Miracle-dz/UniFAR-FTUs huggingface dataset:
Localized reductions in resting‐state functional connectivity in children with prenatal alcohol exposure

Fetal alcohol spectrum disorders (FASD) are characterized by impairment in cognitive function that may or may not be accompanied by craniofacial anomalies, microcephaly, and/or growth retardation. Resting‐state functional MRI (rs‐fMRI), which examines the low‐frequency component of the blood oxygen level dependent (BOLD) signal in the absence of an explicit task, provides an efficient and powerful mechanism for studying functional brain networks even in low‐functioning and young subjects. Studies using independent component analysis (ICA) have identified a set of resting‐state networks (RSNs) that have been linked to distinct domains of cognitive and perceptual function, which are believed to reflect the intrinsic functional architecture of the brain. This study is the first to examine resting‐state functional connectivity within these RSNs in FASD. Rs‐fMRI scans were performed on 38 children with FASD (19 with either full fetal alcohol syndrome (FAS) or partial FAS (PFAS), 19 nonsyndromal heavily exposed (HE)), and 19 controls, mean age 11.3 ± 0.9 years, from the Cape Town Longitudinal Cohort. Nine resting‐state networks were generated by ICA. Voxelwise group comparison between a combined FAS/PFAS group and controls revealed localized dose‐dependent functional connectivity reductions in five regions in separate networks: anterior default mode, salience, ventral and dorsal attention, and R executive control. The former three also showed lower connectivity in the HE group. Gray matter connectivity deficits in four of the five networks appear to be related to deficits in white matter tracts that provide intra‐RSN connections. Hum Brain Mapp 38:5217–5233, 2017. © 2017 Wiley Periodicals, Inc.
SIEVE ELEMENT-LINING CHAPERONE1 Restricts Aphid Feeding on Arabidopsis during Heat Stress

Genome-wide association mapping and protein characterization reveal that the small heat shock-like protein SLI1 restricts phloem feeding by aphids and improves seed set during heat stress. The role of phloem proteins in plant resistance to aphids is still largely elusive. By genome-wide association mapping of aphid behavior on 350 natural Arabidopsis thaliana accessions, we identified the small heat shock-like SIEVE ELEMENT-LINING CHAPERONE1 (SLI1). Detailed behavioral studies on near-isogenic and knockout lines showed that SLI1 impairs phloem feeding. Depending on the haplotype, aphids displayed a different duration of salivation in the phloem. On sli1 mutants, aphids prolonged their feeding sessions and ingested phloem at a higher rate than on wild-type plants. The largest phenotypic effects were observed at 26°C, when SLI1 expression is upregulated. At this moderately high temperature, sli1 mutants suffered from retarded elongation of the inflorescence and impaired silique development. Fluorescent reporter fusions showed that SLI1 is confined to the margins of sieve elements where it lines the parietal layer and colocalizes in spherical bodies around mitochondria. This localization pattern is reminiscent of the clamp-like structures observed in previous ultrastructural studies of the phloem and shows that the parietal phloem layer plays an important role in plant resistance to aphids and heat stress.
Unification of Fuzzy SVMs and Rule Extraction Methods through imprecise Domain Knowledge

In this paper, we want to motivate the combination of kernel-based methods with fuzzy rule extraction methods to describe uncertain domains by fuzzy models. We thus introduce and motivate the concept of a fuzzy support vector machine (FSVM) to incorporate impreciseness into kernel machines. Furthermore, we present the idea of a positive definite fuzzy classifier (PDFC), the rules of which are obtained by kernel-based models. We conclude with two vague conceptions to associate FSVM with PDFC to finally obtain understandable and meaningful fuzzy rules.
Bayesian Experimental Design: A Review

This paper reviews the literature on Bayesian experimental design, both for linear and nonlinear models. A uniied view of the topic is presented by putting experimental design in a decision theoretic framework. This framework justiies many optimality criteria, and opens new possibilities. Various design criteria become part of a single, coherent approach.
Cabazitaxel regimens inhibit the growth of prostate cancer cells and enhances the anti‐tumor properties of PEDF with various efficacy and toxicity

Taxanes chemotherapies represent the major therapeutic alternative for symptomatic mCRPC. While docetaxel is the most commonly prescribed Taxane for mCRPC; cabazitaxel has been approved for patients unresponsive to docetaxel. Still mCRPC remains incurable and patients often experience severe side effects. Recently, the FIRSTANA trial first demonstrated the absence of superiority in overall survival between cabazitaxel and docetaxel in mCRPC patients. Inversely, different toxicity were reported suggesting that cabazitaxel may provide a first line treatment option for some patients urging for a deeper characterization of cabazitaxel mechanisms of action as well as a re‐evaluation of cabazitaxel conventional dose and schedule. In this study, our goal was therefore to evaluate the anti‐tumor efficacy of various cabazitaxel regimens delivered as monotherapy or in combination with PEDF, a known anti‐angiogenic and anti‐neoplastic agent.
Improving the Care of Individuals with Schizophrenia and Substance Use Disorders: Consensus Recommendations

National attention continues to focus on the need to improve care for individuals with co-occurring mental illnesses and substance use disorders, as emphasized in the 2003 President's New Freedom Commission Report on Mental Health and recent publications from the Substance Abuse and Mental Health Services Administration (SAMHSA). These reports document the need for best practice recommendations that can be translated into routine clinical care. Although efforts are underway to synthesize literature in this area, few focused recommendations are available that include expert opinion and evidence-based findings on the management of specific co-occurring disorders, such as schizophrenia and addiction. In response to the need for user-friendly recommendations on the treatment of schizophrenia and addiction, a consensus conference of experts from academic institutions and state mental health systems was organized to 1) frame the problem from clinical and systems-level perspectives; 2) identify effective and problematic psychosocial, pharmacological, and systems practices; and 3) develop a summary publication with recommendations for improving current practice. The results of the consensus meeting served as the foundation for this publication, which presents a broad set of recommendations for clinicians who treat individuals with schizophrenia. "Integrated treatment" is the new standard for evidence-based treatment for this population and recommendations are given to help clinicians implement such integrated treatment. Specific recommendations are provided concerning screening for substance use disorders in patients with schizophrenia, assessing motivation for change, managing medical conditions that commonly occur in patients with dual diagnoses (e.g., cardiovascular disease, liver complications, lung cancer, HIV, and hepatitis B or C infections) and selecting the most appropriate medications for such patients to maximize safety and minimize drug interactions, use of evidence-based psychosocial interventions for patients with dual diagnoses (e.g., Dual Recovery Therapy, modified cognitive-behavioral therapy, modified motivational enhancement therapy, and the Substance Abuse Management Module), and key pharmacotherapy principles for treating schizophrenia, substance use disorders, and comorbid anxiety, depression, and sleep problems in this population. Finally the article reviews programmatic and systemic changes needed to overcome treatment barriers and promote the best outcomes for this patient population. An algorithm summarizing the consensus recommendations is provided in an appendix.
Identification of five highly priced tuna species by quantitative real-time polymerase chain reaction

Abstract Tunas are economically important fishery worldwide, and are often used for commercial processed production. For effective fishery management and protection of consumers′ rights, it is important to develop a molecular method to identify species in canned tuna products rapidly and reliably. Here, we have developed a duplex quantitative real-time PCR (qPCR) for identification of five highly priced tuna species (Thunnus maccoyii, Thunnus obesus, Thunnus albacares, Thunnus alalunga and Katsuwonus pelamis) from processed as well as fresh fish. After amplification and sequencing of seven genetic markers commonly used for species identification, 16S rDNA and control region (CR) of mitochondrial DNA were selected as the reference gene markers for genus Thunnus and tuna species identification, respectively. Subsequently, a 73 bp fragment of 16S rDNA and 85–99 bp fragment of CR were simultaneously amplified from each target species by qPCR. The qPCR efficiency of each reaction was calculated according to the standard curves, and the method was validated by amplification DNA extracted from single or mixed tuna specimen. The developed duplex qPCR system was applied to authenticate species of 14 commercial tuna products successfully, which demonstrated it was really a useful and academic technique to identify highly priced tuna species.
In vivo confocal microscopic and histopathologic correlations of dermoscopic features in 202 melanocytic lesions.

OBJECTIVES To identify in vivo microscopic substrates of the dermoscopic patterns of melanocytic lesions and to correlate them with histopathologic features. DESIGN Before excision, lesion areas that showed characteristic dermoscopic patterns were imaged by dermoscopy and confocal microscopy and directly correlated with histopathologic features. SETTING Departments of Dermatology of the University of Modena and Reggio Emilia and Hospital Clínico of Barcelona, between July 2006 and March 2007. Patients Patients with 202 melanocytic lesions, corresponding to 76 melanomas, 114 nevi, and 12 Spitz or Reed nevi. MAIN OUTCOME MEASURES Correlation of dermoscopic patterns in melanocytic lesions with confocal microscopic findings and conventional histopathologic findings. RESULTS Characteristic architectural and cytologic substrates were identified in vivo with the use of confocal microscopy and correlated with histopathologic features. Pigment network atypia was evidenced through confocal microscopy as a disarrangement of dermoepidermal junction architecture and cellular atypia. Pigmented globules consisted of cell clusters, corresponding to melanocytic nests identified on histopathologic analysis. Black dots correlated with intraepidermal reflective spots or with large pagetoid cells in nevi and melanoma, respectively. Blue structures usually consisted of numerous pleomorphic cells, corresponding to malignant melanocytes and inflammatory cells in melanomas, whereas plump bright cells, corresponding to melanophages on histopathologic analysis, characterized benign lesions. Within regression, a retiform distribution of collagen fibers, which sometimes intermingled with melanophages and rarely with nucleated cells, was observable. CONCLUSIONS The knowledge of the cytologic and architectural aspects of the different dermoscopic patterns, as they appear by in vivo confocal microscopy, may guide the user to the identification of specific substrates in melanocytic lesions and consequently the interpretation of the dermoscopic features.
Role of Smad3 signaling in the epithelial-mesenchymal transition of the lens epithelium following injury

Transforming growth factor-β (TGF-β) is important in the development of posterior capsule opacification (PCO), and inhibition of the TGF-β pathway may represent a novel method of treating PCO. Drosophila protein, mothers against decapentaplegic homolog 3 (Smad3) is a phosphorylated receptor-activated Smad required for the transmission of TGF-β signals. Smad3 knockout (KO) disturbs the activation of TGF-β signaling, thus inhibiting the onset of PCO. In the present study, lens epithelial cell (LEC) damage induced by extracapsular cataract extraction was simulated by puncture of the anterior capsule using a 26-gauge hypodermic needle. The effect of Smad3 in the trauma-induced epithelial-mesenchymal transition (EMT) of the lens epithelium in Smad3-KO and wild-type (WT) mice was then observed. The expression levels of EMT markers and extracellular matrix components were measured in the two groups by reverse transcription-quantitative polymerase chain reaction analysis, western blot analysis and immunofluorescence staining. Apoptosis was also detected in the punctured anterior capsule. The Smad3-KO mice exhibited lower expression levels of α-smooth muscle actin, lumican, osteopontin, fibronectin and collagen, compared with the WT mice. Additionally, the Smad3-KO mice exhibited a higher percentage of apoptotic cells than the WT mice. Smad3 signaling was associated with the induction of trauma-induced EMT, and Smad3 KO interfered with TGF-β signaling pathway activation, but did not completely inhibit the trauma-induced EMT in LECs. Therefore, Smad3 may be a target in the treatment of PCO and other fibrosis-related diseases.
Role of modular and hierarchical structure in making networks dynamically stable

According to the May-Wigner theorem, increasing the complexity of random networks results in their dynamical instability. However, the prevalence of complex networks in nature, where they necessarily have to be robust to survive, appears to contradict this theoretical result. A possible solution to this apparent paradox maybe through the introduction of certain structural features of real-life networks, in particular, modularity and hierarchical levels. In this paper, we first show that the existence of these structures in an otherwise random network will make it more unstable. Next, we introduce the realistic constraint that every link has an associated cost, and, find that modular networks are indeed more stable than homogeneous networks. Increasing modularity in such networks results in the appearance of large number of hubs and heterogeneous degree distribution, a general property shared by many networks including scale-free networks. Our results provide a dynamical setting for explaining the ubiquity of such networks in reality.
Testing and measurement from a multilevel view: Psychometrics and validation.

A growing number of testing and assessment programs gather individual student or child measures, but by design, they do not make inferences or decisions about individual students or children but rather for an aggregate such as a school, school district, neighborhood, or state. We call such measurement practices multilevel measurement. In striking contrast to multilevel measurement, however, the widely used measurement and testing models (including our psychometric and validation models) are, by historical precedent, geared toward individual differences, as are the constructs they measure and related construct validation work. Our purposes herein are to (a) introduce multilevel measurement; (b) contrast it with conventional views of measurement; and (c) discuss its implications for how one defines constructs, considers high stakes, and conducts theoretical and day-to-day work such as evaluating the measurement properties and
Bladder Cancer Genetic Susceptibility. A Systematic Review

Background: The variant/gene candidate approach to explore bladder cancer (BC) genetic susceptibility has been applied in many studies with significant findings reported. However, results are not always conclusive due to the lack of replication by subsequent studies. Objectives: To identify all epidemiological investigations on the genetic associations with BC risk, to quantify the likely magnitude of the associations by applying metaanalysis methodology and to assess whether there is a potential for publication/reporting bias. Methods: To address our aims, we have catalogued all genetic association studies published in the field of BC risk since 2000. Furthermore, we metaanalysed all polymorphisms with data available from at least three independent case-control studies with subjects of Caucasian origin analyzed under the same mode of inheritance. Results: The characterization of the genetic susceptibility of BC is composed of 28 variants, GWAS contributing most of them. Most of the significant variants associated with BC risk are located in genes belonging to chemical carcinogenesis, DNA repair, and cell cycle pathways. Causal relationship was also provided by functional analysis for GSTM1-null, NAT2-slow, APOBEC-rs1014971, CCNE1-rs8102137, SLC14A1-rs10775480, PSCA-rs2294008, UGT1A-rs1189203, and TP63-rs35592567. Conclusions: Genetic susceptibility of BC is still poorly defined, with GWAS contributing most of the strongest evidence. The systematic review did not provide evidence of further genetic associations. The potential public health translation of the existing knowledge on genetic susceptibility on BC is still limited.
Visualizing Basic Words Chosen by Latent Dirichlet Allocation for Serendipitous Recommendation

The use of recommender systems to support users' search and selection of items in an information overloaded environment is widespread. Usually, precision and recall are utilized for evaluating a recommender system. However, an alternative measure should be considered, because a user's satisfaction is the most important factor to be considered when constructing a recommender system. Briefly, there exists a novel technique, serendipitous recommendation that considers this factor. In this paper, we propose a new method for constructing a novel serendipitous recommendation technique. In our method, we utilize a map of basic words that shows the semantic relationships between words. The basic words selected by Latent Dirichlet Allocation (LDA) are arranged on the map by principal components analysis (PCA). As a result, they are composed of semantically connected word pairs. We believe that this map is useful for searching and selecting items, because the user can find serendipitous words.
Variable compliance control for transfer support robot

Recently in Japan, increase in necessity of nursing care with elderly society has been problematic. Transfer task of a person in need of nursing care is one of the heavy load for care-worker. Additionally, the problem of the privacy protection for the disability in the private space such as a toilet and bath is a serious issue. Therefore, the aim of this research is to develop the transfer support robot which enables to promote the independence of the disability in the private space. In this paper, as the first step of the realization, the necessary movements and controls are clarified. The newly-designed variable compliance control method is proposed. In the proposed method, compliance control is applied to the position control based control system. The stiffness of the robot changes smoothly based on the information of disturbance force caused by human motion and weight. It means that safety cooperative work is possible even when humans perform irregular movements. By the proposed method, when a disturbance force occurs downward direction due to a human weight, the robot has highly stiffness value. When a disturbance force occurs upward direction due to a human motion, the robot has lowly stiffness value. The validity of the proposed method was confirmed by simulation and experiment using a 2-link manipulator imitate the transfer support robot.
Maternal Serum Endocan Concentration in Pregnancies Complicated by Intrauterine Growth Restriction

Objectives: Endocan plays a role in the development of vascular tissue in health and disease and is an indicator of endothelial cells activation and angiogenesis. Therefore, this study aimed to investigate the relationship between maternal endocan serum level and intrauterine growth restriction (IUGR) as well as ultrasound Doppler flow measurements indicating placental insufficiency. Methods: This study included a group of women with IUGR (n = 37) and a group of healthy pregnant women (controls, n = 37). The endocan serum concentrations were assessed using commercially available enzyme-linked immunosorbent assay kit. Every woman underwent an ultrasound examination with Doppler flow measurements of the uterine arteries, umbilical vessels, and fetal middle cerebral artery. We used the cerebroplacental ratio (CPR) to determine placental insufficiency. Results: We found significant differences in median (interquartile) endocan serum level (pg/mL) between study and control groups (464 [374-532] vs 339 [189-496], respectively; P < .001). The endocan serum level correlated neither with umbilical cord blood gases nor with Apgar score. Ultrasound Doppler findings revealed significant differences in middle cerebral artery pulsatility index (PI), umbilical artery PI, CPR, as well as mean uterine arteries PI between IUGR group and controls. In the study group, we found significant correlations between the serum endocan and CPR (R = 0.56, P < .001) as well as between serum endocan and mean uterine arteries PI (R = 0.46, P = .006). Conclusion: Endocan is likely involved in the pathogenesis of IUGR in pregnant women and possibly is a useful marker of endothelial dysfunction in these cases.
Central limit theorems for empirical transportation cost in general dimension

We consider the problem of optimal transportation with quadratic cost between a empirical measure and a general target probability on R d , with d $\ge$ 1. We provide new results on the uniqueness and stability of the associated optimal transportation potentials , namely, the minimizers in the dual formulation of the optimal transportation problem. As a consequence, we show that a CLT holds for the empirical transportation cost under mild moment and smoothness requirements. The limiting distributions are Gaussian and admit a simple description in terms of the optimal transportation potentials.
Action-Dependent Photobiomodulation on Health, Suboptimal Health, and Disease

The global photobiomodulation (PBM) on an organism was studied in terms of function-specific homeostasis (FSH) and scale-free functional network in this paper. A function can be classified into a normal function in its FSH and a dysfunctional function far from its FSH. An FSH-specific stress (FSS) disrupting an FSH can also be classified into a successful stress in its FSS-specific homeostasis (FSSH) and a chronic stress far from its FSSH. The internal functions of an organism can be divided into essential, special nonessential, and general nonessential functions. Health may be defined as a state of an organism in which all the essential and special nonessential functions are normal or their stresses are successful. Suboptimal health may be defined as a state of a disease-free organism in which only some special nonessential functions are dysfunctional in comparison with its healthy state. Disease may be defined as a state of an organism which is not in both health and suboptimal health. The global PBM of health, suboptimal health, or disease suggested that the PBM may depend on the organism action.