Miracle-dz/UniFAR-FTUs huggingface dataset:
Type VI secretion system: secretion by a contractile nanomachine

The type VI secretion systems (T6SS) are present in about a quarter of all Gram-negative bacteria. Several key components of T6SS are evolutionarily related to components of contractile nanomachines such as phages and R-type pyocins. The T6SS assembly is initiated by formation of a membrane complex that binds a phage-like baseplate with a sharp spike, and this is followed by polymerization of a long rigid inner tube and an outer contractile sheath. Effectors are preloaded onto the spike or into the tube during the assembly by various mechanisms. Contraction of the sheath releases an unprecedented amount of energy, which is used to thrust the spike and tube with the associated effectors out of the effector cell and across membranes of both bacterial and eukaryotic target cells. Subunits of the contracted sheath are recycled by T6SS-specific unfoldase to allow for a new round of assembly. Live-cell imaging has shown that the assembly is highly dynamic and its subcellular localization is in certain bacteria regulated with a remarkable precision. Through the action of effectors, T6SS has mainly been shown to contribute to pathogenicity and competition between bacteria. This review summarizes the knowledge that has contributed to our current understanding of T6SS mode of action.
Effectiveness of hospital-based video interaction guidance on parental interactive behavior, bonding, and stress after preterm birth: A randomized controlled trial.

OBJECTIVE This study examined the effectiveness of hospital-based Video Interaction Guidance (VIG; Eliëns, 2010; Kennedy, Landor, & Todd, 2011) for mothers and fathers of infants born preterm (25-37 weeks of gestation). METHOD VIG is a preventive video-feedback intervention to support the parent-infant relationship. One hundred fifty families (150 infants, 150 mothers, 144 fathers) participated in a pragmatic randomized controlled trial to evaluate the effects of VIG as adjunct to standard hospital care. Primary outcome was parental interactive behavior (sensitivity, intrusiveness, and withdrawal) as observed in videotaped dyadic parent-infant interaction. Secondary outcomes comprised parental bonding, stress responses, and psychological well-being based on self-report. The intervention effects were assessed at baseline, mid-intervention, 3-week, 3-month, and 6-month follow-ups. Data were analyzed on an intention-to-treat basis, using multilevel modeling and analyses of covariance. RESULTS VIG proved to be effective in enhancing sensitive behavior and diminishing withdrawn behavior in mothers (Cohen's d range = .24-.44) and in fathers (d range: .54-.60). The positive effects of VIG were particularly found in mothers who experienced the preterm birth as very traumatic (d range = .80-1.04). The intervention, however, did not change parents' intrusive behavior. Analyses additionally revealed positive effects on parental bonding, especially for fathers, yet no significant effects on stress and well-being were detected. CONCLUSIONS The results indicate that VIG is a useful addition to standard hospital care, reducing the possible negative impact of preterm birth on the parent-infant relationship. VIG appeared particularly beneficial for fathers, and for mothers with traumatic birth experiences. High levels of parental intrusiveness, however, need complementary intervention. (PsycINFO Database Record
Improvement of skin wound healing in diabetic mice by kinin B2 receptor blockade.

Impaired skin wound healing is a major medical problem in diabetic subjects. Kinins exert a number of vascular and other actions limiting organ damage in ischaemia or diabetes, but their role in skin injury is unknown. We investigated, through pharmacological manipulation of bradykinin B1 and B2 receptors (B1R and B2R respectively), the role of kinins in wound healing in non-diabetic and diabetic mice. Using two mouse models of diabetes (streptozotocin-induced and db/db mice) and non-diabetic mice, we assessed the effect of kinin receptor activation or inhibition by subtype-selective pharmacological agonists (B1R and B2R) and antagonist (B2R) on healing of experimental skin wounds. We also studied effects of agonists and antagonist on keratinocytes and fibroblasts in vitro. Levels of Bdkrb1 (encoding B1R) and Bdkrb2 (encoding B2R) mRNAs increased 1-2-fold in healthy and wounded diabetic skin compared with in non-diabetic skin. Diabetes delayed wound healing. The B1R agonist had no effect on wound healing. In contrast, the B2R agonist impaired wound repair in both non-diabetic and diabetic mice, inducing skin disorganization and epidermis thickening. In vitro, B2R activation unbalanced fibroblast/keratinocyte proliferation and increased keratinocyte migration. These effects were abolished by co-administration of B2R antagonist. Interestingly, in the two mouse models of diabetes, the B2R antagonist administered alone normalized wound healing. This effect was associated with the induction of Ccl2 (encoding monocyte chemoattractant protein 1)/Tnf (encoding tumour necrosis factor α) mRNAs. Thus stimulation of kinin B2 receptor impairs skin wound healing in mice. B2R activation occurs in the diabetic skin and delays wound healing. B2R blockade improves skin wound healing in diabetic mice and is a potential therapeutic approach to diabetic ulcers.
Efficient Construction of Spanners in $d$-Dimensions

In this paper we consider the problem of efficiently constructing $k$-vertex fault-tolerant geometric $t$-spanners in $\dspace$ (for $k \ge 0$ and $t >1$). Vertex fault-tolerant spanners were introduced by Levcopoulus et. al in 1998. For $k=0$, we present an $O(n \log n)$ method using the algebraic computation tree model to find a $t$-spanner with degree bound O(1) and weight $O(\weight(MST))$. This resolves an open problem. For $k \ge 1$, we present an efficient method that, given $n$ points in $\dspace$, constructs $k$-vertex fault-tolerant $t$-spanners with the maximum degree bound O(k) and weight bound $O(k^2 \weight(MST))$ in time $O(n \log n)$. Our method achieves the best possible bounds on degree, total edge length, and the time complexity, and solves the open problem of efficient construction of (fault-tolerant) $t$-spanners in $\dspace$ in time $O(n \log n)$.
SCRAM: Scalable Collision-avoiding Role Assignment with Minimal-Makespan for Formational Positioning

Teams of mobile robots often need to divide up subtasks efficiently. In spatial domains, a key criterion for doing so may depend on distances between robots and the subtasks' locations. This paper considers a specific such criterion, namely how to assign interchangeable robots, represented as point masses, to a set of target goal locations within an open two dimensional space such that the makespan (time for all robots to reach their target locations) is minimized while also preventing collisions among robots. We present scaleable (computable in polynomial time) role assignment algorithms that we classify as being SCRAM (Scalable Collision-avoiding Role Assignment with Minimal-makespan). SCRAM role assignment algorithms use a graph theoretic approach to map agents to target goal locations such that our objectives for both minimizing the makespan and avoiding agent collisions are met. A system using SCRAM role assignment was originally designed to allow for decentralized coordination among physically realistic simulated humanoid soccer playing robots in the partially observable, non-deterministic, noisy, dynamic, and limited communication setting of the RoboCup 3D simulation league. In its current form, SCRAM role assignment generalizes well to many realistic and real-world multiagent systems, and scales to thousands of agents.
Prevalence and distribution of plasmid-mediated quinolone resistance genes in clinical isolates of Escherichia coli lacking extended-spectrum beta-lactamases.

OBJECTIVES The aac(6')-Ib-cr gene has been described in plasmids from CTX-M-15-producing Escherichia coli in the worldwide ST131 lineage, but has not been systematically sought in other quinolone-resistant strains in the UK. A rise in quinolone resistance in bacteraemia isolates in the UK preceded the increased prevalence of CTX-M-producing strains. This study aimed to describe the presence of plasmid-encoded quinolone resistance genes in historical and current strains of E. coli not producing extended-spectrum beta-lactamases (ESBLs). METHODS Ciprofloxacin-resistant, non-ESBL-producing E. coli isolates included nationally distributed isolates from the BSAC UK bacteraemia surveillance programme between 2001 and 2005, urinary isolates from a regional project in 2000 and local strains in 2006. The aac(6')-Ib-cr gene was detected using PCR followed by restriction fragment length polymorphism analysis. Multiplex PCR was used to detect qnr genes. Isolates with aac(6')-Ib-cr were assessed for aminoglycoside susceptibilities and were serotyped. RESULTS The prevalence of the aac(6')-Ib-cr gene was 3% and 9% in current local urinary and historic national bacteraemia quinolone-resistant non-ESBL-producing E. coli, respectively. Of 521 regional urinary E. coli isolates from 2000, 14 were norfloxacin-resistant, none of which carried the aac(6')-Ib-cr gene. National positive bacteraemia isolates from 2001/2 were type O102-ST405 and, in 2004/5, types O1-ST645 and O25-ST131. Positive local urinary isolates from 2006 included serotypes O1 and O25. CONCLUSIONS In the UK, aac(6')-Ib-cr occurs in E. coli in the absence of CTX-M-15, but with a restricted serotype distribution. Its presence in widespread bacteraemia isolates of a single type from 2001 to 2002, prior to the spread of CTX-M-15 in Britain, might suggest a lineage from which plasmid recombination occurred in man or other species.
Clinical impact of neoadjuvant treatment in resectable pancreatic cancer: a systematic review and meta-analysis protocol

Introduction Although the only curative strategy for pancreatic cancer is surgical resection, up to 85% of patients relapse after surgery. The efficacy of neoadjuvant treatment in resectable pancreatic cancer (RPC) remains unclear and there is no systematic review focusing fully on this issue. Recently, two prospective trials of neoadjuvant treatment in RPC were terminated early because of slow recruiting and existing randomised controlled trials (RCTs) have too small sample sizes. Therefore, to overcome probable biases, it would be more reasonable to include both RCTs and non-randomised studies (NRSs) with selected criteria. This review aims to investigate the effect of neoadjuvant chemotherapy (CTx) and chemoradiation therapy (CRT) in RPC using RCTs and specific NRSs. Method and analysis This systematic review will include conventional RCTs as group I, and quasi-randomised controlled trials, non-randomised controlled trials and prospective cohort studies as group II. Two groups will be assessed and analysed separately. Comprehensive literature search will use Medline, Embase, Cochrane library and Scopus databases. Additionally, we will search references from relevant studies and abstracts from major conferences. Two authors will independently identify, screen, include studies, extract data and assess the risk of bias. Discrepancies will be resolved by consensus with another author. An independent methodologist will categorise and assess NRSs to minimise heterogeneity. In each study group, meta-analysis will be conducted using a random-effect model and statistical heterogeneity will be evaluated using I2-statistics. Publication bias will be visualised with contour-enhanced funnel plots and analysed with Egger's test. In group I, cumulative meta-analysis will be considered because the CTx regimen and CRT protocol have changed. The quality of evidence will be summarised using the GRADE (Grading of Recommendations Assessment, Development and Evaluation) approach. Ethics and dissemination This review does not use primary data, and formal ethical approval is not required. Findings will be disseminated through peer-reviewed journals and committee conferences. Trial registration number CRD42015023820.
Hard X-Ray Emission from the Galaxy Cluster A2256

After the positive detection by BeppoSAX of hard X-ray radiation up to ~80 keV in the Coma Cluster spectrum, we present evidence for nonthermal emission from A2256 in excess of thermal emission at a 4.6 σ confidence level. In addition to this power-law component, a second nonthermal component already detected by ASCA could be present in the X-ray spectrum of the cluster, which is not surprising given the complex radio morphology of the cluster central region. The spectral index of the hard tail detected by the Phoswich Detection System on board BeppoSAX is marginally consistent with that expected for the inverse Compton model. A value of ~0.05 μG is derived for the intracluster magnetic field of the extended radio emission in the northern regions of the cluster, while a higher value of ~0.5 μG could be present in the central radio halo, which is likely related to the hard tail detected by ASCA.
Rapid and Specific Detection of Salmonella spp. in Animal Feed Samples by PCR after Culture Enrichment

ABSTRACT A PCR procedure has been developed for routine analysis of viable Salmonella spp. in feed samples. The objective was to develop a simple PCR-compatible enrichment procedure to enable DNA amplification without any sample pretreatment such as DNA extraction or cell lysis. PCR inhibition by 14 different feed samples and natural background flora was circumvented by the use of the DNA polymerase Tth. This DNA polymerase was found to exhibit a high level of resistance to PCR inhibitors present in these feed samples compared to DyNAzyme II, FastStart Taq, Platinum Taq, Pwo, rTth, Taq, and Tfl. The specificity of the Tth assay was confirmed by testing 101 Salmonella and 43 non-Salmonella strains isolated from feed and food samples. A sample preparation method based on culture enrichment in buffered peptone water and DNA amplification with Tth DNA polymerase was developed. The probability of detecting small numbers of salmonellae in feed, in the presence of natural background flora, was accurately determined and found to follow a logistic regression model. From this model, the probability of detecting 1 CFU per 25 g of feed in artificially contaminated soy samples was calculated and found to be 0.81. The PCR protocol was evaluated on 155 naturally contaminated feed samples and compared to an established culture-based method, NMKL-71. Eight percent of the samples were positive by PCR, compared with 3% with the conventional method. The reasons for the differences in sensitivity are discussed. Use of this method in the routine analysis of animal feed samples would improve safety in the food chain.
Extraction of Facial Features from Color Images

In this paper, a method for localization and extraction of faces and characteristic facial features such as eyes, mouth and face boundaries from color image data is proposed. This approach exploits color properties of human skin to localize image regions - face candidates. The facial features extraction is performed only on prese- lected face-candidate regions. Likewise, for eyes and mouth localization color information and local contrast around eyes are used. The ellipse of face boundary is de- termined using gradient image and Hough transform. Algorithm was tested on image database Feret.
A dimorphic fungus causing disseminated infection in South Africa.

BACKGROUND The genus emmonsia contains three species that are associated with human disease. Emmonsia crescens and Emmonsia parva are the agents that cause adiaspiromycosis, and one human case of Emmonsia pasteuriana infection has been described. We report a fungal pathogen within the genus emmonsia that is most closely related to E. pasteuriana in human immunodeficiency virus (HIV)-infected adults in South Africa. METHODS Between July 2008 and July 2011, we conducted enhanced surveillance to identify the cause of systemic, dimorphic fungal infections in patients presenting to Groote Schuur Hospital and other hospitals affiliated with the University of Cape Town, Cape Town, South Africa. DNA sequencing was used to identify pathogenic fungi. RESULTS A total of 24 cases of dimorphic fungal infection were diagnosed, 13 of which were caused by an emmonsia species. All 13 patients were HIV-infected, with a median CD4+ T-cell count of 16 cells per cubic millimeter (interquartile range, 10 to 44), and all had evidence of disseminated fungal disease. Three patients died soon after presentation, but the others had a good response to a variety of antifungal agents and antiretroviral therapy. Phylogenetic analysis of five genes (LSU, ITS1-2, and the genes encoding actin, β-tubulin, and intein PRP8) revealed that this fungus belongs in the genus emmonsia and is most closely related to E. pasteuriana. CONCLUSIONS The findings suggest that these isolates of an emmonsia species represent a new species of dimorphic fungus that is pathogenic to humans. The species appears to be an important cause of infections in Cape Town.
Nitrogen transactions along the digestive tract of lambs concurrently infected with Trichostrongylus colubriformis and Ostertagia circumcincta

Twelve lambs, paired on the basis of live weight, were cannulated in the abomasum, in the proximal jejunum approximately 4 m distal to the pylorus and in the terminal ileum. Six were infected with 3000 Trichostrongylus colubriformis and 3000 Ostertagia circumcincta larvae each day for 18 weeks and the remainder were pair-fed to individual infected lambs. All animals were offered ryegrass (Lolium perenne)–white clover (Trifolium repens) pasture, cut daily. Dry matter (DM) intake, live weight, faecal egg concentration, plasma pepsinogen and plasma protein concentrations were measured weekly. During weeks 7 and 17 after commencement of infection, the flow of digesta along the gastrointestinal tract was measured together with enteric plasma loss and true digestion and absorption of 125I-labelled albumin in the small intestine. DM intake was depressed by parasitism, being 1331, (se 70), 423 (se 32) and 529 (se 52) g/d during weeks 3, 7 and 17 respectively. The flow of nitrogen at the proximal jejunum and in faeces was increased by parasitism during week 7 and at the abomasum and ileum during week 17. Plasma protein-N loss (g/d) into the gastrointestinal tract was 0.68 (se 0.091) and 1.97 (se 0.139) during week 7, and 0.85 (se0.158) and 1.96 (se 0.396) during week 17, in control and infected sheep respectively. True digestion and absorption of albumin in the proximal small intestine, the site of infection, was very low (mean 0.08) and was not affected by parasitism. Between the abomasum and terminal ileum absorption of albumin was high (mean 0.87) and again was not affected by parasitism. It was calculated that of the total increase in endogenous protein passing from the ileum tract as a result of infection, plasma protein comprised only a small percentage (10–36%). The major proportion of digestion and absorption of protein occurred in the distal small intestine beyond the site of infection and was not affected by infection.
Transcriptome Analysis of Murine Macrophages in Response to Infection with Streptococcus pyogenes Reveals an Unusual Activation Program

ABSTRACT The complex response of murine macrophages to infection with Streptococcus pyogenes was investigated at the level of gene expression with a high-density oligomer microarray. More than 400 genes were identified as being differentially regulated. Many of the up-regulated genes encode molecules involved in the immune response and in inflammation, transcription, signaling, apoptosis, the cell cycle, electron transport, and cell adhesion. Of particular interest was the up-regulation of proinflammatory cytokines, typical of the classically activated macrophages (M1 phenotype), such as tumor necrosis factor alpha, interleukin 1 (IL-1), and IL-6, and as well as the up-regulation of anti-inflammatory mediators, such as IL-1 decoy receptor and IL-10, associated with alternative macrophage activation (M2 phenotype). Furthermore, the gene encoding inducible nitric oxide synthase (iNOS), an enzyme typically implicated in classical activation, was not induced in infected macrophages. Instead, the gene encoding arginase, a competitor for the iNOS substrate arginine involved in the alternative activation pathway, was up-regulated in S. pyogenes-infected cells. Thus, the microarray-based gene expression analysis demonstrated that S. pyogenes induces an atypical activation program in macrophages, with some but not all features of the classical or alternative activation phenotypes. The microarray data also suggested that the bactericidal activity of macrophages against S. pyogenes is mediated by phagocyte oxidase, as p47phox was up-regulated in infected cells. Indeed, the in vivo and in vitro killing of S. pyogenes was markedly diminished in the absence of functional phagocyte (p47phox−/−) but not in the absence of iNOS (iNOS−/−). An understanding of how macrophages respond to S. pyogenes at the molecular level may facilitate the development of new therapeutic paradigms.
The capacity region of the symmetric linear deterministic interference channel with partial feedback

The linear deterministic interference channel (LD-IC) with partial feedback is considered. Partial feedback for the LD-IC models a scenario in which the top l most-significant-bits of the channel output of receiver j are received as feedback at transmitter j, for j = 1, 2. The rationale for studying the LD-IC with partial feedback comes from the fact that it is a good approximation to the Gaussian interference channel with output feedback corrupted by additive white Gaussian noise (commonly referred to as noisy feedback). The main contribution of this paper is to characterize the capacity region of the symmetric LD-IC with partial feedback. The main ingredient of the proof is to obtain novel upper bounds on weighted rates 2R1 + R2 and R1 + 2R2.
Loss of Flight and Associated Neuronal Rhythmicity in Inositol 1,4,5-Trisphosphate Receptor Mutants of Drosophila

Coordinated flight in winged insects requires rhythmic activity of the underlying neural circuit. Here, we show that Drosophila mutants for the inositol 1,4,5-trisphosphate (InsP3) receptor gene (itpr) are flightless. Electrophysiological recordings from thoracic indirect flight muscles show increased spontaneous firing accompanied by a loss of rhythmic flight activity patterns normally generated in response to a gentle puff of air. In contrast, climbing speed, the jump response, and electrical properties of the giant fiber pathway are normal, indicating that general motor coordination and neuronal excitability are much less sensitive to itpr mutations. All mutant phenotypes are rescued by expression of an itpr+ transgene in serotonin and dopamine neurons. Pharmacological and immunohistochemical experiments support the idea that the InsP3 receptor functions to modulate flight specifically through serotonergic interneurons. InsP3 receptor action appears to be important for normal development of the flight circuit and its central pattern generator.
A Brief Review of Nature-Inspired Algorithms for Optimization

Swarm intelligence and bio-inspired algorithms form a hot topic in the developments of new algorithms inspired by nature. These nature-inspired metaheuristic algorithms can be based on swarm intelligence, biological systems, physical and chemical systems. Therefore, these algorithms can be called swarm-intelligence-based, bio-inspired, physics-based and chemistry-based, depending on the sources of inspiration. Though not all of them are efficient, a few algorithms have proved to be very effi cient and thus have become popular tools for solving real-world problems. Some algorithms are insuffici ently studied. The purpose of this review is to present a relatively comprehensive list of all the algorithms in the literature, so as to inspire further research.