julilili42/papers huggingface dataset:
The strange role of brain lesion size in cognitive neuropsychology
2021-03-29

Abstract The size of brain lesions is a variable that is frequently considered in cognitive neuropsychology. In particular, lesion-deficit inference studies often control for lesion size, and the association of lesion size with post-stroke cognitive deficits and its predictive value are studied. In the present article, the role of lesion size in cognitive deficits and its computational or design-wise consideration is discussed and questioned. First, I argue that the commonly discussed role or effect of lesion size in cognitive deficits eludes us. A generally valid understanding of the causal relation of lesion size, lesion location, and cognitive deficits is unachievable. Second, founded on the theory of covariate control, I argue that lesion size control is no valid covariate control. Instead, it is identified as a procedure with only situational benefits, which is supported by empirical data. This theoretical background is used to suggest possible research practices in lesion-deficit inference, post-stroke outcome prediction, and behavioural studies. Last, control for lesion size is put into a bigger methodological and also historical context – it is identified to relate to a long-known association problem in neuropsychology, which was previously discussed from the perspectives of a mislocalisation in lesion-deficit mapping and the symptom complex approach. Highlights - Lesion size is a factor that is often considered or controlled in neuropsychology - No general causal relation between lesion size, lesion location and deficit exists - Lesion size in brain mapping, outcome prediction and behavioural study is discussed - Lesion size control is no valid covariate control - Practical suggestions and guidelines how to consider lesion size are provided
Phosphorylation of myosin A regulatesPlasmodiumsporozoite motility and is essential for efficient malaria transmission
2021-03-29

Abstract Malaria-causing parasites rely on an actin-myosin based motor for the invasion of different host cells as well as tissue traversal in mosquitoes and vertebrates. The unusual myosin A of Plasmodium spp. has a unique N-terminal extension which is important for red blood cell invasion by P. falciparum merozoites in vitro and harbors a phosphorylation site at serine 19. Here, using the rodent-infecting P. berghei we show that serine 19 is essential for efficient transmission of Plasmodium by mosquitoes as S19A mutants show defects in mosquito salivary gland entry and migration of salivary gland sporozoites in both 2D and 3D environments. Our data suggests that entry into salivary glands represents the strongest barrier in parasite transmission and hence is the key determinant for evolution of the motility and invasion machinery of these parasites. Highlights The unusual N-terminal extension of Plasmodium myosin A is important for efficient gliding motility Altering the kinetics of the myosin A power stroke impacts Plasmodium life cycle progression and sporozoite motility Myosin A phosphorylation at serine 19 is important for malaria transmission by mosquitoes Salivary gland invasion emerges as key selection step for evolution of the parasite motor
Mustapha Sheikh, Ottoman Puritanism and its Discontents. Aḥmad al-Rūmī al- Āqḥiṣārī and the Qāḍīzādelis, Oxford: Oxford University Press 2016, 191 S., ISBN 978-0-19-879076-1.
2021-03-29

Article Mustapha Sheikh, Ottoman Puritanism and its Discontents. Aḥmad al-Rūmī al- Āqḥiṣārī and the Qāḍīzādelis, Oxford: Oxford University Press 2016, 191 S., ISBN 978-0-19-879076-1. was published on April 1, 2021 in the journal Der Islam (volume 98, issue 1).
CRIP1 expression in monocytes related to hypertension
2021-03-30

Abstract Hypertension is a complex and multifactorial disorder caused by lifestyle and environmental factors, inflammation and disease-related genetic factors and is a risk factor for stroke, ischemic heart disease and renal failure. Although circulating monocytes and tissue macrophages contribute to the pathogenesis of hypertension, the underlying mechanisms are poorly understood. Cysteine rich protein 1 (CRIP1) is highly expressed in immune cells, and CRIP1 mRNA expression in monocytes associates with blood pressure (BP) and is up-regulated by proinflammatory modulation suggesting a link between CRIP1 and BP regulation through the immune system. To address this functional link, we studied CRIP1 expression in immune cells in relation to BP using a human cohort study and hypertensive mouse models. CRIP1 expression in splenic monocytes/macrophages and in circulating monocytes was significantly affected by angiotensin II (Ang II) in a BP-elevating dose (2 mg/kg/day). In the human cohort study, monocytic CRIP1 expression levels were associated with elevated BP, whereas upon differentiation of monocytes to macrophages this association along with the CRIP1 expression level was diminished. In conclusion, CRIP1-positive circulating and splenic monocytes seem to play an important role in hypertension related inflammatory processes through endogenous hormones such as Ang II. These findings suggest that CRIP1 may affect the interaction between the immune system, in particular monocytes, and the pathogenesis of hypertension.
MR-Guided Radiotherapy for Rectal Cancer: Current Perspective on Organ Preservation
2021-03-30

Online MRI-guided radiotherapy (MRgRT) is one of the most recent technological advances in radiotherapy. MRgRT permits the visualization of tumorous and healthy tissue while the patient is on the treatment table and online daily plan adaptations following the observed anatomical changes. In the context of rectal cancer, online MRgRT is a very promising modality due to the pronounced geographical variability of tumor tissues and the surrounding healthy tissues. This current paper will discuss the possible applications of online MRgRT, in particular, in terms of radiotherapy dose escalation and response prediction in organ preservation approaches for rectal cancer.
Spiral structures in gravito-turbulent gaseous disks
2021-03-30

Context. Gravitational instabilities can drive small-scale turbulence and large-scale spiral arms in massive gaseous disks under conditions of slow radiative cooling. These motions affect the observed disk morphology, its mass accretion rate and variability, and could control the process of planet formation via dust grain concentration, processing, and collisional fragmentation. Aims. We study gravito-turbulence and its associated spiral structure in thin gaseous disks subject to a prescribed cooling law. We characterize the morphology, coherence, and propagation of the spirals and examine when the flow deviates from viscous disk models. Methods. We used the finite-volume code P LUTO to integrate the equations of self-gravitating hydrodynamics in three-dimensional spherical geometry. The gas was cooled over longer-than-orbital timescales to trigger the gravitational instability and sustain turbulence. We ran models for various disk masses and cooling rates. Results. In all cases considered, the turbulent gravitational stress transports angular momentum outward at a rate compatible with viscous disk theory. The dissipation of orbital energy happens via shocks in spiral density wakes, heating the disk back to a marginally stable thermal equilibrium. These wakes drive vertical motions and contribute to mix material from the disk with its corona. They are formed and destroyed intermittently, and they nearly corotate with the gas at every radius. As a consequence, large-scale spiral arms exhibit no long-term global coherence, and energy thermalization is an essentially local process. Conclusions. In the absence of radial substructures or tidal forcing, and provided a local cooling law, gravito-turbulence reduces to a local phenomenon in thin gaseous disks.
Fragmentation and kinematics in high-mass star formation
2021-03-30

Context. The formation of high-mass star-forming regions from their parental gas cloud and the subsequent fragmentation processes lie at the heart of star formation research. Aims. We aim to study the dynamical and fragmentation properties at very early evolutionary stages of high-mass star formation. Methods. Employing the NOrthern Extended Millimeter Array and the IRAM 30 m telescope, we observed two young high-mass star-forming regions, ISOSS22478 and ISOSS23053, in the 1.3 mm continuum and spectral line emission at a high angular resolution (~0.8′′). Results. We resolved 29 cores that are mostly located along filament-like structures. Depending on the temperature assumption, these cores follow a mass-size relation of approximately M ∝ r 2.0 ± 0.3 , corresponding to constant mean column densities. However, with different temperature assumptions, a steeper mass-size relation up to M ∝ r 3.0 ± 0.2 , which would be more likely to correspond to constant mean volume densities, cannot be ruled out. The correlation of the core masses with their nearest neighbor separations is consistent with thermal Jeans fragmentation. We found hardly any core separations at the spatial resolution limit, indicating that the data resolve the large-scale fragmentation well. Although the kinematics of the two regions appear very different at first sight – multiple velocity components along filaments in ISOSS22478 versus a steep velocity gradient of more than 50 km s −1 pc −1 in ISOSS23053 – the findings can all be explained within the framework of a dynamical cloud collapse scenario. Conclusions. While our data are consistent with a dynamical cloud collapse scenario and subsequent thermal Jeans fragmentation, the importance of additional environmental properties, such as the magnetization of the gas or external shocks triggering converging gas flows, is nonetheless not as well constrained and would require future investigation.
Simple Baseline Machine Learning Text Classifiers for Small Datasets
2021-03-30

Abstract Text classification is important to better understand online media. A major problem for creating accurate text classifiers using machine learning is small training sets due to the cost of annotating them. On this basis, we investigated how SVM and NBSVM text classifiers should be designed to achieve high accuracy and how the training sets should be sized to efficiently use annotation labor. We used a four-way repeated-measures full-factorial design of 32 design factor combinations. For each design factor combination 22 training set sizes were examined. These training sets were subsets of seven public text datasets. We study the statistical variance of accuracy estimates by randomly drawing new training sets, resulting in accuracy estimates for 98,560 different experimental runs. Our major contribution is a set of empirically evaluated guidelines for creating online media text classifiers using small training sets. We recommend uni- and bi-gram features as text representation, btc term weighting and a linear-kernel NBSVM. Our results suggest that high classification accuracy can be achieved using a manually annotated dataset of only 300 examples.
Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes
2021-03-30

Abstract Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS, are limited in terms of sensitivity, resolution or throughput. Here we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by ∼90% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. It allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics LC-MS/MS measurements. The analysis has been implemented as an open-source application ( https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber based prebiotics. In summary, we demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01% to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.
DataJoint Elements: Data Workflows for Neurophysiology
2021-03-30

Abstract A new resource— DataJoint Elements —provides modular designs for assembling complete workflow solutions to organize data and computations for common neurophysiology experiments. The designs are derived from working solutions developed in leading research groups using the open-source DataJoint framework to integrate data collection and analysis in collaborative workflows.
The Motor Neuron-Like Cell Line NSC-34 and Its Parent Cell Line N18TG2 Have Glycogen that is Degraded Under Cellular Stress
2021-03-30

Abstract Brain glycogen has a long and versatile history: Primarily regarded as an evolutionary remnant, it was then thought of as an unspecific emergency fuel store. A dynamic role for glycogen in normal brain function has been proposed later but exclusively attributed to astrocytes, its main storage site. Neuronal glycogen had long been neglected, but came into focus when sensitive technical methods allowed quantification of glycogen at low concentration range and the detection of glycogen metabolizing enzymes in cells and cell lysates. Recently, an active role of neuronal glycogen and even its contribution to neuronal survival could be demonstrated. We used the neuronal cell lines NSC-34 and N18TG2 and could demonstrate that they express the key-enzymes of glycogen metabolism, glycogen phosphorylase and glycogen synthase and contain glycogen which is mobilized on glucose deprivation and elevated potassium concentrations, but not by hormones stimulating cAMP formation. Conditions of metabolic stress, namely hypoxia, oxidative stress and pH lowering, induce glycogen degradation. Our studies revealed that glycogen can contribute to the energy supply of neuronal cell lines in situations of metabolic stress. These findings shed new light on the so far neglected role of neuronal glycogen. The key-enzyme in glycogen degradation is glycogen phosphorylase. Neurons express only the brain isoform of the enzyme that is supposed to be activated primarily by the allosteric activator AMP and less by covalent phosphorylation via the cAMP cascade. Our results indicate that neuronal glycogen is not degraded upon hormone action but by factors lowering the energy charge of the cells directly.
The impact of TMS‐enhanced cognitive control on forgiveness processes
2021-03-30

Abstract Background Cognitive control is thought to be necessary for forgiveness processes. Materials and Methods To examine this correlation, highly impulsive participants, who often fail to inhibit feelings of revenge, received activating theta burst stimulation (TBS) of a classical cognitive control region of the brain, the right dorsolateral prefrontal cortex (rDLPFC). For testing forgiveness ability participants received verum TBS versus sham TBS in a randomized, double‐blinded, within‐subjects design. In both sessions, they first learned that there are fair and unfair opponents in an ultimatum game, and subsequently played a dictator game with reversed roles with the option to revenge or forgive the opponents from the previous game. Results Contrary to our hypothesis, activating TBS did not increase forgiving behavior toward unfair opponents. However, it increased the generosity toward previously fair opponents. Conclusion As an explanation it is discussed that the TBS can only affect “cold” emotions such as greed, but not the “hot” emotions such as anger.
Complications following REM sleep behavior disorder
2021-03-30

Abstract REM sleep behavior disorder (RBD) is gaining increasing attention as important prodromal marker for the development of neurodegenerative disorders such as Parkinson's Disease. However, the clinical relevance of this disorder and its association with other prodromal markers is often underestimated in clinical routine. We here report a case of severe clinical complications following extensive nocturnal movements due to RBD, aggravated by occurrence of additional prodromal non‐motor symptoms. This case stresses the importance of recognizing RBD as a multisystem disease by all clinical disciplines.
Is the Human Being Redeemable? Consolation as an Integral Meaning of Rosenzweig’s Understanding of Redemption: A Blumenbergian Reflection
2021-03-30

Abstract In this article, I test out Hans Blumenberg’s understanding of consolation as a pattern to interpret Rosenzweig’s “new thinking.” Drawing on Blumenberg’s philosophical anthropology, I explore the connection between the concept of redemption as consolation and the image of the human being that it presupposes. I further examine the function of consolation in concepts and non-conceptual images through a comparison of redemptive consolation in the respective thought of Luther and Rosenzweig.
Liedpoetik und soziale Praxis
2021-03-30

Abstract This article is dedicated to the Leipzig Ovid translator and song poet Johann Georg Schoch. It focusses on Schoch’s major work Neu-erbaueter Poetischer Lust- u[nd] Blumen-Garten (1660). The article analyses the poetics and social references of this collection. The author argues that the bucolic, erotic, and sociable songs are linked by intertextual references to works by other Leipzig authors such as Paul Fleming and Gottfried Finckelthaus. Schoch’s contrafactum of an ode by his student friend David Schirmer (“Immer hin/ fahr immer hin”) shows that the songs function as a keepsake of remembrance and identify both authors as members of a local group. They also provide insights into the social practice of student sociability.
Mochica pronouns: their internal reconstruction and significance for worldwide patterns of paradigmatic resemblances in pronominal shapes
2021-03-31

This article embeds an attempt at internal reconstruction of the pronominal roots of Mochica, an extinct language of the north coast of Peru, into broader comparative perspectives on the consonantism of pronominal paradigms. Mochica presents a case of so-called m-t pronouns (i.e., featuring a bilabial nasal in the first-person pronoun and an alveolar stop or affricate in the second-person pronoun), which is common in Eurasia but rare in the Americas and hitherto not explicitly discussed for South America. An internal reconstruction of pre-Mochica pronominal roots, while fraught with some difficulties that presumably cannot be resolved due to the nature of the available colonial documentation, confirms that the m-t consonantism pertains to the diachronically reconstructable pronominal roots. This finding reaffirms that even paradigmatic resemblances are not immune to the chance factor and underscores the previously advised caution in interpreting such patterns as evidence for deep linguistic prehistory.
Output-Specific Adaptation of Habenula-Midbrain Excitatory Synapses During Cocaine Withdrawal
2021-03-31

Projections from the lateral habenula (LHb) control ventral tegmental area (VTA) neuronal populations’ activity and both nuclei shape the pathological behaviors emerging during cocaine withdrawal. However, it is unknown whether cocaine withdrawal modulates LHb neurotransmission onto subsets of VTA neurons that are part of distinct neuronal circuits. Here we show that, in mice, cocaine withdrawal, drives discrete and opposing synaptic adaptations at LHb inputs onto VTA neurons defined by their output synaptic connectivity. LHb axons innervate the medial aspect of VTA, release glutamate and synapse on to dopamine and non-dopamine neuronal populations. VTA neurons receiving LHb inputs project their axons to medial prefrontal cortex (mPFC), nucleus accumbens (NAc), and lateral hypothalamus (LH). While cocaine withdrawal increases glutamate release from LHb onto VTA-mPFC projectors, it reduces presynaptic release onto VTA-NAc projectors, leaving LHb synapses onto VTA-to-LH unaffected. Altogether, cocaine withdrawal promotes distinct adaptations at identified LHb-to-VTA circuits, which provide a framework for understanding the circuit basis of the negative states emerging during abstinence of drug intake.
Synthesis and Thin Films of Thermally Robust Quartet (S = 3/2) Ground State Triradical
2021-03-31

High-spin (<i>S</i> = 3/2) organic triradicals may offer enhanced properties with respect to several emerging technologies, but those synthesized to date typically exhibit small doublet quartet energy gaps and/or possess limited thermal stability and processability. We report a quartet ground state triradical <b>3</b>, synthesized by a Pd(0)-catalyzed radical-radical cross-coupling reaction, which possesses two doublet-quartet energy gaps, Δ<i>E</i><sub>DQ</sub> ≈ 0.2-0.3 kcal mol<sup>-1</sup> and Δ<i>E</i><sub>DQ</sub>2 ≈ 1.2-1.8 kcal mol<sup>-1</sup>. The triradical has a 70+% population of the quartet ground state at room temperature and good thermal stability with onset of decomposition at >160 °C under an inert atmosphere. Magnetic properties of <b>3</b> are characterized by SQUID magnetometry in polystyrene glass and by quantitative EPR spectroscopy. Triradical <b>3</b> is evaporated under ultrahigh vacuum to form thin films of intact triradicals on silicon substrate, as confirmed by high-resolution X-ray photoelectron spectroscopy. AFM and SEM images of the ∼1 nm thick films indicate that the triradical molecules form islands on the substrate. The films are stable under ultrahigh vacuum for at least 17 h but show onset of decomposition after 4 h at ambient conditions. The drop-cast films are less prone to degradation in air and have a longer lifetime.