julilili42/papers huggingface dataset:
Shallow-marine serpentinization-derived fluid seepage in the Upper Cretaceous Qahlah Formation, United Arab Emirates
2021-03-18

Abstract Serpentinization of ultramafic rocks in the sea and on land leads to the generation of alkaline fluids rich in molecular hydrogen (H 2 ) and methane (CH 4 ) that favour the formation of carbonate mineralization, such as veins in the sub-seafloor, seafloor carbonate chimneys and terrestrial hyperalkaline spring deposits. Examples of this type of seawater–rock interaction and the formation of serpentinization-derived carbonates in a shallow-marine environment are scarce, and almost entirely lacking in the geological record. Here we present evidence for serpentinization-induced fluid seepage in shallow-marine sedimentary rocks from the Upper Cretaceous (upper Campanian to lower Maastrichtian) Qahlah Formation at Jebel Huwayyah, United Arab Emirates. The research object is a metre-scale structure (the Jebel Huwayyah Mound) formed of calcite-cemented sand grains, which formed a positive seafloor feature. The Jebel Huwayyah Mound contains numerous vertically orientated fluid conduits containing two main phases of calcite cement. We use C and O stable isotopes and elemental composition to reconstruct the fluids from which these cements precipitated and infer that the fluids consisted of variable mixtures of seawater and fluids derived from serpentinization of the underlying Semail Ophiolite. Based on their negative δ 13 C values, hardgrounds in the same section as the Jebel Huwayyah Mound may also have had a similar origin. The Jebel Huwayyah Mound shows that serpentinization of the Semail Ophiolite by seawater occurred very soon after obduction and marine transgression, a process that continued through to the Miocene, and, with interaction of meteoric water, up to the present day.
SUBRETINAL AIR USED AS A BALL VALVE TO STABILIZE A RETINAL BLEB
2021-03-18

Purpose: To describe a technique of using subretinal air to create and stabilize a neurosensory detachment performed during placement of a subretinal implant. Methods: A case report of an experiment in a live porcine model. Results: Creation of a neurosensory detachment may be facilitated by instillation of subretinal air. We use a small-gauge cannula to infuse approximately 0.1 mL of subretinal air to create a neurosensory detachment. We then expand the bleb using an additional 0.1 cc to 0.2 cc of subretinal air followed by balanced salt solution and stabilize it further with installation of viscoelastic. The small-gauge retinotomy should be created on the anterior and superior aspect of the bleb so that the air can tamponade the retinotomy both during surgery and postoperatively. Conclusion: This technique may be useful for some newer procedures, such as subretinal implants and perhaps administration of subretinal gene therapy or cell therapy, that require access to the subretinal space.
A neuronal blood marker is associated with mortality in old age
2021-03-18

<strong>Neurofilament light chain (NfL) has emerged as a promising blood biomarker for the progression of various neurological diseases. NfL is a structural protein of nerve cells and elevated levels in blood are thought to mirror damage to the nervous system. We find that plasma NfL levels increase in humans with age (n=122; 21–107 years of age) and correlate with changes in other plasma proteins linked to neural pathways. In centenarians (n=135) plasma NfL levels are associated with mortality equally or better than previously described multi-item scales of cognitive or physical functioning, and this observation was replicated in an independent cohort of nonagenarians (n=180). Plasma NfL also increases in aging mice (n=114; 2–30 months of age) and dietary restriction, a paradigm that extends lifespan in mice, attenuates the age-related increase of plasma NfL. These observations suggest a contribution of nervous system functional deterioration to late life mortality. </strong>
Differentiating the Value Function by using Convex Duality
2021-03-18

We consider the differentiation of the value function for parametric optimization problems. Such problems are ubiquitous in Machine Learning applications such as structured support vector machines, matrix factorization and min-min or minimax problems in general. Existing approaches for computing the derivative rely on strong assumptions of the parametric function. Therefore, in several scenarios there is no theoretical evidence that a given algorithmic differentiation strategy computes the true gradient information of the value function. We leverage a well known result from convex duality theory to relax the conditions and to derive convergence rates of the derivative approximation for several classes of parametric optimization problems in Machine Learning. We demonstrate the versatility of our approach in several experiments, including non-smooth parametric functions. Even in settings where other approaches are applicable, our duality based strategy shows a favorable performance.
Conspiracy Theories and Their Societal Effects During the COVID-19 Pandemic
2021-03-19

During COVID-19, conspiracy theories were intensely discussed in the media. Generally, both believing in conspiracy theories (i.e., explanations for events based on powerholders’ secret arrangements) and being confronted with a conspiracy theory have been found to predict cognition and behavior with negative societal effects, such as low institutional trust. Accordingly, believing in conspiracy theories around COVID-19 should reduce institutional trust, support of governmental regulations and their adoption, and social engagement (e.g., helping members of risk groups). We tested these predictions in a national random sample survey, an experiment, and a longitudinal study ( N total = 1,213; all studies were preregistered). Indeed, believing in and being confronted with a COVID-19 conspiracy theory decreased institutional trust, support of governmental regulations, adoption of physical distancing, and—to some extent—social engagement. Findings underscore the severe societal effects of conspiracy theories in the context of COVID-19.
MR-Guided Radiotherapy for Head and Neck Cancer: Current Developments, Perspectives, and Challenges
2021-03-19

Based on the development of new hybrid machines consisting of an MRI and a linear accelerator, magnetic resonance image guided radiotherapy (MRgRT) has revolutionized the field of adaptive treatment in recent years. Although an increasing number of studies have been published, investigating technical and clinical aspects of this technique for various indications, utilizations of MRgRT for adaptive treatment of head and neck cancer (HNC) remains in its infancy. Yet, the possible benefits of this novel technology for HNC patients, allowing for better soft-tissue delineation, intra- and interfractional treatment monitoring and more frequent plan adaptations appear more than obvious. At the same time, new technical, clinical, and logistic challenges emerge. The purpose of this article is to summarize and discuss the rationale, recent developments, and future perspectives of this promising radiotherapy modality for treating HNC.
Spectrum formation in X-ray pulsars at very low mass accretion rate: Monte Carlo approach
2021-03-19

ABSTRACT Recently, it has been discovered that the transition of X-ray pulsars to the low luminosity state ( ) is accompanied by a dramatic spectral change. That is, the typical power-law-like spectrum with high-energy cut-off transforms into a two-component structure with a possible cyclotron absorption feature on top of it. It was proposed that these spectral characteristics can be explained qualitatively by the emission of cyclotron photons in the atmosphere of the neutron star caused by collisional excitation of electrons to upper Landau levels and further Comptonization of the photons by electron gas. The electron gas are expected to be overheated in a thin top layer of the atmosphere. In this paper, we perform Monte Carlo simulations of the radiative transfer in the atmosphere of an accreting neutron star while accounting for a resonant scattering of polarized X-ray photons by thermally distributed electrons. The spectral shape is shown to be strongly polarization-dependent in soft X-rays ( ) and near the cyclotron scattering feature. The results of our numerical simulations are tested against the observational data of the X-ray pulsar A 0535+262 in the low-luminosity state. We show that the spectral shape of the pulsar can be reproduced by the proposed theoretical model. We discuss applications of the discovery to the observational studies of accreting neutron stars.
HDX-MS for Epitope Characterization of a Therapeutic ANTIBODY Candidate on the Calcium-Binding Protein Annexin-A1
2021-03-19

Annexin-A1 (ANXA1) belongs to a class of highly homologous Ca2+-dependent phospholipid-binding proteins. Its structure consists of a core region composed of four homologous repeats arranged in a compact, hydrolysis-resistant structure and an N-terminal region with a Ca2+-dependent conformation. ANXA1 is involved in several processes, including cell proliferation, apoptosis, metastasis, and the inflammatory response. Therefore, the development of antibodies blocking selected regions on ANXA1 holds great potential for the development of novel therapeutics treating inflammatory and cancer diseases. Here, we report the interaction site between an ANXA1-specific antibody known to inhibit T cell activation without adverse cytotoxic effects and ANXA1 using amide hydrogen–deuterium exchange mass spectrometry (HDX-MS). For the epitope determination, we applied two bottom-up HDX-MS approaches with pepsin digestion in solution and immobilized on beads. Both strategies revealed the interaction region within domain III of ANXA1 in Ca2+-bound conformation. The antibody-binding region correlates with the hydrophobic binding pocket of the N-terminal domain formed in the absence of calcium. This study demonstrates that even cryptic and flexible binding regions can be studied by HDX-MS, allowing a fast and efficient determination of the binding sites of antibodies which will help to define a mode of action profile for their use in therapy.
Black Sea hydroclimate and coupled hydrology was strongly controlled by high-latitude glacial climate dynamics
2021-03-19

Abstract The Black Sea experienced pronounced millennial-scale changes in temperature and rainfall during the last glacial coinciding with Dansgaard-Oeschger cycles. However, little is known regarding the amount and sources of freshwater reaching this inland basin. Here, we present detailed ostracod δ 18 O data from the glacial Black Sea showing subdued Dansgaard-Oeschger cyclicity and four prominent longer-term saw-tooth shaped Bond-like cycles. We propose that the δ 18 O ostracods signature primarily reflects changes in the atmospheric circulation in response to the waxing and waning Eurasian Ice Sheet. The millennial-scale ice sheet variations likely resulted not only in latitudinal migrations of atmospheric frontal systems but also in shifts of dominant moisture sources for the Black Sea. Heavier isotopic precipitation arrived from the North Atlantic-Mediterranean realm during the warmer interstadials and lighter isotopic precipitation from the Eurasian continental interior during the colder stadials. The subdued Dansgaard-Oeschger variability likely reflects an integrated precipitation signal additionally affected by the long mixing times of the large Black Sea volume up to 1,500 years as suggested from hydrologic-isotope-balance modelling.
Expansion of Functional Myeloid-Derived Suppressor Cells in Controlled Human Malaria Infection
2021-03-19

Malaria can cause life-threatening complications which are often associated with inflammatory reactions. More subtle, but also contributing to the burden of disease are chronic, often subclinical infections, which result in conditions like anemia and immunologic hyporesponsiveness. Although very frequent, such infections are difficult to study in endemic regions because of interaction with concurrent infections and immune responses. In particular, knowledge about mechanisms of malaria-induced immunosuppression is scarce. We measured circulating immune cells by cytometry in healthy, malaria-naïve, adult volunteers undergoing controlled human malaria infection (CHMI) with a focus on potentially immunosuppressive cells. Infectious Plasmodium falciparum (Pf) sporozoites (SPZ) (PfSPZ Challenge) were inoculated during two independent studies to assess malaria vaccine efficacy. Volunteers were followed daily until parasites were detected in the circulation by RT-qPCR. This allowed us to analyze immune responses during pre-patency and at very low parasite densities in malaria-naïve healthy adults. We observed a consistent increase in circulating polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) in volunteers who developed P. falciparum blood stage parasitemia. The increase was independent of preceding vaccination with a pre-erythrocytic malaria vaccine. PMN-MDSC were functional, they suppressed CD4 + and CD8 + T cell proliferation as shown by ex-vivo co-cultivation with stimulated T cells. PMN-MDSC reduced T cell proliferation upon stimulation by about 50%. Interestingly, high circulating PMN-MDSC numbers were associated with lymphocytopenia. The number of circulating regulatory T cells (T reg ) and monocytic MDSC (M-MDSC) showed no significant parasitemia-dependent variation. These results highlight PMN-MDSC in the peripheral circulation as an early indicator of infection during malaria. They suppress CD4 + and CD8 + T cell proliferation in vitro . Their contribution to immunosuppression in vivo in subclinical and uncomplicated malaria will be the subject of further research. Pre-emptive antimalarial pre-treatment of vaccinees to reverse malaria-associated PMN-MDSC immunosuppression could improve vaccine response in exposed individuals.
Phloem exudate metabolic content reflects the response to water‐deficit stress in pea plants (Pisum sativum L.)
2021-03-19

Summary Drought stress impacts the quality and yield of Pisum sativum . Here, we show how short periods of limited water availability during the vegetative stage of pea alters phloem sap content and how these changes are connected to strategies used by plants to cope with water deficit. We have investigated the metabolic content of phloem sap exudates and explored how this reflects P. sativum physiological and developmental responses to drought. Our data show that drought is accompanied by phloem‐mediated redirection of the components that are necessary for cellular respiration and the proper maintenance of carbon/nitrogen balance during stress. The metabolic content of phloem sap reveals a shift from anabolic to catabolic processes as well as the developmental plasticity of P. sativum plants subjected to drought. Our study underlines the importance of phloem‐mediated transport for plant adaptation to unfavourable environmental conditions. We also show that phloem exudate analysis can be used as a useful proxy to study stress responses in plants. We propose that the decrease in oleic acid content within phloem sap could be considered as a potential marker of early signalling events mediating drought response.
Spinocerebellar ataxia type 14: refining clinicogenetic diagnosis in a rare adult‐onset disorder
2021-03-19

Abstract Objectives Genetic variant classification is a challenge in rare adult‐onset disorders as in SCA‐PRKCG (prior spinocerebellar ataxia type 14) with mostly private conventional mutations and nonspecific phenotype. We here propose a refined approach for clinicogenetic diagnosis by including protein modeling and provide for confirmed SCA‐PRKCG a comprehensive phenotype description from a German multi‐center cohort, including standardized 3D MR imaging. Methods This cross‐sectional study prospectively obtained neurological, neuropsychological, and brain imaging data in 33 PRKCG variant carriers. Protein modeling was added as a classification criterion in variants of uncertain significance (VUS). Results Our sample included 25 cases confirmed as SCA‐PRKCG (14 variants, thereof seven novel variants) and eight carriers of variants assigned as VUS (four variants) or benign/likely benign (two variants). Phenotype in SCA‐PRKCG included slowly progressive ataxia (onset at 4–50 years), preceded in some by early‐onset nonprogressive symptoms. Ataxia was often combined with action myoclonus, dystonia, or mild cognitive‐affective disturbance. Inspection of brain MRI revealed nonprogressive cerebellar atrophy. As a novel finding, a previously not described T2 hyperintense dentate nucleus was seen in all SCA‐PRKCG cases but in none of the controls. Interpretation In this largest cohort to date, SCA‐PRKCG was characterized as a slowly progressive cerebellar syndrome with some clinical and imaging features suggestive of a developmental disorder. The observed non‐ataxia movement disorders and cognitive‐affective disturbance may well be attributed to cerebellar pathology. Protein modeling emerged as a valuable diagnostic tool for variant classification and the newly described T2 hyperintense dentate sign could serve as a supportive diagnostic marker of SCA‐PRKCG.
Ultra-compact X-ray binaries as dual-line gravitational-wave sources
2021-03-20

ABSTRACT By virtue of their sub-hour orbital periods, ultra-compact X-ray binaries are promising sources for the space-borne gravitational-wave interferometers LISA, Taiji, and TianQin. Some of these systems contain a neutron star primary, whose spin period can be measured directly via pulse timing, or indirectly through rotational modulations of burst phenomena. It is pointed out here that since actively accreting stars, with spin frequencies in the hundreds of Hz, may continuously emit appreciable gravitational waves due to the presence of accretion-built mountains, toroidal magnetic fields, and/or r-mode oscillations, such binaries are also candidate sources for ground-based interferometers. Two Galactic systems (4U 1728−34 and 4U 1820−30) are identified as being potentially detectable by both LISA and aLIGO simultaneously: a dual-line detection of this sort could provide percent-level constraints on the mass, radius, and internal magnetic field strength of the neutron star. With the Einstein Telescope, we find that at least four of the known ultra-compact binaries become dual-line visible.
Occipital sleep spindles predict sequence learning in a visuo-motor task
2021-03-20

Abstract Study Objectives The brain appears to use internal models to successfully interact with its environment via active predictions of future events. Both internal models and the predictions derived from them are based on previous experience. However, it remains unclear how previously encoded information is maintained to support this function, especially in the visual domain. In the present study, we hypothesized that sleep consolidates newly encoded spatio-temporal regularities to improve predictions afterwards. Methods We tested this hypothesis using a novel sequence-learning paradigm that aimed to dissociate perceptual from motor learning. We recorded behavioral performance and high-density electroencephalography (EEG) in male human participants during initial training and during testing two days later, following an experimental night of sleep (n = 16, including high-density EEG recordings) or wakefulness (n = 17). Results Our results show sleep-dependent behavioral improvements correlated with sleep-spindle activity specifically over occipital cortices. Moreover, event-related potential (ERP) responses indicate a shift of attention away from predictable to unpredictable sequences after sleep, consistent with enhanced automaticity in the processing of predictable sequences. Conclusions These findings suggest a sleep-dependent improvement in the prediction of visual sequences, likely related to visual cortex reactivation during sleep spindles. Considering that controls in our experiments did not fully exclude oculomotor contributions, future studies will need to address the extent to which these effects depend on purely perceptual versus oculomotor sequence learning.
Land Use and Soil Organic Carbon Stocks—Change Detection over Time Using Digital Soil Assessment: A Case Study from Kamyaran Region, Iran (1988–2018)
2021-03-21

Land use change and soil organic carbon stock (SOCS) depletion over time is one of the predominant worldwide environmental problems related to global warming and the need to secure food production for an increasing world population. In our research, satellite images from 1988 and 2018 were analyzed for a 177.48 km2 region in Kurdistan Province, Iran. Across the study area. 186 disturbed and undisturbed soil samples were collected at two depths (0–20 cm and 20–50 cm). Bulk density (BD), soil organic carbon (SOC), rock fragments (RockF) and SOCS were measured. Random forest was used to model the spatial variability of SOCS. Land use was mapped with supervised classification and maximum likelihood approaches. The Kappa index and overall accuracy of the supervised classification and maximum likelihood land use maps varied between 83% and 88% and 78% and 85%, respectively. The area of forest and high-quality rangeland covered 5286 ha in 1988 and decreased by almost 30% by 2018. Most of the decrease was due to the establishment of cropland and orchards, and due to overgrazing of high-quality rangeland. As expected, the results of the analysis of variance showed that mean values of SOCS for the high-quality rangeland and forest were significantly higher compared to other land use classes. Thus, transformation of land with natural vegetation like forest and high-quality rangeland led to a loss of 15,494 Mg C in the topsoil, 15,475 Mg C in the subsoil and 15,489 Mg C−1 in total. We concluded that the predominant causes of natural vegetation degradation in the study area were mostly due to the increasing need for food, anthropogenic activities such as cultivation and over grazing, lack of government landuse legislation and the results of this study are useful for land use monitoring, decision making, natural vegetation planning and other areas of research and development in Kurdistan province.
Temporo-parietal brain regions are involved in higher order object perception
2021-03-21

Lesions to posterior temporo-parietal brain regions are associated with deficits in perception of global, hierarchical shapes, but also with impairments in the processing of objects presented under demanding viewing conditions. Evidence from neuroimaging studies and lesion patterns observed in patients with simultanagnosia and agnosia for object orientation suggest similar brain regions to be involved in perception of global shapes and processing of objects in atypical (‘non-canonical’) orientation. In a localizer experiment, we identified individual temporo-parietal brain areas involved in global shape perception and found significantly higher BOLD signals during the processing of non-canonical compared to canonical objects. In a multivariate approach, we demonstrated that posterior temporo-parietal brain areas show distinct voxel patterns for non-canonical and canonical objects and that voxel patterns of global shapes are more similar to those of objects in non-canonical compared to canonical viewing conditions. These results suggest that temporo-parietal brain areas are not only involved in global shape perception but might serve a more general mechanism of complex object perception. Our results challenge a strict attribution of object processing to the ventral visual stream by suggesting specific dorsal contributions in more demanding viewing conditions.