julilili42/papers huggingface dataset:
AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential
2019-04-11

Abstract Understanding the evolutionary background of a bacterial isolate has applications for a wide range of research. However generating an accurate species phylogeny remains challenging. Reliance on 16S rDNA for species identification currently remains popular. Unfortunately, this widespread method suffers from low resolution at the species level due to high sequence conservation. Currently, there is now a wealth of genomic data that can be used to yield more accurate species designations via modern phylogenetic methods and multiple genetic loci. However, these often require extensive expertise and time. The Automated Multi-Locus Species Tree (autoMLST) was thus developed to provide a rapid ‘one-click’ pipeline to simplify this workflow at: https://automlst.ziemertlab.com. This server utilizes Multi-Locus Sequence Analysis (MLSA) to produce high-resolution species trees; this does not preform multi-locus sequence typing (MLST), a related classification method. The resulting phylogenetic tree also includes helpful annotations, such as species clade designations and secondary metabolite counts to aid natural product prospecting. Distinct from currently available web-interfaces, autoMLST can automate selection of reference genomes and out-group organisms based on one or more query genomes. This enables a wide range of researchers to perform rigorous phylogenetic analyses more rapidly compared to manual MLSA workflows.
On the inverse spectrum problem of neutron stars
2019-04-11

In this work we revisit axial perturbations of spherically symmetric and\\nnon-rotating neutron stars. Although it has been object of many studies, it\\nstill offers new insights that are of potential interest for more realistic\\nscenarios or in the study exotic compact objects, which have drawn much\\nattention recently. By using WKB theory, we first derive a new Bohr-Sommerfeld\\nrule that allows to investigate the quasi-normal mode spectrum and address the\\ninverse spectrum problem. The pure analytical treatment of the wave equation is\\nrather involved, because it requires the solution of the TOV equations and the\\nnon-trivial tortoise coordinate transformation depending on the underlying\\nspace-time. Therefore we provide an easy way to construct potentials that\\nsimplifies the analytical treatment, but still captures the relevant physics.\\nThe approximated potential can be used for calculations of the axial\\nperturbation spectrum. These results are also useful in the treatment of the\\ninverse problem. We demonstrate this by reconstructing the time-time component\\nof the metric throughout the star and constraining the equation of state in the\\ncentral region. Our method also provides an analytical explanation of the\\nempirically known asteroseismology relation that connects the fundamental QNM\\nand radius of a neutron star with its compactness.\\n
Paleoecology of sublittoral Miocene echinoids from Sardinia: A case study for substrate controls of faunal distributions
2019-04-11

Abstract A rich echinoid fauna within the middle Miocene carbonate sedimentary succession cropping out along the coast between Santa Caterina di Pittinuri and S'Archittu (central-western Sardinia) allows the comparison of faunal gradients and preservation potentials from both hard and soft substrata. Three echinoid assemblages are recognized. Faunal composition, as well as taphonomic and sedimentological features and functional morphological interpretation of the echinoid test indicate an outer sublittoral setting. Assemblage 1 represents a highly structured environment within the photic zone, with mobile substrata occupied by infaunal irregular echinoids, mainly spatangoids, and localized hard substrata, provided by rhodolith beds, with epibenthic regular echinoids represented by the co-occurrence of the diadematid Diadema Gray, 1825 and the toxopneustids Tripneustes L. Agassiz, 1841 and Schizechinus Pomel, 1869. Assemblage 2 shows a higher diversity of irregular echinoids, dominated by the clypeasteroids Echinocyamus van Phelsum, 1774 and Clypeaster Lamarck, 1801 and different spatangoids, with the minute trigonocidarid Genocidaris A. Agassiz, 1869 among regular echinoids. This assemblage points to a soft-bottom environment with moderate water-energy conditions, periodically affected by storms. A low-diversity echinoid fauna in Assemblage 3, dominated by the spatangoids Brissopsis L. Agassiz, 1840 and Ova Gray, 1825, documents a deeper, soft-bottom environment, possibly below storm-wave base. These results indicate that the diversity of echinoid faunas originating in sublittoral environments is related to: (1) the presence of both soft and hard substrata, (2) differential preservation potentials of the various echinoid taxa, (3) intense bioturbation, and (4) sediment deposition by sporadic storm events.
Measuring circadian preference in adolescence with the Morningness-Eveningness Stability Scale improved (MESSi)
2019-04-11

Differences in daytime preferences are mainly manifested in the variability of sleep and wakefulness. Circadian preference shows a great influence on health and daily routine. Further, circadian preference and chronotype changes throughout the life span. A wide-ranging determination of circadian preference is therefore important. This study presents a validation of the MESSi in adolescents. The MESSi determines the individual circadian phase and amplitude based on three sub-scales: Morningness (MA), Eveningness (EV) and Stability/Distinctness (DI). Based on three studies, the convergent validity of the MESSi was analyzed (N = 215). In study 1 the Pediatric daytime sleepiness scale (PDSS) was applied, in study 2 the Composite Scale of Morningness (CSM) and in study 3 the Children’s ChronoType Questionnaire (CCTQ). The MESSi showed a good convergent validity with all sum-scores of the three measurements. A Confirmatory Factor Analysis (CFA) proved the three-structure model of the MESSi. The fit indices were good (TLI = 0.966, and CFI o = 0.972). The RMSEA was also good with 0.045 and PCLOSE was not significant (p = 0.651). The results support the assumption that the MESSi is a valid instrument with a three-factor structure to measure circadian phase and amplitude in adolescents.
On Structure Priors for Learning Bayesian Networks
2019-04-11

To learn a Bayesian network structure from data, one popular approach is to maximize a decomposable likelihood-based score. While various scores have been proposed, they usually assume a uniform prior, or ``penalty,'' over the possible directed acyclic graphs (DAGs); relatively little attention has been paid to alternative priors. We investigate empirically several structure priors in combination with different scores, using benchmark data sets and data sets generated from benchmark networks. Our results suggest that, in practice, priors that strongly favor sparsity perform significantly better than the uniform prior or even the informed variant that is conditioned on the correct number of parents for each node. For an analytic comparison of different priors, we generalize a known recurrence equation for the number of DAGs to accommodate modular weightings of DAGs, a result that is also of independent interest.
A novel mutant allele uncouples brassinosteroid-dependent and independent functions of BRI1
2019-04-11

Abstract Plants depend on an array of cell surface receptors to integrate extracellular signals with developmental programs. One of the best-studied receptors is BRASSINOSTEROID INSENSITIVE 1 (BRI1), which upon binding of its hormone ligands forms a complex with shape-complimentary co-receptors and initiates a signal transduction cascade leading to a wide range of responses. BR biosynthetic and receptor mutants have similar growth defects on the macroscopic level, which had initially led to the assumption of a largely linear signalling pathway. However, recent evidence suggests that BR signalling is interconnected with a number of other pathways through a variety of different mechanisms. We recently described that feedback information from the cell wall is integrated at the level of the receptor complex through interaction with RLP44. Moreover, BRI1 is required for a second function of RLP44, the control of procambial cell fate. Here, we report on a BRI1 mutant, bri1 cnu4 , which differentially affects canonical BR signalling and RLP44 function in the vasculature. While BR signalling is only mildly impaired, bri1 cnu4 mutants show ectopic xylem in the position of procambium. Mechanistically, this is explained by an increased association of RLP44 and the mutated BRI1 protein, which prevents the former from acting in vascular cell fate maintenance. Consistent with this, the mild BR response phenotype of bri1 cnu4 is a recessive trait, whereas the RLP44-mediated xylem phenotype is semi-dominant. Our results highlight the complexity of plant plasma membrane receptor function and provide a tool to dissect BR signalling-related roles of BRI1 from its non-canonical functions. One sentence summary A novel mutant allows to dissect brassinosteroid signalling related and non-canonical functions of the receptor-like kinase BRI1.
Smartphone biosensor for Salmonella and Amitriptyline
2019-04-11

The proposed application has been developed to detect CRP, salmonella, and amitriptyline (AMT) on the basis of a structured lateral flow chip. It is combined with a read-out system using the camera of a smartphone and software such as ImageJ or a specially programmed app to evaluate color depth proportional to concentration. These strips are structured for multi-channel applications for either multi-analyte or for replica measurements. Calibration curves are provided for analytes, structuring and read-out will be discussed. The results allow the application in the area of POCT (point-of-care diagnostics), Anywhere care, or citizen science.
Adsorption kinetics of proteins to biomaterials measured by reflectometric interference spectroscopy
2019-04-11

In this work we present the investigation of the interaction of fibronectin with different biomaterials. Since the amount, type and possible conformational changes of adsorbed proteins at the body-implant interface strongly influences the performance of implants, this work is focusing on a more comprehensive understanding of these processes. To create very stable and thin surface modification of a glass transducer with PEG, PU and PLA an immobilization strategy based on silane chemistry was developed. To monitor the adsorption and desorption of fibronectin onto these biomaterial surfaces, the reflectometric interference spectroscopy – a direct optical method – was applied. To estimate the association and dissociation rate constants, a biomolecular interaction analysis was performed within the kinetically limited regime of the association process. Additionally, the influence of the pH value on the adsorption behavior is exemplary shown for the interaction of fibronectin on a glass surface. These experiments show high potential to give more detailed insights into the complex processes during the implantation of foreign materials into the human body.
DNA methylation profiling to predict recurrence risk in meningioma: development and validation of a nomogram to optimize clinical management
2019-04-12

Abstract Background Variability in standard-of-care classifications precludes accurate predictions of early tumor recurrence for individual patients with meningioma, limiting the appropriate selection of patients who would benefit from adjuvant radiotherapy to delay recurrence. We aimed to develop an individualized prediction model of early recurrence risk combining clinical and molecular factors in meningioma. Methods DNA methylation profiles of clinically annotated tumor samples across multiple institutions were used to develop a methylome model of 5-year recurrence-free survival (RFS). Subsequently, a 5-year meningioma recurrence score was generated using a nomogram that integrated the methylome model with established prognostic clinical factors. Performance of both models was evaluated and compared with standard-of-care models using multiple independent cohorts. Results The methylome-based predictor of 5-year RFS performed favorably compared with a grade-based predictor when tested using the 3 validation cohorts (ΔAUC = 0.10, 95% CI: 0.03–0.018) and was independently associated with RFS after adjusting for histopathologic grade, extent of resection, and burden of copy number alterations (hazard ratio 3.6, 95% CI: 1.8–7.2, P &lt; 0.001). A nomogram combining the methylome predictor with clinical factors demonstrated greater discrimination than a nomogram using clinical factors alone in 2 independent validation cohorts (ΔAUC = 0.25, 95% CI: 0.22–0.27) and resulted in 2 groups with distinct recurrence patterns (hazard ratio 7.7, 95% CI: 5.3–11.1, P &lt; 0.001) with clinical implications. Conclusions The models developed and validated in this study provide important prognostic information not captured by previously established clinical and molecular factors which could be used to individualize decisions regarding postoperative therapeutic interventions, in particular whether to treat patients with adjuvant radiotherapy versus observation alone.
Research in Social Psychology Changed Between 2011 and 2016: Larger Sample Sizes, More Self-Report Measures, and More Online Studies
2019-04-12

The debate about false positives in psychological research has led to a demand for higher statistical power. To meet this demand, researchers need to collect data from larger samples—which is important to increase replicability, but can be costly in both time and money (i.e., remuneration of participants). Given that researchers might need to compensate for these higher costs, we hypothesized that larger sample sizes might have been accompanied by more frequent use of less costly research methods (i.e., online data collection and self-report measures). To test this idea, we analyzed social psychology studies published in 2009, 2011, 2016, and 2018. Indeed, research reported in 2016 and 2018 (vs. 2009 and 2011) had larger sample sizes and relied more on online data collection and self-report measures. Thus, over these years, research improved in its statistical power, but also changed with regard to the methods applied. Implications for social psychology as a discipline are discussed.
Staphylococcus aureus Colonization of the Human Nose and Interaction with Other Microbiome Members
2019-04-12

ABSTRACT Staphylococcus aureus is usually regarded as a bacterial pathogen due to its ability to cause multiple types of invasive infections. Nevertheless, S. aureus colonizes about 30% of the human population asymptomatically in the nares, either transiently or persistently, and can therefore be regarded a human commensal as well, although carriage increases the risk of infection. Whereas many facets of the infection processes have been studied intensively, little is known about the commensal lifestyle of S. aureus . Recent studies highlight the major role of the composition of the highly variable nasal microbiota in promoting or inhibiting S. aureus colonization. Competition for limited nutrients, trace elements, and epithelial attachment sites, different susceptibilities to host defense molecules and the production of antimicrobial molecules by bacterial competitors may determine whether nasal bacteria outcompete each other. This chapter summarizes our knowledge about mechanisms that are used by S. aureus for efficient nasal colonization and strategies used by other nasal bacteria to interfere with its colonization. An improved understanding of naturally evolved mechanisms might enable us to develop new strategies for pathogen eradication.
Development of a Low-Density DNA Microarray for Detecting Tick-Borne Bacterial and Piroplasmid Pathogens in African Cattle
2019-04-12

In Africa, pathogens transmitted by ticks are of major concern in livestock production and human health. Despite noticeable improvements particularly of molecular screening methods, their widespread availability and the detection of multiple infections remain challenging. Hence, we developed a universally accessible and robust tool for the detection of bacterial pathogens and piroplasmid parasites of cattle. A low-cost and low-density chip DNA microarray kit (LCD-Array) was designed and tested towards its specificity and sensitivity for five genera causing tick-borne diseases. The blood samples used for this study were collected from cattle in Northern Cameroon. Altogether, 12 species of the genera Anaplasma, Ehrlichia, Rickettsia and Theileria, and their corresponding genus-wide probes including Babesia were tested on a single LCD-Array. The detection limit of plasmid controls by PCR ranged from 1 to 75 copies per μL depending on the species. All sequenced species hybridized on the LCD-Array. As expected, PCR, agarose gel electrophoresis and Sanger sequencing found significantly less pathogens than the LCD-Array (p &lt; 0.001). Theileria and Rickettsia had lower detection limits than Anaplasma and Ehrlichia. The parallel identification of some of the most detrimental tick-borne pathogens of livestock, and the possible implementation in small molecular-diagnostic laboratories with limited capacities makes the LCD-Array an appealing asset.
‘Introduction’ to Kingdoms of Elfin (Handheld Press, 2018)
2019-04-12

Originally conceived of as an introduction to a new edition of Sylvia Townsend Warner’s Kingdoms of Elfin (Handheld Press, 2018), this article provides an overview of the place of Kingdoms of Elfin (1977) in Sylvia Townsend Warner’s oeuvre and life, placing it in the final phases of her life as an astonishing new departure. In Kingdoms , Warner experiments with the excision of affect from the narrative process, producing stories which construct the narrative voice uncompromisingly as a voice of observation rather than identification. The playing field on which this is carried through is nothing less than a whole new fictional universe in the form of meticulously worked-out ‘Elfin’ worlds. The narratives’ observational stance unfolds itself as a disinterested ethnography of the strangeness of behaviours both human and non-human, radically decentring human perceptions and moral convictions in the process.
The Impact of Maternal Eating Disorders on Dietary Intake and Eating Patterns during Pregnancy: A Systematic Review
2019-04-13

Maternal nutrition in pregnancy has a key influence on optimum fetal health. Eating disorders (EDs) during pregnancy may have detrimental effects on fetal growth and the child’s early development. There is limited knowledge concerning the eating behavior, dietary intake and derived nutritional biomarkers as well as the nutrient supplementation in women with EDs during pregnancy. We performed a systematic review according to the PRISMA statement to synthesize current evidence in this field. Of N = 1203 hits, 13 full-texts were included in the qualitative synthesis. While women with current Binge Eating Disorder (BED) showed higher energy and fat intakes during pregnancy, women with a lifetime Anorexia Nervosa (AN), Bulimia Nervosa (BN) or both (AN + BN) had similar patterns of nutrient intake and dietary supplement use as healthy women. There is evidence, that women with a history of EDs have a sufficient diet quality and are more likely to be vegetarian. Dieting and bingeing improved substantially with pregnancy. The highlighted differences in the consumption of coffee/caffeine and artificially sweetened beverages as well as the elevated prevalence of iron deficiency anemia in women with a past or active ED during pregnancy might have an important impact on fetal development.
Does text–picture integration also occur with longer text segments?
2019-04-13

Summary Text–picture integration is one of the most important cognitive processes when reading illustrated text. There is empirical evidence that text‐picture integration takes place when learning with pictures combined with single sentences. The present experiment investigated whether text–picture integration also takes place when the single sentences are embedded into longer text segments and hence when materials become more complex. In a within‐subjects design, 43 participants read an illustrated story, in which the different combinations of general and specific sentences and pictures, respectively, were embedded. In line with previous findings, participants were more likely to falsely recognize specific versions of the sentences after having studied their general versions combined with specific pictures. Thus, the experiment shows that text–picture integration also occurs when learners have to read longer text passages combined with pictures.
Tumor‐secreted extracellular vesicles promote the activation of cancer‐associated fibroblasts via the transfer of microRNA‐125b
2019-04-14

ABSTRACT Tumour cells release large quantities of extracellular vesicles (EVs) to mediate their interactions with other cells in the tumour microenvironment. To identify host cells that naturally take up EVs from tumour cells, we created breast cancer cell lines secreting fluorescent EVs. These fluorescent EVs are taken up most robustly by fibroblasts within the tumour microenvironment. RNA sequencing indicated that miR‐125b is one of the most abundant microRNAs secreted by mouse triple‐negative breast cancer 4T1 and 4TO7 cells. Treatment with 4T1 EVs leads to an increase in fibroblast activation in isogenic 4TO7 tumours, which is reversed by blocking miR‐125b in 4T1 EVs; hence, miR‐125b delivery by EVs is responsible for fibroblast activation in mouse tumour models. miR‐125b is also secreted by human breast cancer cells and the uptake of EVs from these cells significantly increases cellular levels of miR‐125b and expression of multiple cancer‐associated fibroblast markers in resident fibroblasts. Overexpression of miR‐125b in both mouse and human fibroblasts leads to an activated phenotype similar to the knockdown of established miR‐125b target mRNAs. These data indicate that miR‐125b is transferred through EVs from breast cancer cells to normal fibroblasts within the tumour microenvironment and contributes to their development into cancer‐associated fibroblasts.
Socially constrained variation in nonmodal phonation for more than 2,500 speakers of British English
2019-04-14

This study examines the status of nonmodal phonation in British English using smartphone recordings from over 2,500 speakers. The acoustic correlates that were examined include fundamental frequency, H1*-H2*, cepstral peak prominence, and harmonic-to-noise ratio. The results confirm that existing findings on nonmodal phonation---such as greater use of creaky voice by male speakers than female speakers---hold for a much larger and more diverse sample than has been considered previously. The study also uncovers effects that have not been reported in past work, such as a relationship between speakers' education levels and their production of nonmodal phonation.