Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus

Strains of the Pseudovibrio genus have been detected worldwide, mainly as part of bacterial communities associated with marine invertebrates, particularly sponges. This recurrent association has been considered as an indication of a symbiotic relationship between these microbes and their host. Until recently, the availability of only two genomes, belonging to closely related strains, has limited the knowledge on the genomic and physiological features of the genus to a single phylogenetic lineage. Here we present 10 newly sequenced genomes of Pseudovibrio strains isolated from marine sponges from the west coast of Ireland, and including the other two publicly available genomes we performed an extensive comparative genomic analysis. Homogeneity was apparent in terms of both the orthologous genes and the metabolic features shared amongst the 12 strains. At the genomic level, a key physiological difference observed amongst the isolates was the presence only in strain P. axinellae AD2 of genes encoding proteins involved in assimilatory nitrate reduction, which was then proved experimentally. We then focused on studying those systems known to be involved in the interactions with eukaryotic and prokaryotic cells. This analysis revealed that the genus harbors a large diversity of toxin-like proteins, secretion systems and their potential effectors. Their distribution in the genus was not always consistent with the phylogenetic relationship of the strains. Finally, our analyses identified new genomic islands encoding potential toxin-immunity systems, previously unknown in the genus. Our analyses shed new light on the Pseudovibrio genus, indicating a large diversity of both metabolic features and systems for interacting with the host. The diversity in both distribution and abundance of these systems amongst the strains underlines how metabolically and phylogenetically similar bacteria may use different strategies to interact with the host and find a niche within its microbiota. Our data suggest the presence of a sponge-specific lineage of Pseudovibrio. The reduction in genome size and the loss of some systems potentially used to successfully enter the host, leads to the hypothesis that P. axinellae strain AD2 may be a lineage that presents an ancient association with the host and that may be vertically transmitted to the progeny.
Performance Evaluation of Energy Consumption in MANET

mobility of nodes in MANET may result in dynamic topology with high rate of link breakage and network partitions leading to interruption in communication and packet loss. Many routing protocols have been proposed in the literature with different characteristics and properties. The routing protocols suffer from various overheads causing energy loss which is further aggravated by link breaks. The present work concentrate on the energy consumption issues of routing protocols. We have evaluated the performance of DSDV, DSR and AODV routing protocols with respect to energy consumption indicating their usage of node's energy.
Fast indirect illumination using two virtual spherical gaussian lights

A virtual spherical Gaussian light (VSGL) [Tokuyoshi 2015] is an approximation of a set of virtual point lights (VPLs) for real-time rendering. Thousands of VSGLs can be dynamically generated using mipmapped specialized reflective shadow maps (RSMs) to render glossy indirect illumination at 20-30 ms. Although this approach is efficient compared to VPLs, rendering at 20-30 ms is still expensive for some time-sensitive applications such as video games. This poster demonstrates glossy indirect illumination in 1 ms using only two VSGLs. In this poster, each VSGL has a single spherical Gaussian lobe to represent radiant intensity, and thus diffuse and specular reflections at the second bounce are represented with two VSGLs. This rough approximation is suitable for scenes which are locally lit by a spot light (e.g., flashlight in a cave). To generate these two VSGLs dynamically, this poster presents a specialized implementation using a parallel summation algorithm. Other than RSMs, our implementation uses only small temporary buffers with a resolution that is 1/64 of an RSM. Therefore, the proposed method is not only fast, but also memory saving.
Recognition of briefly presented familiar and unfamiliar faces

Early processing stages in the perception of familiar and unfamiliar faces were studied in four experiments by varying the type of available facial information in a four alternative forced choice recognition task. Both reaction time and recognition accuracy served as dependent measures. The observed data revealed an asymmetry in processing familiar and unfamiliar faces. A markedly weak inversion effect and strong blurring effect suggest a limited usage of spatial relations within early processing stages of unfamiliar faces. Recognition performance for whole familiar faces did not deteriorate due to blurring or the presentation of isolated internal features, suggesting a low level of representation for featural properties of familiar faces. Based on the data we propose that recognition of familiar faces relies much more on spatial relations among features, particularly internal features, than on featural characteristics. In contrast, recognition of unfamiliar faces resorts mainly to featural information.
Two basic mechanisms for organisational learning in schools

SUMMARY In recent literature on teachers' professional communities and organisational learning in schools the focus is on conditions fostering teacher professional developments. Less attention has been paid to clarifying these concepts and to analysing the processes and the full range of outcomes of organisational learning in schools. The question in this article is whether and how teachers' professional communities can play a role in organisational learning and professional development. Firstly, recent research literature on teachers' workplace conditions, teachers' professional communities, and organisational learning in schools is discussed. Next, two basic mechanisms for organisational learning in schools are presented. Some conclusions are that the opportunities for steering intentional organisational learning in the school context are only weak, and that a balance should be created in the school between diverging conditions for organisational learning
PepCrawler: a fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors

MOTIVATION Design of protein-protein interaction (PPI) inhibitors is a key challenge in structural bioinformatics and computer-aided drug design. Peptides, which partially mimic the interface area of one of the interacting proteins, are natural candidates to form protein-peptide complexes competing with the original PPI. The prediction of such complexes is especially challenging due to the high flexibility of peptide conformations. RESULTS In this article, we present PepCrawler, a new tool for deriving binding peptides from protein-protein complexes and prediction of peptide-protein complexes, by performing high-resolution docking refinement and estimation of binding affinity. By using a fast path planning approach, PepCrawler rapidly generates large amounts of flexible peptide conformations, allowing backbone and side chain flexibility. A newly introduced binding energy funnel 'steepness score' was applied for the evaluation of the protein-peptide complexes binding affinity. PepCrawler simulations predicted high binding affinity for native protein-peptide complexes benchmark and low affinity for low-energy decoy complexes. In three cases, where wet lab data are available, the PepCrawler predictions were consistent with the data. Comparing to other state of the art flexible peptide-protein structure prediction algorithms, our algorithm is very fast, and takes only minutes to run on a single PC. AVAILABILITY http://bioinfo3d.cs. tau.ac. il/PepCrawler/ CONTACT eladdons@tau.ac. il; wolfson@tau.ac. il.
Assessment of Methods for Detection of Infectious Cryptosporidium Oocysts and Giardia Cysts in Reclaimed Effluents

ABSTRACT This study evaluates the occurrence of Cryptosporidium oocysts and Giardia cysts in reclaimed effluents if method 1623 with the Envirochek capsule filters (standard and high-volume [HV] filters) and a modified version of the Information Collection Rule method (ICR) with the polypropylene yarn-wound cartridge filter are used. The recovery efficiency of the analytical methods was evaluated with samples of reagent, tap, and reclaimed water by using flow cytometer-sorted spike suspensions. (Oo)cyst recovery efficiency determined filter performance and method reproducibility in the water matrix tested. Method 1623 with the Envirochek HV capsule filter generated significantly higher recovery rates than did the standard Envirochek filter and the modified ICR method. Notwithstanding, large variations in recovery rates (>80%) occurred with samples of reclaimed water, and none of the water quality parameters analyzed in the reclaimed effluents could explain such variability. The highest concentrations of indigenous oocysts were detected by method 1623 with the HV filter, which provided a sufficient number of oocysts for further confirmation of infectious potential. Confirmation of species and potential infectivity for all positive protozoan samples was made by using a nested PCR restriction fragment polymorphism assay and the focus detection method most-probable-number assay, respectively. The methodology and results described in the present investigation provide useful information for the establishment of pathogen numeric standards for reclaimed effluents used for unrestricted irrigation.
'Gently does it: Ethnicity and cultural identity in Olivier Ducastel and Jacques Martineau's Drôle de Félix (2000)'

Abstract This article argues that Ducastel and Martineau's Drôle de Félix (2000) marked a new departure for representations of people of North African origin within French film. It analyses how the lead character's journey from Dieppe to Marseilles allows the filmmakers to probe the parameters of ethnicity and sexuality throughout France's provinces, and interrogates its portrait of France and construction of Frenchness. Notions of family within the film and Félix's place within fin-de-siècle France are also considered, and an important literary precursor to Félix's road trip is identified.
Shared experience, shared memory: a common structure for brain activity during naturalistic recall

Our daily lives revolve around sharing experiences and memories with others. When different people recount the same events, how similar are their underlying neural representations? In this study, participants viewed a fifty-minute audio-visual movie, then verbally described the events while undergoing functional MRI. These descriptions were completely unguided and highly detailed, lasting for up to forty minutes. As each person spoke, event-specific spatial patterns were reinstated (movie-vs.-recall correlation) in default network, medial temporal, and high-level visual areas; moreover, individual event patterns were highly discriminable and similar between people during recollection (recall-vs.-recall similarity), suggesting the existence of spatially organized memory representations. In posterior medial cortex, medial prefrontal cortex, and angular gyrus, activity patterns during recall were more similar between people than to patterns elicited by the movie, indicating systematic reshaping of percept into memory across individuals. These results reveal striking similarity in how neural activity underlying real-life memories is organized and transformed in the brains of different people as they speak spontaneously about past events.
Derivation, expansion and characterization of clinical grade mesenchymal stem cells from umbilical cord matrix using cord blood serum.

BACKGROUND AND OBJECTIVES With increasing use of mesenchymal stem cells (MSCs) in regenerative medicine, there is greater awareness towards the need to have clinical grade products. The bovine media currently used allow good expansion to give large number of MSCs of the right quality. This report brings the significance of using cord blood serum (CBS) in the derivation of MSCs from umbilical cord matrix, to help its clinical applicability. METHODS AND RESULTS MSCs isolated from the cord by explant cultures were expanded and characterized by flow cytometry. Cord blood serum while helping expansion, has the ability to preserve the immunophenotype and differentiation potential of the MSCs derived from the umbilical cords. CONCLUSIONS Our results suggest that MSCs derived and expanded in cord blood serum are better suited for clinical applications.
Bilateral Vestibular Hypofunction: Insights in Etiologies, Clinical Subtypes, and Diagnostics

Objective To evaluate the different etiologies and clinical subtypes of bilateral vestibular hypofunction (BVH) and the value of diagnostic tools in the diagnostic process of BVH. Materials and methods A retrospective case review was performed on 154 patients diagnosed with BVH in a tertiary referral center, between 2013 and 2015. Inclusion criteria comprised (1) imbalance and/or oscillopsia during locomotion and (2) summated slow phase velocity of nystagmus of less than 20°/s during bithermal caloric tests. Results The definite etiology of BVH was determined in 47% of the cases and the probable etiology in 22%. In 31%, the etiology of BVH remained idiopathic. BVH resulted from more than 20 different etiologies. In the idiopathic group, the percentage of migraine was significantly higher compared to the non-idiopathic group (50 versus 11%, p < 0.001). Among all patients, 23.4% were known with autoimmune disorders in their medical history. All four clinical subtypes (recurrent vertigo with BVH, rapidly progressive BVH, slowly progressive BVH, and slowly progressive BVH with ataxia) were found in this population. Slowly progressive BVH with ataxia comprised only 4.5% of the cases. The head impulse test was abnormal in 94% of the cases. The torsion swing test was abnormal in 66%. Bilateral normal hearing to moderate hearing loss was found in 49%. Blood tests did not often contribute to the determination of the etiology of the disease. Abnormal cerebral imaging was found in 21 patients. Conclusion BVH is a heterogeneous condition with various etiologies and clinical characteristics. Migraine seems to play a significant role in idiopathic BVH and autoimmunity could be a modulating factor in the development of BVH. The distribution of etiologies of BVH probably depends on the clinical setting. In the diagnostic process of BVH, the routine use of some blood tests can be reconsidered and a low-threshold use of audiometry and cerebral imaging is advised. The torsion swing test is not the “gold standard” for diagnosing BVH due to its lack of sensitivity. Future diagnostic criteria of BVH should consist of standardized vestibular tests combined with a history that is congruent with the vestibular findings.
The Gray Haired Gaming Generation

The market for adult computer gamers is growing considerably. However, there are nearly no empirical works that are primarily focusing this age group. Therefore, there is an urgent need for explorative studies on these gamers. In a qualitative in-depth interview study with 21 gamers aged between 35 and 73 years, this article describes their gaming careers, the integration of gaming into their everyday life, and aspects of social interaction within real and virtual life. Overall, the findings of this study sketch a lively picture of adult players. Many of the interviewees show a very strong interest in the social aspects of gaming. However, gaming can put some strain on their family life, and many older gamers feel that their partners and peers regard their hobby as being inappropriate for their age. Still, most of the interview partners successfully manage to combine occupational and private duties with their gaming activities.
Identification of Genetic Mutations in Human Lung Cancer by Targeted Sequencing

Lung cancer remains the most prevalent malignancy and the primary cause of cancer-related deaths worldwide. Unique mutations patterns can be found in lung cancer subtypes, in individual cancers, or within a single tumor, and drugs that target these genetic mutations and signal transduction pathways are often beneficial to patients. In this study, we used the Ion Torrent AmpliSeq Cancer Panel to sequence 737 loci from 45 cancer-related genes and oncogenes to identify genetic mutations in 48 formalin-fixed, paraffin-embedded (FFPE) human lung cancer samples from Chinese patients. We found frequent mutations in EGFR, KRAS, PIK3CA, and TP53 genes. Moreover, we observed that a portion of the lung cancer samples harbored two or more mutations in these key genes. This study demonstrates the feasibility of using the Ion Torrent sequencing to efficiently identify genetic mutations in individual tumors for targeted lung cancer therapy.
Associations between postprandial insulin and blood glucose responses, appetite sensations and energy intake in normal weight and overweight individuals: a meta-analysis of test meal studies

It is unclear whether postprandial blood glucose or insulin exerts a regulatory function in short-term appetite regulation in humans. The aim of this study was to investigate, by use of meta-analysis, the role of blood glucose and insulin in short-term appetite sensation and energy intake (EI) in normal weight and overweight participants. Data from seven test meal studies were used, including 136 healthy participants (ALL) (92 normal weight (NW) and 44 overweight or obese (OW)). All meals were served as breakfasts after an overnight fast, and appetite sensations and blood samples were obtained frequently in the postprandial period. Finally, an ad libitum lunch was served. Data were analysed by fixed effects study level (SL) meta-regression analysis and individual participant data (IPD) regression analysis, using STATA software. In SL analysis, postprandial insulin response was associated with decreased hunger in ALL, NW and OW (P < 0·019), and with increased satiety in NW (P = 0·004) and lower subsequent EI in OW (P = 0·022). Multivariate IPD analysis showed similar associations, but only in NW for hunger, satiety and EI (P < 0·028), and in ALL for EI (P = 0·016). The only association involving blood glucose was the multivariate IPD analysis showing an inverse association between blood glucose and EI in ALL (P = 0·032). Our results suggest that insulin, but not glucose, is associated with short-term appetite regulation in healthy participants, but the relationship is disrupted in the overweight and obese. We conclude that the postprandial insulin response may be an important satiety signal, and that central nervous system insulin resistance in overweight might explain the blunted effect on appetite.
The illusion of cell immortality

Normal cultured cell populations are mortal but cells that are immortal are abnormal and most have properties of cancer cells. Nevertheless, this distinction becomes blurred because the terms ‘mortality’ and ‘immortality’ are subject to enormous variations in understanding. Forty years ago we showed that cell mortality and immortality are inextricably linked to longevity determination, ageing and cancer. We suggested that a counting mechanism existed in normal cells and that has now been identified as telomere attrition. This replicometer, in combination with the discovery of the enzyme telomerase, has gone very far in explaining why most normal somatic cells have a finite capacity to replicate both in vivo and in vitro and how immortal cancer cells circumvent this inevitability. It is suggested that telomere attrition may be better understood as a direct measure of longevity determination and to only have an indirect association with age changes. © 2000 Cancer Research Campaign
A plea for the second functionalist model and the insufficiency of simulation

others; both involve inference to the best explanation of talk and action. Second, it preserves the critical point that mental states are introspected in terms laid down by the available set of concepts, the theory-theory. Introspection, like ascription to others and reconstruction of one's own past, is mediated by the available set of concepts. No concepts, no introspectively available mental states. The weakness of the theory-theory view is that it gives no special place to first-person experience. Above we argued that without experience of failed, fulfilled, and shared expectations and the accompanying emotions, children could never acquire the critical set of mental concepts. Indeed, this seems to be the preferred explanation of why autistic children fail to develop a theory of mind. They appear to manage other "theories" but not the theory of mind. Mental concepts are not like other concepts, contra both Goldman and Gopnik. We conclude with a few suggestions as to how our understanding of these issues may be further advanced. One way is to pay closer attention to the role of concepts in perception. Gombrich (1960) long ago pointed out that perception is served up to consciousness in terms of the concepts available. Perception, he said, is like entering information into a form or formulary if there is no slot available for certain kinds of information, it is just too bad for that information. Putnam (1981) made the same point in his discussion of internalism, namely, that perception is always in terms of available concepts. That, we suggest, is why introspection is governed by concepts, just as ascription and remembering is. But the fact that the perception of our own mental states is mediated by concepts does not make our knowledge of those mental states inferential or the directness of our experience of those states, illusory. Second, we suggest that a more promising approach to the problem of perception and ascription of mental states was set out some time ago by Sellars and Strawson. Sellars (1963) offered an account, in his celebrated "myth of Jones," of the relation between first-person reports of mental states and the ascription of such states to others. Sellars imagines our "Rylean ancestors," who without any knowledge of the mind, came up with the idea that people actually had ideas and beliefs. His "myth" was that Jones, who had access only to the talk and actions of his fellows, could, by adopting a theoretical stance toward such evidence, come up with the simplifying theory that quite diverse utterances or actions could be explained by assuming that they were products of a smaller set of beliefs and desires. Having found them appropriate for characterizing the talk and actions of others, he discovered that such a theory was useful for characterizing oneself as well (Sellars 1963, pp. 188-89).
Junk into urban heritage: the Neon Boneyard, Las Vegas

This short photographic essay is a reflection on the practice of cultural geography in places that are in the process of becoming historically significant. My focus is on a visit I made to the Neon Boneyard in Las Vegas in 2004, where I photographed signs collected from demolished casinos, bars and hotels as part of a research project on waste, decay and cultural memory in Nevada. While I initially explored the site to glean memory-work for my doctoral thesis on high-level nuclear waste disposal at Yucca Mountain, in another life before graduate school, I worked as a cultural heritage consultant in Australia. In making active connections between signs and meanings in-the-present, I wondered if sites such as the Neon Boneyard offer a different approach to practicing heritage in places. The text that accompanies the photographs is a reflection on the relationship between public art, junk and the practices of urban heritage.