Miracle-dz/UniFAR-FTUs huggingface dataset:
Ultracontractive Properties for Directed Graph Semigroups with Applications to Coupled Oscillators

Abstract It is now well known that ultracontractive properties of semigroups with infinitesimal generator given by an undirected graph Laplacian operator can be obtained through an understanding of the geometry of the underlying infinite weighted graph. The aim of this work is to extend these results to semigroups with infinitesimal generators given by a directed graph Laplacian operator through an analogous inspection of the geometry of the underlying directed graph. In particular, we introduce appropriate nomenclature to discuss the geometry of an infinite directed graph, as well as provide sufficient conditions to extend ultracontractive properties of undirected graph Laplacians to those of the directed variety. Such directed graph Laplacians can often be observed in the study of coupled oscillators, where recent work made explicit the link between synchronous patterns to systems of identically coupled oscillators and ultracontractive properties of undirected graph semigroups. Therefore, in this work we demonstrate the applicability of our results on directed graph semigroups by extending the aforementioned investigation beyond the idealized case of identically coupled oscillators.
A Quantum Field Approach for Advancing Optical Coherence Tomography Part I: First Order Correlations, Single Photon Interference, and Quantum Noise

Optical coherence tomography has become an important imaging technology in cardiology and ophthalmology, with other applications under investigations. Major advances in optical coherence tomography (OCT) imaging are likely to occur through a quantum field approach to the technology. In this paper, which is the first part in a series on the topic, the quantum basis of OCT first order correlations is expressed in terms of full field quantization. Specifically first order correlations are treated as the linear sum of single photon interferences along indistinguishable paths. Photons and the electromagnetic (EM) field are described in terms of quantum harmonic oscillators. While the author feels the study of quantum second order correlations will lead to greater paradigm shifts in the field, addressed in part II, advances from the study of quantum first order correlations are given. In particular, ranging errors are discussed (with remedies) from vacuum fluctuations through the detector port, photon counting errors, and position probability amplitude uncertainty. In addition, the principles of quantum field theory and first order correlations are needed for studying second order correlations in part II.
Expression of Indoleamine 2,3-Dioxygenase Induced by IFN-γ and TNF-α as Potential Biomarker of Prostate Cancer Progression

Inflammation has been suggested to play an important role in onset and progression of prostate cancer (PCa). Histological analysis of prostatectomy specimens has revealed focal inflammation in early stage lesions of this malignancy. We addressed the role of inflammatory stimuli in the release of PCa-specific, tumor-derived soluble factors (PCa-TDSFs) already reported to be mediators of PCa morbidity, such as indoleamine 2,3-dioxygenase (IDO) and interleukin (IL)-6. Inflammation-driven production and functions of PCa-TDFSs were tested “in vitro” by stimulating established cell lines (CA-HPV-10 and PC3) with IFN-γ or TNF-α. Expression of genes encoding IDO, IL-6, IFN-γ, TNF-α, and their receptors was investigated in tumor tissues of PCa patients undergoing radical prostatectomy, in comparison with benign prostatic hyperplasia (BPH) specimens. IFN-γ and TNF-α-treatment resulted in the induction of IDO and IL-6 gene expression and release in established cell lines, suggesting that the elicitation of PCa-TDSFs by these cytokines might contribute to progression of cancer into an untreatable phenotype. An analysis based on timing of biochemical recurrence revealed the prognostic value of IDO but not IL-6 gene expression in predicting recurrence-free survival in patients (RFS) with PCa. In addition, a urine-based mRNA biomarker study revealed the diagnostic potential of IDO gene expression in urines of men at risk of PCa development.
Submesoscale evolution of surface drifter triads in the Gulf of Mexico

Triangle shape metrics are analyzed to quantify the evolution of submesoscale (100–500 m initial separation) surface drifter triplets released in the northern Gulf of Mexico. The observations are compared to synthetic drifters advected by geostrophic velocity fields derived from satellite altimetry. Observed submesoscale triads evolve rapidly, reaching highly elongated configurations on timescales of 6 h to 2 days, in contrast to 6 days or longer for altimetry‐derived synthetic data. Estimates of horizontal divergence and strain rate from the drifter triplets indicate the relative importance of divergence in the evolution of triangle shape. Horizontal divergence is scale dependent, on the order of the local Coriolis parameter, and 2 to 3 times larger for initial 100 m scales compared to initial 500 m scales.
Resolving Event Coreference with Supervised Representation Learning and Clustering-Oriented Regularization

We present an approach to event coreference resolution by developing a general framework for clustering that uses supervised representation learning. We propose a neural network architecture with novel Clustering-Oriented Regularization (CORE) terms in the objective function. These terms encourage the model to create embeddings of event mentions that are amenable to clustering. We then use agglomerative clustering on these embeddings to build event coreference chains. For both within- and cross-document coreference on the ECB+ corpus, our model obtains better results than models that require significantly more pre-annotated information. This work provides insight and motivating results for a new general approach to solving coreference and clustering problems with representation learning.
Widespread yet heterogeneous genomic divergence

Genetic differentiation during adaptive divergence and speciation is heterogeneous among genomic regions. Some regions can be highly differentiated between populations, for example, because they harbour genes under divergent selection or those causing reproductive isolation and thus are resistant to gene flow. Other regions might be homogenized by gene flow and thus weakly differentiated. Debates persist about the number of differentiated regions expected under divergence with gene flow, and their causes, size, and genomic distribution. In this issue of Molecular Ecology, a study of freshwater stickleback used next‐generation sequencing to shed novel insight into these issues (Roesti et al. 2012). Many genomic regions distributed across the genome were strongly differentiated, indicating divergence with gene flow can involve a greater number of loci than often thought. Nonetheless, differentiation of some regions, such as those near the centre of chromosomes where recombination is reduced, was strongly accentuated over others. Thus, divergence was widespread yet highly heterogeneous across the genome. Moreover, different population pairs varied in patterns of differentiation, illustrating how genomic divergence builds up across stages of the speciation process. The study demonstrates how variation in different evolutionary processes, such as selection and recombination rate, can combine to result in similar genomic patterns. Future work could focus on teasing apart the contributions of different processes for causing differentiation, a task facilitated by experimental manipulations.
Investigation of co-infections with pathogens associated with gill disease in Atlantic salmon during an amoebic gill disease outbreak.

Gill diseases are a complex and multifactorial challenge for marine farmed Atlantic salmon. Co-infections with putative pathogens are common on farms; however, there is a lack of knowledge in relation to the potential effect co-infections may have on pathology. The objective of this study was to determine the prevalence and potential effects of Neoparamoeba perurans, Desmozoon lepeophtherii, Candidatus Branchiomonas cysticola, Tenacibaculum maritimum and salmon gill poxvirus (SGPV) during a longitudinal study on a marine Atlantic salmon farm. Real-time PCR was used to determine the presence and sequential infection patterns of these pathogens on gill samples collected from stocking until harvest. A number of multilevel models were used to determine the effect of these putative pathogens on gill health (measured as gill histopathology score), while adjusting for the effect of water temperature and time since the last freshwater treatment. Results indicate that between 12 and 16 weeks post-seawater transfer (wpst), colonization of the gills by all pathogens had commenced and by week 16 of marine production each of the pathogens had been detected. D. lepeophtherii and Candidatus B. cysticola were by far the most prevalent of the potential pathogens detected during this study. Detections of T. maritimum were found to be significantly correlated with temperature showing distinct seasonality. Salmon gill poxvirus was found to be highly sporadic and detected in the first sampling point, suggesting a carryover from the freshwater stage of production. Finally, the model results indicated no clear effect between any of the pathogens. Additionally, the models showed that the only variable which had a consistent effect on the histology score was N. perurans.
A Review of Mutual Coupling in MIMO Systems

This paper provides a systematic review of the mutual coupling in multiple-input multiple-output (MIMO) systems, including the effects on performances of MIMO systems and various decoupling techniques. The mutual coupling changes the antenna characteristics in an array, and therefore, degrades the system performance of the MIMO system and causes the spectral regrowth. Although the system performance can be partially improved by calibrating out the mutual coupling in the digital domain, it is more effective to use decoupling techniques (from the antenna point) to overcome the mutual coupling effects. Some popular decoupling techniques for MIMO systems (especially for massive MIMO base station antennas) are also presented.
Out with the old, in with the new: how changes in cricket helmet regulations affect the vision of batters

ABSTRACT The International Cricket Council recently introduced new regulations for helmets in cricket. Amongst other changes, these regulations limit batters from adjusting the gap between the peak and the grille, resulting in some controversy over whether the new helmet design reduces visibility of the ball. This study compared the visual field of individuals when wearing an old helmet that does not conform to the new regulations, and the equivalent replacement which does. The visual field of 10 male participants was tested whilst wearing an old and new helmet. The new helmet resulted in a significant reduction in the visual field of the wearer (M = 66.1 out of 76 points seen in the new helmet vs. 74.8 seen with the old helmet), with the restriction predominantly confined to the superior visual field. The new regulations do appear to restrict the visual field of batters, confirming the anecdotal reports of players. However, the majority of this restriction occurs in the superior field, suggesting that the impact on batting performance may be limited. The importance of considering the impact that new helmet regulations can have on vision, batting performance, and player safety is discussed.
Microbial micropatches within microbial hotspots

The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have ‘hotspots’ of high abundance, and ‘coldspots’ of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur.
A randomized controlled trial on the effect of a silver carboxymethylcellulose dressing on surgical site infections after breast cancer surgery

Background The incidence of surgical site infections (SSIs) after breast cancer surgery is relatively high; ranging from 3 to 19%. The role of wound dressings in the prevention of SSI after breast cancer surgery is unclear. This study compares a silver carboxymethylcellulose dressing (AQUACEL Ag Surgical (Aquacel) with standard wound dressing in SSI rate after breast cancer surgery. Patients and methods A single-centre randomized controlled trial among women ≥18 years, diagnosed with breast cancer, undergoing breast conserving or ablative surgery, was conducted in a combined in and outpatient setting. The intervention was the use of Aquacel, compared with standard gauze dressing. Primary outcome measure was SSI following CDC criteria. Results A total of 230 patients were analysed: 106 in the Aquacel group and 124 controls. Seven patients (6.6%) developed SSI in the Aquacel group and 16 patients (12.9%) in the control group (RR 0.51 [95% Confidence Interval (CI): 0.22–1.20]; p = 0.112; adjusted OR 0.49 [0.19–1.25] p = 0.135)). Unplanned exploratory subgroup analysis of breast conserving surgery patients showed that SSI rate was 1/56 (1.8%) in the Aquacel group vs. 7/65 (10.8%) in controls; adjusted OR 0.15 [0.02–1.31] p = 0.087. The Aquacel group showed better patient satisfaction (median 8 vs. 7 on a Numerical Rating Scale, p = 0.006), fewer dressing changes within 48 hours(adjusted OR 0.12 [0.05–0.27] p<0.001), fewer re-operations (0% vs. 3.2%, p = 0.062), and lower mean wound-related treatment costs, both in a high (€265.42 (SD = 908) vs. €470.65 (SD = 1223) [p<0.001]) and low (€59.12 (SD = 129) vs. €67.55 (SD = 172) [p<0.001]) attributable costs of SSI model. Conclusion In this randomized controlled trial in women undergoing surgery for breast cancer, the use of AQUACEL Ag Surgical wound dressing did not significantly reduce the occurrence of SSIs compared to standard gauze dressing. The use of Aquacel resulted in significantly improved patient satisfaction, reduced dressing changes and reduced wound-related costs. Trial registration www.trialregister. nl: NTR5840
Binary Huygens’ Metasurfaces: Experimental Demonstration of Simple and Efficient Near-Grazing Retroreflectors for TE and TM Polarizations

This paper investigates the retroreflective properties of a type of periodic metasurface, which is aggressively discretized to include only two cells per grating period. The resultant metasurface, which we term the binary Huygens’ metasurface, dramatically simplifies the design toward highly efficient, low cost, and robust metasurface retroreflectors. Using this discretization method, we designed, simulated, and measured two binary Huygens’ metasurfaces that retroreflect an incident plane wave at 82.87° from broadside, for TE and TM polarized waves, respectively. The simulated results for a 2-D infinite structure show power efficiencies of 94% (TE) and 99% (TM). The measured results show a power efficiency of 93% for both TE and TM polarizations. This shows that it is possible to obtain a high retroreflection power efficiency at an angle of choice using a very simple (slot or patch) metasurface design. The proposed design methodology allows one to achieve not only retroreflection but also reflection to arbitrary angles, with very high efficiency, which diversifies its uses.
Data-driven Development of ROTEM and TEG Algorithms for the Management of Trauma Hemorrhage: A Prospective Observational Multicenter Study.

OBJECTIVE Developing pragmatic data-driven algorithms for management of trauma induced coagulopathy (TIC) during trauma hemorrhage for viscoelastic hemostatic assays (VHAs). BACKGROUND Admission data from conventional coagulation tests (CCT), rotational thrombelastometry (ROTEM) and thrombelastography (TEG) were collected prospectively at 6 European trauma centers during 2008 to 2013. METHODS To identify significant VHA parameters capable of detecting TIC (defined as INR > 1.2), hypofibrinogenemia (< 2.0 g/L), and thrombocytopenia (< 100 x10/L), univariate regression models were constructed. Area under the curve (AUC) was calculated, and threshold values for TEG and ROTEM parameters with 70% sensitivity were included in the algorithms. RESULTS A total of, 2287 adult trauma patients (ROTEM: 2019 and TEG: 968) were enrolled. FIBTEM clot amplitude at 5 minutes (CA5) had the largest AUC and 10 mm detected hypofibrinogenemia with 70% sensitivity. The corresponding value for functional fibrinogen (FF) TEG maximum amplitude (MA) was 19 mm. Thrombocytopenia was similarly detected using the calculated threshold EXTEM-FIBTEM CA5 30 mm. The corresponding rTEG-FF TEG MA was 46 mm. TIC was identified by EXTEM CA5 41 mm, rTEG MA 64 mm (80% sensitivity). For hyperfibrinolysis, we examined the relationship between viscoelastic lysis parameters and clinical outcomes, with resulting threshold values of 85% for EXTEM Li30 and 10% for rTEG Ly30.Based on these analyses, we constructed algorithms for ROTEM, TEG, and CCTs to be used in addition to ratio driven transfusion and tranexamic acid. CONCLUSIONS We describe a systematic approach to define threshold parameters for ROTEM and TEG. These parameters were incorporated into algorithms to support data-driven adjustments of resuscitation with therapeutics, to optimize damage control resuscitation practice in trauma.
Association between Sleep-Disordered Breathing during Pregnancy and Maternal and Fetal Outcomes: An Updated Systematic Review and Meta-Analysis

Background Due to the high prevalence in pregnant women and potential association with pregnancy complications or perinatal outcomes, sleep-disordered breathing (SDB) has become an increasing concern. Methods Pubmed and Embase were retrieved from inception until 2017 to conduct a meta-analysis to explore the association of SDB and several outcomes during gestation. A stratified analysis differentiated by the type of SDB [snoring alone/obstructive sleep apnea (OSA)] was also performed. Pooled odds ratios were produced for binary outcomes. Weighted mean differences were also produced for continuous outcomes. Sensitivity analysis was performed to identify the impact of individual studies on summary results and estimation of publication bias was performed by funnel plot. Results 35 studies with a total of 56,751,837 subjects were included. SDB during pregnancy was associated with a significantly increased risk of gestational diabetes mellitus (GDM), pregnancy-induced hypertension (PIH), and preeclampsia (PEC), but not significantly associated with fetal maternal outcomes, namely APGAR score and birth weight. Moreover, OSA was linked with an increasing risk of GDM, PIH, PEC and preterm birth while snoring appeared to increase the risk of GDM, PIH, and PEC. Conclusion The finding provided potential evidence for association between SDB and adverse perinatal outcomes. SDB increased the risk of some pregnancy complications while its influence to fetal outcomes was not clear.
Evaluating local features in high-resolution 3D-PLI data

Even though imaging techniques enhance some local features in histological brain sections, it is often difficult to detect these features. In this paper, we introduce a robust feature detection method for accurate registration of multi-resolution 3D polarized light imaging data of brain sections. Our approach is based on the structure tensor and a scale-space scheme that reduces ambiguity and preserves scale-invariant features. We applied our approach to data from tissue sections of human and rat brain. Quantitative evaluations are performed and compared with state-of-the-art methods.
The Protective Effects of Glycyrrhetinic Acid and Chrysin against Ischemia-Reperfusion Injury in Rat Ovaries

Objective To evaluate the protective effects of glycyrrhetinic acid (GA) and chrysin (CH) on experimental ischemia-reperfusion (I/R) injury in rat ovaries using tissue oxidative stress marker levels, hormone levels, and histopathological scores. Methods Sixty healthy rats were randomly divided into six equal groups: control, I/R, I/R + CH (50 mg/kg/day), I/R + GA (100 mg/kg/day), CH (50 mg/kg/day), and GA (100 mg/kg/day). Biochemical, hormonal, and histopathological evaluations were performed on blood and tissue samples 14 days after CH and GA treatment. Results The antioxidant defense system parameters were significantly higher in the ovarian tissues of the I/R + CH and I/R + GA groups than in those of the I/R group. Serum follicle-stimulating hormone levels were significantly reduced, and serum anti-Müllerian hormone levels were significantly increased in rats treated with CH and GA compared with those in the I/R group. Additionally, the histopathological scores of the I/R + CH and I/R + GA groups were significantly improved compared with those of the I/R group. Conclusions The significant improvements in tissue oxidative stress parameters, serum hormone levels, and histological scores observed in this study indicate that treatment with CH or GA may be a conservative approach to prevent I/R injury in adnexal torsion cases after the ovarian detorsion procedure.
Querying Word Embeddings for Similarity and Relatedness

Word embeddings obtained from neural network models such as Word2Vec Skipgram have become popular representations of word meaning and have been evaluated on a variety of word similarity and relatedness norming data. Skipgram generates a set of word and context embeddings, the latter typically discarded after training. We demonstrate the usefulness of context embeddings in predicting asymmetric association between words from a recently published dataset of production norms (Jouravlev & McRae, 2016). Our findings suggest that humans respond with words closer to the cue within the context embedding space (rather than the word embedding space), when asked to generate thematically related words.
Bayesian Pose Graph Optimization via Bingham Distributions and Tempered Geodesic MCMC

We introduce Tempered Geodesic Markov Chain Monte Carlo (TG-MCMC) algorithm for initializing pose graph optimization problems, arising in various scenarios such as SFM (structure from motion) or SLAM (simultaneous localization and mapping). TG-MCMC is first of its kind as it unites asymptotically global non-convex optimization on the spherical manifold of quaternions with posterior sampling, in order to provide both reliable initial poses and uncertainty estimates that are informative about the quality of individual solutions. We devise rigorous theoretical convergence guarantees for our method and extensively evaluate it on synthetic and real benchmark datasets. Besides its elegance in formulation and theory, we show that our method is robust to missing data, noise and the estimated uncertainties capture intuitive properties of the data.