Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Rearrangements Involved in the Capsid Shell Maturation of Bacteriophage T7*♦

Maturation of dsDNA bacteriophages involves assembling the virus prohead from a limited set of structural components followed by rearrangements required for the stability that is necessary for infecting a host under challenging environmental conditions. Here, we determine the mature capsid structure of T7 at 1 nm resolution by cryo-electron microscopy and compare it with the prohead to reveal the molecular basis of T7 shell maturation. The mature capsid presents an expanded and thinner shell, with a drastic rearrangement of the major protein monomers that increases in their interacting surfaces, in turn resulting in a new bonding lattice. The rearrangements include tilting, in-plane rotation, and radial expansion of the subunits, as well as a relative bending of the A- and P-domains of each subunit. The unique features of this shell transformation, which does not employ the accessory proteins, inserted domains, or molecular interactions observed in other phages, suggest a simple capsid assembling strategy that may have appeared early in the evolution of these viruses.
Acceptance of Corporate Blogs for Collaboration and Knowledge Sharing

ABSTRACT This study investigates employees’ acceptance of corporate Web 2.0 applications for collaboration and knowledge sharing. Results show that altruism, managerial support, and perceived usefulness are good predictors of the intention to use corporate blogs as tools for collaboration and knowledge sharing. The study further explores differences between employees from companies with low and high adoption rates, and uses prediction-oriented segmentation to unveil two different paths to adoption of Web 2.0 collaborative tools in companies.
Monitoring Adolescents' Distress using Social Web data as a Source: the InsideOut Project

English. The role of Social Media in the psychological and social development of adolescents and young adults is increasingly important as it impacts on the quality of their interpersonal communication dynamics. The InsideOut project explores the possibility to use Social Web mining methodologies and technologies to collect information about adolescents’ distress from their micro-blogging activities. The project is promoting a complex language processing workflow to approach the collection, enrichment and summarization of user generated contents over Twitter. This paper presents the general architecture of the InsideOut Web Platform and the resources produced by an integrated effort among computer science and mental health professionals. Italiano. Il ruolo dei Social Media nella crescita psicologica e sociale risulta essere sempre più importante poiché influisce sulla qualità e sulle dinamiche di comunicazioni interpersonali, specialmente riguardo le ultime generazioni. Il progetto InsideOut esplora la applicabilità di metodologie e tecnologie che consentono l’individuazione nel Web di evidenze riferibili a sorgenti di stress negli adolescenti. Il progetto propone un workflow di elaborazione linguistica in grado di gestire la raccolta, l’arricchimento e la sintesi dei contenuti generati dagli utenti su Twitter. Nel paper verrà presentata l’architettura generale della piattaforma Web InsideOut e le risorse che derivano dal lavoro congiunto di ricercatori provenienti dall’ambito informatico e medico.
Draft Genome Sequence of a Sulfide-Oxidizing, Autotrophic Filamentous Anoxygenic Phototrophic Bacterium, Chloroflexus sp. Strain MS-G (Chloroflexi)

ABSTRACT The draft genome sequence of the thermophilic filamentous anoxygenic phototrophic bacterium Chloroflexus sp. strain MS-G (Chloroflexi), isolated from Mushroom Spring (Yellowstone National Park, WY, USA) was sequenced and comprises 4,784,183 bp in 251 contigs. The draft genome is predicted to encode 4,059 protein coding genes, 49 tRNA encoding genes, and 3 rRNA operons.
What we can learn from a tadpole about ciliopathies and airway diseases: Using systems biology in Xenopus to study cilia and mucociliary epithelia

Over the past years, the Xenopus embryo has emerged as an incredibly useful model organism for studying the formation and function of cilia and ciliated epithelia in vivo. This has led to a variety of findings elucidating the molecular mechanisms of ciliated cell specification, basal body biogenesis, cilia assembly, and ciliary motility. These findings also revealed the deep functional conservation of signaling, transcriptional, post‐transcriptional, and protein networks employed in the formation and function of vertebrate ciliated cells. Therefore, Xenopus research can contribute crucial insights not only into developmental and cell biology, but also into the molecular mechanisms underlying cilia related diseases (ciliopathies) as well as diseases affecting the ciliated epithelium of the respiratory tract in humans (e.g., chronic lung diseases). Additionally, systems biology approaches including transcriptomics, genomics, and proteomics have been rapidly adapted for use in Xenopus, and broaden the applications for current and future translational biomedical research. This review aims to present the advantages of using Xenopus for cilia research, highlight some of the evolutionarily conserved key concepts and mechanisms of ciliated cell biology that were elucidated using the Xenopus model, and describe the potential for Xenopus research to address unresolved questions regarding the molecular mechanisms of ciliopathies and airway diseases.
New Transmission Planning Model

A model for optimal long-range transmission planning is proposed. The model is capable of dealing with both static and dynamic modes of transmission planning. Given the existing network and anticipating a requirement for future facilities and loads, an accurate nonlinear cost function for the system is formulated. It includes both the fixed and the variable costs for all planned lines, in addition to the cost of the power losses. The cost function is minimized subject to demand satisfaction and overloading constraints. The model includes security constraints on bus voltage magnitudes and swing angles. The AC load flow solution is included in the optimization model. The results of applying the model to a previously reported power system from the literature are discussed. >
Collecting and Analyzing Patient Experiences of Health Care From Social Media

Background Social Media, such as Yelp, provides rich information of consumer experience. Previous studies suggest that Yelp can serve as a new source to study patient experience. However, the lack of a corpus of patient reviews causes a major bottleneck for applying computational techniques. Objective The objective of this study is to create a corpus of patient experience (COPE) and report descriptive statistics to characterize COPE. Methods Yelp reviews about health care-related businesses were extracted from the Yelp Academic Dataset. Natural language processing (NLP) tools were used to split reviews into sentences, extract noun phrases and adjectives from each sentence, and generate parse trees and dependency trees for each sentence. Sentiment analysis techniques and Hadoop were used to calculate a sentiment score of each sentence and for parallel processing, respectively. Results COPE contains 79,173 sentences from 6914 patient reviews of 985 health care facilities near 30 universities in the United States. We found that patients wrote longer reviews when they rated the facility poorly (1 or 2 stars). We demonstrated that the computed sentiment scores correlated well with consumer-generated ratings. A consumer vocabulary to describe their health care experience was constructed by a statistical analysis of word counts and co-occurrences in COPE. Conclusions A corpus called COPE was built as an initial step to utilize social media to understand patient experiences at health care facilities. The corpus is available to download and COPE can be used in future studies to extract knowledge of patients’ experiences from their perspectives. Such information can subsequently inform and provide opportunity to improve the quality of health care.
Encryption and decryption of tissue factor

Tissue factor (TF) is a transmembrane cofactor that binds and promotes the catalytic activity of factor (F) VIIa. The TF/VIIa complex activates FX by limited proteolysis to initiate blood coagulation and helps provide the thrombin burst that is important for a stable thrombus. TF is present both in the extravascular compartment, where it functions as a hemostatic envelope, and the intravascular compartment, where it contributes to thrombus formation, particularly when endothelial disruption is minimal. The regulation of its cofactor function appears to differ in the two compartments. Intravascular TF derives predominately from leucocytes, with either monocytes or neutrophils implicated in different models of thrombosis. This TF exists mostly in a non‐coagulant or cryptic form and acute events lead to local decryption of TF and FX activation. A variety of experimental observations imply that decryption of leucocyte surface TF involves both a dithiol/disulfide switch and exposure of phosphatidylserine. The dithiol/disulfide switch appears to involve the Cys186‐Cys209 disulfide bond in the membrane‐proximal domain of TF, although this has not been demonstrated in vivo. Activation of a purinergic receptor or complement has recently been observed to decrypt TF on myeloid cells and a dithiol/disulfide switch and the oxidoreductase, protein disulfide isomerase, have been implicated in both systems. The molecular mechanism of action of protein disulfide isomerase in TF encryption/decryption, though, remains to be determined.
Improving learning in MOOCs with Cognitive Science

MOOCs and other platforms for online education are having a tremendous impact on the learning of tens of thousands of students. They offer a chance to build a set of educational resources from the ground up, at a time when scientists know far more about learning and teaching than at the advent of the current education system. This paper presents practical implications of research from cognitive science, showing empirically supported and actionable strategies any designer or instructor can use to improve students’ learning. These all take the form of augmenting online videos and exercises with questions and prompts for students to consider explanations: before, during, and after learning. This class of instructional strategies provides students with direction while allowing them to take charge of their learning, is technically easy to implement, and is applicable to a wide variety of video and exercise content, that ranges across multiple topics.
Control of grid-tied photovoltaic systems with neutral point clamped inverters

This paper presents the operation of a grid-tied photovoltaic power generator considering a two stages configuration for active power injection. A Neutral Point Clamped Inverter (NPC Inverter) was used for the DC-AC conversion and a DC-DC Boost converter complemented the system configuration. The control system includes the following loops: a maximum power point tracking algorithm, a DC bus voltage control, a reference generator, a capacitors voltage balancing loop, a current controller and a Level Shifted Pulse Width Modulation (LS-PWM) technique. The work is mainly focused in balancing the voltages in the DC bus capacitors by adding an offset level to the modulation signal which ensures the good performance of the NPC inverter. The operation of the system was evaluated in a PSIM® software environment for different irradiance conditions. The results show the outstanding performance of the photovoltaic system specifically in the Maximum Power Point Tracking (MPPT), the DC side voltages balance in the NPC inverter and the active power control.
Psychosocial and clinical correlates of ADHD in a community sample of school-age children.

OBJECTIVE To identify the psychosocial and clinical correlates of attention-deficit hyperactivity disorder (ADHD) in a community sample of children and to examine the validity of a subclinical form of ADHD. METHOD The sample of 449 children (mean age 9.2 years, SD 1.78; 53.6% boys) participated in the second stage of a community survey. Of these, 359 (80%) screened positive at stage 1. On the basis of a structured diagnostic interview with a parent, children were classified into 1 of 3 mutually exclusive groups: ADHD (n = 89), subthreshold ADHD (n = 100), and non-ADHD (n = 260). RESULTS As measured by the Children's Global Assessment Scale, the ADHD group was more impaired than the subthreshold group, which was more impaired than the non-ADHD group (p < .05 for each test). Children in the ADHD group were more likely to be male, to have mothers with a history of psychiatric treatment, to have fathers with a history of excessive alcohol use, and to live in low-income families with higher levels of family dysfunction (p < .05 for all variables). A model containing male gender, family dysfunction, and low income was most predictive of ADHD status (p < .01). ADHD was also associated with psychiatric comorbidity, especially disruptive behavior disorders. CONCLUSIONS These results support a dimensional approach to ADHD. More severe forms of ADHD are associated with psychosocial adversity and psychiatric comorbidity.
Postcopy Live Migration with Guest-Cooperative Page Faults

Postcopy live migration is a promising alternative of virtual machine (VM) migration, which transfers memory pages after switching the execution host of a VM. It allows a shorter and more deterministic migration time than precopy migration. There is, however, a possibility that postcopy migration would degrade VM performance just after switching the execution host. In this paper, we propose a performance improvement technique of postcopy migration, extending the para-virtualized page fault mechanism of a virtual machine monitor. When the guest operating system accesses a not-yet-transferred memory page, our proposed mechanism allows the guest kernel to defer the execution of the current process until the page data is transferred. In parallel with the page transfer, the guest kernel can yield VCPU to other active processes. We implemented the proposed technique in our postcopy migration mechanism for Qemu/KVM. Through experiments, we confirmed that our technique successfully alleviated performance degradation of postcopy migration for web server and database benchmarks. key words: virtual machine, live migration, page fault, postcopy migration
Using Multi-Attribute Decision Making For Designing Revised Balanced Scorecard In National Iranian Oil Products Distribution Company

Balanced Scorecard (BSC) is used as a comprehensive method in evaluation of organization's performance. The model emphasizes on organizational strategies and provides a reasonable and perfect relation with all organizational aspects (e.g. financial, customer, internal process, learning and growth), in order to achieve the goals and their evaluations. In this paper, we propose the concepts and procedure of Balanced Scorecard (BSC) evolution in public and private dimensions. Managers want to implemented company's strategy by Balanced Scorecard to archive the vision. But they have not lot of money, time, resource and etc to execute all improved programming that reach performance driver's indicators. Therefore, we want to ranking perspectives and performance drivers to reach vision by Multi-Attribute Decision Making (MADM) methods. The proposed approach is applied to an example problem and is shown to be successful, ultimately providing a new managerial tool for planning and analyzing excellence organization more effectively.
A frame erasure concealment method based on pitch and gain linear prediction for AMR-WB codec

This paper presents a novel error concealment method for AMR-WB codec, using excitation search constraint at the encoder and a linear prediction of the pitch and gains of the adaptive codebook and the innovative codebook at the decoder to enhance speech quality after a frame erasure. The experimental results demonstrate that the proposed method achieves performance improvement over the existing methods.
Novel stator electrically field excited synchronous machines without rare-earth magnet

This paper systematically presents the development of novel stator electrically field excited synchronous machines having salient pole rotors without any coils or magnets. This kind of new machines does not use slip-rings/brushes required in the conventional rotor wound field machines and combines the synergies of wound field machines, permanent magnet machines, switched reluctance and synchronous reluctance machines. The paper describes the machine topologies, winding configurations, electromagnetic performance, torque/power density, and efficiency, as well as acoustic noise and vibration, together with a comparison with Toyota Prius interior permanent magnet machines in terms of torque/power speed characteristics and efficiency.
Population Pharmacokinetics of Liposomal Irinotecan in Patients With Cancer

Nanoliposomal irinotecan (nal‐IRI) is a liposomal formulation of irinotecan with a longer half‐life (t1/2), higher plasma total irinotecan (tIRI), and lower SN‐38 maximum concentration (Cmax) compared with nonliposomal irinotecan. Population pharmacokinetic (PK) analysis of nal‐IRI was performed for tIRI and total SN‐38 (tSN38) using patient samples from six studies. PK‐safety association was evaluated for neutropenia and diarrhea in 353 patients. PK‐efficacy association was evaluated from a phase III study in pancreatic cancer NAPOLI1. Efficacy was associated with longer duration of unencapsulated SN‐38 (uSN38) above a threshold and higher Cavg of tIRI, tSN38, and uSN38. Neutropenia was associated with uSN38 Cmax and diarrhea with tIRI Cmax. Baseline predictive factors were race, body surface area, and bilirubin. Analysis identified PK factors associated with efficacy, safety, and predictive baseline factors. The results support the benefit of nal‐IRI dose of 70 mg/m2 (free‐base; equivalent to 80 mg/m2 salt base) Q2W over 100 mg/m2 Q3W.
Inhibition of thymocyte negative selection by T cell receptor antagonist peptides

The T cell receptor (TCR) recognizes antigenic peptide presented by major histocompatibility complex (MHC) molecules. Analogs of antigenic peptides have been shown to inhibit antigen‐specific T cell responses, a phenomenon described as TCR antagonism. We have examined the effect of a natural variant of an antigenic peptide and a synthetic peptide analog, on the responses of mature T cells and immature thymocytes from an αβ TCR‐transgenic mouse (F5), the TCR of which recognizes a nonamer peptide from the nucleoprotein (NP) of influenza virus in the context of the H‐2Db MHC molecule. Both peptides were shown to antagonize specifically the T cell cytolytic response without being able directly to stimulate mature T cells from these transgenic mice. Furthermore, a negative selection assay in vitro was used to demonstrate for the first time that antagonistic peptides are capable of antagonizing thymocyte deletion induced by antigenic peptides. These data suggest that the final selection of a T cell could be the result of a balance between the positive and negative influences of endogenous peptide ligands.
Microscopic Examination of Distribution and Phenotypic Properties of Phylogenetically Diverse Chloroflexaceae-Related Bacteria in Hot Spring Microbial Mats

ABSTRACT We investigated the diversity, distribution, and phenotypes of uncultivated Chloroflexaceae-related bacteria in photosynthetic microbial mats of an alkaline hot spring (Mushroom Spring, Yellowstone National Park). By applying a directed PCR approach, molecular cloning, and sequence analysis of 16S rRNA genes, an unexpectedly large phylogenetic diversity among these bacteria was detected. Oligonucleotide probes were designed to target 16S rRNAs from organisms affiliated with the genus Chloroflexus or with the type C cluster, a group of previously discovered Chloroflexaceae relatives of this mat community. The application of peroxidase-labeled probes in conjunction with tyramide signal amplification enabled the identification of these organisms within the microbial mats by fluorescence in situ hybridization (FISH) and the investigation of their morphology, abundance, and small-scale distribution. FISH was combined with oxygen microelectrode measurements, microscope spectrometry, and microautoradiography to examine their microenvironment, pigmentation, and carbon source usage. Abundant type C-related, filamentous bacteria were found to flourish within the cyanobacterium-dominated, highly oxygenated top layers and to predominate numerically in deeper orange-colored zones of the investigated microbial mats, correlating with the distribution of bacteriochlorophyll a. Chloroflexus sp. filaments were rare at 60°C but were more abundant at 70°C, where they were confined to the upper millimeter of the mat. Both type C organisms and Chloroflexus spp. were observed to assimilate radiolabeled acetate under in situ conditions.
Occult metastases in the sentinel lymph nodes of patients with early stage breast carcinoma

Thirty percent of lymph node negative patients with operable breast carcinoma experience disease recurrence within 10 years. Retrospective serial sectioning of axillary lymph nodes has revealed undetected metastases in 9–30% of these patients. These occult metastases have been shown to have an adverse effect on survival. Serial sectioning (SS) is impractical for all axillary lymph nodes harvested from Levels I and II, but it is feasible if applied only to sentinel lymph nodes.
Cyclic fatigue resistance of different continuous rotation and reciprocating endodontic systems

Objective: The objective of this study is to compare the cyclic fatigue resistance of nine types of endodontic instruments of nickel–titanium. Materials and Methods: Five files of 25 mm of length of each group: Reciproc (RC) R25; WaveOne (WO) Primary; Unicone (UC) L25 25/0.06; K3XF 25/0.06; ProTaper Universal F2 (PTF2); ProTaper Next X2 (PTX2); Mtwo 25/0.06; BioRaCe 25/0.06; One Shape L25 25/0.06 were subjected to a cyclic fatigue resistance test on a mechanical apparatus. The mean fracture time was analyzed statistically by one-way analysis of variance and Tukey's honest significant difference post hoc test, with significance set at P< 0.05. Conclusion: It was observed that the groups PTX2, RC, R25, UC L25 25/0.06, and WO Primary presented greater cyclic fracture resistance than the other groups (P< 0.001).
Low Frequency Radio Polarization Sensor With Applications in Attitude Estimation

A novel method of attitude (orientation) estimation is proposed, which makes use of measurements of the polarization of the magnetic (H-) field of Low Frequency (LF) radio signals. This offers advantages relative to existing accelerometer-based systems in high-acceleration, cost-constrained environments, such as small fixed-wing unmanned aerial vehicles. In order to validate this method, a sensor system is presented, which is capable of determining the H-field polarization of LF radio signals from three-axis measurements. The sensor system consists of an array of three orthogonal loop antennas, a three channel radio receiver circuit, a datalogging and control module, and data processing algorithms. This system is shown to accurately measure the axis of H-field polarization for signals with linear or almost linear polarization, subject to a sign ambiguity. A representative AM radio broadcast in the LF band is shown to have a substantially linear polarization, measurements of which are used to determine a receiver's heading angle. The stability of these polarization measurements over time and the distorting effect of certain structures are quantified. The feasibility of this method of attitude determination is therefore demonstrated.