Miracle-dz/UniFAR-FTUs huggingface dataset:
Prebiotic synthesis of cysteine peptides that catalyze peptide ligation in neutral water

Cysteine as peptide precursor and catalyst Among amino acids, cysteine is highly reactive as a nucleophile, metal ligand, and participant in redox and radical reactions. These properties make cysteine attractive as a component of prebiotic chemistry, but traditional Strecker synthesis of α-aminonitriles, which can serve as peptide precursors, cannot produce free cysteine. Foden et al. found that a simple acylation of the free amine prevented degradation of cysteine nitrile and enabled synthesis of this cysteine precursor from acetyl dehydroalanine nitrile and a sulfide donor (see the Perspective by Muchowska and Moran). When combined with other proteinogenic α-aminonitriles, acetylcysteine or derivative thiols catalyzed efficient peptide ligation in water. These results highlight how prebiotic synthesis of precursors can also generate function by creating a catalyst for polymerization. Science, this issue p. 865; see also p. 767 Nitrile chemistry unlocks biomimetic cysteine synthesis, fueling catalytic peptide ligation in water. Peptide biosynthesis is performed by ribosomes and several other classes of enzymes, but a simple chemical synthesis may have created the first peptides at the origins of life. α-Aminonitriles—prebiotic α–amino acid precursors—are generally produced by Strecker reactions. However, cysteine’s aminothiol is incompatible with nitriles. Consequently, cysteine nitrile is not stable, and cysteine has been proposed to be a product of evolution, not prebiotic chemistry. We now report a high-yielding, prebiotic synthesis of cysteine peptides. Our biomimetic pathway converts serine to cysteine by nitrile-activated dehydroalanine synthesis. We also demonstrate that N-acylcysteines catalyze peptide ligation, directly coupling kinetically stable—but energy-rich—α-amidonitriles to proteinogenic amines. This rare example of selective and efficient organocatalysis in water implicates cysteine as both catalyst and precursor in prebiotic peptide synthesis.
An Integral Recognition and Signaling for Electrochemical Assay of Protein Kinase Activity and Inhibitor by Reduced Graphene Oxide-Polydopamine-Silver Nanoparticle-Ti4+ Nanocomposite

A novel electrochemical biosensing method for protein kinase (PKA) activity was demonstrated by using a reduced graphene oxide-polydopamine-silver nanoparticle-Ti4+ (rGO-PDA-AgNPs-Ti4+) nanocomposite. The obtained nanocomposite possessed an integral capability for phosphopeptide recognition and signal readout. The polydopamine modified reduced graphene oxide (rGO-PDA) was firstly prepared based on a self-polymerization method of dopamine. The silver ions were adsorbed onto polydopamine (PDA) layer and directly reduced into silver nanoparticles (AgNPs), which was used for electrochemical signal reporting. Then, the Ti4+ cations were attached onto the PDA layer for phosphopeptide recognition according to the strong coordination ability of PDA with Ti4+ and phosphate group. The prepared rGO-PDA-AgNPs-Ti4+ nanocomposites were characterized with different methods. The developed rGO-PDA-AgNPs-Ti4+ nanocomposites were then employed for electrochemical analysis of PKA-catalyzed kemptide phosphorylation. The sensitive detection toward PKA activity was realized with an experimental detection limit of about 0.01 U/mL. It may be also extended for the inhibitor evaluation. Thus, it provided a facile and sensitive means for electrochemical analysis of PKA activity and inhibitor screening.
Humidified and Heated Cascade Impactor for Aerosol Sizing

Aerosol sizing is generally measured at ambient air but human airways have different temperature (37°C) and relative humidity (100%) which can affect particle size in airways and consequently deposition prediction. This work aimed to develop and evaluate a new method using cascade impactor to measure particle size at human physiological temperature and humidity (HPTH) taking into account ambient air conditions. A heated and humidified trachea was built and a cascade impactor was heated to 37°C and humidified inside. Four medical aerosols [jet nebulizer, mesh nebulizer, Presurized Metered Dose Inhaler (pMDI), and Dry Powder Inhaler (DPI)] under ambient conditions and at HPTH were tested. MMAD was lower at HPTH for the two nebulizers; it was similar at ambient conditions and HPTH for pMDI, and the mass of particles smaller than 5 μm decreased for DPI at HPTH (51.9 vs. 82.8 μg/puff). In conclusion, we developed a new method to measure particle size at HPTH affecting deposition prediction with relevance. In vivo studies are required to evaluate the interest of this new model to improve the precision of deposition prediction.
Prevalence and Characterization of Carbapenem-Hydrolyzing Class D β-Lactamase-Producing Acinetobacter Isolates From Ghana

Multidrug resistance, especially carbapenem resistance in Acinetobacter bacteria is a global healthcare concern. However, available data on the phenotypic and genotypic characteristics of Acinetobacter isolates from West Africa, including Ghana is scanty. Our aim was to investigate the antibiotic resistance profile and genotypic characteristics of Acinetobacter isolates from Ghana and to characterize carbapenemase producers using whole-genome sequencing (WGS). A total of 36 Acinetobacter isolates collected at three hospitals in Ghana between 2016 and 2017 were analyzed. MICs were determined by commercial antibiotic plates. Acinetobacter baumannii MLST was determined using the Pasteur scheme. WGS of OXA-carbapenemase producers was performed using short- and long-read sequencing strategies. The resistance rate was highest for trimethoprim/sulfamethoxazole (n = 22; 61%). Six (16.7%) and eight (22.2%) isolates were resistant to ceftazidime and colistin, respectively. Two (5.6%) isolates were resistant and one (2.8%) isolate had intermediate sensitivity to three carbapenems. Fifteen STs were identified in 24 A. baumannii isolates including six new STs (ST1467 ∼ ST1472). ST78 was the predominant (n = 6) followed by ST1469 (n = 3). Four carbapenemase-producing A. baumannii isolates also were identified. Isogenic ST103 isolates Ab-B004d-c and Ab-D10a-a harbored blaOXA–23 within Tn2007 on identical plasmids, pAb-B004d-c_3, and pAb-D10a-a_3. ST1472 isolate Ab-C102 and ST107 isolate Ab-C63 carried blaOXA–58 and blaOXA–420, a rare blaOXA–58 variant, respectively, within novel genetic contexts. Our results show that A. baumannii isolates of diverse and unique genotypes, including OXA-carbapenemase producers, are circulating in Ghana highlighting the need for a wider surveillance of antimicrobial resistance.
Genome Sequence of Citrobacter freundii AMC0703, Isolated from the Intestinal Lumen of an 11-Year-Old Organ Donor

Citrobacter freundii AMC0703 was isolated from the intestinal mucosa of an 11-year-old organ donor. Genome analysis revealed the presence of multiple factors potentially aiding in pathogenicity, including fimbriae, flagella, and genes encoding resistance to fluoroquinolones, cephamycin, fosfomycin, and aminocoumarin. ABSTRACT Citrobacter freundii AMC0703 was isolated from the intestinal mucosa of an 11-year-old organ donor. Genome analysis revealed the presence of multiple factors potentially aiding in pathogenicity, including fimbriae, flagella, and genes encoding resistance to fluoroquinolones, cephamycin, fosfomycin, and aminocoumarin.
Genome Sequences of Bacteria Associated with the Diatom Cyclotella cryptica Strain CCMP332

We report draft genomes of two bacterial strains in the genera Hyphobacterium and Reichenbachiella, which are associated with the diatom Cyclotella cryptica strain CCMP332. Genomes from these strains were 2,691,501 bp and 3,325,829 bp in size, respectively, and will be useful for understanding interactions between diatoms and bacteria. ABSTRACT We report draft genomes of two bacterial strains in the genera Hyphobacterium and Reichenbachiella, which are associated with the diatom Cyclotella cryptica strain CCMP332. Genomes from these strains were 2,691,501 bp and 3,325,829 bp, respectively, and will be useful for understanding interactions between diatoms and bacteria.
Global health and human rights in the time of COVID-19: Response, restrictions, and legitimacy

Abstract Policy responses to the COVID-19 pandemic have impacted a range of human rights, with the pandemic being used to justify police violence, authoritarian power grabs, and corruption. Health systems in high- and low-income countries have struggled to provide adequate COVID-19 testing, tracing, and treatment, with non-COVID-19 healthcare-restricted, vulnerable populations at high risk of infection and negative health and social impacts, and lockdowns exacerbating poverty, domestic violence, and mental health problems. If underresourced health systems are overwhelmed by COVID-19, and individuals are forced to bear testing and treatment costs, there is a stronger likelihood of health system failures, for higher mortality from a range of causes, and for people to be pushed further into poverty and insecurity. COVID-19 thus underscores the urgent need for clearer rules about legitimate restrictions of the right to health in responding to the pandemic, and for safeguarding global health policy initiatives in its aftermath. This article focuses on key right-to-health challenges, including realization of universal health coverage, and potential challenges in access to future COVID-19 therapies and vaccines. We conclude with reflections on what the pandemic may mean for the evolution of human rights, and the right to health in particular.
Evaluating the effect of anticipated emotion on forming environmentally responsible behavior in heritage tourism: developing an extended model of norm activation theory

ABSTRACT Scholars have found that emotional factors, as compared with cognitive factors, have greater effects on explaining behavior. This research incorporated the anticipated emotion into the original model of norm activation theory (NAT) to explain the environmentally responsible behavior in heritage tourism. The results show that the proposed model has greater prediction power than the original NAT. Both positive and negative anticipated emotion form significant relationships with the constructs in the extended model of NAT and play partial mediating roles. The significant relationship among constructs in the original NAT was revealed in a heritage tourism context. This study contributes to the literature in heritage tourism.
3-D navigation – A core driver of brain plasticity in video game interventions

Recent evidence has repeatedly shown that 3D platform video game training leads to substantial brain structural plasticity in hippocampus, prefrontal cortex and cerebellum. However, a great disadvantage of using complex video game interventions is the difficulty to attribute the observed effects to specific game mechanics. In order to address this caveat, we conducted a longitudinal training study in which 40 participants were randomly assigned to train with a 3D platformer game or a 2D platformer game. The main difference between the two games lies within their affordance for spatial exploration. After a training phase of two months, we observed extended brain structural increases in the 3D in comparison to the 2D condition in bilateral prefrontal areas, hippocampus/ entorhinal cortex as well as precuneus and the temporal lobe. In the reverse contrast an increase in bilateral caudate nucleus was observed. The results demonstrate a crucial role of 3D spatial navigation for widespread brain plasticity effects within a two-months training setup. Given the vast complexity of video games, spatial navigation seems to play an outstanding role in structural plasticity. Since prefrontal, temporal and hippocampal volume deficits are prominent risk factors for several psychiatric disorders, daily navigation habits (outdoor movement, using GPS devices etc.) have to be considered in future mental disorders prevention research.
A translation of weighted LTL formulas to weighted Büchi automata over ω-valuation monoids

In this paper we introduce a weighted LTL over product {\omega}-valuation monoids that satisfy specific properties. We also introduce weighted generalized Buchi automata with {\epsilon}-transitions, as well as weighted Buchi automata with {\epsilon}-transitions over product {\omega}-valuation monoids and prove that these two models are expressively equivalent and also equivalent to weighted Buchi automata already introduced in the literature. We prove that every formula of a syntactic fragment of our logic can be effectively translated to a weighted generalized Buchi automaton with {\epsilon}-transitions. Finally, we prove that the number of states of the produced automaton is polynomial in the size of the corresponding formula.
Domain-Speci(cid:28)c Knowledge Graph Construction for Semantic Analysis

Knowledge graphs are widely used for systematic representation of real-world data. Large-scale, general purpose knowledge graphs, having millions of facts, have been constructed through automated techniques from publicly available datasets such as Wikipedia. However, these knowledge graphs are typically incomplete and often fail to correctly capture the semantics of the data. This holds true particularly for domain-speci(cid:28)c data, where the generic techniques for automated knowledge graph creation often fail due to several challenges, such as lack of training data, semantic ambiguities and absence of representative ontologies. The focus of this thesis is on automated knowledge graph construction for the cultural heritage domain. The goal is to tackle the research challenges encountered during the creation of an ontology and a knowledge graph from digitized collections of cultural heritage data. This paper identi(cid:28)es the speci(cid:28)c research problems for these tasks and presents a methodology and approach for a solution, along with prelim-inary results.
Freshwater crayfish in Croatia

Freshwater crayfish of the family Astacidae (phyllum Arthropoda, order Decapoda) are represented with more than 540 species in Europe and four of them are indigenous in Croatia: Astacus astacus (Linnaeus, 1758) or noble crayfish, Astacus leptodactylus (Eschscholtz, 1823), Austropotamobius torrentium (Schrank, 1803) or stone crayfish and Austropotamobius pallipes (Lereboullet, 1858) or white-clawed crayfish. Three species (noble, stone and white-clawed crayfish) are listed in the IUCN Red List of Threatenes Species as vulnerable (VU) and are protected by the Croatian law ; the Law of Nature Conservation and the Rule Book on Protection of Crayfish. Also, the presence of one nonindigenous species (Orconectes limosus) was confirmed in marshes of the Nature Park Kopacki rit, Croatia.
Expression and purification of thioredoxin-his6-ZmDREB2.7 fusion protein in Escherichia coli for raising antibodies

Dehydration-responsive element-binding (DREB) proteins play a critical role in the plant’s drought-tolerance mechanism despite their presence in minor amounts in the cell. In this study, a maize-derived transcription factor protein, ZmDREB2.7, was overexpressed in the Escherichia coli strain Rosetta 1. The interested gene conjugating with the thioredoxin gene (TrxA) and his6 tag in the pET-32a vector encoded a 55.7 kDa fusion protein. The optimum condition for inducing the thioredoxin-his6-ZmDREB2.7 expression was five hours of induction with 0.05 mM IPTG at 300C. The Tris-HCl 20 mM pH 8.0 lysis buffer was harnessed to extract the recombinant protein for the purification process. Using the immobilized-metal affinity chromatography column, the recombinant protein was purified and then injected into rabbits. The antisera containing polyclonal antibodies (pAbs) could specifically recognize the ZmDREB2.7 fusion protein. This study represents updated data on the bacterial expression of the recombinant ZmDREB2.7 protein and the production of anti-ZmDREB2.7 pAbs.
Ty1 Retrotransposition Frequency Assay Using a Chromosomal Ty1his3AI or Ty1kanMXAI Element

[Abstract] Here I describe a simple genetic assay to determine the frequency of retrotransposition of a single chromosomal Ty1 element that is marked with the retrotransposition indicator gene, his3AI or kanMXAI . The assay is used to determine the effect of mutations or environmental conditions on the frequency of Ty1 retrotransposition in the yeast, cerevisiae .
Evolution of Synergistic Epistasis Underlying Complex Disease in Biologically-based Models

Author(s): Gervin, Joshua | Advisor(s): Lander, Arthur D | Abstract: The origins of complex, heritable traits -- such as familial risk for cancer, diabetes, and neuropsychiatric illness -- are poorly understood. For the past decade, genome-wide association studies (GWAS) have been used to search for sites of genetic variation associated with such traits, but the alleles thus discovered account, according to the statistical methods used, for only a small fraction of the probability of displaying the trait. One hypotheses put forth to explain this apparent failure concerns the nature of genetic interaction: If genes often interact synergistically, so that small-effect variants have a much greater than additive effect when combined, such genes will be difficult to discover by GWAS. This hypothesis is often rejected based on empirical evidence that natural genetic variants mostly tend to interact additively. Here I provide evidence that, for deleterious traits, the force of natural selection can alter this situation dramatically, producing inadvertent selection for synergistic interactions among small-effect alleles. To first demonstrate this, I created a variety of dynamical models of real and fictitious biological processes that are required to perform a series of tasks and, to mimic one likely effect of natural selection, optimized their parameters so that their outputs would be more robust to the values of their parameters (considered one at a time). In models of suitable complexity, I observed that optimization drove most parameter combinations (pairs, triples, etc.) toward additive interaction, but invariably drove a subset toward very high synergy (epistasis). Next, I used a simple model of non-additive gene-gene interaction to simulate populations evolving in the presence of “phenotypic noise” (i.e., intrinsic and environmental variability in the relationship between phenotype and genotype) to show the occurrence of common diseases (i.e., unfit phenotypes with frequencies on the order of 1%) can, under the right circumstances, be expected to be driven primarily by synergistic epistatic interactions. These results raise the possibility that the existence of complex, heritable disease traits with synergistic or combinatorial genetic origins may be an inevitable consequence of evolution.
Prosody Features Characterization of Autism Speech for Automated Detection and Classiﬁcation

—The verbal children affected with autism spectrum disorder (ASD) often shows some notable acoustic patterns. This paper represents the classiﬁcation of autism speech, i.e., the speech signal of children affected with ASD. In addition, this work speciﬁcally aims to classify the speech signals of non-native Indo English speakers (children) affected with ASD. Previous studies, however, have focused only on native English speakers. Hence, for this study purpose a speech signal dataset of ASD children and a speech signal dataset of normal children were recorded in English, and all the children selected for the data collection were non-native Indo English speakers. Here, for the ASD and the normal children, the acoustic features explored for classiﬁcation are namely, fundamental frequency (F0), strength of excitation (SoE), formants frequencies (F1 to F5), dominant frequencies (FD1, FD2), signal energy (E), zero-crossing rate (ZCR), mel-frequency cepstral coefﬁcients (MFCC), and linear prediction cepstrum coefﬁcients (LPCC). Further, these feature sets are classiﬁed by utilizing different classiﬁers. The KNN classiﬁer model achieves the highest 96.5% accuracy with respect to other baseline models explored here.
Biogeography and Edaphic Factors Structure Coastal Sediment Microbial Communities More than Vegetation Removal by Sudden Vegetation Dieback

Development of sudden vegetation dieback (SVD), a phenomenon that causes the rapid mortality of salt marsh plants, specifically Spartina alterniflora, has affected large-scale alterations in Atlantic coastal systems, through the often-complete removal of vegetation. In this study, two wetlands that differ in the time since development of SVD were compared in order to study biogeographic and temporal patterns that structure coastal wetland microbial communities and their response to disturbance. Biogeographic and edaphic factors that distinguished the two wetlands, such as differing salinity, water content, and soil carbon and nitrogen between the sites were more strongly associated with sediment microbial community structure than either sampling date or SVD development. In fact, no OTUs differed in abundance due to the season samples were collected, or vegetation loss due to SVD. This is not to say that SVD did not alter the composition of the microbial communities. The taxonomic composition of sediment communities in SVD-affected sediments was more heterogeneous between samples and a small number of OTUs were enriched in the vegetated sediments. Yet, these data suggest that coastal wetland sediment communities are predominantly shaped by environmental conditions and are generally resilient to temporal cycles or ecosystem disturbances. Importance One of the challenges of microbial ecology is predicting how microbial communities will respond to ecosystem change. Yet, few studies have addressed whether microbial responses to disturbance are consistent over space or time. In this study we employ SVD as a natural vegetation removal experiment and compare the sediment microbial communities between two geographically separated wetlands (ca 125 km). In this manner, we uncover a hierarchical structuring of the microbial communities, being predominantly governed by biogeography, with lesser effects due to disturbance, or temporal dynamics.
Carabid beetle (Coleoptera: Carabidae) distribution in a rural landscape based on habitat diversity and habitat characteristics

The spatial arrangement of ecosystems in an ecological landscape is assumed to be of importance with respect to species diversity. In order to improve current knowledge with respect to this aspect, carabid beetles were studied in six study sites, representing differently treated agricultural and post-agricultural areas and their surrounding habitats, over the period 2013-2015. Additionally, phytosociological surveys were elaborated on the study sites, in order to elaborate indicator values for selected environmental characteristics. We wanted to study (1) the similarities between the study sites and their contribution to overall species diversity, (2) the constancy of similarities between the study sites over several years, and (3) influence of environmental factors on the distribution of the species. Altogether, 1402 individuals belonging to 65 species were collected. Numbers of species differed strongly on the individual study sites in single years, but taking into account all three years the differences were much less significant. The number of exclusive species on the individual study sites ranged from 3 to 11 species, with the highest number on an agricultural field. Cluster analysis and correspondence analysis (CA) showed that the samples of the study sites from the different years were generally similar to each other. The distribution of the study sites along the ordination axis indicated a high importance of stages of succession (management intensity) followed by moisture conditions. The analysis of the indicator values, however, indicated light, acidity and humus content as most important. The study confirmed the assumption that a diversified landscape contributes to species diversity. In this context anthropogenic ecosystems should be taken into account.