julilili42/papers huggingface dataset:
Correlating Adaptive Optics Images to Clinical Findings in Juvenile Macular Dystrophy with Hypotrichosis in Siblings with Homozygous <b><i>CDH3</i></b> Pathogenic Variation
2020-01-01

&lt;b&gt;&lt;i&gt;Objective:&lt;/i&gt;&lt;/b&gt; We report on two German siblings diagnosed with congenital hypotrichosis and juvenile macular dystrophy, an extremely rare syndrome affecting both hair growth and visual functions. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; A detailed ophthalmological examination was carried out including fundus examination, visual acuity assessment, visual field determination, color vision testing, and electrophysiology (electroretinography [ERG]). Additionally, fundus photography and autofluorescence imaging (FAF) was performed, along with optical coherence tomography (OCT) and adaptive optics (AO) fundus imaging. Targeted Sanger sequencing and next-generation gene panel sequencing were carried out. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; Macular dystrophy was evident in the fundus of both patients, as was a central scotoma in the static visual field. The kinetic visual field was normal. The ERG recordings were also normal, but the amplitudes of the multifocal ERG were reduced in the central 4–5° of the retina. The FAF images revealed a large central hypofluorescent area surrounded by a hyperfluorescent ring. The OCT images showed atrophy in the outer layers and tubulations. The AO images depicted a loss of central photoreceptors, as well as severe central atrophy in patient 1. A cone mosaic was observable in the peripheral AO fundus images of both patients. The disrupted cone mosaic on the AO images correlated with the hypofluorescent areas on autofluorescence. DNA testing identified the homozygous, likely pathogenic variant c.1508G&amp;#x3e;A/p.(Arg503His) (chr16:68719191) in the &lt;i&gt;CDH3&lt;/i&gt; gene. &lt;b&gt;&lt;i&gt;Conclusions:&lt;/i&gt;&lt;/b&gt; The two siblings revealed hypotrichosis and macular dystrophy in both eyes. The identification of a homozygous &lt;i&gt;CDH3&lt;/i&gt; mutation in each patient confirms the syndromic entity of hypotrichosis with juvenile macular degeneration.
Structural Gravity and the Gains from Trade Under Imperfect Competition
2020-01-01

We extend structural gravity models of bilateral trade flows to oligopolistic competition. We show that conventional gravity estimates do not only reflect trade costs but also market power. Our simple estimation procedure generalizes the standard gravity model and disentangles exogenous trade frictions and endogenous market power distortions. We use our estimated model to counterfactually increase trade costs by abolishing the European Single Market. We find that domestic firms' markups in EU member countries increase by 2 to 6 percent. Importantly, welfare effects of trade liberalization are much more pronounced due to the change in competition among domestic and foreign firms.
Delayed Treatment of a Galeazzi Fracture Using an External Ring Fixator.
2020-01-01

By applying the principles of bone healing and osteosynthesis, even older or unconventional treatment strategies can be indicated and conducted successfully in individual patients, leading to good results and high patient satisfaction.
New Pottery Contexts and Radiocarbon Data from Early Layers on the Byrsa Hill (Carthage): the “Astarte 2”-sequence
2020-01-01

This paper presents the results of a preventive excavation at the south-eastern slope of the Byrsa Hill in Carthage located in the modern Rue Astarte. Early Punic layers in a closed, undisturbed sequence upon the virgin soil were excavated (“Astarte 2”-sequence). According to the ceramic and radiocarbon data, this sequence can be placed to the first half of the 8th century BCE, and remains open to a possible overflow to the end of the 9th century BCE for the early material of the lowest stratigraphic layer. This evidence makes it possible to consider the assemblages in this sequence as being the oldest one found in Carthage so far. Already in this early stage Carthage seems to have been well integrated into a Mediterranean wide network, connecting Sardinian, Libyan, Cypriote, Iberian, Greek and Levantine partners.
GULF OF NUNA: ASTROCHRONOLOGIC CORRELATION OF A MESOPROTEROZOIC OCEANIC EUXINIC EVENT
2020-01-01

The ca. 1.4 Ga Velkerri and Xiamaling Formations, in Australia and the north China craton, respectively, are both carbonaceous shale deposits that record a prominent euxinic interval and were intruded by ca.1.3 Ga dolerite sills.These similarities raise the possibility that these two units correlate, which would suggest the occurrence of widespread euxinia, organic carbon burial, and source rock deposition.Paleomagnetic data are consistent with Australia and the north China craton being neighbors in the supercontinent Nuna and thus permit deposition in a single large basin, and the putative stratigraphic correlation.However, lack of geochronological data has precluded definitive testing.The Xiamaling Formation has been shown to exhibit depositional control by orbital cycles.Here, we tested the putative correlation with the Velkerri Formation by cyclostratigraphic analysis.The Velkerri Formation exhibits sedimentological cycles that can be interpreted to represent the entire hierarchy of orbital cycles, according to a sedimentation rate that is consistent with Re-Os ages.Comparison of the inferred durations of the euxinic intervals preserved in both the Xiamaling and Velkerri Formations reveals a nearly identical ∼10-m.y.-long oceanic euxinic event.This permits the interpretation that the two hydrocarbon-rich units were deposited and matured in the same basin of Nuna, similar to the Gulf of Mexico during the breakup of Pangea.
Energy transfer in supramolecular [Crypt-RE]-[W6I14] solids
2020-01-01

Photophysical properties of tungsten iodides with the [W<sub>6</sub>I<sub>14</sub>]<sup>2−</sup> cluster core have been described with respect to phosphorescence and phosphorescence quenching by molecular oxygen.
P689 Patient-reported outcomes (PRO-2) and intestinal ultrasound in ulcerative colitis patients: subanalysis of the TRUST&UC study cohort
2020-01-01

Abstract Background Patient-reported Outcomes (PRO) are gaining increasing acceptance as new tools to evaluate clinical activity, especially in the context of clinical trials and evaluation of drug efficacy. However, data to support the relevance of these endpoints and their correlation to objective markers of inflammation is still lacking.1 Recently published data demonstrated the feasibility of intestinal ultrasound (IUS) as a routine monitoring technique in clinical practice for Crohn’s disease (CD) and ulcerative colitis (UC) patients.2 Thus, the importance and significance of IUS, as a patient-centric and non-invasive technique has emerged over the last years and will become more relevant in the future.With this sub-analysis of the TRUST&amp;UC study, we aimed to investigate the correlation between improvement in ultrasound parameters and PRO-2 in UC patients. Methods TRUST&amp;UC is a prospective, observational study including 244 patients with an increased bowel wall thickness (BWT) at baseline and active UC (SCCAI ≥ 5). These patients were analysed for the Simple Clinical Colitis Activity Index (SCCAI) subscores stool frequency, urgency and rectal bleeding. These parameters were documented for up to 4 visits (baseline, an optional visit at week 2, week 6 and week 12). Pathological stool frequency was defined as a stool frequency of ≥1 point (≥ 4 stools/day) and pathological rectal bleeding was defined as ≥1 point (traces of blood in stool); the combination of both subscores was defined as PRO-2. Results We found a positive moderate correlation between BWT and the investigated SCCAI-subscores (rectal bleeding and BWT at W12 r = 0.417; stool frequency and BWT at W12, r = 0.483; PRO-2 and BWT at W12, r = 0.518) and even W6, which is in accordance with previously reported correlations of various PROs and endoscopy in UC-patients.3 We demonstrate that patients with normalisation of BWT (sigmoid colon &amp;lt; 4.0 mm) had a significantly higher chance of a non-pathological PRO-2 (pathological PRO-2 yes/no: 4.25 mm and 3.20 mm for week 6 (p &amp;lt; 0.001) and 4.45 mm and 3.00 mm (p &amp;lt; 0.001) for week 12). Conclusion With this sub-analysis of the TRUST&amp;UC study we demonstrated that bowel wall thickness, assessed by intestinal ultrasound, had a moderate correlation with normalisation of patient-reported outcomes as early as week 6 and 12. Furthermore, patients with non-pathological PRO-2 had significantly decreased bowel wall thickness. This again supports the value of intestinal ultrasound in routine medical practice. References
Construction of Antisense RNA-mediated Gene Knock-down Strains in the Cyanobacterium Anabaena sp. PCC 7120
2020-01-01

<i>Anabaena</i> sp. PCC 7120 (hereafter <i>Anabaena</i>) is a model cyanobacterium to study nitrogen fixation, cellular differentiation and several other key biological functions that are analogous in plants. As with any other organism, many genes in <i>Anabaena</i> encode an essential life function and hence cannot be deleted, causing a bottleneck in the elucidation of its genomic function. Antisense RNA (asRNA) mediated approach renders the study of essential genes possible by suppressing (but not completely eliminating) expression of the target gene, thus allowing them to function to some extent. Recently, we have successfully implemented this approach using the strong endogenous promoter of the <i>psbA1</i> gene (D1 subunit of Photosystem II) introduced into a high-copy replicative plasmid (pAM1956) to suppress the transcript level of the target gene <i>alr0277</i> (encoding a sigma factor, SigJ/Alr0277) in <i>Anabaena</i>. This protocol represents an efficient and easy procedure to further explore the functional genomics, expanding the scope of basic and applied research in these ecologically important cyanobacteria.
AnnoXplorer: A Scalable, Integrated Approach for the Visual Analysis of Text Annotations
2020-01-01

Text annotation data in terms of a series of tagged text segments can pose scalability challenges within the dimensions of quantity (long texts bearing many annotations), configuration (overlapping annotations or annotations with multiple tags), or source (annotations by multiple annotators). Accordingly, exploration tasks such as navigating within a long annotated text, recognizing patterns in the annotation data or assessing differences between annotators can be demanding. Our approach of an annotation browser deals with all of these data and task challenges simultaneously by providing a continuous range of views on large amounts of complex annotation data from multiple sources. We achieve this by using a combined geometric/semantic zooming mechanism that operates on an abstract representation of the sequence of a text’s tokens and the annotations thereupon, which is interlinked with a view on the text itself. The approach was developed in the context of a joint project with researc hers from fields concerned with textual sources. We derive our approach’s requirements from a series of tasks that are typical in natural language processing and digital humanities, show how it supports these tasks, and discuss it in the light of the feedback we got from our domain experts.
Cold-climate toolkits: firemaking, lithic recycling and assemblage formation in the Magdalenian of Hohle Fels Cave
2020-01-01

Equipment used for fire-making must have formed an integral part of the toolkits of Palaeolithic hunter-gatherers, especially during cold periods and in regions where caves were exploited. Yet evidence of the use of flint in fire-making only becomes abundant towards the end of the Palaeolithic period. We present here a number of newly identified strike-a-lights from the Magdalenian occupation of Hohle Fels Cave (Swabian Jura, Germany), dated to between 16,300 and 14,700 cal BP. The artefacts are interpreted as strike-a-lights on the basis of relatively heavy rounding, scarring and linear features located at their extremities. Two of them also have deposits of red mineral residue that were deemed the possible degraded remains of sulphuric iron and further analysed with SEM-EDS. All the potential strike-a-lights presented here are recycled tools originally used for other activities. We use them as a basis for discussing the use of lithic raw material in hunter-gatherer toolkits in the younger part of the Upper Palaeolithic sequence of Hohle Fels.
Heteromolecular exciton delocalization and heterofission in tetracene – pentacene blends
2020-01-01

Singlet exciton fission in heteromolecular systems holds great potential for application in organic photovoltaics. We study tetracene:pentacene mixed films using femtosecond transient absorption spectroscopy and find signs of heteromolecular interaction upon excitation of pentacene.
Semantic Variation Graphs: Ontologies for Pangenome Graphs
2020-01-01

Background: Variation graphs are a novel way to describe genomic variation across a population. Variation graph tools present a significant improvement in mitigating reference bias compared to the linear reference ecosystem. Existing toolkits focus on algorithms processing pangenome graphs. Yet, they have limited capabilities in integrating various annotations of the biology and providing an interface for large scale visualizations. Description: To interpret biological meaning in variation graphs by integrating various kinds of annotations for further analysis, FAIR data interchange formats are demanded. Borderless technology such as the Semantic Web allows variation graph toolkits and pangenome tools to focus on their core competence while allowing bioinformaticians to integrate, analyze, and visualize the data. Result: We demonstrate how we can represent a graphical pangenome with pangenome ontologies using a standard declarative graph query language. Then we show how the vg RDF and Pantograph RDF can represent data ready for the Semantic Web and how we can combine existing data from INDSC and UniProt without conversions or loss of information into a single Variation and Knowledge Graph.
The macroeconomic impact of Trump
2020-01-01

How much credit does Donald Trump deserve for the macroeconomic performance of\\nthe US economy? Growth and job creation have been robust during the first 2.5 years\\nof his presidential term, but this does not prove that Trump made a difference. In this\\nnote we develop a counterfactual scenario for how the US economy would have evolved\\nwithout Trump—we let a matching algorithm determine which combination of other\\neconomies best resembles the pre-election path of the US economy. We then compare the\\npost-election performance of the US economy to this synthetic “doppelganger”. There is\\nlittle evidence for a Trump effect.
The birth of bubbles by spinodal decomposition: Solving the tiny bubble paradox
2020-01-01

Energetic ash-producing volcanic eruptions are driven by the diffusive and decompressive growth of bubbles (mostly water) during ascent in a magma conduit. The spatial distribution of bubble nucleation sites is one of the primary controls on ash-forming fragmentation. However, the initial formation of bubbles in a supersaturated magma is problematical, especially for homogeneous nucleation. Excessive surface tension pressure should preclude the existence of small bubbles, because exsolved water is driven back into the melt. This is the “tiny bubble paradox.” We suggest that—under special circumstances—the tiny bubble paradox may be circumvented by spinodal decomposition, a process in which uphill diffusion enables spontaneous unmixing of phases to reduce the free energy of the system. As spinodal decomposition progresses, three dimensional, quasi-spherical, zones of water-rich magma develop. These zones are characterized by an increasingly high concentration of dissolved water at the centers and reducing concentration at the margins. Bubbles are born when the concentration of water in the interior of the water-rich zones goes to 100% and the concentration of melt goes to zero. The small, nascent, bubbles that emerge will be buffered from melt by water-rich shells with increasing melt concentration away from newly formed bubbles. This diffuse concentration gradient of water means that there is no surface, per se, for surface tension to arise. This is the crux of the solution of the tiny bubble paradox. Particle morphology may be used to distinguish ash with spinodal origins from ash associated with typical (metastable) bubble nucleation. Spinodal decomposition occurs at a wavelength determined by the pressure, temperature, and viscosity of the magmatic system. This wavelength should create bubbles of uniform size and bubble walls of equal strength in a fragmenting magmatic foam, leading to sharply mono-modal vesicle and ash particle size distributions. Classical bubble nucleation should create more-variable bubble sizes and bubble wall strengths, leading to a broader particle size distribution. Better understanding the mechanism of bubble formation in magmatic systems will, in turn, enable better understanding of hazardous, explosive, eruptions.
Surgical Treatment of a Neuromucoepidermoid Carcinoma of the Left Main Bronchus via Posterolateral Thoracotomy in a 4-Year-Old Boy
2020-01-01

Abstract We report the case of a 4-year-old boy with a neuromucoepidermoid carcinoma of the left main bronchus. Complete resection of the carcinoma and reconstruction of the carina between lower and upper lobe by means of an end-to-end anastomosis was performed via a left-sided thoracotomy.
A high precision calorimeter for hunting the sterile neutrino in the SOX experiment
2020-01-01

Abstract A thermal calorimetric apparatus was designed, built and calibrated for measuring the activity of the artificial 144 Ce — 144 Pr antineutrino source. This measurement will be performed at the Laboratori Nazionali del Gran Sasso in Italy, just before the source insertion in the tunnel under the Borexino detector and a precision better than 1% is required for a disappearance technique measurement in the SOX (Short distance neutrino Oscillation with BoreXino) project. In this work the apparatus is described and the most important results from the calibration measurements are shown, where the final precision of few per thousand is demonstrated.
Natural and Unnatural History of Isolation of Pulmonary Artery of Ductal Origin (IPADO)
2020-01-01

Objectives: Unilateral isolation of pulmonary artery of ductal origin is rare with a reported incidence of 1:200,000 live births (in the absence of a congenital heart defect). We report our experience in this specific patient group with regard to the treatment options and possible complications.
Prognostic Parameters for a Severe Disease Course in Pediatric Patients with Suspected Myocarditis: Data from the Prospective Multicenter Registry “MYKKE”
2020-01-01

Objectives: Myocarditis is one cause of severe heart failure in childhood. “MYKKE,” a multicenter prospective registry on pediatric patients with suspected myocarditis, aims with its ongoing enrollment to gain knowledge on incidence, diagnostic, therapy, and outcome.
Introduction: A Roadmap
2020-01-01

This chapter is the introduction which offers a roadmap to the structure and the content outline of the book. It lays out to the reader how the different chapters of the book succeed each other and build onto each other.
Justification of the Proposed Paradigm Shift
2020-01-01

This chapter goes into the benefits of the proposed perspective and approach. Arguments from various disciplines are offered to show the impact of a holistic perspective, for the individual, the community he/she lives in, and wider Society. A summary of evidence is drawn from the perspective of psychology and mental health, from biology, personal leadership and self-development, from evolutionary theories, from sociological argumentation, and from an economic viewpoint.
Impact of Histopathological Prostate Inflammation on Urine-Based Prostate Cancer Prediction Using the Prostate Cancer Gene 3 Score
2020-01-01

&lt;b&gt;&lt;i&gt;Introduction:&lt;/i&gt;&lt;/b&gt; The Prostate Cancer gene 3 (PCA3) urine test has gained importance in the diagnostic workup of prostate cancer (PC). Limited evidence suggests that PCA3 is not altered in the presence of inflammation. &lt;b&gt;&lt;i&gt;Objective:&lt;/i&gt;&lt;/b&gt; To assess the impact of histological inflammation on PCA3. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; PCA3 was evaluated in patients prior to prostate biopsy (&lt;i&gt;n&lt;/i&gt; = 193) and to radical prostatectomy (&lt;i&gt;n&lt;/i&gt; = 197). In patients without PC, inflammation was assessed and quantified by individual scores integrating grade and extent. Uni- and multivariate analyses were performed to assess the impact of inflammation grade on PCA3. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; The PCA3 scores prior to prostatectomy were lower (median 45) than those before positive biopsy (57; &lt;i&gt;p&lt;/i&gt; = 0.008). Of 101 negative biopsies, 78% showed inflammation. The median PCA3 scores in the groups with no inflammation and with maximum grade 1 (&lt;i&gt;n&lt;/i&gt; = 22), 2 (&lt;i&gt;n&lt;/i&gt; = 38), and 3 (&lt;i&gt;n&lt;/i&gt; = 19) inflammation were 45, 38, 27, and 25 (&lt;i&gt;p&lt;/i&gt; = 0.016). The multivariate models revealed a decrease in PCA3 proportional to the grade and extent of inflammation (&lt;i&gt;p&lt;/i&gt; &amp;#x3c; 0.04 each). &lt;b&gt;&lt;i&gt;Conclusions:&lt;/i&gt;&lt;/b&gt; The present data imply that the PCA3 score decreases in the presence of inflammation, which is relevant, for instance, to testing after a recently performed biopsy. In general, inflammation should be regarded as a factor putatively influencing PCA3 and other available and upcoming PC tests.
A neutron scattering perspective on the structure, softness and dynamics of the ligand shell of PbS nanocrystals in solution
2020-01-01

Time-averaged and energy-resolved neutron and X-ray scattering reveal the structure of the ligand shell, temperature-dependent diffusion and the phonon spectrum of PbS nanocrystals functionalized with oleic acid in solution.
Indirect Comparison of Combined BRAF and MEK Inhibition in Melanoma Patients with Elevated Baseline Lactate Dehydrogenase
2020-01-01

The approval of BRAF and MEK inhibitors has significantly improved treatment outcomes for patients with BRAF-mutated metastatic melanoma. The 3 first-line targeted therapy trials have provided similar results, and thus the identification of predictive biomarkers may generate a more precise basis for clinical decision-making. Elevated baseline lactate dehydrogenase (LDH) has already been determined as a strong prognostic factor. Therefore, this indirect analysis compared subgroups with elevated baseline LDH across the pivotal targeted therapy trials co-BRIM, COMBI-v and COLUMBUS part 1. The Bucher method was used to compare progression-free survival, objective response rate and overall survival indirectly. The results show a non-significant risk reduction for progression in the subgroup with elevated baseline LDH receiving vemurafenib plus cobimetinib compared with dabrafenib plus trametinib and encorafenib plus binimetinib. Although an indirect comparison, these data might provide some guidance for treatment recommendations in melanoma patients with elevated LDH.