Miracle-dz/UniFAR-FTUs huggingface dataset:
Early activation, motility, and homing of neonatal microglia to injured neurons does not require protein synthesis

Neuronal injury in CNS tissues induces a rapid activation and mobilization of resident microglia (MG). It is widely assumed that changes in gene expression drive the morphological transformation of MG and regulate their mobilization during activation. Here, we used acutely excised neonatal rat brain slices to test whether the morphological transformation and homing of MG to injured neurons requires gene expression and de novo protein synthesis. Traumatic injury during excision of live brain tissue slices induces a rapid and transient translocation of a transcription factor, NF‐κB, to nuclei in MG. This is followed within 4–8 h by an increase in immunolabeling for cell adhesion molecules and lysosomal proteins, accompanied by changes in cell morphology. Application of anisomycin, a protein synthesis inhibitor, prevents the increase in immunolabeling for markers of MG activation but not the morphological transformation. Confocal time‐lapse imaging in live tissue slices indicates that MG cell motility (branch extension and retraction) and locomotion are unaffected by anisomycin at early postinjury time‐points (<4 h), while at later time‐points (4–8 h postinjury) MG locomotion but not motility is inhibited. Thus, activated MG rapidly localize to injured pyramidal neuron cell bodies by 4‐h postinjury, even in the presence of anisomycin. Moreover, this early MG activation and homing to injured neurons is unaffected in tissue slices from β2 integrin deficient mice. These results indicate that gene activation and new protein synthesis coincide with, but are not necessary for, the rapid morphological transformation and early migration‐dependent homing of activated MG to injured neurons in CNS tissues. © 2006 Wiley‐Liss, Inc.
An interactive engine for multilingual video browsing using semantic content

The amount of audio-visual information has increased dramatically with the advent of High Speed Internet. Furthermore, technological advances in recent years in the field of information technology, have simplified the use of video data in various fields by the general public. This made it possible to store large collections of video documents into computer systems. To enable efficient use of these collections, it is necessary to develop tools to facilitate access to these documents and handling them. In this paper we propose a method for indexing and retrieval of video sequences in a video database of large dimension, based on a weighting technique to calculate the degree of membership of a concept in a video also a structuring of the data of the audio-visual (context / concept / video) and a relevance feedback mechanism.
MRS classification based on independent component analysis and support vector machines

A novel scheme is proposed in this paper which combines independent component analysis (ICA) and support vector machines (SVM) to classify MRS. ICA is used to extract features by decomposing MRS into components which correspond to biomedical metabolites. SVM is used to train a classifier based on features extracted by ICA. The new scheme can extract meaningful features and therefore obtain a classifier with good generalization. Experimental results show that the new method has better performance than others previous ones.
Reduced-complexity transmit/receive-diversity systems

We consider wireless systems with transmit and receive diversity. For reduction of complexity, we propose to use hybrid selection/maximal ratio transmission at one link end, choosing L out of N antennas. We analyze the performance of such systems, giving analytical bounds and comparing them to computer simulations. Outage probability, symbol error probability, and capacity are shown. We demonstrate that in typical cases, a small number of used antennas L is sufficient to achieve considerable performance gains.
Associations between Basal Cortisol Levels and Memory Retrieval in Healthy Young Individuals

Cortisol is known to affect memory processes. On the one hand, stress-induced or pharmacologically induced elevations of cortisol levels enhance memory consolidation. On the other hand, such experimentally induced elevations of cortisol levels have been shown to impair memory retrieval. However, the effects of individual differences in basal cortisol levels on memory processes remain largely unknown. Here we tested whether individual differences in cortisol levels predict picture learning and recall in a large sample. A total of 1225 healthy young women and men viewed two different sets of emotional and neutral pictures on two consecutive days. Both sets were recalled after a short delay (10 min). On Day 2, the pictures seen on Day 1 were additionally recalled, resulting in a long-delay (20 hr) recall condition. Cortisol levels were measured three times on Days 1 and 2 via saliva samples before encoding, between encoding and recall as well as after recall testing. We show that stronger decreases in cortisol levels during retrieval testing were associated with better recall performance of pictures, regardless of emotional valence of the pictures or length of the retention interval (i.e., 10 min vs. 20 hr). In contrast, average cortisol levels during retrieval were not related to picture recall. Remarkably during encoding, individual differences in average cortisol levels as well as changes in cortisol did not predict memory recall. Our results support previous findings indicating that higher cortisol levels during retrieval testing hinders recall of episodic memories and extend this view onto interindividual changes in basal cortisol levels.
Chemosensory assessment of sperm competition levels and the evolution of internal spermatophore guarding

Males of many species adjust their reproductive behaviour according to the perceived risk of sperm competition. Although this phenomenon is widespread in insects and other animals, the mechanisms that allow mates to assess sperm competition levels remain largely unexplored. In this study, we analysed the mating behaviour of pairs of Tenebrio molitor beetles under three odour treatments representing increasing levels of sperm competition risk (SCR) and sperm competition intensity (SCI). Copula duration and male and female post-copulatory behaviour varied significantly with odour treatment. Both copula duration and post-copulatory associations (PCAs) increased significantly in odour treatments reflecting high male density. To our knowledge, this is the first study to report that insects may assess the actual density of potential competitors at the time of mating, a cue to SCR and SCI, on the basis of chemical cues. In T. molitor, males inhibit sperm release from the spermatophore of a rival male when remating takes place at short intervals. We show that, when sperm competition levels are high, PCAs increase female remating interval just above that necessary to prevent spermatophore inhibition by rival males. This finding strongly suggests that strategic male behaviour plays a ‘spermatophore guarding’ role in this species. Although common in insects with external spermatophore transfer, spermatophore guarding is not expected in species with rapid ejaculate transfer and internal spermatophore delivery. Our results reveal that spermatophore guarding may evolve, even under these circumstances, as an evolutionary response to short-term spermatophore inhibition or displacement mechanisms.
Taurine supplementation restored the changes in pancreatic islet mitochondria in the fetal protein-malnourished rat

Intra-uterine growth retardation has been linked to the development of type 2 diabetes in later life. Mitochondrial changes have been suggested as a link between fetal malnutrition and adult insulin resistance. Taurine has been implicated in this process. We investigated whether protein malnutrition in early life alters mitochondria of the pancreatic islets in adulthood, and whether taurine supplementation restores these changes. Male offspring of rats fed a control diet, a low-protein diet or a low-protein diet supplemented with taurine during pregnancy and lactation were weaned onto the control diet. In each group, at 20 weeks of age, intravenous glucose tolerance tests, euglycaemic–hyperinsulinaemic clamp studies, morphometric analysis of the pancreatic islets and ultra-structural analysis of the mitochondria of the β-cells were performed. The expressions of cytochrome c oxidase (COX) I and mitochondrial respiratory chain complex II were also measured. Fetal protein-malnourished rats showed decreased pancreatic islet mass and reduced insulin-secretory responses to a glucose load. These rats also showed reduced mitochondrial DNA-encoded COX I gene expression in the islets. Electron microscopic examination showed abnormal mitochondrial shapes in the β-cells of fetal protein-malnourished rats. Taurine supplementation to the low-protein diet restored all these changes. Our findings indicate that a maternal protein-restriction diet causes long-lasting mitochondrial changes that may contribute to the development of type 2 diabetes later in life. The lack of taurine may be a key causative factor for these dysfunctional mitochondrial changes.
Effective Induction of Simian Immunodeficiency Virus-Specific Cytotoxic T Lymphocytes in Macaques by Using a Multiepitope Gene and DNA Prime-Modified Vaccinia Virus Ankara Boost Vaccination Regimen

ABSTRACT DNA and modified vaccinia virus Ankara (MVA) are vaccine vehicles suitable and safe for use in humans. Here, by using a multicytotoxic T-lymphocyte (CTL) epitope gene and a DNA prime-MVA boost vaccination regimen, high levels of CTLs specific for a single simian immunodeficiency virus (SIV) gag-derived epitope were elicited in rhesus macaques. These vaccine-induced CTLs were capable of killing SIV-infected cells in vitro. Fluorescence-activated cell sorter analysis using soluble tetrameric major histocompatibility complex-peptide complexes showed that the vaccinated animals had 1 to 5% circulating CD8+ lymphocytes specific for the vaccine epitope, frequencies comparable to those in SIV-infected monkeys. Upon intrarectal challenge with pathogenic SIVmac251, no evidence for protection was observed in at least two of the three vaccinated animals. This study does not attempt to define correlates of protective immunity nor design a protective vaccine against immunodeficiency viruses, but it demonstrates clearly that the DNA prime-MVA boost regimen is an effective protocol for induction of CTLs in macaques. It also shows that powerful tools for studying the role of CTLs in the control of SIV and human immunodeficiency virus infections are now available: epitope-based vaccines, a protocol for an effective induction of CTLs in primates, and a simple and sensitive method for quantitation of epitope-specific T cells. The advantages of the DNA prime-MVA boost regimen as well as the correlations of tetramer staining of peripheral blood lymphocytes with CTL killing in vitro and postchallenge control of viremia are discussed.
On the ability to self‐monitor cognitive performance during sleep deprivation: a calibration study

SUMMARY The antagonistic effects of extensive sleep deprivation (SD) on human cognitive performance are well documented. However, one aspect of human performance that has not been investigated with respect to its susceptibility to SD is the ‘metacognitive’ ability to self‐monitor overt performance. In the present study, 16 male subjects participated in an experiment requiring sustained cognitive work during a three day period. One of the cognitive tasks required the mental addition of rapidly presented numbers. On each trial, subjects reported the sum and then provided a subjective confidence rating to indicate the degree of certainty in their response. As expected, performance on the sequential addition task deteriorated with increasing fatigue and returned to baseline following a recovery sleep. However, calibration analyses, which quantify a number of properties of the relationship between subjective and overt performance, revealed that the correlation between confidence and performance (calibration), the ability to differentiate correct from incorrect judgments (resolution), and validity of subjective ‘certainty’, were all unaffected by SD. Hence, in the absence of external feedback from the environment, people have access to fairly reliable internal feedback about their performance during periods of sustained and vigilant cognitive activity.
e-NSP: efficient negative sequential pattern mining based on identified positive patterns without database rescanning

Mining Negative Sequential Patterns (NSP) is much more challenging than mining Positive Sequential Patterns (PSP) due to the high computational complexity and huge search space required in calculating Negative Sequential Candidates (NSC). Very few approaches are available for mining NSP, which mainly rely on re-scanning databases after identifying PSP. As a result, they are very inefficient. In this paper, we propose an efficient algorithm for mining NSP, called e-NSP, which mines for NSP by only involving the identified PSP, without re-scanning databases. First, negative containment is defined to determine whether or not a data sequence contains a negative sequence. Second, an efficient approach is proposed to convert the negative containment problem to a positive containment problem. The supports of NSC are then calculated based only on the corresponding PSP. Finally, a simple but efficient approach is proposed to generate NSC. With e-NSP, mining NSP does not require additional database scans, and the existing PSP mining algorithms can be integrated into e-NSP to mine for NSP efficiently. e-NSP is compared with two currently available NSP mining algorithms on 14 synthetic and real-life datasets. Intensive experiments show that e-NSP takes as little as 3% of the runtime of the baseline approaches and is applicable for efficient mining of NSP in large datasets.
The SNP rs6500843 in 16p13.3 is associated with survival specifically among chemotherapy-treated breast cancer patients

We have utilized a two-stage study design to search for SNPs associated with the survival of breast cancer patients treated with adjuvant chemotherapy. Our initial GWS data set consisted of 805 Finnish breast cancer cases (360 treated with adjuvant chemotherapy). The top 39 SNPs from this stage were analyzed in three independent data sets: iCOGS (n=6720 chemotherapy-treated cases), SUCCESS-A (n=3596), and POSH (n=518). Two SNPs were successfully validated: rs6500843 (any chemotherapy; per-allele HR 1.16, 95% C.I. 1.08-1.26, p=0.0001, p(adjusted)=0.0091), and rs11155012 (anthracycline therapy; per-allele HR 1.21, 95% C.I. 1.08-1.35, p=0.0010, p(adjusted)=0.0270). The SNP rs6500843 was found to specifically interact with adjuvant chemotherapy, independently of standard prognostic markers (p(interaction)=0.0009), with the rs6500843-GG genotype corresponding to the highest hazard among chemotherapy-treated cases (HR 1.47, 95% C.I. 1.20-1.80). Upon trans-eQTL analysis of public microarray data, the rs6500843 locus was found to associate with the expression of a group of genes involved in cell cycle control, notably AURKA, the expression of which also exhibited differential prognostic value between chemotherapy-treated and untreated cases in our analysis of microarray data. Based on previously published information, we propose that the eQTL genes may be connected to the rs6500843 locus via a RBFOX1-FOXM1-mediated regulatory pathway.
Epigenetic Control of Effector Gene Expression in the Plant Pathogenic Fungus Leptosphaeria maculans

Plant pathogens secrete an arsenal of small secreted proteins (SSPs) acting as effectors that modulate host immunity to facilitate infection. SSP-encoding genes are often located in particular genomic environments and show waves of concerted expression at diverse stages of plant infection. To date, little is known about the regulation of their expression. The genome of the Ascomycete Leptosphaeria maculans comprises alternating gene-rich GC-isochores and gene-poor AT-isochores. The AT-isochores harbor mosaics of transposable elements, encompassing one-third of the genome, and are enriched in putative effector genes that present similar expression patterns, namely no expression or low-level expression during axenic cultures compared to strong induction of expression during primary infection of oilseed rape (Brassica napus). Here, we investigated the involvement of one specific histone modification, histone H3 lysine 9 methylation (H3K9me3), in epigenetic regulation of concerted effector gene expression in L. maculans. For this purpose, we silenced the expression of two key players in heterochromatin assembly and maintenance, HP1 and DIM-5 by RNAi. By using HP1-GFP as a heterochromatin marker, we observed that almost no chromatin condensation is visible in strains in which LmDIM5 was silenced by RNAi. By whole genome oligoarrays we observed overexpression of 369 or 390 genes, respectively, in the silenced-LmHP1 and -LmDIM5 transformants during growth in axenic culture, clearly favouring expression of SSP-encoding genes within AT-isochores. The ectopic integration of four effector genes in GC-isochores led to their overexpression during growth in axenic culture. These data strongly suggest that epigenetic control, mediated by HP1 and DIM-5, represses the expression of at least part of the effector genes located in AT-isochores during growth in axenic culture. Our hypothesis is that changes of lifestyle and a switch toward pathogenesis lift chromatin-mediated repression, allowing a rapid response to new environmental conditions.
Long-Term Outcome of Laparoscopic Cystogastrostomy Performed Using a Posterior Approach with a Stapling Device

Background: Internal drainage of an acute pancreatic pseudocyst is indicated 6 weeks after its first detection. Laparoscopic treatment of pancreatic pseudocysts enables definitive drainage with faster recovery. Pseudocysts located adjacent to the posterior gastric wall are best drained by pseudocyst gastrostomy. Although the anterior approach for drainage has frequently been reported, reports on the posterior approach are rare. Methods: Seven patients underwent laparoscopic cystogastrostomy for pancreatic pseudocysts. The posterior approach that enables the direct visualization of the posterior gastric wall and pseudocyst was used, and the cyst was drained with a needle. After creating a sufficient drainage orifice, the cyst was thoroughly debrided. Cystogastrostomy was performed using the posterior approach with a stapling device. The insertion site of the stapling device closed using a hernia stapler. Results: Cystogastrostomy was performed using the posterior approach with a stapling device in all patients, without requiring conversion to the anterior approach or open surgery. There were neither operative complications nor late recurrences during the follow-up period (median 65 months). Conclusion: Laparoscopic cystogastrostomy using the posterior approach, which facilitates adequate internal drainage, is a safe and feasible procedure for pancreatic pseudocyst, and it is not accompanied with a risk of recurrence in the long term.
End-to-End Tracking and Semantic Segmentation Using Recurrent Neural Networks

In this work we present a novel end-to-end framework for tracking and classifying a robot's surroundings in complex, dynamic and only partially observable real-world environments. The approach deploys a recurrent neural network to filter an input stream of raw laser measurements in order to directly infer object locations, along with their identity in both visible and occluded areas. To achieve this we first train the network using unsupervised Deep Tracking, a recently proposed theoretical framework for end-to-end space occupancy prediction. We show that by learning to track on a large amount of unsupervised data, the network creates a rich internal representation of its environment which we in turn exploit through the principle of inductive transfer of knowledge to perform the task of it's semantic classification. As a result, we show that only a small amount of labelled data suffices to steer the network towards mastering this additional task. Furthermore we propose a novel recurrent neural network architecture specifically tailored to tracking and semantic classification in real-world robotics applications. We demonstrate the tracking and classification performance of the method on real-world data collected at a busy road junction. Our evaluation shows that the proposed end-to-end framework compares favourably to a state-of-the-art, model-free tracking solution and that it outperforms a conventional one-shot training scheme for semantic classification.
Classification of research efforts in requirements engineering

The article proposes and justifies a trial classification scheme. An earlier version was used to organize the papers submitted to this symposium, and the scheme has been refined somewhat in response to inadequacies discovered during the process of selecting the program. The first issue to be tackled is the heterogeneity of the topics usually considered part of requirements engineering. They include: tasks that must be completed; problems that must be solved; solutions to problems; ways of contributing to knowledge; and types of system. There seems to be a need for several orthogonal dimensions of classification. While multiple dimensions certainly help us cope with the heterogeneity of concerns, there is a danger of making the classification scheme too complex to use. I have compromised by settling on two dimensions.
Data feedback efforts in quality improvement: lessons learned from US hospitals

Background: Data feedback is a fundamental component of quality improvement efforts, but previous studies provide mixed results on its effectiveness. This study illustrates the diversity of hospital based efforts at data feedback and highlights successful strategies and common pitfalls in designing and implementing data feedback to support performance improvement. Methods: Open ended interviews with 45 clinical and administrative staff in eight US hospitals in 2000 concerning their perceptions about the effectiveness of data feedback in supporting performance improvement efforts were analysed. The hospitals were chosen to represent a range of sizes, geographical regions, and β blocker improvement rates over a 3 year period. Data were organized and analyzed in NUD-IST 4 using the constant comparative method of qualitative data analysis. Results: Although the data feedback efforts at the hospitals were diverse, the interviews suggested that seven key themes may be important: (1) data must be perceived by physicians as valid to motivate change; (2) it takes time to develop the credibility of data within a hospital; (3) the source and timeliness of data are critical to perceived validity; (4) benchmarking improves the meaningfulness of data feedback; (5) physician leaders can enhance the effectiveness of data feedback; (6) data feedback that profiles an individual physician’s practices can be effective but may be perceived as punitive; (7) data feedback must persist to sustain improved performance. Embedded in several themes was the view that the effectiveness of data feedback depends not only on the quality and timeliness of the data, but also on the organizational context in which such efforts are implemented. Conclusions: Data feedback is a complex and textured concept. Data feedback strategies that might be most effective are suggested, as well as potential pitfalls in using data to promote performance improvement.