Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of optic nerve regeneration using transgenic zebrafish

In contrast to the adult mammalian central nervous system (CNS), fish are able to functionally regenerate severed axons upon injury. Although the zebrafish is a well-established model vertebrate for genetic and developmental studies, its use for anatomical studies of axon regeneration has been hampered by the paucity of appropriate tools to visualize re-growing axons in the adult CNS. On this account, we used transgenic zebrafish that express enhanced green fluorescent protein (GFP) under the control of a GAP-43 promoter. In adult, naïve retinae, GFP was restricted to young retinal ganglion cells (RGCs) and their axons. Within the optic nerve, these fluorescent axons congregated in a distinct strand at the nerve periphery, indicating age-related order. Upon optic nerve crush, GFP expression was markedly induced in RGC somata and intra-retinal axons at 4 to at least 14 days post injury. Moreover, individual axons were visualized in their natural environment of the optic nerve using wholemount tissue clearing and confocal microscopy. With this novel approach, regenerating axons were clearly detectable beyond the injury site as early as 2 days after injury and grew past the optic chiasm by 4 days. Regenerating axons in the entire optic nerve were labeled from 6 to at least 14 days after injury, thereby allowing detailed visualization of the complete regeneration process. Therefore, this new approach could now be used in combination with expression knockdown or pharmacological manipulations to analyze the relevance of specific proteins and signaling cascades for axonal regeneration in vivo. In addition, the RGC-specific GFP expression facilitated accurate evaluation of neurite growth in dissociated retinal cultures. This fast in vitro assay now enables the screening of compound and expression libraries. Overall, the presented methodologies provide exciting possibilities to investigate the molecular mechanisms underlying successful CNS regeneration in zebrafish.
Averting speed inefficiency in rate-diverse WiFi networks through queueing and aggregation

IEEE 802.11n, the latest version of the widely used standard for wireless LANs, promises significant increases in speed by incorporating multiple enhancements at the physical layer. In this paper we demonstrate that, on the contrary, the straightforward deployment of 802.11n in conjunction with TCP over a simple, single access-point network, can dramatically underachieve the promised speeds. Part of the deficiency is due to overheads and can be improved by the technique of packet aggregation present in the standard. However more subtle problems are identified, in particular the downward equalization of throughputs that occurs under physical rate diversity, or the unreasonable portion of resources taken by uplink flows when competing with the more numerous downlink connections. These difficulties are demonstrated and their causes explained through a sequence of experiments with the ns3 packet simulator. Our analysis leads us to propose a desirable resource allocation for these situations of competition, and an architecture for control in the access-point to achieve it. Our solution involves a combination of packet aggregation, multiple queues and TCPACK isolation, compatible with the standard and where all the control resides at the AP. We demonstrate analytically and through extensive simulation that our method is able to provide significant enhancements in performance under a variety of traffic conditions.
Exploring Spiritual Well‐Being Among Survivors of Colorectal and Lung Cancer

This descriptive, exploratory study is part of a larger observational study of the quality of cancer care delivered to population‐based cohorts of newly diagnosed patients with lung and colorectal cancer. The current study explores the role of spiritual well‐being in adjustment to life after the cancer diagnosis, utilizing the Functional Assessment of Chronic Illness Therapy–Spiritual Well‐Being–Expanded (FACIT‐Sp‐Ex) Scale. Survey data collected from 304 newly diagnosed cancer survivors were analyzed to explore important aspects of spirituality, such as sense of meaning in one's life, harmony, peacefulness, and a sense of strength and comfort from one's faith. Spiritual well‐being scores, particularly meaning/peace, were statistically significant for African Americans, women, and colorectal cancer survivors. These findings amplify a need for oncology social workers and other practitioners to assess spiritual well‐being in cancer survivors in an effort to strengthen psychosocial treatment plans. Implications for social work practice and research are discussed.
Monte Carlo simulation of a solvated ionic polymer with cluster morphology

A multiscale modeling approach for the prediction of material stiffness of the ionic polymer Nafion is presented. Traditional rotational isomeric state theory is applied in combination with a Monte Carlo methodology to develop a simulation model of the conformation of Nafion polymer chains on a nanoscopic level from which a large number of end-to-end chain lengths are generated. The probability density function of end-to-end distances is then estimated and used as an input parameter to enhance existing energetics-based macroscale models of ionic polymer behavior. Several methods for estimating the probability density function are compared, including estimation using Johnson distributions, Bézier distributions, and cubic splines.
Physiologic, Pathologic, and Therapeutic Paracrine Modulation of Cardiac Excitation-Contraction Coupling

Cardiac excitation–contraction coupling (ECC) is the orchestrated process of initial myocyte electrical excitation, which leads to calcium entry, intracellular trafficking, and subsequent sarcomere shortening and myofibrillar contraction. Neurohumoral &bgr;-adrenergic signaling is a well-established mediator of ECC; other signaling mechanisms, such as paracrine signaling, have also demonstrated significant impact on ECC but are less well understood. For example, resident heart endothelial cells are well-known physiological paracrine modulators of cardiac myocyte ECC mainly via NO and endothelin-1. Moreover, recent studies have demonstrated other resident noncardiomyocyte heart cells (eg, physiological fibroblasts and pathological myofibroblasts), and even experimental cardiotherapeutic cells (eg, mesenchymal stem cells) are also capable of altering cardiomyocyte ECC through paracrine mechanisms. In this review, we first focus on the paracrine-mediated effects of resident and therapeutic noncardiomyocytes on cardiomyocyte hypertrophy, electrophysiology, and calcium handling, each of which can modulate ECC, and then discuss the current knowledge about key paracrine factors and their underlying mechanisms of action. Next, we provide a case example demonstrating the promise of tissue-engineering approaches to study paracrine effects on tissue-level contractility. More specifically, we present new functional and molecular data on the effects of human adult cardiac fibroblast conditioned media on human engineered cardiac tissue contractility and ion channel gene expression that generally agrees with previous murine studies but also suggests possible species-specific differences. By contrast, paracrine secretions by human dermal fibroblasts had no discernible effect on human engineered cardiac tissue contractile function and gene expression. Finally, we discuss systems biology approaches to help identify key stem cell paracrine mediators of ECC and their associated mechanistic pathways. Such integration of tissue-engineering and systems biology methods shows promise to reveal novel insights into paracrine mediators of ECC and their underlying mechanisms of action, ultimately leading to improved cell-based therapies for patients with heart disease.
Neighborhood-level cohesion and disorder: measurement and validation in two older adult urban populations.

OBJECTIVES Drawing from collective efficacy and social disorganization theories, we developed and validated measures of neighborhood-level social processes. METHODS Data came from 2 large, population-based cohort studies of urban-dwelling older adults, the Chicago Neighborhood and Disability Study (CNDS, n = 3,882) and the Baltimore Memory Study (BMS, n = 1,140). Data on neighborhood social processes were collected from residents using a standardized instrument identical in the 2 studies. We used confirmatory factor analysis and descriptive statistics to explore reliability and validity of the neighborhood-level measures. RESULTS Confirmatory factor analysis indicated 2 latent factors: social cohesion and exchange (i.e., observations of and interactions with neighbors) and social and physical disorder (i.e., neighborhood problems and unsafe conditions). Neighborhood-level measures of cohesion and disorder showed moderate to high levels of internal consistency (alphas = .78 and .85 in CNDS and .60 and .88 in BMS). Inter-resident agreements were low (intra-neighborhood correlation coefficients = .08 and .11 in CNDS and .05 and .33 in BMS). Cohesion showed a modest, positive association with a composite measure of neighborhood socioeconomic status (SES). Disorder showed a strong, negative association with neighborhood SES. CONCLUSIONS Findings provide initial evidence of the reliability and construct validity of these neighborhood-level social process measures.
Towards optimum query segmentation: in doubt without

Query segmentation is the problem of identifying those keywords in a query, which together form compound concepts or phrases like "new york times". Such segments can help a search engine to better interpret a user's intents and to tailor the search results more appropriately. Our contributions to this problem are threefold. (1) We conduct the first large-scale study of human segmentation behavior based on more than 500000 segmentations. (2) We show that the traditionally applied segmentation accuracy measures are not appropriate for such large-scale corpora and introduce new, more robust measures. (3) We develop a new query segmentation approach with the basic idea that, in cases of doubt, it is often better to (partially) leave queries without any segmentation. This new in-doubt-without approach chooses different segmentation strategies depending on query types. A large-scale evaluation shows substantial improvement upon the state of the art in terms of segmentation accuracy. To draw a complete picture, we also evaluate the impact of segmentation strategies on retrieval performance in a TREC setting. It turns out that more accurate segmentation not necessarily yields better retrieval performance. Based on this insight, we propose an in-doubt-without variant which achieves the best retrieval performance despite leaving many queries unsegmented. But there is still room for improvement: the optimum segmentation strategy which always chooses the segmentation that maximizes retrieval performance, significantly outperforms all other tested approaches.
Experimental posterior penetrating eye injury in the rabbit Table 1 Natural history of posterior perforating injury in the rabbit eye

A technique has been developed which produces an experimental posterior penetrating eye injury that reproducibly results in traction retinal detachment in rabbit eyes. The standard injury is an incision through the pars plana with vitreous prolapse and incarceration; the wound is then carefully closed with microsurgical techniques. It appears that blood in the vitreous is an essential factor in the development of vitreous traction and of traction retinal detachment. The model, which has been successfully transferred to Rhesus monkey eyes, is considered useful for further histological, electromicroscopical, electrophysiological, and ultrasound studies of posterior penetrating injuries of the eye. Our immediate goal is to assess in a controlled experiment whether pars plana vitrectomy can interrupt the sequence of events leading to traction retinal detachment after a posterior penetrating injury.
Cytological events involved in protein synthesis in cellular and syncytial trophoblast of human placenta. An electron microscope autoradiographic study of [3H]leucine incorporation

Electron microscope autoradiography has been used to study protein synthesis in syncytial and cellular trophoblast of term human placental villi incubated in vitro with tritiated leucine ([3H]leu). Autoradiographs were analyzed using the hypothetical grain analysis of Blackett and Parry (1973. J. Cell Biol. 57:9-15). The results of this study demonstrated that both cellular and syncytial trophoblast have marked capacities for protein synthesis. Cellular trophoblast synthesized protein in both its rough endoplasmic reticulum (RER) and its ground plasm which contained abundant free ribosomes. The vast majority of 3H-proteins remained within the cell, with some of the proteins synthesized ultimately appearing in the nucleus. A small percentage of grains was ultimately associated with the trophoblast basement membrane. In syncytial trophoblast, the RER was the dominant site for protein synthesis. The autoradiographic data suggested that, as in the cellular trophoblast, the vast majority of 3H-proteins synthesized by the syncytial trophoblast remained within the syncytial trophoblast throughout the incubation period. The major portion of [3H]leu-labeling present in the syncytial trophoblast of villi incubated the longest times (4 h+) remained in association with the RER. Labeled proteins did not become concentrated in syncytial trophoblast Golgi apparatus, vesicles, or granules. In contrast to cellular trophoblast, the nuclei in the syncytium did not contain 3H-proteins at any time-point studied.
Practical use of English pronunciation system for Japanese students in the CALL classroom

We have developed an English pronunciation learning system which estimates the intelligibility of students’ speech and ranks their errors from the viewpoint of improving their intelligibility. We have begun using this system in a CALL class at Kyoto University. We have evaluated system performance through the use of questionnaires and analysis of speech data logged in the server, and will present our findings in this paper.
Tartrate-resistant acid phosphatase 5b is a useful serum marker for extensive bone metastasis in breast cancer patients.

PURPOSE Previous studies showed that serum tartrate-resistant acid phosphatase 5b (TRACP5b) activity was increased in 70% to 94% of breast cancer (BC) patients with bone metastasis (BM). This study aims to determine whether serum TRACP5b is useful for identifying limited or extensive BM in BC patients. EXPERIMENTAL DESIGN Serum TRACP5b activity was measured in 168 BC patients, including 81 who were newly diagnosed with early BC, 20 with extraosseous metastasis, 24 with limited BM, and 43 with extensive BM. Serum TRACP5b activity was also measured monthly in 151 patients with early BC until they developed BM. Four hundred and twenty-seven (427) healthy women ages 18 to 90 served as control. One-way ANOVA was used to compare serum TRACP5b among groups. The sensitivity and specificity of serum TRACP5b as a marker for BM were estimated by receiver operator characteristic (ROC) curves. RESULTS Serum TRACP5b increased with age in healthy women ( P < 0.0001). It was significantly elevated in patients with extensive BM compared with all other groups ( P < 0.0001). ROC analysis established a cutoff value of 4.026 units/L to identify patients with extensive BM with a specificity of 98% and a sensitivity of 93% (area under the curve = 0.9807; 95% CI = 0.9698-0.9915). Among the 151 patients with early BC, 6 developed limited BM and 2 developed extensive BM during the follow-up period. Serum TRACP5b remained below the cutoff value in patients with limited BM, but became significantly increased in those whose BM became extensive. CONCLUSION Serum TRACP5b activity is a useful diagnostic marker for extensive BM in patients with BC.
Determination of patient set-up error and optimal treatment margin for intensity modulated radiotherapy using image guidance system.

PURPOSE The geometrical uncertainties in the patient positioning during intensity modulated radiotherapy (IMRT) are crucial as there is potential to underdose the tumor and overdose the nearby critical structures. Image guided techniques provide a solution to assess the patient set-up uncertainties and help determine the optimal planning target volume (PTV) margin to the clinical tumor volume (CTV). METHODS A retrospective study was conducted to evaluate patient set-up errors along the three translational directions at different treatment sites such as the brain, the head and neck (H&N) and the prostate. A total of 60 patients' set-up error data was analysed to evaluate the systematic and random errors and the optimal CTV-PTV margin. RESULTS For brain and H&N sites, more than 90, 80 and about 100% of the total image acquisitions were less than 3 mm in lateral, longitudinal and vertical directions respectively. For the prostate cases, the frequency of patient set-up error to be less than 3 mm were 79.7, 75.6 and 80% in lateral, longitudinal and vertical directions respectively. About 0.6% had more than 7 mm error in the lateral and longitudinal directions for the prostate site. CTV-PTV margin of 3.4, 3.4 and 1.9 mm for brain cases, 3.5, 3 and 1.8 mm for H&N cases and 5, 4.6 and 4.5 mm for the prostate cases in the lateral, longitudinal and vertical directions respectively were determined. CONCLUSION Image guidance is an effective method to evaluate the accuracy of IMRT treatment delivery. The optimal CTV-PTV margin can be determined to ensure adequate dose to CTV, specific to the site.
Body composition in psychotic disorders: a general population survey

Background The literature suggests an association between obesity and schizophrenia but fat mass and fat-free mass, which have been shown to be more predictive of all-cause mortality than only waist circumference and obesity [body mass index (BMI) ⩾30 kg/m2], have not been reported in psychotic disorders. We examined the detailed body composition of people with different psychotic disorders in a large population-based sample. Method We used a nationally representative sample of 8082 adult Finns aged ⩾30 years with measured anthropometrics (height, weight, waist circumference, fat percentage, fat-free mass and segmental muscle mass). Psychiatric diagnoses were based on a consensus procedure utilizing the Structured Clinical Interview for DSM-IV (SCID)-interview, case-notes and comprehensive register data. Results Schizophrenia (including schizo-affective disorder) was associated with obesity [odds ratio (OR) 2.3, 95% confidence interval (CI) 1.5–3.6], abdominal obesity (waist circumference ⩾88 cm for women, ⩾102 cm for men) (OR 2.2, 95% CI 1.3–3.6) and with higher fat percentage (mean difference 3.8%, 95% CI 2.0–5.7%), adjusted for age and gender, than in the remaining sample. The associations between schizophrenia and low fat-free mass and decreased muscle mass on trunk and upper limbs became statistically significant after adjusting for BMI. After further adjusting for current antipsychotic medication, education, diet and smoking, schizophrenia remained associated with obesity (OR 1.9, 95% CI 1.1–3.6) and abdominal obesity (OR 3.8, 95% CI 1.5–9.4). Participants with affective psychoses did not differ from the general population. Conclusions Individuals with schizophrenia have metabolically unfavorable body composition, comprising abdominal obesity, high fat percentage and low muscle mass. This leads to increased risk of metabolic and cardiovascular diseases.
An experimental analysis of the heritability of variation in glucocorticoid concentrations in a wild avian population

Glucocorticoid hormones (CORT) are predicted to promote adaptation to variable environments, yet little is known about the potential for CORT secretion patterns to respond to selection in free-living populations. We assessed the heritable variation underlying differences in hormonal phenotypes using a cross-foster experimental design with nestling North American barn swallows (Hirundo rustica erythrogaster). Using a bivariate animal model, we partitioned variance in baseline and stress-induced CORT concentrations into their additive genetic and rearing environment components and estimated their genetic correlation. Both baseline and stress-induced CORT were heritable with heritability of 0.152 and 0.343, respectively. We found that the variation in baseline CORT was best explained by rearing environment, whereas the variation in stress-induced CORT was contributed to by a combination of genetic and environmental factors. Further, we did not detect a genetic correlation between these two hormonal traits. Although rearing environment appears to play an important role in the secretion of both types of CORT, our results suggest that stress-induced CORT levels are underlain by greater additive genetic variance compared with baseline CORT levels. Accordingly, we infer that the glucocorticoid response to stress has a greater potential for evolutionary change in response to selection compared with baseline glucocorticoid secretion patterns.
Evolutionary Synthesis of Deep Neural Networks via Synaptic Cluster-driven Genetic Encoding

There has been significant recent interest towards achieving highly efficient deep neural network architectures. A promising paradigm for achieving this is the concept of evolutionary deep intelligence, which attempts to mimic biological evolution processes to synthesize highly-efficient deep neural networks over successive generations. An important aspect of evolutionary deep intelligence is the genetic encoding scheme used to mimic heredity, which can have a significant impact on the quality of offspring deep neural networks. Motivated by the neurobiological phenomenon of synaptic clustering, we introduce a new genetic encoding scheme where synaptic probability is driven towards the formation of a highly sparse set of synaptic clusters. Experimental results for the task of image classification demonstrated that the synthesized offspring networks using this synaptic cluster-driven genetic encoding scheme can achieve state-of-the-art performance while having network architectures that are not only significantly more efficient (with a ~125-fold decrease in synapses for MNIST) compared to the original ancestor network, but also tailored for GPU-accelerated machine learning applications.