Miracle-dz/UniFAR-FTUs huggingface dataset:
Metagenomics: The Next Culture-Independent Game Changer

A trend towards the abandonment of obtaining pure culture isolates in frontline laboratories is at a crossroads with the ability of public health agencies to perform their basic mandate of foodborne disease surveillance and response. The implementation of culture-independent diagnostic tests (CIDTs) including nucleic acid and antigen-based assays for acute gastroenteritis is leaving public health agencies without laboratory evidence to link clinical cases to each other and to food or environmental substances. This limits the efficacy of public health epidemiology and surveillance as well as outbreak detection and investigation. Foodborne outbreaks have the potential to remain undetected or have insufficient evidence to support source attribution and may inadvertently increase the incidence of foodborne diseases. Next-generation sequencing of pure culture isolates in clinical microbiology laboratories has the potential to revolutionize the fields of food safety and public health. Metagenomics and other ‘omics’ disciplines could provide the solution to a cultureless future in clinical microbiology, food safety and public health. Data mining of information obtained from metagenomics assays can be particularly useful for the identification of clinical causative agents or foodborne contamination, detection of AMR and/or virulence factors, in addition to providing high-resolution subtyping data. Thus, metagenomics assays may provide a universal test for clinical diagnostics, foodborne pathogen detection, subtyping and investigation. This information has the potential to reform the field of enteric disease diagnostics and surveillance and also infectious diseases as a whole. The aim of this review will be to present the current state of CIDTs in diagnostic and public health laboratories as they relate to foodborne illness and food safety. Moreover, we will also discuss the diagnostic and subtyping utility and concomitant bias limitations of metagenomics and comparable detection techniques in clinical microbiology, food and public health laboratories. Early advances in the discipline of metagenomics, however, have indicated noteworthy challenges. Through forthcoming improvements in sequencing technology and analytical pipelines among others, we anticipate that within the next decade, detection and characterization of pathogens via metagenomics-based workflows will be implemented in routine usage in diagnostic and public health laboratories.
Orientation-based FRET sensor for real-time imaging of cellular forces

Mechanical stress is an unmapped source of free energy in cells. Mapping the stress fields in a heterogeneous time-dependent environment like that found in cells requires probes that are specific for different proteins and respond to biologically relevant forces with minimal disturbance to the host system. To meet these goals, we have designed a genetically encoded stress sensor with minimal volume and high sensitivity and dynamic range. The new FRET-based sensor, called cpstFRET, is designed to be modulated by the angles between the donor and acceptor rather than the distance between them. Relative to other probes, it is physically smaller and exhibits a greater dynamic range and sensitivity and expresses well. For in vivo testing, we measured stress gradients in time and space in non-erythroid spectrin in several different cell types and found that spectrin is under constitutive stress in some cells but not in others. Stresses appear to be generated by both F-actin and tubulin. The probe revealed, for the first time, that spectrin undergoes time-dependent force modulation during cell migration. cpstFRET can be employed in vitro, in vivo and in situ, and when incorporated into biologically expressed extracellular polymers such as collagen, it can report multidimensional stress fields.
Oxytocin in the Circadian Timing of Birth

Background The molecular components determining the timing for birth remain an incompletely characterized aspect of reproduction, with important conceptual and therapeutic ramifications for management of preterm, post-term and arrested labor. Methodology/Principal Findings To test the hypothesis that oxytocin mediates circadian regulation of birth, we evaluated parturition timing following shifts in light cycles in oxytocin (OT)-deficient mice. We find that, in contrast to wild type mice that do not shift the timing of birth following a 6-h advance or delay in the light cycle, OT-deficient mice delivered at random times of day. Moreover, shifts in the light-dark cycle of gravid wild type mice have little impact on the pattern of circadian oxytocin release. Conclusions/Significance Our results demonstrate oxytocin plays a critical role in minimizing labor disruption due to circadian clock resetting.
Low-cost accelerometers for robotic manipulator perception

We present a series of experiments which explore the use of consumer-grade accelerometers as joint position sensors for robotic manipulators. We show that 6- and 7-dof joint angle estimation is possible by using one 3-d accelerometer for each pair of joints. We demonstrate two calibration approaches and experimental results using accelerometer-based control in both position-control and torque-control regimes. We present a manipulator design combining accelerometer-based sensing with low-cost actuation, and conclude by demonstrating the utility of consumer-grade accelerometers even on high-precision manipulators.
Layer-Specific Markers as Probes for Neuron Type Identity in Human Neocortex and Malformations of Cortical Development

Malformations of cortical development (MCDs) are heterogeneous disorders caused by abnormalities of cell proliferation, apoptosis, cell migration, cortical organization, and axon pathfinding. In severe MCDs, the cerebral cortex can appear completely disorganized, or may be replaced by aberrant laminar patterns, as in "4-layered" types of lissencephaly and polymicrogyria. Little is known about the abnormal layers in MCDs and whether they bear any relation to normal cortical layers or how MCDs affect specific neuron types. Normally, each layer contains a defined mixture of different types of pyramidal and nonpyramidal neurons. The neuron types are distinguished by molecular expression as well as morphologic, neurochemical, and electrophysiologic criteria. Patterns of layer-specific mRNA and protein expression reflect the segregation of different neuron types into different layers (e.g. corticospinal projection neurons in layer V). Numerous layer-specific markers have been described in rodent cortex, and increasing numbers are being documented in human and monkey cortex. Applied to MCDs, layer-specific markers have the potential to reveal new insights on pathogenesis, treatment possibilities, and genotype-phenotype correlations. However, much work remains before layer-specific markers become practical tools in diagnostic neuropathology. Additional markers, more extensive documentation of normal expression, and better antibodies compatible with paraffin-embedded tissues will be necessary.
Identifying users' behavior purchasing virtual items

Virtual asset has become more important in the virtual worlds. A growing number of users involve in the virtual worlds has created a new business phenomena. An online transaction on virtual goods involves real money. This research mainly focus on finding out what are the factors influence customers’ behavior and how to predict it toward purchasing in virtual worlds. There are thirty eight participants from different countries involve in this study. An online questionnaire is design to get necessary information from the users. The correlation and regression analysis applied in order to predict customer behavior toward purchasing in virtual worlds.
Relative Navigation with Maneuvers Using a Suboptimal Fading Extended Kalman Filtera

Relative navigation is one of the key technologies involved in many spatial missions, including spacecraft formation flight as well as rendezvous and docking. This paper develops an efficient approach of relative orbit determination, especially, the case in which spacecrafts perform unknown maneuvers to change the relative configuration is considered. On the assumption that the inter-spacecraft distance and orientation measurements are available all the time, the orbit states estimation is achieved through a suboptimal fading extended Kalman filter design. The numerical simulation results verify the validity of this navigation approach
Is common method variance a “deadly plague”? Unsolved contention, fresh insights, and practical recommendations

: Common method variance (CMV) is a form of systematic variance attributed to similarities of measurement method facets between constructs. It has potential to distort observational correlations and thus elicits common method bias (CMB). Although it has been noted repeatedly in social science research for almost 60 years, its threat to research validity hasn’t been overwhelmingly acknowledged and remains to be scrutinized. Extant empirical evidence has demonstrated the ubiquity of CMV and identified distinct factors triggering CMB, including data source, time interval, and questionnaire design. As a result, cross-sectional self-reporting surveys are particularly subjected to extensive criticism. Nonetheless, some researchers contend that measurement error and uncommon method variance can offset or alleviate the underlying detriment so that pervasive anxiety regarding CMV is exaggerated and unjustified. The measure-centric approach underlines that CMV originates from the interplay between methods and constructs, and the two-dimensional CMV risk evaluation procedure should be conducted with simultaneous consideration of method and construct. From our view, it is preferable to cultivate a balanced and impartial attitude towards CMV, embrace its existence, discard the prejudice against self-reporting, and, above all, take proactive countermeasures based on the optimization of research design.
Purification, characterization, and in vitro differentiation of cytotrophoblasts from human term placentae.

Highly purified functional cytotrophoblasts have been prepared from human term placentae by adding a Percoll gradient centrifugation step to a standard trypsin-DNase dispersion method. The isolated mononuclear trophoblasts averaged 10 microns in diameter, with occasional cells measuring up to 20-30 microns. Viability was greater than 90%. Transmission electron microscopy revealed that the cells had fine structural features typical of trophoblasts. In contrast to syncytial trophoblasts of intact term placentae, these cells did not stain for hCG, human placental lactogen, pregnancy-specific beta 1-glycoprotein or low mol wt cytokeratins by immunoperoxidase methods. Endothelial cells, fibroblasts, or macrophages did not contaminate the purified cytotrophoblasts, as evidenced by the lack of immunoperoxidase staining with antibodies against vimentin or alpha 1-antichymotrypsin. The cells produced progesterone (1 ng/10(6) cells . 4 h), and progesterone synthesis was stimulated up to 8-fold in the presence of 25-hydroxycholesterol (20 micrograms/ml). They also produced estrogens (1360 pg/10(6) cells . 4 h) when supplied with androstenedione (1 ng/ml) as a precursor. When placed in culture, the cytotrophoblasts consistently formed aggregates, which subsequently transformed into syncytia within 24-48 h after plating. Time lapse cinematography revealed that this process occurred by cell fusion. The presumptive syncytial groups were proven to be true syncytia by microinjection of fluorescently labeled alpha-actinin, which diffused completely throughout the syncytial cytoplasm within 30 min. Immunoperoxidase staining of cultured trophoblasts between 3.5 and 72 h after plating revealed a progressive increase in cytoplasmic pregnancy-specific beta 1-glycoprotein, hCG, and human placental lactogen concomitant with increasing numbers of aggregates and syncytia. At all time points examined, occasional single cells positive for these markers were identified. RIA of the spent culture media for hCG revealed a significant increase in secreted hCG, paralleling the increase in hCG-positive cells and syncytia identified by immunoperoxidase methods. We conclude that human cytotrophoblasts differentiate in culture and fuse to form functional syncytiotrophoblasts.
Simulation of combined shield wire and MOV protection on distribution lines in severe lightning areas

This paper presents the protective effects of shield wire coupled with Metal Oxide Varistor (MOV) arresters in a distribution network located in a severe lightning area. The presented test case is the IEEE 34-node radial distribution test feeder injected with multiple lightning strokes and simulated with the Alternative Transients Program/ Electromagnetic Transients program (ATP/EMTP). The response of the distribution line to lightning strokes was modeled with three different cases: no protection, protection with surge arresters and protection with a combination of shield wire and arresters. Simulations were made to compare the resulting overvoltages on the line for all the analyzed cases.
ATP-dependent glutathione disulphide transport mediated by the MRP gene-encoded conjugate export pump.

We have previously shown that the multidrug resistance protein (MRP) mediates the ATP-dependent membrane transport of the endogenous glutathione conjugate leukotriene C4 (LTC4) and of structurally related anionic conjugates of lipophilic compounds [Jedlitschky, Leier, Buchholz, Center and Keppler (1994) Cancer Res. 54, 4833-4836; Leier, Jedlitschky, Buchholz, Cole, Deeley and Keppler (1994) J. Biol. Chem. 269, 27807-27810]. We demonstrate in the present study that MRP also mediates the ATP-dependent transport of GSSG, as shown in membrane vesicles from human leukaemia cells overexpressing MRP (HL60/ADR cells) or HeLa cells transfected with an MRP expression vector (HeLa T5 cells) in comparison with the respective parental or control cells. The Km value for ATP-dependent transport of GSSG was 93 +/- 26 microM (mean value +/- S.D., n=5) in membrane vesicles from HeLa T5 cells. GSH, at a concentration of 100 microM, was not a substrate for any significant ATP-dependent MRP-mediated transport. The transport of GSSG was competitively inhibited by LTC4, by the leukotriene D4 receptor antagonist 3-([{3-(2-[7-chloro-2-quinolinyl]ethenyl)phenyl}-{(3-dimethylamino-3- oxopropyl)-thio}-methyl]thio)propanoic acid (MK 571) and by S-decylglutathione, with K1 values of 0.3, 0.6 and 0.7 microM respectively. These studies identify MRP as the membrane glycoprotein which mediates the ATP-dependent export of GSSG from these cells.
Disuse atrophy and exercise rehabilitation in humans profoundly affects the expression of genes associated with the regulation of skeletal muscle mass

Skeletal muscle atrophy occurs as a consequence of injury, illness, surgery, and muscle disuse, impacting appreciably on health care costs and patient quality of life, particularly in the absence of appropriate rehabilitation. The molecular mechanisms that regulate muscle mass during atrophy and rehabilitation in humans have not been elucidated, despite several robust candidate pathways being identified. Here, we induced skeletal muscle atrophy in healthy volunteers using two weeks of limb immobilization, and then stimulated the restoration of muscle mass with six weeks of supervised exercise rehabilitation. We determined muscle mass and function and performed targeted gene expression analysis at prescribed time points during immobilization and rehabilitation. For the first time, we have identified novel changes in gene expression following immobilization‐induced atrophy and during a program of rehabilitative exercise that restored muscle mass and function. Furthermore, we have shown that exercise performed immediately following immobilization induces profound changes in the expression of a number of genes in favor of the restoration of muscle mass, within 24 h. This information will be of considerable importance to our understanding of how immobilization and contraction stimulate muscle atrophy and hypertrophy, respectively, and to the development of novel therapeutic strategies aimed at maintaining or restoring muscle mass.
Automatic translation of Arabic queries for bilingual information retrieval

In this paper, we present an automatic query translation in Arabic for information retrieval. This system, implements a method for lexical disambiguation of terms in a query. To choose the best sense, each term of the query is projected on the French EuroWordNet and we extract his related concepts in order to form a semantic network. In a second time using the same type of network, but by integrating LSI (Latent Semantic Index), and extraction of contextual hidden links between the concepts of the list (listSRF). This list extracted by the automatic alignment by Mkalign tool's, from the knowledge base defined by the Monde Diplomatic parallel corpus. This tool will allow us to map between the relevant sentences in Arabic identified in our previous work with French sentences to build a listSRF. This list forms the basis of the lexical disambiguation method. Finally, we propose a mechanism for selecting the best sense of the ambiguous term of the query, based on the matching between each network corresponds to a word in the query with the network listSRF to extract an adequate sense with the highest degree of similarity. An evaluation and comparison are conducted to measure the quality of our translation system.
Entropy Rate Superpixel Classification for Automatic Red Lesion Detection in Fundus Images

Diabetic retinopathy (DR) is the main cause of blindness in the working-age population in developed countries. Digital color fundus images can be analyzed to detect lesions for large-scale screening. Thereby, automated systems can be helpful in the diagnosis of this disease. The aim of this study was to develop a method to automatically detect red lesions (RLs) in retinal images, including hemorrhages and microaneurysms. These signs are the earliest indicators of DR. Firstly, we performed a novel preprocessing stage to normalize the inter-image and intra-image appearance and enhance the retinal structures. Secondly, the Entropy Rate Superpixel method was used to segment the potential RL candidates. Then, we reduced superpixel candidates by combining inaccurately fragmented regions within structures. Finally, we classified the superpixels using a multilayer perceptron neural network. The used database contained 564 fundus images. The DB was randomly divided into a training set and a test set. Results on the test set were measured using two different criteria. With a pixel-based criterion, we obtained a sensitivity of 81.43% and a positive predictive value of 86.59%. Using an image-based criterion, we reached 84.04% sensitivity, 85.00% specificity and 84.45% accuracy. The algorithm was also evaluated on the DiaretDB1 database. The proposed method could help specialists in the detection of RLs in diabetic patients.
DCX‐expressing cells in the vicinity of the hypothalamic neurogenic niche: A comparative study between mouse, sheep, and human tissues

Neural stem and precursor cells persist postnatally throughout adulthood and are capable of responding to numerous endogenous and exogenous signals by modifying their proliferation and differentiation. Whereas adult neurogenesis has been extensively studied in the dentate gyrus of the hippocampal formation and in the subventricular zone adjacent to the wall of the lateral ventricles, we and others have recently reported constitutive adult neurogenesis in other brain structures, including the hypothalamus. In this study, we used immunohistochemistry to study the expression of the neuroblast marker doublecortin (DCX), and compared its expression pattern in adult ovine, mouse, and human hypothalamic tissues. Our results indicate that DCX‐positive cells resembling immature and developing neurons occur in a wide range of hypothalamic nuclei in all three species, although with different distribution patterns. In addition, the morphology of DCX‐positive cells varied depending on their location. DCX‐positive cells near the third ventricle had the morphology of very immature neuroblasts, a round shape with no processes, whereas those located deeper in the parenchyma such as in the ventromedial nucleus were fusiform and showed a bipolar morphology. Extending this observation, we showed that among the cohort of immature neurons entering the ventromedial nucleus, some appeared to undergo maturation, as revealed by the partial colocalization of DCX with markers of more mature neurons, e.g., human neuronal protein C and D (HuC/D). This study provides further confirmation of the existence of an adult hypothalamic neurogenic niche and argues for the potential existence of a migratory path within the hypothalamus. J. Comp. Neurol. 522:1966–1985, 2014. © 2013 Wiley Periodicals, Inc.
Study the Relationship between Early Maladaptive Schemas and Parenting Styles

Everey person may had painfull experiences in his or her past, for example failures which had in his or her life. These experiences form person Maladaptive Schemas. We wanted to know these Schemas, which some of parents had in their life whether can have effect in styles that they apply in upbringing their childeren.So the main objective of this research is to investigate the relationship between Early Maladaptive Schemas and Parenting Styles between married men and women in Sanandaj city at the years 2012 to 2013. This study sought to examine the relationship between Early Maladaptive Schemas (Abandonment,Uncompromising standards ,obedience, punishment, and negativism) with Parenting Styles (Permissiveness, Authoritative and Authoritarian style). The research's population of this study includes married men and women headed households in the Sanandaj city during the years 2012-2013. According to statistical data, 65person of married men and women in the city of Sanandaj were selected based on accessible sampling. For data collection we used standards questionnaire of Baumrind Parenting Styles and questionnaire of Young's Early Maladaptive Schemas; and its reliability and validity have been calculated. For data analysis, Pearson correlation coefficient were used. Findings indicate that there is significant relationship between Early Maladaptive Schemas with Authoritarian style and also Authoritative style among married men and women, but there is no significant relationship between Early Maladaptive Schemas and permissive style, among married men and women.