Miracle-dz/UniFAR-FTUs huggingface dataset:
Induction of apoptosis by overexpression of the DNA-binding and DNA-PK-activating protein C1D.

Apoptosis is induced in various tumor cell lines by vector-dependent overexpression of the conserved gene C1D that encodes a DNA-binding and DNA-PK-activating protein. C1D is physiologically expressed in 50 human tissues tested, which points to its basic cellular function. The expression of this gene must be tightly regulated because elevated levels of C1D protein, e.g. those induced by transient vector-dependent expression, result in apoptotic cell death. Cells transfected with C1D-expressing constructs show terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling of DNA ends. Transfections with constructs in which C1D is expressed in fusion with the (enhanced) green fluorescent protein from A. victoria (EGFP) allow the transfected cells to be identified and the morphological changes induced to be traced. Starting from intense nuclear spots, green fluorescence reflecting C1D expression increases dramatically at 12-24 hours post-transfection. Expression of C1D-EGFP protein is accompanied by morphological changes typical of apoptotic cell death, e.g. cytoplasmic vacuolation, membrane blebbing and nuclear disintegration. Cell shrinkage and detachment from extracellular matrix are observed in monolayer cultures while suspension cells become progressively flattened. The facility to differentiate between transfected and non-transfected cells reveals that non-transfected cells co-cultured with transfected cells also show the morphological changes of apoptosis, which points to a bystander effect. C1D-dependent apoptosis is not induced in cells with non-functional p53. Accordingly, C1D-induced apoptosis is discussed in relation to its potential to activate DNA-PK, which has been considered to act as an upstream activator of p53.
Effects of color spaces and distance norms on graph-based image segmentation

Use of the graph theory tools in image processing field is growing up with each passing day. Graph theory makes the operations easier for image processing applications, and can represent digital image components completely. In image segmentation processes, the graph theory tools are also used widely. These kinds of image segmentation processes are called graph-based image segmentation. In many image processing applications, it seems as a problem that which color space the color values of pixels should be considered according to and which distance norm should be used to measure the difference between two points in the space. In this work, a graph-based image segmentation algorithm is tested on several color spaces with different distance norms. The test is carried out on 100 real world images that take part in a general-purposed image segmentation dataset. The average segmentation results are given as F-measure in this work with regard to both color spaces and distance norms. The results show that L∗a∗b∗ and L∗u∗v∗ color spaces are more appropriate than RGB color space, in general. The squared Euclidean distance norm gives more accurate results than the Euclidean distance norm, used in the source paper, if the Gaussian smoothing is not used as pre-processing.
Canadian government's framing of ageing at work and older workers: Echoing positive ageing models.

BACKGROUND Public representations of ageing can influence how individuals perceive their own experience of ageing. Results of studies on the OECD (Organisation for Economic Co-operation and Development)'s governmental messages on older workers suggest that they are mainly constructed around economic productivity and personal responsibility. OBJECTIVE The goal of this study is to examine how the Canadian government frames issues around ageing, work and older workers. Canada is facing a rapidly ageing workforce, hence the importance of examining how the government discusses ageing at work. METHOD A thematic content analysis was conducted on a total of 154 government web pages. RESULTS Results revealed that predominant themes revolve around economic challenges resulting from an ageing workforce. Older workers are depicted as a key component for the (economic) management of an ageing workforce. More specifically, older workers who intend to continue working are highly valued in the government's messages which present them as productive citizens and role models for "ageing well". CONCLUSION Canada's response to the challenges of an ageing workforce echoes the underlying standards of positive ageing models, which may generate, perhaps inadvertently, a new form of ageism by creating intra-and intergenerational divides in the workplace.
Differential expression of KCC2 accounts for the differential GABA responses between relay and intrinsic neurons in the early postnatal rat olfactory bulb

The rat olfactory bulb is anatomically immature at birth, and considerable neurogenesis and synaptogenesis are known to take place postnatally. In addition, significant physiological changes have also been reported in this period. For example, granule cell‐mediated inhibition following electrical stimulations to the lateral olfactory tract is robust during the first postnatal week, and then decreases abruptly after the second week. However, the mechanism underlying this enhanced inhibition remains to be elucidated. To know the cause of this phenomenon, we investigated the expression patterns of cation‐Cl– co‐transporters (KCC1, KCC2 and NKCC1) mRNAs, which are responsible for the regulation of [Cl–]i. In addition, responses to γ‐aminobutyric acid (GABA) were measured by gramicidin‐perforated patch‐clamp recordings and Ca2+ imaging using fura‐2. We found that in the early postnatal period, mitral cells expressing KCC2 mRNA were inhibited by GABA, while granule cells lacking KCC2 mRNA expression were depolarized or excited by GABA. These results indicate that transient GABA‐mediated excitation on granule cells might be the main cause of the enhanced inhibition on mitral cells, and suggest that these differential GABA responses between relay and intrinsic neurons play pivotal roles in the early postnatal rat olfactory bulb.
Purine Salvage Pathways in the Apicomplexan Parasite Toxoplasma gondii*

We have exploited a variety of molecular genetic, biochemical, and genomic techniques to investigate the roles of purine salvage enzymes in the protozoan parasite Toxoplasma gondii. The ability to generate defined genetic knockouts and target transgenes to specific loci demonstrates that T. gondii uses two (and only two) pathways for purine salvage, defined by the enzymes hypoxanthine-xanthine-guanine phosphoribosyltransferase (HXGPRT) and adenosine kinase (AK). Both HXGPRT and AK are single-copy genes, and either one can be deleted, indicating that either one of these pathways is sufficient to meet parasite purine requirements. Fitness defects suggest both pathways are important for the parasite, however, and that the salvage of adenosine is more important than salvage of hypoxanthine and other purine nucleobases. HXGPRT and AK cannot be deleted simultaneously unless one of these enzymes is provided in trans, indicating that alternative routes of functionally significant purine salvage are lacking. Despite previous reports to the contrary, we found no evidence of adenine phosphoribosyltransferase (APRT) activity when parasites were propagated in APRT-deficient host cells, and no APRT ortholog is evident in the T. gondii genome. Expression of Leishmania donovani APRT in transgenic T. gondii parasites yielded low levels of activity but did not permit genetic deletion of both HXGPRT and AK. A detailed comparative genomic study of the purine salvage pathway in various apicomplexan species highlights important differences among these parasites.
Energy expenditure while playing active and inactive video games.

PURPOSE To examine energy expenditure (EE) when playing active and inactive videogames (VG). METHODS Predicted EE was measured among 51 undergraduate students while playing active and inactive VG (Ontario, Canada). RESULTS Predicted EE was significantly higher playing the active VG compared to the inactive VG according to heart rate monitor (97.4 kcal vs 64.7 kcal) and SenseWear armband (192.4 kcal vs 42.3 kcal) estimates. CONCLUSION Active VG may be a viable intervention tool for increasing EE among students who would otherwise be spending time in sedentary screen-based behaviors.
RNA Triphosphatase Component of the mRNA Capping Apparatus of Paramecium bursaria Chlorella Virus 1

ABSTRACT Paramecium bursaria chlorella virus 1 (PBCV-1) elicits a lytic infection of its unicellular green alga host. The 330-kbp viral genome has been sequenced, yet little is known about how viral mRNAs are synthesized and processed. PBCV-1 encodes its own mRNA guanylyltransferase, which catalyzes the addition of GMP to the 5′ diphosphate end of RNA to form a GpppN cap structure. Here we report that PBCV-1 encodes a separate RNA triphosphatase (RTP) that catalyzes the initial step in cap synthesis: hydrolysis of the γ-phosphate of triphosphate-terminated RNA to generate an RNA diphosphate end. We exploit a yeast-based genetic system to show thatChlorella virus RTP can function as a cap-forming enzyme in vivo. The 193-amino-acid Chlorella virus RTP is the smallest member of a family of metal-dependent phosphohydrolases that includes the RNA triphosphatases of fungi and other large eukaryotic DNA viruses (poxviruses, African swine fever virus, and baculoviruses). Chlorella virus RTP is more similar in structure to the yeast RNA triphosphatases than to the enzymes of metazoan DNA viruses. Indeed, PBCV-1 is unique among DNA viruses in that the triphosphatase and guanylyltransferase steps of cap formation are catalyzed by separate viral enzymes instead of a single viral polypeptide with multiple catalytic domains.
Minimizing pipeline stalls in distributed-controlled coarse-grained reconfigurable arrays with Triggered Instruction issue and execution

The pipeline stall in distributed-controlled coarse-grained reconfigurable arrays is a major source stumbling performance. This work presents a Triggered-Issue and Triggered-Execution (TITE) paradigm motivated from the Triggered Instruction Architecture (TIA) which converts control and data dependencies into predicate dependencies as triggers for spatial parallelism. TITE separately triggers the issuing and execution of instructions to further relax the predicate dependencies in TIA. Triggered dual instructions and tag forwarding are proposed to minimize pipeline stalls of both intra and inter-processing elements. Experiments show that TITE improves performance, energy efficiency, and area efficiency by 21%, 17%, and 12%, respectively, compared with TIA.
Multicenter evaluation of infant lung function tests as cystic fibrosis clinical trial endpoints.

RATIONALE The conducting of clinical trials in infants with cystic fibrosis (CF) has been hindered by lack of sensitive outcome measures. OBJECTIVES To evaluate safety, feasibility, and ability to detect abnormalities in lung function of serial pulmonary function tests (PFTs) in infants with CF. METHODS Multicenter observational study using a commercial device, rigorous training, ongoing quality control, and over-reading of data by an independent panel. Raised volume rapid thoracoabdominal compression technique and plethysmography were performed at enrollment and at 6 and 12 months, with an additional 1-month reproducibility visit. MEASUREMENTS AND MAIN RESULTS A total of 342 procedures were performed in 100 infants with CF at 10 centers. FRC measurements were acceptable at a higher proportion of study visits (89%) than raised volume (72%) or fractional lung volume (68%) measurements. Average Z scores for many parameters differed significantly from historical control values. Mean (95% confidence interval) Z scores were: -0.52 (-0.78 to -0.25) for forced expiratory flow at 75% (FEF₇₅) for FVC; 1.92 (1.39-2.45) for FRC; 1.22 (0.68-1.76) for residual volume; 0.87 (0.60-1.13) for FRC/total lung capacity; and 0.66 (0.27-1.06) for residual volume/total lung capacity. For future multicenter clinical trials using infant PFTs as primary endpoints, minimum detectable treatment effects are presented for several sample sizes. CONCLUSIONS In this 10-center study, key PFT measures were significantly different in infants with CF than in historical control subjects. However, infant PFTs do not yet appear ready as primary efficacy endpoints for multicenter clinical trials, particularly at inexperienced sites, based on acceptability rates, variability, and potentially large sample sizes required to detect reasonable treatment effects.
Src-inducible association of CrkL with procaspase-8 promotes cell migration

Procaspase-8, the zymogen form of the apoptosis-initiator caspase-8, undergoes phosphorylation following integrin-mediated cell attachment to an extracellular matrix substrate. Concordant with cell attachment to fibronectin, a population of procaspase-8 becomes associated with a peripheral insoluble compartment that includes focal complexes and lamellar microfilaments. Phosphorylation of procaspase-8 both impairs its maturation to the proapoptotic form and can promote cell migration. Here we show that the cytoskeletal adaptor protein CrkL promotes caspase-8 recruitment to the peripheral spreading edge of cells, and that the catalytic domain of caspase-8 directly interacts with the SH2 domain of CrkL. We show that the interaction is abolished by shRNA-mediated silencing of Src, in Src-deficient MEFs, and by pharmacologic inhibitors of the kinase. The results provide insight into how tyrosine kinases may act to coordinate the suppression caspase-8 mediated apoptosis, while promoting cell invasion.
Spatiotemporal choreography of chromosome and megaplasmids in the Sinorhizobium meliloti cell cycle

A considerable share of bacterial species maintains multipartite genomes. Precise coordination of genome replication and segregation with cell growth and division is vital for proliferation of these bacteria. The α‐proteobacterium Sinorhizobium meliloti possesses a tripartite genome composed of one chromosome and the megaplasmids pSymA and pSymB. Here, we investigated the spatiotemporal pattern of segregation of these S. meliloti replicons at single cell level. Duplication of chromosomal and megaplasmid origins of replication occurred spatially and temporally separated, and only once per cell cycle. Tracking of FROS (fluorescent repressor operator system)‐labelled origins revealed a strict temporal order of segregation events commencing with the chromosome followed by pSymA and then by pSymB. The repA2B2C2 region derived from pSymA was sufficient to confer the spatiotemporal behaviour of this megaplasmid to a small plasmid. Altering activity of the ubiquitous prokaryotic replication initiator DnaA, either positively or negatively, resulted in an increase in replication initiation events or G1 arrest of the chromosome only. This suggests that interference with DnaA activity does not affect replication initiation control of the megaplasmids.
Antibacterial activity of Ocimum gratissimum L. essential oil.

The essential oil (EO) of Ocimum gratissimum inhibited Staphylococcus aureus at a concentration of 0.75 mg/ml. The minimal inhibitory concentrations (MICs) for Shigella flexineri, Salmonella enteritidis, Escherichia coli, Klebsiella sp. , and Proteus mirabilis were at concentrations ranging from 3 to 12 microg/ml. The endpoint was not reached for Pseudomonas aeruginosa (>=24 mg/ml). The MICs of the reference drugs used in this study were similar to those presented in other reports. The minimum bactericidal concentration of EO was within a twofold dilution of the MIC for this organism. The compound that showed antibacterial activity in the EO of O. gratissimum was identified as eugenol and structural findings were further supported by gas chromatography/mass spectra retention time data. The structure was supported by spectroscopic methods.
Kanadaptin Is a Protein That Interacts with the Kidney but Not the Erythroid Form of Band 3*

Although epithelial membrane proteins are separately targeted to apical or basolateral domains, some are apically located in one cell type but are basolateral in others. More dramatically, the anion exchanger of a clonal cell line of intercalated cells derived from the kidney can be retargeted from the apical to basolateral domain. This Cl:HCO3 exchanger, kAE1, is an alternately spliced form of the erythroid anion exchanger (AE1, band 3), but unlike band 3 it does not bind ankyrin. Here we identify a new protein (kanadaptin) that binds to the cytoplasmic domain of kAE1in vitro and in vivo but not to the erythroid AE1 or to ankyrin. No significant homologous proteins have been reported so far. Kanadaptin is widely expressed in epithelial (kidney, lung, and liver) and non-epithelial cells (brain and skeletal and cardiac muscle). In kidney, we found by immunocytochemistry that kanadaptin was only expressed in the collecting tubule. In the intercalated cells of this segment, it colocalized with kAE1 in cytoplasmic vesicles but not when the exchanger was in the basolateral membrane. These results raised the possibility that this protein is involved in the targeting of kAE1 vesicles to their final destination.
Realization of Ultra Fine Pitch Traces on LCP Substrates

Liquid crystal polymer (LCP) is being utilized in a variety of applications that could benefit from the realization of ultra fine pitch conductive traces on the surface of the LCP substrate. LCP has unique chemical properties that not only benefit the intended application, but can also be exploited to realize ultra fine pitch traces. Through a series of experiments, it was discovered that a thin film of Ti can form TiC with the surface of an Ar ion ablated LCP substrate. This layer then provides sufficient adhesion for other metals to be deposited so that ultra fine pitch traces can be patterned. Using this process, 10 mum wide traces on a 20 mum pitch with high yield were demonstrated and analyzed. Smaller feature size test structures were also demonstrated.
Admission and Power Control for Spectrum Sharing Cognitive Radio Networks

We investigate the problem of admission and power control considering a scenario where licensed, or primary, users and cognitive radios, or secondary users, are transmitting concurrently over the same band. The primary users share a common receiver and the interference on this receiver from secondary users should be strictly limited to a certain level. Each secondary link is assumed to have a minimum quality of service (QoS) requirement that should be satisfied together with the interference limit constraint, otherwise the secondary link is not admitted. Under those constraints, admission and power control for secondary users are investigated for two main optimization objectives. First, we maximize the number of admitted secondary links. Second, we maximize the sum throughput of the admitted secondary links. The first problem is NP-hard, hence we provide a distributed close-to-optimal solution based on local measurements at each user and a limited amount of signaling. For the second problem, which is non-convex, we propose a suboptimal algorithm based on sequential geometric programming. The proposed algorithms are compared with previously related work to demonstrate their relative efficiency in terms of outage probability, complexity and achievable throughput.
Ontology for Geographical Names Management and Retrieval

Geographical Names are key components of all georeferenced information systems, including GIS applications in many diverse fields of knowledge and services. This paper we focus on building an ontology for gazetteers, the ontology will better support the gazetteers applications, maintenances, and usability. The ontology contains place types, spatial and temporal concepts and their relations. We firstly establish a prototype of geographical name ontology. Secondly, we analyzed geographical names concepts and their semantics, to describe the knowledge structure for this field. Then we use OWL to provide a formal description for these concepts and relations and propose a unified semantic framework for the description of the geographical names information. Finally, we make an experiment by establishing ontology-based knowledge base. Through the analysis of examples we showed that ontology-based geographical names information can be shared and reused conveniently, and that the information retrieval by assistant of ontology can be easily realized.
Comparison of Central Corneal Thickness Measurements with a Rotating Scheimpflug Camera, a Specular Microscope, Optical Low-Coherence Reflectometry, and Ultrasound Pachymetry in Keratoconic Eyes

Abstract Objective: To compare central corneal thickness (CCT) measurements with a rotating Scheimpflug camera (RSC), noncontact specular microscopy (SM), optical low-coherence reflectometry (OLCR), and ultrasonic pachymetry (UP) in keratoconus (KC) patients. Method: In this prospective study, four CCT measurements taken with an RSC, SM, OLCR, and UP were compared in 81 eyes of 44 consecutive KC patients. The KC patients were divided into four subgroups according to Amsler-Krumeich’s KC classification. Results: The RSC and UP measurements of the CCT were not statistically significant in all the groups. Comparison of the SM vs. the OLCR measurements yielded statistically significant differences in all the KC patients and in all KC stages. In all the KC patients, RSC and OLCR showed a high correlation coefficient factor (r = 0.87, p = 0.000). Conclusion: CCT measurements with RSC are comparable to those achieved with UP. Compared with the other devices, according to SM measurements, the central cornea is thicker in all keratoconic eyes and in all KC grades, and it is thinner according to OLCR. RSC, UP, SM, and OLCR should not be used interchangeably in keratoconic eyes.
Airway epithelium in obliterative airway disease

Lung transplantation is currently the only available treatment for endstage lung disease patients. Despite the success of improved modern lung transplantation with the introduction of new surgical techniques, improved immunosuppressive agents and innovations in managing of acute rejection and infection, the survival rate of recipients is 75% at 1 year and less than 50% at 5 years. (1) One of the most severe complications after lung transplantation is obliterative bronchiolitis (OB) which affect over 40% of the recipients within 5 years during the posttransplantation period. (1). OB is a chronic disease that develops from months and mostly years after lung transplantation (2-4). It is characterized by progressive bronchial inflammation, epithelial injury and luminal fibrosis. (5-7). There is no treatment for human OB and insight into the understandings of its mechanism is still lacking. Presently, all clinical efforts are directed at slowing down the process. These efforts include pre-transplant treatment to the donor lung to reduce inflammatory inducing factors, employment of aggressive peri-transplant administration with antibiotics (3;8-11) and improved immunosuppressive regimens. Only re-transplantation appears to be a curable solution, but is mostly not possible due to the limited availability of donor organs. Clinical investigation of OB in humans is restricted by the limited amount of patient material available for research. This makes the development of new treatments a difficult and time consuming task (12). Thus, a simple animal model that resembles the development of OB in human is a desirable goal.