bluuebunny/crossref_metadata_2025 huggingface dataset:
Interrupted Time-Series Analysis to Evaluate the Impact of a National Antimicrobial Stewardship Campaign on Antibiotic Prescribing: A Typical Practice in China’s Primary Care
Authors: Li Hui , Gong Yanhong , Han Jing , Zhang Shengchao , Chen Shanquan , Xu Xing , Lu Zuxun , Yin Xiaoxv
Published: July 2020

Background

After implementing the 2011 national antimicrobial stewardship campaign, few studies focused on evaluating its effect in China’s primary care facilities.

Methods

We randomly selected 11 community health centers in Shenzhen, China, and collected all outpatient prescriptions of these centers from 2010 to 2015. To evaluate the impact of local interventions on antibiotic prescribing, we used a segmented regression model of interrupted time series to analyze 7 outcomes (ie, percentage of prescriptions with antibiotics, and percentages of prescriptions with broad-spectrum antibiotics, with parenteral antibiotics, and with 2 or more antibiotics in all prescriptions or antibiotic-containing prescriptions).

Results

Overall, 1 482 223 outpatient prescriptions were obtained. The intervention was associated with a significant immediate change (–5.2%, P = .04) and change in slope (–3.1% per month, P < .01) for the percentage of prescriptions with antibiotics, and its relative cumulative effect at the end of the study was –74.0% (95% confidence interval, –79.0 to –69.1). After the intervention, the percentage of prescriptions with broad-spectrum and with parenteral antibiotics decreased dramatically by 36.7% and 77.3%, respectively, but their percentages in antibiotic-containing prescriptions decreased insignificantly. Percentage of prescriptions with two or more antibiotics in all prescriptions or antibiotic-containing prescriptions only showed immediate changes, but significant changes in slope were not observed.

Conclusions

A typical practice in Shenzhen, China, showed that strict enforcement of the antimicrobial stewardship campaign could effectively reduce antibiotic prescribing in primary care with a stable long-term effect. However, prescribing of broad-spectrum and parenteral antibiotics was still prevalent. More targeted interventions are required to promote appropriate antibiotic use.
Context sensitivity and economic-geographic (re)theorising
Authors: Gong Huiwen , Hassink Robert
Published: July 2020

Drawing upon critical realism and the literature on theorising in social sciences, this article contributes to the understanding of theorising in economic geography by highlighting the role of context throughout the theory development process. By critically reviewing two key concepts in economic geography—related variety and knowledge bases—from a critical realist theory development perspective, scholars’ sensitivity to local context through the whole theorising process is examined. We argue that the particular strength of economic geography with regard to advancing theory lies in the continuous application of concepts and theories (that is, generalities) within new contexts (that is, confrontation with new particularities).
Ultrasensitive DNA Immune Repertoire Sequencing Using Unique Molecular Identifiers
Authors: Johansson Gustav , Kaltak Melita , Rîmniceanu Cristiana , Singh Avadhesh K , Lycke Jan , Malmeström Clas , Hühn Michael , Vaarala Outi , Cardell Susanna , Ståhlberg Anders
Published: July 2020

Background

Immune repertoire sequencing of the T-cell receptor can identify clonotypes that have expanded as a result of antigen recognition or hematological malignancies. However, current sequencing protocols display limitations with nonuniform amplification and polymerase-induced errors during sequencing. Here, we developed a sequencing method that overcame these issues and applied it to γδ T cells, a cell type that plays a unique role in immunity, autoimmunity, homeostasis of intestine, skin, adipose tissue, and cancer biology.

Methods

The ultrasensitive immune repertoire sequencing method used PCR-introduced unique molecular identifiers. We constructed a 32-panel assay that captured the full diversity of the recombined T-cell receptor delta loci in γδ T cells. The protocol was validated on synthetic reference molecules and blood samples of healthy individuals.

Results

The 32-panel assay displayed wide dynamic range, high reproducibility, and analytical sensitivity with single-nucleotide resolution. The method corrected for sequencing-depended quantification bias and polymerase-induced errors and could be applied to both enriched and nonenriched cells. Healthy donors displayed oligoclonal expansion of γδ T cells and similar frequencies of clonotypes were detected in both enrichment and nonenriched samples.

Conclusions

Ultrasensitive immune repertoire sequencing strategy enables quantification of individual and specific clonotypes in a background that can be applied to clinical as well as basic application areas. Our approach is simple, flexible, and can easily be implemented in any molecular laboratory.
Angiopoietin-1 enhanced myocyte mitosis, engraftment, and the reparability of hiPSC-CMs for treatment of myocardial infarction
Authors: Tao Zhonghao , Loo Szejie , Su Liping , Tan Shihua , Tee Guizhen , Gan Shu Uin , Zhang Jianyi , Chen Xin , Ye Lei
Published: July 2020

Aims

To examine whether transient over-expression of angiopoietin-1 (Ang-1) increases the potency of hiPSC-CMs for treatment of heart failure.

Methods and results

Atrial hiPSC-CMs (hiPSC-aCMs) were differentiated from hiPSCs and purified by lactic acid and were transfected with Ang-1 (Ang-1-hiPSC-aCMs) plasmid using lipoSTEM. Ang-1 gene transfection efficiency was characterized in vitro. Gene transfected CMs (1×106) were seeded into a fibrin/thrombin patch and implanted on the rat-infarcted left ventricular (LV) anterior wall after myocardial infarction (MI). Echo function was determined at 1- and 6 weeks post-MI. Immunohistochemistry study was performed at 6 weeks post-MI. Ang-1 (20 and 40 ng/mL) protected hiPSC-aCMs from hypoxia through up-regulating pERK1/2 and inhibiting Bax protein expressions. Ang-1-hiPSC-aCMs transiently secreted Ang-1 protein up to 14 days, with peak level on day-2 post-transfection (24.39 ± 13.02 ng/mL) in vitro. Animal study showed that transplantation of Ang-1-hiPSC-aCM seeded patch more effectively limited rat heart apoptosis at 1 day post-MI as compared with LipoSTEM-Ang-1 or hiPSC-aCMs transplantation. Ang-1-hiPSC-aCMs transplantation induced host (rat) and donor (human) CM mitosis and arteriole formation, improved cell engraftment rate, more effectively limited LV dilation (EDV = 460.7 ± 96.1 μL and ESV = 219.8 ± 72.9 μL) and improved LV global pump function (EF = 53.1 ± 9%) as compared with the MI (EDV = 570.9 ± 91.8 μL, P = 0.033; ESV = 331.6 ± 71.2 μL, P = 0.011; EF = 42.3 ± 4.1%, P = 0.02) or the LipoSTEM-Ang-1 injected (EDV = 491.4 ± 100.4 μL, P = 0.854; ESV = 280.9 ± 71.5 μL, P = 0.287; EF = 43.2 ± 4.6, P = 0.039) or hiPSC-CM transplanted (EDV = 547.9 ± 55.5 μL, P = 0.095; ESV = 300.2 ± 88.4 μL, P = 0.075; EF = 46 ± 10.9%, P = 0.166) animal groups at 6 weeks post-MI and treatment.

Conclusion

Transient over-expression of Ang-1 enhanced hiPSC-aCM mitosis and engraftment and increased the reparability potency of hiPSC-aCMs for treatment of MI.
A novel method for measuring absolute coronary blood flow and microvascular resistance in patients with ischaemic heart disease
Authors: Morris Paul D , Gosling Rebecca , Zwierzak Iwona , Evans Holli , Aubiniere-Robb Louise , Czechowicz Krzysztof , Evans Paul C , Hose D Rodney , Lawford Patricia V , Narracott Andrew J , Gunn Julian P
Published: July 2020

Aims

Ischaemic heart disease is the reduction of myocardial blood flow, caused by epicardial and/or microvascular disease. Both are common and prognostically important conditions, with distinct guideline-indicated management. Fractional flow reserve (FFR) is the current gold-standard assessment of epicardial coronary disease but is only a surrogate of flow and only predicts percentage flow changes. It cannot assess absolute (volumetric) flow or microvascular disease. The aim of this study was to develop and validate a novel method that predicts absolute coronary blood flow and microvascular resistance (MVR) in the catheter laboratory.

Methods and results

A computational fluid dynamics (CFD) model was used to predict absolute coronary flow (QCFD) and coronary MVR using data from routine invasive angiography and pressure-wire assessment. QCFD was validated in an in vitro flow circuit which incorporated patient-specific, three-dimensional printed coronary arteries; and then in vivo, in patients with coronary disease. In vitro, QCFD agreed closely with the experimental flow over all flow rates [bias +2.08 mL/min; 95% confidence interval (error range) −4.7 to +8.8 mL/min; R2 = 0.999, P < 0.001; variability coefficient <1%]. In vivo, QCFD and MVR were successfully computed in all 40 patients under baseline and hyperaemic conditions, from which coronary flow reserve (CFR) was also calculated. QCFD-derived CFR correlated closely with pressure-derived CFR (R2 = 0.92, P < 0.001). This novel method was significantly more accurate than Doppler-wire-derived flow both in vitro (±6.7 vs. ±34 mL/min) and in vivo (±0.9 vs. ±24.4 mmHg).

Conclusions

Absolute coronary flow and MVR can be determined alongside FFR, in absolute units, during routine catheter laboratory assessment, without the need for additional catheters, wires or drug infusions. Using this novel method, epicardial and microvascular disease can be discriminated and quantified. This comprehensive coronary physiological assessment may enable a new level of patient stratification and management.
Agricultural bankers’ farmland price expectations
Authors: Kuethe Todd H , Oppedahl David
Published: July 2020

Previous studies provide conflicting evidence on the degree to which Federal Reserve surveys of agricultural bankers provide useful information on the future direction of farm real estate values. We use unbalanced panel of responses from the Federal Reserve Bank of Chicago’s Land Values and Credit Conditions Survey between 1993Q1 and 2019Q2 to empirically test adaptive, rational and extrapolative expectations. We find that respondents extrapolate recent farmland price experiences but are overly cautious, as observed farmland price changes tend to be greater than expected. This is the first study of individual farmland price expectations collected by Federal Reserve surveys of agricultural bankers.
Assessing health systems’ preparedness for providing care for refugees, asylum seekers and migrants: a scoping review
Authors: Kocot Ewa , Szetela Anna
Published: July 2020

Background

Health care systems and care professionals often face the challenge of providing adequate health care for migrant groups. The objective of this study is to answer the question of whether and how meeting the special health system requirements regarding refugees (R), asylum seekers (AS) and migrants (M) (RASM) is checked and evaluated.

Methods

A scoping review was used as a methodology of the research, with four electronic databases, websites of relevant organizations and European projects searched, using a strictly defined search strategy. Finally, 66 studies were included in the analysis.

Results

The included studies presented assessment of different types, aspects and facilities of health care, as well as various methods of analysis. In the vast majority of the studies (n = 52, 78%) interviews or questionnaires were used to collect data. The studies were mostly declared to be qualitative. The main issues assessed in the studies can be categorized into three groups: (i) legal aspects, (ii) before receiving health care and (iii) during health care usage.

Conclusions

RASM inflow is a big challenge for health care system in many countries. The first step to guarantee adequate health care for RASM is assessing how the system is functioning. This makes it possible to find gaps, indicate the directions of activities needed and monitor progress. Further work on the development of a comprehensive tool, checked in terms of validity and reliability assessment, and enabling examination of many aspects of health care for RASM should be carried out.
Altered bone development with impaired cartilage formation precedes neuromuscular symptoms in spinal muscular atrophy
Authors: Hensel Niko , Brickwedde Hermann , Tsaknakis Konstantinos , Grages Antonia , Braunschweig Lena , Lüders Katja A , Lorenz Heiko M , Lippross Sebastian , Walter Lisa M , Tavassol Frank , Lienenklaus Stefan , Neunaber Claudia , Claus Peter , Hell Anna K
Published: July 2020

Spinal muscular atrophy (SMA) is a fatal neurodegenerative disease of newborns and children caused by mutations or deletions of the survival of motoneuron gene 1 resulting in low levels of the SMN protein. While neuromuscular degeneration is the cardinal symptom of the disease, the reduction of the ubiquitously expressed SMN additionally elicits non-motoneuron symptoms. Impaired bone development is a key feature of SMA, but it is yet unknown whether this is an indirect functional consequence of muscle weakness or caused by bone-intrinsic mechanisms. Therefore, we radiologically examined SMA patients in a prospective, non-randomized cohort study characterizing bone size and bone mineral density (BMD) and performed equivalent measurements in pre-symptomatic SMA mice. BMD as well as lumbar vertebral body size were significantly reduced in SMA patients. This growth defect but not BMD reduction was confirmed in SMA mice by μCT before the onset of neuromuscular symptoms indicating that it is at least partially independent of neuromuscular degeneration. Interestingly, the number of chondroblasts in the hypertrophic zone of the growth plate was significantly reduced. This was underlined by RNAseq and expression data from developing SMA mice vertebral bodies, which revealed molecular changes related to cell division and cartilage remodeling. Together, these findings suggest a bone intrinsic defect in SMA. This phenotype may not be rescued by novel drugs that enhance SMN levels in the central nervous system only.
Introducing a Human Rights-based Disability Research Methodology
Authors: Arstein-Kerslake Anna , Maker Yvette , Flynn Eilionóir , Ward Olympia , Bell Ruby , Degener Theresia
Published: July 2020

Research has the potential to be a powerful tool for the realisation of the rights of disabled people. However, antiquated research practices continue to marginalise disabled people by excluding them from research; inadequately remunerating them for participation in research; undertaking research that assumes difference; and not including their voice in the leadership design or implementation of research. This article builds on emancipatory, participatory and inclusive research methodologies to introduce a new human rights-based disability research methodology that presents a roadmap to overcome these problems and transform research into a means of rights realisation. It presents a protocol for the methodology that was created by the international Disability Human Rights Research Network. Finally, it explores many challenges that researchers may face when endeavouring to implement the methodology.
Association of Myeloid Liver Kinase B1 Depletion With a Reduction in Alveolar Macrophage Numbers and an Impaired Host Defense During Gram-Negative Pneumonia
Authors: Otto Natasja A , de Vos Alex F , van Heijst Jeroen W J , Roelofs Joris J T H , van der Poll Tom
Published: July 2020

Background

Liver kinase B1 (LKB1) has been studied extensively as a tumor suppressor gene (Stk11) in the context of cancer. We hypothesized that myeloid LKB1 plays a role in innate immunity during pneumonia.

Methods

Mice deficient for LKB1 in myeloid cells (LysM-cre × Stk11fl/fl) or neutrophils (Mrp8-cre × Stk11fl/fl) were infected with Klebsiella pneumoniae via the airways. LysM-cre × Stk11fl/fl mice were also intranasally challenged with lipopolysaccharide (LPS).

Results

Mice with myeloid LKB1 deficiency, but not those with neutrophil LKB1 deficiency, had increased bacterial loads in lungs 6–40 hours after infection, compared with control mice, pointing to a role for LKB1 in macrophages. Myeloid LKB1 deficiency was associated with reduced cytokine release into the airways on local LPS instillation. The number of classic (SiglecFhighCD11bneg) alveolar macrophages (AMs) was reduced by approximately 50% in the lungs of myeloid LKB1–deficient mice, which was not caused by increased cell death or reduced proliferation. Instead, these mice had AMs with a “nonclassic” (SiglecFlowCD11bpos) phenotype. AMs did not up-regulate glycolysis in response to LPS, irrespective of LKB1 presence.

Conclusion

Myeloid LKB1 is important for local host defense during Klebsiella pneumonia by maintaining adequate AM numbers in the lung.
Induction of the Coxsackievirus and Adenovirus Receptor in Macrophages During the Formation of Atherosclerotic Plaques
Authors: Nilchian Azadeh , Plant Estelle , Parniewska Malgorzata M , Santiago Ana , Rossignoli Aránzazu , Skogsberg Josefin , Hedin Ulf , Matic Ljubica , Fuxe Jonas
Published: July 2020

Multiple viruses are implicated in atherosclerosis, but the mechanisms by which they infect cells and contribute to plaque formation in arterial walls are not well understood. Based on reports showing the presence of enterovirus in atherosclerotic plaques we hypothesized that the coxsackievirus and adenovirus receptor (CXADR/CAR), although absent in normal arteries, could be induced during plaque formation. Large-scale microarray and mass spectrometric analyses revealed significant up-regulation of CXADR messenger RNA and protein levels in plaque-invested carotid arteries compared with control arteries. Macrophages were identified as a previously unknown cellular source of CXADR in human plaques and plaques from Ldr−/−Apob100/100 mice. CXADR was specifically associated with M1-polarized macrophages and foam cells and was experimentally induced during macrophage differentiation. Furthermore, it was significantly correlated with receptors for other viruses linked to atherosclerosis. The results show that CXADR is induced in macrophages during plaque formation, suggesting a mechanism by which enterovirus infect cells in atherosclerotic plaques.
Trialstreamer: A living, automatically updated database of clinical trial reports
Authors: Marshall Iain J , Nye Benjamin , Kuiper Joël , Noel-Storr Anna , Marshall Rachel , Maclean Rory , Soboczenski Frank , Nenkova Ani , Thomas James , Wallace Byron C
Published: July 2020

Objective

Randomized controlled trials (RCTs) are the gold standard method for evaluating whether a treatment works in health care but can be difficult to find and make use of. We describe the development and evaluation of a system to automatically find and categorize all new RCT reports.

Materials and Methods

Trialstreamer continuously monitors PubMed and the World Health Organization International Clinical Trials Registry Platform, looking for new RCTs in humans using a validated classifier. We combine machine learning and rule-based methods to extract information from the RCT abstracts, including free-text descriptions of trial PICO (populations, interventions/comparators, and outcomes) elements and map these snippets to normalized MeSH (Medical Subject Headings) vocabulary terms. We additionally identify sample sizes, predict the risk of bias, and extract text conveying key findings. We store all extracted data in a database, which we make freely available for download, and via a search portal, which allows users to enter structured clinical queries. Results are ranked automatically to prioritize larger and higher-quality studies.

Results

As of early June 2020, we have indexed 673 191 publications of RCTs, of which 22 363 were published in the first 5 months of 2020 (142 per day). We additionally include 304 111 trial registrations from the International Clinical Trials Registry Platform. The median trial sample size was 66.

Conclusions

We present an automated system for finding and categorizing RCTs. This yields a novel resource: a database of structured information automatically extracted for all published RCTs in humans. We make daily updates of this database available on our website (https://trialstreamer.robotreviewer.net).
Epidemiology and Outcome Analysis of Burns During Explosion Accident at a Major Center in Southwestern China From 2002 to 2016
Authors: Wang Yangping , Zhang Xiaorong , Liu Tengfei , Liu Menglong , Li Haisheng , Huang Yong , Hu Xiaohong , He Weifeng , Luo Gaoxing , Qian Wei
Published: July 2020

Explosions always lead to serious public health, social, and economic problems. We investigated the epidemiology, outcomes, and costs of burn patients caused by explosion accident in Southwest China to explore more effective prevention and treatment strategies. This retrospective study included 497 inpatients with burns during explosion accident admitted to the Institute of Burn Research of Army Medical University from 2002 to 2016. A total of 497 cases (77.78% males) were found, accounting for 2.37% of the total burn patients. The average age was 34.38 ± 15.02 years. The most common etiology was gas explosions (51.51%). Most of the cases were caused by work-related activities. The average TBSA was 31.30 ± 28.32%. The median length of stay (LOS) was 31 days. The LOS was correlated with TBSA, full-thickness burns, older age, number of operations and outcome. The major factors determining the cost were larger TBSA, full-thickness burns, and higher cure rate. The mortality was 6.44%. Larger TBSA and older age were the most important risk factors for the mortality. This study suggested that special attention should be paid to prevent burns during explosion accident in adult males with occupational exposure. In the future, more effective and practical strategies for preventing and treating burns during explosion accident based on related risk factors should be implemented.
Genetic and physiological regulation of folate in pak choi (Brassica rapa subsp. Chinensis) germplasm
Authors: Shohag M J I , Wei Yanyan , Zhang Jie , Feng Ying , Rychlik Michael , He Zhenli , Yang Xiaoe
Published: July 2020

Folates are one of the essential micronutrients for all living organisms. Due to inadequate dietary intake, folate deficiency remains prevalent in humans. Genetically diverse germplasms can potentially be used as parents in breeding programs and also for understanding the folate regulatory network. Therefore, we investigated the natural genetic diversity of folates and their physiological regulation in pak choi (Brassica rapa subsp. Chinensis) germplasm. The total folate concentration ranged from 52.7 μg 100 gFW–1 to 166.9 μg 100 gFW–1, with 3.2-fold variation. The main folate vitamer was represented by 5-CH3-H4folate, with 4.5-fold variation. The activities of GTP cyclohydrolase I and aminodeoxy chorismate synthase, the first step of folate synthesis, were high in high folate accessions and low in low folate accessions. Analysis of the transcription levels of 11 genes associated with folate metabolism demonstrated that the difference in folate concentrations may be primarily controlled at the post-transcriptional level. A general correlation between total folate and their precursors was observed. Folate diversity and chlorophyll content were tightly regulated through the methyl cycle. The diverse genetic variation in pak choi germplasm indicated the great genetic potential to integrate breeding programs for folate biofortification and unravel the physiological basis of folate homeostasis in planta.
Stark broadening of Co ii spectral lines in hot stars and white dwarf spectra
Authors: Majlinger Zlatko , Dimitrijević Milan S , Srećković Vladimir A
Published: July 2020

Stark full widths at half-maximum for 46 Co ii multiplets have been calculated using modified semi-empirical method. The obtained results have been used to demonstrate the importance of Stark broadening mechanism in DA and DB white dwarf and A star atmospheres. With the obtained results we also test possibility of using some approximate methods of Stark width calculations developed on the basis of regularities and systematic trends.
Simulating kilonovae in the ΛCDM universe
Authors: Jiang Zhen , Wang Jie , Zhang Fenghui , Li Li-Xin , Wang Lan , Li Ran , Gao Liang , Han Zhanwen , Pan Jun
Published: July 2020

Kilonovae are optical flashes produced in the aftermath of neutron star–neutron star mergers or neutron star–black hole mergers. In this work, we use the Millennium Simulation, combined with semi-analytic galaxy formation model gabe (Galaxy Assembly with Binary Evolution) to explore the cosmic event rate of kilonovae, and the properties of their host galaxies in a cosmological context. We find that model with supernova kick velocity of $V_{\rm kick}=0\, \, {\rm km}\, \, {\rm s}^{-1}$ fits the observation best, satisfying the preference for low kick velocity binary system in theoretical models. With $V_{\rm kick}=0\, \, {\rm km}\, \, {\rm s}^{-1}$, the cosmic event rate of NNMs and NBMs at z = 0 are 283 and $91\, \, {\rm Gpc}^{-3}\, \, {\rm yr}^{-1}$, respectively, marginally consistent with the constraint from LVC GWTC-1. For Milky Way-mass galaxies, we predict the NNM rate is $25.7^{+59.6}_{-7.1}\, {\rm Myr}^{-1}$, which is also in good agreement with the observed properties of binary neutron stars in the Milky Way. Taking all the kilonovae into account in the history of Milky Way-mass galaxies, we find that the averaged r-process elements yield (A > 79) in an NNM/NBM event should be $0.01\, {\rm M}_\odot$ to be consistent with observation. We conclude that NGC 4993, the host galaxy of GW170817, is a typical host galaxy for NNMs. However, generally, NNMs and NBMs tend to reside in young, blue, star-forming, late-type galaxies, with stellar mass, and gaseous metallicity distribution peaking at $M_{\rm *}=10^{10.65}\, {\rm M}_\odot$ and 12 + log (O/H) = 8.72 − 8.85, respectively. By exploring the connection between kilonovae and their host galaxies in the cosmological background, it is promising to constrain model better when we have more events in the forthcoming future.
The mass, spin, and rotational energy of the remnant black holes from compact binary mergers
Authors: Deng Can-Min
Published: July 2020

Recently, many gravitational wave events from compact binary mergers have been detected by LIGO. Determining the final mass and spin of the remnant black holes (RBHs) is a fundamental issue and is also important in astrophysics. In this paper, unified models for predicting the final mass and spin of the RBHs from compact binary mergers is proposed. The models achieve a good accuracy within the parameter range of interest. In addition, the rotational energy of the RBHs is also studied that relevant to the electromagnetic counterparts of the mergers. It is found the distribution of the rotational energy of the RBHs from different types of mergers of compact binary has its own characteristics, which might help identify the electromagnetic counterparts associated with the mergers.
The interior of Comet 67P/C–G; revisiting CONSERT results with the exact position of the Philae lander
Authors: Kofman Wlodek , Zine Sonia , Herique Alain , Rogez Yves , Jorda Laurent , Levasseur-Regourd Anny-Chantal
Published: July 2020

CONSERT, a bistatic radar onboard the Rosetta spacecraft and its Philae lander, was designed to probe the nucleus of comet 67P/Churyumov–Gerasimenko with radio waves at 90 MHz frequency. In 2016 September, the exact position of Philae was retrieved, within the region previously identified by CONSERT. This allowed us to revisit the measurements and improve our analysis of the properties of the interior, the results of which we present here. The relative permittivity of the materials is found to range from about 1.7 to 1.95 in the shallow subsurface (<25 m) and about 1.2 to 1.32 in the interior. These differences indicate different average densities between the shallow subsurface and the interior of comet. They can be explained by various physical phenomena such as different porosities, the possible compaction of surface materials, or even perhaps different proportions of the same materials. This strongly suggests that the less dense interior has kept its pristine nature.
Intragenic Conflict in Phylogenomic Data Sets
Authors: Smith Stephen A , Walker-Hale Nathanael , Walker Joseph F
Published: July 2020

Most phylogenetic analyses assume that a single evolutionary history underlies one gene. However, both biological processes and errors can cause intragenic conflict. The extent to which this conflict is present in empirical data sets is not well documented, but if common, could have far-reaching implications for phylogenetic analyses. We examined several large phylogenomic data sets from diverse taxa using a fast and simple method to identify well-supported intragenic conflict. We found conflict to be highly variable between data sets, from 1% to >92% of genes investigated. We analyzed four exemplar genes in detail and analyzed simulated data under several scenarios. Our results suggest that alignment error may be one major source of conflict, but other conflicts remain unexplained and may represent biological signal or other errors. Whether as part of data analysis pipelines or to explore biologically processes, analyses of within-gene phylogenetic signal should become common.
Necdin regulates BMAL1 stability and circadian clock through SGT1-HSP90 chaperone machinery
Authors: Lu Renbin , Dong Yufan , Li Jia-Da
Published: July 2020

Circadian clocks are endogenous oscillators that control ∼24-hour physiology and behaviors in virtually all organisms. The circadian oscillator comprises interconnected transcriptional and translational feedback loops, but also requires finely coordinated protein homeostasis including protein degradation and maturation. However, the mechanisms underlying the mammalian clock protein maturation is largely unknown. In this study, we demonstrate that necdin, one of the Prader-Willi syndrome (PWS)-causative genes, is highly expressed in the suprachiasmatic nuclei (SCN), the pacemaker of circadian clocks in mammals. Mice deficient in necdin show abnormal behaviors during an 8-hour advance jet-lag paradigm and disrupted clock gene expression in the liver. By using yeast two hybrid screening, we identified BMAL1, the core component of the circadian clock, and co-chaperone SGT1 as two necdin-interactive proteins. BMAL1 and SGT1 associated with the N-terminal and C-terminal fragments of necdin, respectively. Mechanistically, necdin enables SGT1-HSP90 chaperone machinery to stabilize BMAL1. Depletion of necdin or SGT1/HSP90 leads to degradation of BMAL1 through the ubiquitin–proteasome system, resulting in alterations in both clock gene expression and circadian rhythms. Taken together, our data identify the PWS-associated protein necdin as a novel regulator of the circadian clock, and further emphasize the critical roles of chaperone machinery in circadian clock regulation.
Enhancement of target specificity of CRISPR–Cas12a by using a chimeric DNA–RNA guide
Authors: Kim Hanseop , Lee Wi-jae , Oh Yeounsun , Kang Seung-Hun , Hur Junho K , Lee Hyomin , Song WooJeung , Lim Kyung-Seob , Park Young-Ho , Song Bong-Seok , Jin Yeung Bae , Jun Bong-Hyun , Jung Cheulhee , Lee Dong-Seok , Kim Sun-Uk , Lee Seung Hwan
Published: July 2020

The CRISPR–Cas9 system is widely used for target-specific genome engineering. CRISPR–Cas12a (Cpf1) is one of the CRISPR effectors that controls target genes by recognizing thymine-rich protospacer adjacent motif (PAM) sequences. Cas12a has a higher sensitivity to mismatches in the guide RNA than does Cas9; therefore, off-target sequence recognition and cleavage are lower. However, it tolerates mismatches in regions distant from the PAM sequence (TTTN or TTN) in the protospacer, and off-target cleavage issues may become more problematic when Cas12a activity is improved for therapeutic purposes. Therefore, we investigated off-target cleavage by Cas12a and modified the Cas12a (cr)RNA to address the off-target cleavage issue. We developed a CRISPR–Cas12a that can induce mutations in target DNA sequences in a highly specific and effective manner by partially substituting the (cr)RNA with DNA to change the energy potential of base pairing to the target DNA. A model to explain how chimeric (cr)RNA guided CRISPR–Cas12a and SpCas9 nickase effectively work in the intracellular genome is suggested. Chimeric guide-based CRISPR- Cas12a genome editing with reduced off-target cleavage, and the resultant, increased safety has potential for therapeutic applications in incurable diseases caused by genetic mutations.
Routine serum biomarkers, but not dual-energy X-ray absorptiometry, correlate with cortical bone mineral density in children and young adults with chronic kidney disease
Authors: Lalayiannis Alexander D , Crabtree Nicola J , Ferro Charles J , Askiti Varvara , Mitsioni Andromachi , Biassoni Lorenzo , Kaur Amrit , Sinha Manish D , Wheeler David C , Duncan Neill D , Popoola Joyce , Milford David V , Long Jin , Leonard Mary Beth , Fewtrell Mary , Shroff Rukshana
Published: July 2020

Background. Biomarkers and dual-energy X-ray absorptiometry (DXA) are thought to be poor predictors of bone mineral density (BMD). The Kidney Disease: Improving Global Outcomes guidelines suggest using DXA if the results will affect patient management, but this has not been studied in children or young adults in whom bone mineral accretion continues to 30 years of age. We studied the clinical utility of DXA and serum biomarkers against tibial cortical BMD (CortBMD) measured by peripheral quantitative computed tomography, expressed as Z-score CortBMD, which predicts fracture risk.

Methods. This was a cross-sectional multicentre study in 26 patients with CKD4 and 5 and 77 on dialysis.

Results. Significant bone pain that hindered activities of daily living was present in 58%, and 10% had at least one low-trauma fracture. CortBMD and cortical mineral content Z-scores were lower in dialysis compared with CKD patients (P = 0.004 and P = 0.02). DXA BMD hip and lumbar spine Z-scores did not correlate with CortBMD or biomarkers. CortBMD was negatively associated with parathyroid hormone (PTH; r = −0.44, P < 0.0001) and alkaline phosphatase (ALP; r = −0.22, P = 0.03) and positively with calcium (Ca; r = 0.33, P = 0.001). At PTH <3 times upper limit of normal, none of the patients had a CortBMD below −2 SD (odds ratio 95% confidence interval 7.331 to infinity). On multivariable linear regression PTH (β = −0.43 , P < 0.0001), ALP (β = −0.36, P < 0.0001) and Ca (β = 0.21, P = 0.005) together predicted 57% of variability in CortBMD. DXA measures did not improve this model.

Conclusions. Taken together, routinely used biomarkers, PTH, ALP and Ca, but not DXA, are moderate predictors of cortical BMD. DXA is not clinically useful and should not be routinely performed in children and young adults with CKD 4–5D.
Rapid, label-free detection of diffuse glioma recurrence using intraoperative stimulated Raman histology and deep neural networks
Authors: Hollon Todd C , Pandian Balaji , Urias Esteban , Save Akshay V , Adapa Arjun R , Srinivasan Sudharsan , Jairath Neil K , Farooq Zia , Marie Tamara , Al-Holou Wajd N , Eddy Karen , Heth Jason A , Khalsa Siri Sahib S , Conway Kyle , Sagher Oren , Bruce Jeffrey N , Canoll Peter , Freudiger Christian W , Camelo-Piragua Sandra , Lee Honglak , Orringer Daniel A
Published: July 2020

Background

Detection of glioma recurrence remains a challenge in modern neuro-oncology. Noninvasive radiographic imaging is unable to definitively differentiate true recurrence versus pseudoprogression. Even in biopsied tissue, it can be challenging to differentiate recurrent tumor and treatment effect. We hypothesized that intraoperative stimulated Raman histology (SRH) and deep neural networks can be used to improve the intraoperative detection of glioma recurrence.

Methods

We used fiber laser–based SRH, a label-free, nonconsumptive, high-resolution microscopy method (<60 sec per 1 × 1 mm2) to image a cohort of patients (n = 35) with suspected recurrent gliomas who underwent biopsy or resection. The SRH images were then used to train a convolutional neural network (CNN) and develop an inference algorithm to detect viable recurrent glioma. Following network training, the performance of the CNN was tested for diagnostic accuracy in a retrospective cohort (n = 48).

Results

Using patch-level CNN predictions, the inference algorithm returns a single Bernoulli distribution for the probability of tumor recurrence for each surgical specimen or patient. The external SRH validation dataset consisted of 48 patients (recurrent, 30; pseudoprogression, 18), and we achieved a diagnostic accuracy of 95.8%.

Conclusion

SRH with CNN-based diagnosis can be used to improve the intraoperative detection of glioma recurrence in near-real time. Our results provide insight into how optical imaging and computer vision can be combined to augment conventional diagnostic methods and improve the quality of specimen sampling at glioma recurrence.
Multi-decadal (1972–2019) Mnemiopsis leidyi (Ctenophora) abundance patterns in Narragansett Bay, Rhode Island, USA
Authors: Slesinger Emily , Langan Joseph A , Sullivan Barbara K , Borkman David G , Smayda Theodore J
Published: July 2020

The influence of a warming climate on patterns of abundance and seasonality of the lobate ctenophore Mnemiopsis leidyi is of interest worldwide, especially in regions where the species occurs at or near the limits of its thermal niche or is shifting its spatial distribution poleward. A 47-year (1972–2019) time series of weekly observations of M. leidyi abundance in Narragansett Bay, the northern limit of its distribution in the Northwest Atlantic, was analyzed to identify links between abundance and environmental factors such as temperature. During this entire period, the species exhibited a striking degree of interannual variability with a gradual decline during the most recent years. Temperature influenced ctenophore abundance, with warmer winter and spring temperatures supporting higher abundances and longer bloom durations. Two blooms were typically observed each year, and both the summer and autumn bloom shifted earlier over time. Chlorophyll was an important factor in the abundance and bloom dynamics of reproductive stage ctenophores, where high levels of summer chlorophyll indicated lower autumn ctenophore abundance, suggesting top-down effects by M. leidyi. These results suggest that multiple factors affect M. leidyi abundance and phenology but that ctenophores in both native and introduced ranges may benefit from continued ocean warming.
Sonographically Guided Percutaneous Sectioning of the Coracohumeral Ligament for the Treatment of Refractory Adhesive Capsulitis: Proof of Concept
Authors: Wahezi Sayed , Yerra Sandeep , Rivelis Yulia , Sitapara Kishan , Gonzalez David , Downie Sherry , Jain Ruchi , Deer Tim , Abd-Elsayed Alaa , Gulati Amit
Published: July 2020

Introduction

Treatment options are limited for nonsurgical chronic refractory cases of adhesive capsulitis. We describe a novel percutaneous tenotomy technique for coracohumeral ligament interruption with cadaveric validation.

Objective

The objective of this study was to describe and validate a novel technique for percutaneous interruption of the coracohumeral ligament.

Design

Cadaveric study.

Setting

Academic tertiary care center.

Methods

Eight cadavers underwent ultrasound (US)-guided percutaneous incision of the coracohumeral (CHL) ligament. Performance of the procedure requires that the practitioner make oscillatory motions with a needle that uses ultrasound energy to cut through tissue. Each pass removes a pinhead-sized amount of tissue. The number of passes and the cutting time are recorded during the procedure. As a standard for this procedure does not exist, the authors created their own based on the preclinical information presented here. Postprocedure dissection was performed to assess the extent of CHL interruption and injury to surrounding tissue.

Results

The average resection time was seven minutes, requiring 500 passes. The technique described in this paper completely interrupted the CHL in all subjects. Cadaveric analysis demonstrated interruption of the CHL with respect to control shoulders requiring an average of seven minutes of cutting time and ∼500 micro-perforations.

Conclusion

US-guided percutaneous CHL ligament sectioning is possible with a commercially available ultrasonic probe.
Patient-based reliability of the Outcome Measures in Rheumatology (OMERACT) ultrasound scoring system for salivary gland assessment in patients with Sjögren’s syndrome
Authors: Finzel Stephanie , Jousse-Joulin Sandrine , Costantino Félicie , Hánová Petra , Hocevar Alojzija , Iagnocco Annamaria , Keen Helen , Naredo Esperanza , Ohrndorf Sarah , Schmidt Wolfgang A , D’Agostino Maria Antonietta , Terslev Lene , Bruyn George A
Published: July 2020

Background

To assess the reliability of the consensually agreed US definitions of major salivary gland lesions and the US scoring system for salivary gland assessment in patients with SS.

Methods

Nine experienced sonographers scanned and read the US images of both parotid glands (PGs) and submandibular glands (SMGs) in eight patients with primary and secondary SS in two rounds. A consensually agreed four-grade semi-quantitative scoring was applied in B-mode for morphological lesions: grade 0, normal; grade 1, mild inhomogeneity without anechoic or hypoechoic areas; grade 2, moderate inhomogeneity with focal anechoic or hypoechoic areas; grade 3, severe inhomogeneity with diffuse an- or hypoechoic areas occupying the entire gland or fibrous gland. The presence or absence of typical SS lesions, i.e. the Sjögren’s signature, was scored binary. Intra- and interreader reliabilities were computed using weighted and unweighted Cohen’s and Light’s κ coefficients.

Results

The mean prevalence of grades 0–3 in PG were 43, 17, 23 and 31% and 28, 14, 33 and 32% for the SMGs, respectively. The weighted κ for intrareader reliability ranged from 0.44 to 1 for grading and 0.64 to 1 for the Sjögren’s signature of PG and 0.59 to 1 and −0.09 to 0.6 for SMGs, respectively. The interreader reliability κ for grading in PG was 0.62 (95% CI 0.47, 0.74) and for Sjögren’s signature it was 0.36 (95% CI 0, 0.43); in SMG it was 0.62 (95% CI 0.47, 0.72) and 0.03 (95% CI 0, 0.07) respectively.

Conclusions

The consensually agreed novel US scoring system for major salivary gland lesions showed substantial intra- and interreader reliability in patients with SS. The reliability of the Sjögren’s signature was moderate.
The Proteomics of Resistance to Halo Blight in Common Bean
Authors: Cooper Bret , Campbell Kimberly B. , Beard Hunter S. , Garrett Wesley M. , Ferreira Marcio E.
Published: July 2020

Halo blight disease of beans is caused by a gram-negative bacterium, Pseudomonas syringae pv. phaseolicola. The disease is prevalent in South America and Africa and causes crop loss for indigent people who rely on beans as a primary source of daily nutrition. In susceptible beans, P. syringae pv. phaseolicola causes water-soaking at the site of infection and produces phaseolotoxin, an inhibitor of bean arginine biosynthesis. In resistant beans, P. syringae pv. phaseolicola triggers a hypersensitive response that limits the spread of infection. Here, we used high-throughput mass spectrometry to interrogate the responses to two different P. syringae pv. phaseolicola isolates on a single line of common bean, Phaseolus vulgaris PI G19833, with a reference genome sequence. We obtained quantitative information for 4,135 bean proteins. A subset of 160 proteins with similar accumulation changes during both susceptible and resistant reactions included salicylic acid responders EDS1 and NDR1, ethylene and jasmonic acid biosynthesis enzymes, and proteins enabling vesicle secretion. These proteins revealed the activation of a basal defense involving hormonal responses and the mobilization of extracellular proteins. A subset of 29 proteins specific to hypersensitive immunity included SOBIR1, a G-type lectin receptor–like kinase, and enzymes needed for glucoside and phytoalexin production. Virus-induced gene silencing revealed that the G-type lectin receptor–like kinase suppresses bacterial infection. Together, the results define the proteomics of disease resistance to P. syringae pv. phaseolicola in beans and support a model whereby the induction of hypersensitive immunity reinstates defenses targeted by P. syringae pv. phaseolicola.
Genetic Mapping and Nucleotide Diversity of Two Powdery Mildew Resistance Loci in Melon (Cucumis melo)
Authors: Haonan Cui , Zhuo Ding , Chao Fan , Zicheng Zhu , Hao Zhang , Peng Gao , Feishi Luan
Published: July 2020

Powdery mildew (PM) significantly and negatively affects the yield and quality of melon (Cucumis melo) worldwide. Race 2F is the predominant physiological race of the pathogen Podosphaera xanthii in many regions. We used accessions PMR 6 (P1; resistant to PM) and M1-7 (P2; susceptible to PM) to analyze the inheritance of resistance to PM (race 2F). The ratio between resistant and susceptible individuals fits a Mendelian segregation ratio of 13:3 in a total of 256 F2individuals and 1:1 in BC1P2. The resistance to PM in PMR 6 was governed by two genes: a dominant (AA) gene with an epistatic effect and a recessive gene (bb). Only individuals with aaBB or aaBb genotypes were susceptible to PM. Two PM resistance loci, Pm2.1 and pm12.1, were mapped on chromosomes 2 and 12 by bulked segregant analysis and secondary mapping by quantitative trait loci analysis with 18 markers. A new marker-assisted selection system to identify melon genotypes resistant or susceptible to PM was developed and tested in 93 melon accessions. Nucleotide diversity (π) and fixation index (Fst) for the two PM resistance loci were estimated using resequencing data of 336 melons from three groups: C. melo subsp. agrestis, Cucumis melo subsp. melo, and the intermediate type. The lowest π was observed in C. melo ssp. agrestis, and the highest Fst value was between C. melo ssp. agrestis and C. melo ssp. melo. The findings provide a promising tool that can be used to accelerate breeding for durable resistance to PM.
TOPOGRAPHIC ASSESSMENT OF CHORIOCAPILLARIS FLOW DEFICITS IN THE INTERMEDIATE AGE-RELATED MACULAR DEGENERATION EYES WITH HYPOREFLECTIVE CORES INSIDE DRUSEN
Authors: Byon Iksoo , Ji Yongsok , Alagorie Ahmed R. , Tiosano Liran , Sadda Srinivas R.
Published: July 2020

Purpose:

To evaluate the choriocapillaris (CC) flow deficit (FD) in eyes with hyporeflective cores (HCs) inside drusen in eyes with intermediate age-related macular degeneration.

Methods:

Intermediate age-related macular degeneration subjects underwent optical coherence tomography and optical coherence tomography angiography using a Cirrus HD-optical coherence tomography (Carl Zeiss Meditec, Dublin, CA). All B-scans were inspected for the presence of drusen with an HC that was defined as dark, condense materials inside drusen. Drusen regions delineated in the manufactures advanced retinal pigment epithelium elevation map were superimposed to the compensated CC optical coherence tomography angiography images. Quantitative analysis of CC FD% was performed under drusen with and without HCs, 150-µm-wide ring region around drusen with and without HCs, drusen-free region, and whole macula.

Results:

Fifty eyes were included in this cross-sectional study. Twenty eyes had drusen with HCs. Thirty eyes without HCs were matched for age and sex. The CC FD% of whole macula was significantly greater in eyes with an HC than those without it (46.3% vs. 42.9%; P = 0.001). In eyes with HCs, regional CC FD% was the greater under drusen (59.8%) and in a 150-µm-wide ring surrounding drusen with HCs (53.0%) than corresponding regions for drusen without HCs (52.5% and 47.3%, respectively) (P < 0.005 in all, Bonferroni correction). The CC FD% in macular regions remote from drusen was 43.2%.

Conclusion:

Intermediate age-related macular degeneration eyes with HCs demonstrated more impaired CC flow, compared with those without this featured. The CC was also more severely impaired directly below these drusen with HCs. These findings highlight that the appearance of HCs may be an indicator of a more advanced disease phenotype.