Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards an understanding of human alpha-7 nicotinic acetylcholine receptor selectivity: the creation and characterization of a soluble ligand binding domain template

Receptors play a vital role in the transduction of cell to cell signaling. They are important proteins with recognition capacity in signal transduction, particularly in neurons. Cholinergic neurons in the central and peripheral nervous systems are defined by storage, release, and stimulation of the neurotransmitter acetylcholine. At the synaptic cleft, the release of acetylcholine from presynaptic neurons triggers activation through channel opening of the nicotinic acetylcholine receptors (nAChRs) in the postsynaptic membrane. Previous research implicates the nAChRs in diseases including schizophrenia, drug addiction (specifically nicotine addiction), Alzheimer's and Parkinson's diseases. The work presented here uses a comprehensive approach including structural studies, protein engineering, functional studies, and protein characterization to gain insight into the distinguishing characteristics that may contribute to ligand selectivity and structural components that contribute to receptor function. The main aim of this work was to create a soluble template of the ligand binding domain of human alpha-7-nAChRs to understand pharmacological selectivity, while also creating an efficient tool for therapeutic development. In order to validate this study, methods to test the functional activity of nAChRs were developed and in the process a novel calcium FRET sensor based assay was developed as a cost-effective tool for drug screening and functional ligand characterization on nAChRs and other ligand-gated, calcium-permeable, ion channels. To process the information generated by the developed assay, a novel data storage system in the form of a database was created. The creation of a soluble template fully identical to the ligand binding domain of human alpha-7-nAChR was not successful, but the protein generated served to identify structurally a glycosylation site on the receptor as well as proved to be a better binding homologue for alpha-7- nAChRs than any other proteins currently available. Overall, the mutational conversion of a soluble homologue to the human alpha-7-nAChR gave insight into the structural understanding of the extracellular domain of nAChRs. This template provides a better model to create lead compounds as therapeutics for diseases associated with the nAChRs
A new species of Ochna (Ochnaceae) from the Barberton Mountains of Mpumalanga, South Africa

Ochna barbertonensis is described as a new species from the Barberton Mountains in Mpumalanga, South Africa. The new species is characterised by its suffrutescent habit, elongate-deltoid stipules sometimes with broadened base, mucronate leaf tip and high anther to filament ratio, where the anthers are ca. two times longer than the filaments. It is placed within sect. Ochna due to its poricidal anthers and subglobose drupes, attached at the base. It is most likely to be confused with the superficially similar suffrutescent species Ochna confusa, but that species has longitudinal anther dehiscence and anthers shorter than the filaments. The new species occurs within well protected nature reserves, but is only known from five collections with an Extent of Occurrence (EOO) of 34 km2, making it a ‘Rare’ species under the Red List of South African Plants. A species description, illustration and distribution map are provided.
Particulate arsenic release in a drinking water distribution system

Trace contaminants have been shown to accumulate in solids found in drinking water distribution systems and can potentially be released to the consumer—s tap water. The objective of this study was to identify and evaluate the source of high arsenic in consumers— tap water at a small drinking water system and assess the effect of the installation of a treatment system for iron/arsenic removal. Before treatment, water samples collected from home taps showed high arsenic concentrations (as high as 299 μg/L) that were attributable to iron solids found in the distribution system. In 29% of the tap water samples, arsenic concentrations in first‐draw water samples were greater than arsenic levels in water entering the distribution system. Color measurements proved to be good predictors of arsenic and iron levels in the tap water, and turbidity was a relatively poor predictive measurement.
Nutrient Release Performance of Starch Coated NPK Fertilizers and Their Effects on Corn Growth

One way to control or slow down the nutrient release rate from fertilizer is by coating technique. Nowadays the use of biodegradable coating materials for slow-release fertilizer (SRF) is preferable because of environmental issues. This research was aimed to make SRF using starches and cellulose as the coating materials and to test the release rate of the nutrients. Five kinds of starches (cassava, corn, sago, wheat, and glutinous rice) and carboxymethyl cellulose (CMC) were used as coating material for granulated NPK fertilizer. The coated fertilizers (NPK SRF) were tested for their leaching rate in the soil by percolation experiment. The results showed that the kind of starch used influenced the release rate of the NPK SRFs. The NPK SRF coated with sago starch exhibited slow release rate and low leached nutrients which also resulted in slow growth of corn plant, as expected of SRF. The use of starch and CMC as biodegradable coating materials in this research has a possibility to affect the microbial activity in the soil so that the nutrient release became faster than the uncoated NPK fertilizer.
Analisis Pengaruh Fitur Iklan Pada Media Sosial Instagram Terhadap Purchase Intention (studi Pada Indonesia)

Abstrak Seiring dengan perkembangan waktu, Media sosial semakin digunakan sebagai platform untuk melakukan kegiatan pemasaran dan periklanan. Perusahaan menghabiskan banyak biaya pada iklan di Media soasial. namun. selalu ada tantangan untuk perusahaan dalam mendesain iklan di Media sosial untuk berhasil menarik pelanggan dan memotivasi mereka untuk memberi merekakepercayaan. Instagram merupakan Media sosial yang termasuk memiliki banyak pengguna. Dengan demikian, penelitian ini bertujuan untuk menguji faktor-faktor utama yang terkait dengan social media advertising yang dapat memprediksi purchase intention pada Traveloka. Model konseptual yang digunakan berdasarkan tiga faktor dari teori Unified Theory of Acceptance and Use of Technology (UTAUT2) (performance expectancy, hedonic motivation, dan habit) ditambah dengan interactivity, informativeness, dan perceived relevance. Penelitian ini menggunakan penelitian kuantitatif dengan menggunakan Structural Equation Model (SEM) dengan menggunakan SmartPLS 3.0 sebagai media aplikasinya. Pengumpulan data dilakukan dengan menggunakan penyebaran kuesioner yang disebar kepada 400 responden serta skala ukur yang digunakan dalam penelitian ini adalah Skala Likert dengan skala 1 -5. Kata kunci: Media Sosial, Marketing, Advertising, Customers, Purchase Intetntion, Structural Equation Modeling (SEM) Abstract Over time, social media is increasingly being used as a platform for marketing and advertising activities. The company spends a lot of money on advertising on social media. however. there are always challenges for companies in designing advertisements on social media to successfully attract customers and motivate them to give them trust. Instagram is a social media that includes many users. Thus, this study aims to examine the main factors associated with social media advertising that can predict purchase intention on Traveloka. The conceptual model used is based on three factors from the Unified Theory of Acceptance and Use of Technology (UTAUT2) (performance expectancy, hedonic motivation, and habit) coupled with interactivity, informativeness, and perceived relevance. This research uses quantitative research using Structural Equation Model (SEM) using SmartPLS 3.0 as the application media. Data collection was carried out using a questionnaire distributed to 400 respondents and the measurement scale used in this study was a Likert Scale with a scale of 1-5. Keywords: Social Media, Marketing, Advertising, Customers, Purchase Intetntion, Structural Equation Modeling (SEM).
Screening of Lactic Acid Bacteria from “TapaiPulut” for Biosynthesis of Glutamic Acid

Glutamic acid (glutamate) is an amino acid used in human body to build proteins. Glutamate can be converted to glutamine via glutamine synthetase, and to γ — aminobutyric acid (GABA) via glutamate decarboxylase. The objective of this study is to screen potential of lactic acid bacteria from “tapaiubi” for biosynthesis of glutamic acid. The traditional fermented food, “tapaipulut” was used as a source of lactic acid bacteria (LAB). The sample was cultivated on DeMan-Rogosa-Sharpe MRS agar containing 0.16% bromocresol purple and placed under anaerobic condition at 37°C for 48 hours. A total of 25 strains were isolated with 8 strains were determined to be LAB based on their morphology. The 8 strains were inoculated into 8 bottles of fermentation medium (4% v/v) in duplicate determinations and fermented in rotary shaker (180 rpm, 37°C, 4 days). After 18 hours, the fermented media were centrifuged at 10000 rpm (4°C) for 10 minutes and the supernatants were derivatised at 100°C for 10 minutes. Glutamic acid concentrations were determined by using HPLC with fluorescence detector (C18S) on a 250 × 4.6 mm column at a flow rate of 1.2 ml/min. Cut of 25 strains, 8 strains were shown to have the capability of producing glutamic acid. Five strains, including (TUS 25 (18.409 μg/ml), TUS 17 (18.437 μg/ml), TUS 7 (17.228 μg/ml), TUS 8 (14.033 μg/ml), TUS 3 (7.810 μg/ml) showed the capability of producing glutamic acid after 72 hours fermentation. While the other three strains TUS 11 (4.894 μg/ml), TUS 2 (0.0245 μg/ml), TUS 20 (0.405 μg/ml) were become 48 hours and 72 hours fermentation. The highest glutamate was registered after 48 hours and 96 hours. This study shows that LAB from “tapaipulut” has the capability of producing glutamic acid.
Mathematical Model of Hairy Root Growth.

Hairy roots produce secondary metabolites which have been used as specialty chemicals. The mathematical models o f hairy root growth kinetics can guide the design and scale-up o f root cultures. An unstructured segregated and a chemically structured segregated models for hairy growth kinetics are formulated with rules o f root branching processes. The deterministic branching rule and the stochastic branching rule are studied. For the deterministic rule where two branching parameters are assumed constant, the number o f tips can be obtained by solving a linear difference equation. The conceptual framework established for the deterministic rule is used to formulate a stochastic rule in which two branching parameters change randomly. An age population balance equation is used for the unstructured segregated model in an unchanging environment. In this model, age is assumed sufficient to describe the states o f cells. Using this model, the growth kinetics o f transformed roots o f Tagetes erecta is studied in shake flasks in an unchanging environment. For a transient state, maturity is used as a state parameter because the rate o f change in the maturity depends on its environment. For this case, a maturity population balance equation is used. The solutions o f the age population balance equation and the maturity population balance equation depend explicitly on the number of tips as a function o f time. It is shown how this number can be found from a set o f branching rules which can either be deployed in simulation algorithms or can be used to obtain a difference equation governing the development o f the tip number. Finally, a structured segregated model in the transient state is also formulated. The central assumption used in this model is that the hairy root is divided into two phases, the tip phase and the root body phase. Furthermore, the root body is assumed to consist of two compartments, cytoplasm and vacuole. The medium phase and the tip phase are modeled by the structured distributed model and the root body phase is modeled by the structured segregated model which is based on a maturity. CHAPTER
Diversity and Genetic Structure Inferred with Microsatellites in Natural Populations of Pseudotsuga menziesii (Mirb.) Franco (Pinaceae) in the Central Region of Mexico

The amount and structure of the genetic diversity in Mexican populations of Pseudotsuga menziesii (Mirb.) Franco, is almost unknown, since most genetic studies have been carried out on populations from Canada and the United States. Here, we applied a set of 12 microsatellite markers to 12 populations (234 trees) from the central region of Mexico in order to determine values of genetic diversity and differentiation. Seventy-three different alleles were identified: an average number of alleles per locus (Na) of 6.083, effective number of alleles (Ne) of 2.039, observed heterozygosity (Ho) of 0.229, and expected heterozygosity (Ht) of 0.417. Genetic differentiation was high: the coefficient of differentiation (θ) was 0.270, while the coefficient of structure (Φst) was 0.278. Bayesian analysis identified two genetic groups in central Mexico. The PCoA and the dendrogram were in concordance with the two genetic groups. The results of the analysis of molecular variance (AMOVA) indicate that genetic variation exists mainly within populations (72.149%). Therefore, conservation efforts should focus on as many individuals within populations as possible, to maintain this variation.
Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in C. elegans

The BH3-only family of proteins is key for initiating apoptosis in a variety of contexts, and may also contribute to non-apoptotic cellular processes. Historically, the nematode Caenorhabditis elegans has provided a powerful system for studying and identifying conserved regulators of BH3-only proteins. In C. elegans, the BH3-only protein EGL-1 is expressed during development to cell-autonomously trigger most developmental cell deaths. Here we provide evidence that egl-1 is also transcribed after development in the sensory neuron pair URX without inducing apoptosis. We used genetic screening and epistasis analysis to determine that its transcription is regulated in URX by neuronal activity and/or in parallel by orthologs of Protein Kinase G and the Salt-Inducible Kinase family. Because several BH3-only family proteins are also expressed in the adult nervous system of mammals, we suggest that studying egl-1 expression in URX may shed light on mechanisms that regulate conserved family members in higher organisms.
Winter temperature predicts prolonged diapause in pine processionary moth across its geographic range

Prolonged diapause occurs in a number of insects and is interpreted as a way to evade adverse conditions. The winter pine processionary moths (Thaumetopoea pityocampa and Th. wilkinsoni) are important pest of pines and cedars in the Mediterranean region. They are typically univoltine, with larvae feeding across the winter, pupating in spring in the soil and emerging as adults in summer. Pupae may, however, enter a prolonged diapause with adults emerging one or more years later. We tested the effect of spatial variation in winter temperature on the incidence of prolonged diapause, using a total of 64 individual datasets related to insect cohorts over the period 1964-2015 for 36 sites in 7 countries, covering most of the geographic range of the species. We found high variation in prolonged diapause incidence over the species’ range. Insect cohorts exposed to average winter temperatures lower than 0°C were associated with higher prolonged diapause incidence than cohorts exposed to intermediate temperatures. Prolonged diapause may represent a risk-spreading strategy although it is associated with high mortality because of a longer exposure to mortality factors, desiccation, and energy depletion. Climate change, and in particular the increase of winter temperature, may reduce the incidence of prolonged diapause at the colder sites whereas it may increase it at the warmer ones, with consequences on the population dynamics.
Full circle : genetics, biosynthesis, mode of action and resistance mechanisms of the bacteriocin garvicin ML

Garvicin ML (GarML) is a circular bacteriocin produced by Lactococcus garvieae DCC43. The recently published draft genome of this strain allowed determination of the genetic background for bacteriocin production. Bioinformatic analysis identified a gene cluster consisting of nine open reading frames organized in 4 operons involved in the production of and immunity to GarML. The garA gene encodes the bacteriocin precursor, garX a large transmembrane protein, garBCDE a putative immunity protein (garB) followed by an ATPase and two transmembrane proteins, and garFGH encode an ABC transporter complex. Functional genetic analysis revealed that deletion of garFGH had little effect on sensitivity to or production of GarML. In contrast, deletion of garBCDE or inactivation of garX resulted in high level sensitivity to GarML, and completely abolished production of active bacteriocin. Mass spectrometry of culture supernatants revealed that wild-type cells contain the mature circular form as well as the linear forms of the bacteriocin, both with and without the three amino acid leader sequence, while bacteriocin-negative mutants only contain the linear forms. These results indicate that the cleavage of the leader peptide precedes circularization, and is likely performed by a functional entity separate from the GarML gene cluster. To our knowledge, this is the first evidence for these processes being separated in time. Loss of immunity, antimicrobial activity and our inability to detect the circular bacteriocin in the garBCDE and garX pCG47 mutants demonstrates that both these units are indispensible for GarML biosynthesis, specifically in the circularization process, but also for immunity, and that their functions are interlinked.
Success comes with consistency in hard times: foraging repeatability relates to sex and breeding output in African penguins

The concept of individual behavioural consistency has received a great deal of attention in the past 2 decades. However, the fitness benefits of being consistent in varying environmental conditions remain poorly explored. Such information is strongly relevant to our understanding of ecological processes, but also for predicting how some individuals and populations cope with environmental changes. We investigated short-term consistency in foraging behaviours of African penguins Spheniscus demersus at population and individual levels on Bird Island (Algoa Bay, South Africa) between 2015 and 2017, and related individual levels of consistency to reproductive outputs. Short-term overall consistency in foraging behaviour across individuals of the same population (population level) was generally moderate, although it was high for bearing (i.e. direction) towards the furthest point of the foraging trip. At the individual level, foraging consistency differed between years and was higher when environmental conditions were less profitable. Females were more flexible in their foraging behaviours than males. Overall, these results suggest that both intrinsic and extrinsic factors are responsible for inter-individual differences in foraging consistency in African penguins. Chicks of parents that were consistent in their foraging trip duration had higher growth rates than those of more flexible individuals when conditions were poor. It is not clear whether penguins adapt their level of short-term consistency at sea to the changing conditions or maintain their strategy across years. However, our results have revealed a reproductive advantage of individual foraging consistency during a year when resources were poor. For the first time, we have identified a potential mechanism to explain why some African penguins may cope better than others during poor environmental conditions.
THERMAL ENTRANCE REGION HEAT TRANSFER FOR RECTANGULAR DUCTS OF VARIOUS ASPECT RATIOS AND PECLET NUMBERS

Abstract : In this investigation the thermal entrance region problem is solved for flow in rectangular ducts of various aspect ratios and for various Peclet numbers. The assumptions under which the problem is solved are steady, fully developed laminar velocity profile, constant fluid properties of viscosity, density, specific heat and thermal conductivity, constant wall temperature, and a uniform inlet fluid temperature. Included in the solution are axial conduction and viscous dissipation. The method of B. G. Galerkin is used to formulate an approximate series solution of the problem. The data presented include bulk mean temperature, local Nusselt number, and the ratio of the local heat-transfer rate to the long wall to the local heat-transfer rate to the short wall. It is concluded that for low Peclet numbers, neglecting the axial conduction term leads to considerable error in the solution.
Speed, accuracy, sensitivity and quality control choices for detecting clinically relevant microbes in whole blood from patients

Infections are a serious health concern worldwide, particularly in vulnerable populations such as the immunocompromised, elderly, and young. Advances in metagenomic sequencing availability, speed, and decreased cost offer the opportunity to supplement or replace culture-based identification of pathogens with DNA sequence-based diagnostics. Adopting metagenomic analysis for clinical use requires that all aspects of the pipeline are optimized and tested, including data analysis. We tested the accuracy, sensitivity, and resource requirements of Centrifuge within the context of clinically relevant bacteria. Binary mixtures of bacteria showed Centrifuge reliably identified organisms down to 0.1% relative abundance. A staggered mock bacterial community showed Centrifuge outperformed CLARK while requiring less computing resources. Shotgun metagenomes obtained from whole blood in three febrile neutropenia patients showed Centrifuge could identify both bacteria and viruses as part of a culture-free workflow. Finally, Centrifuge results changed minimally by eliminating time-consuming read quality control and host screening steps. AUTHOR SUMMARY Immunocompromised patients, such as those with febrile neutropenia (FN), are susceptible to infections, yet cultures fail to identify causative organisms ~80% of the time. High-throughput metagenomic sequencing offers a promising approach for identifying pathogens in clinical samples. Mining through metagenomes can be difficult given the volume of reads, overwhelming human contamination, and lack of well-defined bioinformatics methods. The goal of our study was to assess Centrifuge, a leading tool for the identification and quantitation of microbes, and provide a streamlined bioinformatics workflow real-word data from FN patient blood samples. To ensure the accuracy of the workflow we carefully examined each step using known bacterial mixtures that varied by genetic distance and abundance. We show that Centrifuge reliably identifies microbes present at just 1% relative abundance and requires substantially less computer time and resource than CLARK. Moreover, we found that Centrifuge results changed minimally by quality control and host-screening allowing for further reduction in compute time. Next, we leveraged Centrifuge to identify viruses and bacteria in blood draws for three FN patients, and confirmed suspected pathogens using genome coverage plots. We developed a web-based tool in iMicrobe and detailed protocols to promote re-use.