julilili42/papers huggingface dataset:
Clinically Valuable Quality Control for PET/MRI Systems: Consensus Recommendation From the HYBRID Consortium
2019-09-24

Quality control (QC) of medical imaging devices is essential to ensure their proper function and to gain accurate and quantitative results. Therefore, several international bodies have published QC guidelines and recommendations for a wide range of imaging modalities to ensure adequate performance of the systems. Hybrid imaging systems such as positron emission tomography/computed tomography (PET/CT) or PET/magnetic resonance imaging (PET/MRI), in particular, present additional challenges caused by differences between the combined modalities. However, despite the increasing use of this hybrid imaging modality in recent years, there are no dedicated QC recommendations for PET/MRI. Therefore, this work aims at collecting information on QC procedures across a European PET/MRI network, presenting quality assurance procedures implemented by PET/MRI vendors and achieving a consensus on PET/MRI QC procedures across imaging centers. Users of PET/MRI systems at partner sites involved in the HYBRID consortium were surveyed about local frequencies of QC procedures for PET/MRI. Although all sites indicated that they perform vendor-specific daily QC procedures, significant variations across the centers were observed for other QC tests and testing frequencies. Likewise, variations in available recommendations and guidelines and the QC procedures implemented by vendors were found. Based on the available information and our clinical expertise within this consortium, we were able to propose a minimum set of PET/MRI QC recommendations including the daily QC, cross-calibration tests, and an image quality (IQ) assessment for PET and coil checks and MR image quality tests for MRI. Together with regular checks of the PET–MRI alignment, proper PET/MRI performance can be ensured.
Greater effect of warming on community composition with increased precipitation and in moister landscape location
2019-09-24

Abstract Questions We asked how plant community composition responded to experimentally produced warmer and drier climate conditions at the landscape scale with existing variation in local species composition and environmental conditions. We aimed to identify changes in community composition overall and the species with greatest response in abundance, and hypothesized that locally restricted species may be more sensitive to warming than more widespread species within the landscape based on the assumption that they have a narrower niche breadth with respect to environmental conditions. Location Semiarid, northern Mongolian steppe. Methods Open‐top passive warming chambers (OTCs) elevated temperatures at two slope locations that differed in elevation, degree of slope, environmental conditions, and species composition. The OTC treatment was crossed with watering on the drier upper slope. Community composition differences among treatments were examined using canonical analysis of principal coordinates (CAP), which identified species contributing the most to differences. In response to warming, we also compared species locally restricted to one slope location with locally widespread species. Results Open‐top passive warming chambers affected community composition more where soil moisture was greater, at the lower slope location and where warming was combined with supplemental watering on the drier upper slope. Locally restricted species responded negatively to the OTC while locally widespread species showed no overall response. Conclusions Community composition responses to warming differ even within the landscape over and above the initial differences that exist in community structure and abiotic factors. Our results suggest that a warmer and drier climate will impact community composition sooner under more mesic conditions, affect locally restricted species more strongly, and reduce variation in species composition across the landscape. To better predict community responses to future warming, we must consider combined and interactive effects with changes in precipitation and extant water availability.
Field-Scale Co-fermentation of Solid Waste From Urine-Diverting Dry Toilets (UDDT-SW) and Banana Waste to Produce Undissociated Carboxylic Acids to Inactivate Ascaris Eggs
2019-09-24

Innovative, low-cost methods for inactivating pathogens in human fecal material (HFM) are needed, particularly in expanding urban areas where conventional sewer systems and centralized wastewater treatment plants are not feasible. To address this challenge, we have developed a bioprocess that utilizes open cultures of anaerobic bacteria (i.e., microbiomes) to produce carboxylic acids using HFM as substrate. When the pH is sufficiently low, the carboxylic acids exist in the undissociated form and inactivate pathogens. Here, we used real solid waste (SW) collected from container-based, urine-diverting dry toilets (UDDT) in Nairobi, Kenya to conduct lab-scale and field-scale trials. Through these trials, we investigated operating conditions required to use carboxylic acid fermentation in sanitation waste treatment processes. We tested three different inoculum treatments and determined that the microbiome in UDDT-SW is well-suited to produce carboxylic acids without the need for an external inoculum. We also tested co-fermentation of UDDT-SW with carbohydrate-rich food waste as a means of reducing the pH. We found that when food waste was incorporated in a way that maintained the pH between 4.8 and 5.2, then the food waste was quickly converted to carboxylic acids, and the low pH created high concentrations of undissociated carboxylic acids. The resulting concentrations of undissociated carboxylic acids resulted in Ascaris inactivation within 15 days. However, we found that a temperature ≥30°C is required for carboxylic acid production to occur.
Retinal horizontal cells use different synaptic sites for global feedforward and local feedback signaling
2019-09-24

Abstract In the outer plexiform layer (OPL) of the mouse retina, two types of cone photoreceptors (cones) provide input to more than a dozen types of cone bipolar cells (CBCs). This transmission is modulated by a single horizontal cell (HC) type, the only interneuron in the outer retina. Horizontal cells form feedback synapses with cones and feedforward synapses with CBCs. However, the exact computational role of HCs is still debated. Along with performing global signaling within their laterally coupled network, HCs also provide local, cone-specific feedback. Specifically, it has not been clear which synaptic structures HCs use to provide local feedback to cones and global forward signaling to CBCs. Here, we reconstructed in a serial block-face electron microscopy volume the dendritic trees of five HCs as well as cone axon terminals and CBC dendrites to quantitatively analyze their connectivity. In addition to the fine HC dendritic tips invaginating cone axon terminals, we also identified “bulbs”, short segments of increased dendritic diameter on the primary dendrites of HCs. These bulbs are located well below the cone axon terminal base and make contact to other cells mostly identified as other HCs or CBCs. Using immunolabeling we show that HC bulbs express vesicular gamma-aminobutyric acid transporters and co-localize with GABA receptor γ2 subunits. Together, this suggests the existence of two synaptic strata in the mouse OPL, spatially separating cone-specific feedback and feedforward signaling to CBCs. A biophysics-based computational model of a HC dendritic branch supports the hypothesis that the spatial arrangement of synaptic contacts allows simultaneous local feedback and global feedforward signaling.
Revisiting Lorentz violation in Hořava gravity
2019-09-24

In the context of Horava gravity, the most promising known scenarios to\\nrecover Lorentz invariance at low energy are the possibilities that (1) the\\nrenormalization group flow of the system leads to emergent infrared Lorentz\\ninvariance, and (2) that supersymmetry protects infrared Lorentz invariance. A\\nthird scenario proposes that a classically Lorentz invariant matter sector with\\ncontrolled quantum corrections may simply co-exist with Horava gravity under\\ncertain conditions. However, for non-projectable Horava gravity in 3+1\\ndimensions it is known that, in the absence of additional structures, this\\nmechanism is spoiled by unexpected power-law divergences. We confirm this same\\nresult in the projectable version of the theory by employing the recently found\\ngauge-fixing term that renders the shift and graviton propagators regular. We\\nshow that the problem persists for all dimensions , and that the\\ndegree of fine tuning in squared sound speeds between a U(1) gauge field and a\\nscalar field increases with . In particular, this difference in the zero\\nexternal momentum limit is proportional to for , where\\n is the ultraviolet momentum cutoff for loop integrals, while the\\npower-law divergences are absent for and . These results suggest\\nthat not only the gravity sector but also the matter sector should exhibit a\\ntransition to Lifshitz scaling above some scale, and that there should not be a\\nlarge separation between the transition scales in the gravity and matter\\nsectors. We close with a discussion of other more promising scenarios,\\nincluding emergent Lorentz invariance from supersymmetry/strong dynamics, and\\npointing out challenges where they exist.\\n
The 5’-NAD cap of RNAIII modulates toxin production in Staphylococcus aureus isolates
2019-09-24

1 Abstract Nicotinamide adenosine dinucleotide (NAD) has been found to be covalently attached to the 5’-ends of specific RNAs in many different organisms, but the physiological consequences of this modification are largely unknown. Here we report the occurrence of several NAD-RNAs in the opportunistic human pathogen Staphylococcus aureus . Most prominently, RNAIII, a central quorum-sensing regulator of this bacterium’s physiology, was found to be 5’-NAD-capped to a significant extent. NAD incorporation efficiency into RNAIII was found to depend in vivo on the −1 position of the P3 promoter. Reduction of RNAIII’s NAD content led to a decreased expression of alpha- and delta-toxins, resulting in reduced cytotoxicity of the modified strains. These effects to not seem to be due to changes in RNAIII’s secondary structure upon NAD attachment, as indicated by largely unaltered patterns in in vitro chemical probing experiments. Our study represents a large step towards establishing a biological function of the 5’-NAD cap, which for RNAIII in S. aureus is to modulate the expression of virulence factors. 2 Importance Numerous organisms, including bacteria, are endowed with a 5’-NAD cap in specific RNAs. While the presence of the 5’-NAD cap modulates the stability of the modified RNA species, a significant biological function and phenotype have not been assigned so far. Here, we show the presence of a 5’-NAD cap in RNAIII from S. aureus, a dual-function regulatory RNA involved in quorum-sensing processes and regulation of virulence factor expression. We also demonstrate that altering the natural NAD modification ratio of RNAIII leads to a decrease in exotoxin production, thereby modulating bacterium’s virulence. Our work unveils a new layer of regulation of RNAIII and the agr system that might be linked to the redox state of the NAD molecule in the cell.
Notes on Yurumanguí grammar and lexicon
2019-09-25

In this article, I offer a contribution to the philological study of premodern materials of languages of South America that have already become extinct. I am concerned with the Yurumanguí language, whose speakers were encountered in the 18th century in the western lowlands of Colombia by a Spanish expedition. This encounter resulted in the production of a short collection of words and phrases by a priest which is analyzed here anew. Problems of inconsistent and likely highly inadequate orthographic representation of the speech of the Yurumanguí informants and other problems, in this case, make it highly difficult to arrive at consistent analyses, as I show throughout my highly tentative discussion of nominal and verbal morphosyntax. I also offer external comparisons for some of the available Yurumanguí lexical material. Far from being able to demonstrate the genetic connections of the language, such comparisons do allow to identify items the Yurumanguí language shared with neighboring languages and hence to situate it within the former linguistic ecology of this part of South America.
The HLA Ligand Atlas - A resource of natural HLA ligands presented on benign tissues
2019-09-25

ABSTRACT The human leukocyte antigen (HLA) complex controls adaptive immunity by presenting defined fractions of the intracellular and extracellular protein content to immune cells. Here, we describe the HLA Ligand Atlas, an extensive collection of mostly matched HLA-I and -II ligandomes from 225 benign samples (29 tissues, 21 subjects). The initial release covers 51 HLA-I and 86 HLA-II allotypes presenting 89,853 HLA-I- and 140,861 HLA-II ligands. We observe that the immunopeptidomes differ considerably between tissues and individuals on both source protein and HLA-ligand level. 1,407 HLA-I ligands stem from non-canonical genomic regions. We highlight the importance of comparatively analyzing both benign and malignant tissues to inform tumor association, based on a case study in three glioblastoma patients. The resource provides insights into applied and basic immune-associated questions in the context of cancer immunotherapy, infection, transplantation, allergy, and autoimmunity. It is publicly available at www.hla-ligand-atlas.org .
Using Multilevel Mixture Models in Educational Research: An Illustration with Homework Research
2019-09-25

The present study illustrates the utility of applying multilevel mixture models in educational research, using data on the homework behavior of 1,812 Swiss eighth-grade students in French as a second language. A previous person-centered study identified 5 homework learning types characterized by different patterns of high or low homework time and effort. Via multilevel latent profile analyses (MLPAs), the dependence of homework learning types on between-classroom differences was investigated. Based on the proportions of homework learning profiles across classrooms, 3 class-level profiles were identified: A “low time”, “high time” and an “average” profile. Predictors of the latent profiles at the student and class levels were assessed. The study offers insights into the advantages of multilevel mixture models for educational research.
The Gamification of Political Participation
2019-09-25

Abstract Political participation lies at the heart of normative democratic theory. To foster participatory interactions between citizens, some advocates and designers are resorting to gamification as the use of psycho-motivational involvement strategies from games in non-game contexts. The hope is that through gamification mechanisms, citizens will be drawn more easily towards participation platforms, apps, and digital services, as well as remain there longer, thereby effectively enhancing participation numbers and time. In this article, I will explore the potential problems of these involvement strategies, namely the worry that they may be able to undermine citizen’s individual and political autonomy by manipulating them into participating. Depending on the severity of the psycho-motivational effect as well as the covertness of the mechanism, gamification may constitute inadmissible forms of paternalism.
Non-invasive stimulation of vagal afferents reduces gastric frequency
2019-09-25

Abstract Metabolic feedback between the gut and the brain relayed via the vagus nerve contributes to energy homeostasis. We investigated in healthy adults whether non-invasive stimulation of vagal afferents impacts energy homeostasis via efferent effects on metabolism or digestion. In a randomized crossover design, we applied transcutaneous auricular vagus nerve stimulation (taVNS) while recording efferent metabolic effects using simultaneous electrogastrography (EGG) and indirect calorimetry. We found that taVNS reduced gastric myoelectric frequency ( p =.008), but did not alter resting energy expenditure. We conclude that stimulating vagal afferents induces gastric slowing via vagal efferents without acutely affecting net energy expenditure at rest. Collectively, this highlights the potential of taVNS to modulate digestion by activating the dorsal vagal complex. Thus, taVNS-induced changes in gastric frequency are an important peripheral marker of brain stimulation effects.
Therapeutic Touch in Exercise Videos: A Randomized Experiment of the Impact on the Evaluation of Therapists' Competence and Viewers' Self-Reliance
2019-09-25

From a psychological health perspective, being physically touched is highly relevant throughout people's lives. Touch plays an important role in many contexts, such as in instructing movement exercises. Exercise videos have become a well-accepted format to support therapists in instructing movement exercises. In the study presented here we examined the impact of the use of therapeutic touch in exercise videos on people's evaluation of physiotherapists' competence and on their own self-reliance. In a between-group randomized experiment, 125 participants watched one of three videos that showed a physiotherapist who instructed a movement exercise to a patient. The physiotherapist touched the patient during the treatment (therapist-touch, TT), instructed the patient to use self-touch (ST), or provided only exercise instruction without physical touch (no-touch, NT). In the TT condition, the participants' perception was that the physiotherapist exhibited more professional competence. However, participants considered the movement exercise in this TT condition to have less potential for fostering their autonomy. Finally, participants in the ST condition had the biggest increase in perceived self-efficacy. The way of touching a patient in an exercise video influences the perception of the treatment. We conclude that therapeutic touch should be applied in exercise videos in a goal-oriented way: It seems appropriate to use ST if the aim is to strengthen viewers' self-reliance and to use TT to arouse trust in the competence of the therapist.
Mixture-of-Experts Variational Autoencoder for clustering and generating from similarity-based representations
2019-09-25

Clustering high-dimensional data, such as images or biological measurements, is a long-standing problem and has been studied extensively. Recently, Deep Clustering gained popularity due to its flexibility in fitting the specific peculiarities of complex data. Here we introduce the Mixture-of-Experts Similarity Variational Autoencoder (MoE-Sim-VAE), a novel generative clustering model. The model can learn multi-modal distributions of high-dimensional data and use these to generate realistic data with high efficacy and efficiency. MoE-Sim-VAE is based on a Variational Autoencoder (VAE), where the decoder consists of a Mixture-of-Experts (MoE) architecture. This specific architecture allows for various modes of the data to be automatically learned by means of the experts. Additionally, we encourage the lower dimensional latent representation of our model to follow a Gaussian mixture distribution and to accurately represent the similarities between the data points. We assess the performance of our model on the MNIST benchmark data set and a challenging real-world task of defining cell subpopulations from mass cytometry (CyTOF) measurements on hundreds of different datasets. MoE-Sim-VAE exhibits superior clustering performance on all these tasks in comparison to the baselines as well as competitor methods and we show that the MoE architecture in the decoder reduces the computational cost of sampling specific data modes with high fidelity.
Novel box trainer for taTME – prospective evaluation among medical students
2019-09-25

Abstract Background Transanal total mesorectal excision (taTME) has been subject to extensive research and increasing clinical application. It allows further reduction of trauma by accessing via a natural orifice. Manifold platforms and instruments have been introduced and heterogeneity in surgical techniques exists. Because of the technique’s complexity there is a persistent need for dedicated training devices and concepts. Materials and methods The key steps of taTME were analyzed and a box trainer with three modules resembling these steps was designed and manufactured. Twenty-one surgically inexperienced medical students performed five repetitions of the three tasks with the new box trainer. Time and error count were analyzed for assessment of a learning curve. Results A significant reduction of processing time could be demonstrated for tasks 1–3 (p &lt; 0.001; p &lt; 0.001; p = 0.001). The effect size was high for comparison of repetition 1 and 5 and decreased over the course (task 1: r = 0.88 vs. r = 0.21; task 2: r = 0.86 vs. r = 0.23; task 3: r = 0.74 vs. r = 0.44). Also, a significant reduction of errors was demonstrated for tasks 1 and 2. The decrease of effect size was analogously demonstrated. Conclusions The trainer might help to reduce the use of animal models for testing of platforms and instruments as well as gaining first-hand experience in transanal rectal resection.
Final Analysis of DeCOG-SLT Trial: No Survival Benefit for Complete Lymph Node Dissection in Patients With Melanoma With Positive Sentinel Node
2019-09-26

PURPOSE We have previously reported on the 3-year results of the phase III German Dermatologic Cooperative Oncology Group trial (DeCOG; ClinicalTrials.gov identifier: NCT02434107 ) comparing distant metastasis-free survival (DMFS), recurrence-free survival (RFS), and overall survival (OS) in patients with positive sentinel lymph-node biopsy who were randomly assigned to complete lymph node dissection (CLND) or observation. Here, we report the final analysis with 72 months of median follow up. PATIENTS AND METHODS The multicenter randomized phase III trial included patients with cutaneous melanoma of the trunk and extremities who were randomly assigned (1:1) to undergo CLND or observation. DMFS was analyzed as the primary end point, and RFS, OS, and recurrences in the regional lymph node basin were secondary end points. The analysis was by intention to treat. Disease and survival information were collected quarterly. RESULTS From January 2006 to December 2014, 5,547 patients were screened to identify 1,256 with metastases in the sentinel lymph node (SLN). Of these, 483 (39%) were included: 241 in the observation arm and 242 in the CLND arm. In the final analysis, median follow up was 72 months (interquartile range, 67-77 months). No significant treatment-related difference was seen in the 5-year DMFS between the observation and CLND arms (67.6% v 64.9%, respectively; hazard ratio [HR], 1.08; P = .87). The 5-year RFS and OS also showed no difference (HR, 1.01 and 0.99, respectively). Grade 3 and 4 adverse effects occurred in 32 patients (13%) in the CLND arm; lymphedema (n = 20) and delayed wound healing (n = 5) were most common and no serious adverse events were reported. CONCLUSION The final results of the German Dermatologic Cooperative Oncology Group trial with a median follow up of 72 months showed higher event rates, but similar HRs compared with those at the 3-year analysis. These results confirm that immediate CLND in SLN-positive patients is not superior to observation in terms of DMFS, RFS, or OS and support not recommending CLND in patients with SLN metastasis.