julilili42/papers huggingface dataset:
Untangling Faculty Misinformation From an Educational Perspective: Rejoinder to “The Menace of Misinformation: Faculty Misstatements in Management Education and Their Consequences”
2019-04-25

In their thought-provoking article, Giacalone and Promislo point to some problematic ideas in management education such as the adoration of materialism and competition or the notion of the economic model as a natural law. But do students really develop such ideas because they were misinformed by their teachers? Misinformation implies that what is taught is not the truth or at least not the whole truth. We suggest that the question of how to design future management education cannot be answered by only looking at what should be taught. Rather, we suggest that debates about the future of management education should not only be concerned with content but also the epistemology and the teaching of management theory. Not only does the current mainstream of management education misinform students by painting a one-sided picture of economic realities. Rather, and even more importantly, it leads students to develop misconceptions of knowledge in management science as being objective and unambiguous. Teaching students how to reflect on the assumptions behind management theories as well as their own assumptions and values might be a possible way to tackle the challenge of misinformation.
How rhythms of the sleeping brain tune memory and synaptic plasticity
2019-04-26

Abstract Decades of neurobehavioral research has linked sleep-associated rhythms in various brain areas to improvements in cognitive performance. However, it remains unclear what synaptic changes might underlie sleep-dependent declarative memory consolidation and procedural task improvement, and why these same changes appear not to occur across a similar interval of wake. Here we describe recent research on how one specific feature of sleep—network rhythms characteristic of rapid eye movement and non-rapid eye movement—could drive synaptic strengthening or weakening in specific brain circuits. We provide an overview of how these rhythms could affect synaptic plasticity individually and in concert. We also present an overarching hypothesis for how all network rhythms occurring across the sleeping brain could aid in encoding new information in neural circuits.
Soil Abiotic Properties and Plant Functional Traits Mediate Associations Between Soil Microbial and Plant Communities During a Secondary Forest Succession on the Loess Plateau
2019-04-26

In the context of secondary forest succession, aboveground-belowground interactions are known to affect the dynamics and functional structure of plant communities. However, the links between soil microbial communities, soil abiotic properties, plant functional traits in the case of semi-arid and arid ecosystems, are unclear. In this study, we investigated the changes in soil microbial species diversity and community composition, and the corresponding effects of soil abiotic properties and plant functional traits, during a ≥150-year secondary forest succession on the Loess Plateau, which represents a typical semi-arid ecosystem in China. Plant community fragments were assigned to six successional stages: 1-4, 4-8, 8-15, 15-50, 50-100, and 100-150 years after abandonment. Bacterial and fungal communities were analyzed by high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene and the internal transcribed spacer (ITS2) region of the rRNA operon, respectively. A multivariate variation-partitioning approach was used to estimate the contributions of soil properties and plant traits to the observed microbial community composition. We found considerable differences in bacterial and fungal community compositions between the early (S1-S3) and later (S4-S6) successional stages. In total, 18 and 12 unique families were, respectively, obtained for bacteria and fungi, as indicators of microbial community succession across the six stages. Bacterial alpha diversity was positively correlated with plant species alpha diversity, while fungal diversity was negatively correlated with plant species diversity. Certain fungal and bacterial taxa appeared to be associated with the occurrence of dominant plant species at different successional stages. Soil properties (pH, total N, total C, NH<sub>4</sub>-N, NO<sub>3</sub>-N, and PO<sub>4</sub>-P concentrations) and plant traits explained 63.80% and 56.68% of total variance in bacterial and fungal community compositions, respectively. These results indicate that soil microbial communities are coupled with plant communities via the mediation of microbial species diversity and community composition over a long-term secondary forest succession in the semi-arid ecosystem. The bacterial and fungal communities show distinct patterns in response to plant community succession, according to both soil abiotic properties and plant functional traits.
Point of Care Ultrasound in Geriatric Patients: Prospective Evaluation of a Portable Handheld Ultrasound Device
2019-04-26

Abstract Purpose The aim of the current study was to evaluate point of care ultrasound (POCUS) in geriatric patients by echoscopy using a handheld ultrasound device (HHUSD, VScan) at bedside in comparison to a high-end ultrasound system (HEUS) as the gold standard. Materials and Methods Prospective observational study with a total of 112 geriatric patients. The ultrasound examinations were independently performed by two experienced blinded examiners with a portable handheld device and a high-end ultrasound device. The findings were compared with respect to diagnostic findings and therapeutic implications. Results The main indications for the ultrasound examinations were dyspnea (44.6 %), fall (frailty) (24.1 %) and fever (21.4 %). The most frequently found diagnoses were cystic lesions 32.1 % (35/109), hepatic vein congestion 19.3 % (21/109) and ascites 13.6 % (15/110). HHUSD delivered 13 false-negative findings in the abdomen resulting in an “overall sensitivity” of 89.5 %. The respective “overall specificity” was 99.6 % (7 false-positive diagnoses). HHUSD (versus HEUS data) resulted in 13.6 % (17.3 %) diagnostically relevant procedures in the abdomen and 0.9 % (0.9 %) in the thorax. Without HHUSD (HEUS) 95.7 % (100 %) of important pathological findings would have been missed. Conclusion The small HHUSD tool improves clinical decision-making in immobile geriatric patients at the point of care (geriatric ward). In most cases, HHUSD allows sufficiently accurate yes/no diagnoses already at the bedside, thereby clarifying the leading symptoms for early clinical decision-making.
Spread‐spectrum magnetic resonance imaging
2019-04-26

Purpose A novel method for the acceleration of MRI acquisition is proposed that relies on the local modulation of magnetic fields. These local modulations provide additional spatial information for image reconstruction that is used to accelerate image acquisition. Methods In experiments and simulations, eight local coils connected to current amplifiers were used for rapid local magnetic field variation. Acquired and simulated data were reconstructed to quantify reconstruction errors as a function of the acceleration factor and applied modulation frequency and strength. Results Experimental results demonstrate a possible acceleration factor of 2 to 4. Simulations demonstrate the challenges and limits of this method in terms of required magnetic field modulation strengths and frequencies. A normalized mean squared error of below 10% can be achieved for acceleration factors of up to 8 using modulation field strengths comparable to the readout gradient strength at modulation frequencies in the range of 5 to 20 kHz. Conclusion Spread‐spectrum MRI represents a new approach to accelerate image acquisition, and it can be independently combined with traditional parallel imaging techniques based on local receive coil sensitivities.
eDiVA—Classification and prioritization of pathogenic variants for clinical diagnostics
2019-04-27

Mendelian diseases have shown to be an and efficient model for connecting genotypes to phenotypes and for elucidating the function of genes. Whole-exome sequencing (WES) accelerated the study of rare Mendelian diseases in families, allowing for directly pinpointing rare causal mutations in genic regions without the need for linkage analysis. However, the low diagnostic rates of 20-30% reported for multiple WES disease studies point to the need for improved variant pathogenicity classification and causal variant prioritization methods. Here, we present the exome Disease Variant Analysis (eDiVA; http://ediva.crg.eu), an automated computational framework for identification of causal genetic variants (coding/splicing single-nucleotide variants and small insertions and deletions) for rare diseases using WES of families or parent-child trios. eDiVA combines next-generation sequencing data analysis, comprehensive functional annotation, and causal variant prioritization optimized for familial genetic disease studies. eDiVA features a machine learning-based variant pathogenicity predictor combining various genomic and evolutionary signatures. Clinical information, such as disease phenotype or mode of inheritance, is incorporated to improve the precision of the prioritization algorithm. Benchmarking against state-of-the-art competitors demonstrates that eDiVA consistently performed as a good or better than existing approach in terms of detection rate and precision. Moreover, we applied eDiVA to several familial disease cases to demonstrate its clinical applicability.
Stress urinary incontinence and regenerative medicine
2019-04-27

The use of stem cells seems to be a feasible and safe technique with promising results in patients with SUI. However, as a result of heterogeneity of preclinical and clinical trials, the best approach to cell-based therapy in SUI is still under investigation. The definition of the optimal cell type applied for the regeneration of the sphincter, the development of surgical injection advices and adequate tools for the investigation of the muscle regeneration during the follow-up have to be investigated to improve the use of autologous cells in the therapy of SUI.
Engineering Tissues from Induced Pluripotent Stem Cells
2019-04-27

Stem cells hold tremendous promise for replacing or regenerating tissues damaged by injury and disease as well as to study developmental biology and pathomechanisms. The discovery of methods to generate and culture human pluripotent stem cells (hESC and hiPSC) paved the way for producing genetically defined organ and tissue-specific cell types in a controlled laboratory setting. Cell and tissue engineering approaches have proven essential to unlocking the power of human pluripotent stem cells for both disease modeling and regenerative medicine. This editorial summarizes impressive examples of burgeoning research by leading groups that harness cellular and tissue engineering principles to study mechanisms of disease and injury, and in the context of repairing damaged tissue. These studies highlight both the power of these approaches, as well as ongoing challenges in the field.
A Cleared View on Retinal Organoids
2019-04-28

Human induced pluripotent stem cell (hiPSC)-derived organoids mimicking tissues and organs in vitro have advanced medical research, as they opened up new possibilities for in-depth basic research on human organ development as well as providing a human in vitro model for personalized therapeutic approaches. hiPSC-derived retinal organoids have proven to be of great value for modeling the human retina featuring a very similar cellular composition, layering, and functionality. The technically challenging imaging of three-dimensional structures such as retinal organoids has, however, raised the need for robust whole-organoid imaging techniques. To improve imaging of retinal organoids we optimized a passive clearing technique (PACT), which enables high-resolution visualization of fragile intra-tissue structures. Using cleared retinal organoids, we could greatly enhance the antibody labeling efficiency and depth of imaging at high resolution, thereby improving the three-dimensional microscopy output. In that course, we were able to identify the spatial morphological shape and organization of, e.g., photoreceptor cells and bipolar cell layers. Moreover, we used the synaptic protein CtBP2/Ribeye to visualize the interconnection points of photoreceptor and bipolar cells forming the retinal-specific ribbon synapses.
Prognostic relevance of motor tests in elite girls’ soccer: a five-year prospective cohort study within the German talent promotion program
2019-04-28

Introduction: While research has provided valuable information about talent predictors, there is a gap regarding female soccer. This study analyzed the prognostic relevance of motor tests for players' future selection level in female soccer and assessed the role of sex as a moderator variable.Methods: Within the German talent promotion program, N = 499 U12 girls participated in motor diagnostics (sprint, agility, dribbling, ball control, shooting). Five years later, 14.2% of them made the youth national team (NT), 18.8% the regional association team (RA), and 66.9% were not further selected (NS). The tests' predictive validity for achieving one of these levels was analyzed using ANOVAs with post-hoc tests and logistic regressions. Subsequently, results were compared to data from previous research with N = 22,843 male U12 players.Results: Girls' performances in the motor diagnostics significantly discriminated between all three selection levels. Future NT players outperformed NS (d = 1.04) and RA players (d = 0.55), who, in turn, performed better than NS players (d = 0.47). Exception for dribbling, the motor tests demonstrated predictive validity independent of sex.Discussion: Although diagnostics are not sensitive enough to determine individual decisions for talent selection, they provide objective information to supplement coaches' work.
Image content is more important than Bouma’s Law for scene metamers
2019-04-29

We subjectively perceive our visual field with high fidelity, yet peripheral distortions can go unnoticed and peripheral objects can be difficult to identify (crowding). Prior work showed that humans could not discriminate images synthesised to match the responses of a mid-level ventral visual stream model when information was averaged in receptive fields with a scaling of about half their retinal eccentricity. This result implicated ventral visual area V2, approximated ‘Bouma’s Law’ of crowding, and has subsequently been interpreted as a link between crowding zones, receptive field scaling, and our perceptual experience. However, this experiment never assessed natural images. We find that humans can easily discriminate real and model-generated images at V2 scaling, requiring scales at least as small as V1 receptive fields to generate metamers. We speculate that explaining why scenes look as they do may require incorporating segmentation and global organisational constraints in addition to local pooling.
The fate of DNAPL contaminants in non-consolidated subsurface systems – Discussion on the relevance of effective source zone geometries for plume propagation
2019-04-29

Dense non-aqueous phase liquids, i.e., DNAPLs and the evolving contaminant plumes in aquifers provide significant potential to pose hazards affecting both environment and human health. Therefore, a proper assessment of contaminant spreading within the subsurface is critical. This includes a sufficient characterization of governing parameters describing both the subsurface and the contaminant itself. Thereby, knowledge on the contaminant source zone and especially the source zone geometry, i.e., SZG is critically required, yet very uncertain. This study identifies current limitations and open research questions in the formation and shape determination of source zone geometry, as well as its relevance for contaminant plumes. Our literature review reveals that existing characterization methods are subject to data interpretation uncertainties, while the application of these methods on field scale is limited by technical demands and accompanied efforts. In a next step, methods to implement increased source zone information into calculation methods are discussed. By means of an exemplary application of selected assessment tools, i.e., plume response models, results clearly proof the relevance of SZGs for site assessment. However, existing plume response models consider over-simplified geometries that may compromise their suitability. Our findings identify the demand for improved characterization of complex SZGs and the need to better evaluate the dependency of DNAPL migration on system properties and external influences. With emphasized knowledge on the most relevant SZG features, the delineation of "effective" SZGs allowing for straightforward implementation into plume response models and an adaption of the latter to incorporate more information on SZGs should be possible.
Diagnostic Value of the Basic Erosive Wear Examination for the Assessment of Dental Erosion on Patients, Dental Photographs, and Dental Casts
2019-04-29

SUMMARY Objectives: The aim of this trial was to investigate the diagnostic value of the basic erosive wear examination (BEWE) in clinical use, on dental photographs, and on dental casts over a two-year follow-up period (2013-2015). According to the main hypothesis for longitudinal monitoring of dental erosion, the BEWE is equally reproducible by the three assessment methods. Methods and Materials: The clinical assessment included intraoral photographic documentation, dental impressions, oral examination, and assessment of BEWE. Clinical assessment of BEWE was done by one blinded examiner, whereas assessment on photographs and dental casts was performed by three calibrated examiners and repeated after 14 days. The three assessment methods were analyzed separately by longitudinal agreement and inter- and intrarater reliability (intraclass correlation coefficient) alongside 95% confidence intervals (CIs). Results: Comparing the longitudinal data of the years 2013-2015, clinical use and photographs showed no significant difference (p=0.0681-0.9963), whereas the statistical analysis showed a significant difference for dental casts by comparing data from 2013 vs 2014 (p=0.0266) as well as data from 2013 vs 2015 (p=0.0001). Statistical evaluation of overall BEWE showed an intrarater reliability of 0.79-0.91 for photographs and 0.60-0.87 for dental casts. The interrater reliability was 0.77 (95% CI=[0.69; 0.84]) for photographs and 0.63 (95% CI=[0.52; 0.72]) for dental casts. Conclusion: This investigation showed that in longitudinal clinical monitoring, the assessment of the BEWE on patients and dental photographs yielded comparable results. In addition, based on these findings, the assessment of the BEWE on dental casts showed moderate reproducibility. Therefore, dental casts may be better used for laboratory assessment techniques.
Bax mitochondrial residency is more critical than Bax oligomerization for apoptosis
2019-04-29

Abstract The Bax protein plays an important effector role in apoptosis by forming pores in the mitochondrial outer membrane. While doing so, Bax forms higher-order oligomers in the membrane, but it remains unclear whether this oligomer formation is essential for pore formation. Using cell-free and cellular experimental systems, we investigated two Bax C-terminus mutants, T182I and G179P. Neither mutant formed large oligomers when activated in liposomes. Nevertheless, the G179P mutant could produce membrane pores, suggesting that large oligomers are not required for permeabilization. Surprisingly, however, when G179P was transduced into Bax/Bak double knockout mouse embryonic fibroblasts, it was purely cytoplasmic and failed to mediate cell death. T182I behaved in the opposite manner. When mixed with liposomes, T182I was inefficient in both membrane insertion and permeabilization. However, transduced into cells, BaxT182I resided constitutively in mitochondria, owing to its slow retrotranslocation and mediated apoptosis as efficiently as wild-type Bax. We conclude that Bax’s mitochondrial residence (regulated by targeting and retrotranslocation) is more important for apoptosis than its efficiency of membrane insertion and higher-order oligomerization.
Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery
2019-04-30

In summary, we conclude that CRWN1 is a key component of the lamina-chromatin network in plants. It is functionally equivalent to animal lamins, playing critical roles in modulating patterns of chromatin positioning at the nuclear periphery.
Association of Intrathecal Immunoglobulin G Synthesis With Disability Worsening in Multiple Sclerosis
2019-04-30

Patients with new diagnoses of relapsing-remitting multiple sclerosis or clinically isolated syndrome with intrathecal IgG synthesis had a higher risk of and shorter time to EDSS worsening across a 4-year period of follow-up. Intrathecal IgG synthesis is a potentially useful marker for disability worsening in patients with multiple sclerosis and may be useful for early treatment decisions.
ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion
2019-04-30

Abstract The field of computational proteomics is approaching the big data age, driven both by a continuous growth in the number of samples analysed per experiment, as well as by the growing amount of data obtained in each analytical run. In order to process these large amounts of data, it is increasingly necessary to use elastic compute resources such as Linux-based cluster environments and cloud infrastructures. Unfortunately, the vast majority of cross-platform proteomics tools are not able to operate directly on the proprietary formats generated by the diverse mass spectrometers. Here, we presented ThermoRawFileParser, an open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzML. To ensure the broadest possible availability, and to increase integration capabilities with popular workflow systems such as Galaxy or Nextflow, we have also built Conda and BioContainers containers around ThermoRawFileParser. In addition, we implemented a user-friendly interface (ThermoRawFileParserGUI) for those users not familiar with command-line tools. Finally, we performed a benchmark of ThermoRawFileParser and msconvert to verify that the converted mzML files contain reliable quantitative results.
Elastic Wrapping of Lower Extremity Free Flaps during Dangling Improves Microcirculation and Reduces Pain as well as Edema
2019-04-30

Background Free tissue transfer has become a common and safe reconstructive procedure. However, total or partial flap losses remain a looming threat, especially for lower extremity free flaps due to the gravitational challenge associated with dependency. Thus, the majority of microsurgical centers apply some kind of structured flap training. However, due to the lack of evidence, these differ greatly, for example, in the application of an elastic wrapping during dangling. Therefore, the aim of this study was to assess the impact of an elastic wrapping on free flap microcirculation, edema, and pain during dangling. Methods Standardized dangling was performed from postoperative day (POD) 6 to 9 in 30 patients with microvascular reconstruction of the lower extremity. The first dangling per day was performed without elastic wrapping, followed by another session with 30 mm Hg of elastic wrapping. Tissue oxygen saturation (StO2), regional hemoglobin content (rHb), and blood flow (BF) were continuously measured in the free flap; the circumference of the flap as well as pain was assessed. Results During wrapped dangling, BF as well as StO2 was significantly increased, while rHb was significantly lower on all PODs. Wrapped dangling was rated significantly more comfortable and the girth of the free flaps was significantly less after wrapped dependency when compared with unwrapped dangling. Conclusion Dangling with an elastic wrapping with 30 mm Hg pressure improved flap microcirculation and reduced pain and edema formation.