Miracle-dz/UniFAR-FTUs huggingface dataset:
Wikipedia-Based Efficient Sampling Approach for Topic Model

In this paper, we propose a novel approach called Wikipedia-based Collapsed Gibbs sampling (Wikipedia-based CGS) to improve the efficiency of the collapsed Gibbs sampling(CGS), which has been widely used in latent Dirichlet Allocation (LDA) model. Conventional CGS method views each word in the documents as an equal status for the topic modeling. Moreover, sampling all the words in the documents always leads to high computational complexity. Considering this crucial drawback of LDA we propose the Wikipedia-based CGS approach that commits to extracting more meaningful topics and improving the efficiency of the sampling process in LDA by distinguishing different statuses of words in the documents for sampling topics with Wikipedia as the background knowledge. The experiments on real world datasets show that our Wikipedia-based approach for collapsed Gibbs sampling can significantly improve the efficiency and have a better perplexity compared to existing approaches.
Recent advances in laser dermatology

Lasers have revolutionized the practice of modern dermatology. Our understanding of laser physics and selective photothermolysis has expanded greatly over the last 20 years. In the last 2 years, we have looked beyond the traditional lasers and explored new concepts. This article will look at five of these new concepts. A strong understanding of these new techniques will allow dermatologists to use them either primarily or in combination with more conventional methods.
Kinetics, Equilibrium, and Thermodynamics Studies of the Biosorption of Lead(II) and Chromium(III) by Basella alba L.

The ability of a fast growing plant (Basella alba L.) to remove lead(II) and chromium(III) ions from aqueous solutions has been studied in a batch system. The effects of various parameters such as pH, biomass dosage, agitation time; and initial metal concentration were examined and have been found to have direct influence on the uptake of the metals by the biosorbent. Time-dependence experiments for the metal ions showed that optimum binding to the Basella alba L. occurred within 30 min. and 7 min. for Pb 2+ and Cr 3+ , respectively.
Complement Gene Expression in Human Cardiac Allograft Biopsies as a Correlate of Histologic Grade of Injury

Complement activation contributes to antibody-mediated allograft rejection, but increasing evidence also implicates complement proteins produced locally within the graft, in part by infiltrating mononuclear cells, as important mediators of tissue injury. To test this concept in transplant recipients, we evaluated complement, complement regulator, and T cell/proinflammatory marker gene expression by quantitative real-time polymerase chain reaction in 71 archived heart transplant biopsies and correlated the results with the histologic grade of rejection. Significantly more transcripts encoding alternative pathway components factor B, C3 and properdin, and C3a receptor and C5a receptor were detected in grade 3 versus grade 0 or 1 biopsies. The grade 3 rejections also contained significantly higher amounts of CD3, interferon &ggr;, perforin, and granzyme B genes. In addition to providing supportive evidence for a pathogenic role of graft-derived complement in human heart transplant injury, these correlations suggest that molecular profiling of complement gene expression could be useful in the diagnosis of human allograft rejection.
Blood pressure control in patients receiving bevacizumab in an outpatient cancer center

Purpose. Hypertension is a common adverse effect of vascular endothelial growth factor (VEGF) signaling inhibitors, such as bevacizumab, with an incidence upwards of 35%. The management of bevacizumab-induced hypertension is important in order to avoid dose interruption/discontinuation and/or end organ damage. The efficacy of antihypertensive medications for this cause of hypertension has not been demonstrated. This study seeks to determine if antihypertensives are effective in treating anti-VEGF-induced hypertension from bevacizumab and determine which classes of antihypertensive agents are effective. Methods. A retrospective review of all patients who received bevacizumab between January 2007 and September 2009 at two medical centers was conducted. Patients were included if they experienced new onset or exacerbation of preexisting hypertension, during bevacizumab treatment. Efficacy of antihypertensives was determined by recording a 28-day change in systolic blood pressure from the initiation or dose increase of individual antihypertensive medications. Secondary endpoints included an efficacy analysis of antihypertensive classes. Results. Five-hundred thirteen patients were identified as receiving bevacizumab during the indicated time period. Fifty-seven patients met the full inclusion/exclusion criteria for analysis. The average systolic blood pressure declined by 23 mm Hg with 4 weeks of treatment (p < 0.0001). Each class had a statistically significant decline in systolic blood pressure of 15.5–57 mm Hg with the exception of diuretics and a group of miscellaneous antihypertensives. Conclusions. This is the first data that demonstrates individual classes of antihypertensives are effective in bevacizumab-induced hypertension. Most antihypertensives were effective in reducing blood pressure, with the exception of diuretics and miscellaneous antihypertensives, which may be due to a limited sample size.
Messenger RNA‐ Versus Retrovirus‐Based Induced Pluripotent Stem Cell Reprogramming Strategies: Analysis of Genomic Integrity

The use of synthetic messenger RNAs to generate human induced pluripotent stem cells (iPSCs) is particularly appealing for potential regenerative medicine applications, because it overcomes the common drawbacks of DNA‐based or virus‐based reprogramming strategies, including transgene integration in particular. We compared the genomic integrity of mRNA‐derived iPSCs with that of retrovirus‐derived iPSCs generated in strictly comparable conditions, by single‐nucleotide polymorphism (SNP) and copy number variation (CNV) analyses. We showed that mRNA‐derived iPSCs do not differ significantly from the parental fibroblasts in SNP analysis, whereas retrovirus‐derived iPSCs do. We found that the number of CNVs seemed independent of the reprogramming method, instead appearing to be clone‐dependent. Furthermore, differentiation studies indicated that mRNA‐derived iPSCs differentiated efficiently into hepatoblasts and that these cells did not load additional CNVs during differentiation. The integration‐free hepatoblasts that were generated constitute a new tool for the study of diseased hepatocytes derived from patients' iPSCs and their use in the context of stem cell‐derived hepatocyte transplantation. Our findings also highlight the need to conduct careful studies on genome integrity for the selection of iPSC lines before using them for further applications.
Cognition and behavior in pre‐pubertal children with Prader–Willi syndrome and associations with sleep‐related breathing disorders

Prader–Willi syndrome (PWS) is characterized by hypotonia, hypogonadism, obesity, and short stature. Neurobehavioral abnormalities, cognitive impairment, and sleep‐related breathing disorders (SRBD) are common. In the general population associations between neurobehavioral and cognitive abnormalities and SRBD have been found. We investigated cognition, behavior, and SRBD in children with PWS. Thirty‐one pre‐pubertal PWS children were evaluated (5 with paternal deletion, 14 with maternal disomy, 4 with imprinting‐center mutation, and in 8 the defect was not specified). Cognition was assessed by Wechsler scale subtests, and behavior by parent–questionnaires. Polysomnography was performed. Cognition, behavior, and associations with SRBD were evaluated. All cognitive subtests were significantly below O SDS, with the lowest median (interquartile range) scores for the Block design subtest (−2.7 SDS (−3.0 to −0.3)). In 60%, verbal subtests were less affected than performance subtests. Parents reported problem behavior related to “emotions/behavior not adapted to the social situation” and “insensitivity to social information. ” All children had SRBD, with an Apnea Hypopnea Index of 4.1/hr (2.6–7.9). One performance subtest score was significantly higher in children with better sleep efficiency, and daytime sleepiness was associated with more autistic‐like social impairment. In contrast to our expectations, behavior was worse in children with better sleep‐related breathing. In pre‐pubertal PWS children, cognition is impaired. Neurobehavioral abnormalities are common, particularly autistic‐like social impairment. Sleep efficiency was associated with better performance on one of the performance subtests, and neurobehavioral abnormalities were associated with daytime sleepiness. In contrast, we could not confirm a positive association of neurobehavioral abnormalities with SRBD in PWS. © 2008 Wiley‐Liss, Inc.
Report : Verifiable Control for ( Semi ) Autonomous Cars that Learns from Human ( Re ) Actions

Currently, autonomous cars tend to be overly defensive and obliviously opaque. When needing to merge into another lane, they will patiently wait for another driver to pass first. When stopped at an intersection and waiting for the driver on the right to go, they will sit there unable to wave them by. They are very capable when it comes to obstacle avoidance, lane keeping, localization, active steering and braking [1–7]. But when it comes to other human drivers, they tend to rely on simplistic models: for example, assuming that other drivers will be bounded disturbances [8, 9], they will keep moving at the same velocity [10–12], or they will approximately follow one of a set of known trajectories [13, 14]. These simplistic models lead to predictions about what other cars are going to do, and the autonomous car’s task is to do its best to stay out of their way. It will not cut in front of another driver when it is in a rush. It will also be restricted to functional actions, and not execute actions that are communicative. Our goal is to enable autonomous cars to be more efficient, and better at coordinating with human drivers.
Combining Attention Model with Hierarchical Graph Representation for Region-Based Image Retrieval

The manifold-ranking algorithm has been successfully adopted in content-based image retrieval (CBIR) in recent years. However, while the global low-level features are widely utilized in current systems, region-based features have received little attention. In this paper, a novel attention-driven transductive framework based on a hierarchical graph representation is proposed for region-based image retrieval (RBIR). This approach can be characterized by two key properties: (1) Since the issue about region significance is the key problem in region-based retrieval, a visual attention model is chosen here to measure the regions' significance. (2) A hierarchical graph representation which combines region-level with image-level similarities is utilized for the manifold-ranking method. A novel propagation energy function is defined which takes both low-level visual features and regional significance into consideration. Experimental results demonstrate that the proposed approach shows the satisfactory retrieval performance compared to the global-based and the block-based manifold-ranking methods.
Mospd1, a new player in mesenchymal versus epidermal cell differentiation

Mospd1 codes for a small protein with unknown physiological function, which is part of a family of genes, including Mospd2 and Mospd3, defined by the presence of the major sperm protein domain and two transmembrane domains. This work characterizes the Mospd1 gene, the intracellular location of the protein and its expression in different mouse tissues and mesenchymal cell lines during differentiation. The role of Mospd1 in mesenchymal cellular differentiation was studied by siRNA knockdown experiments in mouse osteoblastic MC3T3‐E1 cells. Transfection experiments of the targeted cDNA show MOSPD1 located in the endoplasmatic reticulum and in the Golgi apparatus. Removal of the last exon of the gene resulted in localization of the protein in the nucleus, which was attributed to a nuclear export sequence in the N‐terminal part. In mouse tissues the gene was generally strongly expressed while mesenchymal tissues showed the highest expression. In mesenchymal cell lines Mospd1 mRNA was higher expressed in cells with advanced differentiation status. In osteoblastic, myoblastic, and adipocytic cell lines Mospd1 was up‐regulated during differentiation. Genome‐wide gene expression analysis after knockdown of Mospd1 by siRNA in MC3T3‐E1 cells revealed a shift in the gene expression pattern from mesenchymal to epithelial genes featuring up‐regulation of the epithelial cadherin Cdh1 and down‐regulation of its inhibitors Snail1 and 2 and the mesenchymal cadherin Cdh11, suggesting a mesenchymal to epithelial transition. From these data we conclude that Mospd1 plays a pivotal role in the developmental regulation at the switch between mesenchymal and epithelial cells. J. Cell. Physiol. 226: 2505–2515, 2011. © 2010 Wiley‐Liss, Inc.
Ultrasonic evaluation of cervical metastatic lymphadenopathy.

We investigated the location, size, and shape of cervical lymph nodes in head and neck cancer, using a 7.5‐MHz ultrasound scanner. First, the different criteria for normal size were obtained for cervical lymph nodes in each region; lymph nodes greater than 9 mm in thickness in the internal jugular chain or greater than 7 mm in thickness in the submandibular and submental chains should be suspected of harboring metastatic foci. Second, metastatic nodes showed a more rounded configuration than nonmetastatic ones. Third, a comparative study of metastatic lymph nodes between the in vivo and in vitro ultrasonograms and the corresponding histopathological findings disclosed that an echogenic region in an ultrasonogram of a metastatic node was caused by coagulation necrosis, and a cystic area of liquefaction necrosis.
Computer Vision for Card Games

For this project, we designed a computer vision program that can recognize and accurately classify photos of playing cards lying on a table into one of 52 classes. In conjunction with our CS221 project, where we designed a card playing AI, this allows us to develop a holistic application for a player with a real-world card deck to play against a computer or for a player to use AI support (e.g. via Google glasses), playing a real world game against an adversary. We decided to test a variety of machine learning methods to tackle this computer vision problem. Using classical methods such as multiclass logistic regression and multiclass support vector machines with regularization, we managed to achieve accuracies between 82-89% on the dev and test sets. Using deep learning approaches, we designed a custom convolutional neural network in Tensorflow, that manages to get 100 % on the dev and test sets. Keywords—Computer Vision, Object Classification, Convolutional Neural Networks
Profiles of Sibling Bullying

Considerable research has been done on childhood bullying, including its antecedents and consequences. Yet, with all of the attention on bullying, particularly school bullying, sibling bullying has been vastly overlooked. Sibling bullying is a type of violence prevalent in the lives of most children, but little is known about the phenomenon. The purpose of this study was to profile sibling bullying by examining prevalence rates, the extent to which siblings perceive sibling bullying to be normative, and victim–perpetrator differences in perceptions of sibling bullying. Twenty-seven sibling pairs who wrote stories about personal experiences of sibling bullying and victimization completed questionnaires about these experiences and responded to their sibling partners’ stories. Of the siblings surveyed, 78% reported being bullied by their sibling and 85% reported bullying their sibling during their childhood. This is far greater than published statistics on peer bullying. Not surprisingly, victims viewed sibling bullying more negatively than perpetrators. Sadly, there was a norm of acceptance of sibling bullying among most of the sibling pairs. Practical implications are discussed.
The role of psychological well-being in obese and overweight older adults

Being obese or overweight is often associated with impaired quality of life and psychological well-being (PWB) in comparison with normal-weight people (Giuli et al., 2014), both in developed and developing countries. PWB is considered a very important correlate of subjective well-being in people with excess weight. The concept of PWB is based on Ryff's multidimensional model (Ryff, 2014), which considers well-being as eudaemonic concept, and includes six dimensions: autonomy, environmental mastery, personal growth, positive relations with others, purpose in life, and self-acceptance. Few studies have analyzed the role of specific correlates of perceived well-being in the obese and overweight Italian older population. The purpose of this study was to evaluate the role of perceived well-being in obese and overweight older adults. Our study included 124 overweight and obese older participants, aged 60 years or more, selected from patients attending the Division of Endocrinology, Department of Clinical and Molecular Sciences of Polytechnic University of Marche (Italy). As previously described (Giuli et al., 2014), the participants were recruited on the basis of specific inclusion/exclusion criteria, in a period of three years (January 2010–December 2012).
High-speed, high-accuracy binarization method for recognizing text in images of low spatial resolutions

We propose a new high-speed, high-accuracy binarization method for recognizing text in document images. First character neighborhoods are extracted from input images using a global thresholding value that is shifted to the background pixel value from the thresholding value of conventional global binarization. Second, characters are extracted using an original local binarization process integrated with image interpolation. Our method takes only 1/100 the processing time over the method that performs image interpolation first. Therefore our method binarizes an A4 size text image (150dpi) in an average of only 3.3 seconds using a 166 MHz Pentium processor. Furthermore, our method reduced unrecognized characters by 46.5%, compared with conventional global binarization.
Phosphorylation of CrkII Adaptor Protein at Tyrosine 221 by Epidermal Growth Factor Receptor*

CrkII adaptor protein becomes tyrosine-phosphorylated upon various types of stimulation. We examined whether tyrosine 221, which has been shown to be phosphorylated by c-Abl, was phosphorylated also by other tyrosine kinases, such as epidermal growth factor (EGF) receptor. For this purpose, we developed an antibody that specifically recognizes Tyr221-phosphorylated CrkII, and we demonstrated that CrkII was phosphorylated on Tyr221 upon EGF stimulation. When NRK cells were stimulated with EGF, the tyrosine-phosphorylated CrkII was detected at the periphery of the cells, where ruffling is prominent, suggesting that signaling to CrkII may be involved in EGF-dependent cytoskeletal reorganization. The EGF-dependent phosphorylation of CrkII was also detected in a c-Abl-deficient cell line. Moreover, recombinant CrkII protein was phosphorylated in vitro by EGF receptor. These results strongly suggest that EGF receptor directly phosphorylates CrkII. Mutational analysis revealed that the src homology 2 domain was essential for the phosphorylation of CrkII by EGF receptor but not by c-Abl, arguing that these kinases phosphorylate CrkII by different phosphorylation mechanisms. Finally, we found that the CrkII protein phosphorylated upon EGF stimulation did not bind to the phosphotyrosine-containing peptide and that CrkII initiated dissociation from EGF receptor within 3 min even with the sustained tyrosine phosphorylation of EGF receptor. This result implicated phosphorylation of Tyr221 in the negative regulation of the src homology 2-mediated binding of CrkII to EGF receptor.
Spatial and temporal organization of replicating Escherichia coli chromosomes

The positions of DNA regions close to the chromosome replication origin and terminus in growing cells of Escherichia coli have been visualized simultaneously, using new widely applicable reagents. Furthermore, the positions of these regions with respect to a replication factory‐associated protein have been analysed. Time‐lapse analysis has allowed the fate of origins, termini and the FtsZ ring to be followed in a lineage‐specific manner during the formation of microcolonies. These experiments reveal new aspects of the E. coli cell cycle and demonstrate that the replication terminus region is frequently located asymmetrically, on the new pole side of mid‐cell. This asymmetry could provide a mechanism by which the chromosome segregation protein FtsK, located at the division septum, can act directionally to ensure that the septal region is free of DNA before the completion of cell division.
Diversity and Distribution of Escherichia coli Genotypes and Antibiotic Resistance Phenotypes in Feces of Humans, Cattle, and Horses

ABSTRACT Escherichia coli is the most completely characterized prokaryotic model organism and one of the dominant indicator organisms for food and water quality testing, yet comparatively little is known about the structure of E. coli populations in their various hosts. The diversities of E. coli populations isolated from the feces of three host species (human, cow, and horse) were compared by two subtyping methods: ribotyping (using HindIII) and antibiotic resistance analysis (ARA). The sampling effort required to obtain a representative sample differed by host species, as E. coli diversity was consistently greatest in horses, followed by cattle, and was lowest in humans. The diversity of antibiotic resistance patterns isolated from individuals was consistently greater than the diversity of ribotypes. E. coli populations in individuals sampled monthly, over a 7- to 8-month period, were highly variable in terms of both ribotypes and ARA phenotypes. In contrast, E. coli populations in cattle and humans were stable over an 8-h period. Following the cessation of antibiotic therapy, the E. coli population in the feces of one human experienced a rapid and substantial shift, from a multiply antibiotic-resistant phenotype associated with a particular ribotype to a relatively antibiotic-susceptible phenotype associated with a different ribotype. The high genetic diversity of E. coli populations, differences in diversity among hosts, and temporal variability all indicate complex population dynamics that influence the usefulness of E. coli as a water quality indicator and its use in microbial source tracking studies.
Homogeneous Cooling with Repulsive and Attractive Long‐range Interactions

In granular matter, consisting of discrete particles, long-range interactions imply that each of the particles is interacting with all others. For many charged granular materials with Coulomb repulsion or large-scale gravitationally attractive systems, a Molecular Dynamics environment is developed. In granular systems with long-range interaction forces and dissipative collisions, both effects can lead to large-scale structure formation, whereas already dissipation alone leads to ever growing clusters. For our three-dimensional mono-charged dissipative homogeneous systems we present the effect of both repulsive and attractive mutual long-range forces and make an attempt to predict the collision frequency and the temperature decay in the system by means of a modified pseudo-Liouville operator formalism. The theoretical predictions are in perfect agreement with the simulations, but only in the limit of low density and for not too strong interaction potential enrgy.