Miracle-dz/UniFAR-FTUs huggingface dataset:
ideal: an R/Bioconductor package for interactive differential expression analysis

RNA sequencing (RNA-seq) is an ever increasingly popular tool for transcriptome profiling. A key point to make the best use of the available data is to provide software tools that are easy to use but still provide flexibility and transparency in the adopted methods. Despite the availability of many packages focused on detecting differential expression, a method to streamline this type of bioinformatics analysis in a comprehensive, accessible, and reproducible way is lacking. We developed the ideal software package, which serves as a web application for interactive and reproducible RNA-seq analysis, while producing a wealth of visualizations to facilitate data interpretation. ideal is implemented in R using the Shiny framework, and is fully integrated with the existing core structures of the Bioconductor project. Users can perform the essential steps of the differential expression analysis workflow in an assisted way, and generate a broad spectrum of publication-ready outputs, including diagnostic and summary visualizations in each module, all the way down to functional analysis. ideal also offers the possibility to seamlessly generate a full HTML report for storing and sharing results together with code for reproducibility. ideal is distributed as an R package in the Bioconductor project (http://bioconductor.org/packages/ideal/), and provides a solution for performing interactive and reproducible analyses of summarized RNA-seq expression data, empowering researchers with many different profiles (life scientists, clinicians, but also experienced bioinformaticians) to make the ideal use of the data at hand.
COMPOSITE-TO-METAL TUBULAR LAP JOINT UNDER TORSIONAL LOADING

During the damage evolution of bonded joints, different modes of failure can be detected. These modes include pure modes (Mode I, Mode II, Mode III) or their combinations (Mixed-mode) according to the type and the direction of loading. Some scientifically validated test methods are commonly used to obtain the fracture toughness by loading under pure Mode I, Mode II and their Mixed-mode. Some test methods were established to obtain the fracture toughness by loading under pure Mode III, however further research is required. The aim of this work is to clarify the mode ratio of a tubular lap joint under torsional loading and then to propose a method to determine the cohesive and damage parameters of this joint. The presumed mode of failure is Mode III, or Mixed-mode with a predominance of Mode III. Emphasis is placed on the widespread applicability of the obtained results for similar specimens loaded under similar modes.
Structural Change in Dimyristoyl Phosphatidyl Choline (DMPC) Molecule Alkyl Chains on the Addition of Cholesterol to DMPC Monolayer: Specific Addition Effect of Cholesterol

We have investigated the morphology of dimyristoyl phosphatidyl choline (DMPC)—cholesterol mixed monolayer formed on the water surface by dropping method using surface tension measurement (STm), Brewster angle microscopy (BAM), and infrared external reflection spectroscopy (IERS). STm results showed negative deviation of the limiting molecular area (A0) of cholesterol occurred when cholesterol was added to the DMPC monolayer. BAM images showed the expandable DMPC monolayer changed to the condensed rigid monolayer at more than cholesterol mole fraction (xChol) 0.4. IERS recordings showed that the addition of cholesterol at xChol = 0.4 occurred structural change from gauche- to trans- conformation of two DMPC molecule alkyl chains. From these results, it is found that cholesterol molecule has specific properties that cause structural transition of DMPC molecule alkyl chains.
When poverty becomes detrimental to life satisfaction in the transition to adulthood

This study examines whether poverty becomes more meaningful for young people as they move from youth to adulthood; therefore, the main hypothesis is that poverty becomes increasingly detrimental to individual life satisfaction as young people grow older and – at the same time – enter working life and establish their own households or families. The empirical analysis uses German household panel data and applies indicators for income poverty and material deprivation for a sample of 15- to 29-year-old young men and women. Results show that few facets of poverty impair life satisfaction in youth, and indicators increasingly show significant negative effects as people age. Changes in employment status and household context in the transition to adulthood cannot explain the age differences. Findings indicate that age is an independent reference point for young people in the transition to adulthood. Results also suggest that a more critical discussion is required on the significance of poverty and its measurement during the transition from youth to adulthood.
Demography and dynamics of a partial migrant close to the northern range margin

Climate change causes range expansions, but neither the population parameters nor the ecological mechanisms behind range expansions are well known. I studied population dynamics and demography of the great tit (Parus major) in northern Finland, close to the northern range margin of the species’ distribution. I further examined winter conditions, such as temperature, as limiting factors on winter site fidelity and survival of human-fed great tits. Temporal variation in the population growth rate was large, but indicated an overall increasing population size, which fits the current large scale increase in the north. Importantly, the study population was a sink (or pseudo-sink) in almost all years because of low adult survival and low local recruitment. Immigration formed 39–43% of the annual population growth rate indicating that the population is demographically dependent on immigration. The demography differs most from other great tit populations in terms of adult survival which is lower than estimates from more southern Europe. This difference may reflect the impact of more difficult winters. Results from the wintering population support this line of reasoning. Within-winter movement was lower during mid-winter (January to February) and decreased during cold periods. This pattern is probably linked to energy saving and predator escaping strategies during these demanding periods when energy expenditure is high and birds have limited daylight hours to forage. Site fidelity was lower for juveniles than adults within a winter, but not between winters. In addition, survival showed strong links to winter weather. There was temporal variation within winters, particularly when the winter was colder than usual. Survival of juveniles showed a stronger response to cold temperatures. When mean daily minimum temperatures declined below –15 C° degrees, survival started to decline. Low winter temperatures thus provide one explanation for the lower annual adult survival and the sink nature of the population. The results suggest that great tits suffer from the cold conditions of the north: higher mortality increases turnover allowing for strong immigration. Great tits should benefit from warming winters caused by climate change.
Abnormal persistence of the chorioallantoic membrane is associated with severe developmental abnormalities in freshwater turtles

Development in oviparous reptiles requires the correct formation and function of extra-embryonic membranes in the egg. In 2017, we incubated 2583 eggs from five species of freshwater turtle during a long-term ecological study and opened eggs that failed to hatch. We described a previously unreported developmental anomaly: the retention of an extra-embryonic membrane around 7 turtles (1 Spiny Softshell Turtle (Apalone spinifera (Le Sueur, 1827)), 1 Snapping Turtle (Chelydra serpentina (Linnaeus, 1758)), and 5 Northern Map Turtles (Graptemys geographica (Le Sueur, 1817))) that were alive but unhatched >14 days after their clutch mates had emerged. We investigated the association between retention of this membrane and the exhibition of other developmental deformities of varying severity, and we tested whether this novel abnormality was associated with reduced fertility or hatching success in affected clutches. Consultation of ∼150 years of literature suggests that we observed persistence of the chorioallantoic membrane (CAM; also called the chorioallantois). Our data suggest that clutches where at least one turtle exhibits a persistent CAM may also exhibit slightly reduced fertility or hatch success in the rest of the clutch compared with conspecific clutches that do not contain this anomaly. Future research should investigate the factors predicting CAM retention and other developmental abnormalities.
Integrating International Exchange Students into Local Service-Learning Projects in Hong Kong

Through qualitative research, which involved qualitative interviews and focus group meetings with members of four student teams, we identified a number of barriers to the development of cohesiveness in teams of local and international exchange (IE) students, who were undertaking service-learning (SL) together. Lack of cohesiveness in such teams resulted in the psychological withdrawal of some of the IE students and appeared to reduce opportunities to derive developmental benefits. Barriers to cohesiveness identified by the students included language, conflicting priorities, and East-West cultural differences. We also identified how students took action to remove the barriers to cohesiveness. These actions included conducting internal team meetings in English and arranging for local students to provide interpretation in meetings with community stakeholders. Students reported that the major developmental benefits associated specifically with working cohesively in a cross-cultural team were improved English language skills, greater interpersonal adaptability, and appreciation of diversity. We offer practical suggestions about how educators can prepare local and IE students to work together effectively on SL projects and about further research. Studies of projects undertaken by inter-cultural SL teams at host universities in other jurisdictions would facilitate the generalizability of the findings.
Anomalies vasculaires, neurodégénérescence et réserve cognitive dans la sclérose en plaques : une étude multimodale en IRM.

La sclerose en plaques est une maladie inflammatoire du systeme nerveux central, ayant plusieurs phenotypes cliniques, caracterisee par la coexistence de phenomenes inflammatoires focaux et d’une neurodegenerescence diffuse, dont la physiopathologie est actuellement inconnue. L’apparition de troubles cognitifs marque un tournant evolutif pour les patients, est en lien avec la progression de la maladie, et notamment l’atrophie cerebrale. Neanmoins le statut cognitif de certains patients reste preserve malgre la progression de la maladie. Le concept de reserve cognitive rendrait compte de cette absence de correlation entre statut cognitif et lesions cerebrales en lien de la maladie, mais ses bases physiologiques sont a l’heure actuelle inconnues. Trois techniques d’imagerie : L’etude de la perfusion cerebrale en arterial spin labelling, de la vasoreactivite cerebrale grâce a l’inhalation d’un gaz enrichi en CO2, et des anomalies de substance blanche cerebrale en tenseur de diffusion sont utilisees dans ce manuscrit pour repondre aux questions suivantes :- Existe-t-il des anomalies vasculaires pouvant expliquer la neurodegenerescence diffuse observee dans la sclerose en plaques, et notamment dans les formes progressives ? - Existe-t-il en tenseur de diffusion des anomalies de certains faisceaux de substance blanche qui serait correlees au statut cognitif ou au phenotype clinique des patients? La reserve cognitive est-elle mediee par des phenomenes de plasticite de la substance blanche dans la sclerose en plaques?
Markups, Labor Market Inequality and the Nature of Work

We demonstrate the importance of distinguishing between the traditional use of labor for production, versus alternative uses of labor for overhead, marketing and other expansionary activities, for studying the distribution of both factor income and labor income. We use our framework to assess the impact of changes in markups on the overall labor share and on labor income inequality across occupations. We identify the production and expansionary content of different occupations from the co-movement of occupational income shares with markup-induced changes in the labor share. We find that around one-fifth of US labor income compensates expansionary activities, and that occupations with larger expansionary content have experienced the fastest wage and employment growth since 1980. Our framework can rationalize a counter-cyclical labor share in the presence of sticky prices and can be used to study the distributional effects of demand shocks, monetary policy and secular changes in competition.
Caution from using cardiac glycosides digoxin drug which have properties therapeutic index (Ti) narrow compare with the medications wide therapeutic index

Clinical research will be based on the practical application of randomly assigned patients over the age of 25 who numbered 730 at the Academic Teaching Hospital in Iraq Samawa. We used drugs narrow therapeutic index (NTI), which is used with caution at a specific and calculated dose because it is life-threatening and has high toxicity. Compared to drugs that have wide therapeutic index (WTI) and less serious effects (such as aspirin, acetaminophen (paracetamol), penicillin, etc.), we selected acetaminophen (paracetamol) in patient research (a wide therapeutic index) and the dose and ratio between the toxic dose and the safe therapeutic dose of the drug, the research focuses on dilution To limit the risk of medication to patients (mortality), which is used as a measure of the relative safety of the drug in a particular drug treatment, our main work is limited to digoxin (cardiac glycosides) used in heart disease, discrimination with other drugs and knowledge, and in comparison to drugs. We used acetaminophen (paracetol) which is a broad indicator, so we based on previous knowledge in clinical pharmacy, dosage medications, therapeutic toxic dose, maximum dose, initial dose, maintenance dose, lethal dose, by knowing Therapeutic index for drug identification, therapeutic index, therapeutic ratio, TI can be calculated as a lethal dose of the drug by 50% of the population (LD50) divided by the minimum effective dose for 50% of the population (ED50), that is, TI = LD50 / ED50. This "academic" definition of TI is easier to follow in preclinical trials but opens the door to changing explanations in clinical practice. In fact, the definition of therapeutic and / or toxic effect in humans is highly dependent on the type of therapeutic or toxic effect under study, and the drug is generally considered to have a good safety appearance if its TI values exceed the value of 10. The situation is quite different from so-called narrow TI drugs (NTIDs) , Where only a very small set of doses produce a beneficial effect without causing severe and fatal complications, i.e. small differences in their plasma concentrations can lead to inadequate therapeutic response or the appearance of harmful toxic effects. The term “critical dose medication” is sometimes used to refer to drugs where relatively small differences in dosage or concentration may lead to serious therapeutic failure and / or serious drug reactions. Other terms used also include "narrow therapeutic window drugs", "narrow therapeutic range", "critical anti-dose drugs" or "narrow therapeutic ratio , According to:The US Food and Drug Administration (FDA) defines a medication product as containing NTI when (a) there is less than a double difference in LD50 and medium effective dose values (ED50) or (b) there is less than a double difference in toxic concentrations Minimum (MTC) and minimum effective concentrations (MEC) in the blood and (c) safe and effective use of the drug requires careful calibration and patient monitoring 2018.
I farmaci biologici anti-TNFα e il rischio infettivo nell'artrite reumatoide TNFα blockers and infectious risk in rheumatoid arthritis

SUMMARY Patients suffering from rheumatoid arthritis have increased risk of infections when compared with general population. The risk depends directly from disease activity and severity. Furthermore, risk increases with aging, immunosuppressive agents and comorbidities such as diabetes, pulmonary and cardiac diseases. In particular corticosteroids, even at low doses, are a major risk factor. Due to disease related risk it is difficult to separate the risk deriving from the use of TNF alpha blockers. Data from clinical trials, meta-analysis and national registers are somewhat contradictory. In patients with rheumatoid arthritis on routine follow-up, treatment with TNF alpha blockers seems to carry an increased risk of infections compared to traditional DMARDs but not associated with increased risk of overall serious infection. Physicians should carefully monitor for signs of infection when using TNF alpha blockers, particularly shortly after treatment initiation.
Identifying health education competencies for primary health care nurses in Saudi Arabia : a Delphi Consensus Study

Research Aim The primary aim of this Saudi-based study is to identify health-education competencies (knowledge, skills & attitudes) for Primary Health Care (PHC) nurses. Although the Saudi Ministry of Health (MOH) has highlighted the importance of health education provided in PHC by nurses, there have been no studies into the required competencies in the Saudi context. Methods The Delphi technique was employed with a sample of sixty PHC nurses who matched the study’s inclusion criteria and they took part in a three-round questionnaire. A consensus criterion of 60 per cent was adopted for the study. The first round asked participants’ opinions about what items should be included within health education competencies for PHC nurses by selecting (Yes, No, Uncertain). In the second round, participants were asked to rank the competencies on which there had been no initial consensus, using a five-point Likert scale. In the final round, participants selected agree or disagree for each of the remaining competencies. Following the Delphi technique an interactive workshop was undertaken with primary health care nurses and service users, to consider the next steps and practical piloting and testing of the competencies. Principal Findings The expert Delphi panellists eventually reached consensus on 45 of the 48 competencies for PHC nurses to engage in health-education practice. These competencies were classified into three domains: knowledge (22), skills (10) and attitudes (13). Three competencies related to knowledge did not reach consensus in the three rounds. The main outcomes of the interactive workshop suggest that service users would welcome the introduction of technology within the delivery of health education, and the PHC nurses confirmed the need for more training courses in order to improve their practice of health education. Importance and Relevance This is the first study to identify health-education competencies for PHC nurses in S.A. The results from this study represent a contribution to knowledge in a PHC setting and they can assist the MOH by being an initial step on the road to developing a national competency and curriculum framework for PHC nurses’ practice. Also, it is the first study to involve service users.
Atherosclerosis involves more than just lipids : focus on inflammation

Inflammation in the vessel wall is now considered to play an essential role in the initiation, progression and the final pathophysiological steps of atherosclerosis, plaque erosion, fissure and eventual rupture. Classical pathological studies have demonstrated the presence of inflammatory cells, such as monocyte-derived macrophages and T lymphocytes, at every stage of the disease. These morphological changes are preceded by dysfunction of endothelial cells, which produce adhesion molecules that interact with inflammatory cells. Yet atherosclerosis and its clinical complications are not only characterized by a local inflammation. Recent prospective studies have consistently shown that several markers of systemic inflammation may predict future cardiovascular events, not only in apparently healthy subjects but also in patients with unstable angina. Measurements of inflammatory markers add to the predictive value of total and HDL cholesterol levels in assessing long-term coronary risk. Finally, the results of recent clinical trials indicate that the proven efficacy of various compounds in primary and secondary prevention of coronary heart disease, such as aspirin and statins, may be mediated at least in part by modifying the consequences of the inflammatory response on vascular risk.
Intra-population variation in the diet of an avian top predator: generalist and specialist foraging in Great Black-backed Gulls Larus marinus

ABSTRACT Capsule: Great Black-backed Gulls Larus marinus breeding on Skokholm, UK, fed predominantly on seabirds, rabbits, refuse, and marine prey, with the majority of pairs being dietary generalists, but with some specialist pairs. Aims: To understand the significance of Great Black-backed Gulls as top predators on a small offshore island with internationally important numbers of breeding seabirds (Skokholm, UK) by quantifying their diet and to determine how this varies within the breeding season, to test for pair-level dietary specialization and to examine the consequences of dietary differences for reproductive performance. Methods: Regurgitated pellets were collected and analysed from 26 breeding pairs on Skokholm during 2017 and related to breeding success. Results: Analysis of 1035 pellets revealed that, overall, Great Black-backed Gulls fed on seabirds (48% – mostly Manx Shearwaters Puffinus puffinus), mammals (38% – mostly European Rabbits Oryctolagus cuniculus), anthropogenic waste (7%), and marine prey (7%). Diet varied among pairs with 18 (73%) generalist pairs and 7 (27%) specialist pairs (of which, 5 were bird specialists and 2 were mammal specialists). Diet also varied seasonally, but pair-level dietary diversity was repeatable through the breeding season. Dietary diversity did not covary with breeding success. Conclusion: Great Black-backed Gulls are top predators on Skokholm. Variation in diet among pairs emphasizes that not all individuals contribute equally in terms of predation. Understanding the incidence of this variation has important ecological implications, particularly where apex predators may exert a strong top-down influence.
Anti-money laundering: The world's least effective policy experiment? Together, we can fix it

Abstract This paper uses anti-money laundering as a case study to illustrate the benefits of cross-disciplinary engagement when major policymaking functions develop separately from public policy design principles. It finds that the anti-money laundering policy intervention has less than 0.1 percent impact on criminal finances, compliance costs exceed recovered criminal funds more than a hundred times over, and banks, taxpayers and ordinary citizens are penalized more than criminal enterprises. The data are poorly validated and methodological inconsistencies rife, so findings cannot be definitive, but there is a huge gap between policy intent and results. The scale of the problem not addressed by “solutions” repeatedly “fixing” the same perceived issues suggest that blaming banks for not “properly” implementing anti-money laundering laws is a convenient fiction. Fundamental problems may lie instead with the design of the core policy prescription itself. With an important policymaking function operating largely as an independent silo of specialist knowledge, this paper suggests that active engagement with critical, diverse perspectives, and deeper connections between the anti-money laundering movement and other disciplines (notably, policy effectiveness, outcomes and evaluation principles of public policy) should contribute to better results.