nils-herrmann/clean_scirepeval huggingface dataset:
Comparative Analysis of the miRNome of Bovine Milk Fat, Whey and Cells
Venue: PloS one

Abundant miRNAs have been identified in milk and mammary gland tissues of different species. Typically, RNA in milk can be extracted from different fractions including fat, whey and cells and the mRNA transcriptome of milk could serve as an indicator of the transcriptome of mammary gland tissue. However, it has not been adequately validated if the miRNA transcriptome of any milk fraction could be representative of that of mammary gland tissue. The objectives of this study were to (1) characterize the miRNA expression spectra from three milk fractions fat, whey and cells; (2) compare miRNome profiles of milk fractions (fat, whey and cells) with mammary gland tissue miRNome, and (3) determine which milk fraction miRNome profile could be a better representative of the miRNome profile of mammary gland tissue. Milk from four healthy Canadian Holstein cows in mid lactation was collected and fractionated. Total RNA extracted from each fraction was used for library preparation followed by small RNA sequencing. In addition, miRNA transcripts of mammary gland tissues from twelve Holstein cows in our previous study were used to compare our data. We identified 210, 200 and 249 known miRNAs from milk fat, whey and cells, respectively, with 188 universally expressed in the three fractions. In addition, 33, 31 and 36 novel miRNAs from milk fat, whey and cells were identified, with 28 common in the three fractions. Among 20 most highly expressed miRNAs in each fraction, 14 were expressed in common and 11 were further shared with mammary gland tissue. The three milk fractions demonstrated a clear separation from each other using a hierarchical cluster analysis with milk fat and whey being most closely related. The miRNome correlation between milk fat and mammary gland tissue (rmean 0.866) was significantly higher than the other two pairs (p 0.01) whey/mammary gland tissue (rmean 0.755) and milk cell/mammary gland tissue (rmean 0.75) suggesting that milk fat could be an alternative non invasive source of RNA in assessing miRNA activities in bovine mammary gland. Predicted target genes (1802) of 14 highly expressed miRNAs in milk fractions were enriched in fundamental cellular functions, infection, organ and tissue development. Furthermore, some miRNAs were highly enriched (FDR <0.05) in milk whey (3) cells (11) and mammary gland tissue (14) suggesting specific regulatory functions in the various fractions. In conclusion, we have obtained a comprehensive miRNA profile of the different milk fractions using high throughput sequencing. Our comparative analysis showed that miRNAs from milk fat accurately portrayed the miRNome of mammary gland tissue. Functional annotation of the top expressed miRNAs in milk confirmed their critical regulatory roles in mammary gland functions and potentially to milk recipients.
Sentinel 1 based flood mapping: a fully automated processing chain

This article presents an automated Sentinel 1 based processing chain designed for flood detection and monitoring in near real time (NRT) Since no user intervention is required at any stage of the flood mapping procedure, the processing chain allows deriving time critical disaster information in less than 45 min after a new data set is available on the Sentinel Data Hub of the European Space Agency (ESA) Due to the systematic acquisition strategy and high repetition rate of Sentinel 1, the processing chain can be set up as a web based service that regularly informs users about the current flood conditions in a given area of interest. The thematic accuracy of the thematic processor has been assessed for two test sites of a flood situation at the border between Greece and Turkey with encouraging overall accuracies between 94.0% and 96.1% and Cohen's kappa coefficients (k) ranging from 0.879 to 0.910. The accuracy assessment, which was performed separately for the standard polarizations (VV/VH) of the interferometric wide swath (IW) mode of Sentinel 1, further indicates that under calm wind conditions, slightly higher thematic accuracies can be achieved by using VV instead of VH polarization data.
Automated flood mapping and monitoring using Sentinel 1 data

Flood extent maps derived from Synthetic Aperture Radar (SAR) data can be a key information source for an effective disaster management, helping humanitarian relief organizations and decision makers to obtain spatially explicit information about inundated areas in a time and cost efficient manner. In comparison to manual or semi automatic flood mapping approaches often utilized in the framework of rapid mapping activities, automatic SAR based processing chains can substantially reduce the critical time delay between the delivery of satellite data after a crisis event and the subsequent provision of satellite derived crisis information (e.g. the extent of a flood situation) to emergency management authorities. In this work, an automated Sentinel 1 based processing chain designed for flood detection and monitoring in near real time (NRT) is presented. The work is based upon a TerraSAR X based flood service which has been adapted to Sentinel 1, including a number of enhancements for improving both robustness and thematic accuracy. Since no user intervention is required at any stage of the flood mapping procedure, the processing chain allows deriving time critical disaster information in less than 45 minutes after a new dataset is available on the ESA Sentinel Data Hub. Due to the systematic acquisition strategy and high repeat rate of Sentinel 1, the processing chain can be set up as a web based service which regularly informs users about the current flood conditions in a given area of interest. The processing chain is composed of the following main elements: a) automatic data ingestion through a Python based script which routinely queries the ESA Sentinel Data Hub for new acquisitions matching user defined criteria and subsequently downloads them, b) geometric correction and radiometric calibration using the graph processing tool (GPT) of the ESA Sentinel 1 toolbox (S1TBX) which is embedded in the Sentinel Application Platform (SNAP) c) initial classification using an automatic thresholding methodology, d) fuzzy logic based classification refinement, e) final classification including auxiliary data, and f) dissemination and visualization of the results using a dedicated web client. The thematic accuracy of the processor has been assessed for two test sites of a flood situation at the border between Greece and Turkey with encouraging accuracies. The accuracy assessment, which was performed separately for both standard polarizations (VV/VH) of the interferometric wide swath (IW) mode of Sentinel 1, further indicates that the thematic accuracy of VV polarization is slightly higher than that of VH polarization under calm wind conditions.
An assessment of the Height Above Nearest Drainage terrain descriptor for the thematic enhancement of automatic SAR based flood monitoring services
Venue: Remote Sensing

Flood extent maps derived from Synthetic Aperture Radar (SAR) data can communicate spatially explicit information in a timely and cost effective manner to support disaster management. Automated processing chains for SAR based flood mapping have the potential to substantially reduce the critical time delay between the delivery of post event satellite data and the subsequent provision of satellite derived crisis information to emergency management authorities. However, the accuracy of SAR based flood mapping can vary drastically due to the prevalent land cover and topography of a given scene. While expert based image interpretation with the consideration of contextual information can effectively isolate flood surface features, a fully automated feature differentiation algorithm mainly based on the grey levels of a given pixel is comparatively more limited for features with similar SAR backscattering characteristics. The inclusion of ancillary data in the automatic classification procedure can effectively reduce instances of misclassification. In this work, a near global 'Height Above Nearest Drainage' (HAND) index [10] was calculated with digital elevation data and drainage directions from the HydroSHEDS mapping project  The index can be used to separate flood prone regions from areas with a low probability of flood occurrence. Based on the HAND index, an exclusion mask was computed to reduce water look alikes with respect to the hydrologictopographic setting. The applicability of this near global ancillary data set for the thematic improvement of Sentinel 1 and TerraSAR X based services for flood and surface water monitoring has been validated both qualitatively and quantitatively. Application of a HAND based exclusion mask resulted in improvements to the classification accuracy of SAR scenes with high amounts of water look alikes and considerable elevation differences.
Regularization Of Inverse Problems

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Electric crows: powerlines, climate change and the emergence of a native invader

Climate change and other anthropogenic global change drivers act in complex, mutually exacerbating ways to alter the abundance and distribution of species. In South Africa, pied crows Corvus albus have increased in numbers and range in recent decades. Popular opinion links these changes to urbanisation and infrastructure development, but there has been no empirical test of this idea. We aimed to clarify the drivers of pied crow population changes in South Africa. Location South Africa.  We used publicly available long term datasets, the Southern African Bird Atlas Project and University of Delaware Gridded Climate Database, and spatial data from government bodies, to assess relationships between pied crow population and range changes, land use, infrastructure, urbanisation and climate change.  Pied crow numbers have increased significantly in the past three decades, but rate of increase varied geographically, with crows declining in the northeast and increasing in the south west of South Africa. Pied crow population changes were strongly correlated with climate change. Crows have benefited most from climate warming in the shrubland biomes of south western South Africa. Pied crows are tree nesters, and within these shrublands, there is a strong positive relationship between the rate of population increase and the density of powerline infrastructure, which may facilitate pied crows' increase by providing nesting sites.  Pied crow numbers have increased in response to climate warming, with their spread facilitated by electrical infrastructure in south western South Africa, providing a clear example of compound influence of multiple global change drivers promoting a significant change in species range and reporting rate. Pied crows are generalist predators and there is popular concern about their ecological impact in areas where increases have occurred. We highlight the importance of understanding the ecosystem level implications of increased numbers of pied crows in South Africa's shrubland biomes.
Detecting Pulse from Head Motions Using Smartphone Camera

This paper proposes a touchless system for estimating heart rates using smartphone cameras. It is based on computing subtle and periodic head motions by tracking facial feature points in camera images. However, it suffers from the problem with the shaking movements of the hand that holds the smartphone. To resolve the problem, the proposed system tracks background feature points together with facial feature points. This is based on that the movements of the background feature points are mainly caused by hand shaking. The movements of background feature points are then used to correct locations of the facial feature points. In experiments, the correction improved the accuracy of heart rate estimation by more than 15% As a result, the proposed system could estimate heart rates with high accuracy.
Fatigue and fracture of wires and cables for biomedical applications

Fine wires and cables play a critical role in the design of medical devices and subsequent treatment of a large array of medical diagnoses. Devices such as guide wires, catheters, pacemakers, stents, staples, functional electrical stimulation systems, eyeglass frames and orthodontic braces can be comprised of wires with diameters ranging from 10s to 100s of micrometres. Reliability is paramount as part of either internal or external treatment modalities. While the incidence of verified fractures in many of these devices is quite low, the criticality of these components requires a strong understanding of the factors controlling the fracture and fatigue behaviour.1,2 Additionally, optimisation of the performance and reliability of these devices necessitates characterisation of the fatigue and fracture properties of its constituent wires. A review of cable architecture and stress states experienced during testing is followed by an overview of the effects of changes in material composition, microstructure, processing and test conditions on fracture and fatigue behaviour of wire and cable systems used in biomedical applications. The review concludes with recommendations for future work.
State of the art of diagnosis of rickettsial diseases: the use of blood specimens for diagnosis of scrub typhus, spotted fever group rickettsiosis, and murine typhus
Venue: Current opinion in infectious diseases

With improved malaria control, acute undifferentiated febrile illness studies in tropical regions reveal a startling proportion of rickettsial illnesses, especially scrub typhus, murine typhus, and spotted fever group rickettsioses. Laboratory diagnosis of these infections evolved little over the past 40 years, but combinations of technologies like PCR and loop mediated isothermal amplification, with refined rapid diagnostic tests and/or ELISA, are promising for guidance for early antirickettsial treatment.  The long term reliance on serological tests useful only late in rickettsial infections has led to underdiagnosis, inappropriate therapies, and undocumented morbidity and mortality. Recent approaches integrate nucleic acid amplification and recombinant protein based serological tests for diagnosing scrub typhus. Optimized using Bayesian latent class analyses, this strategy increases diagnostic confidence and enables early accurate diagnosis and treatment a model to follow for lagging progress in murine typhus and spotted fever.  A laboratory diagnostic paradigm shift in rickettsial infections is evolving, with replacement of indirect immunofluorescence assay by the more objective ELISA coupled with nucleic acid amplification assays to expand the diagnostic window toward early infection intervals. This approach supports targeted antirickettsial therapy, reduces morbidity and mortality, and provides a robust evidence base for further development of diagnostics and vaccines.
Probabilistic quantum teleportation in the presence of noise

We extend the research program initiated in 2015) where we restricted our attention to noisy deterministic teleportation protocols, to noisy probabilistic (conditional) protocols. Our main goal now is to study how we can increase the fidelity of the teleported state in the presence of noise by working with probabilistic protocols. We work with several scenarios involving the most common types of noise in realistic implementations of quantum communication tasks and find many cases where adding more noise to the probabilistic protocol increases considerably the fidelity of the teleported state, without decreasing the probability of a successful run of the protocol. Also, there are cases where the entanglement of the channel connecting Alice and Bob leading to the greatest fidelity is not maximal. Moreover, there exist cases where the optimal fidelity for the probabilistic protocols are greater than the maximal fidelity (2/3) achievable by using only classical resources, while the optimal ones for the deterministic protocols under the same conditions lie below this limit. This result clearly illustrates that in some cases we can only get a truly quantum teleportation if we use probabilistic instead of deterministic protocols.
In Situ Confinement of Ultrasmall Pd Clusters within Nanosized Silicalite 1 Zeolite for Highly Efficient Catalysis of Hydrogen Generation.
Venue: Journal of the American Chemical Society

Well dispersed and ultrasmall Pd clusters in nanosized silicalite 1 (MFI) zeolite have been prepared under direct hydrothermal conditions using [Pd(NH2CH2CH2NH2)2]Cl2 as precursor. High resolution scanning transmission electron microscopy studies indicate that the Pd clusters are encapsulated within the intersectional channels of MFI, and the Pd clusters in adjacent channels visually aggregate, forming nanoparticles (NPs) of ~1.8 nm. The resultant catalysts show an excellent activity and highly efficient H2 generation toward the complete decomposition of formic acid (FA) under mild conditions. Notably, thanks to the further reduced Pd NP size ~1.5 nm) and the additionally introduced basic sites, the Pd/S 1 in K catalyst affords turnover frequency values up to 856 h( 1) at 25 degC and 3027 h( 1) at 50 degC. The easy in situ confinement synthesis of metal clusters in zeolites endows the catalysts with superior catalytic activities, excellent recyclability, and high thermal stability, thus opening new perspectives for the practical application of FA as a viable and effective H2 storage material for use in fuel cells.
Direct and selective conversion of methanol to para xylene over Zn ion doped ZSM 5/silicalite 1 core shell zeolite catalyst

We successfully designed Zn ion doped ZSM 5/silicalite 1 core shell zeolite catalyst. On methanol to para xylene (MT p X) over the core shell catalyst, p xylene yield was 40.7 C mol% and para selectivity para xylene selectivity in xylene isomers) was higher than 99 C mol% which substantially exceeds the other results reported in the literature.
Analysing Texts through their Linguistic Properties: A Cross disciplinary Study
Venue: J. Quant. Linguistics

The study reported here focuses on identifying linguistic complexity indices in discussion sections of research articles which can be used to discriminate among various disciplines. Two measures of lexical complexity including lexical diversity and lexical density and two measures of syntactic complexity including average sentence length and ratio of subordination were used as our text complexity model factors. Referring to three major disciplines (humanities, life sciences, and physics) we tried to examine this model. Our corpus consisted of 120 discussion sections of research articles (40 articles from each discipline) Wordsmith Tools software was used to calculate the four complexity measures of each piece of data. To examine the prediction power of our model, MANOVA and discriminant function analysis were run. The results demonstrated substantial predictability (68.3% for the proposed model. Except for average sentence length, all of the complexity measures used in this study indicated significant contribution to discrimination among three disciplines. The study has implications for EAP and ESP teachers and practitioners.
Mechanical Thrombectomy for Isolated M2 Occlusions: A Post Hoc Analysis of the STAR, SWIFT, and SWIFT PRIME Studies
Venue: American Journal of Neuroradiology

Mechanical thrombectomy is beneficial for patients with acute ischemic stroke and a proximal anterior occlusion, but it is unclear if these results can be extrapolated to patients with an M2 occlusion. The purpose of this study was to examine the technical aspects, safety, and outcomes of mechanical thrombectomy with a stent retriever in patients with an isolated M2 occlusion who were included in 3 large multicenter prospective studies.  We included patients from the Solitaire Flow Restoration Thrombectomy for Acute Revascularization (STAR) Solitaire With the Intention For Thrombectomy (SWIFT) and Solitaire With the Intention for Thrombectomy as Primary Endovascular Treatment (SWIFT PRIME) studies, 3 large multicenter prospective studies on thrombectomy for ischemic stroke. We compared outcomes and technical details of patients with an M2 with those with an M1 occlusion. All patients were treated with a stent retriever. Imaging data and outcomes were scored by an independent core laboratory. Successful reperfusion was defined as modified Thrombolysis in Cerebral Infarction score of 2b/3.  We included 50 patients with an M2 and 249 patients with an M1 occlusion. Patients with an M2 occlusion were older (mean age, 71 versus 67 years; P .04) and had a lower NIHSS score (median, 13 versus 17; P .001) compared with those with an M1 occlusion. Procedural time was nonsignificantly shorter in patients with an M2 occlusion (median, 29 versus 35 minutes; P .41) The average number of passes with a stent retriever was also nonsignificantly lower in patients with an M2 occlusion (mean, 1.4 versus 1.7; P .07) There were no significant differences in successful reperfusion (85% versus 82% P .82) symptomatic intracerebral hemorrhages (2% versus 2% P 1.0) device related serious adverse events (6% versus 4% P .46) or modified Rankin Scale score 0 2 at follow up (60% versus 56% P .64)  Endovascular reperfusion therapy appears to be feasible in selected patients with ischemic stroke and an M2 occlusion.
Microglial M1/M2 polarization and metabolic states
Venue: British journal of pharmacology

Microglia are critical nervous system specific immune cells serving as tissue resident macrophages influencing brain development, maintenance of the neural environment, response to injury and repair. As influenced by their environment, microglia assume a diversity of phenotypes and retain the capability to shift functions to maintain tissue homeostasis. In comparison with peripheral macrophages, microglia demonstrate similar and unique features with regards to phenotype polarization, allowing for innate immunological functions. Microglia can be stimulated by LPS or IFN g to an M1 phenotype for expression of pro inflammatory cytokines or by IL 4/IL 13 to an M2 phenotype for resolution of inflammation and tissue repair. Increasing evidence suggests a role of metabolic reprogramming in the regulation of the innate inflammatory response. Studies using peripheral immune cells demonstrate that polarization to an M1 phenotype is often accompanied by a shift in cells from oxidative phosphorylation to aerobic glycolysis for energy production. More recently, the link between polarization and mitochondrial energy metabolism has been considered in microglia. Under these conditions, energy demands would be associated with functional activities and cell survival and thus, may serve to influence the contribution of microglia activation to various neurodegenerative conditions. This review examines the polarization states of microglia and their relationship to mitochondrial metabolism. Additional supporting experimental data are provided to demonstrate mitochondrial metabolic shifts in primary microglia and the BV 2 microglia cell line induced under LPS (M1) and IL 4/IL 13 (M2) polarization.