julilili42/papers huggingface dataset:
Complementary methods for SARS-CoV-2 diagnosis in times of material shortage
2021-06-07

Abstract The pandemic caused by SARS-CoV-2 resulted in increasing demands for diagnostic tests, leading to a shortage of recommended testing materials and reagents. This study reports on the performance of self-sampled alternative swabbing material (ordinary Q-tips tested against flocked swab and rayon swab), of reagents for classical RNA extraction (phenol/guanidine-based protocol against a commercial kit), and of intercalating dye-based one-step quantitative reverse transcription real-time PCRs (RT-qPCR) compared against the gold standard hydrolysis probe-based assays for SARS-CoV-2 detection. The study found sampling with Q-tips, RNA extraction with classical protocol and intercalating dye-based RT-qPCR as a reliable and comparably sensitive strategy for detection of SARS-CoV-2—particularly valuable in the current period with a resurgent and dramatic increase in SARS-CoV-2 infections and growing shortage of diagnostic materials especially for regions limited in resources.
Mutualistic interactions between B. subtilis and seeds dictate plant development
2021-06-07

Abstract A tightly coordinated developmental program controls precise genetic and metabolic reprogramming that dictates efficient transition of the seeds from dormancy to metabolically active seedlings. Beneficial microbes are known to stimulate the germination of the seeds or adaptation of the seedlings; however, investigations of exact mechanisms mediating these interactions and the resulting physiological responses of the plants are only beginning. Bacillus subtilis is commonly detected in the plant holobiont and belongs to the group of microbes that provide multifaceted contribution to the health of the plants. The present study demonstrated that B. subtilis triggered genetic and physiological responses in the seeds that determined subsequent metabolic and developmental status of adult plants. Chemically diverse extracellular matrix of Bacillus was demonstrated to structurally cooperate in bacterial colonization of the seed storage tissues. Additionally, an amyloid protein and fengycin, which are two components of the extracellular matrix, targeted the oil bodies of the seed endosperm, provoking changes in lipid metabolism or accumulation of glutathione-related molecules that stimulated two different plant growth programs: the development of seed radicles or overgrowth and immunization of adult plants. We propose this mutualistic interaction is conserved in Bacilli and plant seeds containing storage oil bodies.
Lying in a 3T MRI Scanner Induces Neglect-Like Spatial Attention Bias
2021-06-07

Summary The static magnetic field of MRI scanners can induce a magneto-hydrodynamic stimulation of the vestibular organ (MVS). In common fMRI settings, this MVS effect leads to a vestibular ocular reflex (VOR). We asked whether – beyond inducing a VOR – putting a healthy subject in a 3T MRI scanner would also alter goal-directed spatial behavior, as is known from other types of vestibular stimulation. We investigated 17 healthy volunteers, all of which exhibited a rightward VOR inside the MRI-scanner as compared to outside-MRI conditions. More importantly, when probing the distribution of overt spatial attention inside the MRI using a visual search task, subjects scanned a region of space that was significantly shifted towards the right. An additional estimate of subjective straight-ahead orientation likewise exhibited an MVC-induced rightward shift. Hence, putting a subject in a 3T MRI-scanner induces a bias of spatial attention, which closely mimics that of stroke patients with spatial neglect.
Spectral evolution of X-ray pulsar 4U 1901+03 during the 2019 outburst based on Insight-HXMT and NuSTAR observations
2021-06-07

We report on a detailed spectral analysis of emission from X-ray pulsar 4U 1901+03 using data obtained by the Insight-HXMT and NuSTAR observatories during the 2019 outburst of the source. Thanks to the extensive coverage of the outburst by Insight-HXMT, we were able to investigate the spectral evolution of the source as a function of flux, and compare these results to the previous reports, focusing on the properties of a putative absorption feature at around 10 keV. In particular, we demonstrate that the broadband X-ray continuum of 4U 1901+03 can be well described with a two-component continuum model without an absorption line at 10 keV, which casts doubt on its interpretation as a cyclotron line. The high quality of the data also allowed us to perform both phase-averaged and phase-resolved spectral analyses as a function of luminosity. Finally, we performed a detailed investigation of another absorption feature in the spectrum of the source around 30 keV recently reported in the NuSTAR data. We show that this feature appears to be significantly detected both in phase-averaged and phase-resolved spectra irrespective of the continuum model.
Medical Education Videos as a Tool for Rehearsal: Efficiency and the Cases of Background Music and Difficulty
2021-06-07

This study reports a field experiment investigating how instructional videos with and without background music contribute to the learning of examination techniques within a formal curriculum of medical teaching. Following a classroom teaching unit on the techniques for examining the knee and the shoulder joint, our participants (N = 175) rehearsed the studied techniques for either the knee or the shoulder joint with an instructional video with or without background music. As dependent measures, we collected a general questionnaire, a judgement of learning, as well as performance on an exam-like knowledge test covering both joints. For both videos, the participants who had watched a particular video during rehearsal were more accurate in answering the corresponding questions than the participants who had seen the other video, signaling that instructional videos provide a useful tool for rehearsal. For the knee video (less difficult), we observed a detrimental effect of the background music, whereas we observed no such effect for the shoulder video (more difficult). Further explorations revealed that background music might be detrimental for learning, as it reduces the perceived demand characteristics. Because the impact of the demand characteristics might be more pronounced in less difficult instructional videos, we discuss video difficulty as a potential moderating factor. Overall, our study provides evidence that instructional videos could be usefully implemented in formal teaching curricula and that such instructional videos probably should be designed without background music.
Exactness of Mean-Field Equations for Open Dicke Models with an Application to Pattern Retrieval Dynamics
2021-06-08

Open quantum Dicke models are paradigmatic systems for the investigation of light-matter interaction in out-of-equilibrium quantum settings. Albeit being structurally simple, these models can show intriguing physics. However, obtaining exact results on their dynamical behavior is challenging, since it requires the solution of a many-body quantum system with several interacting continuous and discrete degrees of freedom. Here, we make a step forward in this direction by proving the validity of the mean-field semiclassical equations for open multimode Dicke models, which, to the best of our knowledge, so far has not been rigorously established. We exploit this result to show that open quantum multimode Dicke models can behave as associative memories, displaying a nonequilibrium phase transition toward a pattern-recognition phase.
T Lymphocytes, Multi-Omic Interactions and Bronchopulmonary Dysplasia
2021-06-08

Bronchopulmonary dysplasia (BPD) remains a significant clinical challenge in neonatal medicine. BPD is clearly a multifactorial disease with numerous antenatal and postnatal components influencing lung development. Extremely immature infants are born in the late canalicular or early saccular stage and usually receive intensive care until the early alveolar stage of lung development, resulting in varying magnitudes of impairment of alveolar septation, lung fibrosis, and abnormal vascular development. The interactions between T lymphocytes, the genome and the epigenome, the microbiome and the metabolome, as well as nutrition and therapeutic interventions such as the exposure to oxygen, volutrauma, antibiotics, corticosteroids, caffeine and omeprazole, play an important role in pathogenesis and disease progression. While our general understanding of these interactions thanks to basic research is improving, this knowledge is yet to be translated into comprehensive prevention and clinical management strategies for the benefit of preterm infants developing BPD and later during infancy and childhood suffering from the disease itself and its sequelae. In this review, we summarise existing evidence on the interplay between T lymphocytes, lung multi-omics and currently used therapeutic interventions in BPD, and highlight avenues for potential future immunology related research in the field.
Potential Protective Protein Components of Cow’s Milk against Certain Tumor Entities
2021-06-08

Milk and dairy products, especially from cow’s milk, play a major role in the daily human diet. It is therefore hardly surprising that the subject of milk is being extensively researched and that many effects of individual milk components have been characterized as a result. With the wealth of results available today, the influence of milk on the development of various types of cancer and, in particular, its often protective effects have been shown both in vitro and in vivo and in the evaluation of large-scale cohort and case-control studies. Various caseins, diverse whey proteins such as α-lactalbumin (α-LA), bovine α-lactalbumin made lethal to tumor cells (BAMLET), β-lactoglobulin (β-LG), or bovine serum albumin (BSA), and numerous milk fat components, such as conjugated linoleic acid (CLA), milk fat globule membrane (MFGM), or butyrate, as well as calcium and other protein components such as lactoferrin (Lf), lactoferricin (Lfcin), and casomorphines, show antitumor or cytotoxic effects on cells from different tumor entities. With regard to a balanced and health-promoting diet, milk consumption plays a major role in a global context. This work provides an overview of what is known about the antitumoral properties of proteins derived from cow’s milk and their modes of action.
Relaxation or Regulation: The Acute Effect of Mind-Body Exercise on Heart Rate Variability and Subjective State in Experienced Qi Gong Practitioners
2021-06-08

Mind-body exercises such as Yoga or Qi Gong have demonstrated a wide range of health benefits and hold great promise for employment in clinical practice. However, the psychophysiological mechanism underlying these effects remains unclear. Theoretical frameworks highlight regulation as a characteristic and specific mechanism of mind-body exercise for which empirical evidence is scarce. To investigate the exact nature of this mechanism, we tracked acute changes in autonomic nervous system (ANS) activity and subjective state over a common form of mind-body exercise (Qi Gong). Heart rate variability (HRV) and subjective state were assessed in 42 Qi Gong practitioners from China and Germany during a standard moving Qi Gong exercise (Baduanjin). Relaxation in supine position prior and after the exercise served as a control condition to Qi Gong and to assess changes before and after the exercise. Following Qi Gong, all practitioners reported significantly increased subjective calmness and perceived body activation, attentional focus, and subjective vitality. On the physiological level, a significant decrease of parasympathetic modulation and increase in heart rate indicated a pattern of moderate general physiological activation during Qi Gong. A significant increase in overall RR-interval modulation and cardiac coherence during Qi Gong were indicative of a mechanism of active regulation. Examination of the RR-interval trajectories revealed a rhythmic pattern of ANS activation and deactivation in sync with activating and relaxing segments of the exercise. Significant changes in subjective state, not on the physiological level, before and after the exercise were observed. Significant associations between Qi-Gong-specific beliefs, age, cultural background, and experiential and physiological measures demonstrated the complexity of mind-body exercises as multicomponent interventions. Overall, this study highlights moderate general physiological activation, exercise-dependent rhythmic ANS modulation, and induction of a characteristic state of eutonic calmness as potential psychophysiological mechanisms underlying the health benefits of mind-body exercise.
Duplicate Detection of Spike Events: A Relevant Problem in Human Single-Unit Recordings
2021-06-08

Single-unit recordings in the brain of behaving human subjects provide a unique opportunity to advance our understanding of neural mechanisms of cognition. These recordings are exclusively performed in medical centers during diagnostic or therapeutic procedures. The presence of medical instruments along with other aspects of the hospital environment limit the control of electrical noise compared to animal laboratory environments. Here, we highlight the problem of an increased occurrence of simultaneous spike events on different recording channels in human single-unit recordings. Most of these simultaneous events were detected in clusters previously labeled as artifacts and showed similar waveforms. These events may result from common external noise sources or from different micro-electrodes recording activity from the same neuron. To address the problem of duplicate recorded events, we introduce an open-source algorithm to identify these artificial spike events based on their synchronicity and waveform similarity. Applying our method to a comprehensive dataset of human single-unit recordings, we demonstrate that our algorithm can substantially increase the data quality of these recordings. Given our findings, we argue that future studies of single-unit activity recorded under noisy conditions should employ algorithms of this kind to improve data quality.
Neuromotor examination in unilateral cerebral palsy: Bilateral impairments in different levels of motor integration
2021-06-08

Unilateral cerebral palsy (UCP) usually results in damage to the unilateral pyramidal system. However, the clinical presentation of neuromotor deficits also suggests lesions to the extrapyramidal and cerebellar systems bilaterally. In this study, we developed and tested a behavioral neuromotor examination protocol assessing impairments at three levels of motor integration for children with UCP, also considering impairments of the non-paretic upper limb as well as the influences of the laterality of the lesion. We included 30 children with UCP (10.79 ± 2.61 years) and 60 healthy children (8.27 ± 1.57 years) in the study. All children were assessed on general cognitive ability and classified according to the manual ability classification system (MACS). Our neuromotor examination protocol incorporated specific tasks for each level of motor integration: pyramidal, extrapyramidal and cerebellar. Children with UCP and controls did not differ with respect to general cognitive abilities and sex but children with UCP were significantly older. Controls performed significantly better than children with UCP on neuromotor tasks at all levels of motor integration. Additionally, performance of the non-plegine hand in children with UCP was significantly inferior to controls. With the exception of fine motor skills (pyramidal level), children with right and left UCP did not differ. Our behavioral neuromotor examination was sensitive to reveal impairments at all three levels of motor integration bilaterally in children with UCP-although more subtle for the non-paretic limb.
Study of Gribov copies in a Yang-Mills ensemble
2021-06-08

Recently, based on a new procedure to quantize the theory in the continuum, it was argued that Singer's theorem points towards the existence of a Yang-Mills ensemble. In the new approach, the gauge fields are mapped into an auxiliary field space used to separately fix the gauge on different sectors labeled by center vortices. In this work, we study this procedure in more detail. We provide examples of configurations belonging to sectors labeled by center vortices and discuss the existence of nonabelian degrees of freedom. Then, we discuss the importance of the mapping injectivity, and show that this property holds infinitesimally for typical configurations of the vortex-free sector and for the simplest example in the one-vortex sector. Finally, we show that these configurations are free from Gribov copies.
Balance of power across the Channel: reassessing Frankish hegemony in southern England (sixth–early seventh century)
2021-06-08

Relations between southern Britain and the Merovingian kingdoms in the sixth and early seventh centuries have largely been understood in terms of a Frankish hegemony extending across the Channel. However, a re‐examination of the small group of written sources on which this idea is based shows that they do not necessarily imply such overlordship. Sixth‐century archaeological evidence points to a different and more complex picture of Frankish influence: displaying links with the Franks was crucial for the self‐representation of elites in southern England, and should be understood in the context of extensive transmarine contacts.
Reply on RC1
2021-06-08

<strong class="journal-contentHeaderColor">Abstract.</strong> Weathering of bedrock to produce regolith is essential for sustaining life on Earth and global biogeochemical cycles. The rate of this process is influenced not only by tectonics, but also by climate and biota. We present new data on soil production, chemical weathering, and physical erosion rates from the large climate and ecological gradient of the Chilean Coastal Cordillera (26Â to 38<span class="inline-formula"><sup>â</sup></span>âS). Four Chilean study areas are investigated and span (from north to south) arid (Pan de AzÃocar), semi-arid (Santa Gracia), Mediterranean (LaÂ Campana), and temperate humid (Nahuelbuta) climate zones. Observed soil production rates in granitoid soil-mantled hillslopes range from <span class="inline-formula">â1⁄47</span>Â to 290âtâkm<span class="inline-formula"><sup>â2</sup></span>âyr<span class="inline-formula"><sup>â1</sup></span> and are lowest in the sparsely vegetated and arid north and highest in the Mediterranean setting. Calculated chemical weathering rates range from zero in the arid north to a high of 211âtâkm<span class="inline-formula"><sup>â2</sup></span>âyr<span class="inline-formula"><sup>â1</sup></span> in the Mediterranean zone. Chemical weathering rates are moderate in the semi-arid and temperate humid zones (<span class="inline-formula">â1⁄420</span>Â to 50âtâkm<span class="inline-formula"><sup>â2</sup></span>âyr<span class="inline-formula"><sup>â1</sup></span>). Similarly, physical erosion rates are lowest in the arid zone (<span class="inline-formula">â1⁄411</span>âtâkm<span class="inline-formula"><sup>â2</sup></span>âyr<span class="inline-formula"><sup>â1</sup></span>) and highest in the Mediterranean climate zone (<span class="inline-formula">â1⁄491</span>âtâkm<span class="inline-formula"><sup>â2</sup></span>âyr<span class="inline-formula"><sup>â1</sup></span>). The contribution of chemical weathering to total denudation rates is lower in the arid north than further south. However, due to heterogeneities in lithologies and ZrÂ concentrations, reported chemical weathering rates and chemical depletion fractions are affected by large uncertainties. Comparison of Chilean results to published global data collected from hillslope settings underlain by granitoid lithologies documents similar patterns in soil production, chemical weathering, and total denudation rates for varying mean annual precipitation and vegetation cover amounts. We discuss the Chilean and global data in the light of contending model frameworks in the literature and find that observed variations in soil production rates bear the closest resemblance to models explicitly accounting for variations in soil thickness and biomass.
Reply on RC2
2021-06-08

<strong class="journal-contentHeaderColor">Abstract.</strong> Weathering of bedrock to produce regolith is essential for sustaining life on Earth and global biogeochemical cycles. The rate of this process is influenced not only by tectonics, but also by climate and biota. We present new data on soil production, chemical weathering, and physical erosion rates from the large climate and ecological gradient of the Chilean Coastal Cordillera (26Â to 38<span class="inline-formula"><sup>â</sup></span>âS). Four Chilean study areas are investigated and span (from north to south) arid (Pan de AzÃocar), semi-arid (Santa Gracia), Mediterranean (LaÂ Campana), and temperate humid (Nahuelbuta) climate zones. Observed soil production rates in granitoid soil-mantled hillslopes range from <span class="inline-formula">â1⁄47</span>Â to 290âtâkm<span class="inline-formula"><sup>â2</sup></span>âyr<span class="inline-formula"><sup>â1</sup></span> and are lowest in the sparsely vegetated and arid north and highest in the Mediterranean setting. Calculated chemical weathering rates range from zero in the arid north to a high of 211âtâkm<span class="inline-formula"><sup>â2</sup></span>âyr<span class="inline-formula"><sup>â1</sup></span> in the Mediterranean zone. Chemical weathering rates are moderate in the semi-arid and temperate humid zones (<span class="inline-formula">â1⁄420</span>Â to 50âtâkm<span class="inline-formula"><sup>â2</sup></span>âyr<span class="inline-formula"><sup>â1</sup></span>). Similarly, physical erosion rates are lowest in the arid zone (<span class="inline-formula">â1⁄411</span>âtâkm<span class="inline-formula"><sup>â2</sup></span>âyr<span class="inline-formula"><sup>â1</sup></span>) and highest in the Mediterranean climate zone (<span class="inline-formula">â1⁄491</span>âtâkm<span class="inline-formula"><sup>â2</sup></span>âyr<span class="inline-formula"><sup>â1</sup></span>). The contribution of chemical weathering to total denudation rates is lower in the arid north than further south. However, due to heterogeneities in lithologies and ZrÂ concentrations, reported chemical weathering rates and chemical depletion fractions are affected by large uncertainties. Comparison of Chilean results to published global data collected from hillslope settings underlain by granitoid lithologies documents similar patterns in soil production, chemical weathering, and total denudation rates for varying mean annual precipitation and vegetation cover amounts. We discuss the Chilean and global data in the light of contending model frameworks in the literature and find that observed variations in soil production rates bear the closest resemblance to models explicitly accounting for variations in soil thickness and biomass.