julilili42/papers huggingface dataset:
An MR-Compatible Haptic Interface With Seven Degrees of Freedom
2018-02-15

Functional magnetic resonance imaging (fMRI) is a powerful tool for neuroscience. It allows the visualization of active areas in the human brain. Combining this method with haptic interfaces allows one to conduct human motor control studies with an opportunity for standardized experimental conditions. However, only a small number of specialized MR-compatible haptic interfaces exist that were mostly built around specific research questions. The devices are designed for pure translational, rotational, or grasping movements. In this work, we present a novel MR-compatible haptic interface with seven degrees of freedom (DoF), which allows for both translations and rotations in three DoF each, as well as a two-finger precision grasp. The presented haptic interface is the first one with these capabilities and is designed as a universal tool for human motor control studies involving fMRI. It allows for the switching of the paradigm to reprogramming rather than redesigning when moving on to a new research question. We introduce its kinematics and control, along with results of MR compatibility tests and a preliminary fMRI study, showing the applicability of the device.
Contributions of Catchment and In-Stream Processes to Suspended Sediment Transport in a Dominantly Groundwater-Fed Catchment
2018-02-15

Abstract. Suspended sediments impact stream water quality by increasing the turbidity and acting as a vector for strongly sorbing pollutants. Understanding their sources is of great importance to develop appropriate river management strategies. In this study, we present an integrated sediment transport model composed of a catchment-scale hydrological model to predict river discharge, a river-hydraulics model to obtain shear stresses in the channel, a sediment-generating model, and a river sediment-transport model. We use this framework to investigate the sediment contributions from catchment and in-stream processes in the Ammer catchment close to Tübingen in South-West Germany. The model is calibrated to stream flow and suspended-sediment concentrations. We use the monthly mean suspended-sediment load to analyze seasonal variations of different processes. The contributions of catchment and in-stream processes to the total loads are demonstrated by model simulations under different flow conditions. The evaluation of shear stresses by the river-hydraulics model allows identifying hotspots and hot moments of bed erosion for the main stem of the Ammer River. The results suggest that the contributions of suspended-sediment loads from urban areas and in-stream processes are higher in the summer months, while deposition has small variations with a slight increase in summer months. The catchment input, bed erosion, and bank erosion increase with an increase in flow rates. Bed erosion and bank erosion are negligible when flow is smaller than the corresponding thresholds of 1.5 m3 s−1 and 2.5 m3 s−1, respectively. The bed-erosion rate is higher during the summer months and varies along the main stem. Over the simulated time period, net sediment trapping is observed in the Ammer River. The present work is the basis to study particle-facilitated transport of pollutants in the system, helping to understand fate and transport of sediments and sediment-bound pollutants.
Baseline-corrected space-by-time non-negative matrix factorization for decoding single trial population spike trains
2018-02-15

Activity of populations of sensory neurons carries stimulus information in both the temporal and the spatial dimensions. This poses the question of how to compactly represent all the information that the population codes carry across all these dimensions. Here, we developed an analytical method to factorize a large number of retinal ganglion cells' spike trains into a robust low-dimensional representation that captures efficiently both their spatial and temporal information. In particular, we extended previously used single-trial space-by-time tensor decomposition based on non-negative matrix factorization to efficiently discount pre-stimulus baseline activity. On data recorded from retinal ganglion cells with strong pre-stimulus baseline, we showed that in situations were the stimulus elicits a strong change in firing rate, our extensions yield a boost in stimulus decoding performance. Our results thus suggest that taking into account the baseline can be important for finding a compact information-rich representation of neural activity.
Spectral methods for coupled channels with a mass gap
2018-02-16

We develop a method to compute the vacuum polarization energy for coupled\\nscalar fields with different masses scattering off a background potential in\\none space dimension. As an example we consider the vacuum polarization energy\\nof a kink-like soliton built from two real scalar fields with different mass\\nparameters.\\n
Breast tomosynthesis for the clarification of mammographic BI-RADS 3 lesions can decrease follow-up examinations and enables immediate cancer diagnosis
2018-02-16

Background The limited sensitivity of mammography in case of a high breast density often produces unclear or false-positive findings, so-called BI-RADS 3 lesions, which have to be followed up to prove benignity. Digital breast tomosynthesis (DBT) was developed to reduce such summation effects. Purpose To evaluate the influence of an additional DBT on the management of mammographic BI-RADS 3 findings and whether DBT can decrease the time to definitive diagnosis or not. Material and Methods We analyzed 87 patients with a mammographic non-calcified BI-RADS 3 lesion who underwent an additional DBT of the affected breast. A follow-up two-dimensional (2D) examination or a histological result of the lesion had to be available. The images were analyzed especially for the BI-RADS category and incremental diagnostic accuracy. Moreover, the inter-reader reliability and the radiation dose were evaluated. Results The BI-RADS category has been changed by the addition of DBT: 57.1% were assessed as BI-RADS 1 or 2, 4.6% as BI-RADS 4, and only 38.3% remained as BI-RADS 3. The intraclass correlation coefficient for the three readers showed a good agreement for inter-reader reliability. No false-negative examination was found in the follow-ups. Nine lesions were biopsied (seven benign, two malignant). Both malignant lesions were suspicious in the DBT (BI-RADS 4). A significant higher glandular dose was necessary for the DBT. Conclusion DBT has the potential to reduce the recall-rate of BI-RADS 3 lesions and to find and diagnose malignant lesions earlier than 2D mammography alone.
Negative emotional face perception is diminished on a very early level of processing in autism spectrum disorder
2018-02-16

Deficits in facial affect recognition (FAR) are often reported in autism spectrum disorder (ASD) due to inappropriate visual search strategies. It is unclear, however, whether or not deficits in subliminal FAR are still present in autism when visual focus is controlled. Thirteen persons with ASD and 13 healthy participants took part in this experiment. Supraliminal FAR was assessed using a standardized, computer-aided test. Subliminal FAR was obtained by an emotional face priming paradigm. By using an eye-tracking technique, it was assured that the initial visual focus was on the eyes of the prime. Persons with ASD showed worse FAR in supraliminal face recognition. Although controlled for initial gaze direction, participants also showed reduced negative face priming. These data confirm that FAR is disturbed already on a pre-attentive level in autism.
Status of the Dibaryon Resonance $d^*(2380)$
2018-02-16

The dibaryon resonance with --- first observed in the double-pionic fusion to the deuteron --- has meanwhile been detected in all relevant two-pion production channels by incident neutron-proton collisions. In addition, its resonance pole has been revealed in neutron-proton scattering. Theoretical calculations describe this state either as a compact hexaquark system or a dilute molecular-like object. Whereas the decay into two-pion channels does not discriminate between these two scenarios, the decay into single-pion channels is very discriminatory. In the hexaquark case this decay is heavily suppressed with a branching of less than 1 . In the molecular-like case a branching of as much as 18 is expected. In order to clarify this situation we have measured the isoscalar single-pion production in the energy region of d*(2380). As a result we find no evidence for such a decay with an upper limit of smaller than 9 . This is in support of the hexaquark interpretation -- at least as the dominant configuration, possibly surrounded by a cloud of molecular-like configurations. Other dibaryon candidates are currently under investigation.
Offshoring and Volatility of Demand
2018-02-16

In this paper we explore the role that demand uncertainty plays for the offshoring decision, and the role that offshoring plays for domestic volatility of employment.Offshoring is modeled as in Antràs & Helpman ( 2004), but we assume complete contracts.Firms are heterogeneous as in Melitz (2003).Uncertainty arises through recurring firm-specific shocks to demand.The presence of a cost of firing or hiring as in Bagliano & Bertola (2004) generates an intertemporal element to a firm's employment decision in its domestic and offshore production.In this environment, offshoring is driven by differential labor market exibility as well as by wage differences.Our most important results are: 1) If the foreign labor market features a high exibility, measured relative to its wage rate, compared to the domestic labor market, then higher uncertainty has a pro-offshoring effect.And 2), under this same condition, offshoring increases volatility in domestic employment of offshoring firms and the volatility of offshore employment of these same firms is larger than volatility of domestic employment.
Wnt-signaling enhances neural crest migration of melanoma cells and induces an invasive phenotype
2018-02-17

We present a novel role for Wnt-signaling in neural crest like melanoma cell invasion and metastasis, stressing the crucial role of embryonic EMT-inducing neural crest signaling for the spreading of malignant melanoma.
The mycotoxin phomoxanthone A disturbs the form and function of the inner mitochondrial membrane
2018-02-19

Abstract Mitochondria are cellular organelles with crucial functions in the generation and distribution of ATP, the buffering of cytosolic Ca 2+ and the initiation of apoptosis. Compounds that interfere with these functions are termed mitochondrial toxins, many of which are derived from microbes, such as antimycin A, oligomycin A, and ionomycin. Here, we identify the mycotoxin phomoxanthone A (PXA), derived from the endophytic fungus Phomopsis longicolla , as a mitochondrial toxin. We show that PXA elicits a strong release of Ca 2+ from the mitochondria but not from the ER. In addition, PXA depolarises the mitochondria similarly to protonophoric uncouplers such as CCCP, yet unlike these, it does not increase but rather inhibits cellular respiration and electron transport chain activity. The respiration-dependent mitochondrial network structure rapidly collapses into fragments upon PXA treatment. Surprisingly, this fragmentation is independent from the canonical mitochondrial fission and fusion mediators DRP1 and OPA1, and exclusively affects the inner mitochondrial membrane, leading to cristae disruption, release of pro-apoptotic proteins, and apoptosis. Taken together, our results suggest that PXA is a mitochondrial toxin with a novel mode of action that might prove a useful tool for the study of mitochondrial ion homoeostasis and membrane dynamics.
Sleep timing is linked to sociosexuality: Evidence from German, Polish, Slovak, and Spanish females
2018-02-19

Given the known relationship between eveningness and sociosexuality among females, the aims of this study were: (a) to analyze this relationship in four countries using midsleep time on free days and morning affect measures of morningness–eveningness and (b) to test the role of dark personality and other relevant control variables in this relationship. Data from 1483 females were collected from Poland, Spain, Germany, and Slovakia. Adjusting for age, relationship status, country, age at first intercourse, and Dark Triad traits, the most universal findings were that females with later sleep timing were less sociosexually restricted (3% shared variance with sociosexuality). Sleep timing played a greater role in sociosexuality compared to morning affect. This finding showed that Dark Triad personality is not involved in association between morningness–eveningness and sociosexuality and it added a value to the importance of sleep–wake habits in mating preferences.
H.E.S.S. discovery of very high energy γ-ray emission from PKS 0625−354
2018-02-19

PKS 0625−354 (z = 0.055) was observed with the four High Energy Stereoscopic System (H.E.S.S.) telescopes in 2012 during 5.5 h. The source was detected above an energy threshold of 200 GeV at a significance level of 6.1σ. No significant variability is found in these observations. The source is well described with a power-law spectrum with photon index Γ = 2.84 ± 0.50 ± 0.10 and normalization (at E = 1.0 TeV) N (E ) = (0.58 ± 0.22 ± 0.12 ) × 10−12 TeV cm s . Multiwavelength data collected with Fermi-LAT, Swift-XRT, Swift-UVOT, ATOM and WISE are also analysed. Significant variability is observed only in the Fermi-LAT γ-ray and Swift-XRT X-ray energy bands. Having a good multiwavelength coverage from radio to very high energy, we performed a broad-band modelling from two types of emission scenarios. The results from a one zone lepto-hadronic and a multizone leptonic models are compared and discussed. On the grounds of energetics, our analysis favours a leptonic multizone model. Models associated to the X-ray variability constraint support previous results, suggesting a BL Lac nature of PKS 0625−354 with, however, a large-scale jet structure typical of a radio galaxy.
Does a change in sleep timing increase testosterone in young adult men?
2018-02-19

Men are more evening oriented than women. These sex difference might be a result of gonadal hormones, especially of testosterone. Here, we tested for a causal relationship by shifting the sleep timing of young men to one hour later and assessed the influence on saliva testosterone. 50 men participated in our study (31 experimental, 19 control group). Sleep timing was measured with actigraphy. One week served as baseline and afterwards, participants were randomly assigned to either the control or the experimental group. In the experimental group, men were asked to go to bed about one hour later and to sleep one hour longer in the morning. Participants in the control group experienced no significant changes in sleep timing. In the experimental group, participants went to bed later and woke up later; therefore, mid-point of sleep was shifted to a later time and sleep duration decreased, because he men went to bed about one hour later but woke up only about 30 min later. The control group experienced a decline in testosterone, but the experimental group not. Changes in mid-point of sleep between baseline week and experimental week were correlated with the change in testosterone (r = 0.285).
Changes in the neuropeptide complement correlate with nervous system architectures in xenacoelomorphs
2018-02-19

Abstract Neuropeptides are essential neurosecretory signaling molecules common in protostomes and deuterostomes (together Nephrozoa). Not much, however, is known about the neuropeptide complement of the sister group Xenacoelomorpha. This group is comprised of the three clades Xenoturbella , Nemertodermatida, and Acoela, which differ strongly in their nervous system anatomy. In order to reconstruct the ancestral bilaterian neuropeptide complement and gain insights into neuropeptide evolution within Xenacoelomorpha, we analyzed transcriptomes of 13 acoels, nemertodermatids, and Xenoturbella species. Together with motif searches, similarity searches, mass spectrometry and phylogenetic analyses of neuropeptide precursors and neuropeptide receptors, we reconstruct the xenacoelomorph neuropeptide complement. Our comparison of xenacoelomorph GPCRs with cnidarian and nephrozoan neuropeptide receptors shows that the neuropeptide signaling diversified into at least 20 ancestral peptidergic systems in the lineage to Bilateria. We find that Xenoturbella species possess many of the ancestral bilaterian peptidergic systems and only a few clade-specific neuropeptides. Nemertodermatids seem to have nearly the complete complement of ancestral bilaterian systems and several novel neuropeptides. Acoels show an extensive loss of conserved bilaterian systems, but gained the highest number of novel and group-specific neuropeptides. While it is difficult to correlate the emergence of the bilaterian neuropeptide complement with the evolution of centralized nervous systems, we find a correlation between nervous system novelties and the expansion of taxon-specific neuropeptides in Xenacoelomorpha.
Beyond maps: Patterns of formation processes at the Middle Pleistocene open-air site of Marathousa 1, Megalopolis basin, Greece
2018-02-19

&amp;lt;p&amp;gt;Recent excavations at the Middle Pleistocene open-air site of Marathousa 1 have unearthed in one of the two investigated areas (Area A) a partial skeleton of a single individual of &amp;lt;em&amp;gt;Palaeoloxodon antiquus&amp;lt;/em&amp;gt; and other faunal remains in spatial and stratigraphic association with lithic artefacts. In Area B, a much higher number of lithic artefacts was collected, spatially and stratigraphically associated also with faunal remains. The two areas are stratigraphically correlated, the main fossiliferous layers representing an &amp;lt;em&amp;gt;en mass&amp;lt;/em&amp;gt; depositional process in a lake margin context. Evidence of butchering (cut-marks) has been identified on bones of the elephant skeleton, as well on elephant and other mammal bones from Area B. However, due to the secondary deposition of the main find-bearing units, it is of primary importance to evaluate the degree and reliability of the spatial association of the lithic artefacts with the faunal remains. Indeed, spatial association does not necessarily imply causation, since natural syn- and post-depositional processes may equally produce spatial association. Assessing the degree and extent of post-depositional reworking processes is crucial to fully comprehend the archaeological record, and therefore to reliably interpret past human behaviours. The present study uses a comprehensive set of spatial statistics in order to disentangle the depositional processes behind the distribution of the archaeological and palaeontological record at Marathousa 1. Preliminary results of our analyses suggest that a high-energy erosional process, attributed to a hyperconcentrated flow deposited at the margin of a swamp, reworked an autochthonous, exposed or slightly buried, scatter of lithic artefacts and faunal remains. Minor reworking and substantial spatial association of the lithic and faunal assemblages support the current interpretation of Marathousa 1 as a butchering site.&amp;lt;/p&amp;gt;
A large, open source dataset of stroke anatomical brain images and manual lesion segmentations
2018-02-20

Abstract Stroke is the leading cause of adult disability worldwide, with up to two-thirds of individuals experiencing long-term disabilities. Large-scale neuroimaging studies have shown promise in identifying robust biomarkers (e.g., measures of brain structure) of long-term stroke recovery following rehabilitation. However, analyzing large rehabilitation-related datasets is problematic due to barriers in accurate stroke lesion segmentation. Manually-traced lesions are currently the gold standard for lesion segmentation on T1-weighted MRIs, but are labor intensive and require anatomical expertise. While algorithms have been developed to automate this process, the results often lack accuracy. Newer algorithms that employ machine-learning techniques are promising, yet these require large training datasets to optimize performance. Here we present ATLAS (Anatomical Tracings of Lesions After Stroke), an open-source dataset of 304 T1-weighted MRIs with manually segmented lesions and metadata. This large, diverse dataset can be used to train and test lesion segmentation algorithms and provides a standardized dataset for comparing the performance of different segmentation methods. We hope ATLAS release 1.1 will be a useful resource to assess and improve the accuracy of current lesion segmentation methods.
Quantifying linear enamel hypoplasia in Virunga Mountain gorillas and other great apes
2018-02-20

Abstract Objective Linear enamel hypoplasia (LEH) is a condition marked by localized reductions in enamel thickness, resulting from growth disruptions during dental development. We use quantitative criteria to characterize the depth of LEH defects and “normal” perikymata in great apes. We test the hypothesis that mountain gorillas have shallow defects compared to other taxa, which may have led to their underestimation in previous studies. Materials and Methods Previous attempts to characterize LEH morphology quantitatively have been limited in sample size and scope. We generated digital elevation models using optical profilometry (Sensofar PLu Neox) and extracted 2D coordinates using ImageJ to quantify depths in canines from three great ape genera ( N = 75 perikymata; 255 defects). Results All defect depths fall outside the distribution of perikymata depths. Mountain gorilla defects are significantly shallower than those of other great ape taxa examined, including western lowland gorillas. Females have significantly deeper defects than males in all taxa. The deepest defect belongs to a wild‐captured zoo gorilla. Virunga mountain gorilla specimens collected by Dian Fossey exhibit deeper defects than those collected recently. Discussion Shallow defect morphology in mountain gorillas may have led to an underestimation of LEH prevalence in past studies. Defect depth is used as a proxy for insult severity, but depth might be influenced by inter‐ and intra‐specific variation in enamel growth. Future studies should test whether severe insults are associated with deeper defects, as might be the case with Haloko, a wild‐captured gorilla. Ongoing histologic studies incorporating associated behavioral records will test possible factors that underlie differences in defect morphology.
Understanding 6th-Century Barbarian Social Organization and Migration through Paleogenomics
2018-02-20

ABSTARCT Despite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies, we obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards , a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized around one large pedigree, suggesting that biological relationships played an important role in these early Medieval societies. Moreover, we identified genetic structure in each cemetery involving at least two groups with different ancestry that were very distinct in terms of their funerary customs. Finally, our data was consistent with the proposed long-distance migration from Pannonia to Northern Italy.