Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles

Background The diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed the largest beetle suborder, Polyphaga, mostly includes plant-eaters among its ~315,000 species. In particular, plants defend themselves with a diversity of specialized toxic chemicals. These may impose selective pressures that drive genomic diversification and speciation in phytophagous beetles. However, evidence of changes in beetle gene repertoires driven by such interactions remains largely anecdotal and without explicit hypothesis testing. Results To address this, we explored the genomic consequences of beetle-plant trophic interactions by performing comparative gene family analyses across 18 species representing the two most species-rich beetle suborders. We contrasted the gene contents of species from the mostly plant-eating suborder Polyphaga with those of the mainly predatory Adephaga. We found gene repertoire evolution to be more dynamic, with significantly more adaptive lineage-specific expansions, in the more speciose Polyphaga. Testing the specific hypothesis of adaptation to plant-feeding, we identified families of enzymes putatively involved in beetle-plant interactions that underwent adaptive expansions in Polyphaga. There was especially strong support for the selection hypothesis on large gene families for glutathione S-transferase and carboxylesterase detoxification enzymes. Conclusions Our explicit modeling of the evolution of gene repertoires across 18 species identifies adaptive lineage-specific gene family expansions that accompany the dietary shift towards plants in beetles. These genomic signatures support the popular hypothesis of a key role for interactions with plant chemical defenses, and for plant-feeding in general, in driving beetle diversification.
Impact of COPD on prognosis of lung cancer: from a perspective on disease heterogeneity

Background COPD is an important comorbidity of lung cancer, but the impact of COPD on the outcomes of lung cancer remains uncertain. Because both COPD and lung cancer are heterogeneous diseases, we evaluated the link between COPD phenotypes and the prognosis of different histological subtypes of lung cancer. Methods In this retrospective study, subjects with a newly and pathologically confirmed diagnosis of lung cancer were enrolled from patients preparing for lung cancer surgery. All participants underwent pulmonary function test (PFT). The diagnosis of COPD was based on GOLD criteria. Lung cancer subtypes and COPD phenotypes were categorized by WHO classification of lung tumors and computer quantitative analysis of PFT. The HRs were estimated by Cox regression analysis. Results Among 2,222 lung cancer patients, 32.6% coexisted with COPD. After adjustment for age, sex, body mass index (BMI), smoking status, and therapy method, COPD was significantly associated with the decreased overall survival (OS) of lung cancer (HR 1.28, 95% CI 1.05–1.57). With the increased severity of COPD, the OS of lung cancer was gradually worsened (HR 1.23, 95% CI 1.08–1.39). But surgical treatment and high BMI were independent prognostic protective factors (HR 0.46, 95% CI 0.37–0.56; HR 0.96, 95% CI 0.94–0.99). Moreover, in terms of disease heterogeneity, emphysema-predominant phenotype of COPD was an independent prognostic risk factor for squamous carcinoma (HR 2.53, 95% CI 1.49–4.30). No significant relationship between COPD phenotype and lung cancer prognosis was observed among adenocarcinoma, small cell lung cancer, large cell lung cancer, and other subtype patients. Conclusion These findings suggest that COPD, especially emphysema-predominant phenotype, is an independent prognostic risk factor for squamous carcinoma only.
Discriminative Variable Subsets in Bayesian Classification with Mixture Models

We discuss the evaluation of subsets of variables for the discriminative evidence they provide in multivariate mixture modeling for classification. Novel development of Bayesian classification analysis uses a natural measure of concordance between mixture component densities, and defines an effective and computationally feasible method for assessing and prioritizing subsets of variables according to their roles in discrimination of one or more mixture components. We relate the new discriminative information measures to Bayesian classification probabilities and error rates, and exemplify their use in Bayesian analysis of Dirichlet process mixture models fitted via Markov chain Monte Carlo methods as well as using a novel Bayesian expectation-maximization algorithm. We present a series of theoretical and simulated data examples to fix concepts and exhibit the utility of the approach, and compare with prior approaches. We demonstrate application in the context of automatic classification and discriminative variable selection in high-throughput systems biology using large flow cytometry data sets.
Characterization of Collision Avoidance in Pedestrian Crowds

The avoidance behavior of pedestrians was characterized in the present paper by simulating the movement of crowds in both unidirectional and bidirectional pedestrian flow. A phase change of alternative lane formation observed in real bidirectional pedestrian flows has been studied, where pedestrians tended to evade individuals in counterflow and simultaneously keep a certain distance from each other in the uniform pedestrian flow when the counterflow disappeared. What is more, the comparison between the effect of evading and pushing behavior on evacuation has been investigated in the room egress scenario. Additionally, the evading and overtaking behavior of fast pedestrians have also been simulated in heterogeneous crowds. The performance of the proposed model was compared to the experimental data and the results obtained using other evacuation models. Numerical results showed that both the phase change of alternative lane formation in bidirectional pedestrian flow and the effective evading behavior in unidirectional pedestrian flow were conductive to reduce the evacuation time of pedestrian crowds. Even though pushing behavior of fast pedestrians seemed to improve the flow through the wide exit, it might lead to the panic and other negative effect on the crowds, such as crowds trample. The proposed model in this paper could provide a theoretical basis for the pedestrian crowd management during emergency evacuation.
Leptin-a mediates transcription of genes that participate in central endocrine and phosphatidylinositol signaling pathways in 72-hour embryonic zebrafish ([i]Danio rerio[i])

We analyzed microarray expression data to highlight biological pathways that respond to embryonic zebrafish Leptin-a (lepa) signaling. Microarray expression measures for 26,046 genes were evaluated from lepa morpholino oligonucleotide “knockdown”, recombinant Leptin-a “rescue”, and uninjected control zebrafish at 72-hours post fertilization. In addition to KEGG pathway enrichment for phosphatidylinositol signaling and neuroactive ligand-receptor interactions, Gene Ontology (GO) data from lepa rescue zebrafish include JAK/STAT cascade, sensory perception, nervous system processes, and synaptic signaling. In the zebrafish lepa rescue treatment, we found changes in the expression of homologous genes that align with mammalian leptin signaling cascades including AMPK (prkaa2), ACC (acacb), Ca/calmodulin-dependent kinase (camkk2), PI3K (pik3r1), Ser/Thr protein kinase B (akt3), neuropeptides (agrp2, cart1), mitogen-activated protein kinase (MAPK), and insulin receptor substrate (LOC794738, LOC100537326). Notch signaling pathway and ribosome biogenesis genes respond to knockdown of Leptin-a. Differentially expressed transcription factors in lepa knockdown zebrafish regulate neurogenesis, neural differentiation, and cell fate commitment. This study presents a role for zebrafish Leptin-a in influencing expression of genes that mediate phosphatidylinositol and central endocrine signaling.
Effects of Human Immunodeficiency Virus Type 1 Resistance to Protease Inhibitors on Reverse Transcriptase Processing, Activity, and Drug Sensitivity

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) variants resistant to protease inhibitors often display a reduced replicative capacity as a result of an impairment of protease function. Such fitness-impaired viruses display Gag precursor maturation defects. Here, we report that some protease inhibitor-resistant viruses also display abnormalities in the processing of reverse transcriptase (RT) by the protease. In three recombinant viruses carrying resistant protease sequences from patient plasma, we observed a marked decrease in the amount of mature RT subunits and of particle-associated RT activity compared to their parental pretherapy counterparts. We investigated the possibility that a decrease in the amount of particle-associated mature RT could affect the sensitivity of the corresponding virus to RT inhibitors. We observed a twofold increase of sensitivity to zidovudine (AZT) when a virus which carried AZT mutations was processed by a resistant protease. Interestingly, the presence of AZT-resistance mutations partially rescued the replication defect associated with the mutated protease. The interplay between resistance to protease inhibitors and to RT inhibitors described here may be relevant to the therapeutic control of HIV-1 infection.
Link to publication record in King ' s Research Portal

Argument-based persuasion dialogues provide an effective mechanism for agents to communicate their beliefs, and their reasons for those beliefs, in order to convince another agent of some topic argument. In such dialogues, the persuader has strategic considerations, and must decide which of its known arguments should be asserted, and the order in which they should be asserted. Recent works consider mechanisms for determining an optimal strategy for persuading the responder. However, computing such strategies is expensive, swiftly becoming impractical as the number of arguments increases. In response, we present a strategy that uses heuristic information of the domain arguments and can be computed with high numbers of arguments. Our results show that not only is the heuristic strategy fast to compute, it also performs significantly better than a random strategy.
Can non‐clinical repolarization assays predict the results of clinical thorough QT studies? Results from a research consortium

Translation of non‐clinical markers of delayed ventricular repolarization to clinical prolongation of the QT interval corrected for heart rate (QTc) (a biomarker for torsades de pointes proarrhythmia) remains an issue in drug discovery and regulatory evaluations. We retrospectively analysed 150 drug applications in a US Food and Drug Administration database to determine the utility of established non‐clinical in vitro IKr current human ether‐à‐go‐go‐related gene (hERG), action potential duration (APD) and in vivo (QTc) repolarization assays to detect and predict clinical QTc prolongation.
Beyond Earth: Designing Root Zone Environments for Reduced Gravity Conditions

Fluid management in plant root zones is critical for long duration space missions including lunar‐ or Martian‐based missions, but key aspects of design and delivery of fluids under these conditions are poorly understood due to limited experimental opportunities. We review theoretical and experimental concepts for advancing understanding of fluid‐porous media interactions to improve design and management of plant‐based life support systems for reduced gravity environments. In situ utilization of native lunar and Martian granular materials for plant‐growth media requires reliable characterization of media physical and hydraulic properties and processes. A key aspect is the enhanced effects of capillarity in reduced gravity resulting in an array of micro‐ and macroscale changes in fluid phase organization relative to conditions on Earth that may affect mass fluxes to plant roots and potentially result in excess water and hypoxia. Increasing the medium particle diameter above 1 mm and narrowing the distribution of particles, and thus pore sizes, may counter reduced gravity effects. Approaches used in previous microgravity systems involving sensor‐based active water management assuming prescribed optimal set points (i.e., water potential) may fail in reduced gravity due to dynamic pore space alterations arising from air‐ or liquid‐phase entrapment and root growth in a restricted volume that may alter the porous medium characteristics on which water management is often based. For example, about a 10% reduction in volumetric pore space was observed following rice (Oryza sativa L.) root growth, which could change a well‐aerated root zone into an anoxic environment if not accounted for. Numerical modeling of plant transpiration and irrigation using volumetrically controlled water content under different gravity environments revealed similar hydraulic responses in fine‐textured porous media typically unsuitable for plant growth in greenhouses. Volumetric water content–based management of plant root environments appears to be a safer approach than other methods discussed here.
Events and Periods as Concepts for Organizing Historical Knowledge

Events and periods are not objectively existing phenomena, but concepts we use to organize our knowledge of history. They make historical change comprehensible and help us orient ourselves with respect to the history of the culture in which we participate. Thus they are indispensable for describing both the content of history scholarship and the context of documents that serve as evidence for that scholarship. As historical discourse shifts its emphases and new aspects of the past come to be considered significant, periods and events are subject to constant change. Despite this change, we can model periods and events in systems of knowledge organization because it is possible to discern and formally describe relatively stable recurrent patterns in their narration.
Effect of porcine epidemic diarrhea virus infectious doses on infection outcomes in naïve conventional neonatal and weaned pigs

Porcine epidemic diarrhea virus (PEDV) has been an important pathogen in Europe and Asia for several decades. It was identified in the United States (U.S.) swine population for the first time in April 2013, and spread rapidly across country and into Canada and Mexico. However, no information has been published regarding the minimum infectious dose (MID) of PEDV in different pig models. The main objective of this study was to determine the oral minimum infectious dose of PEDV in naïve conventional neonatal piglets and weaned pigs. A U.S. virulent PEDV prototype isolate (USA/IA19338/2013) with known infectious titer was serially ten-fold diluted in virus-negative cell culture medium, and inoculated into 5-day-old and 3-week-old pigs. Our data showed that PEDV is infectious in an age-dependent manner with a significantly lower MID for neonatal pigs compared to weaned pigs. Furthermore, it showed that, once an infection was established in pigs, the initial dose of PEDV administered did not affect the extent of fecal viral shedding, severity of histopathologic lesions, or magnitude of antibody titer subsequently developed. This information should be taken into consideration when interpreting clinical relevance of PEDV PCR results, designing a PEDV bioassay model, as well as emphasizes the importance of strict biosecurity and thorough cleaning/disinfection on
Delft University of Technology Automatic Test Case Generation What If Test Code Quality Matters ?

Test case generation tools that optimize code coverage have been extensively investigated. Recently, researchers have suggested to add other non-coverage criteria, such as memory consumption or readability, to increase the practical usefulness of generated tests. In this paper, we observe that test code quality metrics, and test cohesion and coupling in particular, are valuable candidates as additional criteria. Indeed, tests with low cohesion and/or high coupling have been shown to have a negative impact on future maintenance activities. In an exploratory investigation we show that most generated tests are indeed affected by poor test code quality. For this reason, we incorporate cohesion and coupling metrics into the main loop of search-based algorithm for test case generation. Through an empirical study we show that our approach is not only able to generate tests that are more cohesive and less coupled, but can (i) increase branch coverage up to 10% when enough time is given to the search and (ii) result in statistically shorter tests.
Mining Facebook Data of People with Rare Diseases

This research is concerned with the study of Spanish Facebook pages that deal with rare diseases. The objectives of this research are to characterise these pages and to compare them with the priorities of the Decalogue of the Spanish Federation of Rare Diseases (FEDER). This research uses Netvizz to download the data, word clouds in R to perform text mining, TextBlob in Python to perform sentiment analysis, and log-likelihood in R to compare Facebook and Decalogue words. The results obtained show that photos are the type of posts with higher number of likes, reactions and engagement. We can also see that positive polarities have higher level of engagement, and that subjectivity is not so correlated with engagement. In the comparison of the Facebook data with the FEDER Decalogue, we observe that the following words have a lot of presence in the Decalogue and little in Facebook: disability, professionals and diseases. Similarly, these are the most present on Facebook with little representation in the Decalogue: help, life, people and children. In conclusion, we can say that the Decalogue should focus more on help, life, people and children and less on disability, professionals and diseases.
Resilience and quality of life in 161 living kidney donors before nephrectomy and in the 1 aftermath of donation : A naturalistic single center study 2 3

3 Yesim Erim, Yeliz Kahraman, Frank Vitinius, Mingo Beckmann , Sylvia Kröncke, Oliver Witzke 4 Department of Psychosomatic and Psychotherapeutic M edicine, University Hospital, Friedrich-Alexander 5 University Erlangen-Nurnberg, Erlangen, Germany 6 Department of Psychosomatic Medicine and Psychother apy, Medical Center, University of Cologne, Cologne , 7 Germany 8 Department of Psychosomatic Medicine and Psychother apy, University Hospital Essen, University of Duisb urg9 Essen, Essen, Germany 10 Department of Medical Psychology, University Medica l Center, Hamburg-Eppendorf, Hamburg, Germany 11 Department for Nephrology, Medical Faculty, Univers ity Duisburg-Essen, Essen, Germany 12
Forging a Frailty-Ready Healthcare System to Meet Population Ageing

The beginning of the 21st century has seen health systems worldwide struggling to deliver quality healthcare amidst challenges posed by ageing populations. The increasing prevalence of frailty with older age and accompanying complexities in physical, cognitive, social and psychological dimensions renders the present modus operandi of fragmented, facility-centric, doctor-based, and illness-centered care delivery as clearly unsustainable. In line with the public health framework for action in the World Health Organization’s World Health and Ageing Report, meeting these challenges will require a systemic reform of healthcare delivery that is integrated, patient-centric, team-based, and health-centered. These reforms can be achieved through building partnerships and relationships that engage, empower, and activate patients and their support systems. To meet the challenges of population ageing, Singapore has reorganised its public healthcare into regional healthcare systems (RHSs) aimed at improving population health and the experience of care, and reducing costs. This paper will describe initiatives within the RHS frameworks of the National Health Group (NHG) and the Alexandra Health System (AHS) to forge a frailty-ready healthcare system across the spectrum, which includes the well healthy (“living well”), the well unhealthy (“living with illness”), the unwell unhealthy (“living with frailty”), and the end-of-life (EoL) (“dying well”). For instance, the AHS has adopted a community-centered population health management strategy in older housing estates such as Yishun to build a geographically-based care ecosystem to support the self-management of chronic disease through projects such as “wellness kampungs” and “share-a-pot”. A joint initiative by the Lien Foundation and Khoo Teck Puat Hospital aims to launch dementia-friendly communities across the island by building a network comprising community partners, businesses, and members of the public. At the National Healthcare Group, innovative projects to address the needs of the frail elderly have been developed in the areas of: (a) admission avoidance through joint initiatives with long-term care facilities, nurse-led geriatric assessment at the emergency department and geriatric assessment clinics; (b) inpatient care, such as the Framework for Inpatient care of the Frail Elderly, orthogeriatric services, and geriatric surgical services; and (c) discharge to care, involving community transitional care teams and the development of community infrastructure for post-discharge support; and an appropriate transition to EoL care. In the area of EoL care, the National Strategy for Palliative Care has been developed to build an integrated system to: provide care for frail elderly with advance illnesses, develop advance care programmes that respect patients’ choices, and equip healthcare professionals to cope with the challenges of EoL care.