julilili42/papers huggingface dataset:
Osteology of the Italian endemic spectacled salamanders, Salamandrina spp. (Amphibia, Urodela, Salamandridae): selected skeletal elements for palaeontological investigations
2020-09-03

Abstract Salamandrina perspicillata , from Northern and Central Italy, and Salamandrina terdigitata , from Southern Italy, represent a unique case of endemism among the amphibians of Europe. Some efforts were made to study the biology and ecology of these species, but only few studies focused on their comparative osteology. In particular, detailed descriptions of isolated skeletal elements and comparisons with other European urodeles are not available in literature hindering the identification of their fossils that testify for an ancient much broader range. The correct identification of fossil remains, mostly based on careful osteological descriptions, is fundamental to study the evolution of the range of this genus through time and the origin of the current endemic condition. This work is focused on the description of selected skeletal elements (occipito‐otic complex, limb bones, atlas, trunk, sacral, caudosacral and caudal vertebrae) of dry‐prepared skeletons and CT‐scans of wet preserved specimens, which are the most common in the fossil record. We provide osteological comparison of Salamandrina with other genera of Europe, yielding diagnostic characters which allow the identification of fossils at a generic level. No significant differences between the two species S. perspicillata and S. terdigitata were found in the described skeletal elements, thus, the identification of skeletal elements at the species level is, at the moment, impossible.
The European Federation for Medicinal Chemistry (EFMC) Best Practice Initiative: Validating Chemical Probes
2020-09-03

Abstract As part of an initiative aimed to share best practices in Medicinal Chemistry, the European Federation for Medicinal Chemistry (EFMC) is preparing a series of webinars and slide sets focused on the early phase of drug discovery. This educational material is freely accessible through the EFMC. The main target audiences are students or early career scientists and we also believe it will be valuable for experienced practitioners. The first of the series is focused on the generation and validation of high‐quality chemical probes, which are critical for drug discovery and more broadly to further our understanding of human biology and disease.
Single-vessel cerebral blood flow fMRI to map blood velocity by phase-contrast imaging
2020-09-03

Abstract Current approaches to high-field fMRI provide two means to map hemodynamics at the level of single vessels in the brain. One is through changes in deoxyhemoglobin in venules, i.e., blood oxygenation level-dependent (BOLD) fMRI, while the second is through changes in arteriole diameter, i.e., cerebral blood volume (CBV) fMRI. Here we introduce cerebral blood flow (CBF)-fMRI, which uses high-resolution phase-contrast MRI to form velocity measurements of flow and demonstrate CBF-fMRI in single penetrating microvessels across rat parietal cortex. In contrast to the venule-dominated BOLD and arteriole-dominated CBV fMRI signal, the phase-contrast -based CBF signal changes are highly comparable from both arterioles and venules. Thus, we have developed a single-vessel fMRI platform to map the BOLD, CBV, and CBF from penetrating microvessels throughout the cortex. This high-resolution single-vessel fMRI mapping scheme not only enables the vessel-specific hemodynamic mapping in diseased animal models but also presents a translational potential to map vascular dementia in diseased or injured human brains with ultra-high field fMRI. Summary We established a high-resolution PC-based single-vessel velocity mapping method using the high field MRI. This PC-based micro-vessel velocity measurement enables the development of the single-vessel CBF-fMRI method. In particular, in contrast to the arteriole-dominated CBV and venule-dominated BOLD responses, the CBF-fMRI shows similar velocity changes in penetrating arterioles and venules in activated brain regions. Thus, we have built a noninvasive single-vessel fMRI mapping scheme for BOLD, CBV, and CBF hemodynamic parameter measurements in animals.
Cyclotron line energy in Hercules X-1: stable after the decay
2020-09-04

We summarize the results of a dedicated effort made between 2012 and 2019 to follow the evolution of the cyclotron line in Her X-1 through repeated NuSTAR observations. The previously observed nearly 20-year-long decay of the cyclotron line energy has ended in 2012: from then on, the pulse-phase-averaged flux-corrected cyclotron line energy has remained stable and constant at an average value of E cyc = (37.44 ± 0.07) keV (normalized to a flux level of 6.8 RXTE/ASM-cts s −1 ). The flux dependence of E cyc discovered in 2007 is now measured with high precision, giving a slope of (0.675 ± 0.075) keV/(ASM-cts s −1 ), corresponding to an increase of 6.5% of E cyc for an increase in flux by a factor of two. We also find that all line parameters as well as the continuum parameters show a correlation with X-ray flux. While a correlation between E cyc and X-ray flux (both positive and negative) is now known for several accreting binaries with various suggestions for the underlying physics, the phenomenon of a long-term decay has so far only been seen in Her X-1 and Vela X-1, with far less convincing explanations.
Sputtered Iridium Oxide as Electrode Material for Subretinal Stimulation
2020-09-04

The efficiency and safety of neuronal stimulation with implants strongly depend on the electrode material.Microelectrodes composed of iridium oxide are becoming increasingly important as they exhibit excellent charge injection capacity (CIC) as well as charge storage capacity (CSC).We present the development of a robust process for the fabrication of sputtered iridium oxide films (SIROF).This process has been used for the "RETINA IMPLANT Alpha AMS" for several years of subretinal stimulation.In this paper, we describe the full experimental investigation of the electrode material.The electrochemical and morphological properties were investigated by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), voltage transient measurements, and focused ion beam-scanning electron microscopy (FIB-SEM).The implementation on the CMOS chip of the retinal prosthesis is presented.The deposition process window was investigated extensively.Major changes in process parameters lead to a difference in impedance of only 10% of the mean.Accelerated aging tests revealed a long-term stability of the electrodes of at least 10 years under conditions of use.The SIROF electrodes (diameter 30 μm) show low impedance (15.9 kΩ), excellent CSC (50.9 mC/cm 2 ), and high CIC (4.2 mC/cm 2 ).In summary, the robustness of the presented deposition process and the large process window enable the integration of high-quality SIROF microelectrodes in active implants and thus long-term stability in a wide range of safe electrical stimulation.
SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of the immune cells
2020-09-04

Abstract The SARS-CoV-2 virus is the causative agent of the global COVID-19 infectious disease outbreak, which can lead to acute respiratory distress syndrome (ARDS). However, it is still unclear how the virus interferes with immune cell and metabolic functions in the human body. In this study, we investigated the immune response in acute or convalescent COVID19 patients. We characterized the peripheral blood mononuclear cells (PBMCs) using flow cytometry and found that CD8 + T cells were significantly subsided in moderate COVID-19 and convalescent patients. Furthermore, characterization of CD8 + T cells suggested that patients with a mild and moderate course of the COVID-19 disease and convalescent patients have significantly diminished expression of both perforin and granzyme A in CD8 + T cells. Using 1 H-NMR spectroscopy, we characterized the metabolic status of their autologous PBMCs. We found that fructose, lactate and taurine levels were elevated in infected (mild and moderate) patients compared with control and convalescent patients. Glucose, glutamate, formate and acetate levels were attenuated in COVID-19 (mild and moderate) patients. In summary, our report suggests that SARS-CoV-2 infection leads to disrupted CD8 + T cytotoxic functions and changes the overall metabolic functions of immune cells.
Gate-Level Models for Fast Cross-Level Power Density Estimation
2020-09-04

We present a methodology for fast cycle-accurate gate-level power density analysis especially suited for hard macros. It leverages a post-PAR (place and route) design. The proposed model generation flow consists of three automated steps: partitioning the design into estimation regions, generating power models using gate-level simulation, estimating power dissipation and power density using a higher-level simulation engine (RTL or above). Our models are based on signal transition classification, which factors in the changes in circuit state caused by signal transitions, and corresponding lookup-tables. Our implementation shows a speedup of 320x for an open source processor (1800x for a multiplier) compared to a state-of-the-art commercial tool.
Products of Finite Connected Subgroups
2020-09-04

For a non-empty class of groups L, a finite group G=AB is said to be an L-connected product of the subgroups A and B if ⟨a,b⟩∈L for all a∈A and b∈B. In a previous paper, we prove that, for such a product, when L=S is the class of finite soluble groups, then [A,B] is soluble. This generalizes the theorem of Thompson that states the solubility of finite groups whose two-generated subgroups are soluble. In the present paper, our result is applied to extend to finite groups previous research about finite groups in the soluble universe. In particular, we characterize connected products for relevant classes of groups, among others, the class of metanilpotent groups and the class of groups with nilpotent derived subgroup. Additionally, we give local descriptions of relevant subgroups of finite groups.
Proteome dynamics during antibiotic persistence and resuscitation
2020-09-04

Abstract During antibiotic persistence, bacterial cells become transiently tolerant to antibiotics by restraining their growth and metabolic activity. Detailed molecular characterization of antibiotic persistence is hindered by low count of persisting cells and the need for their isolation. Here we used sustained addition of stable isotope-labeled lysine to selectively label the proteome during hipA -induced persistence and hipB -induced resuscitation of E. coli cells in minimal medium after antibiotic treatment. Time-resolved, 24-hour measurement of label incorporation allowed detection of over 500 newly synthesized proteins in viable cells, demonstrating low but widespread protein synthesis during persistance. Many essential proteins were newly synthesized and several ribosome-associated proteins, such as RaiA and Sra showed high synthesis levels, pointing to their roles in maintenance of persistence. At the onset of resuscitation, cells synthesized the ribosome-splitting GTPase HflX and various ABC transporters, restored translation machinery and resumed metabolism by inducing glycolysis and biosynthesis of amino acids.
Meaning maps and saliency models based on deep convolutional neural networks are insensitive to image meaning when predicting human fixations - data
2020-09-04

&lt;p&gt;Data from the paper:&lt;em&gt; Meaning maps and saliency models based on deep convolutional neural networks are insensitive to image meaning when predicting human fixations.&lt;/em&gt;&lt;/p&gt;\\n\\n&lt;p&gt;Preprint: https://www.biorxiv.org/content/10.1101/840256v1&lt;/p&gt;\\n\\n&lt;p&gt;Marek A. Pedziwiatr&lt;br&gt;\\nmarek.pedziwi@gmail.com&lt;br&gt;\\nSeptember 2020&lt;/p&gt;\\n\\n&lt;p&gt; &lt;/p&gt;
Meaning maps and saliency models based on deep convolutional neural networks are insensitive to image meaning when predicting human fixations - data
2020-09-04

Data from the paper:<em> Meaning maps and saliency models based on deep convolutional neural networks are insensitive to image meaning when predicting human fixations.</em> Preprint: https://www.biorxiv.org/content/10.1101/840256v1 Marek A. Pedziwiatr<br> marek.pedziwi@gmail.com<br> September 2020
Investigating obesity‐associated brain inflammation using quantitative water content mapping
2020-09-05

Abstract There is growing evidence that obesity is associated with inflammation in the brain, which could contribute to the pathogenesis of obesity. In humans, it is challenging to detect brain inflammation in vivo. Recently, quantitative magnetic resonance imaging (qMRI) has emerged as a tool for characterising pathophysiological processes in the brain with reliable and reproducible measures. Proton density imaging provides quantitative assessment of the brain water content, which is affected in different pathologies, including inflammation. We enrolled 115 normal weight, overweight and obese men and women (body mass index [BMI] range 20.1‐39.7 kg m ‐2 , age range 20‐75 years, 60% men) to acquire cerebral water content mapping in vivo using MRI at 3 Tesla. We investigated potential associations between brain water content with anthropometric measures of obesity, body fat distribution and whole‐body metabolism. No global changes in water content were associated with obesity. However, higher water content values in the cerebellum, limbic lobe and sub‐lobular region were detected in participants with higher BMI, independent of age. More specifically, the dorsal striatum, hypothalamus, thalamus, fornix, anterior limb of the internal capsule and posterior thalamic radiation showed the strongest relationship with BMI, independent of age. In a subgroup with available measurements (n = 50), we identified visceral adipose tissue to be the strongest tested link between higher water content values and obesity. Individuals with metabolic syndrome had the highest water content values in the hypothalamus and the fornix. There is accumulating evidence that inflammation of the hypothalamus contributed to obesity‐associated insulin resistance in that area. Whether brain inflammation is a cause or consequence of obesity in humans still needs to be investigated using a longitudinal study design. Using qMRI, we were able to detect marked water content changes in young and older obese adults, which is most likely the result of chronic low‐grade inflammation.
Severe COVID-19 infection is associated with increased antibody-mediated platelet apoptosis
2020-09-05

Abstract The pathophysiology of COVID-19 associated thrombosis seems to be multifactorial, involving interplay between cellular and plasmatic elements of the hemostasis. We hypothesized that COVID-19 is accompanied by platelet apoptosis with subsequent alteration of the coagulation system. We investigated depolarization of mitochondrial inner transmembrane potential (ΔΨm), cytosolic calcium (Ca 2+ ) concentration, and phosphatidylserine (PS) externalization by flow cytometry. Platelets from intensive care unit (ICU) COVID-19 patients (n=21) showed higher ΔΨm depolarization, cytosolic Ca 2+ concentration and PS externalization, compared to healthy controls (n=18) and COVID-19 non-ICU patients (n=4). Moreover significant higher cytosolic Ca 2+ concentration and PS was observed compared to septic ICU control group (ICU control). In ICU control group (n=5; ICU non-COVID-19) cytosolic Ca 2+ concentration and PS externalization was comparable to healthy control, with an increase ΔΨm depolarization. Sera from ICU COVID-19 13 patients induced significant increase in apoptosis markers (ΔΨm depolarization, cytosolic Ca 2+ concentration and PS externalization). compared to healthy volunteer and septic ICU control. Interestingly, immunoglobulin G (IgG) fractions from COVID-19 patients induced an Fc gamma receptor IIA dependent platelet apoptosis (ΔΨm depolarization, cytosolic Ca 2+ concentration and PS externalization). Enhanced PS externalization in platelets from ICU COVID-19 patients was associated with increased sequential organ failure assessment (SOFA) score (r=0.5635) and DDimer (r=0.4473). Most importantly, patients with thrombosis had significantly higher PS externalization compared to those without. The strong correlations between apoptosis markers and increased D-Dimer levels as well as the incidence of thrombosis may indicate that antibody-mediated platelet apoptosis potentially contributes to sustained increased thromboembolic risk in ICU COVID-19 patients. Key points Severe COVID-19 is associated with increased antibody-mediated platelet apoptosis. Platelet apoptosis in severe COVID-19 is correlated with D-Dimer and higher incidence of thromboembolisms.
Chris Dixon. African Americans and the Pacific War, 1941–1945: Race, Nationality, and the Fight for Freedom.
2020-09-06

With his latest book, African Americans and the Pacific War, 1941–1945: Race, Nationality, and the Fight for Freedom, Chris Dixon tackles the history of the Pacific War through the lens of the African American experience. The study builds on his previous research and publications on the diverse and complicated nature of African Americans’ involvement in the Pacific theater. Since 2002, Dixon has (co)authored various publications on African Americans and Australia as well as the Pacific during the Second World War. The monograph under review here is broader in scope and features an impressive array of primary sources, from newspapers and archival documents to oral history. The book’s six chapters underline the complex reality of a multiracial conflict in a wide variety of geographical settings, many of them still under colonial rule. They uncover little-known stories of black Americans in the Pacific and their attitudes toward the war. Dixon asserts that African Americans struggled with their national and racial identity in an especially racially charged theater of the war. They observed and challenged their own oppression at home as well as the fate of colonized people of color abroad. Moreover, they contemplated transnational and transracial activism against white supremacy and colonial rule. Throughout his monograph, Dixon demonstrates that even as they attacked white supremacy perpetuated in and by the United States, African Americans were at the same time “instruments of American power” ingrained in Orientalist stereotypes (7).
Spontaneous (minimal) ritual in non-human great apes?
2020-09-06

This is the postprint of the paper Spontaneous (minimal) ritual in non-human great apes? by Tennie &amp; van Schaik. Published by Phil Trans B link here: https://royalsocietypublishing.org/doi/abs/10.1098/rstb.2019.0423?casa_token=utsMwr-2ddsAAAAA:sUY7YaYp0n-GaUzvmTKKGrJBgHApmVKjbgXK2IJTdD2lz5n_SIxON0Y63-JvhojAa133_hNu156c
Shaping the leaf microbiota: plant–microbe–microbe interactions
2020-09-07

Abstract The aerial portion of a plant, namely the leaf, is inhabited by pathogenic and non-pathogenic microbes. The leaf’s physical and chemical properties, combined with fluctuating and often challenging environmental factors, create surfaces that require a high degree of adaptation for microbial colonization. As a consequence, specific interactive processes have evolved to establish a plant leaf niche. Little is known about the impact of the host immune system on phyllosphere colonization by non-pathogenic microbes. These organisms can trigger plant basal defenses and benefit the host by priming for enhanced resistance to pathogens. In most disease resistance responses, microbial signals are recognized by extra- or intracellular receptors. The interactions tend to be species specific and it is unclear how they shape leaf microbial communities. In natural habitats, microbe–microbe interactions are also important for shaping leaf communities. To protect resources, plant colonizers have developed direct antagonistic or host manipulation strategies to fight competitors. Phyllosphere-colonizing microbes respond to abiotic and biotic fluctuations and are therefore an important resource for adaptive and protective traits. Understanding the complex regulatory host–microbe–microbe networks is needed to transfer current knowledge to biotechnological applications such as plant-protective probiotics.
LifeTime and improving European healthcare through cell-based interceptive medicine
2020-09-07

Here we describe the LifeTime Initiative, which aims to track, understand and target human cells during the onset and progression of complex diseases, and to analyse their response to therapy at single-cell resolution. This mission will be implemented through the development, integration and application of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during the progression from health to disease. The analysis of large molecular and clinical datasets will identify molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. The timely detection and interception of disease embedded in an ethical and patient-centred vision will be achieved through interactions across academia, hospitals, patient associations, health data management systems and industry. The application of this strategy to key medical challenges in cancer, neurological and neuropsychiatric disorders, and infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade.
Phytochemical characterization of different yarrow species (Achillea sp.) and investigations into their antimicrobial activity
2020-09-07

Abstract Various Achillea species are rich in bioactive compounds and are important medicinal plants in phytotherapy. In the present study, Achillea millefolium L., Achillea moschata Wulfen, and Achillea atrata L. were compared with respect to their phenolic profile and antibacterial activity against gram-positive bacteria strains ( Staphylococcus, Propionibacterium ). Particular focus was given to A. atrata , which has hardly been studied so far. Based on the metabolite profile, A. atrata exhibited more similarities to A. moschata than to A. millefolium . The former two only differed in the occurrence of four compounds. The flavonols syringetin-3- O -glucoside and mearnsetin-hexoside, not reported for an Achillea species before, have been detected in A. atrata and A. moschata . All Achillea species reduced growth of the tested bacteria. A. atrata demonstrated highest activity against Propionibacterium acnes and Staphylococcus epidermidis , both being involved in the pathogenesis of acne vulgaris. Furthermore, A. atrata has a pronounced anti–methicillin-resistant Staphylococcus aureus potential. Bioassay-guided fractionation revealed that only the most polar fraction of A. moschata displayed antimicrobial activity, which was attributed to phenolics such as apigenin, centaureidin, and nevadensin, being present in high amounts in A. atrata . Thus, this alpine species shows promising antimicrobial activity and might be a potential source for developing novel dermal/topical drugs.