Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence of Oocyte Polarity in Bovine; Implications for Intracytoplasmic Sperm Injection and Somatic Cell Nuclear Transfer

Objective We recently demonstrated spatial regionalization of maternal transcripts and proteins within unfertilized ovine oocyte. Here, we investigated the likelihood of oocyte polarity for the first time in bovine. Materials and Methods In this experimental study, in vitro matured bovine oocytes were used for manual bisection [into oocyte halve that were near-to (HNS) and far-from (FS) spindle] or trisection [into MII-spindle (S), the spindle-side half (NS), and the distal half unassociated with the spindle (FS)]. Prepared pools of oocyte substructures were used for comparative quantitative real-time polymerase chain reaction (RT-qPCR). To map the possible preferential sperm entry point (SEP), the spatial relationship between SEP and MII-spindle was measured 5 hours post-fertilization. Results The proportional amount of maternal mRNA in S oocyte fragment was estimated to be 6 to 11-fold higher than NS and FS counterparts. The relative abundances of Nanog, Oct4, Fgf4 and Tead4 were significantly higher in HNS oocyte fragment compared t0 FS. The relative abundances of Ctnb, Carm1, Rex1, Sox2 and Cdx2 were comparable between HNS and NS oocyte fragments. FS oocyte fragment possessed significantly higher transcripts of Gata4 compared to HNS. The distribution of certain transcripts related to pluripotency and lineage commitment were different depending upon the region of the oocyte; either enriched at S (Tead4, Nanog, Ctnb and Sox2), NS (Oct4), or FS (Gata6). The SEP in almost (90%) fertilized oocytes was located in MII-hemisphere. Conclusion The observation of spatial restriction of mRNAs and SEP within MII-oocyte may indicate that the principal forces of oocyte polarity are evolutionary conserved. This may in turn highlight the need for refinements in the methodology of intracytoplasmic sperm injection (where a sperm is injected far from the MII-spindle) and somatic cell nuclear transfer (where a major amount of regulative mRNAs that are associated with MIIspindle is removed during enucleation).
Stage-Based Mobile Intervention for Substance Use Disorders in Primary Care: Development and Test of Acceptability

Background In 2016, 21 million Americans aged 12 years and older needed treatment for a substance use disorder (SUD). However, only 10% to 11% of individuals requiring SUD treatment received it. Given their access to patients, primary care providers are in a unique position to perform universal Screening, Brief Intervention, and Referral to Treatment (SBIRT) to identify individuals at risk, fill gaps in services, and make referrals to specialty treatment when indicated. Major barriers to SBIRT include limited time among providers and low motivation to change among many patients. Objective The objective of this study was to develop and test the acceptability of a prototype of a mobile-delivered substance use risk intervention (SURI) for primary care patients and a clinical dashboard for providers that can address major barriers to SBIRT for risky drug use. The SURI delivers screening and feedback on SUD risk via mobile tools to patients at home or in the waiting room; for patients at risk, it also delivers a brief intervention based on the transtheoretical model of behavior change (TTM) to facilitate progress through the stages of change for quitting the most problematic drug and for seeking treatment if indicated. The prototype also delivers 30 days of stage-matched text messages and 4 Web-based activities addressing key topics. For providers, the clinical dashboard summarizes the patient’s SUD risk scores and stage of change data, and provides stage-matched scripts to guide in-person sessions. Methods A total of 4 providers from 2 federally qualified health centers (FQHCs) were recruited for the pilot test, and they in turn recruited 5 patients with a known SUD. Furthermore, 3 providers delivered dashboard-guided SBIRT sessions and completed a brief acceptability survey. A total of 4 patients completed a Web-based SURI session and in-person SBIRT session, accessed other program components, and completed 3 acceptability surveys over 30 days. Questions in the surveys were adapted from the National Cancer Institute’s Education Materials Review Form. Response options ranged from 1=strongly disagree to 5=strongly agree. The criterion for establishing acceptability was an overall rating of 4.0 or higher across items. Results For providers, the overall mean acceptability rating was 4.4 (standard deviation [SD] 0.4). Notably, all providers gave a rating of 5.0 for the item, “The program can give me helpful information about my patient. ” For patients, the overall mean acceptability rating was 4.5 (SD 0.3) for the mobile- and provider-delivered SBIRT sessions and 4.0 (SD 0.4) for the text messages and Web-based activities. One highly rated item was “The program could help me make some positive changes” (4.5). Conclusions The SURI program and clinical dashboard, developed to reduce barriers to SBIRT in primary care, were well received by providers and patients.
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo

Motivation In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced “Poisson Tree Processes” (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences. Results We introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently, yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size. Availability mPTP is implemented in C and is available for download at http://github.com/Pas-Kapli/mptp under the GNU Affero 3 license. A web-service is available at http://mptp.h-its.org. Contact Paschalia.Kapli@h-its.org, Alexandros.Stamatakis@hits.org, Tomas.Flouri@h-its.org
Solitary plasmacytoma of the mandible: report of two cases

Plasma cell neoplasms (plasmacytoma) are discrete, solitary masses of lymphoid neoplastic proliferations of B cells. Plasmacytomas comprise three groups: multiple myeloma, solitary plasmacytoma (SP) and extramedullary plasmacytoma. SP originates as a clone of transformed malignant plasma cells in the bone marrow. SP of the jaw is a rare condition; therefore diagnosis is quite difficult and often results in misdiagnosis. MM is a lymphoproliferative disease the prognosis of which is worse than SP. SP can progress to MM in a few months to years after diagnosis. In this regard, early diagnosis of the disease is of utmost importance. This article presents two cases of SP diagnosed in the mandible and documented with clinical, radiographic and histological findings.
Electromyographic evaluation of the effect of ultrasound with muscle stretching in temporomandibular disorder: a clinical trial

Aim: To investigate the electromyographic activity of masticatory muscles in women with myogenic or mixed TMD treated with ultrasound and ultrasound associated with stretching. Methods: Sixteen women with myogenic or mixed TMD, according to the Research Diagnostic Criteria for Temporomandibular Disorder (RDC/TMD), participated in the study. The patients were evaluated using surface electromyography (sEMG) of the masseter and anterior temporalis muscles, during maximum intercuspation, before and immediately after application of therapeutic resources. All patients were treated by ultrasound (US), ultrasound associated with stretching and placebo ultrasound, by turns, once a week with a one-week minimum interval between them. Results: There was greater symmetry of the masseter muscle electrical activity after ultrasound associated with stretching (p=0.03). The electromyographic values for the maximum intercuspation as well as the symmetry of anterior temporal muscle (p=0.47, p=0.84, p=0.84) and anteroposterior coefficient (p=0.07, p=0.84, p=0.57) showed no statistically significant difference after the intervention, placebo, ultrasound and ultrasound with stretching. Conclusions: These results indicate that a single application of ultrasound and ultrasound associated with stretching were not able to modify the activity pattern of the masticatory muscles during maximum intercuspation, except the symmetry of the masseter muscle that increased with the last, in women with myogenic or mixed temporomandibular disorder.
Development of a Three-dimensional Transient Wall Heat Transfer Model of a Rotating Detonation Combustor

Numerical simulation of transient heat transfer characteristics of a Rotating Detonation Combustor (RDC) is presented in this paper. A three-dimensional transient conduction model was developed to study the effect of large variation, periodic gas temperature exposed to the inner walls of the rotating detonation combustor outer body. The objective of the simulation is to predict heat flux transients and the interior wall surface temperatures from start up to 10s operation. The time varying, three-dimensional periodic convective boundary condition used for the heat transfer simulation is representative of the detonation wave propagation and other physical characteristics of RDC operating around 3000Hz and is derived from a separate computational fluid dynamics (CFD) simulation. The complex flow distribution downstream of the detonation/fill region results in a wall temperature and fluid dynamics that varies temporally and spatially in all directions. Simulation results were compared with experimental temperature data from literature on the outer body of an uncooled RDC. Combustor wall temperature variation in the axial direction indicates effect of non-uniformity on gas temperature distribution in the combustor for a non-premixed geometry. The simulation provides an estimate of transient heat load and hot spot locations that are critical to design efficient combustor cooling strategies.
Non-contact video-based vital sign monitoring using ambient light and auto-regressive models

Remote sensing of the reflectance photoplethysmogram using a video camera typically positioned 1 m away from the patient’s face is a promising method for monitoring the vital signs of patients without attaching any electrodes or sensors to them. Most of the papers in the literature on non-contact vital sign monitoring report results on human volunteers in controlled environments. We have been able to obtain estimates of heart rate and respiratory rate and preliminary results on changes in oxygen saturation from double-monitored patients undergoing haemodialysis in the Oxford Kidney Unit. To achieve this, we have devised a novel method of cancelling out aliased frequency components caused by artificial light flicker, using auto-regressive (AR) modelling and pole cancellation. Secondly, we have been able to construct accurate maps of the spatial distribution of heart rate and respiratory rate information from the coefficients of the AR model. In stable sections with minimal patient motion, the mean absolute error between the camera-derived estimate of heart rate and the reference value from a pulse oximeter is similar to the mean absolute error between two pulse oximeter measurements at different sites (finger and earlobe). The activities of daily living affect the respiratory rate, but the camera-derived estimates of this parameter are at least as accurate as those derived from a thoracic expansion sensor (chest belt). During a period of obstructive sleep apnoea, we tracked changes in oxygen saturation using the ratio of normalized reflectance changes in two colour channels (red and blue), but this required calibration against the reference data from a pulse oximeter.
Modeling the adenosine system as a modulator of cognitive performance and sleep patterns during sleep restriction and recovery

Sleep loss causes profound cognitive impairments and increases the concentrations of adenosine and adenosine A1 receptors in specific regions of the brain. Time courses for performance impairment and recovery differ between acute and chronic sleep loss, but the physiological basis for these time courses is unknown. Adenosine has been implicated in pathways that generate sleepiness and cognitive impairments, but existing mathematical models of sleep and cognitive performance do not explicitly include adenosine. Here, we developed a novel receptor-ligand model of the adenosine system to test the hypothesis that changes in both adenosine and A1 receptor concentrations can capture changes in cognitive performance during acute sleep deprivation (one prolonged wake episode), chronic sleep restriction (multiple nights with insufficient sleep), and subsequent recovery. Parameter values were estimated using biochemical data and reaction time performance on the psychomotor vigilance test (PVT). The model closely fit group-average PVT data during acute sleep deprivation, chronic sleep restriction, and recovery. We tested the model’s ability to reproduce timing and duration of sleep in a separate experiment where individuals were permitted to sleep for up to 14 hours per day for 28 days. The model accurately reproduced these data, and also correctly predicted the possible emergence of a split sleep pattern (two distinct sleep episodes) under these experimental conditions. Our findings provide a physiologically plausible explanation for observed changes in cognitive performance and sleep during sleep loss and recovery, as well as a new approach for predicting sleep and cognitive performance under planned schedules.
Accounting for Biomass Carbon Stock Change Due to Wildfire in Temperate Forest Landscapes in Australia

Carbon stock change due to forest management and disturbance must be accounted for in UNFCCC national inventory reports and for signatories to the Kyoto Protocol. Impacts of disturbance on greenhouse gas (GHG) inventories are important for many countries with large forest estates prone to wildfires. Our objective was to measure changes in carbon stocks due to short-term combustion and to simulate longer-term carbon stock dynamics resulting from redistribution among biomass components following wildfire. We studied the impacts of a wildfire in 2009 that burnt temperate forest of tall, wet eucalypts in south-eastern Australia. Biomass combusted ranged from 40 to 58 tC ha−1, which represented 6–7% and 9–14% in low- and high-severity fire, respectively, of the pre-fire total biomass carbon stock. Pre-fire total stock ranged from 400 to 1040 tC ha−1 depending on forest age and disturbance history. An estimated 3.9 TgC was emitted from the 2009 fire within the forest region, representing 8.5% of total biomass carbon stock across the landscape. Carbon losses from combustion were large over hours to days during the wildfire, but from an ecosystem dynamics perspective, the proportion of total carbon stock combusted was relatively small. Furthermore, more than half the stock losses from combustion were derived from biomass components with short lifetimes. Most biomass remained on-site, although redistributed from living to dead components. Decomposition of these components and new regeneration constituted the greatest changes in carbon stocks over ensuing decades. A critical issue for carbon accounting policy arises because the timeframes of ecological processes of carbon stock change are longer than the periods for reporting GHG inventories for national emissions reductions targets. Carbon accounts should be comprehensive of all stock changes, but reporting against targets should be based on human-induced changes in carbon stocks to incentivise mitigation activities.
Kestrel-Prey Dynamic in a Mediterranean Region: The Effect of Generalist Predation and Climatic Factors

Background Most hypotheses on population limitation of small mammals and their predators come from studies carried out in northern latitudes, mainly in boreal ecosystems. In such regions, many predators specialize on voles and predator-prey systems are simpler compared to southern ecosystems where predator communities are made up mostly of generalists and predator-prey systems are more complex. Determining food limitation in generalist predators is difficult due to their capacity to switch to alternative prey when the basic prey becomes scarce. Methodology We monitored the population density of a generalist raptor, the Eurasian kestrel Falco tinnunculus over 15 years in a mountainous Mediterranean area. In addition, we have recorded over 11 years the inter-annual variation in the abundance of two main prey species of kestrels, the common vole Microtus arvalis and the eyed lizard Lacerta lepida and a third species scarcely represented in kestrel diet, the great white-toothed shrew Crocidura russula. We estimated the per capita growth rate (PCGR) to analyse population dynamics of kestrel and predator species. Principal Findings Multimodel inference determined that the PCGR of kestrels was better explained by a model containing the population density of only one prey species (the common vole) than a model using a combination of the densities of the three prey species. The PCGR of voles was explained by kestrel abundance in combination with annual rainfall and mean annual temperature. In the case of shrews, growth rate was also affected by kestrel abundance and temperature. Finally, we did not find any correlation between kestrel and lizard abundances. Significance Our study showed for the first time vertebrate predator-prey relationships at southern latitudes and determined that only one prey species has the capacity to modulate population dynamics of generalist predators and reveals the importance of climatic factors in the dynamics of micromammal species and lizards in the Mediterranean region.
Regional robust stabilisation and domain-of-attraction estimation for MIMO uncertain nonlinear systems with input saturation

ABSTRACT The regional robust stabilisation by means of linear time-invariant state feedback control for a class of uncertain MIMO nonlinear systems with parametric uncertainties and control input saturation is investigated. The nonlinear systems are described in a differential algebraic representation and the regional stability is handled considering the largest ellipsoidal domain-of-attraction (DOA) inside a given polytopic region in the state space. A novel set of sufficient Linear Matrix Inequality (LMI) conditions with new auxiliary decision variables are developed aiming to design less conservative linear state feedback controllers with corresponding larger DOAs, by considering the polytopic description of the saturated inputs. A few examples are presented showing favourable comparisons with recently published similar control design methodologies.
Big Data Modeling and Analysis for Power Transmission Equipment: A Novel Random Matrix Theoretical Approach

This paper explores a novel idea for power equipment monitoring and finds that random matrix theory is suitable for modeling the massive data sets in this situation. Big data analytics are mined from those data. We extract the statistical correlation between key states and those parameters. In particular, the (empirical) eigenvalue spectrum distribution and the (theoretical) single ring law are derived from large-dimensional random matrices whose entries are modeled as time series. The radii of the single ring law are used as statistical analytics to characterize the measured data. The evaluation of key state and anomaly detection are accomplished through the comparison of those statistical analytics.
Rapid biosynthesis of silver nanoparticles using Crotalaria verrucosa leaves against the dengue vector Aedes aegypti: what happens around? An analysis of dragonfly predatory behaviour after exposure at ultra-low doses

Abstract Aedes aegypti is a primary vector of dengue, a mosquito-borne viral disease infecting 50–100 million people every year. Here, we biosynthesised mosquitocidal silver nanoparticles (AgNP) using the aqueous leaf extract of Crotalaria verrucosa. The green synthesis of AgNP was studied by UV–vis spectroscopy, SEM, EDX and FTIR. C. verrucosa-synthesised AgNPs were toxic against A. aegypti larvae and pupae. LC50 of AgNP ranged from 3.496 ppm (I instar larvae) to 17.700 ppm (pupae). Furthermore, we evaluated the predatory efficiency of dragonfly nymphs, Brachydiplax sobrina, against II and III instar larvae of A. aegypti in an aquatic environment contaminated with ultra-low doses of AgNP. Under standard laboratory conditions, predation after 24 h was 87.5% (II) and 54.7% (III). In an AgNP-contaminated environment, predation was 91 and 75.5%, respectively. Overall, C. verrucosa-synthesised AgNP could be employed at ultra-low doses to reduce larval population of dengue vectors enhancing predation rates of dragonfly nymphs. Graphical abstract
Indian Ocean sources of Agulhas leakage

We examine the mean pathways, transit timescales, and transformation of waters flowing from the Pacific and the marginal seas through the Indian Ocean (IO) on their way toward the South Atlantic within a high-resolution ocean/sea-ice model. The model fields are analyzed from a Lagrangian perspective where water volumes are tracked as they enter the IO. The IO contributes 12.6 Sv to Agulhas leakage, which within the model is 14.1 ± 2.2 Sv, the rest originates from the South Atlantic. The Indonesian Through-flow constitutes about half of the IO contribution, is surface bound, cools and salinificates as it leaves the basin within 10–30 years. Waters entering the IO south of Australia are at intermediate depths and maintain their temperature-salinity properties as they exit the basin within 15–35 years. Of these waters, the contribution from Tasman leakage is 1.4 Sv. The rest stem from recirculation from the frontal regions of the Southern Ocean. The marginal seas export 1.0 Sv into the Atlantic within 15–40 years, and the waters cool and freshen on-route. However, the model's simulation of waters from the Gulfs of Aden and Oman are too light and hence overly influenced by upper ocean circulations. In the Cape Basin, Agulhas leakage is well mixed. On-route, temperature-salinity transformations occur predominantly in the Arabian Sea and within the greater Agulhas Current region. Overall, the IO exports at least 7.9 Sv from the Pacific to the Atlantic, thereby quantifying the strength of the upper cell of the global conveyor belt.