bluuebunny/crossref_metadata_2025_split huggingface dataset:
What Caused the Large‐Scale Heat Deficit in the Subtropical South Atlantic Ocean During 2009–2012?
Authors: Dong Shenfu , Lopez Hosmay , Lee Sang‐Ki , Meinen Christopher S. , Goni Gustavo , Baringer Molly 
Published: April 2020

AbstractThe subtropical South Atlantic hosts complex ocean circulation patterns and processes that transport heat to the North Atlantic, thereby playing an important role in global energy redistribution. This study uses several oceanic products to assess ocean heat changes in the subtropical South Atlantic and the associated atmosphere‐ocean processes. A particular focus is placed on the large heat deficit during 2009–2012, which is associated with cooling during 2008–2011 and subsequent warming. This heat deficit was largely driven by a sharp increase in the southward Ekman transport across 35°S during 2008–2011. The anomalous Ekman transport is connected to the persistent positive sea level pressure anomaly over the Atlantic sector of the Southern Ocean, caused by the Southern Annular Mode and the Pacific‐South American Modes. Although the overall correlations of these climate modes with the Ekman transport are modest during 1993–2016, the modes combined to produce large heat content anomalies during 2009–2012.
Oral microbiome: possible harbinger for children’s health
Authors: Xiao Jin , Fiscella Kevin A. , Gill Steven R. 
Published: April 2020

AbstractThe human microbiome functions as an intricate and coordinated microbial network, residing throughout the mucosal surfaces of the skin, oral cavity, gastrointestinal tract, respiratory tract, and reproductive system. The oral microbiome encompasses a highly diverse microbiota, consisting of over 700 microorganisms, including bacteria, fungi, and viruses. As our understanding of the relationship between the oral microbiome and human health has evolved, we have identified a diverse array of oral and systemic diseases associated with this microbial community, including but not limited to caries, periodontal diseases, oral cancer, colorectal cancer, pancreatic cancer, and inflammatory bowel syndrome. The potential predictive relationship between the oral microbiota and these human diseases suggests that the oral cavity is an ideal site for disease diagnosis and development of rapid point-of-care tests. The oral cavity is easily accessible with a non-invasive collection of biological samples. We can envision a future where early life salivary diagnostic tools will be used to predict and prevent future disease via analyzing and shaping the infant’s oral microbiome. In this review, we present evidence for the establishment of the oral microbiome during early childhood, the capability of using childhood oral microbiome to predict future oral and systemic diseases, and the limitations of the current evidence.
The oxidation of hydrocarbons by diverse heterotrophic and mixotrophic bacteria that inhabit deep-sea hydrothermal ecosystems
Authors: Wang Wanpeng , Li Zhenyu , Zeng Lingyu , Dong Chunming , Shao Zongze 
Published: April 2020

Abstract
Hydrothermal activity can generate numerous and diverse hydrocarbon compounds. However, little is known about the influence of such hydrocarbons on deep-sea hydrothermal microbial ecology. We hypothesize that certain bacteria live on these hydrocarbons. Therefore, in this study, the distribution of hydrocarbons and their associated hydrocarbon-degrading bacteria were investigated at deep-sea hydrothermal vents at the Southern Mid-Atlantic Ridge, the Southwest Indian Ridge, and the East Pacific Rise. A variety of hydrocarbon-degrading consortia were obtained from hydrothermal samples collected at the aforementioned sites after low-temperature enrichment under high hydrostatic pressures, and the bacteria responsible for the degradation of hydrocarbons were investigated by DNA-based stable-isotope probing with uniformly 13C-labeled hydrocarbons. Unusually, we identified several previously recognized sulfur-oxidizing chemoautotrophs as hydrocarbon-degrading bacteria, e.g., the SAR324 group, the SUP05 clade, and Sulfurimonas, and for the first time confirmed their ability to degrade hydrocarbons. In addition, Erythrobacter, Pusillimonas, and SAR202 clade were shown to degrade polycyclic aromatic hydrocarbons for the first time. These results together with relatively high abundance in situ of most of the above-described bacteria highlight the potential influence of hydrocarbons in configuring the vent microbial community, and have made the importance of mixotrophs in hydrothermal vent ecosystems evident.
Immunostimulatory oncolytic virotherapy for multiple myeloma targeting 4-1BB and/or CD40
Authors: Wenthe Jessica , Naseri Sedigheh , Hellström Ann-Charlotte , Wiklund Helena Jernberg , Eriksson Emma , Loskog Angelica 
Published: April 2020

AbstractMultiple myeloma (MM) is a plasma cell malignancy that is characterized by immune dysregulation. MM is commonly treated with immunomodulating agents, but still remains incurable. Herein, we proposed and evaluated immunostimulatory Lokon oncolytic adenoviruses (LOAd) for MM treatment. LOAd viruses are serotype 5/35 chimera, which enables infection of hematopoietic cells. Oncolysis is restricted to cells with a dysregulated retinoblastoma protein pathway, which is frequently observed in MM. Further, LOAd viruses are armed with human immunostimulatory transgenes: trimerized membrane-bound CD40L (LOAd700, LOAd703) and 4-1BBL (LOAd703). LOAd viruses were assessed in a panel of MM cell lines (ANBL-6, L363, LP-1, OPM-2, RPMI-8226, and U266-84). All cells were sensitive to infection, leading to viral replication and cell killing as analyzed by quantitative PCR and viability assay. Transgene expression was verified post infection with flow cytometry. Cell phenotypes were further altered with a downregulation of markers connected to MM progression (ICAM-1, CD70, CXCL10, CCL2, and sIL-2Rα) and an upregulation of the death receptor Fas. In a co-culture of immune and MM cells, LOAd viruses promoted activation of cytotoxic T cells as seen by higher CD69, CD107a, and IFNγ expression. This was most prominent with LOAd703. In conclusion, LOAd viruses are of interest for MM therapy.
Fine mapping of the sex locus in Salix triandra confirms a consistent sex determination mechanism in genus Salix
Authors: Li Wei , Wu Huaitong , Li Xiaoping , Chen Yingnan , Yin Tongming 
Published: April 2020

AbstractSalix triandra belongs to section Amygdalinae in genus Salix, which is in a different section from the willow species in which sex determination has been well studied. Studying sex determination in distantly related willow species will help to clarify whether the sexes of different willows arise through a common sex determination system. For this purpose, we generated an intraspecific full-sib F1 population for S. triandra and constructed high-density genetic linkage maps for the crossing parents using restriction site-associated DNA sequencing and following a two-way pseudo-testcross strategy. With the established maps, the sex locus was positioned in linkage group XV only in the maternal map, and no sex linkage was detected in the paternal map. Consistent with previous findings in other willow species, our study showed that chromosome XV was the incipient sex chromosome and that females were the heterogametic sex in S. triandra. Therefore, sex in this willow species is also determined through a ZW sex determination system. We further performed fine mapping in the vicinity of the sex locus with SSR markers. By comparing the physical and genetic distances for the target interval encompassing the sex determination gene confined by SSRs, severe recombination repression was revealed in the sex determination region in the female map. The recombination rate in the confined interval encompassing the sex locus was approximately eight-fold lower than the genome-wide average. This study provides critical information relevant to sex determination in S. triandra.
Exploiting the diversity of tomato: the development of a phenotypically and genetically detailed germplasm collection
Authors: Mata-Nicolás Estefanía , Montero-Pau Javier , Gimeno-Paez Esther , Garcia-Carpintero Víctor , Ziarsolo Peio , Menda Naama , Mueller Lukas A. , Blanca José , Cañizares Joaquín , van der Knaap Esther , Díez María José 
Published: April 2020

AbstractA collection of 163 accessions, including Solanum pimpinellifolium, Solanum lycopersicum var. cerasiforme and Solanum lycopersicum var. lycopersicum, was selected to represent the genetic and morphological variability of tomato at its centers of origin and domestication: Andean regions of Peru and Ecuador and Mesoamerica. The collection is enriched with S. lycopersicum var. cerasiforme from the Amazonian region that has not been analyzed previously nor used extensively. The collection has been morphologically characterized showing diversity for fruit, flower and vegetative traits. Their genomes were sequenced in the Varitome project and are publicly available (solgenomics.net/projects/varitome). The identified SNPs have been annotated with respect to their impact and a total number of 37,974 out of 19,364,146 SNPs have been described as high impact by the SnpEeff analysis. GWAS has shown associations for different traits, demonstrating the potential of this collection for this kind of analysis. We have not only identified known QTLs and genes, but also new regions associated with traits such as fruit color, number of flowers per inflorescence or inflorescence architecture. To speed up and facilitate the use of this information, F2 populations were constructed by crossing the whole collection with three different parents. This F2 collection is useful for testing SNPs identified by GWAs, selection sweeps or any other candidate gene. All data is available on Solanaceae Genomics Network and the accession and F2 seeds are freely available at COMAV and at TGRC genebanks. All these resources together make this collection a good candidate for genetic studies.
Type-specific dendritic integration in mouse retinal ganglion cells
Authors: Ran Yanli , Huang Ziwei , Baden Tom , Schubert Timm , Baayen Harald , Berens Philipp , Franke Katrin , Euler Thomas 
Published: April 2020

AbstractNeural computation relies on the integration of synaptic inputs across a neuron’s dendritic arbour. However, it is far from understood how different cell types tune this process to establish cell-type specific computations. Here, using two-photon imaging of dendritic Ca2+ signals, electrical recordings of somatic voltage and biophysical modelling, we demonstrate that four morphologically distinct types of mouse retinal ganglion cells with overlapping excitatory synaptic input (transient Off alpha, transient Off mini, sustained Off, and F-mini Off) exhibit type-specific dendritic integration profiles: in contrast to the other types, dendrites of transient Off alpha cells were spatially independent, with little receptive field overlap. The temporal correlation of dendritic signals varied also extensively, with the highest and lowest correlation in transient Off mini and transient Off alpha cells, respectively. We show that differences between cell types can likely be explained by differences in backpropagation efficiency, arising from the specific combinations of dendritic morphology and ion channel densities.
The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II
Authors: van der Weegen Yana , Golan-Berman Hadar , Mevissen Tycho E. T. , Apelt Katja , González-Prieto Román , Goedhart Joachim , Heilbrun Elisheva E. , Vertegaal Alfred C. O. , van den Heuvel Diana , Walter Johannes C. , Adar Sheera , Luijsterburg Martijn S. 
Published: April 2020

AbstractThe response to DNA damage-stalled RNA polymerase II (RNAPIIo) involves the assembly of the transcription-coupled repair (TCR) complex on actively transcribed strands. The function of the TCR proteins CSB, CSA and UVSSA and the manner in which the core DNA repair complex, including transcription factor IIH (TFIIH), is recruited are largely unknown. Here, we define the assembly mechanism of the TCR complex in human isogenic knockout cells. We show that TCR is initiated by RNAPIIo-bound CSB, which recruits CSA through a newly identified CSA-interaction motif (CIM). Once recruited, CSA facilitates the association of UVSSA with stalled RNAPIIo. Importantly, we find that UVSSA is the key factor that recruits the TFIIH complex in a manner that is stimulated by CSB and CSA. Together these findings identify a sequential and highly cooperative assembly mechanism of TCR proteins and reveal the mechanism for TFIIH recruitment to DNA damage-stalled RNAPIIo to initiate repair.
Short-Term Outcomes in Patients Undergoing Paraesophageal Hiatal Hernia Repair
Authors: Howell Raelina S. , Liu Helen H. , Petrone Patrizio , Anduaga María Fernanda , Servide María José , Hall Keneth , Barkan Alexander , Islam Shahidul , Brathwaite Collin E. M. 
Published: April 2020

AbstractMany patients with hiatal hernias (HH) are asymptomatic; however, symptoms may include heartburn, regurgitation, dysphagia, nausea, or vague epigastric pain depending on the hernia type and severity. The ideal technique and timing of repair remains controversial. This report describes short-term outcomes and readmissions of patients undergoing HH repair at our institution. All patients who underwent HH repair from January 2012 through April 2017 were reviewed. Patients undergoing concomitant bariatric surgery were excluded. 239 patients were identified and 128 were included. Eighty-eight were female (69%) and 40 were male (31%) with a mean age of 59 years (range 20–91 years) and a mean BMI of 29.2 kg/m2(17–42). Worsening GERD was the most common presenting symptom in 79 (61.7%) patients. Eighty-four laparoscopic cases (65.6%) and 44 robotic assisted (34.4%) procedures were performed. Mesh was used in 59 operations (3 polytetrafluoroethylene; 56 biologic). All hiatal hernia types (I-IV) were collected. Majority were initial operations (89%). Techniques included: Toupet fundoplication in 68 cases (63.0%), Nissen fundoplication in 36 (33.3%), Dor fundoplication in 4 (3.7%), concomitant Collis gastroplasty in 4 (3.1%), and primary suture repair in 20 (15.6%). Outcomes between robotic and laparoscopic procedures were compared. Length of stay was reported as median and interquartile range for laparoscopic and robotic: 1.0 day (1.0–3.0) and 2.0 days (1.0–2.5); p = 0.483. Thirty-day readmission occurred in 9 patients, 7 (8.3%) laparoscopic and 2 (4.6%) robotic; p = 0.718. Two 30-day reoperations occurred, both laparoscopic; p = 0.545. Total of 16 complications occurred; 18.6% had a complication with the use of mesh compared to 8.7% without the use of mesh, p = 0.063. There were no conversion to open modality and no mortalities were reported. Hiatal hernia repair can be performed safely with a low incidence of complications.
Controlling the nonadiabatic electron-transfer reaction rate through molecular-vibration polaritons in the ultrastrong coupling regime
Authors: Phuc Nguyen Thanh , Trung Pham Quang , Ishizaki Akihito 
Published: April 2020

AbstractRecent experiments showed that the chemical reaction rate is modified, either increased or decreased, by strongly coupling a nuclear vibration mode to the single mode of an optical cavity. Herein we investigate how the rate of an electron-transfer reaction depends on the molecule-cavity coupling in the ultrastrong coupling regime, where the coupling strength is comparable in magnitude with both the vibrational and the cavity frequencies. We found two main factors that determine the modification of the reaction rate: the relative shifts of the energy levels induced by the coupling and the mixing of the ground and excited states of molecular vibration in the ground state of the hybrid molecule-plus-cavity system through which the Franck-Condon factor between the initial and final states of the transition is altered. The former is the dominant factor if the molecule-cavity coupling strengths for the reactant and product states differ significantly from each other and gives rise to an increase in the reaction rate over a wide range of system’s parameters. The latter dominates if the coupling strengths and energy levels of the reactant and product states are close to each other and it leads to a decrease in the reaction rate. The effect of the mixing of molecular vibrational states on the reaction rate is, however, suppressed in a system containing a large number of molecules due to the collective nature of the resulting polariton, and thus should be observed in a system containing a small number of molecules. In contrast, the effect of the relative shifts of the energy levels should be essentially independent of the number of molecules coupled to the cavity.
The greenhouse gas offset potential from seagrass restoration
Authors: Oreska Matthew P. J. , McGlathery Karen J. , Aoki Lillian R. , Berger Amélie C. , Berg Peter , Mullins Lindsay 
Published: April 2020

AbstractAwarding CO2 offset credits may incentivize seagrass restoration projects and help reverse greenhouse gas (GHG) emissions from global seagrass loss. However, no study has quantified net GHG removal from the atmosphere from a seagrass restoration project, which would require coupled Corg stock and GHG flux enhancement measurements, or determined whether the creditable offset benefit can finance the restoration. We measured all of the necessary GHG accounting parameters in the 7-km2Zostera marina (eelgrass) meadow in Virginia, U.S.A., part of the largest, most cost-effective meadow restoration to date, to provide the first seagrass offset finance test-of-concept. Restoring seagrass removed 9,600 tCO2 from the atmosphere over 15 years but also enhanced both CH4 and N2O production, releasing 950 tCO2e. Despite tripling the N2O flux to 0.06 g m−2 yr−1 and increasing CH4 8-fold to 0.8 g m−2 yr−1, the meadow now offsets 0.42 tCO2e ha−1 yr−1, which is roughly equivalent to the seagrass sequestration rate for GHG inventory accounting but lower than the rates for temperate and tropical forests. The financial benefit for this highly successful project, $87 K at $10 MtCO2e−1, defrays ~10% of the restoration cost. Managers should also consider seagrass co-benefits, which provide additional incentives for seagrass restoration.
CRISPR/Cas9 mediated genetic resource for unknown kinase and phosphatase genes in Drosophila
Authors: Wu Menghua , Zhang Xuedi , Wei Wei , Long Li , An Sainan , Gao Guanjun 
Published: April 2020

AbstractKinases and phosphatases are crucial for cellular processes and animal development. Various sets of resources in Drosophila have contributed significantly to the identification of kinases, phosphatases and their regulators. However, there are still many kinases, phosphatases and associate genes with unknown functions in the Drosophila genome. In this study, we utilized a CRISPR/Cas9 strategy to generate stable mutants for these unknown kinases, phosphatases and associate factors in Drosophila. For all the 156 unknown gene loci, we totally obtained 385 mutant alleles of 105 candidates, with 18 failure due to low efficiency of selected gRNAs and other 33 failure due to few recovered F0, which indicated high probability of lethal genes. From all the 105 mutated genes, we observed 9 whose mutants were lethal and another 4 sterile, most of which with human orthologs referred in OMIM, representing their huge value for human disease research. Here, we deliver these mutants as an open resource for more interesting studies.
Development but not diet alters microbial communities in the Neotropical arboreal trap jaw ant Daceton armigerum: an exploratory study
Authors: Ramalho Manuela O. , Duplais Christophe , Orivel Jérôme , Dejean Alain , Gibson Joshua C. , Suarez Andrew V. , Moreau Corrie S. 
Published: April 2020

AbstractTo better understand the evolutionary significance of symbiotic interactions in nature, microbiome studies can help to identify the ecological factors that may shape host-associated microbial communities. In this study we explored both 16S and 18S rRNA microbial communities of D. armigerum from both wild caught individuals collected in the Amazon and individuals kept in the laboratory and fed on controlled diets. We also investigated the role of colony, sample type, development and caste on structuring microbial communities. Our bacterial results (16S rRNA) reveal that (1) there are colony level differences between bacterial communities; (2) castes do not structure communities; (3) immature stages (brood) have different bacterial communities than adults; and 4) individuals kept in the laboratory with a restricted diet showed no differences in their bacterial communities from their wild caught nest mates, which could indicate the presence of a stable and persistent resident bacterial community in this host species. The same categories were also tested for microbial eukaryote communities (18S rRNA), and (5) developmental stage has an influence on the diversity recovered; (6) the diversity of taxa recovered has shown this can be an important tool to understand additional aspects of host biology and species interactions.
Replication analysis of variants associated with multiple sclerosis risk
Authors: Dashti Mohammad , Ateyah Khadijah , Alroughani Raed , Al-Temaimi Rabeah 
Published: April 2020

AbstractMultiple Sclerosis (MS) is a complex chronic neurodegenerative disorder resulting from an autoimmune reaction against myelin. So far, many genetic variants have been reported to associate with MS risk however their association is inconsistent across different populations. Here we investigated the association of the most consistently reported genetic MS risk variants in the Kuwaiti MS population in a case-control study designs. Of the 94 reported MS risk variants four variants showed MS risk association in Arabs exome analysis (EVI5 rs11808092 p = 0.0002; TNFRSF1A rs1800693 p = 0.00003; MTHFR rs1801131 p = 0.038; and CD58 rs1414273 p = 0.00007). Replication analysis in Kuwaiti MS cases and healthy controls confirmed EVI5 rs11808092A (OR: 1.6, 95%CI: 1.19–2.16, p = 0.002) and MTHFR rs1801131G (OR: 1.79, 95%CI: 1.3–2.36, p = 0.001) as MS risk genetic factors, while TNFRSF1A rs1800693C had a marginal MS risk association (OR: 1.36, 95%CI: 1.04–1.78, p = 0.025) in the Kuwaiti population. CD58 rs1414273 did not sustain risk association (p = 0.37). In conclusion, EVI5 rs11808092A, TNFRSF1A rs1800693C and MTHFR rs1801131G are MS risk factors in the Kuwaiti population. Further investigations into their roles in MS pathogenesis and progression are merited.