bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevention of adrenal crisis: cortisol responses to major stress compared to stress dose hydrocortisone delivery in adrenal insufficiency
Authors: Prete Alessandro , Taylor Angela E , Bancos Irina , Smith David J , Foster Mark A , Kohler Sibylle , Fazal-Sanderson Violet , Komninos John , O’Neil Donna M , Vassiliadi Dimitra A , Mowatt Christopher J , Mihai Radu , Fallowfield Joanne L , Annane Djillali , Lord Janet M , Keevil Brian G , Wass John AH , Karavitaki Niki , Arlt Wiebke 
Published: February 2020

ABSTRACTContextPatients with adrenal insufficiency require increased hydrocortisone cover during major stress to avoid life-threatening adrenal crisis. However, current treatment recommendations are not evidence-based.ObjectiveTo identify the most appropriate mode of hydrocortisone delivery in patients with adrenal insufficiency exposed to major stress.Design and ParticipantsCross-sectional study: 122 unstressed healthy subjects and 288 subjects exposed to different stressors (major trauma [N=83], sepsis [N=100], and combat stress [N=105]). Longitudinal study: 22 patients with preserved adrenal function undergoing elective surgery. Pharmacokinetic study: 10 patients with primary adrenal insufficiency undergoing administration of 200mg hydrocortisone over 24 hours in four different delivery modes (continuous intravenous infusion; six-hourly oral, intramuscular or intravenous bolus administration).Main Outcome MeasureWe measured total serum cortisol and cortisone, free serum cortisol and urinary glucocorticoid metabolite excretion by mass spectrometry. Linear pharmacokinetic modelling was used to determine the most appropriate mode and dose of hydrocortisone administration in patients with adrenal insufficiency exposed to major stress.ResultsSerum cortisol was increased in all stress conditions, with the highest values observed in surgery and sepsis. Continuous intravenous hydrocortisone was the only administration mode persistently achieving median cortisol concentrations in the range observed during major stress. Linear pharmacokinetic modelling identified continuous intravenous infusion of 200mg hydrocortisone over 24 hours, preceded by an initial bolus of 50-100mg hydrocortisone, as best suited for maintaining cortisol concentrations in the required range.ConclusionsContinuous intravenous hydrocortisone infusion should be favored over intermittent bolus administration in the prevention and treatment of adrenal crisis during major stress.
Genetic variants drive altered epigenetic regulation of endotoxin tolerance in BTBR macrophages
Authors: Ciernia Annie Vogel , Link Verena M. , Careaga Milo , LaSalle Janine , Ashwood Paul 
Published: February 2020

AbstractThe BTBR T+Itpr3tf/J (BTBR) mouse has been used as a complex genetic model of Autism Spectrum Disorders (ASD). While the specific mechanisms underlying BTBR behavioral phenotypes are poorly understood, prior studies have implicated profound differences in innate immune system control of pro-inflammatory cytokines. Innate immune activation and elevated pro-inflammatory cytokines are also detected in blood of children with ASD. In this study, we examined how underlying BTBR genetic variants correspond to strain-specific changes in chromatin accessibility, resulting in a pro-inflammatory response specifically in BTBR bone marrow derived macrophages (BMDM). In response to repeated lipopolysaccharide (LPS) treatments, C57BL/6J (C57) BMDM exhibited intact endotoxin tolerance. In contrast, BTBR BMDM exhibited hyper-responsive expression of genes that were normally tolerized in C57. This failure in formation of endotoxin tolerance in BTBR was mirrored at the level of chromatin accessibility. Using ATAC-seq, we specifically identified promoter and enhancer regions with strain-specific differential chromatin accessibility both at baseline and in response to LPS. Regions with strain-specific differences in chromatin accessibility were significantly enriched for BTBR genetic variants, such that an average of 22% of the differential chromatin regions had at least one variant. Together, these results demonstrate that BTBR genetic variants contribute to altered chromatin responsiveness to endotoxin challenge and a failure in formation of tolerance, resulting in a hyper-responsive innate immunity in BTBR. These findings provide evidence for an interaction between complex genetic variants and differential epigenetic regulation of innate immune responses. Our findings also provide novel mechanistic insight into the complex genetic architecture and immune abnormalities observed in ASD.
The lockdown of Hubei Province causing different transmission dynamics of the novel coronavirus (2019-nCoV) in Wuhan and Beijing
Authors: Li Xinhai , Zhao Xumao , Sun Yuehua 
Published: February 2020

AbstractBackgroundAfter the outbreak of novel coronavirus (2019-nCoV) starting in late 2019, a number of researchers have reported the predicted the virus transmission dynamics. However, under the strict control policy the novel coronavirus does not spread naturally outside Hubei Province, and none of the prediction closes to the real situation.Methods and findingsWe used the traditional SEIR model, fully estimated the effect of control measures, to predict the virus transmission in Wuhan, the capital city of Hubei Province, and Beijing. We forecast that the outbreak of 2019-nCoV would reach its peak around March 6±10 in Wuhan and March 20±16 in Beijing, respectively. The infectious population in Beijing would be much less (only 0.3%) than those in Wuhan at the peak of this transmission wave. The number of confirmed cases in cities inside Hubei Province grow exponentially, whereas those in cities outside the province increase linearly.ConclusionsThe unprecedented province lockdown substantially suspends the national and global outbreak of 2019-nCoV.
The GINS complex is required for the survival of rapidly proliferating retinal and tectal progenitor cells during zebrafish development
Authors: Varga Máté , Csályi Kitti , Bertyák István , Menyhárd Dóra K. , Poole Richard J. , Cerveny Kara L. , Kövesdi Dorottya , Barátki Balázs , Rouse Hannah , Vad Zsuzsa , Hawkins Thomas A. , Stickney Heather L. , Cavodeassi Florencia , Schwarz Quenten , Young Rodrigo M. , Wilson Stephen W. 
Published: February 2020

AbstractEfficient and accurate DNA replication is particularly critical in stem and progenitor cells for successful proliferation and survival. The replisome, an amalgam of protein complexes, is responsible for binding potential origins of replication, unwinding the double helix, and then synthesizing complimentary strands of DNA. According to current models, the initial steps of DNA unwinding and opening are facilitated by the CMG complex, which is composed of a GINS heterotetramer that connects Cdc45 with the mini-chromosome maintenance (Mcm) helicase. In this work, we provide evidence that in the absence of GINS function DNA replication is cell autonomously impaired, and we also show thatgins1andgins2mutants exhibit elevated levels of apoptosis restricted to actively proliferating regions of the central nervous system (CNS). Intriguingly, our results also suggest that the rapid cell cycles during early embryonic development in zebrafish may not require the function of the GINS complex as neither Gins1 nor Gins2 seem to be present during these stages.
Wnt-regulated lncRNA discovery enhanced byin vivoidentification and CRISPRi functional validation
Authors: Liu Shiyang , Harmston Nathan , Glaser Trudy Lee , Wong Yunka , Zhong Zheng , Madan Babita , Virshup David M. , Petretto Enrico 
Published: February 2020

AbstractBackgroundWnt signaling is an evolutionarily conserved developmental pathway that is frequently hyperactivated in cancer. While multiple protein-coding genes regulated by Wnt signaling are known, the functional lncRNAs regulated by Wnt signaling have not been systematically characterized.ResultsWe comprehensively mapped lncRNAs from an orthotopic Wnt-addicted pancreatic cancer model, identifying 3,633 lncRNAs, of which 1,503 were regulated by Wnt signaling. We found lncRNAs were much more sensitive to changes in Wnt signaling in xenografts than in cultured cells. To functionally validate Wnt-regulated lncRNAs, we performed CRISPRi screens to assess their role in cancer cell proliferation. Consistent with previous genome-wide lncRNA CRISPRi screens, around 1% (13/1,503) of the Wnt-regulated lncRNAs could modify cancer cell growthin vitro. This includedCCAT1andLINC00263, previously reported to regulate cancer growth. Using anin vivoCRISPRi screen, we doubled the discovery rate, identifying twice as many Wnt-regulated lncRNAs (25/1,503) that had a functional effect on cancer cell growth.ConclusionsOur study demonstrates the value of studying lncRNA functionsin vivo, provides a valuable resource of lncRNAs regulated by Wnt signaling and establishes a framework for systematic discovery of functional lncRNAs.
Cognitive impairments in sporadic cerebral small vessel disease (SVD): a systematic review and meta-analysis of cohorts with stroke, dementia and non-clinical presentations of SVD
Authors: Hamilton Olivia KL , Backhouse Ellen V , Janssen Esther , Jochems Angela CC , Maher Caragh , Stevenson Anna J , Ritakari Tuula E , Xia Lihua , Deary Ian J , Wardlaw Joanna M 
Published: February 2020

AbstractBackgroundCognitive impairment is a key clinical feature of cerebral small vessel disease (SVD), but the full range of SVD-related cognitive impairments is unclear, and little is known about how they might vary across clinical and non-clinical manifestations of SVD.MethodsIn systematic searches of OVID MEDLINE, Embase, and PsychINFO from 1st January 1985 to 6th October 2019, we identified studies reporting cognitive test results for study participants with SVD and control participants without SVD. Using standardised group-level cognitive test data, we performed random effects meta-analyses in seven cognitive domains to test whether cognitive test scores differed between SVD and control groups. We conducted meta-regression analyses to test whether differences in age, education, or vascular risk factors between SVD and control groups, or whether different clinical manifestations of SVD (e.g. stroke, cognitive impairment, or non-clinical presentations) accounted for cognitive effect sizes.FindingsOf 8562 studies identified, we included 69 studies from six continents, published in four languages. These studies included 3229 participants with SVD and 3679 controls. Meta-analyses demonstrated that on average, control groups outperformed SVD cohorts on cognitive tests in all cognitive domains examined: executive function (estimate: -0.928; 95%CI: -1.08, -0.78); processing speed (-0.885; -1.17, -0.60); delayed memory (-0.898; -1.10, -0.69); language (-0.808; -1.01, -0.60); visuospatial ability (-0.720; -0.96, -0.48); reasoning (-0.634; -0.93, -0.34); and attention (-0.622; -0.94, -0.31; all p≤0.001). Meta-regression analyses suggested that differences in years of education between SVD and control groups may account for a proportion of the differences in performance on tests of executive function, visuospatial ability and language, and that cohorts with cognitive impairments performed more poorly on tests of executive function, delayed memory and visuospatial ability than cohorts with stroke or non-clinical presentations of SVD.InterpretationParticipants with SVD demonstrated poorer cognitive performance relative to control groups in all cognitive domains we examined. This effect was present for all presentations of SVD, reinforcing the need to test a range of cognitive domains in both clinical and research settings. Lower levels of education in SVD versus control participants may contribute to these effects, highlighting the need to account for educational level in the assessment of SVD-related cognitive impairment.FundingNone.
Going off the rails: Impaired coherence in the speech of patients with semantic control deficits
Authors: Hoffman Paul , Cogdell-Brooke Lucy , Thompson Hannah E 
Published: February 2020

AbstractThe ability to speak coherently, maintaining focus on the topic at hand, is critical for effective communication and is commonly impaired following brain damage. Recent data suggests that executive processes that regulate access to semantic knowledge (i.e., semantic control) are critical for maintaining coherence during speech. To test this hypothesis, we assessed speech coherence in a case-series of fluent stroke aphasic patients with deficits in semantic control. Patients were asked to speak about a series of topics and their responses were analysed using computational linguistic methods to derive measures of their global coherence (the degree to which they spoke about the topic given) and local coherence (the degree to which they maintained a topic from one moment to the next). Compared with age-matched controls, patients showed severe impairments to global coherence and milder impairments to local coherence, suggesting that semantic control deficits give rise to being “led up the garden path”, i.e., one sentence automatically cueing another, with the topic becoming increasingly less relevant to the original question. Global coherence was strongly correlated with the patients’ performance on tests of semantic control, with poorer ability to maintain top-down global coherence being associated with greater semantic control deficits. Other aspects of speech production were also impaired but were not correlated with semantic control deficits. This is the first study to investigate the impact of semantic control impairments within a naturalistic setting, and indicates patients with these impairments are likely to find maintaining focus in everyday conversation difficult.
Par3A and Par3B orchestrate podocyte architecture by regulating RhoA levels
Authors: Koehler Sybille , Odenthal Johanna , Jess David Unnersjö , Höhne Martin , Jüngst Christian , Grawe Ferdi , Helmstädter Martin , Hagmann H. Henning , Walz Gerd , Bloch Wilhelm , Niessen Carien , Schermer Bernhard , Wodarz Andreas , Denholm Barry , Benzing Thomas , Iden Sandra , Brinkkoetter Paul Thomas 
Published: February 2020

AbstractGlomerular diseases are a major cause for chronic kidney disorders. In the majority of cases podocyte injury is causative for disease development. Cytoskeletal rearrangements and morphological changes are hallmark features of podocyte injury and result in dedifferentiation and subsequent loss of podocytes. Here, we establish a link between components of the Par3 polarity complex and actin regulators, which are necessary to establish and maintain the podocytes architecture utilizing both, mouse andDrosophilamodels. We demonstrate that the two mammalian Par3 proteins, Par3A and Par3B, share redundant functions despite differing in their ability to interact with other components of the Par complex. Only simultaneous inactivation of both Par3 proteins causes a severe disease phenotype in mouse podocytes by regulating Rho-GTP levels involving the actin regulators Synaptopodin and CD2AP in an aPKC independent manner.
Assessing thein vitroresistance development in Enterovirus 71 in the context of combination antiviral treatment
Authors: Lanko Kristina , Shi Chenyan , Patil Shivaprasad , Delang Leen , Matthijnssens Jelle , Mirabelli Carmen , Neyts Johan 
Published: February 2020

AbstractThere are currently no antivirals available to treat infection with enterovirus A71 (EV-A71) or any other enterovirus. The extensively studied capsid binders select rapidly for drug-resistant variants. We here explore whether the combination of two direct-acting enterovirus inhibitors with a different mechanism of action may delay or prevent resistance development to the capsid binders. To that end, the in vitro dynamics of resistance development to the capsid binder pirodavir was studied either alone or in combination with (i) a viral 2C-targeting compound (SMSK_0213), (ii) a viral 3C-protease inhibitor (rupintrivir) or (iii) a viral RNA-dependent RNA polymerase (RdRp) inhibitor [7-deaza-2’C-methyladenosine (7DMA)]. We demonstrate that combining pirodavir with either rupintrivir or the nucleoside analogue 7DMA delays the development of resistance to pirodavir and that no resistance to the protease or polymerase inhibitor develops. The combination of pirodavir with the 2C inhibitor results in a double-resistant virus population. The deep sequencing analysis of resistant populations revealed that even though resistant mutations are present in less than 30% of the population, this still provides the resistant phenotype.
Alpha-ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication
Authors: Zhang Linlin , Lin Daizong , Kusov Yuri , Nian Yong , Ma Qingjun , Wang Jiang , von Brunn Albrecht , Leyssen Pieter , Lanko Kristina , Neyts Johan , de Wilde Adriaan , Snijder Eric J. , Liu Hong , Hilgenfeld Rolf 
Published: February 2020

ABSTRACTThe main protease of coronaviruses and the 3C protease of enteroviruses share a similar active-site architecture and a unique requirement for glutamine in the P1 position of the substrate. Because of their unique specificity and essential role in viral polyprotein processing, these proteases are suitable targets for the development of antiviral drugs. In order to obtain near-equipotent, broad-spectrum antivirals against alphacoronaviruses, betacoronaviruses, and enteroviruses, we pursued structure-based design of peptidomimetic α-ketoamides as inhibitors of main and 3C proteases. Six crystal structures of protease:inhibitor complexes were determined as part of this study. Compounds synthesized were tested against the recombinant proteases as well as in viral replicons and virus-infected cell cultures; most of them were not cell-toxic. Optimization of the P2 substituent of the α-ketoamides proved crucial for achieving near-equipotency against the three virus genera. The best near-equipotent inhibitors,11u(P2 = cyclopentylmethyl) and11r(P2 = cyclohexylmethyl), display low-micromolar EC50values against enteroviruses, alphacoronaviruses, and betacoronaviruses in cell cultures. In Huh7 cells,11rexhibits three-digit picomolar activity against Middle East Respiratory Syndrome coronavirus.
Fatty Acyl Availability Modulates Cardiolipin Composition and Alters Mitochondrial Function in HeLa Cells
Authors: Oemer Gregor , Edenhofer Marie-Luise , Lackner Katharina , Leman Geraldine , Koch Jakob , Lindner Herbert H. , Dubrac Sandrine , Zschocke Johannes , Keller Markus A. 
Published: February 2020

AbstractThe molecular assembly of cells depends not only on their balance between anabolism and catabolism, but to a large degree also on the building blocks available in the environment. For cultivated mammalian cells, this is largely determined by the composition of the growth medium used. Here we study the impact of medium lipids on mitochondrial membrane architecture and function by combining LC-MS/MS lipidomics and functional tests with lipid supplementation experiments in an otherwise serum- and lipid-free cell culture model. We demonstrate that the composition of mitochondrial cardiolipins (CL) strongly depends on the lipid environment in cultured cells and prefers the incorporation of essential linoleic acid over other fatty acids. Simultaneously, the mitochondrial respiratory complex I activity was altered, whereas the matrix-localized enzyme citrate synthase was unaffected. This suggests a link between membrane composition and respiratory capacity. In summary, we find a strong dependency of central mitochondrial features on the type of lipids contained in the growth medium. Thus, this underlines the importance of considering these factors when using and establishing cell culture models in biomedical research.Abstract Figure
CRISPR-Cas12a exploits R-loop asymmetry to form double-strand breaks
Authors: Cofsky Joshua C. , Karandur Deepti , Huang Carolyn J. , Witte Isaac P. , Kuriyan John , Doudna Jennifer A. 
Published: February 2020

ABSTRACTMost type V CRISPR-Cas interference proteins use a single RuvC active site to make RNA-guided breaks in double-stranded DNA substrates, an activity essential for both bacterial immunity and genome editing applications. The best-studied of these enzymes, Cas12a, initiates DNA cutting by forming a 20-nucleotide R-loop in which the guide RNA displaces one of the DNA strands of a double-helical substrate, positioning the DNase active site for first-strand cleavage. However, crystal structures and biochemical data have not explained how the second strand is cut to complete the double-strand break. Here, we show that Cas12a-mediated R-loop formation destabilizes DNA at the second-strand cleavage site, which is located outside of the R-loop structure and beyond the 3′ end of the guide RNA. Chemical and fluorescent DNA probes reveal that this destabilization is an intrinsic feature of DNA flanking the RNA-3′ side of R-loops and does not require direct protein interactions. Interestingly, DNA flanking the RNA-5′ side of R-loops is not intrinsically unstable. This asymmetry in R-loop structure may explain the uniformity of guide RNA architecture and the single-active-site cleavage mechanism that are fundamental features of all type V CRISPR-Cas systems.
Genetic predictors of participation in optional components of UK Biobank
Authors: Tyrrell Jessica , Zheng Jie , Beaumont Robin , Hinton Kathryn , Richardson Tom G , Wood Andrew R , Smith George Davey , Frayling Timothy M , Tilling Kate 
Published: February 2020

AbstractLarge studies (e.g. UK Biobank) are increasingly used for GWAS and Mendelian randomization (MR) studies. Selection into and dropout from studies may bias genetic and phenotypic associations. We examine genetic factors affecting participation in four optional components in up to 451,306 UK Biobank participants. We used GWAS to identify genetic variants associated with participation, MR to estimate effects of phenotypes on participation, and genetic correlations to compare participation bias across different studies. 32 variants were associated with participation in one of the optional components (P<6×10-9), including loci with known links to intelligence and Alzheimer’s disease. Genetic correlations demonstrated that participation bias was common across studies. MR showed that longer educational duration, older menarche and taller stature increased participation, whilst higher levels of adiposity, dyslipidaemia, neuroticism, Alzheimer’s and schizophrenia reduced participation. Our effect estimates can be used for sensitivity analysis to account for selective participation biases in genetic or non-genetic analyses.