Miracle-dz/UniFAR-FTUs huggingface dataset:
Meningococcal Factor H Binding Protein Vaccine Antigens with Increased Thermal Stability and Decreased Binding of Human Factor H

ABSTRACT Neisseria meningitidis causes cases of bacterial meningitis and sepsis. Factor H binding protein (FHbp) is a component of two licensed meningococcal serogroup B vaccines. FHbp recruits the complement regulator factor H (FH) to the bacterial surface, which inhibits the complement alternative pathway and promotes immune evasion. Binding of human FH impairs the protective antibody responses to FHbp, and mutation of FHbp to decrease binding of FH can increase the protective responses. In a previous study, we identified two amino acid substitutions in FHbp variant group 2 that increased its thermal stability by 21°C and stabilized epitopes recognized by protective monoclonal antibodies (MAbs). Our hypothesis was that combining substitutions to increase stability and decrease FH binding would increase protective antibody responses in the presence of human FH. In the present study, we generated four new FHbp single mutants that decreased FH binding and retained binding of anti-FHbp MAbs and immunogenicity in wild-type mice. From these mutants, we selected two, K219N and G220S, to combine with the stabilized double-mutant FHbp antigen. The two triple mutants decreased FH binding >200-fold, increased the thermal stability of the N-terminal domain by 21°C, and bound better to an anti-FHbp MAb than the wild-type FHbp. In human-FH-transgenic mice, the FHbp triple mutants elicited 8- to 15-fold-higher protective antibody responses than the wild-type FHbp antigen. Collectively, the data suggest that mutations to eliminate binding of human FH and to promote conformational stability act synergistically to optimize FHbp immunogenicity.
Distributed Online Convex Optimization on Time-Varying Directed Graphs

This paper introduces a class of discrete-time distributed online optimization algorithms, with a group of agents whose communication topology is given by a uniformly strongly connected sequence of time-varying networks. At each time, a private locally Lipschitz strongly convex objective function is revealed to each agent. In the next time step, each agent updates its state using its own objective function and the information gathered from its immediate in-neighbors at that time. Under the assumption that the sequence of communication topologies is uniformly strongly connected, we design an algorithm, distributed over the sequence of time-varying topologies, which guarantees that the individual regret, the difference between the network cost incurred by the agent's states estimation and the cost incurred by the best fixed choice, grows only sublinearly. This algorithm consists of a subgradient flow along with a push-sum step to adjust for the directed nature of the network topologies. We implement the proposed algorithm in a collaborative localization problem, and the results show the proper performance of the algorithm.
Risk factors of perioperative morbimortality after laparoscopic sleeve gastrectomy: a club coelio multicenter study

Abstract Objectives: Postoperative complications after Laparoscopic sleeve gastrectomy (LSG) can dramatically compromise patient’s outcome. The aim of this study is to analyze the per- and postoperative short-term outcomes after LSG and to assess predictive risk factors of complications. Methods: The study group consisted of 790 patients (610 women and 180 men) who underwent LSG In 2014. All interventions were performed by 18 experienced surgeons members of the Club Coelio. Data about preoperative work-up, surgical techniques, 30-days postoperative morbidity and mortality were collected. Endpoints were perioperative morbidity and mortality and assessment of potential risk factors for complications. Results: Mean age and body mass index were respectively 39 years and 41.5kg/m2. Ninety-one patients (11.5%) had previous bariatric surgery. Morbidity rate was 4.7% (37/790) including 16 leaks (2.0%) and 9 bleedings (1.1%) and no deaths. Risk factors for leak were: previous adjustable banding (p = .0051), with no difference between removal of the banding and LSG in 1 or 2 steps, and type of endostapler (p = .0129). Conclusions: Leakage after Sleeve was rare but still observed even in experienced hands. The leak rate is particularly high when LSG is performed after adjustable gastric banding removal.
Educating Software Engineering Managers - Revisited What Software Project Managers Need to Know Today

In 2003, the original paper with this title was published as part of CSEET 2003. It focused on resolving communication issues between software project managers and developers and introduced a corporate strategy based means of evaluating software engineers. Now, more than a decade later, we could benefit from what we have learned in other fields about managing people involved in knowledge work and how to improve our success in software development. But are we? This paper is intended to present what Software Engineering students can be taught today that will help them to be successful as software project managers now and in the future. It is based on the premise that effective software project managers are not born but made through education.
Highly sensitive strain sensors based on fragmentized carbon nanotube/polydimethylsiloxane composites

Wearable strain sensors based on nanomaterial/elastomer composites have potential applications in flexible electronic skin, human motion detection, human–machine interfaces, etc. In this research, a type of high performance strain sensors has been developed using fragmentized carbon nanotube/polydimethylsiloxane (CNT/PDMS) composites. The CNT/PDMS composites were ground into fragments, and a liquid-induced densification method was used to fabricate the strain sensors. The strain sensors showed high sensitivity with gauge factors (GFs) larger than 200 and a broad strain detection range up to 80%, much higher than those strain sensors based on unfragmentized CNT/PDMS composites (GF < 1). The enhanced sensitivity of the strain sensors is ascribed to the sliding of individual fragmentized-CNT/PDMS-composite particles during mechanical deformation, which causes significant resistance change in the strain sensors. The strain sensors can differentiate mechanical stimuli and monitor various human body motions, such as bending of the fingers, human breathing, and blood pulsing.
Identification of Diverse Mycoviruses through Metatranscriptomics Characterization of the Viromes of Five Major Fungal Plant Pathogens

ABSTRACT Mycoviruses can have a marked effect on natural fungal communities and influence plant health and productivity. However, a comprehensive picture of mycoviral diversity is still lacking. To characterize the viromes of five widely dispersed plant-pathogenic fungi, Colletotrichum truncatum, Macrophomina phaseolina, Diaporthe longicolla, Rhizoctonia solani, and Sclerotinia sclerotiorum, a high-throughput sequencing-based metatranscriptomic approach was used to detect viral sequences. Total RNA and double-stranded RNA (dsRNA) from mycelia and RNA from samples enriched for virus particles were sequenced. Sequence data were assembled de novo, and contigs with predicted amino acid sequence similarities to viruses in the nonredundant protein database were selected. The analysis identified 72 partial or complete genome segments representing 66 previously undescribed mycoviruses. Using primers specific for each viral contig, at least one fungal isolate was identified that contained each virus. The novel mycoviruses showed affinity with 15 distinct lineages: Barnaviridae, Benyviridae, Chrysoviridae, Endornaviridae, Fusariviridae, Hypoviridae, Mononegavirales, Narnaviridae, Ophioviridae, Ourmiavirus, Partitiviridae, Tombusviridae, Totiviridae, Tymoviridae, and Virgaviridae. More than half of the viral sequences were predicted to be members of the Mitovirus genus in the family Narnaviridae, which replicate within mitochondria. Five viral sequences showed strong affinity with three families (Benyviridae, Ophioviridae, and Virgaviridae) that previously contained no mycovirus species. The genomic information provides insight into the diversity and taxonomy of mycoviruses and coevolution of mycoviruses and their fungal hosts. IMPORTANCE Plant-pathogenic fungi reduce crop yields, which affects food security worldwide. Plant host resistance is considered a sustainable disease management option but may often be incomplete or lacking for some crops to certain fungal pathogens or strains. In addition, the rising issues of fungicide resistance demand alternative strategies to reduce the negative impacts of fungal pathogens. Those fungus-infecting viruses (mycoviruses) that attenuate fungal virulence may be welcome additions for mitigation of plant diseases. By high-throughput sequencing of the RNAs from 275 isolates of five fungal plant pathogens, 66 previously undescribed mycoviruses were identified. In addition to identifying new potential biological control agents, these results expand the grand view of the diversity of mycoviruses and provide possible insights into the importance of intracellular and extracellular transmission in fungus-virus coevolution.
Tissue dual RNA-seq allows fast discovery of infection-specific functions and riboregulators shaping host–pathogen transcriptomes

Significance Our knowledge of the functions required by extracellular bacterial pathogens to grow in host tissues is still limited. Most available information refers to studies conducted under laboratory growth conditions that mimic host environments but exclude the influence of the host immune system. Tissue dual RNA sequencing allows simultaneous transcript profiling of a pathogen and its infected host. This sensitive approach led to the identification of host immune responses and virulence-relevant bacterial functions that were not previously reported in the context of a Yersinia infection. Application of this tool will allow transcript profiling of other pathogens to unravel concealed gene functions that are crucial for survival in different host niches and will improve identification of potential drug targets. Pathogenic bacteria need to rapidly adjust their virulence and fitness program to prevent eradication by the host. So far, underlying adaptation processes that drive pathogenesis have mostly been studied in vitro, neglecting the true complexity of host-induced stimuli acting on the invading pathogen. In this study, we developed an unbiased experimental approach that allows simultaneous monitoring of genome-wide infection-linked transcriptional alterations of the host and colonizing extracellular pathogens. Using this tool for Yersinia pseudotuberculosis-infected lymphatic tissues, we revealed numerous alterations of host transcripts associated with inflammatory and acute-phase responses, coagulative activities, and transition metal ion sequestration, highlighting that the immune response is dominated by infiltrating neutrophils and elicits a mixed TH17/TH1 response. In consequence, the pathogen’s response is mainly directed to prevent phagocytic attacks. Yersinia up-regulates the gene and expression dose of the antiphagocytic type III secretion system (T3SS) and induces functions counteracting neutrophil-induced ion deprivation, radical stress, and nutritional restraints. Several conserved bacterial riboregulators were identified that impacted this response. The strongest influence on virulence was found for the loss of the carbon storage regulator (Csr) system, which is shown to be essential for the up-regulation of the T3SS on host cell contact. In summary, our established approach provides a powerful tool for the discovery of infection-specific stimuli, induced host and pathogen responses, and underlying regulatory processes.
Experimental Evaluation of Large Scale WiFi Multicast Rate Control

WiFi multicast to very large groups has gained attention as a solution for multimedia delivery in crowded areas. Yet, the most recently proposed schemes do not provide performance guarantees and none have been tested at scale. To address the issue of providing high multicast throughput with performance guarantees, we present the design and experimental evaluation of the multicast dynamic rate adaptation (MuDRA) algorithm. MuDRA balances fast adaptation to channel conditions and stability, which is essential for multimedia applications. MuDRA relies on feedback from some nodes collected via a light-weight protocol and dynamically adjusts the RA response time. Our experimental evaluation of MuDRA on the ORBIT testbed with over 150 nodes shows that MuDRA outperforms other schemes and supports high throughput multicast flows to hundreds of receivers while meeting quality requirements. MuDRA can support multiple high-quality video streams, where 90% of the nodes report excellent or very good video quality.
Rogue Access Point Detector Using Characteristics of Channel Overlapping in 802.11n

In this work, we introduce a powerful hardware-based rogue access point (PrAP), which can relay traffic between a legitimate AP and a wireless station back and forth, and act as a man-in-the-middle attacker. Our PrAP is built of two dedicated wireless routers interconnected physically, and can relay traffic rapidly between a station and a legitimate AP. Through extensive experiments, we demonstrate that the state-of-the-art time-based rogue AP (rAP) detectors cannot detect our PrAP, although effective against software-based rAP. To defend against PrAPs, we propose PrAP-Hunter based on intentional channel interference. PrAP-Hunter is highly accurate, even under heavy traffic scenarios. Using a high-performance (desktop) and low-performance (mobile) experimental setups of our PrAP-Hunter in various deployment scenarios, we demonstrate close to 100% of detection rate, compared to 60% detection rate by the state-of-the-art. We show that PrAP-Hunter is fast (takes 5-10 sec), does not require any prior knowledge, and can be deployed in the wild by real world experiments at 10 coffee shops.
The Rosetta all-atom energy function for macromolecular modeling and design

Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta’s success is the energy function: amodel parameterized from small molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, beta_nov15. Applying these concepts,we explain how to use Rosetta energies to identify and analyze the features of biomolecular models.Finally, we discuss the latest advances in the energy function that extend capabilities from soluble proteins to also include membrane proteins, peptides containing non-canonical amino acids, carbohydrates, nucleic acids, and other macromolecules.
Cell Culture Isolation of Piscine Nodavirus (Betanodavirus) in Fish-Rearing Seawater

ABSTRACT Piscine nodavirus (betanodavirus) is the causative agent of viral nervous necrosis (VNN) in a variety of cultured fish species, particularly marine fish. In the present study, we developed a sensitive method for cell culture isolation of the virus from seawater and applied the method to a spontaneous fish-rearing environment. The virus in seawater was concentrated by an iron-based flocculation method and subjected to isolation with E-11 cells. A real-time reverse transcriptase PCR (RT-PCR) assay was used to quantify the virus in water. After spiking into seawater was performed, a betanodavirus strain (redspotted grouper nervous necrosis virus [RGNNV] genotype) was effectively recovered in the E-11 cells at a detection limit of approximately 105 copies (equivalent to 102 50% tissue culture infective doses [TCID50])/liter seawater. In an experimental infection of juvenile sevenband grouper (Epinephelus septemfasciatus) with the virus, the virus was isolated from the drainage of a fish-rearing tank when the virus level in water was at least approximately 105 copies/liter. The application of this method to sevenband grouper-rearing floating net pens, where VNN prevailed, resulted in the successful isolation of the virus from seawater. No differences were found in the partial sequences of the coat protein gene (RNA2) between the clinical virus isolates of dead fish and the cell-cultured virus isolates from seawater, and the viruses were identified as RGNNV. The infection experiment showed that the virus isolates from seawater were virulent to sevenband grouper. These results showed direct evidence of the horizontal transmission of betanodavirus via rearing water in marine aquaculture.
Gradient-Based Energy Balancing and Current Control for Alternate Arm Converters

The alternate arm converter (AAC) is an emerging fault-tolerant multilevel converter topology from the same family of multilevel converters as the modular multilevel converter (MMC). Due to the alternate operation of the converter arms, energy balancing in the AAC is not continuous, but restricted to small time intervals. This paper develops a gradient-based current control and energy-balancing method for the AAC. The proposed strategy enforces the dynamic limits on the redundant submodules (SMs) during the overlap period and allocates effectively the maximum available number of redundant SMs to control the circulating current. The choice of the gradient as the circulating current control parameter improves the energy regulation capability of the AAC, and the enforcement of dynamic limitations avoids distortions of the output voltage. Results from an AAC-based HVDC converter model derived from the CIGRE benchmark MMC system demonstrate that the proposed strategy delivers improved energy control and balancing with good harmonic performance compared to existing current control methods for the AAC while also maintaining zero-current switching of the director switches of the AAC arms.
Pharmacokinetics of Piperacillin in Critically Ill Australian Indigenous Patients with Severe Sepsis

ABSTRACT There are no available pharmacokinetic data to guide piperacillin dosing in critically ill Australian Indigenous patients despite numerous reported physiological differences. This study aimed to describe the population pharmacokinetics of piperacillin in critically ill Australian Indigenous patients with severe sepsis. A population pharmacokinetic study of Indigenous patients with severe sepsis was conducted in a remote hospital intensive care unit. Plasma samples were collected over two dosing intervals and assayed by validated chromatography. Population pharmacokinetic modeling was conducted using Pmetrics. Nine patients were recruited, and a two-compartment model adequately described the data. The piperacillin clearance (CL), volume of distribution of the central compartment (Vc), and distribution rate constants from the central to the peripheral compartment and from the peripheral to the central compartment were 5.6 ± 3.2 liters/h, 14.5 ± 6.6 liters, 1.5 ± 0.4 h−1, and 1.8 ± 0.9 h−1, respectively, where CL and Vc were found to be described by creatinine clearance (CLCR) and total body weight, respectively. In this patient population, piperacillin demonstrated high interindividual pharmacokinetic variability. CLCR was found to be the most important determinant of piperacillin pharmacokinetics.
Mistakes, Too Few to Mention? Impaired Self-conscious Emotional Processing of Errors in the Behavioral Variant of Frontotemporal Dementia

Anosognosia, or lack of awareness of one's deficits, is a core feature of the behavioral variant of frontotemporal dementia (bvFTD). We hypothesized that this deficit has its origins in failed emotional processing of errors. We studied autonomic and facial emotional reactivity to errors in patients with bvFTD (n = 17), Alzheimer's disease (AD, n = 20), and healthy controls (HC, n = 35) during performance of a timed two-alternative-choice button press task. Performance-related behavioral responses to errors were quantified using rates of error correction and post-error slowing of reaction times. Facial emotional responses were measured by monitoring facial reactivity via video and subsequently coding the type, duration and intensity of all emotional reactions. Skin conductance response (SCR) was measured via noninvasive sensors. SCR and total score for each facial emotion expression were quantified for each trial. Facial emotions were grouped into self-conscious (amusement, embarrassment) and negative (fear, sadness, anger, disgust, contempt) emotions. HCs corrected 99.4% of their errors. BvFTD patients corrected 94% (not statistically different compared with HC) and AD corrected 74.8% of their errors (p < 0.05 compared with HC and bvFTD). All groups showed similar post-error slowing. Errors in HCs were associated with greater facial reactivity and SCRs compared with non-error trials, including both negative and self-conscious emotions. BvFTD patients failed to produce self-conscious emotions or an increase in SCR for errors, although they did produce negative emotional responses to a similar degree as HCs. AD showed no deficit in facial reactivity to errors. Although, SCR was generally reduced in AD during error trials, they showed a preserved increase in SCR for errors relative to correct trials. These results demonstrate a specific deficit in emotional responses to errors in bvFTD, encompassing both physiological response and a specific deficit in self-conscious emotions, despite intact awareness and correction of errors. The findings provide a potential mechanism for anosognosia and possibly other behavioral abnormalities in bvFTD and highlight the importance of studying multiple channels of reactivity to errors, including performance related responses and emotional responses, in order to understand how impaired error processing could influence behavior.
Comparative study of hematopoietic stem and progenitor cells between sexes in mice under physiological conditions along time

Hematopoietic stem and progenitor cells (HSPCs) are attractive targets in regenerative medicine, although the differences in their homeostatic maintenance between sexes along time are still under debate. We accurately monitored hematopoietic stem cells (HSCs), common lymphoid progenitors (CLPs), and common myeloid progenitors (CMPs) frequencies by flow cytometry, by performing serial peripheral blood extractions from male and female B6SJL wild‐type mice and found no significant differences. Only modest differences were found in the gene expression profile of Slamf1 and Gata2. Our findings suggest that both sexes could be used indistinctly to perform descriptive studies in the murine hematopoietic system, especially for flow cytometry studies in peripheral blood. This would allow diminishing the number of animals needed for the experimental procedures. In addition, the use of serial extractions in the same animals drastically decreases the number of animals needed.
Sensitivity study of temperature and strain rate dependent properties on solder joint fatigue life

Tensile tests of 63Sn/37Pb solder were carried out at various strain rates over a wide range of temperatures to study the effect of strain rates and testing temperatures on the mechanical properties of solder. A statistical method incorporating multiple linear regression was also employed successfully and a set of empirical formulae was derived to describe the effects of temperature and strain rate quantitatively. These mechanical properties were applied to finite element analysis to study the sensitivity of these material properties on the fatigue life of solder joints in a plastic ball grid array (PBGA) package. From this study, the strain rate effect on solder response to different ramp rates during thermal cycling or thermal shock reliability tests can be modeled in finite element analysis.