Miracle-dz/UniFAR-FTUs huggingface dataset:
Scientific Communication--A Vanity Fair?

Success in science is rewarded with attention. Citation represents a fee paid through transfer of some of the attention earned by the citing author to the cited author. An economy of attention links the collectively most rewarding allocation of attention with the maximum value of the attention its holder can earn. In terms of the resulting collective efficiency it attains, the intelligence of science as a whole surpasses that which individual scientists can attain in isolation.
Chapter 2 Influences of Doping on Photocatalytic Properties of TiO 2 Photocatalyst

As a kind of highly effective, low‐cost, and stable photocatalysts, TiO2 has received substantial public and scientific attention. However, it can only be activated under ultraviolet light irradiation due to its wide bandgap, high recombination, and weak separation efficiency of carriers. Doping is an effective method to extend the light absorption to the visible light region. In this chapter, we will address the importance of doping, different doping modes, preparation method, and photocatalytic mechanism in TiO2 photocatalysts. Thereafter, we will concentrate on Ti3+ self‐doping, nonmetal doping, metal doping, and codoping. Examples of progress can be given for each one of these four doping modes. The influencing factors of preparation method and doping modes on photocatalytic performance (spectrum response, carrier transport, interfacial electron transfer reaction, surface active sites, etc.) are summed up. The main objective is to study the photocatalytic processes, to elucidate the mechanistic models for a better understand‐ ing the photocatalytic reactions, and to find a method of enhancing photocatalytic activities.
DiSL: a domain-specific language for bytecode instrumentation

Many dynamic analysis tools for programs written in managed languages such as Java rely on bytecode instrumentation. Tool development is often tedious because of the use of low-level bytecode manipulation libraries. While aspect-oriented programming (AOP) offers high-level abstractions to concisely express certain dynamic analyses, the join point model of mainstream AOP languages such as AspectJ is not well suited for many analysis tasks and the code generated by weavers in support of certain language features incurs high overhead. In this paper we introduce DiSL (domain-specific language for instrumentation), a new language especially designed for dynamic program analysis. DiSL offers an open join point model where any region of bytecodes can be a shadow, synthetic local variables for efficient data passing, efficient access to comprehensive static and dynamic context information, and weave-time execution of user-defined static analysis code. We demonstrate the benefits of DiSL with a case study, recasting an existing dynamic analysis tool originally implemented in AspectJ. We show that the DiSL version offers better code coverage, incurs significantly less overhead, and eases the integration of new analysis features that could not be expressed in AspectJ.
Mathematical and computational foundations of infectious disease epidemiology

As recent pandemics, such as the Zika and Ebola outbreaks have shown, diseases spread very fast in today’s interconnected world, making public health an important research area. Some of the basic questions are: How can an outbreak be contained before it becomes an epidemic, and what disease surveillance strategies should be implemented? These are challenging problems at the interface of dynamical systems, graph theory, data mining, machine learning, high performance computing, theoretical computer science, economics and statistics. In this tutorial, we provide an overview of the state of the art in mathematical and computational epidemiology, which have typically not been studied from a multi-disciplinary perspective. The tutorial is suitable for both novice and expert researchers, and will be at a level that is accessible to most ICSB attendees who work in these areas.
Interactions between calcium regulatory pathways and mechanosensitive channels in airways

ABSTRACT Introduction Asthma is a chronic lung disease influenced by environmental and inflammatory triggers and involving complex signaling pathways across resident airway cells such as epithelium, airway smooth muscle, fibroblasts, and immune cells. While our understanding of asthma pathophysiology is continually progressing, there is a growing realization that cellular microdomains play critical roles in mediating signaling relevant to asthma in the context of contractility and remodeling. Mechanosensitive pathways are increasingly recognized as important to microdomain signaling, with Piezo and transient receptor protein (TRP) channels at the plasma membrane considered important for converting mechanical stimuli into cellular behavior. Given their ion channel properties, particularly Ca2+ conduction, a question becomes whether and how mechanosensitive channels contribute to Ca2+ microdomains in airway cells relevant to asthma. Areas covered Mechanosensitive TRP and Piezo channels regulate key Ca2+ regulatory proteins such as store operated calcium entry (SOCE) involving STIM and Orai channels, and sarcoendoplasmic (SR) mechanisms such as IP3 receptor channels (IP3Rs), and SR Ca2+ ATPase (SERCA) that are important in asthma pathophysiology including airway hyperreactivity and remodeling. Expert opinion Physical and/or functional interactions between Ca2+ regulatory proteins and mechanosensitive channels such as TRP and Piezo can toward understanding asthma pathophysiology and identifying novel therapeutic approaches.
Biological properties of paleosols and present-day soils in Arkaim and its surrounding area, south Urals, Russia.

We investigated biological properties of paleosols in comparison to those of present-day soils in Arkaim, Kizilskoe and Sintachta, south Urals, Russia. Soil microbial biomass C and N were detected not only in present-day soils but also in paleosols. The past cultivation history such as plowing and differences in parent materials (e.g., illite-montmorillonitic vs. kaolinitic) had significant effects on microbial biomass and activities of microbes. These results indicated that effects of human activity in the past (20 years ago) on soil microbes still remained and varied depending on the type of parent material. Soils originated from a riparian topography emitted more CO2 and CH4 as compared with extremely dried soils in grassland landscapes in Arkaim. N2O flux was positive (1.3 mg N m /h) on average in a soil with middle water content (28%), while almost zero in soils with minimum (11%) and maximum water content (33%).
Overcoming the Uncanny Valley

What makes some near-human characters scary while others are merely laughable? More important, why do some human and humanlike characters fail to arouse our sympathy? Visual artists and roboticists face these questions as they seek to alternately frighten and endear. Recent attempts to create accurate human replicas have brought these questions to the fore with increased urgency.
Feed resources availability and livestock production in the central rift valley of Ethiopia

This study was conducted to investigate feed resource availability in association with livestock production in the Central Rift Valley of Ethiopia. Random sampling was used to select target farms. A total of 60 livestock owners were selected from two districts namely Admi Tullu Jidokombolcha and Dugda Bora both in the central Rift Valley. Structured questionnaire, focused group discussions, secondary data sources and field observations were employed to generate data on household structure, farm size, land use pattern, herd size, herd composition, purpose of livestock raising, major crops grown, crop grain yield, livestock feed types and quantity of total feed. The results of the study indicated that natural pastures and crop residues were the main basal diets in both districts, with crop residues supplying the largest proportion of dry matter.The total livestock population is estimated as 15 and 16 TLU in Adami Tullu Jidokombolcha and Dugda Bora districts, respectively. The total annual DM production met 81 and 80% of the total livestock requirement per annum per farm in Admi Tullu Jidokombolcha and Dugda Bora districts, respectively. From the current study, it was concluded that the available basal roughage feeds were not sufficient to meet livestock dry matter requirement. Alternative means of feed production and supply should be sought with the involvement of all stakeholders. Key words: Dry matter, feed resources, livestock.
Seed dispersal in limber and southwestern white pine: Comparing core and peripheral populations

According to the geographic mosaic theory of coevolution (Thompson 2005), the potential for coevolutionary relationships between interacting species varies with the presence of other species within a community. This implies that the strength of coevolution between two species may vary geographically. In this study, we ask whether there is a shift in vertebrate seed dispersers between core range and peripheral populations in two related five-needle white pines, limber (Pinus flexilis) and southwestern white (P. strobiformis). In the Rocky Mountains, limber pine ranges from southern British Columbia and Alberta south to New Mexico. Southwestern white pine ranges through the higher mountains of northern Mexico north to southern Colorado and Utah, and northern Arizona. The pines overlap in southern Colorado, southern Utah, northern New Mexico, and northern Arizona.
Impact of the Hunga Tonga volcanic eruption on stratospheric composition

Significance The Hunga Tonga-Hunga Ha’apai (HTHH) volcanic eruption on 15 January 2022 is unprecedented in the modern era in both the amount of water vapor injected into the stratosphere and the depth of penetration. The perturbation to water vapor and sulfate aerosols from this volcano significantly altered temperatures, dynamics, and chemistry in the stratosphere, including reductions in stratospheric column ozone, which is essential for protecting life on Earth from harmful ultraviolet radiation. Here, the global evolution of the injected water vapor in latitude, altitude, and time is analyzed for the year following the eruption using satellite data. Significant changes in the concentrations of various chemical compounds in the stratosphere are identified and linked to the HTHH eruption.
Thermal and Quantum Barrier Passage as Potential-Driven Markovian Dynamics

Rapidly progressing laser technologies provide powerful tools to study potential barrier-passage dynamics in physical, chemical, and biological systems with unprecedented temporal and spatial resolution and a remarkable chemical and structural specificity. The available theories of barrier passage, however, operate with equations, potentials, and parameters that are best suited for a specific area of research and a specific class of systems and processes. Making connections among these theories is often anything but easy. Here, we address this problem by presenting a unified framework for the description of a vast variety of classical and quantum barrier-passage phenomena, revealing an innate connection between various types of barrier-passage dynamics and providing closed-form equations showing how the signature exponentials in classical and quantum barrier-passage rates relate to and translate into each other. In this framework, the Arrhenius-law kinetics, the emergence of the Gibbs distribution, Hund’s molecular wave-packet well-to-well oscillatory dynamics, Keldysh photoionization, and Kramers’ escape over a potential barrier are all understood as manifestations of a potential-driven Markovian dynamics whereby a system evolves from a state of local stability. Key to the irreducibility of quantum tunneling to thermally activated barrier passage is the difference in the ways the diffusion-driving potentials emerge in these two tunneling settings, giving rise to stationary states with a distinctly different structure.
Exposure to Low Doses of Phthalates in Male Rodents: Effects on Reproductive and Cognitive Behaviors

Background: The nervous system is a sensitive target for exposure to environmental endocrine-disrupting compounds (EDC). This vulnerability is particularly important during the critical windows of development and puberty and lasts even at later stages of life. Among these environmental EDC, phthalates have largely been described for their neurotoxic effects. These effects have been reported for a large majority of studies using high to very high doses of these substances, which are not relevant for environmental exposure. Summary: The aim of this review was to analyze specifically the male rodent studies using low doses of phthalates. This analysis focuses on reproductive and cognitive behaviors, given the described antiandrogenic effects of phthalates and the known regulation of these behaviors by sex steroids. We also analyze the other neural effects in the hypothalamus and hippocampus/cortex, the brain regions governing these behaviors. A particular focus is on the neurovascular unit, which is newly investigated in the field of endocrine disruption. Key Messages: Exposure to low doses of phthalates can induce modifications in reproductive and cognitive behaviors. Whether these changes are triggered by common initiating cellular and molecular mechanisms in the brain areas controlling these behaviors still needs to be extensively investigated. In this context, given the high sensitivity of the neurovascular unit to sex steroid regulation and its impairment by low doses of phthalates, it could represent a possible initiating trigger for behavioral alterations to assess for phthalate exposure.
The Study of the Influence of IL5RA Variants on Chronic Obstructive Pulmonary Disease

Abstract Chronic obstructive pulmonary disease (COPD) is a complex disease, and its pathogenesis is influenced by genetic factors. This study aimed to evaluate the role of IL5RA genetic variation in the risk of COPD. In this study, 498 patients with COPD and 498 normal controls were recruited. Subsequently, five SNPs (rs3804795, rs2290610, rs13097407, rs334782, and rs3856850) in the IL5RA gene were genotyped. Logistic analysis examined the association of five single nucleotide polymorphisms (SNPs) in IL5RA with the risk of COPD under various genetic models. Furthermore, the association between IL5RA and susceptibility to COPD was comprehensively analyzed with stratification based on age, sex, smoking, and alcohol consumption. Our study showed that IL5RA rs13097407 reduced susceptibility to COPD (OR = 0.43, p < 0.001, p (FDR)< 0.001). On the other hand, rs3856850 was associated with an increased risk of COPD (OR = 1.71, p = 0.002, p (FDR) = 0.002). Interestingly, the effect of IL5RA SNPs on susceptibility to COPD was found to be influenced by factors such as sex and smoking. IL5RA gene variants were significantly associated with susceptibility to COPD.
Zinc effects on bacteria: insights from Escherichia coli by multi-omics approach

ABSTRACT In this study, we investigated the impact of zinc oxide (ZnO) and zinc oxide nanoparticles (ZnONPs) on Escherichia coli. These compounds are commonly used as fertilizers and feed additives and may have unintended consequences on bacteria. We conducted phenotypic and multi-omics analyses of E. coli exposed to sub-lethal concentrations of ZnO and ZnONPs for 40 sub-culturings and 20 sub-culturings with zinc followed by 20 sub-culturings without zinc in an attempt to reverse zinc effects. An extended treatment with ZnO for 40 sub-culturings had the greatest impact leading to bacterial resistance to aminoglycosides, cephalosporins, and sulfonamides while the treatment with ZnONPs for 40 sub-culturings led to the elevated MIC to chloramphenicol only. Cells exposed to these treatments were thicker and had retarded growth in elevated temperatures. Importantly, zinc withdrawal reversed most phenotypic changes. Zinc exposure caused dramatic changes in cell transcripts and proteins with a role in antibiotic response, heat stress, growth regulation, cell shape, and biofilm formation. An extended zinc exposure led to overall major alterations in E. coli biology and resulted in multi-drug resistance. IMPORTANCE A long-term exposure of bacteria to zinc oxide and zinc oxide nanoparticles leads to major alterations in bacterial morphology and physiology. These included biochemical and physiological processes promoting the emergence of strains with multi-drug resistance and virulence traits. After the removal of zinc pressure, bacterial phenotype reversed back to the original state; however, certain changes at the genomic, transcriptomic, and proteomic level remained. Why is this important? The extensive and intensive use of supplements in animal feed effects the intestinal microbiota of livestock and this may negatively impact the health of animals and people. Therefore, it is crucial to understand and monitor the impact of feed supplements on intestinal microorganisms in order to adequately assess and prevent potential health risks. A long-term exposure of bacteria to zinc oxide and zinc oxide nanoparticles leads to major alterations in bacterial morphology and physiology. These included biochemical and physiological processes promoting the emergence of strains with multi-drug resistance and virulence traits. After the removal of zinc pressure, bacterial phenotype reversed back to the original state; however, certain changes at the genomic, transcriptomic, and proteomic level remained. Why is this important? The extensive and intensive use of supplements in animal feed effects the intestinal microbiota of livestock and this may negatively impact the health of animals and people. Therefore, it is crucial to understand and monitor the impact of feed supplements on intestinal microorganisms in order to adequately assess and prevent potential health risks.
Biogenesis, inheritance, and 3D ultrastructure of the microsporidian mitosome

Quantitative electron and light microscopy combined with bioinformatics reveal that microsporidian mitosomes grow and divide incrementally and are inherited at the microsporidian centrosome (spindle pole body), whereas mitochondrial dynamins participate in mitosome division. During the reductive evolution of obligate intracellular parasites called microsporidia, a tiny remnant mitochondrion (mitosome) lost its typical cristae, organellar genome, and most canonical functions. Here, we combine electron tomography, stereology, immunofluorescence microscopy, and bioinformatics to characterise mechanisms of growth, division, and inheritance of this minimal mitochondrion in two microsporidia species (grown within a mammalian RK13 culture-cell host). Mitosomes of Encephalitozoon cuniculi (2–12/cell) and Trachipleistophora hominis (14–18/nucleus) displayed incremental/non-phasic growth and division and were closely associated with an organelle identified as equivalent to the fungal microtubule-organising centre (microsporidian spindle pole body; mSPB). The mitosome–mSPB association was resistant to treatment with microtubule-depolymerising drugs nocodazole and albendazole. Dynamin inhibitors (dynasore and Mdivi-1) arrested mitosome division but not growth, whereas bioinformatics revealed putative dynamins Drp-1 and Vps-1, of which, Vps-1 rescued mitochondrial constriction in dynamin-deficient yeast (Schizosaccharomyces pombe). Thus, microsporidian mitosomes undergo incremental growth and dynamin-mediated division and are maintained through ordered inheritance, likely mediated via binding to the microsporidian centrosome (mSPB).
The novel bacteriocin romsacin from Staphylococcus haemolyticus inhibits Gram-positive WHO priority pathogens

ABSTRACT Staphylococcus haemolyticus is an increasingly relevant nosocomial pathogen. The combination of multi-drug resistance and ability to form biofilms makes S. haemolyticus infections difficult to treat. Bacteriocins are ribosomally synthesized antimicrobial peptides produced by bacteria to inhibit growth of often closely related bacteria. Due to differences in the modes of action between bacteriocins and antibiotics, bacteriocins are normally equally potent against antibiotic-resistant and antibiotic-sensitive strains. To find bacteriocins able to inhibit S. haemolyticus and related species, clinical and commensal S. haemolyticus isolates (n = 174) were assayed for bacteriocin production. One commensal isolate produced an antimicrobial substance inhibiting S. haemolyticus and Staphylococcus aureus. The substance had physicochemical properties that are characteristic of bacteriocins. Purification, whole-genome sequencing, and mass spectrometry identified the antimicrobial as a novel two-peptide lantibiotic, hereafter named romsacin. The bacteriocin was active against a broad range of Gram-positive bacteria, such as the World Health Organization priority pathogens S. aureus [methicillin-resistant S. aureus (MRSA)] and Enterococcus faecium [vancomycin-resistant E. faecium (VRE)]. Importantly, the bacteriocin also eradicated S. haemolyticus, Staphylococcus epidermidis, MRSA, and VRE biofilms. IMPORTANCE Bacteria produce bacteriocins to inhibit growth of other bacterial species. We have studied the antimicrobial activity of a new bacteriocin produced by the skin bacterium S. haemolyticus. The bacteriocin is effective against several types of Gram-positive bacteria, including highly virulent and antibiotic-resistant strains such as Staphylococcus aureus and Enterococcus faecium. Effective antimicrobials are important for the treatment of infections and the success of major surgery and chemotherapy. Bacteriocins can be part of the solution to the global concern of antimicrobial resistance. Bacteria produce bacteriocins to inhibit growth of other bacterial species. We have studied the antimicrobial activity of a new bacteriocin produced by the skin bacterium S. haemolyticus. The bacteriocin is effective against several types of Gram-positive bacteria, including highly virulent and antibiotic-resistant strains such as Staphylococcus aureus and Enterococcus faecium. Effective antimicrobials are important for the treatment of infections and the success of major surgery and chemotherapy. Bacteriocins can be part of the solution to the global concern of antimicrobial resistance.
Change of Tide, Tidal Current, and Sediment due to Reclamation in Tokyo Bay.

Change of M2 tide and tidal current due to the reclamation in Tokyo Bay is investigated using a three-dimensional numerical model. The sea surface area and volume of Tokyo Bay decreased by 25% and 8%, respectively, from 1923 to 1983 due to the reclamation. As a result, M2 tidal amplitude in the bay and its water exchange volume across the bay mouth decreased by 8% and 35%, respectively. The surface sediment around the mouth of Tokyo Bay changed from sand to silt due to the decrease of tidal current amplitude there.