Miracle-dz/UniFAR-FTUs huggingface dataset:
Node sampling for protein complex estimation in bait-prey graphs

Abstract In cellular biology, node-and-edge graph or “network” data collection often uses bait-prey technologies such as co-immunoprecipitation (CoIP). Bait-prey technologies assay relationships or “interactions” between protein pairs, with CoIP specifically measuring protein complex co-membership. Analyses of CoIP data frequently focus on estimating protein complex membership. Due to budgetary and other constraints, exhaustive assay of the entire network using CoIP is not always possible. We describe a stratified sampling scheme to select baits for CoIP experiments when protein complex estimation is the main goal. Expanding upon the classic framework in which nodes represent proteins and edges represent pairwise interactions, we define generalized nodes as sets of adjacent nodes with identical adjacency outside the set and use these as strata from which to select the next set of baits. Strata are redefined at each round of sampling to incorporate accumulating data. This scheme maintains user-specified quality thresholds for protein complex estimates and, relative to simple random sampling, leads to a marked increase in the number of correctly estimated complexes at each round of sampling. The R package seqSample contains all source code and is available at http://vault.northwestern. edu/~dms877/Rpacks/.
Orientation, sphericity and roundness evaluation of particles using alternative 3D representations

Sphericity and roundness indices have been used mainly in geology to analyze the shape of particles. In this paper, geometric methods are proposed as an alternative to evaluate the orientation, sphericity and roundness indices of 3D objects. In contrast to previous works based on digital images, which use the voxel model, we represent the particles with the Extreme Vertices Model, a very concise representation for binary volumes. We define the orientation with three mutually orthogonal unit vectors. Then, some sphericity indices based on length measurement of the three representative axes of the particle can be computed. In addition, we propose a ray-casting-like approach to evaluate a 3D roundness index. This method provides roundness measurements that are highly correlated with those provided by the Krumbein's chart and other previous approach. Finally, as an example we apply the presented methods to analyze the sphericity and roundness of a real silica nano dataset.
Physiological regulation in infants of women with a mood disorder: examining associations with maternal symptoms and stress.

BACKGROUND The offspring of mothers with mood disorders may evidence increased behavioral problems as early as preschool; however, no study to date has examined psychophysiological characteristics during infancy, particularly among offspring of mothers diagnosed with bipolar disorder. Elucidating psychobiological mechanisms of risk early in development is critical to inform prevention and early intervention efforts. METHOD This study compared physiological and behavioral responsivity in 6-month-old infants (N = 329) of mothers with lifetime histories of bipolar disorder (BD, n = 44), major depressive disorder (MDD, n = 244), or no history of Axis I disorders (CTL, n = 41). Infant respiratory sinus arrhythmia (RSA) was measured in a laboratory stressor paradigm. Measures of infant affect and behavior during mother-infant interaction, current maternal depressive symptoms, and exposure to stressful life events were examined with respect to diagnostic group and RSA. RESULTS Groups did not differ in baseline RSA or infant affect measures. However, during the stressor task, infants of mothers with BD evidenced increases in RSA, while infants of MDD and CTL mothers evidenced decreases in RSA. Though levels of postnatal stress and current levels of maternal depressive symptoms differed among groups, neither of these factors predicted infant psychophysiological responses. CONCLUSIONS At 6 months of age, infants of mothers with BD show differences in psychophysiological regulation. These differences cannot be accounted for by perinatal outcome, current maternal depressive symptoms, or exposure to stressful life events, and thus may reflect endophenotypic markers of psychopathological risk.
POSTER: A Unified Framework of Differentially Private Synthetic Data Release with Generative Adversarial Network

Many differentially private data release solutions have been proposed for different types of data with the sacrifice of inherent correlation structure. Here, we propose a unified framework of releasing differentially private data. In particular, our proposed generative adversarial network (GAN)-based framework learns the input distribution, irrespective of tabular data and graphs, and generates synthetic data in a differentially private manner. Our preliminary results show the acceptable utility of the synthetic dataset.
Self-Learning Monitoring and Control of Manufacturing Processes Based on Rule Induction and Event Processing

- Manufacturing enterprises are trying to cope with turbulent market situations by enhancing their existing monitoring and control of manufacturing processes. Enterprise integration within and across the enterprise can assist to realize the aforementioned goal. Further, event processing (EP) techniques can be employed to monitor and control manufacturing processes in real-time. Rules derived from stored process data using the knowledge discovery in databases process can be managed in an EP engine as event patterns. Nonetheless, rule identification is usually an offline activity whereas the control of manufacturing processes is a real-time activity. Consequently, the rule identification process should be transformed from an offline activity to an online or (near) real-time activity. In the contribution, a methodology is presented to overcome the previously mentioned drawback. Machine learning (i.e., rule induction) methods are used to automatically adapt the existing set of event patterns. The implementation of the presented methodology has been started in a casting enterprise.
Evaluación de la Adhesión a la Terapia Antiretroviral Altamente Activa en Adultos en Jamaica

Background and Purpose: Highly active antiretroviral therapy (HAART) has improved morbidity and mortality and quality of life, revitalized communities and transformed the perception of HIV/AIDS from being a “death sentence” to a chronic illness. Strict and sustained adherence to medication is essential long-term viral suppression. In April 2005, an Adherence Support Programme was introduced to Jamaica’s HIV Programme, whereby Persons Living with HIV/ AIDS (PLWHA) who had achieved high levels of adherence were trained to provide support to other PLWHA in order to increase their adherence to HAART regimens. Methods: A cross-sectional survey of 116 individuals with advanced HIV and on HAART was performed in June and July 2006. Results: Many participants were unemployed, poor persons with limited education. Based on selfreport of seven-day adherence, 54.8% of persons were 95–100% adherent, 37.5% were 80–94% adherent and 7.7% were < 80% adherent. Having interacted with an adherence counsellor was not associated with adherence levels. Factors associated with nonadherence were: being away from home (38%), sleeping through dose-time (37%), forgetfulness (37%) and running out of pills (31%). Having no food (26.9%), not wanting to be seen taking medication (20%) and intolerable side effects (18.8%) were also reasons given. Only 44% of persons used aids to remind them of dose times. Conclusion: Adherence in this study group is low and may have worsened since 2005. More emphasis must be placed on preparing adults to start HAART. The use of pillboxes and other reminders such as alarm clocks and cell phones must be reinforced. Evaluación de la Adhesión a la Terapia Antiretroviral Altamente Activa en Adultos en Jamaica KM Harvey1, D Carrington1, J Duncan1, JP Figueroa1, L Hirschorn2, D Manning1, S Jackson1
Module Dynamique et Angle de Phase des EnrobÃ©s C-LTPP

Le dimensionnement des chaussA©es selon une approche mA©caniste-empirique requiert les caractA©ristiques mA©caniques des matA©riaux de chaussA©e. Le module dynamique et lâ€™angle de phase de 11 enrobA©s A©chantillonnA©s sur 11 sites C-LTPP ont A©tA© caractA©risA©es A diffA©rentes frA©quences et tempA©ratures A lâ€™aide dâ€™un A©quipement de flexion A chargement aux tiers-points cyclique. Les courbes maA®tresses de module dynamique ont A©tA© modA©lisA©es en fonction de la tempA©rature et de la frA©quence selon le principe dâ€™A©quivalence frA©quence-tempA©rature. Les courbes de Black dâ€™angle de phase ont A©tA© modA©lisA©es en fonction du module dynamique. Une courbe maA®tresse et une courbe de Black gA©nA©rales ont A©tA© dA©veloppA©es A partir de la moyenne des courbes individuelles.
Female Growth and Offspring Quality over Successive Spawnings in a Caridean Shrimp Neocaridina davidi (Decapoda, Atyidae) with Direct Development

This study analyzed the quality of recently spawned eggs and of juveniles over five and six consecutive spawns, respectively, in a caridean shrimp Neocaridina davidi with direct development. The potential energetic antagonism between reproduction and somatic growth was also evaluated. The number of eggs per spawn per female was highest in the first spawn, while the number of recently hatched juveniles per spawn per female declined in the sixth spawn. Lower lipid concentration and energy content were detected in eggs of the fourth and fifth spawns, which may indicate for the first time a decrease in maternal provisioning as a result of multiple spawning in a decapod with direct development. This result had no effect on the size of eggs or of recently hatched juveniles, nor on the growth performance of juveniles during a 30-day period following hatching. Lipids were the most abundant biochemical component of eggs, followed by proteins and glycogen; the relative proportion of each component was probably related to embryonic development type. Egg volume was unsuitable as an indicator of nutrient content, as no correlation was found between these variables. The physiological costs of reproduction were evident from the lower energy content of females that reproduced versus females that remained virgin. The lower body weight of the reproductive females at the end of the experiment showed that allocation of resources to reproduction occurred at the expense of somatic growth. To our knowledge, this is the first empirical demonstration of a decapod with direct development.
Analysis of the immune response against tetanus toxoid: enumeration of specific T helper cells by the Elispot assay.

Tetanus toxoid (TT) is an antigen known to induce strong T cell specific immune responses in humans after vaccination. Here we have used the Elispot assay to assess the number of TT-specific Interferon-gamma (IFN-gamma) secreting T cells present in individuals and monitored the number of TT specific T cells present in the donors for more than two years. In each of the 22 healthy volunteers tested, TT-specific T cells could be detected. Six out of 7 repetitively tested donors showed a remarkably constant number of TT-specific IFN-gamma secreting T cells over several months, whereas one donor demonstrated a transient increase during a flu-like infection. Three healthy donors received TT booster-immunizations and showed significant increases in the number of TT-specific IFN-gamma secreting T cells which reached peak levels by 4 weeks after vaccination. Depletion of either CD4+ T cells, CD8+ T cells or CD16+/CD56+ T cells by immunomagnetic separation demonstrated that TT-specific IFN-gamma secretion is mediated exclusively by CD4+ T cells. In addition, HLA class-I and -II blocking studies showed that IFN-gamma production is performed by HLA class-II restricted cells. Our data show that the Elispot assay can be reliably used to assess the number of TT-specific CD4+ IFN-gamma producing cells (i.e. probably T helper cells) and therefore maybe also useful for the assessment of reactions to other helper antigens.
Lightweight, Viewpoint-Invariant Visual Place Recognition in Changing Environments

This letter presents a viewpoint-invariant place recognition algorithm which is robust to changing environments while requiring only a small memory footprint. It demonstrates that condition-invariant local features can be combined with Vectors of Locally Aggregated Descriptors to reduce high-dimensional representations of images to compact binary signatures while retaining place matching capability across visually dissimilar conditions. This system provides a speed-up of two orders of magnitude over direct feature matching, and outperforms a bag-of-visual-words approach with near-identical computation speed and memory footprint. The experimental results show that single-image place matching from nonaligned images can be achieved in visually changing environments with as few as 256 b (32 B) per image.
Cyclin dependent kinase 5 , cdk 5 , is a positive regulator of myogenesis in mouse C 2 cells

We have examined the expression, activity and localization of cyclin dependent kinase 5 (cdk5), during myogenesis. Cdk5 protein was found expressed in adult mouse muscle. In murine C2 cells, both the protein level and kinase activity of cdk5 showed a marked increase during early myogenesis with a peak between 36 and 48 hours of differentiation, decreasing as myotubes fuse after 60 to 72 hours. This increase in cdk5 protein level was specific for differentiation and not simply related to cell cycle arrest since it was not observed in fibroblasts grown for 48 hours in low serum medium. Indirect immunofluorescence using monospecific purified anti-cdk5 antibodies showed a low level cytoplasmic staining in proliferative myoblasts, a rapid increase in nuclear staining during the initial 12 hours of differentiation and a predominant nuclear staining in myotubes. Microinjection of plasmids encoding wild-type cdk5 into C2 myoblasts enhanced differentiation as assessed by both myogenin and troponin T expression after 48 hours of differentiation. In contrast, microinjection of plasmids encoding a dominant negative mutant of cdk5 inhibited the onset of differentiation. These data imply a previously unsuspected role for cdk5 protein kinase as a positive modulator of early myogenesis.
Edge detection from high-resolution remotely sensed imagery based on Gabor filter in frequency domain

Edge detection is important to image processing, and there are many approaches to detect the edge features from image. However, the high-resolution remotely sensed imagery including complex features is difficult to extract the edge features. This paper introduces a new method to detect edge from the high-resolution remotely sensed imagery. By using FFT, the high-resolution remotely sensed imagery is transformed into the magnitude spectrum image (frequency image). Then, the frequency image is analyzed by the Radius sampling and angle sample. Finally, Gabor filter is used to extract the edge features by setting the proper parameter. The experimental result shows that the proposed method gives a better solution for extract edge feature from the high-resolution remotely sensed imagery.
Design of an energy management system for an autonomous hybrid micro-grid based on Labview IDE

In this paper, we present a design and implementation of an energy management system for stand-alone micro grid supplied by multi-sources. This system which controls several mixed sources of energy such as Photovoltaic panel, wind turbine, diesel generator and Battery pack equilibrates efficiently the production to the load (consumption). The actual system design is based on a microcontroller board for acquisition, preprocessing and transmitting data to a host computer which responsible for receiving, processing, management and supervising locally or remotely using Labview Application. The developed application includes several user controls and graph visualization that make it ergonomic and powerful.
Should We Screen Asymptomatic Individuals for Coronary Artery Disease or Implement Universal Lipid-Lowering Therapy?

The lifetime risk of developing coronary heart disease after age 40 has been estimated to be 49% and 32% in men and women, respectively. Including other diseases secondary to atherosclerosis makes the likelihood of developing cardiovascular disease even greater. Lacking an adequate screening test for subclinical cardiovascular disease, or for those in whom it will develop, our current national prevention and treatment strategy is to screen for risk factors of coronary artery disease (CAD), treating only those at greatest risk. Although pharmacologic lipid-lowering therapy has proven to be effective at reducing the development and manifestations of CAD, as well as remarkably safe, our current strategy withholds treatment of many in whom cardiovascular disease will ultimately develop. An alternate strategy is to implement universal lipid-lowering therapy, initiated in men at age 30 and at the time of menopause in women. Such a policy would not limit effective treatment to only those at greatest risk. While the cost of such a program would be substantial, although decreasing with the increasing availability of generic agents, this must be weighed against the direct and indirect costs of cardiovascular disease, estimated to be $368 billion in 2004. If such a strategy were implemented, the goal of screening would shift from CAD detection to detection of a disease burden such that therapies shown to decrease events among those with manifest CAD would be expected to benefit. Such treatments currently include aspirin, beta blockers, angiotensin-converting enzyme inhibitors, and revascularization.
Valores de referência de medidas de pico de fluxo expiratório máximo em escolares

A avaliacao da funcao pulmonar nas doencas obstrutivas e importante tanto para quantificar o grau de obstrucao das vias aereas quanto para avaliar a evolucao funcional paralela as informacoes obtidas atraves do exame fisico do paciente. Atualmente, ha diversos testes para avaliar aspectos relacionados a funcao pulmonar, entre eles a avaliacao do pico de fluxo expiratorio maximo. O medidor Wright e um pequeno aparelho portatil feito de material plastico, de facil manejo e compreensao, baixo custo, utilizado para medir o pico de fluxo expiratorio maximo (PFE), indicador da funcao pulmonar. E utilizado tambem como parâmetro de melhora no tratamento do paciente. O estudo apresenta tabelas contendo valores ao pico de fluxo expiratorio obtidos com medidor Wright em 1.024 escolares saudaveis com idade entre 12 a 18 anos oriundos da rede publica estadual de ensino, localizada em uma area central das cidades de Uberlândia e Araguari. As equacoes de regressao calculadas e a media para PFE foram, respectivamente, para o sexo masculino: 295,75 x altura + (24,96 x Idade) – 478,24; 346,12 1/min e para sexo feminino: 212,82 x altura + (5,93 x Idade) – 131,81; 300,24 1/min.
Development of a Medical Specialty Recurring Bibliography-Index of Rheumatology*f

The Index of Rheumatology is a newly-devel-oped, recurring bibliography produced by the Medical Literature Analysis and Retrieval System (MEDLARS) of the National Library of Medicine. It is published semimonthly by the American Rheu-matism Association. This report describes prelimi-nary testing of MEDLARS output, modification of MEDLARS Medical Subject Headings (MeSH), and the computer formulation for retrieval of the bibliographic citations comprising the Index. As
Neutrophil Elastase Inhibitor Attenuates Lipopolysaccharide-Induced Hepatic Microvascular Dysfunction in Mice

The present study was conducted to elucidate the role of neutrophil elastase in lipopolysaccharide (LPS)-induced hepatic microvascular injury by using in vivo microscopy. The intravenous (i.v.) injection of LPS (0.1 mg/kg) in male C3H/HeN mice caused significant hepatic microcirculatory dysfunction: leukocyte adhesion to the sinusoids as well as to the venule, and reduced sinusoidal perfusion, in comparison with vehicle-treated mice. Concomitantly, the serum alanine aminotransferase (ALT) activity at 4 h after LPS injection was significantly increased. The serum concentrations of tumor necrosis factor (TNF&agr;) and interleukin-1&bgr; (IL-1&bgr;) at 1 h and at 4 h after LPS injection, respectively, were significantly elevated. Neutrophil elastase inhibitors, ONO-5046 (30 and 90 mg/kg, i.v., 0 and 2 h after LPS injection) or FK706 (30 and 100 mg/kg, i.v., 0 and 2 h after LPS injection) minimized the LPS-induced hepatic microcirculatory dysfunction in a dose-dependent manner. Treatment with ONO-5046 and FK706 significantly reduced the ALT level as well as the serum concentrations of TNF&agr; and IL-1&bgr;. In addition, ONO-5046 and FK706 attenuated both hepatic microcirculatory dysfunction and liver injury mediated by TNF&agr; and IL-1&bgr; (10 &mgr;g/kg i.v.). Furthermore, both ONO-5046 and FK706 improved human neutrophil elastase (10 &mgr;g/kg i.v.)-induced hepatic microcirculatory dysfunction, although neutrophil elastase did not increase the levels of TNF&agr; and IL-1&bgr;. These results suggest that neutrophil elastase aggravates the LPS-induced hepatic microvascular dysfunction. Neutrophil elastase inhibitors attenuate hepatic microvascular dysfunction in response to LPS by inhibiting TNF&agr; and IL-1&bgr; production. Neutrophil elastase inhibitors also reduce the microvascular dysfunction mediated by TNF&agr; and IL-1&bgr; as well as by neutrophil elastase.
Projection Peak Analysis for Rapid Eye Localization

This paper presents a new method of projection peak analysis for rapid eye localization. First, the eye region is segmented from the face image by setting appropriate candidate window. Then, a threshold is obtained by histogram analysis of the eye region image to binarize and segment the eyes out of the eye region. Thus, a series of projection peak will be derived from vertical and horizontal gray projection curves on the binary image, which is used to confirm the positions of the eyes. The proposed eye-localization method does not need any a priori knowledge and training process. Experiments on three face databases show that this method is effective, accurate and rapid in eye localization, which is fit for real-time face recognition system.
Chitosan Biomaterials for Current and Potential Dental Applications

Chitosan (CHS) is a very versatile natural biomaterial that has been explored for a range of bio-dental applications. CHS has numerous favourable properties such as biocompatibility, hydrophilicity, biodegradability, and a broad antibacterial spectrum (covering gram-negative and gram-positive bacteria as well as fungi). In addition, the molecular structure boasts reactive functional groups that provide numerous reaction sites and opportunities for forging electrochemical relationships at the cellular and molecular levels. The unique properties of CHS have attracted materials scientists around the globe to explore it for bio-dental applications. This review aims to highlight and discuss the hype around the development of novel chitosan biomaterials. Utilizing chitosan as a critical additive for the modification and improvement of existing dental materials has also been discussed.
Peripheral nerve abnormality in multiple sclerosis

Biopsy specimens of sural nerve from 10 patients with multiple sclerosis (MS), of whom only 1 was severely disabled, were assessed by morphometric techniques and compared to nerves from age‐matched controls. The frequency of abnormal teased fibers was increased in MS nerve, with many intenodes showing at least a 50% reduction in myelin thickness. Myelinated nerve fiber densities were not significantly different in MS and control nerves. Regression analysis of axonal area on number of myelin lamellae indicated a generalized reduction of myelin lamellae in this disorder. It is suggested that peripheral myelin may be involved in multiple sclerosis.