Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel ARMS-based assay for the quantification of EGFR mutations in patients with lung adenocarcinoma

Quantification of epidermal growth factor receptor (EGFR) mutations is important for the prediction of tyrosine kinase inhibitor (TKI) efficacy in patients with non-small cell lung cancer (NSCLC). However, clinicians lack a sensitive and convenient method to quantify EGFR mutant abundance. The present study introduces a novel method, namely amplification refractory mutation system (ARMS)-Plus, for the quantitative analysis of EGFR exon 19 deletion (19Del), L858R and T790M mutations. Formalin-fixed paraffin-embedded tumor samples were collected from 77 patients with lung adenocarcinoma. DNA was extracted and analyzed for EGFR mutations using ARMS-Plus. The performance of ARMS-Plus was then compared with that of conventional ARMS-polymerase chain reaction (ARMS-PCR) and droplet digital PCR (ddPCR). The results demonstrated that the concordance rate of EGFR mutation testing between ARMS-Plus and ddPCR was 98.7% (76/77, Kappa=0.9739). 19Del and L858R mutations were detected in 23 and 12 patients, respectively. There was a significant difference between ARMS-Plus and ddPCR in the evaluation of 19Del mutant abundance (P=0.0002); however, not in that of L858R mutant abundance (P=0.7334). The ARMS-Plus results in L858R mutant abundance were concordant with that of ddPCR (R2=0.8081). These results indicated that the sensitivity and specificity of ARMS-Plus in identifying EGFR mutations were similar to that of ddPCR. For quantitative analysis, the results of ARMS-Plus in evaluating L858R mutant abundance revealed a positive correlation with the ddPCR results. Thus, ARMS-Plus provides an alternative method, which is reliable and cost-effective, to quantify EGFR mutations and thereby, aid treatment decisions in patients with lung adenocarcinoma.
Detection of saliency map as image feature outliers using random projections based method

We describe a novel method based on Random Projections for construction of image saliency maps. The method identifies outliers in the 2D projections of image point features as salient image points using Random Projections and kernel density estimation. We compare the method with other known methods in the area and validated on a number of benchmark images. The robustness of the method when Gaussian blurring is applied to an image is demonstrated and evaluated using F-statistics of several image quality metrics. Application of the proposed method for image processing is discussed.
Antibacterial activity of male and female sperm-storage organs in ants

ABSTRACT Bacteria can damage sperm and thus reduce the reproductive success of both males and females; selection should therefore favour the evolution of antimicrobial protection. Eusocial hymenopterans might be particularly affected by such bacterial infections because of their mating ecology. In both sexes, mating is restricted to a short window early in the adult stage; there are no further chances to mate later in life. Males die shortly after mating, but queens use the acquired sperm to fertilise their eggs for years, sometimes decades. The reproductive success of both sexes is, thus, ultimately sperm-limited, which maintains strong selection for high sperm viability before and after storage. We tested the antibacterial activity of the contents of the male and female sperm-storage organs – the accessory testes and the spermatheca, respectively. As our study species, we used the bacterium Escherichia coli and the garden ant Lasius niger, whose queens can live for several decades. Our results provide the first empirical evidence that male and female sperm-storage organs display different antibacterial activity. While the contents of the accessory testes actually enhanced bacterial growth, the contents of the spermatheca strongly inhibited it. Furthermore, mating appears to activate the general immune system in queens. However, antimicrobial activity in both the spermatheca and the control tissue (head–thorax homogenate) declined rapidly post-mating, consistent with a trade-off between immunity and reproduction. Overall, this study suggests that ejaculates undergo an immune ‘flush’ at the time of mating, allowing storage of sperm cells free of bacteria. Highlighted Article: Male and female sperm-storage organs display different antibacterial activity in ants. This activity varies over time in females after mating, allowing long-term storage of sperm cells free of bacteria.
Coherent destruction of tunneling in graphene irradiated by elliptically polarized lasers

Photo-induced transition probabilities in graphene are studied theoretically from the viewpoint of Floquet theory. Conduction band populations are computed for a strongly, periodically driven graphene sheet under linear, circular, and elliptic polarization. Features of the momentum spectrum of excited quasi-particles can be directly related to the avoided crossing of the Floquet quasi-energy levels. In particular, the impact of the ellipticity and the strength of the laser excitation on the avoided crossing structure—and on the resulting transition probabilities—is studied. It is shown that the ellipticity provides an additional control parameter over the phenomenon of coherent destruction of tunneling in graphene, allowing one to selectively suppress multiphoton resonances.
Universality of some models of random matrices and random processes

Many limit theorems in probability theory are universal in the sense that the limiting distribution of a sequence of random variables does not depend on the particular distribution of these random variables. This universality phenomenon motivates many theorems and conjectures in probability theory. For example the limiting distribution in the central limit theorem for the suitably normalized sums of independent random variables which satisfy some moment conditions are independent of the distribution of the summands. In this thesis we establish universality-type results for two classes of random objects: random matrices and stochastic processes. In the first part of the thesis we study ensembles of random matrices with dependent elements. We consider ensembles of random matrices Xn with independent vectors of entries (Xij , Xji)i 6=j . Under the assumption that max(EX4 12,EX 21) <∞ it is proved that the empirical spectral distribution of eigenvalues converges in probability to the uniform distribution on an ellipse. The axes of the ellipse are determined by the correlation between X12 and X21. This result is called Elliptic Law. Here the limit distribution is universal, that is it doesn’t depend on the distribution of the matrix elements. These ensembles generalize ensembles of symmetric random matrices and ensembles of random matrices with independent entries. We also generalize ensembles of random symmetric matrices and consider symmetric matrices Xn = {Xij}i,j=1 with a random field type dependence, such that EXij = 0, EX2 ij = σ2 ij , where σij may be different numbers. Assuming that the average of the normalized sums of variances in each row converges to one and Lindeberg condition holds true we prove that the empirical spectral distribution of eigenvalues converges to Wigner’s semicircle law. In the second part of the thesis we study some classes of stochastic processes. For martingales with continuous parameter we provide very general sufficient conditions for the strong law of large numbers and prove analogs of the Kolmogorov and Brunk–Prokhrov strong laws of large numbers. For random processes with independent homogeneous increments we prove analogs of the Kolmogorov and Zygmund– Marcinkiewicz strong laws of large numbers. A new generalization of the Brunk– Prokhorov strong law of large numbers is given for martingales with discrete times. Along with the almost surely convergence, we also prove the convergence in average.
Locality and context-aware top-down saliency

In this study, the authors propose a novel framework for top-down (TD) saliency detection, which is well suited to locate category-specific objects in natural images. Saliency value is defined as the probability of a target based on its visual feature. They introduce an effective coding strategy called locality constrained contextual coding (LCCC) that enforces locality and contextual constraints. Furthermore, a contextual pooling operation is presented to take advantages of feature contextual information. Benefiting from LCCC and contextual pooling, the obtained feature representation has high discriminative power, which makes the authors' saliency detection method achieving competitive results with existing saliency detection algorithms. They also include bottom-up cues into their framework to supplement the proposed TD saliency algorithm. Experimental results on three datasets (Graz-02, Weizmann Horse and PASCAL VOC 2007) show that the proposed framework outperforms state-of-the-art methods in terms of visual quality and accuracy.
Linear Polarization Properties of Parsec-Scale AGN Jets

We used 15 GHz multi-epoch Very Long Baseline Array (VLBA) polarization sensitive observations of 484 sources within a time interval 1996–2016 from the MOJAVE program, and also from the NRAO data archive. We have analyzed the linear polarization characteristics of the compact core features and regions downstream, and their changes along and across the parsec-scale active galactic nuclei (AGN) jets. We detected a significant increase of fractional polarization with distance from the radio core along the jet as well as towards the jet edges. Compared to quasars, BL Lacs have a higher degree of polarization and exhibit more stable electric vector position angles (EVPAs) in their core features and a better alignment of the EVPAs with the local jet direction. The latter is accompanied by a higher degree of linear polarization, suggesting that compact bright jet features might be strong transverse shocks, which enhance magnetic field regularity by compression.
Differences in genetic structure assessed using Y‐chromosome and mitochondrial DNA markers do not shape the contributions to diversity in African sires

Up to 173 African sires belonging to 11 different subpopulations representative of four cattle groups were analysed for six Y-specific microsatellite loci and a mitochondrial DNA fragment. Differences in Y-chromosome and mtDNA haplotype structuring were assessed. In addition, the effect of such structuring on contributions to total genetic diversity was assessed. Thirty-five Y-chromosome and 71 mtDNA haplotypes were identified. Most Y-chromosomes analysed (73.4%) were of zebu origin (11 haplotypes). Twenty-two Y-haplotypes (44 samples) belonged to the African taurine subfamily Y2a. All mtDNA haplotypes belonged to the "African" taurine T1 haplogroup with 16 samples and nine haplotypes belonging to a recently identified subhaplogroup (T1e). Median-joining networks showed that Y-chromosome phylogenies were highly reticulated with clear separation between zebu and taurine clusters. Mitochondrial haplotypes showed a clear star-like shape with small number of mutations separating haplotypes. Mitochondrial-based FST -statistics computed between cattle groups tended to be statistically non-significant (p > .05). Most FST values computed among groups and subpopulations using Y-chromosome markers were statistically significant. AMOVA confirmed that divergence between cattle groups was only significant for Y-chromosome markers (ΦCT = 0.209). At the mitochondrial level, African sires resembled an undifferentiated population with individuals explaining 94.3% of the total variance. Whatever the markers considered, the highest contributions to total Nei's gene diversity and allelic richness were found in West African cattle. Genetic structuring had no effect on patterns of contributions to diversity.
Syllabic Rate and Utterance Length in French

Abstract This third article in a series presenting the results of a computer-assisted analysis of a vast data file, based on recordings of upper middle-class Parisian conversations, deals with syllabic rate and utterance length. Performance standards are established for teaching, linguistic theory and voice-processing technology. Variations in these aspects of speech are studied as functions of a number of demographic, psychological, intellectual and phonetic background parameters. Syllabic rate is found to vary as a function of sex, age, occupation and certain intentions, while utterance length varies as a function of age, occupation, certain intentions, certain attitudes and loudness. Overall rate averages turn out to be strikingly consistent, most speakers showing about 344 syll/min. Finally, a positive correlation exists between utterance length and syllabic rate; the longer the utterance, the faster the rate and vice versa. A hypothesis is suggested that these results reflect language universals.
Pythagorean fuzzy Bonferroni mean aggregation operator and its accelerative calculating algorithm with the multithreading

In this paper, we study the well‐known Bonferroni mean and develop its generalized aggregation operators in the Pythagorean fuzzy environment. More specifically, by considering the interrelationship between arguments with Pythagorean fuzzy information, we develop the Pythagorean fuzzy Bonferroni mean (PFBM) and some special properties and cases of them are also discussed. Furthermore, taking the multicriteria decision making environment into consideration, we extend the results of PFBM and develop the weighted Pythagorean fuzzy Bonferroni mean (WPFBM). Meanwhile, we also propose an approach for the application of WPFBM. However, during the application of the WPFBM operator, the calculation is very complex and time consuming. Hence, we introduce the multithreading into the application of the WPFBM operator and develop an accelerative calculating algorithm for it. To validate the performance of the accelerative calculating algorithm, we further design the corresponding experimental analysis.
Bonding strength of universal adhesives to Er,Cr:YSGG Laser-Irradiated Dentin

Objectives: Universal adhesives have been recently introduced for use as self-etch or etch-and-rinse adhesives depending on the dental substrate and clinical condition. However, their bonding effectiveness to laser-irradiated dentin is still not well known. Therefore, the aim of this study was to compare the shear bond strength (SBS) of two universal adhesives (Single Bond Universal, Nova Compo-B Plus) applied following laser-etching with SBS of the same adhesives applied in self-etch and acid-etch modes, respectively. Materials and Methods: Sixty bovine incisors were used to obtain the flattened dentin surfaces. Specimens were divided into two groups according to universal adhesives. Each universal adhesive was applied with one of the following modes, self-etch, acid-etch, or laser-etch (n = 10). Er,Cr:YSGG laser was used for laser-etching with 1.5 W–20 Hz parameters. After adhesive applications and composite buildups, SBS was determined after storage in water for 24 h using a universal testing machine with a crosshead speed of 0.5 mm/min. Failure modes were evaluated using a stereomicroscope. Data were analyzed using two-way of analyses of variances (ANOVA) (P = 0.05). Results: Two-way ANOVA revealed that adhesive had no effect on SBS (P > 0.05), but application mode significantly influenced SBS (P < 0.001). Laser-etch significantly increased SBS for NCP when compared to self-etch mode, whereas laser-etch provided similar SBS with self-etch mode for SBU. Conclusions: The influence of different application modes on dentin bond strength of universal adhesives was dependent on the adhesive material. Clinical Significance: For universal adhesives, laser etching may provide some benefits on bonds strength but this would depend on product.
Mood effects on attentional control: a preregistered replication study and critical analysis

ABSTRACT In a widely cited paper, Jefferies et al. (2008) report a study in which they manipulated participants’ mood and examined the effects of this manipulation on their performance on the Attentional Blink task. Their results revealed an interaction between emotional valence and arousal: attentional control of participants who experienced a negative mood with low arousal (i.e. sadness) was best, whereas it was worst for participants who experienced a negative mood with high arousal (i.e. anxiety). Performance for participants who were in a positive mood, either with low arousal (i.e. calmness) or high arousal (i.e. happiness) had intermediate scores. In this study, I examined the replicability of this effect and performed additional analyses to investigate the extent to which this effect is due to perceptual or attentional processes and to examine the role of distraction on AB performance. Importantly, the results showed that the crucial interaction between emotional valence and arousal did not reach significance. This could be due a diversity of factors that are addressed in the discussion.
Addressing barriers to vaccine acceptance: an overview

ABSTRACT Addressing the drivers of vaccine hesitancy and the barriers to vaccine acceptance is a complex but important task. While the percentage of hesitant does vary from country to country and in time few, if any, countries are ever free from this problem. Overcoming hesitancy requires detection, diagnosis and tailored intervention as there is no simple strategy that can address all of the barriers to vaccine acceptance. Immunization program managers and health care workers need to become adept at recognizing and tackling hesitancy in all of its incarnations if high levels of vaccine acceptance are to be achieved but must also actively support immunization acceptors in order to build and support vaccine acceptance resiliency. This paper presents evidence-informed strategies to achieve these goals.
Do‐Not‐Attempt‐Resuscitation orders for people with intellectual disabilities: dilemmas and uncertainties for ID physicians and trainees. The importance of the deliberation process

BACKGROUND Not much is known about Do-Not-Attempt-Resuscitation (DNAR) decision-making for people with intellectual disabilities (IDs). The aim of this study was to clarify the problems and pitfalls of non-emergency DNAR decision-making for people with IDs, from the perspective of ID physicians. METHODS This qualitative study was based on semi-structured individual interviews, focus group interviews and an expert meeting, all recorded digitally and transcribed verbatim. Forty ID physicians and trainees were interviewed about problems, pitfalls and dilemmas of DNAR decision-making for people with IDs in the Netherlands. Data were analysed using Grounded Theory procedures. RESULTS The core category identified was 'Patient-related considerations when issuing DNAR orders'. Within this category, medical considerations were the main contributory factor for the ID physicians. Evaluation of quality of life was left to the relatives and was sometimes a cause of conflicts between physicians and relatives. The category of 'The decision-maker role' was as important as that of 'The decision procedure in an organisational context'. The procedure of issuing a non-emergency DNAR order and the embedding of this procedure in the health care organisation were important for the ID physicians. CONCLUSION The theory we developed clarifies that DNAR decision-making for people with IDs is complex and causes uncertainties. This theory offers a sound basis for training courses for physicians to deal with uncertainties regarding DNAR decision-making, as well as a method for advance care planning. Health care organisations are strongly advised to implement a procedure regarding DNAR decision-making.
Peripheral Hypoechoic Lesions of the Prostate: Evaluation with Color and Power Doppler Ultrasound

Objective: To assess the usefulness of color and power Doppler ultrasound in predicting the benignity and malignancy of the peripheral hypoechoic lesion of the prostate.Methods: Thirty–nine patients who had peripheral hypoechoic lesions on transrectal ultrasound were evaluated with color and power Doppler ultrasound followed by lesion–specific transrectal ultrasound–guided biopsies. The interpretation of color and power Doppler ultrasound was not performed separately and flow signals were categorized using a combination of the two modalities. The amount of flow signals within the lesion was evaluated and categorized into three groups: increased/equal/decreased flow compared to surrounding normal tissue on ultrasound. Doppler spectra could be obtained from the lesions in 23 patients. The amount of flow signals and resistive indexes of the spectra of the lesions were compared with those of surrounding normal tissue using the Mann–Whithney U test.Results: Transrectal ultrasound–guided biopsy of the hypoechoic lesions revealed prostate cancer in 20 patients and benign prostatic diseases in 19. Flow signals within the lesions were of increasded/equal/decreased flow compared to surrounding normal tissue in 16/2/2 in the prostate cancer group and 3/9/7 in the benign disease group, respectively. The difference was statistically significant (p = 0.0003). Resistive indexes of the lesion were 0.58–1.0 (mean 0.75) in the prostate cancer group and 0.57–1.0 (mean 0.80) in the benign disease group, and there was no significant difference between the two groups (p = 0.82). If we consider an increased flow signal within a peripheral hypoechoic lesion as a sign of prostate cancer, color power Doppler ultrasound has a sensitivity of 80%, a specificity of 84%, and an accuracy of 82%. Conclusion: Evaluation of peripheral hypoechoic lesions of the prostate with color and power Doppler may enhance the diagnostic capability of transrectal ultrasound.
Peritransplant Energy Changes and Their Correlation to Outcome After Human Liver Transplantation

Background The ongoing shortage of donor livers for transplantation and the increased use of marginal livers necessitate the development of accurate pretransplant tests of viability. Considering the importance energy status during transplantation, we aimed to correlate peritransplant energy cofactors to posttransplant outcome and subsequently model this in an ex vivo setting. Methods Sequential biopsies were taken from 19 donor livers postpreservation, as well as 30 minutes after portal venous reperfusion and hepatic arterial reperfusion and analyzed by liquid chromatography-mass spectrometry for energetic cofactors (adenosine triphosphate [ATP]/adenosine diphosphate [ADP]/adenosine monophosphate [AMP], nicotinamide adenine dinucleotide /NAD+, nicotinamide adenine dinucleotide phosphate / nicotinamide adenine dinucleotide phosphate +, flavin adenine dinucleotide +, glutathione disulfide/glutathione). Energy status was correlated to posttransplant outcome. In addition, 4 discarded human donation after circulatory death livers were subjected to ex vivo reperfusion, modeling reperfusion injury and were similarly analyzed for energetic cofactors. Results A rapid shift toward higher energy adenine nucleotides was observed following clinical reperfusion, with a 2.45-, 3.17- and 2.12-fold increase in ATP:ADP, ATP:AMP and energy charge after portal venous reperfusion, respectively. Seven of the 19 grafts developed early allograft dysfunction. Correlation with peritransplant cofactors revealed a significant difference in EC between early allograft dysfunction and normal functioning grafts (0.09 vs 0.31, P < 0.05). In the simulated reperfusion model, a similar trend in adenine nucleotide changes was observed. Conclusions A preserved energy status appears critical in the peritransplant period. Levels of adenine nucleotides change rapidly after reperfusion and ratios of ATP/ADP/AMP after reperfusion are significantly correlated to graft function. Using these markers as a viability test in combination with ex vivo reperfusion may provide a useful predictor of outcome that incorporates donor, preservation, and reperfusion factors.