cross-reactive pathogens to estimate levels of virus circulation.
Multispecies and individual gas molecule detection using Stokes solitons in a graphene over-modal microresonator
Authors: Tan Teng , Yuan Zhongye , Zhang Hao , Yan Guofeng , Zhou Siyu , An Ning , Peng Bo , Soavi Giancarlo , Rao Yunjiang , Yao Baicheng 
Published: November 2021

AbstractSoliton frequency combs generate equally-distant frequencies, offering a powerful tool for fast and accurate measurements over broad spectral ranges. The generation of solitons in microresonators can further improve the compactness of comb sources. However the geometry and the material’s inertness of pristine microresonators limit their potential in applications such as gas molecule detection. Here, we realize a two-dimensional-material functionalized microcomb sensor by asymmetrically depositing graphene in an over-modal microsphere. By using one single pump, spectrally trapped Stokes solitons belonging to distinct transverse mode families are co-generated in one single device. Such Stokes solitons with locked repetition rate but different offsets produce ultrasensitive beat notes in the electrical domain, offering unique advantages for selective and individual gas molecule detection. Moreover, the stable nature of the solitons enables us to trace the frequency shift of the dual-soliton beat-note with uncertainty <0.2 Hz and to achieve real-time individual gas molecule detection in vacuum, via an optoelectronic heterodyne detection scheme. This combination of atomically thin materials and microcombs shows the potential for compact photonic sensing with high performances and offers insights toward the design of versatile functionalized microcavity photonic devices.
Ecdysone regulates Drosophila wing disc size via a TORC1 dependent mechanism
Authors: Strassburger Katrin , Lutz Marilena , Müller Sandra , Teleman Aurelio A. 
Published: November 2021

AbstractMost cells in a developing organ stop proliferating when the organ reaches a correct, final size. The underlying molecular mechanisms are not understood. We find that in Drosophila the hormone ecdysone controls wing disc size. To study how ecdysone affects wing size, we inhibit endogenous ecdysone synthesis and feed larvae exogenous ecdysone in a dose-controlled manner. For any given ecdysone dose, discs stop proliferating at a particular size, with higher doses enabling discs to reach larger sizes. Termination of proliferation coincides with a drop in TORC1, but not Dpp or Yki signaling. Reactivating TORC1 bypasses the termination of proliferation, indicating that TORC1 is a main downstream effector causing proliferation termination at the maximal ecdysone-dependent size. Experimental manipulation of Dpp or Yki signaling can bypass proliferation termination in hinge and notum regions, but not the pouch, suggesting that the mechanisms regulating proliferation termination may be distinct in different disc regions.
Mapping propagation of collective modes in Bi2Se3 and Bi2Te2.2Se0.8 topological insulators by near-field terahertz nanoscopy
Authors: Pogna Eva Arianna Aurelia , Viti Leonardo , Politano Antonio , Brambilla Massimo , Scamarcio Gaetano , Vitiello Miriam Serena 
Published: November 2021

AbstractNear-field microscopy discloses a peculiar potential to explore novel quantum state of matter at the nanoscale, providing an intriguing playground to investigate, locally, carrier dynamics or propagation of photoexcited modes as plasmons, phonons, plasmon-polaritons or phonon-polaritons. Here, we exploit a combination of hyperspectral time domain spectroscopy nano-imaging and detectorless scattering near-field optical microscopy, at multiple terahertz frequencies, to explore the rich physics of layered topological insulators as Bi2Se3 and Bi2Te2.2Se0.8, hyperbolic materials with topologically protected surface states. By mapping the near-field scattering signal from a set of thin flakes of Bi2Se3 and Bi2Te2.2Se0.8 of various thicknesses, we shed light on the nature of the collective modes dominating their optical response in the 2-3 THz range. We capture snapshots of the activation of transverse and longitudinal optical phonons and reveal the propagation of sub-diffractional hyperbolic phonon-polariton modes influenced by the Dirac plasmons arising from the topological surface states and of bulk plasmons, prospecting new research directions in plasmonics, tailored nanophotonics, spintronics and quantum technologies.
Overactivated transport in the localized phase of the superconductor-insulator transition
Authors: Humbert V. , Ortuño M. , Somoza A. M. , Bergé L. , Dumoulin L. , Marrache-Kikuchi C. A. 
Published: November 2021

AbstractBeyond a critical disorder, two-dimensional (2D) superconductors become insulating. In this Superconductor-Insulator Transition (SIT), the nature of the insulator is still controversial. Here, we present an extensive experimental study on insulating NbxSi1−x close to the SIT, as well as corresponding numerical simulations of the electrical conductivity. At low temperatures, we show that electronic transport is activated and dominated by charging energies. The sample thickness variation results in a large spread of activation temperatures, fine-tuned via disorder. We show numerically and experimentally that this originates from the localization length varying exponentially with thickness. At the lowest temperatures, there is an increase in activation energy related to the temperature at which this overactivated regime is observed. This relation, observed in many 2D systems shows that conduction is dominated by single charges that have to overcome the gap when entering superconducting grains.
Proteogenomic discovery of neoantigens facilitates personalized multi-antigen targeted T cell immunotherapy for brain tumors
Authors: Rivero-Hinojosa Samuel , Grant Melanie , Panigrahi Aswini , Zhang Huizhen , Caisova Veronika , Bollard Catherine M. , Rood Brian R. 
Published: November 2021

AbstractNeoantigen discovery in pediatric brain tumors is hampered by their low mutational burden and scant tissue availability. Here we develop a proteogenomic approach combining tumor DNA/RNA sequencing and mass spectrometry proteomics to identify tumor-restricted (neoantigen) peptides arising from multiple genomic aberrations to generate a highly target-specific, autologous, personalized T cell immunotherapy. Our data indicate that aberrant splice junctions are the primary source of neoantigens in medulloblastoma, a common pediatric brain tumor. Proteogenomically identified tumor-specific peptides are immunogenic and generate MHC II-based T cell responses. Moreover, polyclonal and polyfunctional T cells specific for tumor-specific peptides effectively eliminate tumor cells in vitro. Targeting tumor-specific antigens obviates the issue of central immune tolerance while potentially providing a safety margin favoring combination with other immune-activating therapies. These findings demonstrate the proteogenomic discovery of immunogenic tumor-specific peptides and lay the groundwork for personalized targeted T cell therapies for children with brain tumors.
Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo
Authors: Lähnemann David , Köster Johannes , Fischer Ute , Borkhardt Arndt , McHardy Alice C. , Schönhuth Alexander 
Published: November 2021

AbstractAccurate single cell mutational profiles can reveal genomic cell-to-cell heterogeneity. However, sequencing libraries suitable for genotyping require whole genome amplification, which introduces allelic bias and copy errors. The resulting data violates assumptions of variant callers developed for bulk sequencing. Thus, only dedicated models accounting for amplification bias and errors can provide accurate calls. We present ProSolo for calling single nucleotide variants from multiple displacement amplified (MDA) single cell DNA sequencing data. ProSolo probabilistically models a single cell jointly with a bulk sequencing sample and integrates all relevant MDA biases in a site-specific and scalable—because computationally efficient—manner. This achieves a higher accuracy in calling and genotyping single nucleotide variants in single cells in comparison to state-of-the-art tools and supports imputation of insufficiently covered genotypes, when downstream tools cannot handle missing data. Moreover, ProSolo implements the first approach to control the false discovery rate reliably and flexibly. ProSolo is implemented in an extendable framework, with code and usage at: https://github.com/prosolo/prosolo
Mechanochemical synthesis of magnesium-based carbon nucleophiles in air and their use in organic synthesis
Authors: Takahashi Rina , Hu Anqi , Gao Pan , Gao Yunpeng , Pang Yadong , Seo Tamae , Jiang Julong , Maeda Satoshi , Takaya Hikaru , Kubota Koji , Ito Hajime 
Published: November 2021

AbstractSince the discovery of Grignard reagents in 1900, the nucleophilic addition of magnesium-based carbon nucleophiles to various electrophiles has become one of the most powerful, versatile, and well-established methods for the formation of carbon−carbon bonds in organic synthesis. Grignard reagents are typically prepared via reactions between organic halides and magnesium metal in a solvent. However, this method usually requires the use of dry organic solvents, long reaction times, strict control of the reaction temperature, and inert-gas-line techniques. Despite the utility of Grignard reagents, these requirements still represent major drawbacks from both an environmental and an economic perspective, and often cause reproducibility problems. Here, we report the general mechanochemical synthesis of magnesium-based carbon nucleophiles (Grignard reagents in paste form) in air using a ball milling technique. These nucleophiles can be used directly for one-pot nucleophilic addition reactions with various electrophiles and nickel-catalyzed cross-coupling reactions under solvent-free conditions.
ABHD5 inhibits YAP-induced c-Met overexpression and colon cancer cell stemness via suppressing YAP methylation
Authors: Gu Yan , Chen Yanrong , Wei Lai , Wu Shuang , Shen Kaicheng , Liu Chengxiang , Dong Yan , Zhao Yang , Zhang Yue , Zhang Chi , Zheng Wenling , He Jiangyi , Wang Yunlong , Li Yifei , Zhao Xiaoxin , Wang Hongwei , Tan Jun , Wang Liting , Zhou Qi , Xie Ganfeng , Liang Houjie , Ou Juanjuan 
Published: November 2021

AbstractCancer stemness represents a major source of development and progression of colorectal cancer (CRC). c-Met critically contributes to CRC stemness, but how c-Met is activated in CRC remains elusive. We previously identified the lipolytic factor ABHD5 as an important tumour suppressor gene in CRC. Here, we show that loss of ABHD5 promotes c-Met activation to sustain CRC stemness in a non-canonical manner. Mechanistically, we demonstrate that ABHD5 interacts in the cytoplasm with the core subunit of the SET1A methyltransferase complex, DPY30, thereby inhibiting the nuclear translocation of DPY30 and activity of SET1A. In the absence of ABHD5, DPY30 translocates to the nucleus and supports SET1A-mediated methylation of YAP and histone H3, which sequesters YAP in the nucleus and increases chromatin accessibility to synergistically promote YAP-induced transcription of c-Met, thus promoting the stemness of CRC cells. This study reveals a novel role of ABHD5 in regulating histone/non-histone methylation and CRC stemness.
Repeated exposure with short-term behavioral stress resolves pre-existing stress-induced depressive-like behavior in mice
Authors: Lee Eun-Hwa , Park Jin-Young , Kwon Hye-Jin , Han Pyung-Lim 
Published: November 2021

AbstractChronic stress induces adaptive changes in the brain via the cumulative action of glucocorticoids, which is associated with mood disorders. Here we show that repeated daily five-minute restraint resolves pre-existing stress-induced depressive-like behavior in mice. Repeated injection of glucocorticoids in low doses mimics the anti-depressive effects of short-term stress. Repeated exposure to short-term stress and injection of glucocorticoids activate neurons in largely overlapping regions of the brain, as shown by c-Fos staining, and reverse distinct stress-induced gene expression profiles. Chemogenetic inhibition of neurons in the prelimbic cortex projecting to the nucleus accumbens, basolateral amygdala, or bed nucleus of the stria terminalis results in anti-depressive effects similarly to short-term stress exposure, while only inhibition of neurons in the prelimbic cortex projecting to the bed nucleus of the stria terminalis rescues defective glucocorticoid release. In summary, we show that short-term stress can reverse adaptively altered stress gains and resolve stress-induced depressive-like behavior.
A model of tension-induced fiber growth predicts white matter organization during brain folding
Authors: Garcia Kara E. , Wang Xiaojie , Kroenke Christopher D. 
Published: November 2021

AbstractThe past decade has experienced renewed interest in the physical processes that fold the developing cerebral cortex. Biomechanical models and experiments suggest that growth of the cortex, outpacing growth of underlying subcortical tissue (prospective white matter), is sufficient to induce folding. However, current models do not explain the well-established links between white matter organization and fold morphology, nor do they consider subcortical remodeling that occurs during the period of folding. Here we propose a framework by which cortical folding may induce subcortical fiber growth and organization. Simulations incorporating stress-induced fiber elongation indicate that subcortical stresses resulting from folding are sufficient to induce stereotyped fiber organization beneath gyri and sulci. Model predictions are supported by high-resolution ex vivo diffusion tensor imaging of the developing rhesus macaque brain. Together, results provide support for the theory of cortical growth-induced folding and indicate that mechanical feedback plays a significant role in brain connectivity.
Magnetization dependent tunneling conductance of ferromagnetic barriers
Authors: Wang Zhe , Gutiérrez-Lezama Ignacio , Dumcenco Dumitru , Ubrig Nicolas , Taniguchi Takashi , Watanabe Kenji , Giannini Enrico , Gibertini Marco , Morpurgo Alberto F. 
Published: November 2021

AbstractRecent experiments on van der Waals antiferromagnets have shown that measuring the temperature (T) and magnetic field (H) dependence of the conductance allows their magnetic phase diagram to be mapped. Similarly, experiments on ferromagnetic CrBr3 barriers enabled the Curie temperature to be determined at H = 0, but a precise interpretation of the magnetoconductance data at H ≠ 0 is conceptually more complex, because at finite H there is no well-defined phase boundary. Here we perform systematic transport measurements on CrBr3 barriers and show that the tunneling magnetoconductance depends on H and T exclusively through the magnetization M(H, T) over the entire temperature range investigated. The phenomenon is reproduced by the spin-dependent Fowler–Nordheim model for tunneling, and is a direct manifestation of the spin splitting of the CrBr3 conduction band. Our analysis unveils a new approach to probe quantitatively different properties of atomically thin ferromagnetic insulators related to their magnetization by performing simple conductance measurements.
Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma
Authors: Phillips Darci , Matusiak Magdalena , Gutierrez Belén Rivero , Bhate Salil S. , Barlow Graham L. , Jiang Sizun , Demeter Janos , Smythe Kimberly S. , Pierce Robert H. , Fling Steven P. , Ramchurren Nirasha , Cheever Martin A. , Goltsev Yury , West Robert B. , Khodadoust Michael S. , Kim Youn H. , Schürch Christian M. , Nolan Garry P. 
Published: November 2021

AbstractCutaneous T cell lymphomas (CTCL) are rare but aggressive cancers without effective treatments. While a subset of patients derive benefit from PD-1 blockade, there is a critically unmet need for predictive biomarkers of response. Herein, we perform CODEX multiplexed tissue imaging and RNA sequencing on 70 tumor regions from 14 advanced CTCL patients enrolled in a pembrolizumab clinical trial (NCT02243579). We find no differences in the frequencies of immune or tumor cells between responders and non-responders. Instead, we identify topographical differences between effector PD-1+ CD4+ T cells, tumor cells, and immunosuppressive Tregs, from which we derive a spatial biomarker, termed the SpatialScore, that correlates strongly with pembrolizumab response in CTCL. The SpatialScore coincides with differences in the functional immune state of the tumor microenvironment, T cell function, and tumor cell-specific chemokine recruitment and is validated using a simplified, clinically accessible tissue imaging platform. Collectively, these results provide a paradigm for investigating the spatial balance of effector and suppressive T cell activity and broadly leveraging this biomarker approach to inform the clinical use of immunotherapies.
Psychological stress impairs IL22-driven protective gut mucosal immunity against colonising pathobionts
Authors: Shaler Christopher R. , Parco Alexandra A. , Elhenawy Wael , Dourka Jasmeen , Jury Jennifer , Verdu Elena F. , Coombes Brian K. 
Published: November 2021

AbstractCrohn’s disease is an inflammatory disease of the gastrointestinal tract characterized by an aberrant response to microbial and environmental triggers. This includes an altered microbiome dominated by Enterobacteriaceae and in particular adherent-invasive E. coli (AIEC). Clinical evidence implicates periods of psychological stress in Crohn’s disease exacerbation, and disturbances in the gut microbiome might contribute to the pathogenic mechanism. Here we show that stress-exposed mice develop ileal dysbiosis, dominated by the expansion of Enterobacteriaceae. In an AIEC colonisation model, stress-induced glucocorticoids promote apoptosis of CD45+CD90+ cells that normally produce IL-22, a cytokine that is essential for the maintenance of ileal mucosal barrier integrity. Blockade of glucocorticoid signaling or administration of recombinant IL-22 restores mucosal immunity, prevents ileal dysbiosis, and blocks AIEC expansion. We conclude that psychological stress impairs IL-22-driven protective immunity in the gut, which creates a favorable niche for the expansion of pathobionts that have been implicated in Crohn’s disease. Importantly, this work also shows that immunomodulation can counteract the negative effects of psychological stress on gut immunity and hence disease-associated dysbiosis.