bluuebunny/crossref_metadata_2025_split huggingface dataset:
miR-23a/b suppress cGAS-mediated innate and autoimmunity
Authors: Yu Qiuya , Chu Lei , Li Yongxing , Wang Quanyi , Zhu Juanjuan , Wang Chen , Cui Shufang 
Published: March 2021

AbstractCyclic GMP-AMP synthase (cGAS), a key sensor of intracellular DNA, is essential for eliciting innate immunity against infection, whereas aberrant activation of cGAS by endogenous DNA promotes severe autoimmune diseases. However, it is largely unknown how cGAS expression is regulated during pathogen infection and autoimmunity. Here, we report that during herpes simplex virus type 1 (HSV-1) infection, two microRNAs (miR-23a and miR-23b) whose levels significantly decrease due to their interaction with the lncRNA Oasl2-209 directly regulate the expression of cGAS. Overexpression of miR-23a/b markedly dampens cytosolic DNA-induced innate immune responses, whereas inhibition of miR-23a/b enhances these responses. Mice treated with miR-23a/b agomirs exhibit increased susceptibility to HSV-1 infection. Moreover, cGAS is significantly upregulated in the Trex1−/− mouse autoimmune disease model. Administration of miR-23a/b blunts self DNA-induced autoinflammatory responses in Trex1−/− mice. Collectively, our study not only reveals a novel regulatory mechanism of cGAS expression by miRNAs but also identifies a potential therapy for cGAS-related autoimmune diseases.
Manganese salts function as potent adjuvants
Authors: Zhang Rui , Wang Chenguang , Guan Yukun , Wei Xiaoming , Sha Mengyin , Yi Mengran , Jing Miao , Lv Mengze , Guo Wen , Xu Jing , Wan Yi , Jia Xin-Ming , Jiang Zhengfan 
Published: March 2021

AbstractAluminum-containing adjuvants have been used for nearly 100 years to enhance immune responses in billions of doses of vaccines. To date, only a few adjuvants have been approved for use in humans, among which aluminum-containing adjuvants are the only ones widely used. However, the medical need for potent and safe adjuvants is currently continuously increasing, especially those triggering cellular immune responses for cytotoxic T lymphocyte activation, which are urgently needed for the development of efficient virus and cancer vaccines. Manganese is an essential micronutrient required for diverse biological activities, but its functions in immunity remain undefined. We previously reported that Mn2+ is important in the host defense against cytosolic dsDNA by facilitating cGAS-STING activation and that Mn2+ alone directly activates cGAS independent of dsDNA, leading to an unconventional catalytic synthesis of 2′3′-cGAMP. Herein, we found that Mn2+ strongly promoted immune responses by facilitating antigen uptake, presentation, and germinal center formation via both cGAS-STING and NLRP3 activation. Accordingly, a colloidal manganese salt (Mn jelly, MnJ) was formulated to act not only as an immune potentiator but also as a delivery system to stimulate humoral and cellular immune responses, inducing antibody production and CD4+/CD8+ T-cell proliferation and activation by either intramuscular or intranasal immunization. When administered intranasally, MnJ also worked as a mucosal adjuvant, inducing high levels of secretory IgA. MnJ showed good adjuvant effects for all tested antigens, including T cell-dependent and T cell-independent antigens, such as bacterial capsular polysaccharides, thus indicating that it is a promising adjuvant candidate.
Design of buried charged networks in artificial proteins
Authors: Baumgart Mona , Röpke Michael , Mühlbauer Max E. , Asami Sam , Mader Sophie L. , Fredriksson Kai , Groll Michael , Gamiz-Hernandez Ana P. , Kaila Ville R. I. 
Published: March 2021

AbstractSoluble proteins are universally packed with a hydrophobic core and a polar surface that drive the protein folding process. Yet charged networks within the central protein core are often indispensable for the biological function. Here, we show that natural buried ion-pairs are stabilised by amphiphilic residues that electrostatically shield the charged motif from its surroundings to gain structural stability. To explore this effect, we build artificial proteins with buried ion-pairs by combining directed computational design and biophysical experiments. Our findings illustrate how perturbation in charged networks can introduce structural rearrangements to compensate for desolvation effects. We validate the physical principles by resolving high-resolution atomic structures of the artificial proteins that are resistant towards unfolding at extreme temperatures and harsh chemical conditions. Our findings provide a molecular understanding of functional charged networks and how point mutations may alter the protein’s conformational landscape.
Multi-task weak supervision enables anatomically-resolved abnormality detection in whole-body FDG-PET/CT
Authors: Eyuboglu Sabri , Angus Geoffrey , Patel Bhavik N. , Pareek Anuj , Davidzon Guido , Long Jin , Dunnmon Jared , Lungren Matthew P. 
Published: March 2021

AbstractComputational decision support systems could provide clinical value in whole-body FDG-PET/CT workflows. However, limited availability of labeled data combined with the large size of PET/CT imaging exams make it challenging to apply existing supervised machine learning systems. Leveraging recent advancements in natural language processing, we describe a weak supervision framework that extracts imperfect, yet highly granular, regional abnormality labels from free-text radiology reports. Our framework automatically labels each region in a custom ontology of anatomical regions, providing a structured profile of the pathologies in each imaging exam. Using these generated labels, we then train an attention-based, multi-task CNN architecture to detect and estimate the location of abnormalities in whole-body scans. We demonstrate empirically that our multi-task representation is critical for strong performance on rare abnormalities with limited training data. The representation also contributes to more accurate mortality prediction from imaging data, suggesting the potential utility of our framework beyond abnormality detection and location estimation.
Viral infection of cells within the tumor microenvironment mediates antitumor immunotherapy via selective TBK1-IRF3 signaling
Authors: Brown Michael C. , Mosaheb Mubeen M. , Mohme Malte , McKay Zachary P. , Holl Eda K. , Kastan Jonathan P. , Yang Yuanfan , Beasley Georgia M. , Hwang E. Shelley , Ashley David M. , Bigner Darell D. , Nair Smita K. , Gromeier Matthias 
Published: March 2021

AbstractActivating intra-tumor innate immunity might enhance tumor immune surveillance. Virotherapy is proposed to achieve tumor cell killing, while indirectly activating innate immunity. Here, we report that recombinant poliovirus therapy primarily mediates antitumor immunotherapy via direct infection of non-malignant tumor microenvironment (TME) cells, independent of malignant cell lysis. Relative to other innate immune agonists, virotherapy provokes selective, TBK1-IRF3 driven innate inflammation that is associated with sustained type-I/III interferon (IFN) release. Despite priming equivalent antitumor T cell quantities, MDA5-orchestrated TBK1-IRF3 signaling, but not NFκB-polarized TLR activation, culminates in polyfunctional and Th1-differentiated antitumor T cell phenotypes. Recombinant type-I IFN increases tumor-localized T cell function, but does not mediate durable antitumor immunotherapy without concomitant pattern recognition receptor (PRR) signaling. Thus, virus-induced MDA5-TBK1-IRF3 signaling in the TME provides PRR-contextualized IFN responses that elicit functional antitumor T cell immunity. TBK1-IRF3 innate signal transduction stimulates eventual function and differentiation of tumor-infiltrating T cells.
Near-room temperature ferromagnetic insulating state in highly distorted LaCoO2.5 with CoO5 square pyramids
Authors: Zhang Qinghua , Gao Ang , Meng Fanqi , Jin Qiao , Lin Shan , Wang Xuefeng , Xiao Dongdong , Wang Can , Jin Kui-juan , Su Dong , Guo Er-Jia , Gu Lin 
Published: March 2021

AbstractDedicated control of oxygen vacancies is an important route to functionalizing complex oxide films. It is well-known that tensile strain significantly lowers the oxygen vacancy formation energy, whereas compressive strain plays a minor role. Thus, atomic reconstruction by extracting oxygen from a compressive-strained film is challenging. Here we report an unexpected LaCoO2.5 phase with a zigzag-like oxygen vacancy ordering through annealing a compressive-strained LaCoO3 in vacuum. The synergetic tilt and distortion of CoO5 square pyramids with large La and Co shifts are quantified using scanning transmission electron microscopy. The large in-plane expansion of CoO5 square pyramids weaken the crystal field splitting and facilitated the ordered high-spin state of Co2+, which produces an insulating ferromagnetic state with a Curie temperature of ~284 K and a saturation magnetization of ~0.25 μB/Co. These results demonstrate that extracting targeted oxygen from a compressive-strained oxide provides an opportunity for creating unexpected crystal structures and novel functionalities.
scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses
Authors: Wang Juexin , Ma Anjun , Chang Yuzhou , Gong Jianting , Jiang Yuexu , Qi Ren , Wang Cankun , Fu Hongjun , Ma Qin , Xu Dong 
Published: March 2021

AbstractSingle-cell RNA-sequencing (scRNA-Seq) is widely used to reveal the heterogeneity and dynamics of tissues, organisms, and complex diseases, but its analyses still suffer from multiple grand challenges, including the sequencing sparsity and complex differential patterns in gene expression. We introduce the scGNN (single-cell graph neural network) to provide a hypothesis-free deep learning framework for scRNA-Seq analyses. This framework formulates and aggregates cell–cell relationships with graph neural networks and models heterogeneous gene expression patterns using a left-truncated mixture Gaussian model. scGNN integrates three iterative multi-modal autoencoders and outperforms existing tools for gene imputation and cell clustering on four benchmark scRNA-Seq datasets. In an Alzheimer’s disease study with 13,214 single nuclei from postmortem brain tissues, scGNN successfully illustrated disease-related neural development and the differential mechanism. scGNN provides an effective representation of gene expression and cell–cell relationships. It is also a powerful framework that can be applied to general scRNA-Seq analyses.
No hints at glyphosate-induced ruminal dysbiosis in cows
Authors: Billenkamp Fabian , Schnabel Karina , Hüther Liane , Frahm Jana , von Soosten Dirk , Meyer Ulrich , Höper Dirk , Beer Martin , Seyboldt Christian , Neubauer Heinrich , Dänicke Sven 
Published: March 2021

AbstractGlyphosate-based herbicides are among the most used non-selective herbicides worldwide and inhibit synthesis of aromatic amino acids in plants, bacteria, and fungi. Given the broad usage, controversies concerning potential effects of glyphosate on health and especially on gut microbiomes arose. For cattle, it has been proposed based on in vitro data that glyphosate has detrimental effects on the ruminal microbiome, which manifest as a specific inhibition of bacteria involved in fiber degradation and as an enrichment of specific pathogens. In the present study, glyphosate effects on the ruminal microbiome were analyzed in vivo using glyphosate contaminated feedstuffs with strong differences in dietary fiber and dietary energy content in order to reproduce the proposed detrimental glyphosate effects on the rumen microbiome. While significant impact of dietary factors on the ruminal microbiome and its products are pointed out, no adverse glyphosate effects on ruminal microbiome composition, diversity, and microbial metabolites are observed.
De-escalation of radiation therapy in patients with stage I, node-negative, HER2-positive breast cancer
Authors: Bazan Jose G. , Jhawar Sachin R. , Stover Daniel , Park Ko Un , Beyer Sasha , Healy Erin , White Julia R. 
Published: March 2021

AbstractIn the modern era, highly effective anti-HER2 therapy is associated with low local-regional recurrence (LRR) rates for early-stage HER2+ breast cancer raising the question of whether local therapy de-escalation by radiation omission is possible in patients with small-node negative tumors treated with lumpectomy. To evaluate existing data on radiation omission, we used the National Cancer Database (NCDB) to test the hypothesis that RT omission results in equivalent overall survival (OS) in stage 1 (T1N0) HER2+ breast cancer. We excluded patients that received neoadjuvant systemic therapy. We stratified the cohort by receipt of adjuvant radiation. We identified 6897 patients (6388 RT; 509 no RT). Patients that did not receive radiation tended to be ≥70 years-old (odds ratio [OR] = 3.69, 95% CI: 3.02–4.51,p < 0.0001), to have ≥1 comorbidity (OR = 1.33, 95% CI: 1.06–1.68,p = 0.0154), to be Hispanic (OR = 1.49, 95% CI: 1.00–2.22,p = 0.049), and to live in lower income areas (OR = 1.32, 95% CI: 1.07–1.64,p = 0.0266). Radiation omission was associated with a 3.67-fold (95% CI: 2.23–6.02,p < 0.0001) increased risk of death. While other selection biases that influence radiation omission likely persist, these data should give caution to radiation omission in T1N0 HER2+ breast cancer.
Structural and chemical mechanisms governing stability of inorganic Janus nanotubes
Authors: Bölle Felix T. , Mikkelsen August E. G. , Thygesen Kristian S. , Vegge Tejs , Castelli Ivano E. 
Published: March 2021

AbstractOne-dimensional inorganic nanotubes hold promise for technological applications due to their distinct physical/chemical properties, but so far advancements have been hampered by difficulties in producing single-wall nanotubes with a well-defined radius. In this work we investigate, based on Density Functional Theory (DFT), the formation mechanism of 135 different inorganic nanotubes formed by the intrinsic self-rolling driving force found in asymmetric 2D Janus sheets. We show that for isovalent Janus sheets, the lattice mismatch between inner and outer atomic layers is the driving force behind the nanotube formation, while in the non-isovalent case it is governed by the difference in chemical bond strength of the inner and outer layer leading to steric effects. From our pool of candidate structures we have identified more than 100 tubes with a preferred radius below 35 Å, which we hypothesize can display distinctive properties compared to their parent 2D monolayers. Simple descriptors have been identified to accelerate the discovery of small-radius tubes and a Bayesian regression approach has been implemented to assess the uncertainty in our predictions on the radius.
Optimal band structure for thermoelectrics with realistic scattering and bands
Authors: Park Junsoo , Xia Yi , Ozoliņš Vidvuds , Jain Anubhav 
Published: March 2021

AbstractUnderstanding how to optimize electronic band structures for thermoelectrics is a topic of long-standing interest in the community. Prior models have been limited to simplified bands and/or scattering models. In this study, we apply more rigorous scattering treatments to more realistic model band structures—upward-parabolic bands that inflect to an inverted-parabolic behavior—including cases of multiple bands. In contrast to common descriptors (e.g., quality factor and complexity factor), the degree to which multiple pockets improve thermoelectric performance is bounded by interband scattering and the relative shapes of the bands. We establish that extremely anisotropic “flat-and-dispersive” bands, although best-performing in theory, may not represent a promising design strategy in practice. Critically, we determine optimum bandwidth, dependent on temperature and lattice thermal conductivity, from perfect transport cutoffs that can in theory significantly boost zT beyond the values attainable through intrinsic band structures alone. Our analysis should be widely useful as the thermoelectric research community eyes zT > 3.
NLM-Chem, a new resource for chemical entity recognition in PubMed full text literature
Authors: Islamaj Rezarta , Leaman Robert , Kim Sun , Kwon Dongseop , Wei Chih-Hsuan , Comeau Donald C. , Peng Yifan , Cissel David , Coss Cathleen , Fisher Carol , Guzman Rob , Kochar Preeti Gokal , Koppel Stella , Trinh Dorothy , Sekiya Keiko , Ward Janice , Whitman Deborah , Schmidt Susan , Lu Zhiyong 
Published: March 2021

AbstractAutomatically identifying chemical and drug names in scientific publications advances information access for this important class of entities in a variety of biomedical disciplines by enabling improved retrieval and linkage to related concepts. While current methods for tagging chemical entities were developed for the article title and abstract, their performance in the full article text is substantially lower. However, the full text frequently contains more detailed chemical information, such as the properties of chemical compounds, their biological effects and interactions with diseases, genes and other chemicals. We therefore present the NLM-Chem corpus, a full-text resource to support the development and evaluation of automated chemical entity taggers. The NLM-Chem corpus consists of 150 full-text articles, doubly annotated by ten expert NLM indexers, with ~5000 unique chemical name annotations, mapped to ~2000 MeSH identifiers. We also describe a substantially improved chemical entity tagger, with automated annotations for all of PubMed and PMC freely accessible through the PubTator web-based interface and API. The NLM-Chem corpus is freely available.
New insights into structure and function of bis-phosphinic acid derivatives and implications for CFTR modulation
Authors: Bitam Sara , Elbahnsi Ahmad , Creste Geordie , Pranke Iwona , Chevalier Benoit , Berhal Farouk , Hoffmann Brice , Servel Nathalie , Baatalah Nesrine , Tondelier Danielle , Hatton Aurelie , Moquereau Christelle , Faria Da Cunha Mélanie , Pastor Alexandra , Lepissier Agathe , Hinzpeter Alexandre , Mornon Jean-Paul , Prestat Guillaume , Edelman Aleksander , Callebaut Isabelle , Gravier-Pelletier Christine , Sermet-Gaudelus Isabelle 
Published: March 2021

AbstractC407 is a compound that corrects the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein carrying the p.Phe508del (F508del) mutation. We investigated the corrector effect of c407 and its derivatives on F508del-CFTR protein. Molecular docking and dynamics simulations combined with site-directed mutagenesis suggested that c407 stabilizes the F508del-Nucleotide Binding Domain 1 (NBD1) during the co-translational folding process by occupying the position of the p.Phe1068 side chain located at the fourth intracellular loop (ICL4). After CFTR domains assembly, c407 occupies the position of the missing p.Phe508 side chain. C407 alone or in combination with the F508del-CFTR corrector VX-809, increased CFTR activity in cell lines but not in primary respiratory cells carrying the F508del mutation. A structure-based approach resulted in the synthesis of an extended c407 analog G1, designed to improve the interaction with ICL4. G1 significantly increased CFTR activity and response to VX-809 in primary nasal cells of F508del homozygous patients. Our data demonstrate that in-silico optimized c407 derivative G1 acts by a mechanism different from the reference VX-809 corrector and provide insights into its possible molecular mode of action. These results pave the way for novel strategies aiming to optimize the flawed ICL4–NBD1 interface.
Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution
Authors: Serna-Sánchez Maria Alejandra , Pérez-Escobar Oscar A. , Bogarín Diego , Torres-Jimenez María Fernanda , Alvarez-Yela Astrid Catalina , Arcila-Galvis Juliana E. , Hall Climbie F. , de Barros Fábio , Pinheiro Fábio , Dodsworth Steven , Chase Mark W. , Antonelli Alexandre , Arias Tatiana 
Published: March 2021

AbstractRecent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.
A modality selective effect of functional laterality in pain detection sensitivity
Authors: Zhang Huijuan , Lu Xuejing , Bi Yanzhi , Hu Li 
Published: March 2021

AbstractThe ability to detect environmental changes is essential to determine the appropriate reaction when facing potential threats. Both detection and reaction functions are critical to survival, and the superior performance of motor reaction for the dominant hand is well recognized in humans. However, it is not clear whether there exists laterality in sensitivity to detect external changes and whether the possible laterality is associated with sensory modality and stimulus intensity. Here, we tested whether the perceptual sensitivity and electrophysiological responses elicited by graded sensory stimuli (i.e., nociceptive somatosensory, non-nociceptive somatosensory, auditory, and visual) that were delivered on/near the left and right hands would be different for right-handed individuals. We observed that perceived intensities and most brain responses were significantly larger when nociceptive stimuli were delivered to the left side (i.e., the non-dominant hand) than to the right side (i.e., the dominant hand). No significant difference was observed between the two sides for other modalities. The higher sensitivity to detect nociceptive stimuli for the non-dominant hand would be important to provide a prompt reaction to noxious events, thus compensating for its worse motor performance. This laterality phenomenon should be considered when designing experiments for pain laboratory studies and evaluating regional sensory abnormalities for pain patients.