Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0

Plant-pathogenic fungi secrete effector proteins to facilitate infection. We describe extensive improvements to EffectorP, the first machine learning classifier for fungal effector prediction. EffectorP 2.0 is now trained on a larger set of effectors and utilizes a different approach based on an ensemble of classifiers trained on different subsets of negative data, offering different views on classification. EffectorP 2.0 achieves accuracy of 89%, compared to 82% for EffectorP 1.0 and 59.8% for a small size classifier. Important features for effector prediction appear to be protein size, protein net charge as well as the amino acids serine and cysteine. EffectorP 2.0 decreases the number of predicted effectors in secretomes of fungal plant symbionts and saprophytes by 40% when compared to EffectorP 1.0. However, EffectorP 1.0 retains value and combining EffectorP 1.0 and 2.0 results in a stringent classifier with low false positive rate of 9%. EffectorP 2.0 predicts significant enrichments of effectors in 12 out of 13 sets of infection-induced proteins from diverse fungal pathogens, whereas a small cysteine-rich classifier detects enrichment only in 7 out of 13. EffectorP 2.0 will fast-track prioritization of high-confidence effector candidates for functional validation and aid in improving our understanding of effector biology. EffectorP 2.0 is available at http://effectorp.csiro. au.
Safety and Efficacy of a Fully Covered Self-Expandable Metallic Stent in Benign Airway Stenosis

Background: The use of self-expandable metallic stents (SEMS) in benign airway disease was the object of a boxed warning from the United States Food and Drug Administration in 2005 due to the risk of stent-related complications and difficulties associated with their removal. Third-generation fully covered SEMS have been commercialized since this warning and theoretically should not present the same difficulties associated with removal as they cannot become embedded in the airway mucosa. Objectives: We aimed to examine the safety and efficacy of a specific third-generation SEMS, the Silmet stent. Methods: We reviewed the records of all patients treated for benign airway stenosis with third-generation Silmet SEMS from January 2011 to December 2015 at the North Hospital of Marseilles, France. Results: Forty SEMS were inserted in 30 patients over this period. Twenty (50.0%) stents were removed because of stent-related complications after a median of 77.0 ± 96.6 days (migration 32.5%, granulation tissue formation 7.5%, subjective intolerance 5.0%, mucus plugging 2.5%, laryngeal edema 2.5%). There were no cases of stent-related mortality. All complications were managed successfully endoscopically. Thirty-six stents (90.0%) were removed successfully after a median of 122.0 ± 113.2 days without any complications. The clinical success rate of stent treatment was 40.7%. Conclusion: Third-generation SEMS are a safe treatment option for complex benign airway stenosis, but complications requiring stent removal are frequent. Further studies are needed to compare the performance of third-generation SEMS and silicone stents in benign airway stenosis.
Effects of uniaxial and biaxial orientation on fiber percolation in conductive polymer composites

A Monte Carlo simulation was built to estimate the percolation threshold of fibers in a system under different fiber orientations. A 3-D model was built. The orientation effect was modeled by introducing a degree of alignment in the randomly generated fibers via appropriate mathematical relationships and various degrees of uniaxial strain were applied. The critical volume fraction was then analyzed in both normal direction (through-plane) and parallel direction (in-plane) to that of the cross-section plane. The effect of uniaxial orientation was modeled by measuring the through-plane percolation threshold under tensile strain. The effect of biaxial orientation was modeled by measuring the in-plane percolation threshold under compressive strain. The results indicated that the introduction of fiber alignment changed both through-plane and in-plane threshold values, albeit with different trends. With the introduction of slight uniaxial orientation, the through-plane percolation threshold reached a minimum va.
Unexpected overnight stay following ENT day-case surgery: a 5-year audit.

Unexpected overnight stay following ENT day-case surgery: a 5-year audit. PROBLEMS/OBJECTIVES Recent decades have seen a steady reduction in the average duration of hospitalization for all surgical patients, including those undergoing ENT procedures. Correspondingly, the proportion of day surgeries relative to in-patient surgeries has progressively increased. In the present observational study, we aimed to evaluate the proportion of unplanned overnight stays following planned day surgeries in our ENT unit, and the major causes of these unexpected overnight admissions. METHODS From databases, we collected data from all patients who underwent ENT day-case surgery in Ziekenhuis Oost- Limburg between January 2008 and December 2013. RESULTS A total of 10,440 patients underwent ENT day-case surgery during this period. The overall rate of unexpected overnight admission was 1.86%, with these overnight admissions most commonly due to anaesthetic (46.91%), surgical (19.59%), and organizational (17.01%) reasons. The types of ENT surgery at the greatest risk for prolonged hospitalisation were hemithyroidectomy (12.50%), tympanoplasty (12.15%), and uvulopalatopharyngoplasty (UPPP) (7.81%). We further identified a clear difference in the rate of unexpected overnight stay between surgery scheduled in the morning (1.17%) versus in the afternoon (12.98%). CONCLUSIONS Our present findings highlight the various reasons for unexpected overnight admission after day-case surgery. To reduce the rate of unexpected overnight stays, we need to better understand these different reasons to support the ongoing search for possible solutions.
Mario Becomes Cognitive

In line with Allen Newell's challenge to develop complete cognitive architectures, and motivated by a recent proposal for a unifying subsymbolic computational theory of cognition, we introduce the cognitive control architecture SEMLINCS. SEMLINCS models the development of an embodied cognitive agent that learns discrete production rule-like structures from its own, autonomously gathered, continuous sensorimotor experiences. Moreover, the agent uses the developing knowledge to plan and control environmental interactions in a versatile, goal-directed, and self-motivated manner. Thus, in contrast to several well-known symbolic cognitive architectures, SEMLINCS is not provided with production rules and the involved symbols, but it learns them. In this paper, the actual implementation of SEMLINCS causes learning and self-motivated, autonomous behavioral control of the game figure Mario in a clone of the computer game Super Mario Bros. Our evaluations highlight the successful development of behavioral versatility as well as the learning of suitable production rules and the involved symbols from sensorimotor experiences. Moreover, knowledge- and motivation-dependent individualizations of the agents' behavioral tendencies are shown. Finally, interaction sequences can be planned on the sensorimotor-grounded production rule level. Current limitations directly point toward the need for several further enhancements, which may be integrated into SEMLINCS in the near future. Overall, SEMLINCS may be viewed as an architecture that allows the functional and computational modeling of embodied cognitive development, whereby the current main focus lies on the development of production rules from sensorimotor experiences.
Prophylactic Strategy for Peritoneal Metastasis from Gastric Cancer

The prognosis of advanced gastric cancer patients with peritoneal metastasis is extremely poor. We advocate extensive intraoperative peritoneal lavage (EIPL) as a useful and practical adjuvant surgical technique for gastric cancer patients who are likely to suffer from peritoneal recurrence. In this article, we review the ability of EIPL to prevent peritoneal recurrence in patients with peritoneal free cancer cells, but not overt peritoneal metastasis (CY+/P-), and describe its potential as a prophylactic therapeutic strategy against peritoneal recurrence.
A scalable high frequency noise model for bipolar transistors with application to optimal transistor sizing for low-noise amplifier design

Fully scalable, analytical HF noise parameter equations for bipolar transistors are presented and experimentally tested on high speed Si and SiGe technologies. A technique for extracting the complete set of transistor noise parameters from Y parameter measurements only is developed and verified. Finally, the usefulness of the noise model is demonstrated in the design of tuned LNAs in the 1.9 GHz, 2.4 GHz, and 5.8 GHz bands.
Dynamic Capability Building in Service Value Networks for Achieving Service Innovation

Service organizations increasingly create new service offerings that are the result of collaborative arrangements operating on a value network level. This leads to the notion of “elevated service offerings,” our definition of service innovation, implying new or enhanced service offerings that can only be eventuated as a result of partnering, and one that could not be delivered on individual organizational merits. Using empirical data from a large telecommunications company, we demonstrate through structural equation modeling (SEM) that higher-order dynamic capabilities in services are generated as a result of collaboration between stakeholders. Furthermore, it is through collaboration and education of the stakeholders that additional higher-order capabilities emerge (customer engagement [CuE], collaborative agility [CA], entrepreneurial alertness [EA], and collaborative innovative capacity), all of which influence the service innovation outcome. Our study also reveals empirical evidence for an ongoing process of continuous dynamic capability building in accordance with the changing dynamics of business. Managers of service organizations should recognize the potential embedded in these higher-order skill sets, starting from collaboration, learning, and management of creative ideas for both strategic and operational benefits. Moreover, the capabilities of CA, EA, and CuE are even more important in managing the flexibility, timely delivery, and reliability of service offerings. Managers should take measures to inculcate, promote, and manage these dynamic capability skill sets to foster innovation in services.
Classifying dynamic transitions in high dimensional neural mass models: A random forest approach

Neural mass models (NMMs) are increasingly used to uncover the large-scale mechanisms of brain rhythms in health and disease. The dynamics of these models is dependent upon the choice of parameters, and therefore it is crucial to be able to understand how dynamics change when parameters are varied. Despite being considered low dimensional in comparison to micro-scale, neuronal network models, with regards to understanding the relationship between parameters and dynamics, NMMs are still prohibitively high dimensional for classical approaches such as numerical continuation. Therefore, we need alternative methods to characterise dynamics of NMMs in high dimensional parameter spaces. Here, we introduce a statistical framework that enables the efficient exploration of the relationship between model parameters and selected features of the simulated, emergent model dynamics of NMMs. We combine the classical machine learning approaches of trees and random forests to enable studying the effect that varying multiple parameters has on the dynamics of a model. The method proceeds by using simulations to transform the mathematical model into a database. This database is then used to partition parameter space with respect to dynamic features of interest, using random forests. This allows us to rapidly explore dynamics in high dimensional parameter space, capture the approximate location of qualitative transitions in dynamics and assess the relative importance of all parameters in the model in all dimensions simultaneously. We apply this method to a commonly used NMM in the context of transitions to seizure dynamics. We find that the inhibitory sub-system is most crucial for the generation of seizure dynamics, confirm and expand previous findings regarding the ratio of excitation and inhibition, and demonstrate that previously overlooked parameters can have a significant impact on model dynamics. We advocate the use of this method in future to constrain high dimensional parameter spaces enabling more efficient, person-specific, model calibration.
Long-term effects of interleukin-17A inhibition with secukinumab in active ankylosing spondylitis: 3-year efficacy and safety results from an extension of the Phase 3 MEASURE 1 trial.

OBJECTIVES Secukinumab, a fully human anti-IL-17A monoclonal antibody, provided rapid and sustained improvements in signs and symptoms of ankylosing spondylitis (AS) over 2 years in the Phase 3 MEASURE 1 trial. Here, we report efficacy and safety after 3 years of treatment. METHODS AS subjects completing 2 years of treatment every 4 weeks with subcutaneous secukinumab 150 or 75 mg (following intravenous loading or initial placebo treatment to 16/24 weeks) entered a separate 3-year extension study (NCT01863732). Assessments included ASAS20/40, ASAS5/6, BASDAI, BASDAI 50, BASFI, BASMI, SF-36 physical component summary, ASAS partial remission and ASDAS-CRP. Results were also analysed by prior anti-TNF treatment status. RESULTS Among 290 subjects completing the core trial, 274 entered the extension study, with 260 subjects (94.9%) completing 156 weeks of treatment. ASAS20/40 response (observed) was 80.2%/61.6% in the IV→150 mg group and 75.5%/50.0% in the IV→75 mg group after 156 weeks. Sustained improvements were also seen in BASDAI, BASFI, BASMI and across all other endpoints regardless of previous exposure to anti-TNF agents. Mean secukinumab exposure was 964.3 days (137.8 weeks). Discontinuation rates were low, and secukinumab had a favourable safety profile, consistent with previous reports. Exposure-adjusted incidence rates for serious infections, Candida infections, Crohn's disease, ulcerative colitis, malignant/unspecified tumours, and adjudicated major adverse cardiac events were 1.1, 0.4, 0.5, 0.1, 0.5 and 0.7 per 100 subject-years, respectively. CONCLUSIONS Secukinumab provided sustained efficacy in signs, symptoms and physical function in subjects with AS over 3 years. No new safety signals were observed.
Surgical treatments for snoring.

Surgical treatments for snoring. OBJECTIVES To compare the results on snoring and sleepiness of different surgical treatments for sleep disordered breathing (SDB) including uvulopalatopharyngoplasty (UPPP), functional expansion pharyngoplasty (FEP), osteotomy, septoplasty with turbinoplasty, and somnoplasty. METHODOLOGY Between May 2011 and December 2015, 329 patients presenting with SDB underwent a dedicated clinical examination, drug-induced sleep endoscopy (DISE), and polysomnography (PSG). Of these, 84 patients underwent surgical treatment. Treatments were evaluated through 4 questionnaires (snoring intensity, snoring severity, Epworth Sleepiness Scale [ESS], and global snoring score) before and 6 weeks and 6 months after treatment. Treatment success was defined as a global snoring visual analog scale score (VAS) ≤3 at 6 months. RESULTS The average age of the surgical group was 43 ± 11 years; the mean body mass index was 26 ±3 kg/m; and 88% were male. The snoring scores decreased significantly for every surgical technique at 6 weeks and 6 months. A higher reduction in the median snoring scores was observed in patients receiving UPPP/FEP and osteotomy compared to somnoplasty and septoplasty. Treatment was successful in 88% of the UPPP/FEP group, 92% of the osteotomy group, 61% of the septoplasty group, and 64% of the somnoplasty group. CONCLUSIONS All surgical treatments effectively and persistently reduced snoring and sleepiness symptom scores. The highest rates of success were observed with osteotomies and UPPP/FEP procedures.
Gender differences in the association of smartphone use with the vitality and mental health of adolescent students

ABSTRACT Objective: The present study examined variations in the degree of smartphone use behavior among male and female adolescents as well as the association between various degrees of smartphone use behavior and the vitality and mental health of each gender. Participants: A total of 218 adolescents were recruited from a junior college in September 2014. Methods: All the participants were asked to answer questionnaires on smartphone use. Results: The findings showed that adolescent females as compared with adolescent males exhibited significantly higher degrees of smartphone dependence and smartphone influence. Positive correlations were observed between the duration of smartphone use on weekends and the vitality/mental health of the male adolescents; negative correlations were found between smartphone dependence and the vitality/mental health of males. Conclusion: The findings demonstrate that adolescent females are deeply affected by their smartphone use. Smartphone dependence may decrease the vitality and mental health of male adolescents.
Pharmacological Behavior of Systemically Administered Nanoparticles of Defined Properties: Mechanistic Investigations at the Organ, Tissue, and Cellular Levels

The objective of this thesis is to establish design rules for nanoparticle properties that enable their in vivo transport to target destinations. Gold nanoparticles containing surface-engrafted polyethylene glycol (PEG) chains are prepared with controlled physicochemical properties (hydrodynamic size, surface charge, targeting ligand density). Upon systemic injection into mice, the transport of nanoparticles is monitored by blood pharmacokinetics as well as distribution at the organ, tissue, and subcellular levels from the same injection in an individual animal. At a constant, slightly negative surface charge (ca. -10 mV), most PEGylated gold nanoparticles (PEG-AuNPs) deposit in the liver, spleen, and kidney of normal mice 24 hours after injection. Increasing retention in the liver (Kupffer cells) and spleen correlate positively with increasing nanoparticle diameter over the range of 25-165 nm, largely due to phagocytic uptake. Accumulation in the kidney is size-dependent, but shows a maximum uptake at ca. 75 ± 25 nm that also gives the highest deposition in the mesangium (uptake by mesangial cells). Tumor-bearing mice received injections of PEG-AuNPs of near-constant size (ca. 75 nm) and surface charge (ca. -10 mV) but with variable amounts of ligands that target cancer cells (0-144 ligands per nanoparticle). Independent of ligand content, nanoparticles accumulate in the tumor by the enhanced permeation and retention effect to the same magnitude, and adjacent to leukocytes. Nanoparticles only enter cancer cells in significant amounts when they contain targeting ligands above a threshold amount (between 18 and 144 ligands per nanoparticle). Mechanistic studies from model nanoparticles provide insights for the delivery of therapeutic nanoparticles. Systemic administrations of targeted, cyclodextrin-based, siRNA-containing nanoparticles are investigated in animals and humans (Phase I clinical trial). A fluorescent chemical stain with exposed adamantane molecules for binding into the cyclodextrin cups of the targeted nanoparticles is created, allowing for the examination of tumor tissue sections from animals and patient biopsies. Results from both animal and human tissues reveal intracellular, dose-dependent accumulation of targeted nanoparticles in cancer cells of the tumor.
Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777; Use of NGS to analyse genomic and sub-genomic RNAs

Porcine epidemic diarrhoea virus, strain CV777, was initially characterized in 1978 as the causative agent of a disease first identified in the UK in 1971. This coronavirus has been widely distributed among laboratories and has been passaged both within pigs and in cell culture. To determine the variability between different stocks of the PEDV strain CV777, sequencing of the full-length genome (ca. 28kb) has been performed in 6 different laboratories, using different protocols. Not surprisingly, each of the different full genome sequences were distinct from each other and from the reference sequence (Accession number AF353511) but they are >99% identical. Unique and shared differences between sequences were identified. The coding region for the surface-exposed spike protein showed the highest proportion of variability including both point mutations and small deletions. The predicted expression of the ORF3 gene product was more dramatically affected in three different variants of this virus through either loss of the initiation codon or gain of a premature termination codon. The genome of one isolate had a substantially rearranged 5´-terminal sequence. This rearrangement was validated through the analysis of sub-genomic mRNAs from infected cells. It is clearly important to know the features of the specific sample of CV777 being used for experimental studies.
Immunological biomarkers associated with brain structure and executive function in late‐life depression: exploratory pilot study

Several immunological biomarkers are altered in late‐life major depressive disorder (LLD). Immunological alterations could contribute to LLD's consequences, but little is known about the relations between specific immunological biomarkers and brain health in LLD. We performed an exploratory pilot study to identify, from several candidates, the specific immunological biomarkers related to important aspects of brain health that are altered in LLD (brain structure and executive function).
Comparison of chemical composition of selected winter wheat species

Chemical composition of common wheat – Triticum aestivum ssp. vulgare Vill. Host. , hard wheat – Triticum durum Desf. , and spelt – Triticum aestivum ssp. spelta (L.) Thell grains was investigated. Total protein, wet gluten, fiber, ash, carbohydrates, falling number, macronutrients (phosphorus, potassium, calcium, magnesium), and microelements (copper, iron, manganese, zinc) were determined. Also standard deviation, variability and correlation coefficients were calculated. Hard wheat and spelt lines were characterized by much higher contents of total protein, wet gluten, and falling number value than common wheat; however, the highest protein concentration and falling number was recorded in grains of hard wheat. Common wheat was distinguished by low ash content and the highest carbohydrates level. Higher percentage of macronutrients and microelements in grains of spelt and hard wheat, as compared to common wheat, confirms the usefulness of these species for foodstuff production. Among the qualitative traits studied, content of carbohydrates appeared to be the least variable (cv = 2.2%), while the highest variability (cv = 31.1%) was shown by fat content. Significant correlations for the following trait pairs were observed: protein–gluten, protein–carbohydrates, fat–ash, fat–falling number, carbohydrates–gluten, and ash–falling number.