Miracle-dz/UniFAR-FTUs huggingface dataset:
Recent Progress in the Understanding and Engineering of Coenzyme B12-Dependent Glycerol Dehydratase

Coenzyme B12-dependent glycerol dehydratase (GDHt) catalyzes the dehydration reaction of glycerol in the presence of adenosylcobalamin to yield 3-hydroxypropanal (3-HPA), which can be converted biologically to versatile platform chemicals such as 1,3-propanediol and 3-hydroxypropionic acid. Owing to the increased demand for biofuels, developing biological processes based on glycerol, which is a byproduct of biodiesel production, has attracted considerable attention recently. In this review, we will provide updates on the current understanding of the catalytic mechanism and structure of coenzyme B12-dependent GDHt, and then summarize the results of engineering attempts, with perspectives on future directions in its engineering.
Data Triangulation in Consumer Neuroscience: Integrating Functional Neuroimaging With Meta-Analyses, Psychometrics, and Behavioral Data

This article reviews a wide range of functional magnetic resonance imaging (fMRI) studies conducted in the field of consumer neuroscience to (1) highlight common interpretative approaches of neuroimaging data (i.e., forward inference and reverse inference), (2) discuss potential interpretative issues associated with these approaches, and (3) provide a framework that employs a multi-method approach aimed to possibly raise the explanatory power and, thus, the validity of functional neuroimaging research in consumer neuroscience. Based on this framework, we argue that the validity of fMRI studies can be improved by the triangulation of (1) careful design of neuroimaging studies and analyses of data, (2) meta-analyses, and (3) the integration of psychometric and behavioral data with neuroimaging data. Guidelines on when and how to employ triangulation methods on neuroimaging data are included. Moreover, we also included discussions on practices and research directions that validate fMRI studies in consumer neuroscience beyond data triangulation.
Mechanisms of Pyrite Formation Promoted by Sulfate-Reducing Bacteria in Pure Culture

Pyrite, or iron disulfide, is the most common sulfide mineral on the Earth’s surface and is widespread through the geological record. Because sulfides are mainly produced by sulfate-reducing bacteria (SRB) in modern sedimentary environments, microorganisms are assumed to drive the formation of iron sulfides, in particular, pyrite. However, the exact role played by microorganisms in pyrite formation remains unclear and, to date, the precipitation of pyrite in microbial cultures has only rarely been achieved. The present work relies on chemical monitoring, electron microscopy, X-ray diffraction, and synchrotron-based spectroscopy to evaluate the formation of iron sulfides by the sulfate-reducing bacteria Desulfovibrio desulfuricans as a function of the source of iron, either provided as dissolved Fe 2 + or as FeIII-phosphate nanoparticles. Dissolved ferrous iron led to the formation of increasingly crystalline mackinawite (FeS) with time, encrusting bacterial cell walls, hence preventing further sulfate reduction upon day 5 and any evolution of iron sulfides into more stable phases, e.g., pyrite. In contrast, ferric phosphate was transformed into a mixture of large flattened crystals of well-crystallized vivianite ( Fe 3 ( PO 4 ) 2 ⋅ 8 H 2 O ) and a biofilm-like thin film of poorly crystallized mackinawite. Although being hosted in the iron sulfide biofilm, most cells were not encrusted. Excess sulfide delivered by the bacteria and oxidants (such as polysulfides) promoted the evolution of mackinawite into greigite ( Fe 3 S 4 ) and the nucleation of pyrite spherules. These spherules were several hundreds of nanometers wide and occurred within the extracellular polymeric substance (EPS) of the biofilm after only 1 month. Altogether, the present study demonstrates that the mineral assemblage induced by the metabolic activity of sulfate-reducing bacteria strongly depends on the source of iron, which has strong implications for the interpretation of the presence of pyrite and vivianite in natural environments.
Tensile and Flexural Properties of Untreated Sisal Fibers Reinforced Unsaturated Polyester Resin Composites

Biobased products have been widely used to prevent damage to the environment. In this context, the use of composites reinforced with natural fibers, replacing synthetics ones, has motivated several researches in last years. The objective of the present work was to characterize composites prepared with unsaturated polyester resin and untreated sisal fibers by tensile and flexural tests. The untreated sisal fibers reinforcement was investigated using 25 g and 50 g masses. The fibers were randomly arranged into the resin to mold composite boards, using the compression molding technique without heating, in a curing process at 25°C for 48 hours. The results indicated that composite with 50 g presented better tensile strength (49%), flexural strength (71%) and flexural modulus (137%). The increase of fibers content improved the mechanical behavior of the composite. In addition, the use of natural fibers replacing a portion of petroleum-based resin can increase the sustainable concept of the products and reduce manufacturing costs, because it can be used less resin.
Subtletee: Augmenting Posture Awareness for Beginner Golfers

While the sport of golf offers unique opportunities for people of all ages to be active, it also requires mastering complex movements before it can be fully enjoyed. Extensive training is required to begin achieving any success, which may demotivate prospective players away from the sport. To aid beginner golfers and enable them to practice without supervision, we designed Subtletee---a system that enhances the bodily awareness of golfers by providing feedback on the position of their feet and elbows. We first identified key problems golf beginners face through expert interviews. We then evaluated different feedback modalities for Subtletee---visual, tactile and auditory in an experiment with 20 beginner golfers. We found that providing proprioception feedback increased the users' performance on the driving range, with tactile feedback providing the most benefits. Our work provides insights on delivering feedback during physical activity that requires high precision movements.
The Modeling of Interfacial Contacts in Composites Using the Sitting Drop - Solid Body System as an Example

The paper presents an analysis of positions, which a theory of a liquid wetting a solid surface is based on, using the sitting drop equilibrium as an example. Certain inconsistencies are indicated in these positions, which is the subject of the discussion. The paper explains why the interfacial tension of solid-gas has no effect on the equilibrium of a drop. It proposes a mechanism to form a liquid-solid interface layer, the tensor of interfacial tensions of which is represented as a pressure tensor. It is established that the surface tension of the interface layer is variable and changes in magnitude and direction depending on the wetting conditions. It is determined that it is not possible to present a range of phenomena accompanying the wetting of a solid surface with a liquid by examining the equilibrium of a three-phase contact line.
Supporting the Generation of Data Narratives

Data narration has received increasing interest in several communities while lacking models and tools for handling, building and structuring data narratives. We present a simple prototype for supporting data narrative, based on a conceptual model deﬁned in [4]. It guides a data narrator from scratch: fetch and explore data, abstract important messages based on an intentional goal, structure the contents of the data story, and render it in a visual manner. This prototype is implemented in Java as a web application using Spring, d3.js, JFreeChart and Apache PDFBox.
Combining Models for Better User Satisfaction in Video Recommendation

Watch time has been a subject of interest for recommender systems in recent years. Music, podcast and video recommendations based on or amplified by consumption time optimization are often employed to boost perceived user satisfaction, subscriptions, engagement or to decrease number of bounces. Finding a fragile balance between several different metrics describing users' behaviour might be challenging, especially in the area of video recommendation. In this paper, we design online algorithms for modelling relationship between click probability and expected watch time on a video. We explore means of combining and balancing click-based and watch time optimizing models in an online multi-criteria setting. We present experiments that involve watch time, CTR and watch ratio. Furthermore, the paper describes empirical evaluations on live traffic and illustrates that our approach has succeeded in outperforming a non-trivial baseline in a controlled manner.
Modeling the Interactions Between Sodium Channels Provides Insight Into the Negative Dominance of Certain Channel Mutations

Background Nav1.5 cardiac Na+ channel mutations can cause arrhythmogenic syndromes. Some of these mutations exert a dominant negative effect on wild-type channels. Recent studies showed that Na+ channels can dimerize, allowing coupled gating. This leads to the hypothesis that allosteric interactions between Na+ channels modulate their function and that these interactions may contribute to the negative dominance of certain mutations. Methods To investigate how allosteric interactions affect microscopic and macroscopic channel function, we developed a modeling paradigm in which Markovian models of two channels are combined. Allosteric interactions are incorporated by modifying the free energies of the composite states and/or barriers between states. Results Simulations using two generic 2-state models (C-O, closed-open) revealed that increasing the free energy of the composite states CO/OC leads to coupled gating. Simulations using two 3-state models (closed-open-inactivated) revealed that coupled closings must also involve interactions between further composite states. Using two 6-state cardiac Na+ channel models, we replicated previous experimental results mainly by increasing the energies of the CO/OC states and lowering the energy barriers between the CO/OC and the CO/OO states. The channel model was then modified to simulate a negative dominant mutation (Nav1.5 p.L325R). Simulations of homodimers and heterodimers in the presence and absence of interactions showed that the interactions with the variant channel impair the opening of the wild-type channel and thus contribute to negative dominance. Conclusion Our new modeling framework recapitulates qualitatively previous experimental observations and helps identifying possible interaction mechanisms between ion channels.
Dynamics of Photoinduced Energy Transfer in Fully and Partially Conjugated Polymers Bearing π-Extended Donor and Acceptor Monomers

The photophysical properties of donor (D)-acceptor (A) polymers were studied by designing two types of polymers, (D-σ-A)n and (D-π-A)n, with non-conjugated alkyl (sp3) and π-conjugated (sp2) linkers using π-extended donor and acceptor monomers that exhibit planar A-D-A structures. The non-conjugated alkyl linker provides structural flexibility to the (D-σ-A)n polymers, while the π-conjugated linker retains the rigid structure of the (D-π-A)n polymers. Photoinduced energy transfer occurs from the large donor to acceptor units in both polymers. However, the photoinduced energy transfer dynamics are found to be dependent on the conformation of the polymers, where the difference is dictated by the types of linkers between the donor and acceptor units. In solution, intramolecular energy transfer is relatively favorable for the (D-σ-A)n polymers with flexible linkers that allow the donor and acceptor units to be proximally located in the polymers. On the other hand, intermolecular (or interchain) energy transfer is dominant in the two polymer films because the π-extended donor and acceptor units in polymers are closely packed. The structural flexibility of the linkers between the donor and acceptor repeating units in the polymers affects the efficiency of energy transfer between the donor and acceptor units and the overall photophysical properties of the polymers.
SHORT AND NARROW ROADS CAUSE SUBSTANTIAL IMPACTS ON WILDLIFE

Short and narrow roads are generally overlooked when assessing road impacts on biodiversity. However, these roads bisect natural environments and may cause significant impacts on wildlife in local scale. Thus, we monitored roadkills along a short two-lane road (CPM road) in Southeastern Brazil and propose mitigation strategies to reduce wildlife mortality. We monitored roadkilled vertebrates along 5 km of CPM road from 2010 to 2016 and we also compiled data from previous studies along the same road. We conducted a hotspot analysis to identify CPM road areas with significant roadkill aggregation. We recorded 77 roadkilled vertebrates from 14 taxonomic groups along the CPM road. Mammals were the most frequently recorded group (91% of roadkills), which represented 56% of all medium- and large-sized mammal species known to occur in the study area. We identified three roadkill hotspots along the CPM road. Two of them were located at two stream crossings, where the road cut across the associated riparian forests, and the other was at a road section with water drainage from a pond, also connected to a riparian forest. These riparian forests are part of the remaining natural habitat that provides connectivity between the forest remnants in the landscape, and therefore, for wildlife. Our results showed that even short and narrow roads can have considerable roadkill, which may have severe effects for wildlife on a local scale. The results stress the need to carefully look at these types of roads and propose measures to reduce impacts. We propose the creation of safe crossing opportunities in the hotspot zones combined with wildlife fencing to keep the animals off the road and guide them towards the safe crossing opportunities.
Virtual Screening for Novel SarA Inhibitors to Prevent Biofilm Formation of Staphylococcus aureus in Prosthetic Joint Infections

Staphylococcus aureus is one of the predominant causes of periprosthetic joint infections (PJIs). Bacterial adhesion and biofilm formation are important factors in the pathogenesis of PJIs. S. aureus biofilm formation is regulated by several factors, including S. aureus regulator A (SarA). Previous studies have found that SarA mutants have limited ability to develop biofilms. In this study, we identified a SarA-targeting antibiofilm compound, ZINC00990144, and evaluated its efficacy and toxicity. According to static biofilm assay, the antibiofilm ability of the compound was concentration dependent. ZINC00990144 reduced biofilm in multiple strains by 40–86% at a concentration of 11.5 μM. Additionally, ZINC00990144 inhibited biofilm formation on different orthopedic implant materials including Titanium and UHMWPE disc. Furthermore, quantitative polymerase chain reaction results demonstrated that ZINC00990144 upregulated the expression of S. aureus exoproteases to inhibit the formation of biofilms. Moreover, ZINC00990144 prevented biofilm formation when exposed to sub-inhibitory doses of vancomycin, which is known to promote biofilm formation. CCK-8 results demonstrated ZINC00990144 has no significant effect on cell viability at concentration of 11.5 μM or below. Finally, we verified the antibiofilm function of the compound in vivo using implant infection mice model with/without exposure to sub-inhibitory vancomycin. In conclusion, ZINC00990144 acts by modulating between biofilm and planktonic state of S. aureus instead of being bactericidal. Therefore, it has the potential to be used in combination with other antibiotics to prevent PJIs.
Internal Model Variability of Ensemble Simulations With a Regional Coupled Wave-Atmosphere Model GCOAST

Ensemble simulations are performed to quantify the internal variability of both regional atmospheric models and wave-atmosphere coupled model systems. Studies have shown that the internal variability in atmospheric models (e.g., wind or pressure fields) is increased during extreme events, such as storms. Comparing the magnitude of the internal variability of the atmospheric model with the internal variability of the coupled model system reveals that the internal variability can be reduced by coupling a wave model to the atmospheric model. While this effect is most evident during extreme events, it is still present in a general assessment of the mean internal variability during the whole study period. Furthermore, the role of this wave-atmosphere coupling can be distinguished from that of the internal variability of the atmospheric model since the impact of the wave-atmosphere interaction is larger than the internal variability. This is shown to be robust to different boundary conditions. One method to reduce the internal variability of the atmospheric model is to apply spectral nudging, the role of which in both the stand-alone atmospheric model and the coupled wave-atmosphere system is evaluated. Our analyses show that spectral nudging in both coupled and stand-alone ensemble simulations keeps the internal variability low, while the impact of the wave-atmosphere interaction remains approximately the same as in simulations without spectral nudging, especially for the wind speed and significant wave height. This study shows that in operational and climate research systems, the internal variability of the atmospheric model is reduced when the ocean waves and atmosphere are coupled. Clear influences of the wave-atmosphere interaction on both of these earth system components can be detected and differentiated from the internal model variability. Furthermore, the wave-atmosphere coupling has a positive effect on the agreement of the model results with both satellite and in situ observations.
Neuromodulation by mGluRs in Sound Localization Circuits in the Auditory Brainstem

The ability of humans and animals to localize the source of a sound in a complex acoustic environment facilitates communication and survival. Two cues are used for sound localization at horizontal planes, interaural time and level differences (ITD and ILD), which are analyzed by distinct neural circuits in the brainstem. Here, we review the studies on metabotropic glutamate receptor (mGluR)-mediated neuromodulation of both intrinsic and synaptic properties of brainstem neurons in these circuits. Both mammalian and avian animal models have been used, with each having their advantages that are not present in the other. For the mammalian model, we discuss mGluR neuromodulation in the ILD circuit, with an emphasis on the recent discovery of differential modulation of synaptic transmission of different transmitter release modes. For the avian model, we focus on reviewing mGluR neuromodulation in the ITD pathway, with an emphasis on tonotopic distribution and synaptic plasticity of mGluR modulation in coincidence detector neurons. Future works are proposed to further investigate the functions and mechanisms of mGluRs in the sound localization circuits.
THE EFFECTS OF ANTI-MITOTIC AGENTS ON DIHAPLOIDIZATION AND FERTILITY IN WINTER SQUASH (Cucurbita maxima Duch.) AND PUMPKIN (Cucurbita moschata Duch.) ANDROGENIC HAPLOIDS

Double-haploidization (DH) is one of the favorable techniques to obtain 100% pure double haploid plants (DH’s) for generating the new F1 cultivars in a short time. The fecundity of this technique depends on the high quantity of haploids and also fertile DH’s. However, there are no comprehensive reports on the chromosome doubling and fertility (fruit and seed-set) of winter squash and pumpkin haploids, currently. Thus, to obtain high frequency and fertile DH’s, the efficiency of different anti-mitotic agents (colchicine, amiprophos methyl, trifluralin and oryzalin) was tested at various concentrations and exposure times for both in vitro and in vivo conditions. Haploid plantlets recovered from anther cultures of winter squash and pumpkin lines were used for DH program. The haploid plants were wholly immersed in aqueous solutions of antimitotic agents in vitro and apical parts of haploid plantlets were treated with anti-mitotic agents three times in vivo. Since some plants remained haploid, and the highest DH efficiency was obtained from multiple treatments of colchicine to shoot tips of haploid plants in the rate of 93.3%. In vivo multiple treatments of 1% colchicine for an hour was found to be the best doubling procedure for the recovery of high-frequency fertile DH’s in our winter squash and pumpkin breeding program.
Distribution of Antibiotic-Resistant Enterobacteriaceae Pathogens in Potable Spring Water of Eastern Indian Himalayas: Emphasis on Virulence Gene and Antibiotic Resistance Genes in Escherichia coli

Every year millions of people die due to fatal waterborne diseases around the world especially in developing countries like India. Sikkim, a northeastern state of India, greatly depends on natural water sources. About 80% of the population of Sikkim depends on natural spring water for domestic as well as agricultural use. Recent waterborne disease outbreaks in the state raises a concerning question on water quality. In this study, we analyzed water quality especially for the detection of Enterobacteriaceae members from four districts of the state. Isolation with selective culture media techniques and taxonomic characterization of Enterobacteriaceae bacteria with 16S rRNA gene showed the prevalence of Escherichia coli (37.50%), Escherichia fergusonii (29.41%), Klebsiella oxytoca (36.93%), Citrobacter freundii (37.92%), Citrobacter amalonaticus (43.82%), Enterobacter sp. (43.82%), Morganella morganii (43.82%), Hafnia alvei (32.42%), Hafnia paralvei (38.74%), and Shigella flexneri (30.47%) in the spring water of Sikkim. Antibiotic susceptibility test (AST) showed resistance of the isolates to common antibiotics like ampicillin, amoxicillin as well as to third generation antibiotics like ceftazidime and carbapenem. None of the isolates showed resistance to chloramphenicol. E. coli isolated from spring water of Sikkim showed presence of different virulence genes such as stx1 (81.81%), elt (86.66%), and eae (66.66%) along with resistance gene for ampicillin (CITM) (80%), quinolones (qnrB) (44.44%), tetracycline (tetO) (66.66%), and streptomycin (aadA1) (66.66%). The data indicates a high incidence rate of multiple antibiotic resistant enteric bacteria in the spring water of Sikkim. Additionally, the presence of enteric bacteria in the water samples indicates widespread fecal contamination of the spring water.