Miracle-dz/UniFAR-FTUs huggingface dataset:
Waveguiding in Photonic Crystals: An Envelope Approximation Using Multiple Scales Analysis

Inspired by the envelope approximation commonly applied to semiconductor heterostructures, an analytical approach to study photonic crystal waveguides is presented. By treating the waveguide core as a slowly-varying perturbation in the cladding photonic crystal, multiple scales analysis is used to derive an envelope equation which solves for the propagation constants and frequencies of the guided modes. The envelope approximation is completely general for sufficiently weak perturbations and applies to photonic crystal waveguides of any dimensionality. The multiple scales approach is verified through comparisons between the envelope approximation and results from full numerical simulations. Heterostructure slab waveguides in three dimensional photonic crystal and a slab waveguide with a homogeneous dielectric core surrounded by photonic crystal cladding are studied. The mode shapes are in excellent agreement with simulations. The computed waveguide dispersion relations agree with simulated results to 1%. The implications and limitations of the envelope approximation are discussed and quantified by examining the validity of the underlying assumptions in the multiple scales framework. Accurate dispersion relations can be obtained with the envelope approximation even when the assumptions are not completely valid. With the aim of enabling efficient forward-engineering of photonic crystal waveguides, the envelope approximation eliminates the need for computationally intensive simulations and provides a physically intuitive picture to the understanding of waveguiding phenomena in photonic crystals.
Lactation Duration and Progression to Diabetes in Women Across the Childbearing Years: The 30-Year CARDIA Study

Importance Lactation duration has shown weak protective associations with incident diabetes (3%-15% lower incidence per year of lactation) in older women based solely on self-report of diabetes, studies initiated beyond the reproductive period are vulnerable to unmeasured confounding or reverse causation from antecedent biochemical risk status, perinatal outcomes, and behaviors across the childbearing years. Objective To evaluate the association between lactation and progression to diabetes using biochemical testing both before and after pregnancy and accounting for prepregnancy cardiometabolic measures, gestational diabetes (GD), and lifestyle behaviors. Design, Setting, and Participants For this US multicenter, community-based 30-year prospective cohort study, there were 1238 women from the Coronary Artery Risk Development in Young Adults (CARDIA) study of young black and white women ages 18 to 30 years without diabetes at baseline (1985-1986) who had 1 or more live births after baseline, reported lactation duration, and were screened for diabetes up to 7 times during 30 years after baseline (1986-2016). Exposures Time-dependent lactation duration categories (none, >0 to 6 months, >6 to <12 months, and ≥12 months) across all births since baseline through 30 years. Main Outcomes and Measures Diabetes incidence rates per 1000 person-years and adjusted relative hazards (RH) with corresponding 95% CIs, as well as proportional hazards regression models adjusted for biochemical, sociodemographic, and reproductive risk factors, as well as family history of diabetes, lifestyle, and weight change during follow-up. Results Overall 1238 women were included in this analysis (mean [SD] age, 24.2 [3.7] years; 615 black women). There were 182 incident diabetes cases during 27 598 person-years for an overall incidence rate of 6.6 cases per 1000 person-years (95% CI, 5.6-7.6); and rates for women with GD and without GD were 18.0 (95% CI, 13.3-22.8) and 5.1 (95% CI, 4.2-6.0), respectively (P for difference < .001). Lactation duration showed a strong, graded inverse association with diabetes incidence: adjusted RH for more than 0 to 6 months, 0.75 (95% CI, 0.51-1.09); more than 6 months to less than 12 months, 0.52 (95% CI, 0.31-0.87), and 12 months or more 0.53 (0.29-0.98) vs none (0 days) (P for trend = .01). There was no evidence of effect modification by race, GD, or parity. Conclusions and Relevance This study provides longitudinal biochemical evidence that lactation duration is independently associated with lower incidence of diabetes. Further investigation is required to elucidate mechanisms that may explain this relationship.
Evidence for Different Trajectories of Delay Discounting in Older Adults With Mild Cognitive Impairment and Mild Alzheimer’s Disease

Objectives To examine whether delay discounting (DD) develops differently within individuals diagnosed with mild cognitive impairment (MCI) or mild Alzheimer's disease (AD). Method We set out to study trajectories of DD in N = 111 older adults (Mage = 75.2 years, range: 55-94, 53% female) with MCI (n = 64) or mild AD (n = 47). Data were repeatedly assessed on three measurement times over a period of 2 years. Results Results indicated a meaningful difference in the trajectories of DD between MCI and mild AD (t = 2.99, p = .004), with AD patients displaying higher DD rates compared with MCI. Lower intelligence (t = -2.50, p = .013) was related to higher DD. We also found reward-dependent group differences in DD (small: p = .079; medium: p = .258; large: p = .007). Age, functional ability, general cognitive ability, living situation, and marital status were not meaningfully linked to DD (all non significant). Further explorative analyses revealed an increase in DD in patients whose cognitive symptoms had progressed at time 2, compared with more stable courses of mild AD or MCI (diagnosed at time 2). Discussion Our results point toward an increase in DD as a function of advanced cognitive decline.
Guilt in bereavement: Its relationship with complicated grief and depression.

This study investigated the relationship between guilt and well-being of bereaved persons, and explored potential differences in the associations between guilt-complicated grief (CG) and guilt-depression. In total, 1358 Chinese bereaved adults were recruited to fill out questionnaires. Participants (N = 194) who had been bereaved within 2 years of the first survey, filled out the same questionnaires 1 year later. Higher guilt was associated with higher degrees of both CG and depression. The level of guilt predicted CG and depression symptoms 1 year later. Bereavement-related guilt has a closer association with CG than depression. Responsibility guilt, indebtedness guilt and degree of guilt feeling are more prominent aspects of guilt in CG than in depression. These findings demonstrate the significant role of guilt (perhaps a core symptom) in mental health of the bereaved, having implications for identifying persons with grief complications and depression.
PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the coding regions are frequently associated with the development of various genetic diseases. Computational tools for the prediction of the effects of mutations on protein function are very important for analysis of single nucleotide variants and their prioritization for experimental characterization. Many computational tools are already widely employed for this purpose. Unfortunately, their comparison and further improvement is hindered by large overlaps between the training datasets and benchmark datasets, which lead to biased and overly optimistic reported performances. In this study, we have constructed three independent datasets by removing all duplicities, inconsistencies and mutations previously used in the training of evaluated tools. The benchmark dataset containing over 43,000 mutations was employed for the unbiased evaluation of eight established prediction tools: MAPP, nsSNPAnalyzer, PANTHER, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT and SNAP. The six best performing tools were combined into a consensus classifier PredictSNP, resulting into significantly improved prediction performance, and at the same time returned results for all mutations, confirming that consensus prediction represents an accurate and robust alternative to the predictions delivered by individual tools. A user-friendly web interface enables easy access to all eight prediction tools, the consensus classifier PredictSNP and annotations from the Protein Mutant Database and the UniProt database. The web server and the datasets are freely available to the academic community at http://loschmidt.chemi. muni.cz/predictsnp.
The genotype-phenotype map of an evolving digital organism

To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable.
Neuromodulatory Correlates of Pupil Dilation

Pupillometry has long been used as a measure of brain state. Changes in pupil diameter are thought to coincide with the activity of neuromodulators, including noradrenaline and acetylcholine, producing alterations in the brain state and corresponding changes in behavior. Here we review mechanisms underlying the control of pupil diameter and how these mechanisms are correlated with changes in cortical activity and the recruitment of neuromodulatory circuits.
Fast online deconvolution of calcium imaging data

Fluorescent calcium indicators are a popular means for observing the spiking activity of large neuronal populations, but extracting the activity of each neuron from raw fluorescence calcium imaging data is a nontrivial problem. We present a fast online active set method to solve this sparse non-negative deconvolution problem. Importantly, the algorithm 3progresses through each time series sequentially from beginning to end, thus enabling real-time online estimation of neural activity during the imaging session. Our algorithm is a generalization of the pool adjacent violators algorithm (PAVA) for isotonic regression and inherits its linear-time computational complexity. We gain remarkable increases in processing speed: more than one order of magnitude compared to currently employed state of the art convex solvers relying on interior point methods. Unlike these approaches, our method can exploit warm starts; therefore optimizing model hyperparameters only requires a handful of passes through the data. A minor modification can further improve the quality of activity inference by imposing a constraint on the minimum spike size. The algorithm enables real-time simultaneous deconvolution of O(105) traces of whole-brain larval zebrafish imaging data on a laptop.
Learning SMaLL Predictors

We present a new machine learning technique for training small resource-constrained predictors. Our algorithm, the Sparse Multiprototype Linear Learner (SMaLL), is inspired by the classic machine learning problem of learning $k$-DNF Boolean formulae. We present a formal derivation of our algorithm and demonstrate the benefits of our approach with a detailed empirical study.
Psychoanalytic / psychodynamic developmental theories

There has now been more than a hundred years of psychoanalytic theorizing on the development of personality, and there are consequently a variety of different psychodynamic models. Despite sharing common origins, each of these theories has a different emphasis. Some theorists have sought to adapt existing ideas to remain within the psychoanalytic approach, while others have redefined them as distinct and separate.
Contrasting Patterns of Population History and Seed-mediated Gene Flow in Two Endemic Costa Rican Oak Species

Lower Central America is an important area to study recent population history and diversification of Neotropical species due to its complex and dynamic geology and climate. Phylogeographic studies in this region are few in comparison with other regions and even less for tree species. The aim of the present study was to characterize the phylogeographic structure in 2 partially co-distributed endemic oak species (Quercus costaricensis and Q. bumelioides) of the Costa Rican mountains using chloroplast short sequence repeats (cpSSRs), and to test for the effect of geological and palaeoclimatic processes on their population history. Genetic diversity and structure, haplotype networks, patterns of seed-mediated gene flow and historical demography were estimated for both species. Results suggested contrasting patterns. Quercus costaricensis exhibited high values of genetic diversity, a marked phylogeographic structure, a north-to-south genetic diversity gradient and evidence of a demographic expansion during the Quaternary. Quercus bumelioides did not show significant genetic structure and the haplotype network and historical demography estimates suggested a recent population expansion probably during the Pleistocene-Holocene transition. The phylogeographic structure of Q. costaricensis seems to be related to Pleistocene altitudinal migration due to its higher altitudinal distribution. Meanwhile, historical seed-mediated gene flow through the lower altitudinal distribution of Q. bumelioides may have promoted the homogenization of genetic variation. Population expansion and stable availability of suitable climatic areas in both species probably indicate that palaeoclimatic changes promoted downwards altitudinal migration and formation of continuous forests allowing oak species to expand their distribution into the Panamanian mountains during glacial stages.
In Vitro Evaluation of Antimicrobial Activity of Alimentary Canal Extracts from the Red Palm Weevil, Rhynchophorus ferrugineus Olivier Larvae

The invasive red palm weevil, Rhynchophorus ferrugineus Olivier (Coleoptera: Curculionidae), is considered one of the world's most devastating insect pests to palm trees. It was observed that larvae of this pest are able to inhibit microbial growth on the rearing media when they start feeding and this observation has led us to study the effect of red palm weevils on various microbial species. The antimicrobial effect of extracts from different parts of the alimentary canal on Gram positive bacteria (Enterococcus faecalis and Staphylococcus aureus), Gram negative bacteria (Escherichia coli and Klebsiella spp.), Candida albicans, and Penicillium sp. was tested using the agar well diffusion method. All extracts inhibited the tested microbial species. Foregut extracts had the greatest zones of growth inhibition. Enterococcus faecalis, Staphylococcus aureus, and Penicillium sp. were significantly sensitive to the extracts and had the largest growth inhibition zones. It is concluded that the gut extracts contain potent antimicrobial activity and may provide a new source of antimicrobial peptides.
Atomic Force Microscopy Studies on Morphology and Distribution of Surface Modified Silica and Clay Fillers in an Ethylene-Octene Copolymer Rubber

Topographic and phase imaging in tapping mode atomic force microscopy (TMAFM) has been performed to investigate the effect of surface modification of silica and clay fillers on the morphology and the microdispersion of the filler particles in the rubber matrix. The above fillers have been modified by using surface coating agents like an acrylate monomer (trimethylolpropane triacrylate, TMPTA) or a silane coupling agent (triethoxy vinylsilane, TEVS) followed by electron beam modification at room temperature. Both unmodified and surface modified fillers have been incorporated in an ethylene-octene copolymer rubber. The phase images of the above composites elucidate the reduction in aggregate size due to the filler surface modification, which is more pronounced in the case of silane modification. The results obtained from the section analysis and the histogram of the filler distribution further corroborate the above findings. The corresponding topographic images are characterized by various statistical quantities like roughness parameters and two-dimensional power spectral density (2-D PSD). As compared to the control silica and clay filled rubbers, a noticeable reduction in the surface roughness is observed in the case of modified filled composites. Thus, the whole study based on AFM suggests that the surface modification of the above fillers significantly reduces the filler-filler interaction, which in turn reduces the filler aggregate size and helps in improving the filler dispersion.
The Association between Hearing Loss, Postural Control, and Mobility in Older Adults: A Systematic Review

Background: Degraded hearing in older adults has been associated with reduced postural control and higher risk of falls. Both hearing loss (HL) and falls have dramatic effects on older persons’ quality of life (QoL). A large body of research explored the comorbidity between the two domains. Purpose: The aim of the current review is to describe the comorbidity between HL and objective measures of postural control, to offer potential mechanisms underlying this relationship, and to discuss the clinical implications of this comorbidity. Data Collection and Analysis: PubMed and Google Scholar were systematically searched for articles published in English up until October 15, 2015, using combinations of the following strings and search words: for hearing: Hearing loss, “Hearing loss,” hearing, presbycusis; for postural control: postural control, gait, postural balance, fall, walking; and for age: elderly, older adults. Results: Of 211 screened articles, 7 were included in the systematic review. A significant, positive association between HL and several objective measures of postural control was found in all seven studies, even after controlling for major covariates. Severity of hearing impairment was connected to higher prevalence of difficulties in walking and falls. Physiological, cognitive, and behavioral processes that may influence auditory system and postural control were suggested as potential explanations for the association between HL and postural control. Conclusions: There is evidence for the independent relationship between HL and objective measures of postural control in the elderly. However, a more comprehensive understanding of the mechanisms underlying this relationship is yet to be elucidated. Concurrent diagnosis, treatment, and rehabilitation of these two modalities may reduce falls and increase QoL in older adults.
Effective and less invasive diagnostic strategy for gastrointestinal GVHD

Abstract Background and study aims Rectosigmoidoscopy with biopsy has been regarded to be a useful procedure to diagnose gastrointestinal graft-versus-host disease (GVHD). However, little is known about the specific colonoscopic features of gastrointestinal GVHD. In this study, we focused on the 4 unique colonoscopic findings – orange peel appearance, spotty redness, small mucosal sloughing, and diffuse mucosal defect – which are possible specific findings of gastrointestinal GVHD. We aimed to estimate the usefulness of these four unique colonoscopic findings in the rectosigmoid portion to diagnose gastrointestinal GVHD. Patients and methods Seventy patients who were histologically diagnosed with gastrointestinal GVHD at our institute were retrospectively enrolled. Colonoscopic findings were reviewed, focusing on the four characteristic findings. The percentage of the positive cases for the characteristic findings was calculated. The final scoping portion and the number of cases showing any of the four characteristic findings in the rectosigmoid portion were also evaluated. The relationships between biopsy sites and the histological findings were also evaluated. Results Orange peel appearance was observed in 66 cases (94.3 %). Spotty redness was observed in 45 cases (64.3 %). Small mucosal sloughing was observed in 49 cases (70.0 %). Diffuse mucosal defect was observed in six cases (8.6 %). The number of cases that were concurrently positive for one, two, and three findings were 16 (20.8 %), 20 (26.0 %), and 34 (48.6 %), respectively. Fifty-eight cases (82.9 %) were investigated up to the rectosigmoid portion, and 12 (17.1 %) were investigated beyond the sigmoid colon. All of the cases showed at least 1 of the 4 characteristics in the rectosigmoid portion. The percentage of crypt apoptosis in the biopsy specimen from orange peel appearance, spotty redness, small mucosal sloughing, and diffuse mucosal defect were 87.5 %, 83.3 %, 87.2 %, and 88.9 %, respectively. Conclusion Orange peel appearance, spotty redness, small mucosal sloughing, and diffuse mucosal defect are the characteristic colonoscopic findings useful for diagnosis of gastrointestinal GVHD. These findings are frequently observed in the rectosigmoid portion. The histological detection rates for crypt cell apoptosis from these findings are high. Identifying the four characteristic findings on rectosigmoidoscopy and taking biopsies from these areas could be essential for the diagnostic strategy for gastrointestinal GVHD.
Shear stress-regulated miR-27b controls pericyte recruitment by repressing SEMA6A and SEMA6D

Aims Vessel maturation involves the recruitment of mural cells such as pericytes and smooth muscle cells. Laminar shear stress is a major trigger for vessel maturation, but the molecular mechanisms by which shear stress affects recruitment of pericytes are unclear. MicroRNAs (miRs) are small non-coding RNAs, which post-transcriptionally control gene expression. The aim of the present study was to unveil the mechanism by which shear stress-regulated microRNAs contribute to vessel maturation. Methods and results Here, we show that laminar shear stress increased miR-27a and miR-27b expression in vitro and in ex vivo in mouse femoral artery explants. Overexpression of miR-27b in endothelial cells increased pericyte adhesion and pericyte recruitment in vitro . In vitro barrier function of endothelial-pericyte co-cultures was augmented by miR-27b overexpression, whereas inhibition of miR-27a/b reduced adhesion and pericyte coverage and decreased barrier functions. In vivo , pharmacological inhibition of miR-27a/b by locked nucleic acid antisense oligonucleotides significantly reduced pericyte coverage and increased water content in the murine uterus. MiR-27b overexpression repressed semaphorins (SEMA), which mediate repulsive signals, and the vessel destabilizing human but not mouse Angiopoietin-2 (Ang-2). Silencing of SEMA6A and SEMA6D rescued the reduced pericyte adhesion by miR-27 inhibition. Furthermore, inhibition of SEMA6D increased barrier function of an endothelial-pericyte co-culture in vitro . Conclusion The present study demonstrates for the first time that shear stress-regulated miR-27b promotes the interaction of endothelial cells with pericytes, partly by repressing SEMA6A and SEMA6D.