julilili42/papers huggingface dataset:
Thromboprophylaxis in Patients with COVID-19: Systematic Review of National and International Clinical Guidance Reports
2021-08-26

Background: Venous thromboembolism (VTE) is common among patients with severe coronavirus disease 2019 (COVID-19). Anticoagulation in hospitalized COVID-19 patients has been associated with survival benefit; however, the optimal thromboprophylaxis strategy has not yet been defined. Objective: To identify published guidance reports by national and international societies regarding thromboprophylaxis strategies in COVID-19 patients in different settings (outpatients, hospitalized, post-discharge). Methods: A systematic review of the literature (Pubmed/EMBASE) was conducted independently by two investigators. Results: Among 1942 initially identified articles, 33 guidance documents were included: 20 published by national and 13 by international societies. These documents provide recommendations mainly for hospitalized (97% of reports) and post-discharge (75%) COVID-19 patients, and less so for outpatients (34%). Thrombotic and bleeding risk stratification prior to any treatment decision is the cornerstone of all suggested thromboprophylaxis strategies; 81% of the documents recommend thromboprophylaxis for all hospitalized patients with a prophylactic dosage of low molecular weight heparin irrespective of VTE risk. Intermediate or therapeutic dose intensity is recommended in high VTE risk patients by 56% and 28% of documents, respectively. Mechanical thromboprophylaxis is suggested in case of high bleeding risk or contraindication to pharmacological thromboprophylaxis (59% of documents). Extended pharmacological thromboprophylaxis is recommended for patients with high VTE risk after hospital discharge (63% of documents). For non-hospitalized outpatients, 28% of documents recommend pharmacological thromboprophylaxis for high VTE risk. Conclusion: The current guidance identifies thromboprophylaxis in COVID-19 patients, especially during hospitalization, as of major importance for the prevention of VTE. Recommendations are derived from limited evidence from observational studies.
Identifying mixtures of metals by multi‐isotope analysis: Disentangling the relationships of the Early Bronze Age swords of the Apa–Hajdúsámson type and associated objects
2021-08-26

Abstract This pilot study addresses the analytical characterisation of 26 well‐known bronze objects of the Early and Middle Bronze Age of Central and Northern Europe. Besides swords and axes of the hoards from Apa, Téglás and Hajdúsámson, the investigation includes the famous Sky Disc and its accompanying finds from the Nebra hoard and several full‐hilted swords from Period I in Denmark. In contrast to former publications, the isotopic systematics of lead, tin and copper are the focus of the present investigation. With a combined approach, we try to relate the typologically closely linked or otherwise related artefacts with chemical and isotopic proxies by identifying mixing scenarios. The results demonstrate that artefacts from different locations are most likely not directly linked, but mixing lines across isotope systems suggest a production of the items from common sources by mixing of bronze batches (e.g., bronze ingots), which were probably disseminated between 1600 and 1500 bce . This helps to correlate objects of different locations with each other and to draw conclusions upon typological and cultural connections. Isotopic and chemical correlations of objects within the individual hoards, on the other hand, allow reconstructions of metallurgical practices in single workshops, which, for example, implies recycling of metal scrap.
Effect of rock uplift and Milankovitch timescale variations in precipitation and vegetation cover on catchment erosion rates
2021-08-26

Abstract. Catchment erosion and sedimentation are influenced by variations in the rates of rock uplift (tectonics) and periodic fluctuations in climate and vegetation cover. This study focuses on quantifying the effects of changing climate and vegetation on erosion and sedimentation over distinct climate–vegetation settings by applying the Landlab–SPACE landscape evolution model. As catchment evolution is subjected to tectonic and climate forcings at millennial to million-year timescales, the simulations are performed for different tectonic scenarios and periodicities in climate–vegetation change. We present a series of generalized experiments that explore the sensitivity of catchment hillslope and fluvial erosion as well as sedimentation for different rock uplift rates (0.05, 0.1, 0.2 mm a−1) and Milankovitch climate periodicities (23, 41, and 100 kyr). Model inputs were parameterized for two different climate and vegetation conditions at two sites in the Chilean Coastal Cordillera at ∼26∘ S (arid and sparsely vegetated) and ∼33∘ S (Mediterranean). For each setting, steady-state topographies were produced for each uplift rate before introducing periodic variations in precipitation and vegetation cover. Following this, the sensitivity of these landscapes was analyzed for 3 Myr in a transient state. Results suggest that regardless of the uplift rate, transients in precipitation and vegetation cover resulted in transients in erosion rates in the direction of change in precipitation and vegetation. The transients in sedimentation were observed to be in the opposite direction of change in the precipitation and vegetation cover, with phase lags of ∼1.5–2.5 kyr. These phase lags can be attributed to the changes in plant functional type (PFT) distribution induced by the changes in climate and the regolith production rate. These effects are most pronounced over longer-period changes (100 kyr) and higher rock uplift rates (0.2 mm yr−1). This holds true for both the vegetation and climate settings considered. Furthermore, transient changes in catchment erosion due to varying vegetation and precipitation were between ∼35 % and 110 % of the background (rock uplift) rate and would be measurable with commonly used techniques (e.g., sediment flux histories, cosmogenic nuclides). Taken together, we find that vegetation-dependent erosion and sedimentation are influenced by Milankovitch timescale changes in climate but that these transient changes are superimposed upon tectonically driven rates of rock uplift.
Vacancy control in acene blends links exothermic singlet fission to coherence
2021-08-26

Abstract The fission of singlet excitons into triplet pairs in organic materials holds great technological promise, but the rational application of this phenomenon is hampered by a lack of understanding of its complex photophysics. Here, we use the controlled introduction of vacancies by means of spacer molecules in tetracene and pentacene thin films as a tuning parameter complementing experimental observables to identify the operating principles of different singlet fission pathways. Time-resolved spectroscopic measurements in combination with microscopic modelling enables us to demonstrate distinct scenarios, resulting from different singlet-to-triplet pair energy alignments. For pentacene, where fission is exothermic, coherent mixing between the photoexcited singlet and triplet-pair states is promoted by vibronic resonances, which drives the fission process with little sensitivity to the vacancy concentration. Such vibronic resonances do not occur for endothermic materials such as tetracene, for which we find fission to be fully incoherent; a process that is shown to slow down with increasing vacancy concentration.
A cultural ecosystem service perspective on the interactions between humans and soils in gardens
2021-08-26

Abstract Gardens are culturally shaped environments in which natural processes can be experienced. Thus, they offer insights into the relation people have with these processes and the biophysical domain. This includes soils and plants, as these are the natural materials gardeners work with regularly. A cultural ecosystem service (CES) perspective might help to understand interactions between the gardeners and the environment, for example, soils. This could provide insights for scientists, public stakeholders and non‐governmental organizations to raise awareness for ecosystem services (ES) of soils. Understanding how gardens are created and used, requires studies from the natural sciences but also from the humanities and social sciences. The natural sciences provide insights into soil properties, biodiversity, plant requirements and the water cycle, while the humanities and social sciences are needed to understand identity formation, social and cultural practices, belief systems and psychological aspects connected to gardening. Inter‐ and transdisciplinary research can then inform scientists, gardeners, policy makers and educators as well as the general public about CES. This can be used to develop educational programs and measures to protect these valuable CES as well as the general ES of gardens and soils.
Altered Secretome of Diabetic Monocytes Could Negatively Influence Fracture Healing—An In Vitro Study
2021-08-26

Diabetes mellitus is a main risk factor for delayed fracture healing and fracture non-unions. Successful fracture healing requires stimuli from different immune cells, known to be affected in diabetics. Especially, application of mononuclear cells has been proposed to promote wound and fracture healing. Thus, aim was to investigate the effect of pre-/diabetic conditions on mononuclear cell functions essential to promote osteoprogenitor cell function. We here show that pre-/diabetic conditions suppress the expression of chemokines, e.g., CCL2 and CCL8 in osteoprogenitor cells. The associated MCP-1 and MCP-2 were significantly reduced in serum of diabetics. Both MCPs chemoattract mononuclear THP-1 cells. Migration of these cells is suppressed under hyperglycemic conditions, proposing that less mononuclear cells invade the site of fracture in diabetics. Further, we show that the composition of cytokines secreted by mononuclear cells strongly differ between diabetics and controls. Similar is seen in THP-1 cells cultured under hyperinsulinemia or hyperglycemia. The altered secretome reduces the positive effect of the THP-1 cell conditioned medium on migration of osteoprogenitor cells. In summary, our data support that factors secreted by mononuclear cells may support fracture healing by promoting migration of osteoprogenitor cells but suggest that this effect might be reduced in diabetics.
Global network structure and local transcriptomic vulnerability shape atrophy in sporadic and genetic behavioral variant frontotemporal dementia
2021-08-26

Abstract Connections among brain regions allow pathological perturbations to spread from a single source region to multiple regions. Patterns of neurodegeneration in multiple diseases, including behavioral variant of frontotemporal dementia (bvFTD), resemble the large-scale functional systems, but how bvFTD-related atrophy patterns relate to structural network organization remains unknown. Here we investigate whether neurodegeneration patterns in sporadic and genetic bvFTD are conditioned by connectome architecture. Regional atrophy patterns were estimated in both genetic bvFTD (75 patients, 247 controls) and sporadic bvFTD (70 patients, 123 controls). We first identify distributed atrophy patterns in bvFTD, mainly targeting areas associated with the limbic intrinsic network and insular cytoarchitectonic class. Regional atrophy was significantly correlated with atrophy of structurally- and functionally-connected neighbors, demonstrating that network structure shapes atrophy patterns. The anterior insula was identified as the predominant group epicenter of brain atrophy using data-driven and simulation-based methods, with some secondary regions in frontal ventromedial and anteromedial temporal areas. Finally, we find that FTD-related genes, namely C9orf72 and TARDBP, confer local transcriptomic vulnerability to the disease, effectively modulating the propagation of pathology through the connectome. Collectively, our results demonstrate that atrophy patterns in sporadic and genetic bvFTD are jointly shaped by global connectome architecture and local transcriptomic vulnerability.
Dataset of ipsilateral motor-evoked potentials induced by transcranial magnetic stimulation
2021-08-26

&lt;p&gt;The dataset includes 4244 trials of EMG recordings after ipsilateral TMS under muscle contraction. This data was used for the evaluation of the DiMEP toolbox https://pypi.org/project/dimep/&lt;/p&gt; &lt;p&gt;All subjects provided written, informed consent before participation and following approval by the local ethics committee. Subjects had no contraindications to TMS. TMS was delivered with a MagVenture MagPro-R30 with MagOption and a MCF-B70 figure 8-coil at an orientation of 45&deg; to the midsagittal plane (see figure 1A). First, the motor hotspot of the contralateral, i.e., right, extensor digitorum communis (EDC) was determined by applying 40 stimuli to the left hemisphere. 40% MSO was used as the starting intensity and increased in steps of 5% MSO in case no MEPs could be elicited. Next, at the locations of the three stimuli that resulted in the greatest MEP, i.e., the largest MEP peak-to-peak amplitude, additional three stimuli were applied. The stimulation location that consistently elicited the largest MEPs in the contralateral EDC was then selected as the hotspot. A neuro-navigation system (TMS Navigator, Localite GmbH, Germany) supported coil positioning throughout the measurements. In order to measure ipsilateral MEPs, TMS pulses were applied to the motor hotspot with 5s &plusmn; 1.25 s between pulses (at an intensity of 90% MSO). To increase the likelihood of exhibiting ipsilateral MEPs, subjects were requested to isometrically contract their left biceps brachii (BB) to 30% of its maximum voluntary contraction while receiving visual feedback of the BB activity relative to the required target level of contraction on a computer display. The electromyographical response (EMG) to TMS was recorded with a BrainProducts ExG bipolar amplifier from the ipsilateral EDC. All trials were divided into 1s segments, i.e., 500 ms before and after each TMS pulse, and sampled at 1000 Hz.&lt;/p&gt;
Trait Rumination and Social Anxiety Separately Predict Stress Induced Rumination and Hemodynamic Responses
2021-08-26

Abstract We aimed to investigate the stress-reactive rumination response to social stress and its association with social anxiety and trait rumination. From previous investigations we know that people with a certain vulnerability to rumination show increased stress-reactive rumination. However, up to date the possible influence of social anxiety to this relationship is still unclear. Therefore, we reanalyzed the data of two of our previous studies assessing healthy low and high trait ruminators and depressed patients performing the Trier Social Stress Test (TSST). We measured cortical oxygenation using functional Near-Infrared Spectroscopy (fNIRS) as well as different behavioral outcome measures (subjective stress levels, negative affect, state rumination). On a behavioral level, we found an influence of both, social anxiety and trait rumination, on state rumination, even when correcting for the other factor, respectively, implying two potentially independent factors of influence. On a neural level, we observed reduced activation in socially anxious subjects in the right inferior frontal gyrus (IFG), as well as time-dependent changes in the left IFG and in the right dorsolateral prefrontal cortex. Results indicate a specific role of social anxiety, at least on a behavioral level, and therefore implicate a crucial factor to be considered in the treatment of depression.
Alpha-Synuclein PET Tracer Development—An Overview about Current Efforts
2021-08-26

&lt;p&gt;Neurodegenerative diseases such as Parkinson&rsquo;s disease (PD) are manifested by inclusion&lt;br&gt; bodies of alpha-synuclein (-syn) also called -synucleinopathies. Detection of these inclusions is&lt;br&gt; thus far only possible by histological examination of postmortem brain tissue. The possibility of&lt;br&gt; non-invasively detecting -syn will therefore provide valuable insights into the disease progression&lt;br&gt; of -synucleinopathies. In particular, -syn imaging can quantify changes in monomeric, oligomeric,&lt;br&gt; and fibrillic -syn over time and improve early diagnosis of various -synucleinopathies or monitor&lt;br&gt; treatment progress. Positron emission tomography (PET) is a non-invasive in vivo imaging technique&lt;br&gt; that can quantify target expression and drug occupancies when a suitable tracer exists. As such,&lt;br&gt; novel -syn PET tracers are highly sought after. The development of an -syn PET tracer faces&lt;br&gt; several challenges. For example, the low abundance of -syn within the brain necessitates the&lt;br&gt; development of a high-affinity ligand. Moreover, -syn depositions are, in contrast to amyloid&lt;br&gt; proteins, predominantly localized intracellularly, limiting their accessibility. Furthermore, another&lt;br&gt; challenge is the ligand selectivity over structurally similar amyloids such as amyloid-beta or tau,&lt;br&gt; which are often co-localized with -syn pathology. The lack of a defined crystal structure of -syn&lt;br&gt; has also hindered rational drug and tracer design efforts. Our objective for this review is to provide a&lt;br&gt; comprehensive overview of current efforts in the development of selective -syn PET tracers.&lt;/p&gt;
Dataset of ipsilateral motor-evoked potentials induced by transcranial magnetic stimulation
2021-08-26

The dataset includes 2546 trials of EMG recordings after ipsilateral TMS under muscle contraction. This data was used for the evaluation of the DiMEP toolbox https://pypi.org/project/dimep/ All subjects provided written, informed consent before participation and following approval by the local ethics committee. Subjects had no contraindications to TMS. TMS was delivered with a MagVenture MagPro-R30 with MagOption and a MCF-B70 figure 8-coil at an orientation of 45° to the midsagittal plane (see figure 1A). First, the motor hotspot of the contralateral, i.e., right, extensor digitorum communis (EDC) was determined by applying 40 stimuli to the left hemisphere. 40% MSO was used as the starting intensity and increased in steps of 5% MSO in case no MEPs could be elicited. Next, at the locations of the three stimuli that resulted in the greatest MEP, i.e., the largest MEP peak-to-peak amplitude, additional three stimuli were applied. The stimulation location that consistently elicited the largest MEPs in the contralateral EDC was then selected as the hotspot. A neuro-navigation system (TMS Navigator, Localite GmbH, Germany) supported coil positioning throughout the measurements. In order to measure ipsilateral MEPs, TMS pulses were applied to the motor hotspot with 5s ± 1.25 s between pulses (at an intensity of 90% MSO). To increase the likelihood of exhibiting ipsilateral MEPs, subjects were requested to isometrically contract their left biceps brachii (BB) to 30% of its maximum voluntary contraction while receiving visual feedback of the BB activity relative to the required target level of contraction on a computer display. The electromyographical response (EMG) to TMS was recorded with a BrainProducts ExG bipolar amplifier from the ipsilateral EDC. All trials were divided into 1s segments, i.e., 500 ms before and after each TMS pulse, and sampled at 1000 Hz. We removed artifacts due to coil placement with a Heaviside fit removal, a Hampel filter of 20 ms width, and a polynomial detrending of 5<sup>th</sup> order. Trials with remaining artifacts were rejected, resulting in an average of 47 trials per subject.
Dataset of ipsilateral motor-evoked potentials induced by transcranial magnetic stimulation
2021-08-26

The dataset includes 4244 trials of EMG recordings after ipsilateral TMS under muscle contraction. This data was used for the evaluation of the DiMEP toolbox https://pypi.org/project/dimep/ All subjects provided written, informed consent before participation and following approval by the local ethics committee. Subjects had no contraindications to TMS. TMS was delivered with a MagVenture MagPro-R30 with MagOption and a MCF-B70 figure 8-coil at an orientation of 45° to the midsagittal plane (see figure 1A). First, the motor hotspot of the contralateral, i.e., right, extensor digitorum communis (EDC) was determined by applying 40 stimuli to the left hemisphere. 40% MSO was used as the starting intensity and increased in steps of 5% MSO in case no MEPs could be elicited. Next, at the locations of the three stimuli that resulted in the greatest MEP, i.e., the largest MEP peak-to-peak amplitude, additional three stimuli were applied. The stimulation location that consistently elicited the largest MEPs in the contralateral EDC was then selected as the hotspot. A neuro-navigation system (TMS Navigator, Localite GmbH, Germany) supported coil positioning throughout the measurements. In order to measure ipsilateral MEPs, TMS pulses were applied to the motor hotspot with 5s ± 1.25 s between pulses (at an intensity of 90% MSO). To increase the likelihood of exhibiting ipsilateral MEPs, subjects were requested to isometrically contract their left biceps brachii (BB) to 30% of its maximum voluntary contraction while receiving visual feedback of the BB activity relative to the required target level of contraction on a computer display. The electromyographical response (EMG) to TMS was recorded with a BrainProducts ExG bipolar amplifier from the ipsilateral EDC. All trials were divided into 1s segments, i.e., 500 ms before and after each TMS pulse, and sampled at 1000 Hz.
The molecular hallmarks of primary and secondary vitreoretinal lymphoma
2021-08-27

Vitreoretinal lymphoma (VRL) is a rare subtype of diffuse large B-cell lymphoma (DLBCL) considered a variant of primary central nervous system lymphoma (PCNSL). Diagnosis of VRL requires examination of vitreous fluid, but cytologic differentiation from uveitis remains difficult. Due to its rarity and difficulty in obtaining diagnostic material, little is known about the genetic profile of VRL. The aim of our study was to investigate the mutational profile of a large series of primary and secondary VRL. Targeted next generation sequencing using a custom panel containing the most frequent mutations in PCNSL was performed on 34 vitrectomy samples of 31 patients with VRL and negative controls with uveitis. In a subset of cases, genome-wide copy number alterations (CNA) were assessed using the Oncoscan platform. Mutations in MYD88 (74%), PIM1 (71%), CD79B (55%), IGLL5 (52%), TBL1XR1 (48%), ETV6 (45%) and 9p21/CDKN2A deletions (85%) were the most common alterations, with similar frequencies in primary (15), synchronous (3) or secondary (13) VRL. This mutational spectrum is similar to MYD88mut/CD79Bmut (MCD or cluster 5) DLBCL with activation of Toll-like and B-cell receptor pathways and CDKN2A loss, confirming their close relationship. Oncoscan analysis demonstrated a high number of CNAs (mean 18.6/case). Negative controls lacked mutations or CNAs. Using cell free DNA of vitreous fluid supernatant, mutations present in cellular DNA were reliably detected in all examined cases. Mutational analysis is a highly sensitive and specific tool for the diagnosis of VRL and can also be applied successfully to cell free DNA derived from the vitreous.