julilili42/papers huggingface dataset:
Early Marine Isotope Stage 3 human occupation of the Shandong Peninsula, coastal North China
2018-10-24

ABSTRACT Archeological studies of coastal sites have yielded a large body of information regarding the dispersal of modern humans from Africa and the coastal adaptations of various hominin groups. Coastal areas have been attractive to humans since at least the late Middle Pleistocene, according to research conducted in Africa and the circum‐Mediterranean region. However, little information concerning Paleolithic occupations has come to light in coastal areas of China. Here, we report on the chronology, archeology and paleoenvironmental reconstruction of the Pleistocene Dazhushan site on the east coast of the Shandong Peninsula in North China. Evidence indicates that prehistoric humans employing a flake technology occupied the current coastal area of the peninsula by at least early Marine Isotope Stage 3 (MIS 3; c . 57–29 ka) when the region was an inland area dominated by a mixed broadleaved forest and grassland environment occupied by terrestrial herbivores. Based on archeological evidence brought to light along the current Chinese coastline, correlated with sea level changes that have occurred since MIS 3, we suggest that future studies of coastal migrations and adaptations in eastern China will be considerably enhanced by a deeper understanding of the geomorphological evolution of those coastal regions.
The art of using t-SNE for single-cell transcriptomics
2018-10-25

Abstract Single-cell transcriptomics yields ever growing data sets containing RNA expression levels for thousands of genes from up to millions of cells. Common data analysis pipelines include a dimensionality reduction step for visualising the data in two dimensions, most frequently performed using t-distributed stochastic neighbour embedding (t-SNE). It excels at revealing local structure in high-dimensional data, but naive applications often suffer from severe shortcomings, e.g. the global structure of the data is not represented accurately. Here we describe how to circumvent such pitfalls, and develop a protocol for creating more faithful t-SNE visualisations. It includes PCA initialisation, a high learning rate, and multi-scale similarity kernels; for very large data sets, we additionally use exaggeration and downsampling-based initialisation. We use published single-cell RNA-seq data sets to demonstrate that this protocol yields superior results compared to the naive application of t-SNE.
Stimulus domain transfer in recurrent models for large scale cortical population prediction on video
2018-10-25

Abstract To better understand the representations in visual cortex, we need to generate better predictions of neural activity in awake animals presented with their ecological input: natural video. Despite recent advances in models for static images, models for predicting responses to natural video are scarce and standard linear-nonlinear models perform poorly. We developed a new deep recurrent network architecture that predicts inferred spiking activity of thousands of mouse V1 neurons simulta-neously recorded with two-photon microscopy, while accounting for confounding factors such as the animal’s gaze position and brain state changes related to running state and pupil dilation. Powerful system identification models provide an opportunity to gain insight into cortical functions through in silico experiments that can subsequently be tested in the brain. However, in many cases this approach requires that the model is able to generalize to stimulus statistics that it was not trained on, such as band-limited noise and other parameterized stimuli. We investigated these domain transfer properties in our model and find that our model trained on natural images is able to correctly predict the orientation tuning of neurons in responses to artificial noise stimuli. Finally, we show that we can fully generalize from movies to noise and maintain high predictive performance on both stimulus domains by fine-tuning only the final layer’s weights on a network otherwise trained on natural movies. The converse, however, is not true.
Regulatory focus, coping strategies and symptoms of anxiety and depression: A comparison between Syrian refugees in Turkey and Germany
2018-10-25

Civil war, flight, escape and expulsion are extremely stressful and assert a negative impact on refugees' mental health. However scientific research about resilience and coping of refugees is scarce. Especially in the recent refugee crisis, calls have been made to consider factors contributing to coping and resilience in this vulnerable population. Therefore, the current research sought to investigate individual differences that could serve as antecedents of coping and contextual factors that might moderate these effects. Specifically, it took into account individual's self-regulatory differences in terms of regulatory focus (i.e., a promotion focus on nurturance needs, ideals and gains vs. a prevention focus on security needs, oughts and losses). It furthermore explored contextual influences by considering Syrian refugees in Turkey (Sample 1, N = 273) and Germany (Sample 2, N = 169). Compared to Syrian refugees in Turkey, those in Germany had a stronger promotion focus. They also reported more problem-focused and less maladaptive coping, as well as less symptoms. Both promotion and prevention focus were positively related to problem-focused coping. Problem-focused coping, in turn, predicted more symptoms in Turkey but not in Germany. Furthermore, a stronger promotion focus was associated with less symptoms and maladaptive coping was associated with more symptoms in both samples. These results contribute to the coping literature in demonstrating that under certain conditions problem-focused coping can be maladaptive and extend the scarce previous work on self-regulation and coping. Most importantly, they highlight a promotion focus as a clear resilience factor and the role of maladaptive coping in increasing vulnerability. As such, they might inform the design of effective interventions among Syrian refugees and beyond.
Multiple Proxy Estimates of Atmospheric CO2 From an Early Paleocene Rainforest
2018-10-25

Abstract Proxy estimates of atmospheric CO 2 are necessary to reconstruct Earth's climate history. Confidence in paleo‐CO 2 estimates can be increased by comparing results from multiple proxies at a single site, but so far this strategy has been implemented only for marine‐based techniques. Here we present CO 2 estimates for the well‐studied early Paleocene Castle Rock site in Colorado using four paleobotanical proxies. Median estimates range from 470 to 813 ppm, demonstrating fair correspondence. The synthesis yields a median of 616 ppm (352–1110 ppm at 95% confidence), considerably higher than previous early Paleocene CO 2 estimates (~300 ppm). Ash bed geochronology by the high‐precision U‐Pb method places the Castle Rock assemblage at 63.844 ± 0.097 Ma (fully propagated 2σ error). When these results are placed into the broader context of other Cenozoic CO 2 estimates from plant‐gas‐exchange approaches and coeval estimates of global mean surface temperature, a pattern emerges of an Earth system sensitivity around 3 °C per CO 2 doubling during the Paleocene and Eocene, a time with little land ice, then steepening to &gt;7 °C after the Eocene once land ice was present on Antarctica.
Crystal Engineering of Dibenzothiophenothieno[3,2-b]thiophene (DBTTT) Isomers for Organic Field-Effect Transistors
2018-10-25

Three thiophene ring-terminated benzothieno[3,2-b]benzothiophene (BTBT) derivatives, C-C6-DBTTT, C-C12-DBTTT, and L-C12-DBTTT, were designed and synthesized, differing in the isomerization of alkyl chain position as well as aromatic core construction. A study of crystal structure and electronic properties combined with a theoretical investigation was performed to understand the structure-property relationships for the application of these molecules in organic field-effect transistors (OFETs). Different crystal packing structures were observed for these three isomers by single-crystal X-ray diffraction as a result of a crystal engineering molecular design approach. The highest charge-carrier mobility was observed for the isomer with a collinear core, L-C12-DBTTT. Preliminary results demonstrated a promising hole mobility of 2.44 cm V s, despite the polymorphism observed in ambient conditions.
Synchronization of Slow Cortical Rhythms During Motor Imagery-Based Brain–Machine Interface Control
2018-10-25

Modulation of sensorimotor rhythm (SMR) power, a rhythmic brain oscillation physiologically linked to motor imagery, is a popular Brain–Machine Interface (BMI) paradigm, but its interplay with slower cortical rhythms, also involved in movement preparation and cognitive processing, is not entirely understood. In this study, we evaluated the changes in phase and power of slow cortical activity in delta and theta bands, during a motor imagery task controlled by an SMR-based BMI system. In Experiment I, EEG of 20 right-handed healthy volunteers was recorded performing a motor-imagery task using an SMR-based BMI controlling a visual animation, and during task-free intervals. In Experiment II, 10 subjects were evaluated along five daily sessions, while BMI-controlling same visual animation, a buzzer, and a robotic hand exoskeleton. In both experiments, feedback received from the controlled device was proportional to SMR power (11–14[Formula: see text]Hz) detected by a real-time EEG-based system. Synchronization of slow EEG frequencies along the trials was evaluated using inter-trial-phase coherence (ITPC). Results: cortical oscillations of EEG in delta and theta frequencies synchronized at the onset and at the end of both active and task-free trials; ITPC was significantly modulated by feedback sensory modality received during the tasks; and ITPC synchronization progressively increased along the training. These findings suggest that phase-locking of slow rhythms and resetting by sensory afferences might be a functionally relevant mechanism in cortical control of motor function. We propose that analysis of phase synchronization of slow cortical rhythms might also improve identification of temporal edges in BMI tasks and might help to develop physiological markers for identification of context task switching and practice-related changes in brain function, with potentially important implications for design and monitoring of motor imagery-based BMI systems, an emerging tool in neurorehabilitation of stroke.
Does Social Exclusion Alter Sensory and Pain Thresholds in Children and Adolescents with Functional Abdominal Pain? – Results from a Preliminary Study
2018-10-25

Abstract Objective Functional abdominal pain (AP) is a prevalent issue in childhood and adolescence. The contribution of psychosocial factors in the development and maintenance of this health problem is rather unclear, and experimental studies about underlying mechanisms are lacking. This study investigates whether experimentally induced social exclusion decreases sensory and pain thresholds in children suffering from AP. Subjects Twenty children/adolescents with AP and 22 healthy controls. Methods Children/adolescents participated in the Cyberball paradigm, which affects an experience of social exclusion. Thermal sensory and pain thresholds were measured before and after Cyberball. Results Children/adolescents with AP showed a divergent reaction regarding their sensory threshold after social exclusion: The control group exhibited a tendency toward a decreased sensory threshold whereas the AP group remained stable. Concerning the pain threshold, no effect of social exclusion could be identified. The increase of both thresholds (“numbing”) after Cyberball was positively correlated with symptoms of mental health issues. Conclusions This is the first study to investigate changes in sensory and pain thresholds following painful social interactions in a sample of children/adolescents with a chronic pain condition. Results suggest that AP and control children differ in their reaction of sensory thresholds, which might indicate an altered processing of social exclusion. Replication and further methodological improvements are needed.
Zeitgebers and their association with rest-activity patterns
2018-10-26

Zeitgebers such as light, eating and physical activity provide input to the circadian clock. Chronic circadian misalignment is associated with significant adverse health effects. An improved understanding of the impact of the timing of zeitgebers on the stability of 24-hour rest-activity rhythm in free-living settings may identify behavioural and environmental intervention targets. A total of 133 healthy adults, aged 21-60 years, wore a wrist actigraph for 7 consecutive days. We applied a non-parametric analysis to activity counts to derive rest-activity patterns. We administered a questionnaire through a smartphone app to collect self-reported timing of light exposure, eating episodes and physical activity. To assess the relationship between timing exposures (first and last exposure to outdoor light, first exposure to indoor light, last eating episode, first eating episode, morning physical activity proportion, evening physical activity proportion) and rest-activity or sleep outcomes (bedtimes, total sleep time, inter-daily stability, intra-daily variability, L5 and M10 midpoint), we first calculated Spearman correlations, using the false discovery rate method to control for multiple comparisons. From those significant associations, we then fit regression models adjusting for age, sex, race, household income, education level, study site, body mass index, as well as physical activity. Finally, we tested for interaction between chronotype and each timing-related exposure and stratified the analysis by morning type. All zeitgebers, except for evening physical activity proportion, were correlated with at least four of the seven sleep and rest-activity outcomes. In adjusted analysis, later timing of first (after 6:30 to 7:45 AM versus earlier) and last exposure to indoor light (after 11:00 PM versus earlier) and first (after 7:45-9:45 AM versus earlier) and last eating episode (after 8:00-09:00 PM versus earlier) were associated with a shift of 0.60-1.39 hours to later bedtimes, M10 and L5 midpoints (i.e. timing of peak activities or inactivities). Later timing of first exposure to outdoor light (after 09:30 AM versus earlier) was also associated with 0.51 (95% CI: 0.19 to 0.83) hours longer total sleep time. Higher morning physical activity proportion (> 33%) was associated with 0.95 (95% CI: -1.38 to -0.53) hours earlier in-bed time and 0.69 (95% CI: -1.14 to -0.24) hours earlier out-of-bed time, 0.92 (95% CI: -1.41 to -0.42) hours earlier M10 and 0.96 (95% CI: -1.42 to -0.49) min earlier L5 midpoint. The results did not change substantially with further adjustment for total activity. There was a significant interaction between morning chronotype and first eating episode with rest-activity patterns (p < 0.05), with first eating episode associating with timing of activities only in non-morning type adults. Timing of zeitgebers was associated with sleep and rest-activity patterns, including bedtimes, L5 and M10 midpoint. Future research should evaluate the impact of manipulating zeitgebers on both circadian rhythms and health outcomes.
Cytoreductive surgery and hyperthermic intraperitoneal chemotherapy: A safe treatment option for intraperitoneal rhabdomyosarcoma in children below 5 years of age
2018-10-26

Abstract Advanced and relapsed intraperitoneal rhabdomyosarcomas in young children represent an oncological challenge and options for local tumor control are limited. Cytoreductive surgery (CRS) combined with hyperthermic intraperitoneal chemotherapy (HIPEC) is commonly used in advanced peritoneal tumors in adults. However, no studies are available regarding CRS and HIPEC in young children. We report our experiences treating six patients with intraperitoneal rhabdomyosarcoma with CRS and HIPEC using cisplatin and doxorubicin focusing on safety and outcomes. No procedure‐associated mortalities occurred and no major short‐ or long‐term toxicities were recorded. All patients showed no evidence of disease after 12‐month median (7–41) follow‐up.
Spikeling: A low-cost hardware implementation of a spiking neuron for neuroscience teaching and outreach
2018-10-26

Understanding how neurons encode and compute information is fundamental to our study of the brain, but opportunities for hands-on experience with neurophysiological techniques on live neurons are scarce in science education. Here, we present Spikeling, an open source in silico implementation of a spiking neuron that costs £25 and mimics a wide range of neuronal behaviours for classroom education and public neuroscience outreach. Spikeling is based on an Arduino microcontroller running the computationally efficient Izhikevich model of a spiking neuron. The microcontroller is connected to input ports that simulate synaptic excitation or inhibition, to dials controlling current injection and noise levels, to a photodiode that makes Spikeling light sensitive, and to a light-emitting diode (LED) and speaker that allows spikes to be seen and heard. Output ports provide access to variables such as membrane potential for recording in experiments or digital signals that can be used to excite other connected Spikelings. These features allow for the intuitive exploration of the function of neurons and networks mimicking electrophysiological experiments. We also report our experience of using Spikeling as a teaching tool for undergraduate and graduate neuroscience education in Nigeria and the United Kingdom.
Measuring intergenerational justice for public policy
2018-10-26

We review dominant approaches to evaluate the intergenerational justice of public policies. We distinguish between justice over complete lives (for which we analyse birth cohorts) and at a given moment in time (for which we study age groups). We note that it is not prima facie problematic if at one given point in time different age groups receive an unequal treatment from the state. But if such inequalities are perpetuated across different birth cohorts over the entire life cycle, then this does point to intergenerational inequities.
Speed tuning to real-world-and retinal motion in cortical motion regions
2018-10-26

Abstract Motion signals can arise for two reasons in the retina: due to self-motion or due to real motion in the environment. Prior studies on speed tuning always measured joint responses to real and retinal motion, and for some of the more recently identified human motion processing regions, speed tuning has not been examined in at all. We localized motion regions V3A, V6, V5/MT, MST and cingulate sulcus visual area (CSv) in 20 human participants, and then measured their responses to motion velocities from 1-24 degrees per second. Importantly, we used a pursuit paradigm that allowed us to quantify responses to objective and retinal motion separately. In order to provide optimal stimulation, we used stimuli with natural image statistics derived from Fourier scrambles of natural images. The results show that all regions increased responses with higher speeds for both, retinal and objective motion. V3A stood out in that it was the only region whose slope of the speed-response function for objective motion was higher than that for retinal motion. V6, V5/MT, MST and CSv did not differ in objective and retinal speed slopes, even though V5/MT and MST tended to respond more to objective motion at all speeds. These results reveal highly similar speed tuning functions for early and high-level motion regions, and support the view that human V3A encodes primarily objective rather than retinal motion signals.
Reviewing Wind Measurement Approaches for Fixed-Wing Unmanned Aircraft
2018-10-28

One of the biggest challenges in probing the atmospheric boundary layer with small unmanned aerial vehicles is the turbulent 3D wind vector measurement. Several approaches have been developed to estimate the wind vector without using multi-hole flow probes. This study compares commonly used wind speed and direction estimation algorithms with the direct 3D wind vector measurement using multi-hole probes. This was done using the data of a fully equipped system and by applying several algorithms to the same data set. To cover as many aspects as possible, a wide range of meteorological conditions and common flight patterns were considered in this comparison. The results from the five-hole probe measurements were compared to the pitot tube algorithm, which only requires a pitot-static tube and a standard inertial navigation system measuring aircraft attitude (Euler angles), while the position is measured with global navigation satellite systems. Even less complex is the so-called no-flow-sensor algorithm, which only requires a global navigation satellite system to estimate wind speed and wind direction. These algorithms require temporal averaging. Two averaging periods were applied in order to see the influence and show the limitations of each algorithm. For a window of 4 min, both simplifications work well, especially with the pitot-static tube measurement. When reducing the averaging period to 1 min and thereby increasing the temporal resolution, it becomes evident that only circular flight patterns with full racetracks inside the averaging window are applicable for the no-flow-sensor algorithm and that the additional flow information from the pitot-static tube improves precision significantly.
Diplomatic relations between the eastern Roman empire and the “barbarian” successor states, 527–565
2018-10-28

Abstract Diplomatic relations between the eastern Roman emperor, Justinian, and “barbarian” Ostrogothic, Vandal, Visigothic, and Frankish successor states in Italy, Africa, Spain, and Gaul, were framed by competing claims to Romanitas during a period often viewed as a crossroads between Antiquity and the Middle Ages. Modern works examining these relations and the wars which resulted disagree as to whether the ruling elites of the successor states were politically “integrated” into Roman society or were barbarian interlopers, awkwardly trying to balance the interests of Germanic military aristocracies and native Roman senatorial and ecclesiastical elites. They thus reflect competing eastern Roman and western ideologies in the aftermath of the political disintegration of the western Roman empire in the fifth century.
A Secreted Bacterial Peptidylarginine Deiminase Can Neutralize Human Innate Immune Defenses
2018-10-29

Bacterial pathogens do not only succeed in breaking the barriers that protect humans from infection, but they also manage to evade insults from the human immune system. The importance of the present study resides in the fact that protein citrullination is shown to represent a new bacterial mechanism for immune evasion. In particular, the oral pathogen P. gingivalis employs this mechanism to defuse innate immune responses by secreting a protein-citrullinating enzyme. Of note, this finding impacts not only the global health problem of periodontitis, but it also extends to the prevalent autoimmune disease rheumatoid arthritis, which has been strongly associated with periodontitis, PPAD activity, and loss of tolerance against citrullinated proteins, such as the histone H3.