bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perforated acute abdomen in a patient with COVID-19: an atypical manifestation of the disease
Authors: Corrêa Neto Isaac José Felippe , Viana Kaline Fortes , Silva Milena Braga Soares da , Silva Leandro Mariano da , Oliveira Gustavo de , Cecchini Angelo Rossi da Silva , Rolim Alexander Sá , Robles Laercio 
Published: May 2020

Abstract
Introduction The Coronavirus belongs to a family of RNA viruses that can cause respiratory infection, with the possibility of gastrointestinal manifestations in approximately 5—50% of the cases.
Objective To report a surgical case with a diagnosis of COVID-19 that developed acute perforated abdomen and pneumothorax.
Case report This was an 80-year-old female patient with respiratory symptoms, with dry cough and fever and diffuse abdominal pain with signs of peritonitis. She had leukocytosis, kidney dysfunction and an increase in D-dimer with positive PCR for COVID. Computed tomography of the chest and abdomen showed pneumothorax on the right and extensive pneumoperitoneum.
Conclusion The presentation of COVID-19 with severe pulmonary and abdominal complications requires specialized and emergency treatments, but it has high mortality rates.
On the structure of Dense graphs with bounded clique number
Authors: Oberkampf Heiner , Schacht Mathias 
Published: June 2020

AbstractWe study structural properties of graphs with bounded clique number and high minimum degree. In particular, we show that there exists a function L = L(r,ɛ) such that every Kr-free graph G on n vertices with minimum degree at least ((2r–5)/(2r–3)+ɛ)n is homomorphic to a Kr-free graph on at most L vertices. It is known that the required minimum degree condition is approximately best possible for this result.For r = 3 this result was obtained by Łuczak (2006) and, more recently, Goddard and Lyle (2011) deduced the general case from Łuczak’s result. Łuczak’s proof was based on an application of Szemerédi’s regularity lemma and, as a consequence, it only gave rise to a tower-type bound on L(3, ɛ). The proof presented here replaces the application of the regularity lemma by a probabilistic argument, which yields a bound for L(r, ɛ) that is doubly exponential in poly(ɛ).
Numerical Modeling of Instream Wood Transport, Deposition, and Accumulation in Braided Morphologies Under Unsteady Conditions: Sensitivity and High‐Resolution Quantitative Model Validation
Authors: Ruiz‐Villanueva V. , Gamberini C. , Bladé E. , Stoffel M. , Bertoldi W. 
Published: May 2020

AbstractLarge wood promotes fundamental changes in river hydraulics and morphology, playing a relevant role in river ecology but also in flood hazard. Accurate predictions of large wood dynamics in terms of deposition patterns and travel distance are still lacking and only recently have numerical models been developed to this end. In this work we enhance the capabilities of the numerical model Iber‐Wood in reproducing large wood dynamics in shallow braided rivers and validate it by comparing simulations with the results of previous laboratory experiments. The flume experiments provide high‐resolution observations of wood travel distances and depositional patterns of wood. The comparison proves useful to improve the numerical simulation of (i) the interactions between wood pieces and the riverbed (e.g., when wood pieces are transported by dragging), (ii) wood pieces with roots, and (iii) the formation of wood jams (i.e., accumulations of greater than three wood pieces). A sensitivity analysis reveals the crucial role of bed topography, with limited effect played by drag and restitution coefficients. Taking advantage of a controlled environment with similar simplifying hypotheses, we combine the strengths of both physical and numerical modeling to explore the parameters that are most effective in controlling wood dynamics. We use the numerical model to explore the effect of unsteady flow conditions, with different wood supply input. The resulting wood depositional patterns, jam formation, and travel distances during floods may improve our understanding of some of the controls on biogeomorphic evolutionary trajectories of braided rivers.
Scalable nanolaminated SERS multiwell cell culture assay
Authors: Ren Xiang , Nam Wonil , Ghassemi Parham , Strobl Jeannine S. , Kim Inyoung , Zhou Wei , Agah Masoud 
Published: May 2020

AbstractThis paper presents a new cell culture platform enabling label-free surface-enhanced Raman spectroscopy (SERS) analysis of biological samples. The platform integrates a multilayered metal-insulator-metal nanolaminated SERS substrate and polydimethylsiloxane (PDMS) multiwells for the simultaneous analysis of cultured cells. Multiple cell lines, including breast normal and cancer cells and prostate cancer cells, were used to validate the applicability of this unique platform. The cell lines were cultured in different wells. The Raman spectra of over 100 cells from each cell line were collected and analyzed after 12 h of introducing the cells to the assay. The unique Raman spectra of each cell line yielded biomarkers for identifying cancerous and normal cells. A kernel-based machine learning algorithm was used to extract the high-dimensional variables from the Raman spectra. Specifically, the nonnegative garrote on a kernel machine classifier is a hybrid approach with a mixed nonparametric model that considers the nonlinear relationships between the higher-dimension variables. The breast cancer cell lines and normal breast epithelial cells were distinguished with an accuracy close to 90%. The prediction rate between breast cancer cells and prostate cancer cells reached 94%. Four blind test groups were used to evaluate the prediction power of the SERS spectra. The peak intensities at the selected Raman shifts of the testing groups were selected and compared with the training groups used in the machine learning algorithm. The blind testing groups were correctly predicted 100% of the time, demonstrating the applicability of the multiwell SERS array for analyzing cell populations for cancer research.
Dissecting the genome of star fruit (Averrhoa carambola L.)
Authors: Fan Yannan , Sahu Sunil Kumar , Yang Ting , Mu Weixue , Wei Jinpu , Cheng Le , Yang Jinlong , Mu Ranchang , Liu Jie , Zhao Jianming , Zhao Yuxian , Xu Xun , Liu Xin , Liu Huan 
Published: May 2020

AbstractAverrhoa carambola is commonly known as star fruit because of its peculiar shape, and its fruit is a rich source of minerals and vitamins. It is also used in traditional medicines in countries such as India, China, the Philippines, and Brazil for treating various ailments, including fever, diarrhea, vomiting, and skin disease. Here, we present the first draft genome of the Oxalidaceae family, with an assembled genome size of 470.51 Mb. In total, 24,726 protein-coding genes were identified, and 16,490 genes were annotated using various well-known databases. The phylogenomic analysis confirmed the evolutionary position of the Oxalidaceae family. Based on the gene functional annotations, we also identified enzymes that may be involved in important nutritional pathways in the star fruit genome. Overall, the data from this first sequenced genome in the Oxalidaceae family provide an essential resource for nutritional, medicinal, and cultivational studies of the economically important star-fruit plant.
Molecular dynamics of pre-germinative metabolism in primed eggplant (Solanum melongena L.) seeds
Authors: Forti Chiara , Ottobrino Valentino , Bassolino Laura , Toppino Laura , Rotino Giuseppe Leonardo , Pagano Andrea , Macovei Anca , Balestrazzi Alma 
Published: May 2020

AbstractSeed priming, a pre-sowing technique that enhances the antioxidant/DNA repair activities during the pre-germinative metabolism, still retains empirical features. We explore for the first time the molecular dynamics of pre-germinative metabolism in primed eggplant (Solanum melongena L.) seeds in order to identify hallmarks (expression patterns of antioxidant/DNA repair genes combined with free radical profiles) useful to discriminate between high- and low-quality lots. The hydropriming protocol hereby developed anticipated (or even rescued) germination, when applied to lots with variable quality. ROS (reactive oxygen species) raised during hydropriming and dropped after dry-back. Upregulation of antioxidant/DNA repair genes was observed during hydropriming and the subsequent imbibition. Upregulation of SmOGG1 (8-oxoguanine glycosylase/lyase) gene detected in primed seeds at 2 h of imbibition appeared as a promising hallmark. On the basis of these results, the investigation was restricted within the first 2 h of imbibition, to verify whether the molecular landscape was reproducible in different lots. A complex pattern of antioxidant/DNA repair gene expression emerged, reflecting the preponderance of seed lot-specific profiles. Only the low-quality eggplant seeds subjected to hydropriming showed enhanced ROS levels, both in the dry and imbibed state, and this might be a useful signature to discriminate among lots. The plasticity of eggplant pre-germinative metabolism stimulated by priming imposes a plethora of heterogeneous molecular responses that might delay the search for quality hallmarks. However, the information hereby gained could be translated to eggplant wild relatives to speed-up their use in breeding programs or other agronomical applications.
Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato
Authors: Zhang Lei , Yu Yicheng , Shi Tianye , Kou Meng , Sun Jian , Xu Tao , Li Qiang , Wu Shaoyuan , Cao Qinghe , Hou Wenqian , Li Zongyun 
Published: May 2020

AbstractDissecting the genetic regulation of gene expression is critical for understanding phenotypic variation and species evolution. However, our understanding of the transcriptional variability in sweet potato remains limited. Here, we analyzed two publicly available datasets to explore the landscape of transcriptomic variations and its genetic basis in the storage roots of sweet potato. The comprehensive analysis identified a total of 724,438 high-confidence single nucleotide polymorphisms (SNPs) and 26,026 expressed genes. Expression quantitative trait locus (eQTL) analysis revealed 4408 eQTLs regulating the expression of 3646 genes, including 2261 local eQTLs and 2147 distant eQTLs. Two distant eQTL hotspots were found with target genes significantly enriched in specific functional classifications. By combining the information from regulatory network analyses, eQTLs and association mapping, we found that IbMYB1-2 acts as a master regulator and is the major gene responsible for the activation of anthocyanin biosynthesis in the storage roots of sweet potato. Our study provides the first insight into the genetic architecture of genome-wide expression variation in sweet potato and can be used to investigate the potential effects of genetic variants on key agronomic traits in sweet potato.
Loading calcium fluorescent probes into protoplasts to detect calcium in the flesh tissue cells of Malus domestica
Authors: Qiu Lina , Wang Yongzhang , Qu Haiyong 
Published: May 2020

AbstractCytosolic Ca2+ plays a key role in signal transduction in plants. Calcium imaging is the most common approach to studying dynamic changes in the cytoplasmic Ca2+ content. Here, we used mature ‘Fuji’ apples (Malus pumila Mill.) to obtain viable protoplasts from flesh tissue cells by enzymatic hydrolysis; then, three small-molecule fluorescent probes (fluo-8/AM, fluo-4/AM, and rhod-2/AM) were loaded into the protoplasts. All three Ca2+ fluorescent probes successfully entered the cytoplasm but did not enter the vacuole. Both the Ca2+ chelator (EGTA) and Ca2+ channel blocker (La3+) reduced the fluorescence intensity in the cytoplasm. The calcium ionophore A23187 increased the fluorescence intensity in the cytoplasm at 5 µmol/L but decreased it at 50 µmol/L. Additionally, A23187 reversed the fluorescence intensity in the cytoplasm, which was decreased by La3+. Ionomycin is also a calcium ionophore that can increase the fluorescence intensity of calcium in the cytoplasm. These results suggest that small-molecule Ca2+ fluorescent probes can be used to detect changes in cytosolic calcium levels in the cells of fruit flesh tissue. In addition, the optimum concentration of fluo-8/AM was determined to be 5 µmol/L. This was the first time that protoplasts have been isolated from apple flesh tissue cells and small-molecule fluorescent probes have been used to detect calcium in the cytoplasm of flesh tissue cells. This study provides a new method to study calcium signal transduction in fruit flesh tissue.
Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’
Authors: Patel Sagar , Robben Michael , Fennell Anne , Londo Jason P. , Alahakoon Dilmini , Villegas-Diaz Roberto , Swaminathan Padmapriya 
Published: May 2020

AbstractVitis riparia, a critically important Native American grapevine species, is used globally in rootstock and scion breeding and contributed to the recovery of the French wine industry during the mid-19th century phylloxera epidemic. This species has abiotic and biotic stress tolerance and the largest natural geographic distribution of the North American grapevine species. Here we report an Illumina short-read 369X coverage, draft de novo heterozygous genome sequence of V. riparia Michx. ‘Manitoba 37’ with the size of ~495 Mb for 69,616 scaffolds and a N50 length of 518,740 bp. Using RNAseq data, 40,019 coding sequences were predicted and annotated. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models found 96% of the complete BUSCOs in this assembly. The assembly continuity and completeness were further validated using V. riparia ESTs, BACs, and three de novo transcriptome assemblies of three different V. riparia genotypes resulting in >98% of respective sequences/transcripts mapping with this assembly. Alignment of the V. riparia assembly and predicted CDS with the latest V. vinifera ‘PN40024’ CDS and genome assembly showed 99% CDS alignment and a high degree of synteny. An analysis of plant transcription factors indicates a high degree of homology with the V. vinifera transcription factors. QTL mapping to V. riparia ‘Manitoba 37’ and V. vinifera PN40024 has identified genetic relationships to phenotypic variation between species. This assembly provides reference sequences, gene models for marker development and understanding V. riparia’s genetic contributions in grape breeding and research.
Robust dynamic community detection with applications to human brain functional networks
Authors: Martinet L.-E. , Kramer M. A. , Viles W. , Perkins L. N. , Spencer E. , Chu C. J. , Cash S. S. , Kolaczyk E. D. 
Published: June 2020

AbstractWhile current technology permits inference of dynamic brain networks over long time periods at high temporal resolution, the detailed structure of dynamic network communities during human seizures remains poorly understood. We introduce a new methodology that addresses critical aspects unique to the analysis of dynamic functional networks inferred from noisy data. We propose a dynamic plex percolation method (DPPM) that is robust to edge noise, and yields well-defined spatiotemporal communities that span forward and backwards in time. We show in simulation that DPPM outperforms existing methods in accurately capturing certain stereotypical dynamic community behaviors in noisy situations. We then illustrate the ability of this method to track dynamic community organization during human seizures, using invasive brain voltage recordings at seizure onset. We conjecture that application of this method will yield new targets for surgical treatment of epilepsy, and more generally could provide new insights in other network neuroscience applications.
Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships
Authors: Sánchez-Valle Jon , Tejero Héctor , Fernández José María , Juan David , Urda-García Beatriz , Capella-Gutiérrez Salvador , Al-Shahrour Fátima , Tabarés-Seisdedos Rafael , Baudot Anaïs , Pancaldi Vera , Valencia Alfonso 
Published: June 2020

AbstractComorbidity is a medical condition attracting increasing attention in healthcare and biomedical research. Little is known about the involvement of potential molecular factors leading to the emergence of a specific disease in patients affected by other conditions. We present here a disease interaction network inferred from similarities between patients’ molecular profiles, which significantly recapitulates epidemiologically documented comorbidities. Furthermore, we identify disease patient-subgroups that present different molecular similarities with other diseases, some of them opposing the general tendencies observed at the disease level. Analyzing the generated patient-subgroup network, we identify genes involved in such relations, together with drugs whose effects are potentially associated with the observed comorbidities. All the obtained associations are available at the disease PERCEPTION portal (http://disease-perception.bsc.es).
Control of criticality and computation in spiking neuromorphic networks with plasticity
Authors: Cramer Benjamin , Stöckel David , Kreft Markus , Wibral Michael , Schemmel Johannes , Meier Karlheinz , Priesemann Viola 
Published: June 2020

AbstractThe critical state is assumed to be optimal for any computation in recurrent neural networks, because criticality maximizes a number of abstract computational properties. We challenge this assumption by evaluating the performance of a spiking recurrent neural network on a set of tasks of varying complexity at - and away from critical network dynamics. To that end, we developed a plastic spiking network on a neuromorphic chip. We show that the distance to criticality can be easily adapted by changing the input strength, and then demonstrate a clear relation between criticality, task-performance and information-theoretic fingerprint. Whereas the information-theoretic measures all show that network capacity is maximal at criticality, only the complex tasks profit from criticality, whereas simple tasks suffer. Thereby, we challenge the general assumption that criticality would be beneficial for any task, and provide instead an understanding of how the collective network state should be tuned to task requirement.
Systemic lupus erythematosus favors the generation of IL-17 producing double negative T cells
Authors: Li Hao , Adamopoulos Iannis E. , Moulton Vaishali R. , Stillman Isaac E. , Herbert Zach , Moon James J. , Sharabi Amir , Krishfield Suzanne , Tsokos Maria G. , Tsokos George C. 
Published: June 2020

AbstractMature double negative (DN) T cells are a population of αβ T cells that lack CD4 and CD8 coreceptors and contribute to systemic lupus erythematosus (SLE). The splenic marginal zone macrophages (MZMs) are important for establishing immune tolerance, and loss of their number or function contributes to the progression of SLE. Here we show that loss of MZMs impairs the tolerogenic clearance of apoptotic cells and alters the serum cytokine profile, which in turn provokes the generation of DN T cells from self-reactive CD8+T cells. Increased Ki67 expression, narrowed TCR V-beta repertoire usage and diluted T-cell receptor excision circles confirm that DN T cells from lupus-prone mice and patients with SLE undergo clonal proliferation and expansion in a self-antigen dependent manner, which supports the shared mechanisms for their generation. Collectively, our results provide a link between the loss of MZMs and the expansion of DN T cells, and indicate possible strategies to prevent the development of SLE.
m5C modification of mRNA serves a DNA damage code to promote homologous recombination
Authors: Chen Hao , Yang Haibo , Zhu Xiaolan , Yadav Tribhuwan , Ouyang Jian , Truesdell Samuel S. , Tan Jun , Wang Yumin , Duan Meihan , Wei Leizhen , Zou Lee , Levine Arthur S. , Vasudevan Shobha , Lan Li 
Published: June 2020

AbstractRecruitment of DNA repair proteins to DNA damage sites is a critical step for DNA repair. Post-translational modifications of proteins at DNA damage sites serve as DNA damage codes to recruit specific DNA repair factors. Here, we show that mRNA is locally modified by m5C at sites of DNA damage. The RNA methyltransferase TRDMT1 is recruited to DNA damage sites to promote m5C induction. Loss of TRDMT1 compromises homologous recombination (HR) and increases cellular sensitivity to DNA double-strand breaks (DSBs). In the absence of TRDMT1, RAD51 and RAD52 fail to localize to sites of reactive oxygen species (ROS)-induced DNA damage. In vitro, RAD52 displays an increased affinity for DNA:RNA hybrids containing m5C-modified RNA. Loss of TRDMT1 in cancer cells confers sensitivity to PARP inhibitors in vitro and in vivo. These results reveal an unexpected TRDMT1-m5C axis that promotes HR, suggesting that post-transcriptional modifications of RNA can also serve as DNA damage codes to regulate DNA repair.
Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host
Authors: Gouveia Duarte , Pible Olivier , Culotta Karen , Jouffret Virginie , Geffard Olivier , Chaumot Arnaud , Degli-Esposti Davide , Armengaud Jean 
Published: June 2020

AbstractMetaproteomics of gut microbiomes from animal hosts lacking a reference genome is challenging. Here we describe a strategy combining high-resolution metaproteomics and host RNA sequencing (RNA-seq) with generalist database searching to survey the digestive tract of Gammarus fossarum, a small crustacean used as a sentinel species in ecotoxicology. This approach provides a deep insight into the full range of biomasses and metabolic activities of the holobiont components, and differentiates between the intestine and hepatopancreatic caecum.
Pleomorphic adenomas and mucoepidermoid carcinomas of the breast are underpinned by fusion genes
Authors: Pareja Fresia , Da Cruz Paula Arnaud , Gularte-Mérida Rodrigo , Vahdatinia Mahsa , Li Anqi , Geyer Felipe C. , da Silva Edaise M. , Nanjangud Gouri , Wen Hannah Y. , Varga Zsuzsanna , Brogi Edi , Rakha Emad A. , Weigelt Britta , Reis-Filho Jorge S. 
Published: June 2020

AbstractPrimary pleomorphic adenomas (PAs) and mucoepidermoid carcinomas (MECs) of the breast are vanishingly rare. Here we sought to determine whether breast PAs and MECs would be underpinned by the fusion genes reported to occur in their salivary gland counterparts. Our study included three breast PAs and one breast MEC, which were subjected to RNA sequencing (PAs, n = 2; MEC, n = 1) or to Archer FusionPlex sequencing (PA, n = 1). Our analyses revealed the presence of the HMGA2-WIF1 fusion gene in breast PA3, the CTNNB1-PLAG1 fusion gene in breast PA2, and the CRTC1-MAML2 fusion gene in the breast MEC analyzed (1/1). No oncogenic fusion genes were detected in breast PA1, and no additional oncogenic fusion genes were detected in the cases studied. The presence of the fusion genes identified was validated by fluorescence in situ hybridization (n = 1), reverse transcription-PCR (n = 1), or by both methods (n = 1). Taken together, our findings indicate that PAs and MECs arising in the breast resemble their salivary gland counterparts not only phenotypically but also at the genetic level. Furthermore, our data suggest that the molecular analysis of breast PAs and MECs might constitute a useful tool to aid in their differential diagnosis.