Miracle-dz/UniFAR-FTUs huggingface dataset:
Diarrhoea-causing enteric protist species in intensively and extensively raised pigs (Sus scrofa domesticus) in Southern Spain. Part II: Association with Hepatitis E virus susceptibility.

Enteropathogenic parasites can infect a wide range of mammals, including humans, supposing an important zoonotic risk. Hepatitis E virus (HEV) is an emerging foodborne pathogen of increasing public health relevance, affecting both human and animal populations. Because both microorganisms share faecal-oral transmission route they may constitute an excellent model to evaluate the interplay between them. Thus, we aim to evaluate the viral-parasite interactions at the enteric interface in swine. We included pigs of two different breeds farming in South Spain under different production systems. We compared the HEV prevalence by the presence of Giardia duodenalis, Cryptosporidium spp. , Balantioides coli, Blastocystis sp. , and Enterocytozoon bieneusi in faecal samples. The HEV prevalence was 13.1 (62 out 475, 95% CI: 10.2-16.4). Those pigs infected with Cryptosporidium spp. showed a higher prevalence of HEV (30.8% vs. 12%; p = 0.012). In the same way, animals bearing E. bieneusi seem to have a higher rate of HEV infection (24.2% vs. 12.2%; p = 0.06). According to their location in the gut, animals bearing intracellular enteroparasites showed a higher HEV prevalence than those uninfected (29.6% vs. 12.7%; p = 0.038), meanwhile those carrying extracellular enteroparasites had a lower likelihood to be infected by HEV than those uninfected (12.1% vs. 23.1%; p = 0.071). Those animals bearing both type of enteroparasites showed a similar prevalence of HEV infection than those exhibiting negative for both (20.8% vs. 26.1%; p = 0.763). Our study provides evidence that intracellular and extracellular enteroparasites modulate the susceptibility to HEV infection in pigs. Meanwhile, the presence of extracellular enteroparasites shows a protective effect on the risk of HEV acquisition in swine, whereas intracellular enteroparasites seems to have the opposite effect, favouring the HEV infection. This article is protected by copyright. All rights reserved.
TRANSPORTATION PLANNING PERFORMANCE MEASURES

Oregon transportation plans, including the statewide Oregon Transportation Plan, and current regional transportation plans for the Portland, Salem, Eugene, and Medford metropolitan areas, contain some policy areas that are not adequately addressed by performance measures. These include policies related to the following: balance and adaptability; economic vitality; safety and security; environmental justice; land use compatibility; and quality of life. This research, while acknowledging the importance of assessing current system performance, focuses on performance measures that can also employ model forecast data for evaluating future plan alternatives. To address some of the deficiencies and to better address other plan policies, this research developed and tested six performance measures. The Urban Mobility Measures and Freight Delay Costs used performance measures developed by others and extended them for use in Oregon plans. The Transportation Cost Index represents a novel approach to measuring accessibility and to address, in part, issues related to balance, environmental justice, land use compatibility, and quality of life. The Percent of Market Basket Accessible by Non-auto Modes and the Auto Dependence Index measures are designed to address issues related to automobile reliance in the Oregon Transportation Planning Rule. The Road Network Concentration Index represents a novel approach to measuring transportation system security and efficiency. Other potential performance measures were considered but dropped because current models do not generate the appropriate data. The results of testing and analysis indicate that the Urban Mobility Measures and the Freight Delay Costs could be implemented immediately in Oregon. The others could be implemented soon following further refinement. Further research is recommended into policies related to the following: balance, particularly regarding transportation investments; safety, focusing on the influence of long range planning decisions; reliability; and other aspects of economic vitality.
Plant circadian clock control of Medicago truncatula nodulation via regulation of nodule cysteine-rich peptides

Abstract Legumes house nitrogen-fixing endosymbiotic rhizobia in specialized polyploid cells within root nodules, which undergo tightly regulated metabolic activity. By carrying out expression analysis of transcripts over time in Medicago truncatula nodules, we found that the circadian clock enables coordinated control of metabolic and regulatory processes linked to nitrogen fixation. This involves the circadian clock-associated transcription factor LATE ELONGATED HYPOCOTYL (LHY), with lhy mutants being affected in nodulation. Rhythmic transcripts in root nodules include a subset of nodule-specific cysteine-rich peptides (NCRs) that have the LHY-bound conserved evening element in their promoters. Until now, studies have suggested that NCRs act to regulate bacteroid differentiation and keep the rhizobial population in check. However, these conclusions came from the study of a few members of this very large gene family that has complex diversified spatio-temporal expression. We suggest that rhythmic expression of NCRs may be important for temporal coordination of bacterial activity with the rhythms of the plant host, in order to ensure optimal symbiosis.
Immunosenescence in the wild? A longitudinal study in a long-lived seabird.

1. Longitudinal studies of various vertebrate populations have demonstrated senescent declines in reproductive performance and survival probability to be almost ubiquitous. Longitudinal studies of potential underlying proximate mechanisms, however, are still scarce. 2. Due to its critical function in the maintenance of health and viability, the immune system is among the potential (mediators of) proximate mechanisms that could underlie senescence. 3. Here, we studied three innate immune parameters - hemagglutination titre, haemolysis titre and haptoglobin concentration - in a population of common terns (Sterna hirundo) known to undergo actuarial senescence. We repeatedly sampled birds of known sex and age across 11 years and used random regression models to (i) quantify how immune parameters vary among individuals, and (ii) describe within-individual age-specific changes in, and potential trade-offs between, immune parameters. 4. Our models revealed no differences between males and females in hemagglutination titre and haptoglobin concentration, and very low among-individual variation in these parameters in general. Within individuals, hemagglutination titre increased with age, while haptoglobin concentration did not change. We found no indication for selective (dis)appearance in relation to hemagglutination titre or haptoglobin concentration, nor for the existence of a trade-off between them. Haemolysis was absent in the majority (76%) of samples. 5. Common terns do not exhibit clear senescence in hemagglutination titre and haptoglobin concentration and show very little among-individual variation in these parameters in general. This may be explained by canalisation of the immune parameters or by the colonial breeding behaviour of our study species, but more longitudinal studies are needed to facilitate investigation of links between species' characteristics and immunosenescence in wild animals.
Fuzzy logic control of a variable speed, variable pitch wind turbine

In this paper a system to evaluate a variable speed and pitch angle wind turbine by fuzzy logic techniques is described. A fuzzy logic control has been proposed based on the wind speed estimation in order to get maximum power and stability of the system. An 11 kW prototype system using two inverters connected by a DC-link capacitor has been used: the first one works as a controlled rectifier implementing vector control and the second one handles the power injected into the utility grid. Experimental result of an 11 kW generator are shown.
Dual Mechanism to Detect DDOS Attack

Cloud computing has emerged as computing paradigm which shares resources and services with its customers. In its early days we does not heard of the Denial of service attack. But since 2000, a series of DDOS attacks by multiple nodes is accomplished of blocking the services of cloud servers. The attack can be for many reasons. It became a major threat for cloud environment. Significant problem of DDOS attacks is that they are difficult to detect. The effects of various attacks can shut the organization off from network. The main goal of this attack is to make cloud services unavailable for the legitimate users. This paper aims at proposing an efficient method for security in cloud. We propose an algorithm which modifies the confidence Based Filtering method (CBF) by adding the IP Spoofing filtering method before applying CBF.
Impact of corona-phobia on attitudes and acceptance towards COVID-19 vaccine among cancer patients: a single-center study

Aim: This study aimed to assess the impact of coronavirus disease 2019 (COVID-19) phobia and related factors on attitude towards COVID-19 vaccine in cancer patients. Methods: A prospective cross-sectional descriptive study was conducted with 300 adult patients using a validated COVID-19 Phobia Scale (C19P-S) and related survey to determine the factors affecting vaccine acceptance between May–June 2021. Results: Regarding the COVID-19 vaccine willingness, 86.7% accepted vaccination, 6.3% were hesitant and 7% refused vaccination. Patients that accepted vaccination had significantly higher C19P-S scores in general, and in psychological and psychosomatic subdivisions. Univariate analysis revealed that increased age, being retired, and being married were significantly associated with willingness to be vaccinated against COVID-19. Conclusion: The majority of patients had high coronophobia levels which were associated with increased willingness for the COVID-19 vaccines. Minimizing negative attitudes towards vaccines will most likely be achieved by raising awareness in the cancer population about COVID-19 vaccine.
A bond-wire inductor-MOS varactor VCO tunable from 1.8 to 2.4 GHz

This paper presents a technique that optimizes LC-tank CMOS voltage-controlled oscillators (VCOs) by minimizing the product of phase noise and power consumption. Moreover, it shows that the minimum depends on the tank's quality factor Q, the device noise coefficient /spl gamma/, and the ratio between the maximum oscillation amplitude and supply voltage /spl alpha/. Prototypes, realized in a 0.35-/spl mu/m process, show the following performances: -122.5 dBc/Hz at 600 kHz from a 1.9-GHz carrier, with 2-V supply voltage and 1-mA current consumption. The VCO can be tuned between 1.8-2.4 GHz, when the varactor control voltage is varied between 0-3.5 V. In the proposed realization, the tank is made of a metal-oxide-silicon varactor (operated between accumulation and deep depletion) and a bond-wire inductor, realized connecting two pads to a package frame lead to be compatible with the production environment.
Cancer stem cells: advances in biology and clinical translation-a Keystone Symposia report.

The test for the cancer stem cell (CSC) hypothesis is to find a target expressed on all, and only CSCs in a patient tumor, then eliminate all cells with that target that eliminates the cancer. That test has not yet been achieved, but CSC diagnostics and targets found on CSCs and some other cells have resulted in a few clinically relevant therapies. However, it has become apparent that eliminating the subset of tumor cells characterized by self-renewal properties is essential for long-term tumor control. CSCs are able to regenerate and initiate tumor growth, recapitulating the heterogeneity present in the tumor before treatment. As great progress has been made in identifying and elucidating the biology of CSCs as well as their interactions with the tumor microenvironment, the time seems ripe for novel therapeutic strategies that target CSCs to find clinical applicability. On May 19-21, 2021, researchers in cancer stem cells met virtually for the Keystone eSymposium "Cancer Stem Cells: Advances in Biology and Clinical Translation" to discuss recent advances in the understanding of CSCs as well as clinical efforts to target these populations.
Lower Driving Pressure and Neuromuscular Blocker Use Are Associated With Decreased Mortality in Patients With COVID-19 ARDS

BACKGROUND: The impact of mechanical ventilation parameters and management on outcomes of patients with coronavirus disease 2019 (COVID-19) ARDS is unclear. METHODS: This multi-center observational study enrolled consecutive mechanically ventilated patients with COVID-19 ARDS admitted to one of 7 Korean ICUs between February 1, 2020–February 28, 2021. Patients who were age < 17 y or had missing ventilation parameters for the first 4 d of mechanical ventilation were excluded. Multivariate logistic regression was used to identify which strategies or ventilation parameters that were independently associated with ICU mortality. RESULTS: Overall, 129 subjects (males, 60%) with a median (interquartile range) age of 69 (62–78) y were included. Neuromuscular blocker (NMB) use and prone positioning were applied to 76% and 16% of subjects, respectively. The ICU mortality rate was 37%. In the multivariate analysis, higher dynamic driving pressure (ΔP) values during the first 4 d of mechanical ventilation were associated with increased mortality (adjusted odds ratio 1.16 [95% CI 1.00–1.33], P = .046). NMB use was associated with decreased mortality (adjusted odds ratio 0.27 [95% CI 0.09–0.81], P = .02). The median tidal volume values during the first 4 d of mechanical ventilation and the ICU mortality rate were significantly lower in the NMB group than in the no NMB group. However, subjects who received NMB for ≥ 6 d (vs < 6 d) had higher ICU mortality rate. CONCLUSIONS: In subjects with COVID-19 ARDS receiving mechanical ventilation, ΔP during the first 4 d of mechanical ventilation was independently associated with mortality. The short-term use of NMB facilitated lung-protective ventilation and was independently associated with decreased mortality.
Artificial intelligence in the prediction of protein–ligand interactions: recent advances and future directions

Abstract New drug production, from target identification to marketing approval, takes over 12 years and can cost around $2.6 billion. Furthermore, the COVID-19 pandemic has unveiled the urgent need for more powerful computational methods for drug discovery. Here, we review the computational approaches to predicting protein–ligand interactions in the context of drug discovery, focusing on methods using artificial intelligence (AI). We begin with a brief introduction to proteins (targets), ligands (e.g. drugs) and their interactions for nonexperts. Next, we review databases that are commonly used in the domain of protein–ligand interactions. Finally, we survey and analyze the machine learning (ML) approaches implemented to predict protein–ligand binding sites, ligand-binding affinity and binding pose (conformation) including both classical ML algorithms and recent deep learning methods. After exploring the correlation between these three aspects of protein–ligand interaction, it has been proposed that they should be studied in unison. We anticipate that our review will aid exploration and development of more accurate ML-based prediction strategies for studying protein–ligand interactions.
ConsensusPathDB 2022: molecular interactions update as a resource for network biology

Abstract Molecular interactions are key drivers of biological function. Providing interaction resources to the research community is important since they allow functional interpretation and network-based analysis of molecular data. ConsensusPathDB (http://consensuspathdb.org) is a meta-database combining interactions of diverse types from 31 public resources for humans, 16 for mice and 14 for yeasts. Using ConsensusPathDB, researchers commonly evaluate lists of genes, proteins and metabolites against sets of molecular interactions defined by pathways, Gene Ontology and network neighborhoods and retrieve complex molecular neighborhoods formed by heterogeneous interaction types. Furthermore, the integrated protein–protein interaction network is used as a basis for propagation methods. Here, we present the 2022 update of ConsensusPathDB, highlighting content growth, additional functionality and improved database stability. For example, the number of human molecular interactions increased to 859 848 connecting 200 499 unique physical entities such as genes/proteins, metabolites and drugs. Furthermore, we integrated regulatory datasets in the form of transcription factor–, microRNA– and enhancer–gene target interactions, thus providing novel functionality in the context of overrepresentation and enrichment analyses. We specifically emphasize the use of the integrated protein–protein interaction network as a scaffold for network inferences, present topological characteristics of the network and discuss strengths and shortcomings of such approaches.
Estimation of stapes piston motion from uniaxial interferometer measurements along observation directions at an angle with the piston axis is prone to substantial errors

We have shown that the vibration of the stapes in human, cat and gerbil exhibits all 3-D components of translation and rotation, but also that non-piston components do not contribute to the transmission path. In most experiments access for direct measurement of stapes motion in line with the piston axis is not available and piston motion is estimated from single component interferometric measurements done under observation directions that make angles up to 50° with the piston axis. We used a heterodyne microscope/interferometer to measure the vibration velocity of the stapes in human, cat and gerbil from different observation angles and calculated the complete set of 3-D motion components for the stapes. Using micro CT scans of the experimental ears, we could express the components in an intrinsic reference system and foretell the motion component that will be obtained when a single axis interferometric measurement is done under various angles with the piston axis. For low frequencies (f<2kHz) a cosine factor provides a good correction for the axis off-set, at higher frequencies the piston component can not correctly be estimated from a single off-axis observation. We will show that this may lead to serious misinterpretations of experimental results.
Evidence That Hypothalamic Gliosis Is Related to Impaired Glucose Homeostasis in Adults With Obesity.

OBJECTIVE Preclinical research implicates hypothalamic glial cell responses in the pathogenesis of obesity and type 2 diabetes (T2D). In the current study we sought to translate such findings to humans by testing whether radiologic markers of gliosis in the mediobasal hypothalamus (MBH) were greater in individuals with obesity and impaired glucose homeostasis or T2D. RESEARCH DESIGN AND METHODS Using cross-sectional and prospective cohort study designs, we applied a validated quantitative MRI approach to assess gliosis in 67 adults with obesity and normal glucose tolerance, impaired glucose tolerance (IGT), or T2D. Assessments of glucose homeostasis were conducted via oral glucose tolerance tests (OGTT) and β-cell modeling. RESULTS We found significantly greater T2 relaxation times (a marker of gliosis by MRI), that were independent of adiposity, in the groups with IGT and T2D as compared with the group with normal glucose tolerance. Findings were present in the MBH, but not control regions. Moreover, positive linear associations were present in the MBH but not control regions between T2 relaxation time and glucose area under the curve during an OGTT, fasting glucose concentrations, hemoglobin A1c, and visceral adipose tissue mass, whereas negative linear relationships were present in the MBH for markers of insulin sensitivity and β-cell function. In a prospective cohort study, greater MBH T2 relaxation times predicted declining insulin sensitivity over 1 year. CONCLUSIONS Findings support a role for hypothalamic gliosis in the progression of insulin resistance in obesity and thus T2D pathogenesis in humans.
Inevitable Progress—Relying on the Immune System, Not Chance

Locoregional recurrence of head and neck cancer after curative therapy portends a poor prognosis even when resectable. Immunotherapy has opened the door to novel strategic approaches in the curative treatment paradigm. Potentially improving outcomes for patients with recurrent, resectable disease through combination immune modulators highlights a new frontier. See related article by Hanna et al., p. 468
Requirements for packaging from an ageing consumer's perspective

The overall objective of this research was to explore ageing consumers' attitudes towards currently available food packaging in New Zealand. Ninety‐nine individuals (over the age of 60) in New Zealand were surveyed to determine packaging attributes of importance when selecting food products. This was followed with a focus group of 13 individuals to discuss improvements to packaging. Frequencies of responses were calculated for the survey data, and cross‐tabulations and chi‐square tests were used to determine the relationships between variables. Price, safety, size of packaging and ability to recycle were of most importance to these individuals. Problems encountered with food packaging included tight lids, small printing and spillage during opening. Of the types of package closures investigated, opening of packages, rather than resealing of packages proved problematic. Fifty percent or more of respondents indicated that peelable induction seals, lug closures and continuous thread closures were problems that occurred ‘very often’ or ‘frequently’. Sixty‐one percent of the participants surveyed had asked for assistance opening some types of packages, and this was particularly prevalent among individuals who had weakness in their arms, hands or wrists. Changes to package closures suggested during the focus groups included increasing the size of twist off caps, larger ring pulls on aluminium cans and including more sliding resealable closures on foil and plastic packaging. Larger printing on labels was also recommended by the participants. Copyright © 2008 John Wiley & Sons, Ltd.
Development and Evaluation of Enhanced IntelliDrive-Enabled Lane Changing Advisory Algorithm to Address Freeway Merge Conflict

Freeway merge conflicts contribute significantly to freeway congestion. With the capabilities that will be available in an IntelliDrive environment, which enables vehicle-to-vehicle and vehicle-to-infrastructure communications, new approaches to managing freeway merges are possible. In this paper, an enhanced IntelliDrive enabled lane changing advisory algorithm was developed with a variable gap size concept. This algorithm first calculates anticipated lead–lag gap sizes with the equations of motion prepared for a car and a truck and for three vehicle dynamics (accelerating, maintaining current speed, and decelerating). The algorithm then provides lane changing advisories to freeway main-line vehicles (selected on the basis of the calculated variable gap sizes) to create more space within the ramp merging area. Evaluation conducted with a VISSIM microscopic traffic simulation model of a freeway network in Virginia showed that the proposed algorithm has the potential to address freeway merge conflicts. The maximum operational improvement observed was 6.4% higher average speed in the freeway main line within a merge area. Up to a 5.2% reduction in emissions was achieved. Further analysis conducted in terms of the sensitivity of algorithm performance to driver compliance rates suggested that a very high compliance rate (90% or higher) was necessary for the proposed algorithm to work as intended.