Miracle-dz/UniFAR-FTUs huggingface dataset:
Social Attitudes of AI Rebellion: A Framework

Human attitudes of objection, protest, and rebellion have undeniable potential to bring about social benefits, from social justice to healthy balance in relationships. At times, they can even be argued to be ethically obligatory. Conversely, AI rebellion is largely seen as a dangerous, destructive prospect. With the increase of interest in collaborative human/AI environments in which synthetic agents play social roles or, at least, exhibit behavior with social and ethical implications, we believe that AI rebellion could have benefits similar to those of its counterpart in humans. We introduce a framework meant to help categorize and design Rebel Agents, discuss their social and ethical implications, and assess their potential benefits and the risks they may pose. We also present AI rebellion scenarios in two considerably different contexts (military unmanned vehicles and computational social creativity) that exemplify components of the framework.
Virtual Screening Using Protein-Ligand Docking: Avoiding Artificial Enrichment

This study addresses a number of topical issues around the use of protein-ligand docking in virtual screening. We show that, for the validation of such methods, it is key to use focused libraries (containing compounds with one-dimensional properties, similar to the actives), rather than "random" or "drug-like" libraries to test the actives against. We also show that, to obtain good enrichments, the docking program needs to produce reliable binding modes. We demonstrate how pharmacophores can be used to guide the dockings and improve enrichments, and we compare the performance of three consensus-ranking protocols against ranking based on individual scoring functions. Finally, we show that protein-ligand docking can be an effective aid in the screening for weak, fragment-like binders, which has rapidly become a popular strategy for hit identification. All results presented are based on carefully constructed virtual screening experiments against four targets, using the protein-ligand docking program GOLD.
External electric field effect on the PR neuronal firing under the ephaptic transmission

The external electric field (EF) has shown to have great influence on neurons. On account of the effects of applied fields on neural activity through the induced EF in the extracellular medium, the electrical characteristics of the extracellular medium should not be ignored for accurately reflecting the biological field effect. Here considering the electrical characteristic of extracellular medium i.e. ephaptic transmission, neuronal firing is studied based on a PR neuron model in the presence of the external (EF), including direct current (DC) and alternating current (AC) EF. Moreover, three key parameters (the inner conductance gc, the inverted potential of potassium ion VK and the extracellular resistance between dendrite and soma RoutDS), which are crucial for the dynamics of neurons, are introduced to develop the neuronal firing. Different firing rhythms of neuron imply different stimulus information, and in some particular stimulus frequency the synchronization between the firing rhythm and EF signal is observed.
Kpax3: Bayesian bi-clustering of large sequence datasets

Motivation: Estimation of the hidden population structure is an important step in many genetic studies. Often the aim is also to identify which sequence locations are the most discriminative between groups of samples for a given data partition. Automated discovery of interesting patterns that are present in the data can help to generate new biological hypotheses. Results: We introduce Kpax3, a Bayesian method for bi‐clustering multiple sequence alignments. Influence of individual sites will be determined in a supervised manner by using informative prior distributions for the model parameters. Our inference method uses an implementation of both split‐merge and Gibbs sampler type MCMC algorithms to traverse the joint posterior of partitions of samples and variables. We use a large Rotavirus sequence dataset to demonstrate the ability of Kpax3 to generate biologically important hypotheses about differential selective pressures across a virus protein. Availability and implementation: Kpax3 is implemented as a Julia package and released under the MIT license. Source code and documentation are available at: https://github.com/albertopessia/Kpax3.jl. Supplementary information: Supplementary data are available at Bioinformatics online.
Adversarial Extreme Multi-label Classification

The goal in extreme multi-label classification is to learn a classifier which can assign a small subset of relevant labels to an instance from an extremely large set of target labels. Datasets in extreme classification exhibit a long tail of labels which have small number of positive training instances. In this work, we pose the learning task in extreme classification with large number of tail-labels as learning in the presence of adversarial perturbations. This view motivates a robust optimization framework and equivalence to a corresponding regularized objective. Under the proposed robustness framework, we demonstrate efficacy of Hamming loss for tail-label detection in extreme classification. The equivalent regularized objective, in combination with proximal gradient based optimization, performs better than state-of-the-art methods on propensity scored versions of precision@k and nDCG@k(upto 20% relative improvement over PFastreXML - a leading tree-based approach and 60% relative improvement over SLEEC - a leading label-embedding approach). Furthermore, we also highlight the sub-optimality of a sparse solver in a widely used package for large-scale linear classification, which is interesting in its own right. We also investigate the spectral properties of label graphs for providing novel insights towards understanding the conditions governing the performance of Hamming loss based one-vs-rest scheme vis-\`a-vis label embedding methods.
Effects of dietary protein level and age at photo stimulation on reproduction traits of broiler breeders and progeny performance

ABSTRACT A study with a 2 × 2 factorial arrangement was conducted to determine the effects of 2 dietary crude protein levels, high (CPh) or low (CPl), supplemented with free amino acids (AA), and 2 ages at photo stimulation (PS)—early (21 wk; PSe) or late (23 wk; PSl)—on reproduction traits of broiler breeders and progeny performance. Diets were isocaloric, and calculated CP content of the CPl diets was 15 g/kg lower than the CPh diets during all phases. A total of 480 female and 64 male Ross 308 breeders of 20 wk of age were used. Total egg production was similar between CPl and CPh birds during phase 1 and 2 but was reduced by 2.8 eggs for CPl birds during phase 3. For the overall laying period, CPl birds tended (P = 0.075) to produce 4.7 fewer total eggs. Hatchability of set eggs was similar between CPl and CPh birds during phases 1 and 2 but tended (P = 0.064) to be lower for CPl birds in phase 3. PSe birds showed an advanced age at sexual maturity and age at peak production of 4.6 and 5.3 d, respectively, resulting in 2.5 more total eggs during phase 1. During phase 1, PSe birds showed an almost 5% increased fertility. Chick production in phase 1 was higher for PSe birds resulting in a tendency (P = 0.071) to higher overall chick production of almost 8 chicks. Progeny from early PS breeders showed an overall significant lower feed conversion ratio (FCR). It was concluded that egg and chick production during phases 1 and 2 were not affected by dietary CP level, but egg and chick production was reduced for CPl birds during phase 3. On the other hand, PSe birds showed an increased number of chicks. It is possible to decrease CP level of breeder diets with comparable reproduction from 22 to 46 wk; however, this is questionable for phase 3. For maximal chick production, early PS is recommended.
A Hierarchical Z‑Scheme α‐Fe2O3/g‐C3N4 Hybrid for Enhanced Photocatalytic CO2 Reduction

The challenge in the artificial photosynthesis of fossil resources from CO2 by utilizing solar energy is to achieve stable photocatalysts with effective CO2 adsorption capacity and high charge‐separation efficiency. A hierarchical direct Z‐scheme system consisting of urchin‐like hematite and carbon nitride provides an enhanced photocatalytic activity of reduction of CO2 to CO, yielding a CO evolution rate of 27.2 µmol g−1 h−1 without cocatalyst and sacrifice reagent, which is >2.2 times higher than that produced by g‐C3N4 alone (10.3 µmol g−1 h−1). The enhanced photocatalytic activity of the Z‐scheme hybrid material can be ascribed to its unique characteristics to accelerate the reduction process, including: (i) 3D hierarchical structure of urchin‐like hematite and preferable basic sites which promotes the CO2 adsorption, and (ii) the unique Z‐scheme feature efficiently promotes the separation of the electron–hole pairs and enhances the reducibility of electrons in the conduction band of the g‐C3N4. The origin of such an obvious advantage of the hierarchical Z‐scheme is not only explained based on the experimental data but also investigated by modeling CO2 adsorption and CO adsorption on the three different atomic‐scale surfaces via density functional theory calculation. The study creates new opportunities for hierarchical hematite and other metal‐oxide‐based Z‐scheme system for solar fuel generation.
At the Crossroads: Does the Configuration of Roadside Vegetation Affect Woodland Bird Communities in Rural Landscapes?

In agricultural regions worldwide, linear networks of vegetation such as hedges, fencerows and live fences provide habitat for plant and animal species in heavily modified landscapes. In Australia, networks of remnant native vegetation along roadsides are a distinctive feature of many rural landscapes. Here, we investigated the richness and composition of woodland-dependent bird communities in networks of eucalypt woodland vegetation along roadsides, in an agricultural region in which >80% of native woodland and forest vegetation has been cleared. We stratified sites in a) cross sections and b) linear strips of roadside vegetation, to test the influence on woodland birds of site location and configuration in the linear network (the ‘intersection effect’). We also examined the influence of tree size at the site, the amount of wooded vegetation surrounding the site, and the abundance of an aggressive native species, the noisy miner Manorina melanocephala. Birds were surveyed at 26 pairs of sites (cross section or linear strip) on four occasions. A total of 66 species was recorded, including 35 woodland species. The richness of woodland bird species was influenced by site configuration, with more species present at cross sections, particularly those with larger trees (>30 cm diameter). However, the strongest influence on species richness was the relative abundance of the noisy miner. The richness of woodland birds at sites where noisy miners were abundant was ~20% of that where miners were absent. These results recognise the value of networks of roadside vegetation as habitat for woodland birds in depleted agricultural landscapes; but highlight that this value is not realised for much of this vast vegetation network because of the dominance of the noisy miner. Nevertheless, roadside vegetation is particularly important where the configuration of networks create nodes that facilitate movement. Globally, the protection, conservation and restoration of such linear networks has an important influence on the persistence of biota within human-dominated landscapes.
Maximum Entropy Deep Inverse Reinforcement Learning

This paper presents a general framework for exploiting the representational capacity of neural networks to approximate complex, nonlinear reward functions in the context of solving the inverse reinforcement learning (IRL) problem. We show in this context that the Maximum Entropy paradigm for IRL lends itself naturally to the efficient training of deep architectures. At test time, the approach leads to a computational complexity independent of the number of demonstrations, which makes it especially well-suited for applications in life-long learning scenarios. Our approach achieves performance commensurate to the state-of-the-art on existing benchmarks while exceeding on an alternative benchmark based on highly varying reward structures. Finally, we extend the basic architecture - which is equivalent to a simplified subclass of Fully Convolutional Neural Networks (FCNNs) with width one - to include larger convolutions in order to eliminate dependency on precomputed spatial features and work on raw input representations.
High Rates of Enteric Fever Diagnosis and Lower Burden of Culture-Confirmed Disease in Peri-urban and Rural Nepal

Abstract Background In South Asia, data on enteric fever are sparse outside of urban areas. We characterized enteric fever diagnosis patterns and the burden of culture-confirmed cases in peri-urban and rural Nepal. Methods We used national reports to estimate enteric fever diagnosis rates over 20 years (1994–2014) and conducted a prospective study of patients presenting with a >72-hour history of fever to 4 peri-urban and rural healthcare facilities (during August 2013–June 2016). We compared clinical characteristics of patients with culture-confirmed Salmonella Typhi or Paratyphi infection to those of patients without enteric fever. We used generalized additive models with logistic link functions to evaluate associations of age and population density with culture positivity. Results National rates of enteric fever diagnosis were high, reaching 18.8 cases per 1000 during 2009–2014. We enrolled 4309 participants with acute febrile illness. Among those with a provisional clinical diagnosis, 55% (1334 of 2412) received a diagnosis of enteric fever; however, only 4.1% of these had culture-confirmed typhoidal Salmonella infection. Culture positivity was highest among young adults and was strongly associated with higher population density (P < .001). Conclusions Enteric fever diagnosis rates were very high throughout Nepal, but in rural settings, few patients had culture-confirmed disease. Expanded surveillance may inform local enteric fever treatment and prevention strategies.
Predicted distribution and movement of Glossina palpalis palpalis (Diptera: Glossinidae) in the wet and dry seasons in the Kogo trypanosomiasis focus (Equatorial Guinea)

ABSTRACT The aim of this study was to predict the distribution and movement of populations of the tsetse fly, Glossina palpalis palpalis (Diptera: Glossinidae), in the wet and dry seasons and to analyze the impact of the use of mono-pyramidal traps on fly populations in the Kogo focus in 2004 and 2005. Three Glossina species are present in Kogo: Glossina palpalis palpalis, major HAT vector in West-Central Africa, Glossina caliginea, and Glossina tabaniformis. The apparent density (AD) G. p. palpalis clearly fell from 1.23 tsetse/trap/day in July 2004 to 0.27 in December 2005. A significant reduction in the mean AD for this species was noted between seasons and years. The diversity of Glossina species was relatively low at all the sampling points; G. p. palpalis clearly predominated over the other species and significantly dropped as a consequence of control activities. The predictive models generated for the seasonal AD showed notable differences not only in the density but in the distribution of the G. p. palpalis population between the rainy and dry season. The mono-pyramidal traps have proven to be effective instrument for reducing the density of the tsetse fly populations, although given that the Kogo trypanosomiasis focus extends from the southern Equatorial Guinea to northern Gabon, interventions need to be planned on a larger scale, involving both countries, to guarantee the long-term success of control.
Effects of Azilsartan, Aliskiren or their Combination on High Fat Diet-induced Non-alcoholic Liver Disease Model in Rats

Introduction: In addition to its role in regulation of blood pressure, fluid and electrolyte homeostasis, the renin-angiotensin system (RAS) components were expressed in many other tissues suggesting potential roles in their functions. Aim: The present study aims to evaluate the protective effect aliskiren, when used alone or in combination with azilsartan against high fat diet-induced liver disease in rats. Material and methods: Thirty-two Wistar male rats, weighing 150-200 gm were allocated evenly into four groups and treated as follow: group I, rats were fed a specially formulated high-fat diet for 8 weeks to induce non-alcoholic liver disease and considered as control group; groups II, III and IV, the rats were administered azilsartan (0.5 mg/kg), aliskiren (25 mg/kg) or their combination orally via gavage tube once daily, and maintained on high fat diet for 8 weeks. The possible treatment outcome was evaluated through measuring serum levels of glucose, insulin, lipid profile, TNF-α, IL-1β and liver enzymes. Additionally, the liver tissue contents of glycogen and lipids and histological changes were also evaluated. Result: The results showed that azilsartan significantly improves the studied markers greater than aliskiren, and their combination o has no additive or synergistic effects on the activity of each one of them. Conclusion: Both azilsartan and aliskiren protects the rats against high-fat diet induced NAFLD with predominant effects for the former, and their combination showed no beneficial synergistic or additive effects.
Inhibition of epidermal growth factor receptor attenuates LPS-induced inflammation and acute lung injury in rats

Acute lung injury (ALI) and its severe form acute respiratory distress syndrome remain the leading cause of morbidity and mortality in intensive care units. Inhibition of epidermal growth factor receptor (EGFR) has been found to be able to reduce inflammatory response. However, it is still unclear whether EGFR inhibition can prevent ALI. This study aimed to validate the EGFR's role in ALI and investigated the effects of EGFR inhibition on lipopolysaccharides (LPS)-induced ALI in rats. In vitro, both pharmacological inhibitors (AG1478 and 451) and si-RNA silencing of EGFR significantly inhibited LPS-induced EGFR signaling activation and inflammatory response in human lung epithelial cells or macrophages. Mechanistically, LPS induced EGFR activation via TLR4 and c-Src signaling. In vivo, rat model with ALI induced by intratracheal instillation of LPS was treated by oral administration of AG1478 and 451. It was observed that AG1478 and 451 blocked the activation of EGFR signaling in lung tissue and reduced the LPS-induced infiltration of inflammatory cells, inflammatory gene expression, and lung injuries. This study demonstrates that TLR4/c-Src-dependent EGFR signaling plays an important role in LPS-induced ALI, and that EGFR may be a potential target in treating ALI.
Increasing Campylobacter Infections, Outbreaks, and Antimicrobial Resistance in the United States, 2004–2012

Background Campylobacteriosis, a leading cause of foodborne illness in the United States, was not nationally notifiable until 2015. Data describing national patterns and trends are limited. We describe the epidemiology of Campylobacter infections in the United States during 2004-2012. Methods We summarized laboratory-confirmed campylobacteriosis data from the Nationally Notifiable Disease Surveillance System, National Outbreak Reporting System, National Antimicrobial Resistance Monitoring System, and Foodborne Diseases Active Surveillance Network. Results During 2004-2012, 303520 culture-confirmed campylobacteriosis cases were reported. Average annual incidence rate (IR) was 11.4 cases/100000 persons, with substantial variation by state (range, 3.1-47.6 cases/100000 persons). IRs among patients aged 0-4 years were more than double overall IRs. IRs were highest among males in all age groups. IRs in western states and rural counties were higher (16.2/100000 and 14.2/100000, respectively) than southern states and metropolitan counties (6.8/100000 and 11.0/100000, respectively). Annual IRs increased 21% from 10.5/100000 during 2004-2006 to 12.7/100000 during 2010-2012, with the greatest increases among persons aged >60 years (40%) and in southern states (32%). The annual median number of Campylobacter outbreaks increased from 28 in 2004-2006 to 56 in 2010-2012; in total, 347 were reported. Antimicrobial susceptibility testing of isolates from 4793 domestic and 1070 travel-associated infections revealed that, comparing 2004-2009 to 2010-2012, ciprofloxacin resistance increased among domestic infections (12.8% vs 16.1%). Conclusions During 2004-2012, incidence of campylobacteriosis, outbreaks, and clinically significant antimicrobial resistance increased. Marked demographic and geographic differences exist. Our findings underscore the importance of national surveillance and understanding of risk factors to guide and target control measures.
Effects of texture shape and fluid–solid interfacial slip on the hydrodynamic lubrication performance of parallel sliding contacts

The aim of this paper is to study the effect of texture shape and fluid–solid interfacial slip on the hydrodynamic lubrication performance of parallel sliding contact. The modified Reynolds equation is solved using finite difference method with a Gauss–Seidel relaxation scheme. The two-component slip length model has been used in order to calculate the slip velocity terms. Results indicate that the consideration of fluid slip around the surface texture enhances the hydrodynamic performance of textured parallel sliding contact as compared to the conventional textured surface. It is concluded that the surface texture should be designed with lower texture height ratio and aspect ratio in order to achieve better hydrodynamic lubrication performance. Furthermore, it is observed that the lower critical threshold shear stress and the higher slip length coefficient improve the performance of parallel sliding contact.
Preoperative Anxiety in the Tertiary Care Hospitals of Sousse, Tunisia: Prevalence and Predictors

Background: Preoperative anxiety is crucial for the surgery outcome, the post operative recovery and the hospitalization cost. Aims: To determine the prevalence of preoperative anxiety and its predictors among elective surgery patients in Sousse, Tunisia. Methods: Cross sectional study was conducted in the 2 tertiary care hospitals of the region of Sousse, Tunisia during March 2016. All patients scheduled for elective surgery in 5 randomly selected surgery departments were included. Data were collected on the hospitals wards within 24 hours before surgery using the Amsterdam Preoperative Anxiety Information Scale. Results: Participants accounted for 332. Their mean age was 47.5 (±15.5) years. Females represented 53%. Preoperative anxiety was identified among 67.5% of them while 42.2% had important need for information, High grade of surgery and high level of information requirement were the main predictors of preoperative anxiety with adjusted odds ratios of 9 (CI95% : 3.4-23.8) and 1.5 (CI95% : 1.3-1.7) respectively. Conclusion: High prevalence of preoperative anxiety and important need for information were identified among elective surgery patients of Sousse. Doctors should enhance their communication skills and attribute much more time for communication with their patients before surgery.