Miracle-dz/UniFAR-FTUs huggingface dataset:
Breast cancer detected with screening US: reasons for nondetection at mammography.

PURPOSE To retrospectively review the mammograms of women with breast cancers detected at screening ultrasonography (US) to determine the reasons for nondetection at mammography. MATERIALS AND METHODS This study received institutional review board approval, and informed consent was waived. Between 2003 and 2011, a retrospective database review revealed 335 US-depicted cancers in 329 women (median age, 47 years; age range, 29-69 years) with Breast Imaging Reporting and Data System breast density type 2-4. Five blinded radiologists independently reviewed the mammograms to determine whether the findings on negative mammograms should be recalled. Three unblinded radiologists re-reviewed the mammograms to determine the reasons for nondetection by using the reference location of the cancer on mammograms obtained after US-guided wire localization or breast magnetic resonance imaging. The number of cancers recalled by the blinded radiologists were compared with the reasons for nondetection determined by the unblinded radiologists. RESULTS Of the 335 US-depicted cancers, 63 (19%) were recalled by three or more of the five blinded radiologists, and 272 (81%) showed no mammographic findings that required immediate action. In the unblinded repeat review, 263 (78%) cancers were obscured by overlapping dense breast tissue, and nine (3%) were not included at mammography owing to difficult anatomic location or poor positioning. Sixty-three (19%) cancers were considered interpretive errors. Of these, 52 (82%) were seen as subtle findings (46 asymmetries, six calcifications) and 11 (18%) were evident (six focal asymmetries, one distortion, four calcifications). CONCLUSION Most breast cancers (81%) detected at screening US were not seen at mammography, even in retrospect. In addition, 19% had subtle or evident findings missed at mammography.
Elastic model of DNA supercoiling in the infinite-length limit

The energies of plectonemic and toroidal supercoiled DNA are calculated by treating DNA as an elastic rod with a finite radius. End effects are ignored and all extensive quantities (e.g., writhe, bend energy) are treated as linear densities (writhe per unit length, bend energy per unit length). Minimum energy configurations are found. For plectonemic DNA, the superhelical pitch angle α is in the range 45°<α≤90°. For low values of specific linking difference, most superhelicity is in writhe. As specific linking difference increases, a greater proportion of superhelicity is in twist. Under physiological conditions, roughly 88% of superhelicity is in writhe. Ionic strength effects are discussed, and it is found that variation of excluded volume with ionic strength has a large effect, resulting in significantly greater torsional stress in supercoiled DNA at low ionic strength. For biologically relevant values of specific linking difference, the plectonemic conformation is energetically favored over toroidal conformations. Results are compared with electron microscopy data. The application of the model to DNA conformational transitions is discussed.
Functional Selectivity of Natural and Synthetic Prostaglandin EP4 Receptor Ligands

Classically, the prostaglandin E2 (PGE2) receptor EP4 has been classified as coupling to the Gαs subunit, leading to intracellular cAMP increases. However, EP4 signaling has been revealed to be more complex and also involves coupling to pertussis toxin-sensitive Gαi proteins and β-arrestin-mediated effects. There are now many examples of selective activation of independent pathways by G protein-coupled receptor (GPCR) ligands, a concept referred to as functional selectivity. Because most EP4 ligands had thus far only been functionally characterized by their ability to stimulate cAMP production, we systematically determined the potencies and efficacies of a panel of EP4 ligands for activation of Gαs, Gαi, and β-arrestin relative to the endogenous ligand PGE2. For this purpose, we adapted three bioluminescence resonance energy transfer (BRET) assays to evaluate the respective pathways in living cells. Our results suggest considerable functional selectivity among the tested, structurally related agonists. PGE2 was the most selective in activating Gαs, whereas PGF2α and PGE1 alcohol were the most biased for activating Gαi1 and β-arrestin, respectively. We observed reversal in order of potencies between β-arrestin 2 and Gαi1 functional assays comparing PGE1 alcohol and either PGF2α, PGD2, or 7-[(1R,2R)-2-[(E,3R)-3-hydroxy-4-(phenoxy)but-1-enyl]-5-oxocyclopentyl]heptanoic acid (M&B28767). Most ligands were full agonists for the three pathways tested. Our results have implications for the use of PGE2 analogs in experimental and possibly clinical settings, because their activity spectra on EP4 differ from that of the native agonist. The BRET-based methodology used for this first systematic assessment of a set of EP4 agonists should be applicable for the study of other GPCRs.
Role of the Two Catalytic Domains of DSR-E Dextransucrase and Their Involvement in the Formation of Highly α-1,2 Branched Dextran

ABSTRACT The dsrE gene from Leuconostoc mesenteroides NRRL B-1299 was shown to encode a very large protein with two potentially active catalytic domains (CD1 and CD2) separated by a glucan binding domain (GBD). From sequence analysis, DSR-E was classified in glucoside hydrolase family 70, where it is the only enzyme to have two catalytic domains. The recombinant protein DSR-E synthesizes both α-1,6 and α-1,2 glucosidic linkages in transglucosylation reactions using sucrose as the donor and maltose as the acceptor. To investigate the specific roles of CD1 and CD2 in the catalytic mechanism, truncated forms of dsrE were cloned and expressed in Escherichia coli. Gene products were then small-scale purified to isolate the various corresponding enzymes. Dextran and oligosaccharide syntheses were performed. Structural characterization by 13C nuclear magnetic resonance and/or high-performance liquid chromatography showed that enzymes devoid of CD2 synthesized products containing only α-1,6 linkages. On the other hand, enzymes devoid of CD1 modified α-1,6 linear oligosaccharides and dextran acceptors through the formation of α-1,2 linkages. Therefore, each domain is highly regiospecific, CD1 being specific for the synthesis of α-1,6 glucosidic bonds and CD2 only catalyzing the formation of α-1,2 linkages. This finding permitted us to elucidate the mechanism of α-1,2 branching formation and to engineer a novel transglucosidase specific for the formation of α-1,2 linkages. This enzyme will be very useful to control the rate of α-1,2 linkage synthesis in dextran or oligosaccharide production.
DISMORFIA MUSCULAR: PERSPECTIVA HISTÓRICA Y ACTUALIZACIÓN EN SU DIAGNÓSTICO, EVALUACIÓN Y TRATAMIENTO

The growing scientific production related to Muscular dysmorphia (MD) makes it clear that men also suffer body image pressures. This article aims to describe the historical background and recent studies that clarify its diagnostic conceptualization and different etiological models; also, an update on the assessment tools and treatment is presented. According to the DSM- 5, the MD represents a specific type of body dysmorphic disorder. However, the new scientific findings relate MD more closely to eating disorders, both in the clinical profile and the proposed treatment. In turn, the etiological models underscore the importance of assessing body image in the development of MD, which is modulated by psychosocial factors. Also, in recent years specific instruments have been developed to assess male body dissatisfaction and DM. However, the lack of
Executive function processes: inhibition, working memory, planning and attention in children and youth with Attention Deficit Hyperactivity Disorder

Executive Function Processes: Inhibition, Working Memory, Planning and Attention in Children and Youth with Attention Deficit Hyperactivity Disorder. (December 2004). Monica Eileen Wolfe, B.A., Texas Woman’s University Co-Chairs of Advisory Committee: Dr. Cynthia A. Riccio Dr. Michael J. Ash This study examines the roles of inhibition, attention, working memory, and planning in youth with and without ADHD. As conceptualized in theories of attention, inhibition, and working memory, difficulties with these executive processes interact to manifest in the behavioral syndrome(s) of ADHD. Barkley (1997) proposed disinhibition as the primary deficit of ADHD. Rapport, Chung, Shore, Denney, & Isaacs, (2000) theorized that ADHD results from a primary deficit in working memory. Mirsky (1987) proposed a model of attention which children with ADHD have deficits in abilities to focus/execute, encode and sustain attention. Posner and Petersen (1990) proposed that three attentional networks are responsible for attentional processes and those children with ADHD have deficits in the vigilance network. To investigate the contributions of inhibition, working memory, attention, and planning in executive dysfunction in children with ADHD, measures were selected from factor analytic studies. Children with ADHD-Combined Type demonstrated poorer inhibition and working memory than children with no diagnosis after controlling for IQ effects. No differences in planning and attention were indicated after controlling for IQ effects.
The IPATCH System for Maritime Surveillance and Piracy Threat Classification

In the EU FP7 project IPATCH, we are researching components for a maritime piracy early detection and avoidance system for deployment on merchant vessels. The system combines information from on-board sensors with intelligence from external sources in order to give early warnings about piracy threats. In this paper we present the ongoing work with the development of an integrated system fusing heterogeneous data.
A Comparative Study of Methods for Hypermedia Development

This paper presents a comparative study of the most relevant methodologies for hypermedia and Web development published in the last few years. Most of these methods focus on the design of hypermedia applications; only a few cover more aspects of the life cycle, such as requirements capture, implementation and/or testing. One common characteristic is the separation of the domain analysis from the specification of the navigation space structure as well as from the design of the user interface. A brief description of each of these methodologies is given as well as a set of comparisons. We compare the main concepts, the phases o steps of the model, CASE Tool support as well as the modelling technique, notation and graphical representation. A list of the most relevant characteristics of the Unified Process is given as well comparing it to hypermedia development methodologies.
The single-referent collector: Optimizing compaction for the common case

Compactors that move or copy objects need to adjust pointers. In extant compactors, pointer adjustment involves inspecting every pointer in the heap and computing the target address for each pointer. At the same time, in modern Managed Runtime Environments (MREs), only a fraction of pointers in the heap changes during compaction. This is because state-of-the-art MREs do not compact the prefix of the heap that contains few dead objects, allowing gaps between live objects and tolerating small space overhead. We describe the design and implementation of the Single-Referent Collector (SRC), a new compactor that reduces the cost of pointer manipulation by avoiding inspection and adjustment of pointers that do not change. SRC exploits the fact that in modern applications, most live objects have only one incoming pointer. For such objects, SRC stores the address of the referent in the object header. Only objects that move have their referent inspected and adjusted. The remaining pointers in the heap are not processed. SRC uses an overflow table to handle objects with multiple incoming pointers. We investigate a number of standard benchmarks and open-source applications to substantiate key statistical observations that underlie the design of SRC. We implement SRC in the HotSpot JVM as part of a generational collection system and compare it empirically with the Lisp2 compactor. We find that, by decreasing the cost of pointer processing, SRC enables significant reduction in pause times and improves application throughput.
A Novel Online Event Analysis Framework for Micro-blog Based on Incremental Topic Modeling

In this paper, we present a scalable implementation of a topic modeling (Adaptive Link-IPLSA) based method for online event analysis, which summarize the gist of massive amount of changing tweets and enable users to explore the temporal trends in topics. This model also can simultaneously maintain the continuity of the latent semantics to better capture the time line development of events. With the help of this model, users can quickly grasp major topics in these twitters. The preliminary results show that our method leads to more balanced and comprehensive improvement for online event detection compared to benchmark approaches. Additionally our algorithm is computationally feasible in near real-time scenarios making it an attractive alternative for capturing the rapidly changing dynamics of microblogs.
ECG classification using ensemble of features

In the literature, countless efforts have been made to analyze and classify electrocardiogram (ECG) signals belonging to various heart problems. In all these efforts, many feature extraction strategies have been used to expose discriminative information from ECG signals. In this paper, the contributions of widely used features to the classification performance and the required processing times to extract those features are comparatively analyzed. The utilized features can be briefly listed as time domain (TD), wavelet transform (WT), and power spectral density (PSD) based features. These feature sets are employed individually and in combination within well-known pattern classifiers, namely decision tree and artificial neural network, to assess classification performance in each case. Later, a wrapper-based feature selection strategy is used to reveal the most discriminative feature subset among the entire feature set containing all the three previously mentioned feature sets. The proposed framework is assessed considering four classes of heart conditions including normal, congestive heart failure, ventricular tachyarrhythmia and atrial fibrillation. The results of the experiments conducted on a large dataset reveal that appropriate subset of TD, WT, and PSD features rather than individual features offer higher classification performance. On the other hand, if the processing time is of concern, TD features come out on top with moderate classification performance.
Nanomaterials and Nanotechnology Synchrotron X-ray Absorption and In Vitro Bioactivity of Magnetic Macro / Mesoporous Bioactive Glasses Regular Paper

Iron oxides in macro/mesoporous bioactive glasses were characterized by synchrotron X-ray absorption near edge structure (XANES) spectroscopy. This magnetic phase was introduced by adding Fe(NO3)3 9H2O during the sol-gel synthesis. The obtained bioactive glass scaffolds exhibited superparamagnetism, in which the magnetization was increased with the increase in the Fe molar ratio from 10 to 20%. The linear combination fits of the XANES spectra indicated that the increase in the Fe molar ratio to 20% enhanced the γ-Fe2O3 formation at the expense of the αFe2O3 phase. This variation also promoted the formation of fine-grained bone-like apatites on the surface of the scaffolds in the in vitro test. The apatite growth between three and seven days was confirmed by the changing elemental compositions. However, the highest magnetic proportion led to the distortion of the skeleton walls and the collapse of the porous networks.
Synaptic Mechanisms of Thiopental‐induced Alterations in Synchronized Cortical Activity

Background Anesthetic depth after barbiturate administration has been correlated with distinct electroencephalogram (EEG) patterns. The current study used a rat neocortical brain slice micro‐EEG preparation to investigate synaptic mechanisms underlying thiopental‐induced transitions in synchronized neuronal activity. Methods Concentration‐dependent cellular actions of thiopental were investigated in brain slices using specific pharmacologic probes, whole cell patch clamps, and extracellular field recordings. Theta‐Like micro‐EEG oscillations were elicited in neocortical slices by mimicking subcortical cholinergic and gamma‐aminobutyric acid (GABA) afferent input with carbachol (100 micro Meter), a cholinergic agonist, and bicuculline (10 micro Meter) a GABAA antagonist. Results In the presence of 20 micro Meter thiopental, micro‐EEG slowing from theta (7.3+/‐0.9 Hz, mean+/‐SD, n = 19) to delta frequencies (2.5+/‐0.5 Hz, n = 11) was associated with a threefold prolongation of inhibitory currents. Burst suppression activity occurred at 50 micro Meter thiopental, and appeared to result from direct activation of GABAA ‐gated chloride currents, observed with voltage clamp recordings, and mimicked with a direct acting GABAA agonist, muscimol (1 micro Meter). Isoelectric activity occurred at 100 micro Meter thiopental, and likely resulted from reduced glutamatergic transmission, evidenced by depressed excitatory postsynaptic potentials. Glutamatergic excitation was required for burst suppression activity, because glutamate receptor antagonists blocked thiopental‐induced bursts; forcing a transition to isoelectric activity. Conclusions Thiopental produced a continuum of EEG‐like states in brain slices similar to those observed in vivo. The progression of thiopental‐induced effects appear to have resulted from specific cellular actions that were recruited in a concentration‐dependent manner. Progressive enhancement of synaptic inhibition followed by depression of excitatory transmission led to micro‐EEG frequency slowing, burst suppression, and isoelectric activity.
Online optimal gait generation for bipedal walking robots using legendre pseudospectral optimization

This paper presents an optimal gait synthesis method that exploits the full body dynamics of robots using the Hybrid Zero Dynamics (HZD) control framework and-for the first time-experimentally realizes online HZD gait generation for a planar underactuated robot. Hybrid zero dynamics is an established theoretical framework that formally enables stable control of dynamic locomotion by enforcing virtual constraints through feedback controllers. An essential part of successfully realizing dynamic walking with HZD framework is determining parameters of the virtual constraints that satisfy hybrid invariant condition via nonlinear constrained optimization. Due to the complexity of the full hybrid system model of the robot, these optimization problems often suffer from slow convergence and local minima. In this paper, we improve the reliability of the HZD gait optimization and significantly increase the convergence speed by taking advantage of the direct transcription formulation and the exponential convergence of the global orthogonal collocation (a.k.a. pseudospectral) method. As a result, generating HZD gaits online becomes feasible with an average computation time less than 0.5 seconds, as will be demonstrated experimentally on a bipedal robot.
Theatre-Arts Pedagogy for Social Justice: Case Study of the Area Youth Foundation in Jamaica

In this paper I describe and analyse the socio-educational significance of a theatre arts approach to learning for young adults in Jamaica, implemented by the Area Youth Foundation (AYF). Briefly outlining the genesis and development of the AYF, I provide snapshots of the experiences and destinations of some of its young participants. The paper discusses AYF workshops to show how the pedagogy was shaped by the expressive arts and based on the critical praxis approach systematized by Paulo Freire in adult education and Augusto Boal in theatre. Based on interviews with AYF’s leader and some of the learners, I discuss how the foundation’s motto, “Youth Empowerment Through the Arts,” is played out in workshops and creative productions that are simultaneously learner-driven and teacher-guided, with the powerful impact of inspiring politically thoughtful creativity and skills in youths from less-privileged communities. This paper is a case study of a theatre-arts approach to learning for young adults in Jamaica, implemented by the Area Youth Foundation (AYF), a non-profit, non-government organisation. The essay is based on qualitative methods that describe and reflect on the socio-educational significance of the pedagogy and learning practised in AYF. Following a case study approach proposed by Robert Yin (1984), I study the phenomenon within its real-life context, when the boundaries between phenomenon and context are fluid, using multiple sources of evidence. I first set the Jamaican context that frames the work and development of the AYF. The content of the case is drawn from information that I obtained from AYF participants—students and the executive director/leader—through semi-structured interviews, conversations, and observation of their workshops and rehearsals. Themes that arose from the transcribed material are described and analysed. I relate this to my theoretical understandings of literacies (Hickling-Hudson, 2007) and Freirean pedagogy (Hickling-Hudson, 1988), and I apply these to explore the significance of the work of AYF. Stating my background, in the tradition of qualitative research, I start by indicating that I was introduced to the AYF by Sheila Lowe Graham, a Jamaican friend and colleague who established AYF and leads the implementation of its work. Over several visits to Jamaica between 2000 and 2012, I was excited to see more of the work of the group, for it seemed to be establishing the kind of alternative approach to education that I knew was desperately needed. My interest in this field stems from my Caribbean origins, upbringing, and experience as an educator working in the 1970s and 1980s in the less-privileged schools, teachers colleges, and adult education programs in Jamaica and Grenada (see Evans, 2009; Hickling-Hudson, 1995). My commitment gradually became one of developing a postcolonial approach to curriculum
Mutation testing as a safety net for test code refactoring

Refactoring is an activity that improves the internal structure of the code without altering its external behavior. When performed on the production code, the tests can be used to verify that the external behavior of the production code is preserved. However, when the refactoring is performed on test code, there is no safety net that assures that the external behavior of the test code is preserved. In this paper, we propose to adopt mutation testing as a means to verify if the behavior of the test code is preserved after refactoring. Moreover, we also show how this approach can be used to identify the part of the test code which is improperly refactored.
Interpolation-Based Image Super-Resolution Using Multisurface Fitting

In this paper, we propose a new interpolation-based method of image super-resolution reconstruction. The idea is using multisurface fitting to take full advantage of spatial structure information. Each site of low-resolution pixels is fitted with one surface, and the final estimation is made by fusing the multisampling values on these surfaces in the maximum a posteriori fashion. With this method, the reconstructed high-resolution images preserve image details effectively without any hypothesis on image prior. Furthermore, we extend our method to a more general noise model. Experimental results on the simulated and real-world data show the superiority of the proposed method in both quantitative and visual comparisons.