Miracle-dz/UniFAR-FTUs huggingface dataset:
Inflation and Long-Term Maintenance of CD8 T Cells Responding to a Latent Herpesvirus Depend upon Establishment of Latency and Presence of Viral Antigens1

Following the priming and contraction phases of the T cell response, latent persistent herpesviruses lead to an accumulation of large pools of virus-specific CD8 T cells, also known as memory inflation (MI). The mechanism of this inflation is incompletely understood, largely because the molecular reactivation of these viruses in vivo and its impact upon T cell biology have not been resolved in mice, and because the relevant observations in humans remain, by necessity, correlative. Understanding these processes is essential from the standpoint of the proposed critical role for latent herpesviruses in aging of the immune system. We studied the causes of memory CD8 T cell accumulation following systemic HSV-1 administration as a model of widespread latent viral infection in humans. A direct role of viral latency and Ag-specific restimulation in driving the accumulation and maintenance of inflated CD8 T cells and a strongly suggested role of viral reactivation in that process were shown by the following: 1) lack of MI in the absence of established latency; 2) prevention or delay of MI with drugs that curtail viral replication; and 3) abrogation of MI by the transfer of inflated T cells into a virus-free environment. These results strongly suggest that periodic, subclinical reactivations of a latent persistent virus cause dysregulation of memory CD8 T cell homeostasis, similar to the one in humans. Moreover, results with antiviral drugs suggest that this approach could be considered as a treatment modality for maintaining T cell diversity and/or function in old age.
LAR tyrosine phosphatase receptor: alternative splicing is preferential to the nervous system, coordinated with cell growth and generates novel isoforms containing extensive CAG repeats

Receptor-linked tyrosine phosphatases regulate cell growth by dephosphorylating proteins involved in tyrosine kinase signal transduction. The leukocyte common antigen-related (LAR) tyrosine phosphatase receptor has sequence similarity to the neural cell adhesion molecule N-CAM and is located in a chromosomal region (1p32- 33) frequently altered in neuroectodermal tumors. To understand the function of receptor-linked tyrosine phosphatases in neural development, we sought to identify LAR isoforms preferentially expressed in the nervous system and cellular processes regulating LAR alternative splicing. We report here the isolation of a series of rat LAR cDNA clones arising from complex combinatorial alternative splicing, not previously demonstrated for the tyrosine phosphatase- receptor gene family in general. Isoforms included: (a) deletions of the fourth, sixth and seventh fibronectin type III-like domains; (b) an alternatively spliced novel cassette exon in the fifth fibronectin type III-like domain; (c) two alternatively spliced novel cassette exons in the juxtamembrane region; (d) a retained intron in the extracellular region with in-frame stop codons predicting a secreted LAR isoform; and (e) an LAR transcript including an alternative 3' untranslated region containing multiple stretches of tandem CAG repeats up to 21 repeats in length. This number of repeats was in the range found in normal alleles of genes in which expansions of repeats are associated with neurodegenerative disease and the genetic phenomenon of anticipation. RT-PCR and Northern analysis demonstrated that LAR alternative splicing occurred preferentially in neuromuscular tissue in vivo and in neurons compared to astrocytes in vitro and was developmentally regulated. Alternative splicing was also regulated in PC12 cells by NGF, in 3T3 fibroblasts by cell confluence and in sciatic nerve and muscle subsequent to nerve transection. Western blot analysis demonstrated that alternatively spliced cassette exons result in the presence of corresponding amino acid segments of LAR protein in vivo. These studies suggest specialized functions of LAR isoforms in the nervous system and support our hypothesis that LAR-like tyrosine phosphatase receptors play a role in neural development and regeneration.
Small RNA Sequencing Reveals Differential miRNA Expression in the Early Development of Broccoli (Brassica oleracea var. italica) Pollen

Pollen development is an important and complex biological process in the sexual reproduction of flowering plants. Although the cytological characteristics of pollen development are well defined, the regulation of its early stages remains largely unknown. In the present study, miRNAs were explored in the early development of broccoli (Brassica oleracea var. italica) pollen. A total of 333 known miRNAs that originated from 235 miRNA families were detected. Fifty-five novel miRNA candidates were identified. Sixty of the 333 known miRNAs and 49 of the 55 predicted novel miRNAs exhibited significantly differential expression profiling in the three distinct developmental stages of broccoli pollen. Among these differentially expressed miRNAs, miRNAs that would be involved in the developmental phase transition from uninucleate microspores to binucleate pollen grains or from binucleate to trinucleate pollen grains were identified. miRNAs that showed significantly enriched expression in a specific early stage of broccoli pollen development were also observed. In addition, 552 targets for 127 known miRNAs and 69 targets for 40 predicted novel miRNAs were bioinformatically identified. Functional annotation and GO (Gene Ontology) analysis indicated that the putative miRNA targets showed significant enrichment in GO terms that were related to plant organ formation and morphogenesis. Some of enriched GO terms were detected for the targets directly involved in plant male reproduction development. These findings provided new insights into the functions of miRNA-mediated regulatory networks in broccoli pollen development.
Derivation of road network from land parcels

This paper presents an adapted algorithm to derive road network from land parcels based on skeleton operator. The spaces among the neighboring parcels are assumed to be occupied by roads. These potential roads are decomposed and approximated to generate road centerlines. The proposed algorithm minimizes unwanted artifacts by computing the negative minima curvature of the boundary. The algorithm includes three parts: 1) shape decomposition; 2) skeleton approximation; and 3) topology reconstruction. A pruning procedure is followed by the decomposition results, which can yield shared edges for neighboring sub-regions, so the direction of the centerline has been smoothed when it passes the shared edges. The straight skeleton (SS) algorithm can generate straight line, and the result is most reasonable for road network. Our proposed algorithm keeps the time complexity of straight skeleton algorithm, however, it partitions the target region into subregions where the skeletons have been computed in individual subregion instead of the whole region, and crossing patterns have been found and utilized to prune the results, hence it is not only much faster in practical computation, but also it is more suited to human perceptions. It can generate centerlines with correct topology in our cadastral test datasets from part of Barcelona. 97% of the decomposed region can get reasonable centerlines compared to a reference dataset, whereas 2% reveals incorrect reconstruction, and only 1% keep the original results from straight skeleton algorithm.
Identification of phosphate starvation-inducible genes in Escherichia coli K-12 by DNA sequence analysis of psi::lacZ(Mu d1) transcriptional fusions

Twenty-four independent phosphate starvation-inducible (psi) transcriptional fusions made with Mu d1(lacZbla) were analyzed by sequencing the psi::lacZ(Mu d1) chromosomal junctions by using DNAs amplified with the polymerase chain reaction or mini-Mu cloning. Our DNA sequence analysis showed that the MuR DNA in Mu d1 has an unexpected structure that is comprised of 104 bases of MuR DNA in the form of a large inverted repeat, which we denoted Mu d1-R. Also, Mu d1s in the phoA and phn (psiD) loci of the phosphate regulon showed regional specificities for the insertion sites despite the randomness of Mu d1 insertions into the genome as a whole. Gene products or open reading frames were identified for seven unknown psi::lacZ(Mu d1) transcriptional fusions by searching DNA data bases with the sequences adjacent and upstream of the Mu d1s. One psiC::lacZ(Mu d1) lies in the ugpB gene of the ugpBAEC operon, which encodes a periplasmic sn-glycerol-3-phosphate-binding protein; two psiQ::lacZ(Mu d1)s lie in the gltB gene, and one psiQ::lacZ(Mu d1) lies in the gltD gene of the gltBDF operon, encoding the large and small subunits of glutamate synthase, respectively; and the psi-51::lacZ(Mu d1) lies in the glpB gene of the glpABC operon, which codes for the anaerobically regulated glycerol-3-phosphate dehydrogenase. psiE and psiF::lacZ(Mu d1)s lie in uncharacterized open reading frames near the xylE and phoA genes, respectively. Six other psi::lacZ(Mu d1)s lie in yet unreported Escherichia coli sequences.
A splice site polymorphism in the G-protein &bgr; subunit influences antidepressant efficacy in depression

Objective Recent evidence suggests that signalling cascades located downstream of monoamine receptors are altered following antidepressant treatment. Our objective was to investigate whether genetic polymorphisms in genes involved in these signalling cascades influenced antidepressant efficacy. Methods Polymorphisms in the G-protein &bgr; subunit GNB3, the cAMP response element binding protein 1 gene (CREB1), the brain derived neurotrophic factor (BDNF) and CREB binding protein (CREBBP) were studied in well characterised unipolar (n=166) and early onset (n=102) depressive populations and correlated with treatment response. Results The GNB3 C825T polymorphism, which results in a 41 amino acid deletion, was significantly associated with lack of remission (OR=0.18, P=0.02) and lack of response (OR=0.26, P=0.03) following 2nd switch treatment. A cytosine deletion 16 base pairs from the start of exon 8 in CREB1 was found more frequently in remitters and responders to 2nd switch antidepressant drug therapy, although these differences failed to reach significance. Polymorphisms detected BDNF (G196A) and CREBBP (T651 C) did not appear to influence antidepressant response. Conclusions These results suggest that inheritance of the GNB3C825T allele may significantly influence antidepressant response and emphasises the potential importance of polymorphisms in genes in signalling cascades activated by commonly prescribed antidepressants.
ENViz: a Cytoscape App for integrated statistical analysis and visualization of sample-matched data with multiple data types

Summary: ENViz (Enrichment Analysis and Visualization) is a Cytoscape app that performs joint enrichment analysis of two types of sample matched datasets in the context of systematic annotations. Such datasets may be gene expression or any other high-throughput data collected in the same set of samples. The enrichment analysis is done in the context of pathway information, gene ontology or any custom annotation of the data. The results of the analysis consist of significant associations between profiled elements of one of the datasets to the annotation terms (e.g. miR-19 was associated to the cell-cycle process in breast cancer samples). The results of the enrichment analysis are visualized as an interactive Cytoscape network. Availability and implementation: ENViz is publically available in the Cytoscape App Store (http://apps.cytoscape.org/apps/enviz). For additional information please visit the tool website: http://www.agilent.com/labs/research/compbio/enviz/ Contact: israel_steinfeld@agilent.com
Individual Flagellar Waveform Affects Collective Behavior of Chlamydomonas reinhardtii

Bioconvection is a form of collective motion that occurs spontaneously in the suspension of swimming microorganisms. In a previous study, we quantitatively described the “pattern transition,” a phase transition phenomenon that so far has exclusively been observed in bioconvection of the unicellular green alga Chlamydomonas. We suggested that the transition could be induced by changes in the balance between the gravitational and shear-induced torques, both of which act to determine the orientation of the organism in the shear flow. As both of the torques should be affected by the geometry of the Chlamydomonas cell, alteration in the flagellar waveform might change the extent of torque generation by altering overall geometry of the cell. Based on this working hypothesis, we examined bioconvection behavior of two flagellar mutants of Chlamydomonas reinhardtii, ida1 and oda2, making reference to the wild type. Flagella of ida1 beat with an abnormal waveform, while flagella of oda2 show a normal waveform but lower beat frequency. As a result, both mutants had swimming speed of less than 50% of the wild type. ida1 formed bioconvection patterns with smaller spacing than those of wild type and oda2. Two-axis view revealed the periodic movement of the settling blobs of ida1, while oda2 showed qualitatively similar behavior to that of wild type. Unexpectedly, ida1 showed stronger negative gravitaxis than did wild type, while oda2 showed relatively weak gravitaxis. These findings suggest that flagellar waveform, not swimming speed or beat frequency, strongly affect bioconvection behavior in C. reinhardtii.
HEFT: A hybrid system-level framework for enabling energy-efficient fault-tolerance in NoC based MPSoCs

In emerging CMOS process technologies, network-on-chip (NoC) fabrics are increasingly becoming susceptible to transient faults. Fault-tolerance mechanisms that are typically employed in NoCs usually entail significant energy overheads that are expected to become prohibitive as fault rates increase in future CMOS technologies. We propose a system-level framework called HEFT to trade-off energy consumption and fault-tolerance in the NoC fabric. Our hybrid framework tackles the challenge of enabling energy-efficient resilience in NoCs in two phases: at design time and at runtime. At design time, we implement an algorithm to guide the robust mapping of cores on to a die while satisfying application bandwidth and latency constraints. At runtime we devise a prediction algorithm to monitor and detect changes in fault susceptibility of NoC components, to intelligently balance energy consumption and reliability. Experimental results show that HEFT improves energy/reliability ratio of synthesized solutions by 8-20%, while meeting application performance goals, when compared to multiple prior works on reliable system-level NoC design.
Fast tagging of medical terms in legal text

Medical terms occur across a wide variety of legal, medical, and news corpora. Documents containing these terms are of particular interest to legal professionals operating in such fields as medical malpractice, personal injury, and product liability. This paper describes a novel method of tagging medical terms in legal, medical, and news text that is very fast and also has high recall and precision. To date, most research in medical term spotting has been confined to medical text and has approached the problem by extracting noun phrases from sentences and mapping them to a list of medical concepts via a fuzzy lookup. The medical term tagging described in this paper relies on a fast finite state machine that finds within sentences the longest contiguous sets of words associated with medical terms in a medical term authority file, converts word sets into medical term hash keys, and looks up medical concept ids associated with the hash keys. Additionally our system relies on a probabilistic term classifier that uses local context to disambiguate terms being used in a medical sense from terms being used in a non-medical sense. Our method is two orders of magnitude faster than an approach based on noun phrase extraction and has better precision and recall for terms pertaining to injuries, diseases, drugs, medical procedures, and medical devices. The methods presented here have been implemented and are the core engines for a Thomson West product called the Medical Litigator. Thus far, the Medical Litigator has processed over 100 million documents and generated over 165 million tags representing approximately 164,000 unique medical concepts. The resulting system is very fast and posted a recall from 0.79 to 0.93 and precision between 0.94 and 0.97, depending on the document type.
Improving the stability of SEIG based microgrids with predominance of dynamic loads by using supercapacitor-based storage

This paper focuses on improving the dynamic behaviour of a microgrid (MG) supplied by a self-excited induction generator (SEIG) when feeding mainly induction motors (IMs) of significant power. In order to sustain the MG during the transitory regime induced by the IMs connection, a short-term energy storage system based on a supercapacitor (SC) is added to the MG control system. Also, a stepped capacitor bank is employed to compensate the reactive power required by the dynamic loads. A voltage source inverter (VSI), having on its DC side a Dump Load (DL), is responsible for the MG voltage and frequency stability during steady-state. When the DC voltage decreases under a certain threshold, the SC system starts injecting power into the VSI DC-link, thus improving the stability of the MG parameters. Simulations are used to validate the effectiveness of the proposed control structure.
Behavior-based Robotics And The Reactive Paradigm A Survey

Behavior-based robots have come under the spotlight in recent years by making their presence known in diverse fields of human interest. Applications in behavior-based robotics have continued to grow in areas such as demining, search and rescue, office automation, health care, etc and continue to replace human beings in risky and menial tasks. With this inspiration, this paper investigates a variety of aspects in behavior-based robotics and the reactive paradigm in the context of their origins, concepts, applications and current research and is intended to provide a comprehensive overview about this area in robotics. The paper will review several central issues including a brief history of robotics, transition of robotic systems from hierarchical paradigm to reactive paradigm, biological/ethological inspiration for behavior-based robots, fundamentals of the reactive paradigm, architectures for controlling robotic behavior and the hybrid deliberative/reactive paradigm.
Consequences of domain insertion on sequence-structure divergence in a superfold

Significance Here, we determine the impact of large-domain insertions on the sequence and structure divergence of a ubiquitous protein scaffold (superfold). By performing quantitative analysis on a distinctive dataset of >150 protein structures, unique protein-design principles have been uncovered. Our work suggests that superfolds are tolerant to relatively large domain insertions when followed by accommodating mutations in the scaffold. This structural robustness may facilitate the development of directed evolution technologies that incorporate domains into existing scaffolds. Although the universe of protein structures is vast, these innumerable structures can be categorized into a finite number of folds. New functions commonly evolve by elaboration of existing scaffolds, for example, via domain insertions. Thus, understanding structural diversity of a protein fold evolving via domain insertions is a fundamental challenge. The haloalkanoic dehalogenase superfamily serves as an excellent model system wherein a variable cap domain accessorizes the ubiquitous Rossmann-fold core domain. Here, we determine the impact of the cap-domain insertion on the sequence and structure divergence of the core domain. Through quantitative analysis on a unique dataset of 154 core-domain-only and cap-domain-only structures, basic principles of their evolution have been uncovered. The relationship between sequence and structure divergence of the core domain is shown to be monotonic and independent of the corresponding type of domain insert, reflecting the robustness of the Rossmann fold to mutation. However, core domains with the same cap type share greater similarity at the sequence and structure levels, suggesting interplay between the cap and core domains. Notably, results reveal that the variance in structure maps to α-helices flanking the central β-sheet and not to the domain–domain interface. Collectively, these results hint at intramolecular coevolution where the fold diverges differentially in the context of an accessory domain, a feature that might also apply to other multidomain superfamilies.
Involvement of JNK and Caspase Activation in Hoiamide A-Induced Neurotoxicity in Neocortical Neurons

The frequent occurrence of Moorea producens (formerly Lyngbya majuscula) blooms has been associated with adverse effects on human health. Hoiamide A is a structurally unique cyclic depsipeptide isolated from an assemblage of the marine cyanobacteria M. producens and Phormidium gracile. We examined the influence of hoiamide A on neurite outgrowth in neocortical neurons and found that it suppressed neurite outgrowth with an IC50 value of 4.89 nM. Further study demonstrated that hoiamide A stimulated lactic acid dehydrogenase (LDH) efflux, nuclear condensation and caspase-3 activity with EC50 values of 3.66, 2.55 and 4.33 nM, respectively. These data indicated that hoiamide A triggered a unique neuronal death profile that involves both necrotic and apoptotic mechanisms. The similar potencies and similar time-response relationships between LDH efflux and caspase-3 activation/nuclear condensation suggested that both necrosis and apoptosis may derive from interaction with a common molecular target. The broad-spectrum caspase inhibitor, Z-VAD-FMK completely inhibited hoiamide A-induced neurotoxicity. Additionally, hoiamide A stimulated JNK phosphorylation, and a JNK inhibitor attenuated hoiamide A-induced neurotoxicity. Collectively, these data demonstrate that hoiamide A-induced neuronal death requires both JNK and caspase signaling pathways. The potent neurotoxicity and unique neuronal cell death profile of hoiamide A represents a novel neurotoxic chemotype from marine cyanobacteria.
Adaptive Spatial Channel Mapping in MIMO Relay Systems: A Unified Framework

In multi-input-multi-output relay systems with amplify-and-forward protocols, the source-relay and the relay-destination links can be treated as two groups of spatial channels. In this letter, an adaptive spatial channel mapping matrix is presented to be used between the two groups. A unified framework of the spatial channel mapping matrix design is presented, which includes various relay protocols. The spatial channel matrix is designed to reduce the relaying noise power or the local noise in the destination node. Simulation results demonstrate the advantage of the adaptive spatial channel mapping on the system reliability and capacity with different relay protocols.