julilili42/papers huggingface dataset:
Description of spreading dynamics by microscopic network models and macroscopic branching processes can differ due to coalescence
2020-02-03

Spreading processes are conventionally monitored on a macroscopic level by counting the number of incidences over time. The spreading process can then be modeled either on the microscopic level, assuming an underlying interaction network, or directly on the macroscopic level, assuming that microscopic contributions are negligible. The macroscopic characteristics of both descriptions are commonly assumed to be identical. In this work we show that these characteristics of microscopic and macroscopic descriptions can be different due to coalescence, i.e., a node being activated at the same time by multiple sources. In particular, we consider a (microscopic) branching network (probabilistic cellular automaton) with annealed connectivity disorder, record the macroscopic activity, and then approximate this activity by a (macroscopic) branching process. In this framework we analytically calculate the effect of coalescence on the collective dynamics. We show that coalescence leads to a universal nonlinear scaling function for the conditional expectation value of successive network activity. This allows us to quantify the difference between the microscopic model parameter and established estimates of the macroscopic branching parameter. To overcome this difference, we propose a nonlinear estimator that correctly infers the microscopic model parameter for all system sizes.
Physiological changes during prolonged standing and walking considering age, gender and standing work experience
2020-02-03

Occupational standing is associated with musculoskeletal and venous disorders. The aim was to investigate whether lower leg oedema and muscle fatigue development differ between standing and walking and whether age, gender and standing work habituation are factors to consider. Sixty participants (15 young females, 15 young males, 15 older males, and 15 young males habituated to standing work) were included and required to stand/walk for 4.5<b> </b>hours in three periods with two seated breaks. Waterplethysmography/bioelectrical impedance, muscle twitch force and surface electromyography were used to assess lower leg swelling (LLS) and muscle fatigue as well as gastrocnemius muscle activity, respectively. While standing led to LLS and muscle fatigue, walking did not. Low-level medial gastrocnemius activity was not continuous during standing. No significant influence of age, gender and standing habituation was observed. Walking can be an effective prevention measure to counteract the detrimental effects of quasi-static standing.<b>Practitioner summary:</b> Prolonged standing leads to lower leg oedema and muscle fatigue while walking does not. The primary cause of fatigue may be in other muscles than the medial gastrocnemius. Walking may be an effective prevention measure for health risks of occupational standing when included intermittently.<b>Abbreviation:</b> BI: bioelectrical impedance; LLS: lower leg swelling; SEMG: surface electromyography; MTF: muscle twitch force; WP: waterplethysmography; Bsl: Baseline; L: Lunch; E: Evening; MTM: method times measurement; EA: electrical activity; IQR: interquartile range; p: percentile; M: mean; SE: standard error; Adj: adjusted.
Tailored ensembles of neural networks optimize sensitivity to stimulus statistics
2020-02-03

The dynamic range of stimulus processing in living organisms is much larger\\nthan a single neural network can explain. For a generic, tunable spiking\\nnetwork we derive that while the dynamic range is maximal at criticality, the\\ninterval of discriminable intensities is very similar for any network tuning\\ndue to coalescence. Compensating coalescence enables adaptation of\\ndiscriminable intervals. Thus, we can tailor an ensemble of networks optimized\\nto the distribution of stimulus intensities, e.g., extending the dynamic range\\narbitrarily. We discuss potential applications in machine learning.\\n
Beta-Glycerophosphate-Induced ORAI1 Expression and Store Operated Ca2+ Entry in Megakaryocytes
2020-02-03

Abstract Impairment of renal phosphate elimination in chronic kidney disease (CKD) leads to enhanced plasma and tissue phosphate concentration, which in turn up-regulates transcription factor NFAT5 and serum &amp; glucocorticoid-inducible kinase SGK1. The kinase upregulates ORAI1, a Ca 2+ -channel accomplishing store-operated Ca 2+ -entry (SOCE). ORAI1 is stimulated following intracellular store depletion by Ca 2+ -sensors STIM1 and/or STIM2. In megakaryocytes and blood platelets SOCE and thus ORAI1 are powerful regulators of activity. The present study explored whether the phosphate-donor ß-glycerophosphate augments NFAT5, ORAI1,2,3 and/or STIM1,2 expressions and thus SOCE in megakaryocytes. Human megakaryocytic Meg01cells were exposed to 2 mM of phosphate-donor ß-glycerophosphate for 24 hours. Platelets were isolated from blood samples of patients with impaired kidney function or control volunteers. Transcript levels were estimated utilizing q-RT-PCR, cytosolic Ca 2+ -concentration ([Ca 2+ ] i ) by Fura-2-fluorescence, and SOCE from increase of [Ca 2+ ] i following re-addition of extracellular Ca 2+ after store depletion with thapsigargin (1 μM). NFAT5 and ORAI1 protein abundance was estimated with Western blots. As a result, ß-glycerophosphate increased NFAT5, ORAI1/2/3, STIM1/2 transcript levels, as well as SOCE. Transcript levels of NFAT5, SGK1, ORAI1/2/3, and STIM1/2 as well as NFAT5 and ORAI1 protein abundance were significantly higher in platelets isolated from patients with impaired kidney function than in platelets from control volunteers. In conclusion, phosphate-donor ß-glycerophosphate triggers a signaling cascade of NFAT5/SGK1/ORAI/STIM, thus up-regulating store-operated Ca 2+ -entry.
SOMC@Periodic Mesoporous Silica Nanoparticles: Meerwein–Ponndorf–Verley Reduction Promoted by Immobilized Rare-Earth-Metal Alkoxides
2020-02-03

The Meerwein–Ponndorf–Verley (MPV) reduction is a reaction that offers a mild reduction of aldehydes and ketones to the corresponding alcohols. Although described as a catalytic reaction, its real-life applicability suffers from the necessity of using the standard catalyst [Al(OiPr)3] in stoichiometric amounts or even in excess. Rare-earth-metal-based catalysts are capable of performing in these reactions in a truly catalytic fashion. The ceric alkoxide [Ce(OiPr)4]3 has been synthesized via silylamine elimination from Ce[N(SiHMe2)2]4 with isopropyl alcohol, its trimetallic solid-state structure has been determined by X-ray diffraction, and its performance in the MPV reduction of 4-tBu-cyclohexanone has been examined and compared to that of cerous [Ce(OCH2tBu)3]4. Spherical mesoporous silica nanoparticles with an MCM-41-type honeycomb pore symmetry, termed MSN-MCM-41 (particle size, ca. 250 nm diameter; pore size, 2.6 nm diameter), are employed for grafting the molecular precursors Ce[N(SiHMe2)2]4, [Ce(OiPr)4]3, Ce[N(SiMe3)2]3, and La[N(SiMe3)2]3 according to the methods of surface organometallic chemistry (SOMC). The MPV reductions carried out with the homogeneous and heterogeneous catalysts reveal (a) a better performance of Ce(III) in comparison to Ce(IV), (b) better performance of La[N(SiMe3)2]3@MSN-MCM-41 in comparison to Ce[N(SiMe3)2]3@MSN-MCM-41 (high sensitivity of Ce(III)-grafted materials), and (c) reusability of the grafted catalyst systems. All hybrid materials were characterized by PXRD, N2 physisorption, and 1H/13C/29Si MAS NMR and FTIR spectroscopies as well as elemental analysis.
Dataset for Male Eurasian jays flexibly alter their food sharing in line with partners' choices
2020-02-03

This is the raw data for Exp. 1 and Exp. 2 from "Male Eurasian jays flexibly alter their food sharing in line with partners’ choices" by Rachel C Crosby, Edward W Legg, Katharina F. Brecht, Michael T Mendl, Ljerka Ostojic and Nicola S. Clayton in a machine-readable format.
Dataset for Male Eurasian jays flexibly alter their food sharing in line with partners' choices
2020-02-03

This is the raw data for Exp. 1 and Exp. 2 from "Investigating the flexibility of male Eurasian jays' food-sharing behavior' by Rachel C Crosby, Edward W Legg, Katharina F. Brecht, Michael T Mendl, Ljerka Ostojic and Nicola S. Clayton in a machine-readable format. It was previously pre-printed under the title of "Male Eurasian jays flexibly alter their food sharing in line with partners’ choices".
Data for: Dose Finding Study of Pentoxifylline in Children With Cerebral Malaria
2020-02-03

&lt;p&gt;Pentoxifylline (PTX) affects many processes that may contribute to the pathogenesis of severe malaria and it has been shown to reduce the duration of coma in children with cerebral malaria. This pilot study was performed to assess pharmacokinetics, safety and efficacy of PTX in African children with cerebral malaria.&lt;/p&gt; &lt;p&gt;Ten children admitted to the high dependency unit of the Kilifi District Hospital in Kenya with cerebral malaria (Blantyre coma score of 2 or less) received quinine plus a continuous infusion of 10 mg/kg/24 hours PTX for 72 hours. Five children were recruited as controls and received normal saline instead of PTX. Plasma samples were taken for PTX and tumour necrosis factor (TNF) levels. Blantyre Coma Score, parasitemia, hematology and vital signs were assessed 4 hourly.&lt;/p&gt; &lt;p&gt;The dataset contains: &lt;ul&gt; &lt;li&gt;Demographic details of the patient, history of disease, and clinical findings (vital signs, oxygen saturation, respiratory status, Blantyre coma score recorded on admission &lt;/li&gt; &lt;li&gt;Laboratory on admission included parasitaemia, full blood count and differential white cell count, glucose, blood culture, blood gas analysis, electrolytes, creatinine, lactate, and aspartate transaminase (AST). Parasite density was counted per 100 white blood cells or, for high parasitaemia, per 500 red blood cells and expressed in parasites per μL&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;A detailed description of the study design is given in the study protocol and results as reported by Lell, B., Köhler, C., Wamola, B., Olola, C.H., Kivaya, E., Kokwaro, G., Wypij, D., Mithwani, S., Taylor, T.E., Kremsner, P.G. and Newton, C.R., 2010. Pentoxifylline as an adjunct therapy in children with cerebral malaria. Malaria journal, 9(1), p.368. doi: &lt;a href="https://dx.doi.org/10.1186%2F1475-2875-9-368"&gt;10.1186/1475-2875-9-368&lt;/a&gt;. The study is also registered on ClinicalTrials.gov &lt;a href="https://clinicaltrials.gov/ct2/show/NCT00133393"&gt;NCT00133393&lt;/a&gt;.
Phenotypic variation within and across transcriptomic cell types in mouse motor cortex
2020-02-04

Cortical neurons exhibit astounding diversity in gene expression as well as in morphological and electrophysiological properties. Most existing neural taxonomies are based on either transcriptomic or morpho-electric criteria, as it has been technically challenging to study both aspects of neuronal diversity in the same set of cells. Here we used Patch-seq to combine patch-clamp recording, biocytin staining, and single-cell RNA sequencing of over 1300 neurons in adult mouse motor cortex, providing a comprehensive morpho-electric annotation of almost all transcriptomically defined neural cell types. We found that, although broad families of transcriptomic types ( Vip , Pvalb , Sst , etc.) had distinct and essentially non-overlapping morpho-electric phenotypes, individual transcriptomic types within the same family were not well-separated in the morpho-electric space. Instead, there was a continuum of variability in morphology and electrophysiology, with neighbouring transcriptomic cell types showing similar morpho-electric features, often without clear boundaries between them. Our results suggest that neural types in the neocortex do not always form discrete entities. Instead, neurons follow a hierarchy consisting of distinct non-overlapping branches at the level of families, but can form continuous and correlated transcriptomic and morpho-electrical landscapes within families.
Format-dependent and format-independent representation of sequential and simultaneous numerosity in the crow endbrain
2020-02-04

Abstract Humans’ symbolic counting skills are built on a primordial ability to approximately estimate the number of items, or numerosity. To date it is debated whether numerosities presented in categorically different formats, that is as temporal sequences versus spatial arrays, are represented abstractly in the brain. To address this issue, we identified the behavioral characteristics and neuronal codes for sequential and simultaneous number formats in crows. We find a format-dependent representation by distinct groups of selective neurons during the sensory encoding stage. However, an abstract and format-independent numerosity code emerges once the encoding phase is completed and numerosities needed to be memorized. These results suggest a successive two-stage code for categorically different number formats and help to reconcile conflicting findings observed in psychophysics and brain imaging.
Biogenesis pathways of α-helical mitochondrial outer membrane proteins
2020-02-04

Abstract Mitochondria harbor in their outer membrane (OM) proteins of different topologies. These proteins are encoded by the nuclear DNA, translated on cytosolic ribosomes and inserted into their target organelle by sophisticated protein import machineries. Recently, considerable insights have been accumulated on the insertion pathways of proteins into the mitochondrial OM. In contrast, little is known regarding the early cytosolic stages of their biogenesis. It is generally presumed that chaperones associate with these proteins following their synthesis in the cytosol, thereby keeping them in an import-competent conformation and preventing their aggregation and/or mis-folding and degradation. In this review, we outline the current knowledge about the biogenesis of different mitochondrial OM proteins with various topologies, and highlight the recent findings regarding their import pathways starting from early cytosolic events until their recognition on the mitochondrial surface that lead to their final insertion into the mitochondrial OM.
Inhibition of IRF4 in dendritic cells by PRR-independent and -dependent signals inhibit Th2 and promote Th17 responses
2020-02-04

Cyclic AMP (cAMP) is involved in many biological processes but little is known regarding its role in shaping immunity. Here we show that cAMP-PKA-CREB signaling (a pattern recognition receptor [PRR]-independent mechanism) regulates conventional type-2 Dendritic Cells (cDC2s) in mice and reprograms their Th17-inducing properties via repression of IRF4 and KLF4, transcription factors essential for cDC2-mediated Th2 induction. In mice, genetic loss of IRF4 phenocopies the effects of cAMP on Th17 induction and restoration of IRF4 prevents the cAMP effect. Moreover, curdlan, a PRR-dependent microbial product, activates CREB and represses IRF4 and KLF4, resulting in a pro-Th17 phenotype of cDC2s. These in vitro and in vivo results define a novel signaling pathway by which cDC2s display plasticity and provide a new molecular basis for the classification of novel cDC2 and cDC17 subsets. The findings also reveal that repressing IRF4 and KLF4 pathway can be harnessed for immuno-regulation.
Accessing the Hotspots of Cavity Plasmon Modes in Vertical Metal–Insulator–Metal Structures for Surface Enhanced Raman Scattering
2020-02-04

Abstract In metal–insulator–metal structures such as Au nanodiscs on an Au film separated by a thin oxide spacer layer, the metal/insulator interfaces can form a Fabry–Perot cavity in which gap surface plasmons are confined. As a result, these cavity plasmon modes show the advantageous properties of strong field enhancement and very narrow resonance line shapes due to the confinement in a cavity. In this work, the hotspots of the electromagnetic near‐field of cavity plasmon modes are exposed to make the strongly enhanced field accessible to Raman molecules. This is achieved by creating an undercut in the spacer between the Au discs and the gold film by wet etching of the spacer. The electromagnetic field distributions as well as the resonance wavelengths of two different cavity plasmon modes in such cavities both with and without undercut are studied by simulations based on the finite element method. The size of the undercut is estimated by relating the measured spectral shift before and after reducing the spacer disc to the one obtained in simulations. Surface enhanced Raman scattering measurements are conducted on arrays of cavities. The effect of the undercut on the Raman scattering intensity is investigated and a notable increase is found.
Utilization of 1-phenylimidazo[1,5-a]quinoline as partner in 1,4-dipolar cycloaddition reactions
2020-02-04

Abstract A Selected set of 2-(quinolin-2-yl)-1,3-oxazepino[7,6- b ]indoles 4a–d and dihydroacenaphtho[1,2- f ][1,3]oxazepine 5 have been prepared via 1,4-dipolar cycloaddition reaction involving 1-phenylimidazo[1,5- a ]quinoline, dimethyl acetylenedicarboxylate, and N -(substituted)isatins or acenaphthoquinone. Structures of the new heterocycles 4a–d and 5 are supported by NMR and HRMS spectral data, and confirmed by single-crystal X-ray crystallography for 4c and 5 .
Novel Tat-Dependent Protein Secretion
2020-02-04

The transcription initiation signal elicited by the binding of ferric citrate to the outer membrane FecA protein is transmitted by the FecR protein across the cytoplasmic membrane to the FecI extracytoplasmic function (ECF) sigma factor. In this issue of Journal of Bacteriology , I. J. Passmore, J. M. Dow, F. Coll, J. Cuccui, et al. (J Bacteriol 202:e00541-19, 2020, https://doi.org/10.1128/JB.00541-19 ) report that the FecR sequence contains both the twin-arginine signal motif and the secretory (Sec) avoidance motif typical of proteins secreted by the twin-arginine translocation (TAT) system.
Performance of two Methods for Cardiac MRI Edema Mapping: Dual-Contrast Fast Spin-Echo and T2 Prepared Balanced Steady State Free Precession
2020-02-04

Purpose To compare true positive and false negative results of myocardial edema mapping in two methods. Myocardial edema may be difficult to detect on cardiac MRI. Materials and Methods 76 patients (age 59 ± 11 years, 15 female) with acute myocardial infarction (MI) and 10 healthy volunteers were prospectively included in this single-center study. 1.5 T cardiac MRI was performed in patients 2.5 days after revascularization (median) for edema mapping: Steady State Free Precession (SSFP) mapping sequence with T2-preparation pulses (T2prep); and dual-contrast Fast Spin-Echo (dcFSE) signal decay edema mapping. Late gadolinium enhancement (LGE) was used as the reference for expected edema in acute MI. Results 311 myocardial segments in patients were acutely infarcted with mean T2 73 ms for T2prep SSFP vs. 87 ms for dcFSE edema mapping. In healthy volunteers the mean T2 was 56 ms for T2prep SSFP vs. 50 ms for dcFSE edema mapping. Receiver operating characteristic (ROC) curve for T2prep SSFP show area under the curve (AUC) 0.962, p &lt; 0.0001, Youden index J 0.8266, associated criterion &gt; 60 ms, sensitivity 94 %, specificity 89 %. dcFSE ROC AUC 0.979, p &lt; 0.0001, J 0.9219, associated criterion &gt; 64 ms, sensitivity 93 %, specificity 99 %. Conclusion Both edema mapping methods indicate high-grade edema with high sensitivity. Nevertheless, edema in acute infarction may be focally underestimated in both mapping methods. Key Points: Citation Format
Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing
2020-02-05

Abstract Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer.
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition
2020-02-05

Abstract About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 38 histological cancer subtypes within the framework of the Pan-Cancer Analysis of Whole Genomes (PCAWG) project. We identified 19,166 somatically acquired retrotransposition events, which affected 35% of samples and spanned a range of event types. Long interspersed nuclear element (LINE-1; L1 hereafter) insertions emerged as the first most frequent type of somatic structural variation in esophageal adenocarcinoma, and the second most frequent in head-and-neck and colorectal cancers. Aberrant L1 integrations can delete megabase-scale regions of a chromosome, which sometimes leads to the removal of tumor-suppressor genes, and can induce complex translocations and large-scale duplications. Somatic retrotranspositions can also initiate breakage–fusion–bridge cycles, leading to high-level amplification of oncogenes. These observations illuminate a relevant role of 22 L1 retrotransposition in remodeling the cancer genome, with potential implications for the development of human tumors.
Proton magnetic resonance spectroscopy in skeletal muscle: Experts' consensus recommendations
2020-02-05

1 H‐MR spectroscopy of skeletal muscle provides insight into metabolism that is not available noninvasively by other methods. The recommendations given in this article are intended to guide those who have basic experience in general MRS to the special application of 1 H‐MRS in skeletal muscle. The highly organized structure of skeletal muscle leads to effects that change spectral features far beyond simple peak heights, depending on the type and orientation of the muscle. Specific recommendations are given for the acquisition of three particular metabolites (intramyocellular lipids, carnosine and acetylcarnitine) and for preconditioning of experiments and instructions to study volunteers.