bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Comparative Evaluation of Cardiothoracic Radiology Fellowship Website Content
Authors: Gibney Brian , Redmond Ciaran E. , Niu Bonnie , Hamid Saira , Kim Gio , O’Neill Siobhán B. , Khosa Faisal 
Published: February 2020

Purpose:
Prospective radiology fellows often rely on the internet to obtain information with regard to the application process for and the unique qualities of different fellowship programs. The aim of this study was to analyze the content of websites of the United States’ and Canadian cardiothoracic radiology fellowships.

Methods:
All active Cardiothoracic Radiology fellowship websites as of July 2019 were evaluated and compared using 25 criteria in the following domains: Application, Recruitment, Clinical Training, Education/Research, and Incentives. Program website information availability was compared by geographic region.

Results:
There were 60 active cardiothoracic radiology fellowships, and 59 of these fellowships had a dedicated fellowship website. Websites, on average, had 9.3 of the 25 criteria (37.2%). The mean number of schools that satisfied the criterion in the “Incentives” domain ([7.75/59] 10.5%±2.8%) was significantly lower than that for the “Application Process” domain ([40.50/59]; 68.7%±40.6%) (P=0.01). There was no significant difference in the information content of programs in different geographic regions (P=0.246).

Conclusion:
Most cardiothoracic radiology fellowship websites were lacking content relevant to prospective fellows. Provision of more relevant and easily accessible online content may support programs to better inform and recruit residents and to promote the specialty of cardiothoracic radiology.
Accelerating availability of clinically-relevant parameter estimates from thromboelastogram point-of-care device
Authors: Pressly Michelle A. , Parker Robert S. , Neal Matthew D. , Sperry Jason L. , Clermont Gilles 
Published: February 2020

BACKGROUND
Modeling approaches offer a novel way to detect and predict coagulopathy in trauma patients. A dynamic model, built and tested on thromboelastogram (TEG) data, was used to generate a virtual library of over 160,000 simulated RapidTEGs. The patient-specific parameters are the initial platelet count, platelet activation rate, thrombus growth rate, and lysis rate (P(0), k1, k2, and k3, respectively).

METHODS
Patient data from both STAAMP (n = 182 patients) and PAMPer (n = 111 patients) clinical trials were collected. A total of 873 RapidTEGs were analyzed. One hundred sixteen TEGs indicated maximum amplitude (MA) below normal and 466 TEGs indicated lysis percent above normal. Each patient's TEG response was compared against the virtual library of TEGs to determine library trajectories having the least sum-of-squared error versus the patient TEG up to each specified evaluation time ∈ (3, 4, 5, 7.5, 10, 15, 20 minutes). Using 10 nearest-neighbor trajectories, a logistic regression was performed to predict if the patient TEG indicated MA below normal (<50 mm), lysis percent 30 minutes after MA (LY30) greater than 3%, and/or blood transfusion need using the parameters from the dynamic model.

RESULTS
The algorithm predicts abnormal MA values using the initial 3 minutes of RapidTEG data with a median area under the curve of 0.95, and improves with more data to 0.98 by 10 minutes. Prediction of future platelet and packed red blood cell transfusion based on parameters at 4 and 5 minutes, respectively, provides equivalent predictions to the traditional TEG parameters in significantly less time. Dynamic model parameters could not predict abnormal LY30 or future fresh-frozen plasma transfusion.

CONCLUSION
This analysis could be incorporated into TEG software and workflow to quickly estimate if the MA would be below or above threshold value within the initial minutes following a TEG, along with an estimate of what blood products to have on hand.

LEVEL OF EVIDENCE
Therapeutic/Care Management: Level IV.
Insulin-like signalling influences the coordination ofDrosophilalarval hemocyte number with body size
Authors: Bakopoulos Daniel , Beadle Lauren Forbes , Esposito Katherine M. , Mirth Christen K. , Warr Coral G. , Johnson Travis K. 
Published: February 2020

AbstractBlood cells, known as hemocytes in invertebrates, play important and conserved roles in immunity, wound healing and tissue remodelling. The control of hemocyte number is therefore critical to ensure these functions are not compromised, and studies usingDrosophilaare proving useful for understanding how this occurs. Recently, the well characterised embryonic patterning gene,torso-like(tsl), was identified as being required both for normal hemocyte number and for providing immunity against certain pathogens. Here, we report that Tsl is required specifically during the larval phase of hematopoiesis, and that the reduced hemocyte number found intslmutant larvae is likely the result of a reduced larval growth rate and compromised insulin signalling. Consistent with this, we find that impairing insulin-mediated growth, either by nutrient deprivation or genetically, results in fewer hemocytes. This is likely the result of impaired insulin-like signalling in the hemocytes themselves since modulation of Insulin-like Receptor (InR) activity specifically in hemocytes causes concomitant changes to their population size in developing larvae. Taken together, our work reveals the strong relationship that exists between body size and hemocyte number, and suggests that insulin-like signalling contributes to, but is not solely responsible for, keeping these tightly aligned during larval development.
Growth differentiation factor-15 is associated with age-related monocyte immunosenescence
Authors: Pence Brandt D. , Yarbro Johnathan R. , Emmons Russell S. 
Published: February 2020

ABSTRACTBackgroundImmunosenescence is an age-associated decrease in function of immune cells precipitated by a variety of mechanisms and affecting nearly every immune cell subset. In myeloid cell subsets, aging reduces numbers of phagocytes and impairs their functional abilities, including antigen presentation, phagocytosis, and bacterial clearance. Recently, we have described an aging effect on several functions indicating immunosenescence in monocytes, including impaired mitochondrial function and reduced inflammatory cytokine gene expression during stimulation with lipopolysaccharide (LPS). We hypothesized that circulating factors altered by the aging process underly these changes. Growth/differentiation factor-15 (GDF-15) is a distant member of the transforming growth factor-beta superfamily that has known anti-inflammatory effects in macrophages and has recently been shown to be highly differentially expressed during aging. We used biobanked serum and plasma samples to assay circulating GDF-15 levels in subjects from our previous studies and examined correlations between GDF-15 levels and monocyte mitochondrial function and inflammatory responses.ResultsMonocyte interleukin-6 production due to lipopolysaccharide stimulation was negatively correlated to plasma GDF-15 levels. Additionally, serum GDF-15 was positively correlated to circulating CD16+ monocyte proportions and negatively correlated to monocyte mitochondrial respiratory capacity.ConclusionsThe results of these analyses suggest that GDF-15 is a potential circulating factor affecting a variety of monocyte functions and promoting monocyte immunosenescence, and thus may be an attractive candidate for therapeutic intervention to ameliorate this.
Mucosal-associated invariant T (MAIT) cells mediate protective host responses in sepsis
Authors: Trivedi Shubhanshi , Labuz Daniel , Anderson Cole P. , Araujo Claudia V. , Blair Antoinette , Middleton Elizabeth A. , Tran Alex , Mulvey Matthew A. , Campbell Robert A. , Hale J. Scott , Rondina Matthew T. , Leung Daniel T. 
Published: February 2020

AbstractSepsis is a systemic inflammatory response to infection and a leading cause of death. Mucosal-associated invariant T (MAIT) cells are innate-like T cells enriched in mucosal tissues that recognize bacterial ligands. We investigated MAIT cells during clinical and experimental sepsis, and their contribution to host responses. In experimental sepsis, MAIT-deficient mice had significantly increased mortality and bacterial load, and reduced tissue-specific cytokine responses. MAIT cells of WT mice expressed lower levels of IFN-γ and IL-17a during sepsis compared to sham surgery, changes not seen in non-MAIT T cells. MAIT cells of patients presenting with sepsis were significantly reduced in frequency, more activated, and had decreased IFN-γ production when stimulated, compared to healthy donors and paired 90-day post-sepsis samples. Our data suggest that MAIT cells are highly activated and become dysfunctional during clinical sepsis, and contribute to tissue-specific cytokine responses that are protective against mortality during experimental sepsis.
The Endothelial Protein C Receptor plays an essential role in the maintenance of Pregnancy
Authors: Castillo Michelle M , Yang Qiuhui , Sigala Abril Solis , McKinney Dosia T , Zhan Min , Chen Kristen L , Jarzembowski Jason A , Sood Rashmi 
Published: February 2020

ABSTRACTPlacenta-mediated pregnancy complications are a major challenge in the management of maternal-fetal health. Maternal thrombophilia is a suspected risk factor but the role of thrombotic processes in these complications and the potential for antithrombotic treatment have remained unclear. Endothelial Protein C Receptor (EPCR) is an anticoagulant protein highly expressed in the placenta. EPCR autoantibodies and specific gene variants of EPCR are associated with poor pregnancy outcomes. In mice, fetal EPCR deficiency results in placental failure andin uterodeath. Adult EPCR-deficient mice generated by maintaining placental expression exhibit plasma markers of thrombophilia without overt thrombosis. We demonstrate that inactivation of clotting factor VIII or Protease Activated Receptor 4 (Par4), Par3 or integrin αIIb in the mother allows placental development and intrauterine survival of murine embryos lacking EPCR. Rescued EPCR-deficient embryos exhibit thrombosis in placental venous sinuses at late gestation and a high rate of neonatal lethality. In contrast to fetal EPCR deficiency, maternal deficiency of EPCR results in frequent stillbirths and maternal death accompanied by pathological findings that resemble placental abruption and consumptive coagulopathy. Inactivation of Par4, but not clotting factor VIII, prevents maternal death and restores normal pregnancy outcomes. These observations establish a cause-effect relationship between maternal thrombophilia and placental abruption. They demonstrate that sites of uteroplacental thrombosis and the potential response to antithrombotic intervention may differ with gestational age and maternal versus fetal origin of thrombophilia. Our findings highlight the potential for therapeutic inhibition of thrombin-mediated platelet activation in a subset of pregnancy complications.KEY POINTSMurine model establishes a cause-effect relationship between maternal thrombophilia, retroplacental hemorrhage and severe pregnancy complications.Thrombin-mediated activation of maternal platelets is a key event in thrombophilia-associated pregnancy complications and a potential target of therapeutic intervention.Maternal venous channels in uteroplacental circulation are additional sites of thrombotic pathology associated with adverse neonatal outcomes.
Direct Observation Of Vesicle Transport On The Synaptic Ribbon Provides Evidence That Vesicles Are Mobilized And Prepared Rapidly For Release
Authors: Joselevitch Christina , Zenisek David 
Published: February 2020

SUMMARYSynaptic ribbons are thought to provide vesicles for continuous synaptic transmission in some retinal non-spiking neurons, yet recent studies indicate that genetic removal of the ribbon has little effect on vesicle release kinetics. To investigate vesicle replenishment at synaptic ribbons, we imaged synaptic vesicles and ribbons in retinal bipolar cells with TIRF microscopy during stimulation with trains of 30-ms depolarizations. Analysis of vesicles released by the stimuli revealed that the vast majority of releasable vesicles reside within 300 nm of the ribbon center. A single 30-ms step to 0 mV was sufficient to deplete the most membrane-proximal vesicle pool, while triggering rapid stepwise movements of distal vesicles along the ribbon and toward the plasma membrane.Replenishment only becomes rate-limiting for recovery from paired-pulse depression for interstimulus intervals shorter than 250 ms. For longer interstimulus intervals, vesicle movement down the ribbon is fast enough to replenish released vesicles, but newly arrived vesicles are not release-ready. Notably, vesicle re-supply is 40-to 50-fold faster than previously measured in non-ribbon conventional synapses, whereas vesicle maturation rate is comparable. Moreover, in contrast to conventional synapses, vesicles docked at the base of the ribbon release with high fidelity. Lastly, our data show that with multiple stimuli, the delay in vesicle departure increases. Our results support a role for ribbons in the rapid supply and efficient preparation of vesicles for release, provide direct measurements of vesicle movement down the synaptic ribbon and suggest that multiple factors contribute to paired-pulse depression.
Bud23 promotes the progression of the Small Subunit Processome to the pre-40S ribosome inSaccharomyces cerevisiae
Authors: Black Joshua J. , Sardana Richa , Elmir Ezzeddine W. , Johnson Arlen W. 
Published: February 2020

AbstractThe first metastable assembly intermediate of the eukaryotic ribosomal small subunit (SSU) is the SSU Processome, a large complex of RNA and protein factors that is thought to represent an early checkpoint in the assembly pathway. Transition of the SSU Processome towards continued maturation requires the removal of the U3 snoRNA and biogenesis factors as well as ribosomal RNA processing. While the factors that drive these events are largely known, how they do so is not well understood. The methyltransferase Bud23 has a role during this transition, but its function, beyond the nonessential methylation of 18S rRNA, is not characterized. Here, we have carried out a comprehensive genetic screen to understand Bud23 function. We identified 67 unique extragenicbud23Δ-suppressing mutations that mapped to genes encoding the SSU Processome factorsDHR1, IMP4, UTP2(NOP14),BMS1and the SSU proteinRPS28A. These factors form a physical interaction network that links the binding site of Bud23 to the U3 snoRNA and many of the suppressing mutations weaken protein-protein and protein-RNA interactions. Importantly, this network links Bud23 to the GTPase Bms1 and the RNA helicase Dhr1. Bms1 is thought to drive conformational changes to promote rRNA cleavage, and we previously showed that Dhr1 is required for unwinding the U3 snoRNA. Moreover, particles isolated from cells lacking Bud23 accumulated late SSU Processome factors and pre-rRNAs not cleaved at sites A1 and A2. We propose a model in which Bud23 dissociates factors surrounding its binding site to promote SSU Processome progression.Author summaryRibosomes are the molecular machines that synthesize proteins and are composed of a large and a small subunit which carry out the essential functions of polypeptide synthesis and mRNA decoding, respectively. Ribosome production is tightly linked to cellular growth as cells must produce enough ribosomes to meet their protein needs. However, ribosome assembly is a metabolically expensive pathway that must be balanced with other cellular energy needs and regulated accordingly. In eukaryotes, the small subunit (SSU) Processome is a metastable intermediate that ultimately progresses towards a mature SSU through the release of biogenesis factors. The decision to progress the SSU Processome is thought to be an early checkpoint in the SSU assembly pathway, but what drives this checkpoint is unknown. Previous studies suggest that Bud23 plays an uncharacterized role during SSU Processome progression. Here, we used a genetic approach to understand its function and found that Bud23 is connected to a network of factors that stabilize the particle. Interestingly, two of these factors are enzymes that facilitate structural rearrangements needed for progression. We conclude that Bud23 promotes the release of factors surrounding its binding site to drive rearrangements during the progression of the SSU Processome.
Escherichia coli σ38promoters use two UP elements instead of a −35 element: resolution of a paradox and discovery thatσ38transcribes ribosomal promoters
Authors: Franco Kevin S. , Sun Zhe , Chen Yixiong , Cagliero Cedric , Zuo Yuhong , Zhou Yan Ning , Kashlev Mikhail , Jin Ding Jun , Schneider Thomas D. 
Published: February 2020

1AbstractInE. coli, one RNA polymerase (RNAP) transcribes all RNA species, and different regulons are transcribed by employing different sigma (σ) factors. RNAP containingσ38(σS) activates genes responding to stress conditions such as stationary phase. The structure ofσ38promoters has been controversial for more than two decades. To construct a model ofσ38promoters using information theory, we aligned proven transcriptional start sites to maximize the sequence information, in bits, and identified a −10 element similar toσ70promoters. We could not align any −35 sequence logo; instead we found two patterns upstream of the −35 region. These patterns have dyad symmetry sequences and correspond to the location of UP elements in ribosomal RNA (rRNA) promoters. Additionally the UP element dyad symmetry suggests that the two polymeraseαsubunits, which bind to the UPs, should have two-fold dyad axis of symmetry on the polymerase and this is indeed observed in an X-ray crystal structure. Curiously theαCTDs should compete for overlapping UP elements.In vitroexperiments confirm thatσ38recognizes therrnBP1 promoter, requires a −10, UP elements and no −35. This clarifies the long-standing paradox of howσ38promoters differ from those ofσ70.
Random access DNA memory in a scalable, archival file storage system
Authors: Banal James L. , Shepherd Tyson R. , Berleant Joseph , Huang Hellen , Reyes Miguel , Ackerman Cheri M. , Blainey Paul C. , Bathe Mark 
Published: February 2020

ABSTRACTDNA is an ultra-high-density storage medium that could meet exponentially growing worldwide demand for archival data storage if DNA synthesis costs declined sufficiently and random access of files within exabyte-to-yottabyte-scale DNA data pools were feasible. To overcome the second barrier, here we encapsulate data-encoding DNA file sequences within impervious silica capsules that are surface-labeled with single-stranded DNA barcodes. Barcodes are chosen to represent file metadata, enabling efficient and direct selection of sets of files with Boolean logic. We demonstrate random access of image files from an image database using fluorescence sorting with selection sensitivity of 1 in 106files, which thereby enables 1 in 106NperNoptical channels. Our strategy thereby offers retrieval of random file subsets from exabyte and larger-scale long-term DNA file storage databases, offering a scalable solution for random-access of archival files in massive molecular datasets.
Genome sequence analysis of a giant-rooted ‘Sakurajima daikon’ radish (Raphanus sativus)
Authors: Shirasawa Kenta , Hirakawa Hideki , Fukino Nobuko , Kitashiba Hiroyasu , Isobe Sachiko 
Published: February 2020

AbstractDaikon radish (Raphanus sativus) roots vary in size and shape between cultivars. This study reports the genome sequence assembly of a giant-rooted ‘Sakurajima daikon’ radish variety, ‘Okute-Sakurajima’, which produces extremely large round roots. Radish genome assembly is hampered by the repetitive and complex nature of the genome. To address this, single-molecule real-time technology was used to obtain long-read sequences at 60× genome coverage.De novoassembly of the long reads generated 504.5 Mb contig sequences consisting of 1,437 sequences with contig N50 length of 1.2 Mb, including 94.1% of the core eukaryotic genes. Nine pseudomolecule sequences, comprising 69.3% of the assembled contig length, were generated with high-density SNP genetic maps. The chromosome-level sequences revealed structure variations and rearrangements among Brassicaceae genomes. In total, 89,915 genes were predicted in the ‘Okute-Sakurajima’ genome, 30,033 of which were unique to the assembly in this study. The improved genome information generated in this study will not only form a new baseline resource for radish genomics, but will also provide insights into the molecular mechanisms underlying formation of giant radish roots.
Loss of Sister Kinetochore Co-orientation and Peri-centromeric Cohesin Protection after Meiosis I Depends on Cleavage of Centromeric REC8
Authors: Ogushi Sugako , Rattani Ahmed , Godwin Jonathan , Metson Jean , Schermelleh Lothar , Nasmyth Kim 
Published: February 2020

SummaryProtection of peri-centromeric REC8 cohesin from separase and sister kinetochore attachment to microtubules emanating from the same spindle pole (co-orientation) ensure that sister chromatids remain associated after meiosis I. Both features are lost during meiosis II, when sister kinetochores bi-orient and lose peri-centromeric REC8 protection, resulting in sister chromatid disjunction and the production of haploid gametes. By transferring spindle-chromosome complexes (SCCs) between meiosis I and II cells, we have discovered that both sister kinetochore co-orientation and peri-centromeric cohesin protection depend on the SCC and not the cytoplasm. Moreover, the catalytic activity of separase at meiosis I is necessary not only for converting kinetochores from a co-to a bi-oriented state but also for deprotection of peri-centromeric cohesin and that cleavage of REC8 may be the key event. Crucially, we show that selective cleavage of REC8 in the vicinity of kinetochores is sufficient to destroy co-orientation in univalent chromosomes, albeit not in bivalents where resolution of chiasmata through cleavage of Rec8 along chromosome arms may also be required.
Freshwater monitoring by nanopore sequencing
Authors: Urban Lara , Holzer Andre , Baronas J Jotautas , Hall Michael , Braeuninger-Weimer Philipp , Scherm Michael J , Kunz Daniel J , Perera Surangi N , Martin-Herranz Daniel E , Tipper Edward T , Salter Susannah J , Stammnitz Maximilian R 
Published: February 2020

ABSTRACTWhile traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet,in situmetagenomic water surveys face substantial challenges in cost and logistics. Here we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices.