Miracle-dz/UniFAR-FTUs huggingface dataset:
Generating and Employing Witness Automata for ACTLW Formulae

When verifying the validity of a formula in a system model by a model checker, a common feature is the generation of a linear witness or counterexample, which is a computation path usually showing a single reason why the formula is valid or, respectively, not. For systems represented with Labeled Transition Systems (LTS) and a subset of ACTLW (Action-based Computation Tree Logic with Unless operator) formulae, a procedure exists for the generation of witness automata, which contain all the interesting finite linear witnesses, thus revealing all the reasons of the validity of a formula. Although this procedure uses a symbolic representation of LTSs, transitions of a given LTS are traversed one by one. In this paper, we propose a procedure which exploits the symbolic representation efficiently to traverse several transitions at once. We evaluate the procedure on models of a communication protocol from industry and a biological system. The results show it to be at least several times faster than the former one. Witness automata were first introduced to allow for compositional generation of test sequences. We propose two more possible uses. One is for the detection of multiple errors in a model by exploring the witness automaton for a formula, instead of only one, which is usually the case with a single witness. The other one is for the detection of previously unknown system properties. As witness automata can be rather large, we show how some existing tools could help in examining them through visualization and simulation.
An Integrative Analysis of Transcriptomics and Proteomics Reveals Novel Insights into the Response in the Midgut of Spodoptera frugiperda Larvae to Vip3Aa

The insecticidal Vip3 proteins, secreted by Bacillus thuringiensis (Bt) during its vegetative growth phase, are currently used in Bt crops to control insect pests, and are genetically distinct from known insecticidal Cry proteins. Compared with Cry toxins, the mechanisms of Vip3 toxins are still poorly understood. Here, the responses of Spodoptera frugiperda larvae after Vip3Aa challenge are characterized. Using an integrative analysis of transcriptomics and proteomics, we found that Vip3Aa has enormous implications for various pathways. The downregulated genes and proteins were mainly enriched in metabolic pathways, including the insect hormone synthesis pathway, whereas the upregulated genes and proteins were mainly involved in the caspase-mediated apoptosis pathway, along with the MAPK signaling and endocytosis pathways. Moreover, we also identified some important candidate genes involved in apoptosis and MAPKs. The present study shows that exposure of S. frugiperda larvae to Vip3Aa activates apoptosis pathways, leading to cell death. The results will promote our understanding of the host response process to the Vip3Aa, and help us to better understand the mode of action of Vip3A toxins.
Epigenome-Wide DNA Methylation Profiling in Colorectal Cancer and Normal Adjacent Colon Using Infinium Human Methylation 450K

The aims were to profile the DNA methylation in colorectal cancer (CRC) and to explore cancer-specific methylation biomarkers. Fifty-four pairs of CRCs and the adjacent normal tissues were subjected to Infinium Human Methylation 450K assay and analysed using ChAMP R package. A total of 26,093 differentially methylated probes were identified, which represent 6156 genes; 650 probes were hypermethylated, and 25,443 were hypomethylated. Hypermethylated sites were common in CpG islands, while hypomethylated sites were in open sea. Most of the hypermethylated genes were associated with pathways in cancer, while the hypomethylated genes were involved in the PI3K-AKT signalling pathway. Among the identified differentially methylated probes, we found evidence of four potential probes in CRCs versus adjacent normal; HOXA2 cg06786372, OPLAH cg17301223, cg15638338, and TRIM31 cg02583465 that could serve as a new biomarker in CRC since these probes were aberrantly methylated in CRC as well as involved in the progression of CRC. Furthermore, we revealed the potential of promoter methylation ADHFE1 cg18065361 in differentiating the CRC from normal colonic tissue from the integrated analysis. In conclusion, aberrant DNA methylation is significantly involved in CRC pathogenesis and is associated with gene silencing. This study reports several potential important methylated genes in CRC and, therefore, merit further validation as novel candidate biomarker genes in CRC.
Population demography maintains biogeographic boundaries

Global biodiversity is organized into biogeographic regions that comprise distinct biotas. The contemporary factors maintaining differences in species composition between biogeographic regions are poorly understood. Given the evidence that populations with sufficient genetic variation can adapt to fill new habitats, it is surprising that we do not see more homogenization of species assemblages among regions. Theory suggests that the expansion of populations across biogeographic transition zones could be limited by environmental gradients that affect population demography in ways that could limit adaptive capacity, but this has not been empirically explored. Using three independently curated data sets describing continental patterns of mammalian demography and population genetics, we show that populations closer to biogeographic transition zones have lower effective population sizes and genetic diversity, and are more genetically differentiated. These patterns are consistent with reduced adaptive capacity near biogeographic transition zones. The consistency of these patterns across mammalian species suggests they are stable, predictable, and generalizable in their contribution to long-term limits on expansion and homogenization of biodiversity across biogeographic transition zones. Understanding the contemporary processes acting on populations that maintain differences in the composition of regional biotas is crucial for our basic understanding of the current and future organization of global biodiversity. The importance of contemporary, population-level processes on the maintenance of global biogeographic regions suggests that biogeographic boundaries are susceptible to environmental perturbation associated with human-caused global change.
A Survey on Machine Learning in Chemical Spectral Analysis

: Chemical spectral analysis is contemporarily undergoing a revolution and drawing much attention of scientists owing to machine learning algorithms, in particular convolutional networks. Hence, this paper outlines the major machine learning and especially deep learning methods contributed to interpret chemical images, and overviews the current application, development and breakthrough in different spectral characterization. Brief categorization of reviewed literatures is provided for studies per application apparatus: X-Ray spectra, UV-Vis-IR spectra, Micro-scope, Raman spectra, Photoluminescence spectrum. End with the overview of existing circumstances in this research area, we provide unique insight and promising directions for the chemical imaging field to fully couple machine learning subsequently.
Lateral entorhinal cortex inputs modulate hippocampal dendritic excitability by recruiting a local disinhibitory microcircuit

The lateral entorhinal cortex (LEC) provides information about multi-sensory environmental cues to the hippocampus through direct inputs to the distal dendrites of CA1 pyramidal neurons. A growing body of work suggests that LEC neurons perform important functions for episodic memory processing, coding for contextually-salient elements of an environment or the experience within it. However, we know little about the functional circuit interactions between LEC and the hippocampus. In this study, we combine functional circuit mapping and computational modeling to examine how long-range glutamatergic LEC projections modulate compartment-specific excitation-inhibition dynamics in hippocampal area CA1. We demonstrate that glutamatergic LEC inputs can drive local dendritic spikes in CA1 pyramidal neurons, aided by the recruitment of a disinhibitory vasoactive intestinal peptide (VIP)-expressing inhibitory neuron microcircuit. Our circuit mapping further reveals that, in parallel, LEC also recruits cholecystokinin (CCK)-expressing inhibitory neurons, which our model predicts act as a strong suppressor of dendritic spikes. These results provide new insight into a cortically-driven GABAergic microcircuit mechanism that gates non-linear dendritic computations, which may support compartment-specific coding of multi-sensory contextual features within the hippocampus. HIGHLIGHTS Slice electrophysiology experiments investigate how lateral entorhinal cortex influences hippocampal area CA1 LEC drives local spikes in distal dendrites but not in somata of CA1 pyramidal neurons LEC inputs recruit VIP IN and CCK IN populations in CA1, but not SST INs Computational modeling and circuit manipulation experiments identify a VIP IN-mediated disinhibitory microcircuit for gating local dendritic spike generation IN BRIEF Bilash et al. found that a distal cortical input is capable of driving local dendritic spikes in hippocampal pyramidal neurons. This dendritic spike generation is promoted by cortical recruitment of a local VIP interneuron-mediated disinhibitory microcircuit. Their results highlight new circuit mechanisms by which dynamic interaction of excitation, inhibition, and disinhibition support supralinear single-cell computations.
Engagement of the CXCL12–CXCR4 Axis in the Interaction of Endothelial Progenitor Cell and Smooth Muscle Cell to Promote Phenotype Control and Guard Vascular Homeostasis

Endothelial progenitor cells (EPCs) are involved in vascular repair and modulate properties of smooth muscle cells (SMCs) relevant for their contribution to neointima formation following injury. Considering the relevant role of the CXCL12–CXCR4 axis in vascular homeostasis and the potential of EPCs and SMCs to release CXCL12 and express CXCR4, we analyzed the engagement of the CXCL12–CXCR4 axis in various modes of EPC–SMC interaction relevant for injury- and lipid-induced atherosclerosis. We now demonstrate that the expression and release of CXCL12 is synergistically increased in a CXCR4-dependent mechanism following EPC–SMC interaction during co-cultivation or in response to recombinant CXCL12, thus establishing an amplifying feedback loop Additionally, mechanical injury of SMCs induces increased release of CXCL12, resulting in enhanced CXCR4-dependent recruitment of EPCs to SMCs. The CXCL12–CXCR4 axis is crucially engaged in the EPC-triggered augmentation of SMC migration and the attenuation of SMC apoptosis but not in the EPC-mediated increase in SMC proliferation. Compared to EPCs alone, the alliance of EPC–SMC is superior in promoting the CXCR4-dependent proliferation and migration of endothelial cells. When direct cell–cell contact is established, EPCs protect the contractile phenotype of SMCs via CXCL12–CXCR4 and reverse cholesterol-induced transdifferentiation toward a synthetic, macrophage-like phenotype. In conclusion we show that the interaction of EPCs and SMCs unleashes a CXCL12–CXCR4-based autoregulatory feedback loop promoting regenerative processes and mediating SMC phenotype control to potentially guard vascular homeostasis.
An Easy Method on Fuzzy Interpolative Control for Automatic Truck Backerupper

An easy method on fuzzy interpolative control is introduced to solve the problem of truck backer-upper.Without the effect of optimal control rules,a simple and efficient automatic truck backer-upper is achieved.The simulations show that the control performance has many advantages,such as rapid response and high control precision.The method is strongly universal.Under the same conditions,it is significantly better than conventional fuzzy control.
Coupling Decision Support Systems For The Optimization of The Management of Water Distribution Networks

The analysis of the current situation of water distribution networks is based on all the alternatives that are technically feasible and implemented from the decision-maker's point of view. Taking the water distribution network of Tourville city as a case study, this paper combines a set of Decision Support Systems (DSS) including the Geographic Information Systems (GIS), multi-criteria analysis and hydraulic simulation models to establish a multi-criteria decision-making aid method for renovation and rehabilitation of water distribution networks. This combination creates an expert management system based on multi-criteria decision making that strengthens the optimization of the management of water distribution networks in terms of renovation and rehabilitation. After dividing the water distribution network into three emergency levels, it was concluded that 26% of the network is in urgent need of rehabilitation.
Does Ethical Climate, Rewards, and Protections Matter for Individual Intention to Blow The Whistle?

This paper aims to examine factors that can predict an individual intention to take whistleblowing action. This study examines the effect of ethical climate-egoism, ethical climate-benevolence, ethical climate-principle, rewards, and legal protection of whistleblower on the intention of Batam public procurement agency employees to do whistleblowing. This study used a quantitative approach with questionnaire data collected technique using census sampling as a sampling method. Partial Least Square (PLS) via SmartPLS 3.0 program is used as the analytical method to running the data. This study analyzes all civil servants in The Batam Public Procurement Agency. The results show that ethical climate-principle and legal protection of whistleblower affect the intention to do whistleblowing significantly. While the ethical climate-egoism, ethical climate-benevolence, and giving rewards to whistleblower showed that the results did not affect the intention of Batam Public Procurement agency employees to do whistleblowing significantly.
Post-industrial society and the economy of leisure: A new personnel paradigm

The transition to the post-industrial society is linked with the fundamental restructuring of the national economy, large-scale lay-offs and altering requirements to occupational qualification. The paper aims to determine the main thrusts of the upcoming changes. Methodologically, the research relies on the theories of vital resources and technological change. The author applies an interdisciplinary approach based on the findings from ethology, medicine, sociology, psychology, political science and economics, and methods of system analysis. In particular, he projects the theory of vital resources onto the economic development of the civilisation to elaborate on the character of the fourth vital mega-wave connected with the emergence of the industry of leisure as a dominant economic sector. The author demonstrates that such a course of events brings the managerial problem of inter-action between the ruling elites and the masses to a new level. Having considered Calhoun’s law, Maslow’s pyramid of needs and Bauman’s rule, the researcher reveals social ambiva-lence of the economy of leisure, which has the potential for both the evolution and degradation of humankind. He discusses the initiative of the Russian government bodies to introduce a four-day working week, and points to the necessity and feasibility of this measure. The researcher suggests abandoning ambitious global projects in favour of regionalisation of the labour market when managing the economy and the higher education system. Taking into account the results of the projection of the Guex – Crevoisier matrix on the university sector, he argues that Russian universities should switch to stronger orientation towards the economic needs of the territories where they are located.
Relationship between Eating Alone and Poor Appetite Using the Simplified Nutritional Appetite Questionnaire

One prominent factor associated with malnutrition is poor appetite. In Japan, the number of older adults living alone has increased annually. Those living alone tended to eat alone, which may lead to poor appetite. This study aimed to investigate the association between eating alone and poor appetite using an index called the Simplified Nutritional Appetite Questionnaire (SNAQ). We surveyed 818 people aged 70 and over in Takashimadaira, Itabashi-ku, Tokyo, Japan, in 2016. Comparisons were made between two groups, a poor appetite group (n = 295) and a good appetite group (n = 523), and results indicate that the poor appetite group had a higher rate of eating alone than the good appetite group (38.0% vs. 20. 1%: p < 0.001). Multivariable logistic regression (OR; 95%CI) was performed and poor appetite was significantly associated with the Geriatric Depression Scale (GDS) score (1.707; 1.200–2.427), the number of medications (1.061; 1.007–1.118), JST score (0.894; 0.841–0.950), the indication of “very healthy” on a self-rated health scale (0.343; 0.152–0.774), and reports of eating alone (1.751; 1.130–2.712). Our results suggest that eating alone is associated with a poor appetite.
Air Pollution in Poland: A 2022 Narrative Review with Focus on Respiratory Diseases

According to the World Bank Group, 36 of the 50 most polluted cities in the European Union are in Poland. Thus, ambient air pollution and its detrimental health effects are a matter of immense importance in Poland. This narrative review aims to analyse current findings on air pollution and health in Poland, with a focus on respiratory diseases, including COVID-19, as well as the Poles’ awareness of air pollution. PubMed, Scopus and Google Scholar databases were searched. In total, results from 71 research papers were summarized qualitatively. In Poland, increased air pollution levels are linked to increased general and respiratory disease mortality rates, higher prevalence of respiratory diseases, including asthma, lung cancer and COVID-19 infections, reduced forced expiratory volume in one second (FEV1) and forced vital capacity (FVC). The proximity of high traffic areas exacerbates respiratory health problems. People living in more polluted regions (south of Poland) and in the winter season have a higher level of air pollution awareness. There is an urgent need to reduce air pollution levels and increase public awareness of this threat. A larger number of multi-city studies are needed in Poland to consistently track the burden of diseases attributable to air pollution.
It Works! Organic-Waste-Assisted Trichoderma spp. Solid-State Fermentation on Agricultural Digestate

This study aimed at valorizing digestate through Trichoderma spp. solid-state fermentation (SSF) to produce a potentially ameliorated fertilizer combined with fungal biomass as a value-added bioproduct. Plant-growth-promoting Trichoderma atroviride Ta13, T. reesei RUT-C30, T. asperellum R, and T. harzianum T-22 were tested on different SSF substrates: whole digestate (WD), digestate dried up with wood sawdust (SSF1), and digestate enriched with food waste and dried up with wood sawdust (SSF2). The fungal biomass was quantified by using a qPCR assay. The growth of the four Trichoderma spp. was only observed on the SSF2 substrate. The highest quantity of mycelium was produced by T. reesei RUT-30 (689.80 ± 80.53 mg/g substrate), followed by T. atroviride Ta13, and T. asperellum R (584.24 ± 13.36 and 444.79 ± 91.02 mg/g substrate). The germination of Lepidium sativum seeds was evaluated in order to assess the phytoxicity of the Trichoderma-enriched substrate. The treatments with 7.5% SSF2-R, 3.75% SSF2-T-22, and 1.8% SSF2-Ta13 equally enhanced the root elongation in comparison to the non-fermented SSF-2. This study demonstrated that digestate, mixed with agro-food waste, was able to support the cultivation of Trichoderma spp. , paving the way to the valorization of fermented digestate as a proper biofertilizer.
Late Pleistocene glaciation history of the southern Black Forest, Germany: 10Be cosmic‐ray exposure dating and equilibrium line altitude reconstructions in Sankt Wilhelmer Tal

During the Late Pleistocene, an ice cap temporarily rested on the highest summit of the Black Forest, Feldberg, and on the surrounding region. Moraines inside the last glaciation maximum ice extent document subsequent glacial standstills and/or re‐advances, but the chronology of the deglaciation remains largely unknown. In Sankt Wilhelmer Tal, moraines were mapped, and suitable moraine boulders were sampled for 10Be cosmic ray exposure (CRE) dating. Equilibrium line altitudes (ELAs) during moraine formation were reconstructed to evaluate whether these can be used for local stratigraphical correlations. Geomorphological mapping revealed numerous ice‐marginal positions in the main valley and in two tributary valleys. CRE ages and ELAs indicate two discrete phases of glacial standstills and/or re‐advances by 17–16 ka at the latest and no later than 14 ka, respectively. Differing ELAs across the study area preclude the use of ELAs for local stratigraphical correlations. Recalculated 10Be CRE ages from other localities in Central Europe indicate similar periods of moraine formation, thus raising the question of a common climatic forcing. Additional sets of CRE ages are needed to answer this question. In addition, future studies should concentrate on determining the age of the last glaciation maximum in the Black Forest.
Clinical-Pathological and Molecular Evaluation of 451 NIFTP Patients from a Single Referral Center

Simple Summary Non-invasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTP) are follicular thyroid neoplasm with an indolent clinical behaviour. In this study, we evaluated a retrospective series of 451 NIFTPs, of which 197 (43.7%) presented in coexistence with collateral thyroid tumours. Unifocal and multifocal NIFTPs did not show peculiar ultrasound, cytological, molecular, and histo-pathological characteristics. Considering the high rate of coexisting carcinomas, NIFTP patients might benefit from monitoring of the contralateral lobe. Abstract Background: Non-invasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTPs) were introduced in thyroid pathology in 2016. NIFTPs are a group of follicular neoplasm with an indolent behaviour. In this study, we gathered a large retrospective cohort of NIFTPs and compared those presenting as solitary lesions and NIFTPs found in multifocal setting. Methods: A retrospective search of NIFTPs was performed, and the clinico-pathological features were recorded. For a subgroup of patients, pre-surgical ultrasound (US) evaluation, cytological diagnosis, and molecular analysis were available. Results: We collected 451 NIFTPs; 254 (56.3%) were truly solitary tumours, while 197 coexisted with one or more NIFTP/cancer. Contrasting unifocal and multifocal settings, NIFTPs size was the only significantly different parameter. Preoperatively, NIFTP nodules mostly showed low-risk US characteristics, indeterminate cytology and a RAS-like molecular profile. Conclusion: NIFTPs often coexist with collateral thyroid tumours. However, no clinical-pathological differences can be observed between solitary and “multifocal” NIFTPs. Despite the well-established clinical indolence of NIFTP, a careful monitoring of the contralateral lobe should not be excluded.