Miracle-dz/UniFAR-FTUs huggingface dataset:
Precisely modulated pathogenicity island interference with late phage gene transcription

Significance Highly mobile staphylococcal pathogenicity islands (SaPIs) are the only source of toxic shock toxin and certain other superantigens, especially enterotoxin B. To promote their survival and spread, the SaPIs parasitize and interfere with certain bacteriophages. Unlike the interference of the clustered regularly interspaced short palindromic repeats (CRISPRs), the interference of SaPIs is never complete, allowing horizontal gene transfer and adaptation. We report a novel SaPI-determined interference mechanism that targets a phage gene essential for both phage and SaPI. Because SaPI is not self-destructive, it must modulate this inhibition to ensure production of its own infectious particles, as well as those of the phage, and it does so by means of a novel SaPI protein that binds to the inhibitor. Having gone to great evolutionary lengths to develop resistance to bacteriophages, bacteria have come up with resistance mechanisms directed at every aspect of the bacteriophage life cycle. Most genes involved in phage resistance are carried by plasmids and other mobile genetic elements, including bacteriophages and their relatives. A very special case of phage resistance is exhibited by the highly mobile phage satellites, staphylococcal pathogenicity islands (SaPIs), which carry and disseminate superantigen and other virulence genes. Unlike the usual phage-resistance mechanisms, the SaPI-encoded interference mechanisms are carefully crafted to ensure that a phage-infected, SaPI-containing cell will lyse, releasing the requisite crop of SaPI particles as well as a greatly diminished crop of phage particles. Previously described SaPI interference genes target phage functions that are not required for SaPI particle production and release. Here we describe a SaPI-mediated interference system that affects expression of late phage gene transcription and consequently is required for SaPI and phage. Although when cloned separately, a single SaPI gene totally blocks phage production, its activity in situ is modulated accurately by a second gene, achieving the required level of interference. The advantage for the host bacteria is that the SaPIs curb excessive phage growth while enhancing their gene transfer activity. This activity is in contrast to that of the clustered regularly interspaced short palindromic repeats (CRISPRs), which totally block phage growth at the cost of phage-mediated gene transfer. In staphylococci the SaPI strategy seems to have prevailed during evolution: The great majority of Staphylococcus aureus strains carry one or more SaPIs, whereas CRISPRs are extremely rare.
Rad51 and Dmc1 Form Mixed Complexes Associated with Mouse Meiotic Chromosome Cores and Synaptonemal Complexes

The eukaryotic RecA homologues RAD51 and DMC1 function in homology recognition and formation of joint-molecule recombination intermediates during yeast meiosis. The precise immunolocalization of these two proteins on the meiotic chromosomes of plants and animals has been complicated by their high degree of identity at the amino acid level. With antibodies that have been immunodepleted of cross-reactive epitopes, we demonstrate that RAD51 and DMC1 have identical distribution patterns in extracts of mouse spermatocytes in successive prophase I stages, suggesting coordinate functionality. Immunofluorescence and immunoelectron microscopy with these antibodies demonstrate colocalization of the two proteins on the meiotic chromosome cores at early prophase I. We also show that mouse RAD51 and DMC1 establish protein–protein interactions with each other and with the chromosome core component COR1(SCP3) in a two-hybrid system and in vitro binding analyses. These results suggest that the formation of a multiprotein recombination complex associated with the meiotic chromosome cores is essential for the development and fulfillment of the meiotic recombination process.
The Digital Distributed System Security Architecture

The Digital Distributed System Security Architecture is a comprehensive speci cation for security in a distributed system that employs state-of-the-art concepts to address the needs of both commercial and government environments. The architecture covers user and system authentication, mandatory and discretionary security, secure initialization and loading, and delegation in a general-purpose computing environment of heterogeneous systems where there are no central authorities, no global trust, and no central controls. The architecture prescribes a framework for all applications and operating systems currently available or to be developed. Because the distributed system is an open OSI environment, where functional interoperability only requires compliance with selected protocols needed by a given application, the architecture must be designed to securely support systems that do not implement or use any of the security services, while providing extensive additional security capabilities for those systems that choose to implement the architecture.
Complementary Split-Ring Resonator-Loaded Microfluidic Ethanol Chemical Sensor

In this paper, a complementary split-ring resonator (CSRR)-loaded patch is proposed as a microfluidic ethanol chemical sensor. The primary objective of this chemical sensor is to detect ethanol’s concentration. First, two tightly coupled concentric CSRRs loaded on a patch are realized on a Rogers RT/Duroid 5870 substrate, and then a microfluidic channel engraved on polydimethylsiloxane (PDMS) is integrated for ethanol chemical sensor applications. The resonant frequency of the structure before loading the microfluidic channel is 4.72 GHz. After loading the microfluidic channel, the 550 MHz shift in the resonant frequency is ascribed to the dielectric perturbation phenomenon when the ethanol concentration is varied from 0% to 100%. In order to assess the sensitivity range of our proposed sensor, various concentrations of ethanol are tested and analyzed. Our proposed sensor exhibits repeatability and successfully detects 10% ethanol as verified by the measurement set-up. It has created headway to a miniaturized, non-contact, low-cost, reliable, reusable, and easily fabricated design using extremely small liquid volumes.
Remote Ischemic Conditioning

Although remote ischemic conditioning promises significant benefit to patients with a variety of acute and chronic illnesses, development of automated, clinically applicable devices has been slow. At least 3 small companies have launched efforts to develop useful tools intended for sale in European and North American markets. The market challenges and opportunities linked to the development of a cost-effective, reliable, and clinically effective device for the application of remote ischemic conditioning are presented in this article.
Acute inflammation regulates neuroregeneration through the NF-κB pathway in olfactory epithelium

Significance After injury to the olfactory mucosa, neural progenitor cells residing in the basal layer are capable of completely reconstituting the neuroepithelium. The molecular events underlying this striking regenerative capacity are not fully understood. We present evidence that damage to the mouse olfactory mucosa results in a transient acute inflammatory response. Using genetic manipulations in a model of olfactory epithelial repair we demonstrate a key role of inflammation in driving the reparative activity of basal olfactory progenitor cells, in a process involving TNF-α signaling via TNF receptor 1 and the NF-κB pathway. This study, revealing cross-talk between the immune system and olfactory neural stem cells, provides insight into the endogenous activation of neuroregeneration. Adult neural stem cells/progenitor cells residing in the basal layer of the olfactory epithelium are capable of reconstituting the neuroepithelium even after severe damage. The molecular events underlying this regenerative capacity remain elusive. Here we show that the repair of neuroepithelium after lesioning is accompanied by an acute, but self-limited, inflammatory process. Attenuation of inflammatory cell recruitment and cytokine production by dexamethasone impairs proliferation of progenitor horizontal basal cells (HBCs) and subsequent neuronal differentiation. Using TNF-α receptor-deficient mice, we identify TNF-α signaling as an important contributor to this inflammatory and reparative process, mainly through TNF-α receptor 1. HBC-selective genetic ablation of RelA (p65), the transcriptional activator of the NF-κB pathway, retards inflammation and impedes proliferation at the early stages of regeneration and suggests HBCs directly participate in cross-talk between immune response and neurogenesis. Loss of RelA in the regenerating neuroepithelium perturbs the homeostasis between proliferation and apoptosis while enhancing JNK signaling. Together, our results support a model in which acute inflammation after injury initiates important regenerative signals in part through NF-κB–mediated signaling that activates neural stem cells to reconstitute the olfactory epithelium.
World Journal of Surgical Oncology the Significance of the Van Nuys Prognostic Index in the Management of Ductal Carcinoma in Situ

Background: Debate regarding the benefit of radiotherapy after local excision of ductal carcinoma in situ (DCIS) continues. The Van Nuys Prognostic Index (VNPI) is thought to be a useful aid in deciding which patients are at increased risk of local recurrence and who may benefit from adjuvant radiotherapy (RT). Recently published interim data from the Sloane project has showed that the VNPI score did significantly affect the chances of getting planned radiotherapy in the UK, suggesting that British clinicians may already be using this scoring system to assist in decision making. This paper independently assesses the prognostic validity of the VNPI in a British population.
Collective intelligence: analysis and modelling

Purpose – The purpose of this paper is to focus on the underpinning dynamics that explain collective intelligence. Design/methodology/approach – Collective intelligence can be understood as the capacity of a collective system to evolve toward higher order complexity through networks of individual capacities. The authors observed two collective systems as examples of the dynamic processes of complex networks – the wiki course PeSO at the Universidad de Los Andes, Bogota, Colombia, and an agent-based model inspired by wiki systems. Findings – The results of the wiki course PeSO and the model are contrasted with a random network baseline model. Both the wiki course and the model show dynamics of accumulation, in which statistical properties of non-equilibrium networks appear. Research limitations/implications – The work is based on network science. The authors analyzed data from two kinds of networks: the wiki course PeSO and an agent-based model. Limitations due to the number of computations and complexity .
Covert Reorganization of Implicit Task Representations by Slow Wave Sleep

Background There is evidence that slow wave sleep (SWS) promotes the consolidation of memories that are subserved by mediotemporal- and hippocampo-cortical neural networks. In contrast to implicit memories, explicit memories are accompanied by conscious (attentive and controlled) processing. Awareness at pre-sleep encoding has been recognized as critical for the off-line memory consolidation. The present study elucidated the role of task-dependent cortical activation guided by attentional control at pre-sleep encoding for the consolidation of hippocampus-dependent memories during sleep. Methodology A task with a hidden regularity was used (Number Reduction Task, NRT), in which the responses that can be implicitly predicted by the hidden regularity activate hippocampo-cortical networks more strongly than responses that cannot be predicted. Task performance was evaluated before and after early-night sleep, rich in SWS, and late-night sleep, rich in rapid eye movement (REM) sleep. In implicit conditions, slow cortical potentials (SPs) were analyzed to reflect the amount of controlled processing and the localization of activated neural task representations. Principal Findings During implicit learning before sleep, the amount of controlled processing did not differ between unpredictable and predictable responses, nor between early- and late-night sleep groups. A topographic re-distribution of SPs indicating a spatial reorganization occurred only after early, not after late sleep, and only for predictable responses. These SP changes correlated with the amount of SWS and were covert because off-line RT decrease did not differentiate response types or sleep groups. Conclusions It is concluded that SWS promotes the neural reorganization of task representations that rely on the hippocampal system despite absence of conscious access to these representations. Significance Original neurophysiologic evidence is provided for the role of SWS in the consolidation of memories encoded with hippocampo-cortical interaction before sleep. It is demonstrated that this SWS-mediated mechanism does not depend critically on explicitness at learning nor on the amount of controlled executive processing during pre-sleep encoding.
Concept disambiguation exploiting semantic databases

This paper presents a novel approach for resolving ambiguities in concepts that already reside in semantic databases such as Freebase and DBpedia. Different from standard dictionaries and lexical databases, semantic databases provide a rich hierarchy of semantic relations in ontological structures. Our disambiguation approach decides on the implied sense by computing concept similarity measures as a function of semantic relations defined in ontological graph representation of concepts. Our similarity measures also utilize Wikipedia descriptions of concepts. We performed a preliminary experimental evaluation, measuring disambiguation success rate and its correlation with input text content. The results show that our method outperforms well-known disambiguation methods.
Non-nutritive sucking relieves pain for preterm infants during heel stick procedures in Taiwan.

AIMS This study examined the effectiveness of non-nutritive sucking on preterm infant pain, changes in infant behaviour and frequency of abnormal physiological signals during heel stick procedures in Taiwan. BACKGROUND Preterm infants' repetitive exposure to painful procedures may result in changes to brain organisation. Pain management should be a priority in neonatal care. DESIGN Randomised control trial. METHODS Preterm infants (gestational age 28.9-37 weeks) were randomised to two groups: those receiving (experimental, n = 52) or not receiving non-nutritive sucking (control, n = 52) during heel stick procedures. Pain was measured before (for three minutes), during and after (during 10-minute recovery) heel stick procedures by the Premature Infant Pain Profile, changes in infant behaviour and abnormal physiological parameters. Results. Infants in both groups had similar odds ratios for pain and moderate-to-severe pain (0.57 and 0.58, respectively), after adjusting for time effects, postconceptional age, heel stick duration, painful experiences and baseline Premature Infant Pain Profile score. The pain scores of infants with non-nutritive sucking were significantly lower than those of non-nutritive sucking infants at all eight phases of the heel stick procedures. Infants undergoing heel stick procedures in the experimental group had lower rates ratios for 'grimace' and 'hand to mouth or face' behaviours than control infants (0.73 and 0.78, respectively). CONCLUSION Non-nutritive sucking effectively reduced pain, particularly mild to moderate pain and behavioural responses to pain in infants receiving heel stick procedures, suggesting that nurses can offer this intervention to relieve pain in preterm infants undergoing invasive procedures. RELEVANCE TO CLINICAL PRACTICE Infants should be given an appropriate-sized pacifier for comfort during painful procedures. Nurses need to be informed about the effectiveness of non-nutritive sucking, its analgesic mechanisms and how to use and incorporate it into practice.
Coordinated Patterns on Smooth Curves

We show methods that control cooperative Newtonian particles to generate patterns on smooth curves. The spacing between neighboring particles is measured by the relative arc-length and the distance between a particle and the desired curve is measured using an orbit function. The orbit value and the relative arc-length are then used as feedback to control the motion of each particle to a pattern on the desired curve asymptotically. Possible applications of the methods to underwater mobile sensor networks are discussed
LC-StatCom with symmetrical I-V characteristic — Power loss analysis

In this paper a comparative loss analysis between a cascaded H-bridge (CHB) low-capacitance static compensator (LC-StatCom) with symmetrical I-V characteristics and a conventional CHB StatCom is presented. Effect of the capacitor voltage ripples on switching and conduction losses are determined through theoretical analysis. Simulation-based analyses on a 350-VA three-cell CHB LC-StatCom system are provided to confirm the theoretical predictions.
Localization of Electrical Flows

We show that in any graph, the average length of a flow path in an electrical flow between the endpoints of a random edge is $O(\log^2 n)$. This is a consequence of a more general result which shows that the spectral norm of the entrywise absolute value of the transfer impedance matrix of a graph is $O(\log^2 n)$. This result implies a simple oblivious routing scheme based on electrical flows in the case of transitive graphs.
Adaptive self-management of teams of autonomous vehicles

Unmanned Autonomous Vehicles (UAVs) are increasingly deployed for missions that are deemed dangerous or impractical to perform by humans in many military and disaster scenarios. Collaborating UAVs in a team form a Self-Managed Cell (SMC) with at least one commander. UAVs in an SMC may need to operate independently or in sub-groups, out of contact with the commander and the rest of the team in order to perform specific tasks, but must still be able to eventually synchronise state information. The SMC must also cope with intermittent and permanent communication failures as well permanent UAV failures. This paper describes a failure management scheme that copes with both communication link and UAV failures, which may result in temporary disjoint sub-networks within the SMC. A communication management protocol is proposed to control UAVs performing disconnected individual operations, while maintaining the SMC's structure by trying to ensure that all members of the mission regardless of destination or task, can communicate by moving UAVs to act as relays or by allowing the UAVs to rendezvous at intermittent intervals.
Some aspects of Quality of Service in wireless LAN

IEEE 802.11 MAC protocol is the de facto standard for wireless local area networks (WLANs). In today’s Internet, the emerging widespread use of real-time voice, audio, and video applications makes QoS (Quality of Service) a key problem. This article tries to show that implementation of some mechanisms of traffic shaping causes some improvement of the level of QoS in WLANs.
Seasonal Prediction of Winter Precipitation Anomalies over Central Southwest Asia: A Canonical Correlation Analysis Approach

AbstractCentral southwest Asia (CSWA: 20˚-47˚N and 40˚-85˚E) is a water-stressed region prone to significant variations in precipitation during its winter precipitation season of November-April. Wintertime precipitation is crucial for regional water resources, agriculture, and livelihood; however, in recent years droughts have been a notable feature of CSWA’s interannual variability. Here, the predictability of CSWA wintertime precipitation is explored based on its time-lagged relationship with the preceding months’ (September-October) sea surface temperature (SST), using a canonical correlation analysis (CCA) approach.For both periods, results indicate that for CSWA much of the seasonal predictability arises from SST variations in the Pacific related to the El Nino–Southern Oscillation (ENSO) and Pacific Decadal Oscillation (PDO). Additional sources of skill that play a weaker predictive role include long-term SST trends, North Atlantic variability and regional teleconnections. CCA cross-validation skill.
Exclusion of Int-6 from PML Nuclear Bodies by Binding to the HTLV-I Tax Oncoprotein

The Tax transactivator of the human T cell leukemia virus type I (HTLV-I) exhibits oncogenic properties. A screen for proteins interacting with Tax yielded a complementary DNA (cDNA) encoding the human Int-6 protein. In mice, the Int-6 gene can be converted into a putative dominant negative oncogene after retroviral insertion. Here, Int-6 was localized in the cell nucleus to give a speckled staining pattern superposed to that of the promyelocytic leukemia (PML) protein. The binding of Tax to Int-6 caused its redistribution from the nuclear domains to the cytoplasm. Thus, Int-6 is a component of the PML nuclear bodies and Tax disrupts its normal cellular localization by binding to it.
Mesenchymal Stem Cells as Therapeutics Agents: Quality and Environmental Regulatory Aspects

Mesenchymal stem cells (MSCs) are one of the main stem cells that have been used for advanced therapies and regenerative medicine. To carry out the translational clinical application of MSCs, their manufacturing and administration in human must be controlled; therefore they should be considered as medicine: stem cell-based medicinal products (SCMPs). The development of MSCs as SCMPs represents complicated therapeutics due to their extreme complex nature and rigorous regulatory oversights. The manufacturing process of MSCs needs to be addressed in clean environments in compliance with requirements of Good Manufacturing Practice (GMP). Facilities should maintain these GMP conditions according to international and national medicinal regulatory frameworks that introduce a number of specifications in order to produce MSCs as safe SCMPs. One of these important and complex requirements is the environmental monitoring. Although a number of environmental requirements are clearly defined, some others are provided as recommendations. In this review we aim to outline the current issues with regard to international guidelines which impact environmental monitoring in cleanrooms and clean areas for the manufacturing of MSCs.
Agent teaching agent framework

We address the problem of knowledge transfer between a trainer and a trainee agent. The knowledge being transferred is a concept description, a boolean-valued function that classifies input examples as members or non-members of the target concept. We assume that the trainer agent does not have access to the internal knowledge representation of the trainee agent, but can evaluate its concept recognition abilities by asking it to categorize selected exemplars and non-exemplars of the target concept. The trainer agent also do not have access to the original training set from which it learned its concept description, and hence has to rely only on that learned knowledge to train the trainee agent. We present an Agent Teaching Agent (ATA) framework which focuses on incremental selection of training examples by the trainer to expedite the learning of the trainee agent. We envisage an iterative training procedure in which alternatively the trainer selects a set of training and testing exemplars, the trainee trains using the training set and then classifies the testing set, the trainer observes errors made by the trainee in classifying the instances in the last testing set and accordingly generates the next training and testing sets. This iterative process converges when error of the trainee falls below a given threshold. We now present these iterative training steps in an algorithmic form: