julilili42/papers huggingface dataset:
Feasibility and accuracy of a voxel-based neuronavigation system with 3D image rendering in preoperative planning and as a learning tool for young neurosurgeons, exemplified by the anatomical localization of the superior sagittal sinus
2019-01-27

It is essential for a neurosurgeon to know individual anatomy and the corresponding anatomical landmarks before starting a surgery. Continuous training, especially of young neurosurgeons, is crucial for understanding complex neuroanatomy. In this study, we used a neuronavigation system with 3D volumetric image rendering to determine the anatomical relationship between the sagittal suture and the superior sagittal sinus (SSS) in patients with intracranial lesions. Furthermore, we discussed the applicability of such system in preoperative planning, residency training, and research. The study included 30 adult patients (18 female/12 male) who underwent a cranial computed tomography (CT) scan combined with venous angiography, for preoperative planning. The position of the sagittal suture in relation to the SSS was assessed in 3D CT images using an image guidance system (IGS) with 3D volumetric image rendering. Measurements were performed along the course of the sagittal sinus at the bregma, lambda, and in the middle between these two points. The SSS deviated to the right side of the sagittal suture in 50% of cases at the bregma, and in 46.7% at the midpoint and lambda. The SSS was displaced to the left of the sagittal suture in 10% of cases at the bregma and lambda and in 13% at the midpoint. IGSs with 3D volumetric image rendering enable simultaneous visualization of bony surfaces, soft tissue and vascular structures and interactive modulation of tissue transparency. They can be used in preoperative planning and intraoperative guidance to validate external landmarks and to determine anatomical relationships. In addition, 3D IGSs can be utilized for training of surgical residents and for research in anatomy.
Quantitative Data Extraction from Orthopyroxene Trace Element Maps and Its Potential to Examine the Formation of the UG2 Unit, Bushveld Complex
2019-01-27

We present a mineral chemical stratigraphy across the UG2 Unit, situated in the Upper Critical Zone of the Bushveld Complex. The magmatic evolution of the rocks hosting this world-class ore deposit for chromium and platinum group elements (PGEs) is still under debate. Orthopyroxene is a common phase across the magmatic stratigraphy of the unit. It hosts trace metals, whose relative contents can record information about magmatic processes. This study determined laser ablation inductively-coupled plasma mass spectrometry (LA-ICP-MS) trace element data for orthopyroxene and spot LA multi-collector ICP-MS Sr-isotope data for plagioclase. Mapping of trace element distributions revealed internal zoning in Cr, V, Y, and Th. Unlike in conventional spot analysis, quantitative trace element concentrations were extracted post-analysis from two-dimensional LA-ICP-MS maps. This approach offered advantages over spot analysis. The maps revealed internal complexities (e.g., inclusions, exsolved phases, zonations and diffusion halos) that could be avoided with suitable thresholds for chemical filter elements (i.e., 100 ppm &lt; Cr &lt; 4000 ppm, Y &lt; 6 ppm), permitting fast, automated extraction of pure orthopyroxene data pixels from elemental maps covering noritic, troctolitic, anorthositic and chromititic mineral assemblages. Diffusive equilibration in orthopyroxene was evaluated by comparing zonations in elements with different known diffusivities. Magnesium and Ni are homogenously distributed, indicative of rapid diffusive processes, while Cr and V show zonations, interpreted to largely reflect primary distribution. Thorium and Y apparently diffused along discrete pathways, indicated by concentration anomalies following orthopyroxene lamellae. A systematic study of the trace element inventory of orthopyroxene across the succession of the UG2 Unit, complemented with Sr isotope signatures of plagioclase, revealed clear evidence for open-system processes: compatible elements (Cr, Ni) are decoupled from Mg# variations in orthopyroxene from specific UG2 subunits; distinct Mg# peaks coincide with negative V excursions in orthopyroxene from chromite-bearing subunits; towards the top of the unit, plagioclase shows a distinct 87Sr/86Srinitial peak and orthopyroxene shows Cr-depleted and Th-enriched rims. These chemical features cannot be explained by crystal mixing alone and argue for the involvement of at least two chemically distinct melts in the formation of the studied UG2 section.
mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics
2019-01-28

This FAIRsharing record describes: Consortia efforts from the Metabolomics Standards Initiative, Proteomics Standards Initiative, and the Metabolomics Society have created mzTab-M to act as a common output format for analytical approaches using MS on small molecules. The intention of this specification, mzTab for Metabolomics (mzTab-M), is to extend the concepts established in the previous specification, so that more detail can be captured about the evidence trail for quantification, including MS features (different charge states or adducts) and the evidence trail for identifications, specifically for MS-based experiments on small molecules (metabolites, lipids, contaminants, etc.). mzTab-M is not formally backwards compatible, but follows a similar design pattern to simplify adaptation of existing software and to facilitate its integration into bioinformatics processing and submission workflows.
Reproducibility of the peritoneal regression grading score for assessment of response to therapy in peritoneal metastasis
2019-01-28

Aims The four‐tiered peritoneal regression grading score ( PRGS ) assesses the response to chemotherapy in peritoneal metastasis ( PM ). The PRGS is used, for example, to assess the response to pressurised intraperitoneal aerosol chemotherapy ( PIPAC ). However, the reproducibility of the PRGS is currently unknown. We aimed to evaluate the inter‐ and intraobserver variability of the PRGS . Methods and results Thirty‐three patients who underwent at least three PIPAC treatments as part of the PIPAC ‐ OPC 1 or PIPAC ‐ OPC 2 clinical trials at Odense University Hospital, Denmark, were included. Prior to each therapy cycle, peritoneal quadrant biopsies were obtained and three haematoxylin and eosin (H&amp;E)‐stained step sections were scanned and uploaded to a pseudonymised web library. For determining interobserver variability, eight pathologists assessed the PRGS for each quadrant biopsy, and Krippendorff's alpha and intraclass correlation coefficients ( ICC s) were calculated. For determining intraobserver variability, three pathologists repeated their own assessments and Cohen's kappa and ICC s were calculated. A total of 331 peritoneal biopsies were analysed. Interobserver variability for PRGS of each biopsy and for the mean and maximum PRGS per biopsy set was moderate to good/substantial. The intraobserver variability for PRGS of each biopsy and for the mean and maximum PRGS per biopsy set was good to excellent/almost perfect. Conclusions Our data support the PRGS as a reproducible and useful tool to assess response to intraperitoneal chemotherapy in PM. Future studies should evaluate the prognostic and predictive role of the PRGS .
Discovery of a sub-Keplerian disk with jet around a 20 M⊙ young star
2019-01-28

It is well established that solar-mass stars gain mass via disk accretion, until the mass reservoir of the disk is exhausted and dispersed, or condenses into planetesimals. Accretion disks are intimately coupled with mass ejection via polar cavities in the form of jets and less collimated winds, which allow mass accretion through the disk by removing a substantial fraction of its angular momentum. Whether disk accretion is the mechanism leading to the formation of stars with much higher masses is still unclear. Here, we are able to build a comprehensive picture of the formation of an O-type star by directly imaging a molecular disk, which rotates and undergoes infall around the central star, and drives a molecular jet that arises from the inner disk regions. The accretion disk is truncated between 2000 and 3000 au, it has a mass of about a tenth of the central star mass, and is infalling towards the central star at a high rate (6 × 10 −4 M ⊙ yr −1 ), so as to build up a very massive object. These findings, obtained with the Atacama Large Millimeter/submillimeter Array at 700 au resolution, provide observational proof that young massive stars can form via disk accretion much like solar-mass stars.
Impact of Alternatively Polyadenylated Isoforms of ETHYLENE RESPONSE FACTOR4 with Activator and Repressor Function on Senescence in Arabidopsis thaliana L.
2019-01-28

Leaf senescence is highly regulated by transcriptional reprogramming, implying an important role for transcriptional regulators. ETHYLENE RESPONSE FACTOR4 (ERF4) was shown to be involved in senescence regulation and to exist in two different isoforms due to alternative polyadenylation of its pre-mRNA. One of these isoforms, ERF4-R, contains an ERF-associated amphiphilic repression (EAR) motif and acts as repressor, whereas the other form, ERF4-A, is lacking this motif and acts as activator. Here, we analyzed the impact of these isoforms on senescence. Both isoforms were able to complement the delayed senescence phenotype of the erf4 mutant with a tendency of ERF4-A for a slightly better complementation. However, overexpression led to accelerated senescence of 35S:ERF4-R plants but not of 35S:ERF4-A plants. We identified CATALASE3 (CAT3) as direct target gene of ERF4 in a yeast-one-hybrid screen. Both isoforms directly bind to the CAT3 promoter but have antagonistic effects on gene expression. The ratio of ERF4-A to ERF4-R mRNA changed during development, leading to a complex age-dependent regulation of CAT3 activity. The RNA-binding protein FPA shifted the R/A-ratio and fpa mutants are pointing towards a role of alternative polyadenylation regulators in senescence.
Clinical, radiological, and genetic characteristics of 16 patients with ACO2 gene defects: Delineation of an emerging neurometabolic syndrome
2019-01-28

Abstract Mitochondrial aconitase is the second enzyme in the tricarboxylic acid (TCA) cycle catalyzing the interconversion of citrate into isocitrate and encoded by the nuclear gene ACO2. A homozygous pathogenic variant in the ACO2 gene was initially described in 2012 resulting in a novel disorder termed “infantile cerebellar retinal degeneration” (ICRD, OMIM#614559). Subsequently, additional studies reported patients with pathogenic ACO2 variants, further expanding the genetic and clinical spectrum of this disorder to include milder and later onset manifestations. Here, we report an international multicenter cohort of 16 patients (of whom 7 are newly diagnosed) with biallelic pathogenic variants in ACO2 gene. Most patients present in early infancy with severe truncal hypotonia, truncal ataxia, variable seizures, evolving microcephaly, and ophthalmological abnormalities of which the most dominant are esotropia and optic atrophy with later development of retinal dystrophy. Most patients remain nonambulatory and do no acquire any language, but a subgroup of patients share a more favorable course. Brain magnetic resonance imaging (MRI) is typically normal within the first months but global atrophy gradually develops affecting predominantly the cerebellum. Ten of our patients were homozygous to the previously reported c.336C&gt;G founder mutation while the other six patients were all compound heterozygotes displaying 10 novel mutations of whom 2 were nonsense predicting a deleterious effect on enzyme function. Structural protein modeling predicted significant impairment in aconitase substrate binding in the additional missense mutations. This study provides the most extensive cohort of patients and further delineates the clinical, radiological, biochemical, and molecular features of ACO2 deficiency.
Glucose Measurements at Various Time Points During the OGTT and Their Role in Capturing Glucose Response Patterns
2019-01-28

Intermediate time points during the oral glucose tolerance test (OGTT) have received more attention recently (1), with some researchers even suggesting to use 1-h glucose when screening for prediabetes (2). We demonstrated that characterization of glucose response patterns from OGTTs with five time points provides useful insights into the heterogeneity of type 2 diabetes development (3). Although such analyses are feasible in small pathophysiological investigations, they are not common in large epidemiological studies where the number of glucose measurements during an OGTT is often limited. Therefore, we aimed to study how well different combinations of fewer than five time points during an OGTT approximate glucose response patterns based on five time points. We analyzed data from the Relationship between Insulin Sensitivity and Cardiovascular disease (RISC) study, which we previously used to develop a glucose pattern classification model (3). The Tubingen Family Study (TUEF) cohort was used for external validation (4). Both studies included five-point OGTTs with glucose measurements at 0, 30, 60, 90, and 120 min. We excluded participants with self-reported diabetes or screen-detected diabetes (fasting plasma glucose ≥7.0 mmol/L or 2-h postload plasma glucose ≥11.1 mmol/L), participants taking glucose-lowering medication, and those with missing measurements at any of the five time points. We previously identified four glucose ...
Evolutionary models of cold and low-mass planets: cooling curves, magnitudes, and detectability
2019-01-28

Context. Future instruments like the Near Infrared Camera (NIRCam) and the Mid Infrared Instrument (MIRI) on the James Webb Space Telescope (JWST) or the Mid-Infrared E-ELT Imager and Spectrograph (METIS) at the European Extremely Large Telescope (E-ELT) will be able to image exoplanets that are too faint (because they have a low mass, and hence a small size or low effective temperature) for current direct imaging instruments. On the theoretical side, core accretion formation models predict a significant population of low-mass and/or cool planets at orbital distances of ~10–100 au. Aims. Evolutionary models predicting the planetary intrinsic luminosity as a function of time have traditionally concentrated on gas-dominated giant planets. We extend these cooling curves to Saturnian and Neptunian planets. Methods. We simulated the cooling of isolated core-dominated and gas giant planets with masses of 5 M ⊕ –2 M ♃ . The planets consist of a core made of iron, silicates, and ices surrounded by a H/He envelope, similar to the ice giants in the solar system. The luminosity includes the contribution from the cooling and contraction of the core and of the H/He envelope, as well as radiogenic decay. For the atmosphere we used grey, AMES-Cond , petitCODE , and HELIOS models. We considered solar and non-solar metallicities as well as cloud-free and cloudy atmospheres. The most important initial conditions, namely the core-to-envelope-mass ratio and the initial (i.e. post formation) luminosity are taken from planet formation simulations based on the core accretion paradigm. Results. We first compare our cooling curves for Uranus, Neptune, Jupiter, Saturn, GJ 436b, and a 5 M ⊕ planet with a 1% H/He envelope with other evolutionary models. We then present the temporal evolution of planets with masses between 5 M ⊕ and 2 M ♃ in terms of their luminosity, effective temperature, radius, and entropy. We discuss the impact of different post formation entropies. For the different atmosphere types and initial conditions, magnitudes in various filter bands between 0.9 and 30 micrometer wavelength are provided. Conclusions. Using blackbody fluxes and non-grey spectra, we estimate the detectability of such planets with JWST. We found that a 20 (100) M ⊕ planet can be detected with JWST in the background limit up to an age of about 10 (100) Myr with NIRCam and MIRI, respectively.
Treatment of Anorexia Nervosa—New Evidence-Based Guidelines
2019-01-29

Anorexia nervosa is the most severe eating disorder; it has a protracted course of illness and the highest mortality rate among all psychiatric illnesses. It is characterised by a restriction of energy intake followed by substantial weight loss, which can culminate in cachexia and related medical consequences. Anorexia nervosa is associated with high personal and economic costs for sufferers, their relatives and society. Evidence-based practice guidelines aim to support all groups involved in the care of patients with anorexia nervosa by providing them with scientifically sound recommendations regarding diagnosis and treatment. The German S3-guideline for eating disorders has been recently revised. In this paper, the new guideline is presented and changes, in comparison with the original guideline published in 2011, are discussed. Further, the German guideline is compared to current international evidence-based guidelines for eating disorders. Many of the treatment recommendations made in the revised German guideline are consistent with existing international treatment guidelines. Although the available evidence has significantly improved in quality and amount since the original German guideline publication in 2011, further research investigating eating disorders in general, and specifically anorexia nervosa, is still needed.
Is There a Positive Side to T Cell Exhaustion?
2019-01-29

T cell "exhaustion" describes a state of late-stage differentiation usually associated with active prevention of functionality via ligation of negative signaling receptors on the cell surface, and which can be reversed by blocking these interactions. This contrasts with T cell "senescence," which has been defined as a state that is maintained by intrinsic internal cell signaling (caused by DNA damage or other stresses) and which can be reversed pharmacologically. Interventions to alleviate these two different categories of inhibitory pathways may be desirable in immunotherapy for cancer and possibly certain infectious diseases, but reciprocally inducing and maintaining these states, or some properties thereof, may be beneficial in organ transplantation and autoimmunity. Even under physiological non-pathological conditions, T cell exhaustion and senescence may play a role in the retention of T cell clones required for immunosurveillance, and prevent their loss via elimination at the Hayflick limit. This essay briefly reviews T cell exhaustion in contrast to replicative senescence, and circumstances under which their modulation may be beneficial.
Facile synthesis of Al/Fe bimetallic (oxyhydr)oxide-coated magnetite for efficient removal of fluoride from water
2019-01-29

In this work, we developed a novel magnetic bimetallic Al/Fe (oxyhydr)oxide adsorbent through a facile and cost-effective method and explored its potential to adsorb fluoride in water. Its synthesis involved corrosion of natural magnetite in aluminium chloride solution, followed by titration with NaOH solution for <i>in-situ</i> synthesis of Al/Fe (oxyhydr)oxide-coated magnetite (Mag@Al<sub>2</sub>Fe). Characterization data indicated a uniform coating of Al/Fe (oxyhydr)oxide on magnetite, and the resulting composite possessed large specific surface area (∼90 m<sup>2</sup>/g) and good magnetic property. In batch adsorption experiments, the isotherm and kinetic data fitted well to the Langmuir model and pseudo-second-order model, respectively. The maximum adsorption capacity of Mag@Al<sub>2</sub>Fe is 26.5 mg/g, which was much higher than natural magnetite (0.44 mg/g). Moreover, this material retained high adsorption capacity toward fluoride within a wide pH range (3.0-8.0) and offered facile magnetic separation from water. Influence of competing ions was also evaluated which showed that the presence of Cl<sup>-</sup> and NO<sub>3</sub> <sup>-</sup> posed negligible interference, while HCO<sub>3</sub> <sup>-</sup> and SO<sub>4</sub> <sup>2-</sup> had negative effects on fluoride adsorption. Thermodynamic investigations revealed that fluoride adsorption was exothermic and spontaneous. The observed increase in solution pH and formation of Al-F and Fe-F bonds (as indicated by XPS analysis) after fluoride adsorption suggested the major adsorption mechanism of ligand exchange. Besides, the adsorption/desorption cycle studies demonstrated the well-retained performance of Mag@Al<sub>2</sub>Fe for repeated application after regeneration by 0.5 mol/L NaOH solution. Facile synthesis, high defluoridation, lower cost, and quick separation of Mag@Al<sub>2</sub>Fe indicates its promising potential for drinking water defluoridation.
Molecular recognition patterns of anti-topoisomerase I-antibodies in patients with systemic sclerosis before and after autologous stem cell transplantation.
2019-01-29

Reactivity towards topo-I-epitopes is heterogeneous in SSc, but peptide 39 (aa647-671) may be another immunodominant epitope besides the published epitope aa489-573. Antibody reactivity to this peptide 39 was higher in group 2- than in group 1-patients. Peptide recognition pattern did not change after aSCT.
Distinct ROPGEFs successively drive polarization and outgrowth of root hairs
2019-01-29

SUMMARY Root hairs are tubular protrusions of the root epidermis that significantly enlarge the exploitable soil volume in the rhizosphere. Trichoblasts, the cell type responsible for root hair formation, switch from cell elongation to tip growth through polarization of the growth machinery to a pre-defined root hair initiation domain (RHID) at the plasma membrane. The emergence of this polar domain resembles the establishment of cell polarity in other eukaryotic systems [1–3]. Rho-type GTPases of plants (ROPs) are among the first molecular determinants of the RHID [4, 5] and later play a central role in polar growth [6]. Numerous studies have elucidated mechanisms that position the RHID in the cell [7–9] or regulate ROP activity [10–18]. The molecular players that target ROPs to the RHID and initiate outgrowth, however, have not been identified. We dissected the timing of the growth machinery assembly in polarizing hair cells and found that positioning of molecular players and outgrowth are temporally separate processes that are each controlled by specific ROP guanine nucleotide exchange factor (GEFs). A functional analysis of trichoblast-specific GEFs revealed GEF3 to be required for normal ROP polarization and thus efficient root hair emergence, while GEF4 predominantly regulates subsequent tip growth. Ectopic expression of GEF3 induced the formation of spatially confined, ROP-recruiting domains in other cell types, demonstrating the role of GEF3 to serve as a membrane landmark during cell polarization. Our findings suggest that morphogenetic programs in plants employ distinct regulatory modules for the alignment and activation of the cellular growth machinery.