julilili42/papers huggingface dataset:
A new host cell internalisation pathway for SadA‐expressing staphylococci triggered by excreted neurochemicals
2019-05-17

Staphylococcus aureus is a facultative intracellular pathogen that invades a wide range of professional and nonprofessional phagocytes by triggering internalisation by interaction of surface-bound adhesins with corresponding host cell receptors. Here, we identified a new concept of host cell internalisation in animal-pathogenic staphylococcal species. This new mechanism exemplified by Staphylococcus pseudintermedius ED99 is not based on surface-bound adhesins but is due to excreted small neurochemical compounds, such as trace amines (TAs), dopamine (DOP), and serotonin (SER), that render host cells competent for bacterial internalisation. The neurochemicals are produced by only one enzyme, the staphylococcal aromatic amino acid decarboxylase (SadA). Here, we unravelled the mechanism of how neurochemicals trigger internalisation into the human colon cell line HT-29. We found that TAs and DOP are agonists of the α2-adrenergic receptor, which, when activated, induces a cascade of reactions involving a decrease in the cytoplasmic cAMP level and an increase in F-actin formation. The signalling cascade of SER follows a different pathway. SER interacts with 5HT receptors that trigger F-actin formation without decreasing the cytoplasmic cAMP level. The neurochemical-induced internalisation in host cells is independent of the fibronectin-binding protein pathway and has an additive effect. In a sadA deletion mutant, ED99ΔsadA, internalisation was decreased approximately threefold compared with that of the parent strain, and treating S. aureus USA300 with TAs increased internalisation by approximately threefold.
KCNJ6 variants modulate reward‐related brain processes and impact executive functions in attention‐deficit/hyperactivity disorder
2019-05-17

Abstract KCNJ6 , encoding a potassium channel subunit, regulates the excitability of dopaminergic neurons and is expressed in attention‐deficit/hyperactivity disorder (ADHD)‐relevant brain regions. As a potential ADHD risk gene, KCNJ6 , therefore, may contribute to the endophenotypic variation of the disorder. The impact of two SNPs, rs7275707 and rs6517442, both located in the transcriptional control region of KCNJ6 , on reporter gene expression was explored in cultured cells. The KCNJ6 variants were then tested for association with ADHD and personality traits in a family‐based sample (165 affected children) and an adult case–control sample (450 patients, 426 controls). Furthermore, the genotypic influence on performance in an n ‐back task and a cued continuous performance test (cCPT) was investigated by electroencephalography recordings. Finally, rs6517442 function was assessed by a reward anticipation paradigm using functional magnetic resonance imaging. Different haplotypes of rs7275707 and rs6517442 significantly influenced KCNJ6 gene expression proving their functional relevance on the molecular level. In the family‐based children sample rs7275707 was associated with ADHD ( p = .038). Moreover, rs7275707 showed association with the personality trait of Reward Dependence ( p = .031). In the ADHD group, both rs7275707 and rs6517442 influenced the Go‐centroid location in the cCPT and the N200 amplitude in the n ‐back task. Furthermore, ventral striatal activation was impacted by rs6517442 during reward anticipation. Our data indicate that functional variants of KCNJ6 influence brain activity during reward‐related and executive processes supporting the view of a differential, age‐dependent modulatory impact of dopamine‐related brain processes in ADHD risk.
Novel telemetric sensor capsule for EGD urgency triage: a feasibility study
2019-05-17

Abstract Background and study aims Upper gastrointestinal bleeding (UGIB) is a frequent cause of hospitalization. Because of the lack of reliable noninvasive diagnostic tools, the decision to proceed with emergency endoscopy in these cases is made based on clinical parameters. A novel non-imaging telemetric real-time sensor capsule (HemoPill Acute, Ovesco Endoscopy AG) has shown promising results for noninvasive detection of UGIB in preclinical studies. Patients and methods We conducted a prospective non-randomized, single center, open-label study to investigate feasibility and safety of the novel sensor capsule in patients with symptoms of UGIB. The primary aim of the first clinical study was to investigate feasibility and safety of the device in a clinical setting. All patients underwent endoscopy within 12 hours after capsule ingestion. Sensor data from the capsule within 10 minutes after ingestion were compared with endoscopic findings. Results From April 2015 to February 2016, 30 consecutive patients with symptoms of acute UGIB were included; 27 were eligible for analysis. Capsule ingestion was well tolerated in all patients and there were no device-related adverse events. Endoscopy showed blood or hematin in the upper gastrointestinal tract of 10 of 27 patients; in 2 of 10 patients it was estimated to be more than 20 mL; in 4 of 8 patients it was between 5 and 20 mL and in 4 of 8 it was estimated to &lt; 5 mL. The sensor capsule was positive in 2 of 2 patients (100 %) with &gt; 20 mL of blood or hematin and in 1 of 8 patients (12.5 %) between 5 and 20 mL. All patients (17/17; 100 %) were correctly identified as non-bleeders. Conclusion Both device and procedure proved to be safe and feasible. Larger studies will be necessary to evaluate the role of the sensor capsule in risk stratification of patients with acute UGIB.
Tracking of antibiotic resistance transfer and rapid plasmid evolution in a hospital setting by Nanopore sequencing
2019-05-17

Abstract Background Infection of patients with multidrug-resistant (MDR) bacteria often leave very limited or no treatment options. The transfer of antimicrobial resistance genes (ARG) carrying plasmids between bacterial species by horizontal gene transfer represents an important mode of expansion of ARGs. Here, we evaluated the application of Nanopore sequencing technology in a hospital setting for monitoring the transfer and rapid evolution of antibiotic resistance plasmids within and across multiple species. Results In 2009 we experienced an outbreak with an extensively multidrug resistant P. aeruginosa harboring the carbapenemase enzyme bla IMP-8 , and in 2012 the first Citrobacter freundii and Citrobacter werkmanii harboring the same enzyme were detected. Using Nanopore and Illumina sequencing we conducted a comparative analysis of all bla IMP-8 bacteria isolated in our hospital over a 6-year period (n = 54). We developed the computational platforms pathoLogic and plasmIDent for Nanopore-based characterization of clinical isolates and monitoring of ARG transfer, comprising de-novo assembly of genomes and plasmids, polishing, QC, plasmid circularization, ARG annotation, comparative genome analysis of multiple isolates and visualization of results. Using plasmIDent we identified a 40 kb plasmid carrying bla IMP-8 in P. aeruginosa and C. freundii , verifying that plasmid transfer had occurred. Within C. freundii the plasmid underwent further evolution and plasmid fusion, resulting in a 164 kb mega-plasmid, which was transferred to C. werkmanii . Moreover, multiple rearrangements of the multidrug resistance gene cassette were detected in P. aeruginosa , including deletions and translocations of complete ARGs. Conclusion Plasmid transfer, plasmid fusion and rearrangement of the multidrug resistance gene cassette mediated the rapid evolution of opportunistic pathogens in our hospital. We demonstrated the feasibility of tracking plasmid evolution dynamics and ARG transfer in clinical settings in a timely manner. The approach will allow for successful countermeasures to contain not only clonal, but also plasmid mediated outbreaks.
Root microbiota assembly and adaptive differentiation among European Arabidopsis populations
2019-05-17

Summary Factors that drive continental-scale variation in root microbiota and plant adaptation are poorly understood. We monitored root-associated microbial communities in Arabidopsis thaliana and co-occurring grasses at 17 European sites across three years. Analysis of 5,625 microbial community profiles demonstrated strong geographic structuring of the soil biome, but not of the root microbiota. Remarkable similarity in bacterial community composition in roots of A. thaliana and grasses was explained by the presence of a few diverse and geographically widespread taxa that disproportionately colonize roots across sites. In a reciprocal transplant between two A. thaliana populations in Sweden and Italy, we uncoupled soil from location effects and tested their respective contributions to root microbiota variation and plant adaptation. The composition of the root microbiota was affected by location and soil origin, and to a lesser degree by host genotype. The filamentous eukaryotes were particularly strongly affected by location. Strong local adaptation between the two A. thaliana populations was observed, with difference in soil properties and microbes of little importance for the observed magnitude of adaptive differentiation. Our results suggest that, across large spatial scales, climate is more important than are soil conditions for plant adaptation and variation in root-associated filamentous eukaryotic communities.
Dietary Adaptations of Early and Middle Pleistocene Equids From the Anagni Basin (Frosinone, Central Italy)
2019-05-17

The intermontane Anagni Basin (Frosinone, central Italy) is an important region for Italian biochronology and paleoecology due to the presence of two rich fossil assemblages dated to the Early (Coste San Giacomo) and Middle Pleistocene (Fontana Ranuccio). These sites have yielded a vast collection of large fossil mammals with a well-documented presence of fossil equids in both localities (represented mostly by isolated teeth). Coste San Giacomo is dated to around 2.1 Ma, thereby having recorded the effects of the onset of the Quaternary glacial cycles, which led to a gradual trend toward colder and more arid conditions in the Northern Hemisphere. The fossil equids of this site belong to the first group of grazing stenonid equids of the genus Equus that spread to the Italian Peninsula during the so called "Elephant- Equus" event, which marked the appearance of new large mammals living in herds in open and arid environments. The site of Fontana Ranuccio is dated to around 400 ka, close to the MIS 12-11 succession (the "Mid-Brunhes event"), which marked the end of the Middle Pleistocene Transition. The fossil horses from Fontana Ranuccio represent one of the oldest caballoid (or "true horses") populations of the Italian Peninsula. The Anagni Basin, thus, provides important data to investigate paleoecological adaptations of these groups of equids in response to two critical environmental and climatic shifts of the Pleistocene. We explore their niche occupation by examining long-term dental wear patterns and tooth enamel carbon and oxygen stable isotopic composition. Both taxa appear to have exhibited a narrow dietary niche, displaying a clear abrasive (highly specialized) grass-rich diet. In particular, caballoid equids from Fontana Ranuccio show a more abrasion-dominated mesowear signature. Stenonid equids from Coste San Giacomo exploited broader and more diverse landscapes during the Early Pleistocene, whereas caballoid horses from Fontana Ranuccio appeared to have limited their dietary adaptations to a stricter grazing behavior in more closed environments.
A Bayesian Conjugate Gradient Method (with Discussion)
2019-05-18

A fundamental task in numerical computation is the solution of large linear systems. The conjugate gradient method is an iterative method which offers rapid convergence to the solution, particularly when an effective preconditioner is employed. However, for more challenging systems a substantial error can be present even after many iterations have been performed. The estimates obtained in this case are of little value unless further information can be provided about, for example, the magnitude of the error. In this paper we propose a novel statistical model for this error, set in a Bayesian framework. Our approach is a strict generalisation of the conjugate gradient method, which is recovered as the posterior mean for a particular choice of prior. The estimates obtained are analysed with Krylov subspace methods and a contraction result for the posterior is presented. The method is then analysed in a simulation study as well as being applied to a challenging problem in medical imaging.
A novel biallelic loss‐of‐function mutation in TMCO1 gene confirming and expanding the phenotype spectrum of cerebro‐facio‐thoracic dysplasia
2019-05-18

Abstract The main clinical features of cerebro‐facio‐thoracic dysplasia (CFTD) syndrome, which were described over four decades ago, include facial dysmorphism, multiple malformations of the vertebrae and ribs, and intellectual disability. Recently, a TMCO1 gene mutation was shown to be responsible for an autosomal recessive CFTD syndrome characterized by craniofacial dysmorphism, skeletal anomalies, and intellectual disability. In the current report, we describe two members of a consanguineous family from an Arab community in Israel who were clinically diagnosed as suffering from craniofacial dysmorphism, skeletal anomalies, intellectual disability, and epilepsy. Both affected siblings had behavioral difficulties such as anxiety and emotional instability with impulsive behaviors. Whole‐exome sequencing revealed a homozygous stop‐gain mutation NM_019026.4: c.616C &gt; T; p.(Arg206*) in exon 6 of the TMCO1 gene. Bioinformatics analysis suggested a structural model for the TMCO1 protein and its homologues. The clinical features of our patients were compared with those of the only other five studies available in the literature. We conclude that this mutation in the TMCO1 gene is responsible for the various clinical manifestations of CFTD syndrome exhibited by the patients studied that expand the phenotypic spectrum of the disease to include epilepsy as a characteristic feature of this syndrome.
Nintedanib for Systemic Sclerosis–Associated Interstitial Lung Disease
2019-05-20

Among patients with ILD associated with systemic sclerosis, the annual rate of decline in FVC was lower with nintedanib than with placebo; no clinical benefit of nintedanib was observed for other manifestations of systemic sclerosis. The adverse-event profile of nintedanib observed in this trial was similar to that observed in patients with idiopathic pulmonary fibrosis; gastrointestinal adverse events, including diarrhea, were more common with nintedanib than with placebo. (Funded by Boehringer Ingelheim; SENSCIS ClinicalTrials.gov number, NCT02597933.).
Pembrolizumab (pembro) plus axitinib (axi) versus sunitinib as first-line therapy for metastatic renal cell carcinoma (mRCC): Outcomes in the combined IMDC intermediate/poor risk and sarcomatoid subgroups of the phase 3 KEYNOTE-426 study.
2019-05-20

4500 Background: In KEYNOTE-426, pembro + axi significantly improved OS (HR 0.53, P &lt; .0001), PFS (HR 0.69, P = .0001), and ORR (59.3% vs 35.7%, P &lt; .0001) vs sunitinib and had manageable toxicity as first-line therapy for mRCC (NCT02853331). The pembro + axi benefit was observed across all IMDC risk groups and regardless of PD-L1 expression. We present data for the combined intermediate/poor risk group and for patients (pts) with sarcomatoid features. Methods: 861 eligible pts with clear-cell mRCC, no prior systemic therapy for mRCC, and KPS ≥70 were randomized 1:1 to pembro 200 mg IV Q3W for a maximum of 35 cycles plus axi 5 mg orally BID (N = 432) or sunitinib 50 mg orally QD (4-wk on/2-wk off) (N = 429). Primary endpoints were OS and PFS (RECIST v1.1 by blinded, independent central review [BICR]). ORR (RECIST v1.1 by BICR) was the key secondary endpoint. The intermediate/poor risk group was prespecified; the sarcomatoid group was exploratory. HRs and their 95% CIs were calculated with a Cox proportional hazards model. None of the analyses were multiplicity-controlled. Results: 592 (68.8%) of all randomized pts were of IMDC intermediate/poor risk — 294 in the pembro + axi arm, 298 in the sunitinib arm. Pembro + axi improved OS (HR 0.52, 95% CI 0.37-0.74; 12-mo rate 87.3% vs 71.3%), PFS (HR 0.67, 95% CI 0.53-0.85; median 12.6 vs 8.2 mo), and ORR (55.8% [95% CI 49.9-61.5] vs 29.5% [24.4-35.1]) in pts with intermediate/poor risk; CR rates were 4.8% (95% CI 2.6-7.9) vs 0.7% (0.1-2.4). Of the 578 pts with known status, 105 (18.2%) had sarcomatoid features — 51 in the pembro + axi arm, 54 in the sunitinib arm. Pembro + axi improved OS (HR 0.58, 95% CI 0.21-1.59; 12-mo rate 83.4% vs 79.5%), PFS (HR 0.54, 95% CI 0.29-1.00; median not reached vs 8.4 mo), and ORR (58.8% [95% CI 44.2-72.4] vs 31.5% [19.5-45.6]) in pts with sarcomatoid features; CR rates were 11.8% (95% CI 4.4-23.9) vs 0% (0.0-6.6). Conclusions: Pembro + axi provides benefit in the combined population of pts with IMDC intermediate or poor risk and in pts whose tumors had sarcomatoid features. The observed benefits were consistent with those seen in the total population. Clinical trial information: NCT02853331.
Gauss-Bonnet black holes with a massive scalar field
2019-05-20

In the present paper we consider the extended scalar-tensor-Gauss-Bonnet\\ngravity with a massive scalar field. We prove numerically the existence of\\nGauss-Bonnet black holes for three different forms of the coupling function\\nincluding the case of spontaneous scalarization. We have performed a systematic\\nstudy of the black hole characteristics such as the area of the horizon, the\\nentropy and the temperature for these coupling functions and compared them to\\nthe Schwarzschild solutions. The introduction of scalar field mass leads to a\\nsuppression of the scalar field and the increase of this mass brings the black\\nholes closer to the Schwarzschild case. For linear and exponential coupling, a\\nnonzero scalar field mass expands the domain of existence of black holes\\nsolutions. Larger deviations from the GR case are observed only for small\\nmasses and these differences decrease with the increase of the scalar field\\nmass. In the case of a coupling function which leads to scalarization the\\nscalar field mass has a significant influence on the bifurcation points where\\nthe scalarized black holes branch out of the Schwarzschild solution. The\\nlargest deviation from the case with a massless scalar field are observed for\\nblack hole masses close to the bifurcation point.\\n
The Augmentation of Retinogeniculate Communication during Thalamic Burst Mode
2019-05-20

Retinal signals are transmitted to cortex via neurons in the lateral geniculate nucleus (LGN), where they are processed in burst or tonic response mode. Burst mode occurs when LGN neurons are sufficiently hyperpolarized for T-type Ca<sup>2+</sup> channels to deinactivate, allowing them to open in response to depolarization, which can trigger a high-frequency sequence of Na<sup>+</sup>-based spikes (i.e., burst). In contrast, T-type channels are inactivated during tonic mode and do not contribute to spiking. Although burst mode is commonly associated with sleep and the disruption of retinogeniculate communication, bursts can also be triggered by visual stimulation, thereby transforming the retinal signals relayed to the cortex. To determine how burst mode affects retinogeniculate communication, we made recordings from monosynaptically connected retinal ganglion cells and LGN neurons in male/female cats during visual stimulation. Our results reveal a robust augmentation of retinal signals within the LGN during burst mode. Specifically, retinal spikes were more effective and often triggered multiple LGN spikes during periods likely to have increased T-type Ca<sup>2+</sup> channel activity. Consistent with the biophysical properties of T-type Ca<sup>2+</sup> channels, analysis revealed that effect magnitude was correlated with the duration of the preceding thalamic interspike interval and occurred even in the absence of classically defined bursts. Importantly, the augmentation of geniculate responses to retinal input was not associated with a degradation of visual signals. Together, these results indicate a graded nature of response mode and suggest that, under certain conditions, bursts facilitate the transmission of visual information to the cortex by amplifying retinal signals.<b>SIGNIFICANCE STATEMENT</b> The thalamus is the gateway for retinal information traveling to the cortex. The lateral geniculate nucleus, like all thalamic nuclei, has two classically defined categories of spikes-tonic and burst-that differ in their underlying cellular mechanisms. Here we compare retinogeniculate communication during burst and tonic response modes. Our results show that retinogeniculate communication is enhanced during burst mode and visually evoked thalamic bursts, thereby augmenting retinal signals transmitted to cortex. Further, our results demonstrate that the influence of burst mode on retinogeniculate communication is graded and can be measured even in the absence of classically defined thalamic bursts.
Circulating FGF21 Levels in Human Health and Metabolic Disease
2019-05-20

Abstract Human fibroblast growth factor 21 (FGF21) is primarily produced and secreted by the liver as a hepatokine. This hormone circulates to its target tissues (e. g., brain, adipose tissue), which requires two components, one of the preferred FGF receptor isoforms (FGFR1c and FGFR3c) and the co-factor beta-Klotho (KLB) to trigger downstream signaling pathways. Although targeting FGF21 signaling in humans by analogues and receptor agonists results in beneficial effects, e. g., improvements in plasma lipids and decreased body weight, it failed to recapitulate the improvements in glucose handling shown for many mouse models. FGF21’s role and metabolic effects in mice and its therapeutic potential have extensively been reviewed elsewhere. In this review we focus on circulating FGF21 levels in humans and their associations with disease and clinical parameters, focusing primarily on obesity and obesity-associated diseases such as type-2 diabetes. We provide a comprehensive overview on human circulating FGF21 levels under normal physiology and metabolic disease. We discuss the emerging field of inactivating FGF21 in human blood by fibroblast activation protein (FAP) and its potential clinical implications.