Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Association Study and Pathway-Level Analysis of Kernel Color in Maize

Rapid development and adoption of biofortified, provitamin A-dense orange maize (Zea mays L.) varieties could be facilitated by a greater understanding of the natural variation underlying kernel color, including as it relates to carotenoid biosynthesis and retention in maize grain. Greater abundance of carotenoids in maize kernels is generally accompanied by deeper orange color, useful for distinguishing provitamin A-dense varieties to consumers. While kernel color can be scored and selected with high-throughput, low-cost phenotypic methods within breeding selection programs, it remains to be well established as to what would be the logical genetic loci to target for selection for kernel color. We conducted a genome-wide association study of maize kernel color, as determined by colorimetry, in 1,651 yellow and orange inbreds from the Ames maize inbred panel. Associations were found with y1, encoding the first committed step in carotenoid biosynthesis, and with dxs2, which encodes the enzyme responsible for the first committed step in the biosynthesis of the isoprenoid precursors of carotenoids. These genes logically could contribute to overall carotenoid abundance and thus kernel color. The lcyE and zep1 genes, which can affect carotenoid composition, were also found to be associated with colorimeter values. A pathway-level analysis, focused on genes with a priori evidence of involvement in carotenoid biosynthesis and retention, revealed associations for dxs3 and dmes1, involved in isoprenoid biosynthesis; ps1 and vp5, within the core carotenoid pathway; and vp14, involved in cleavage of carotenoids. Collectively, these identified genes appear relevant to the accumulation of kernel color.
Fractionation of three different lignins by thermal separation techniques—A comparative study

Separation of the heterogeneous lignin macromolecule in fractions with increased homogeneity, as well as different structural (molar mass) and functional (hydroxy groups, ‐OH) features is important in terms of its use as a chemical building block. For this purpose, three thermal separation techniques were investigated and compared: solvent extraction, successive precipitation and ultrafiltration. One important issue in this context is the utilization of organic solvents with low boiling points to ensure a simple and efficient recovery. In addition to a softwood Kraft lignin (Indulin AT) as reference lignin, two sulfur‐free Organosolv lignins from short rotation coppice (“poplar with bark”) and from the energy grass Miscanthus × gigantheus were investigated. The lignins were separated into low, medium and high molecular weight fractions. Due to the different initial structural features and the associated varying solubility properties in such lignins, different organic solvents were needed for dissolution and precipitation of the individual lignin fractions. The polarity of the used solvent is one key factor regarding the yield of the soluble fraction and the success of molecular sorting into low, medium, and high molecular weight. Further structural features, for example the aliphatic OH‐group content increased with rising molecular weight of poplar, miscanthus, and Kraft lignin from minimum 0.72, 0.3, and 1.6 mmol/g to maximum 2.4, 1.6, and 2.8 mmol/g, respectively. The number of phenolic OH‐groups decreased from maximum 3.8, 4.3, and 4.2 to minimum 1.4, 2.7, and 2.9, respectively. The presented work illustrate options regarding the molecular sorting of several lignin types with three thermal techniques into fractions differing in key properties (yield, molecular weight, polydispersity, functional groups) for material applications.
Indonesian health professions students’ perceptions toward an interprofessional education program: Findings after five years of implementation

Background: The Interprofessional Education (IPE) program is important for preparing health professions students to provide future interprofessional collaborative practice. The Universitas Indonesia Health Sciences Cluster has been implementing the IPE program since 2013. A comprehensive evaluation is required following the implementation of the IPE program. The aim of the study was to evaluate the IPE course based on perceptions of undergraduate students at the Universitas Indonesia from 2013 to 2017. Methods: A mixed-methods study utilizing a semi-structured questionnaire was conducted with first year students following the completion of the first stage of the IPE course. A total of 2355 students (56.35%) from the 2013–2017 academic years completed the questionnaire. Results: The results showed that students’ perceptions of the IPE course improved each year on the domains of clear and relevant learning objectives, studentcentered teaching methods, staff support, and supporting infrastructures. However, some room for improvement was identified, such as the need for tutors to have a more neutral attitude toward every student despite their background differences. Conclusion: The IPE course has been well perceived by students because of its comprehensive instructional design and principles of IPE that are implemented in the curriculum. The continuous cycles of improvement to maintain the quality of the IPE program will remain a challenge.
Variation of almond yield, biometry, α‐tocopherol levels, and antioxidant properties with nitrogen fertilization

A two years’ experiment (2015–2016) was set in a factorial design in which the effect of two application forms of nitrogen (N) (soil and soil + foliar spray) in different doses (0, 25, 50, and 100 kg N ha ‐1 ) on almond ( Prunus dulcis Mill. cv. “Masbovera”) was evaluated. Kernel yield, biometric properties, phytochemicals, and antioxidant activi‐ ties were assessed. The results showed that almond kernel yield increases with an increment in N rate doses ( p < 0.001) and was positively correlated with kernel weight and thickness, and negatively with fruit weight. The levels of α ‐tocopherol and total polyphenol content were higher with lower N doses (25 and 50 kg N ha –1 ). The antioxidant activities were positively correlated with polyphenol content. Based on our results, excessive N rates over 50 kg/ha depreciate the levels of α ‐tocopherol, total polyphenols, and antioxidant bioactivities of kernels.
Prediction of Properties of Sclerolobium paniculatum and Qualea grandiflora Charcoal

There is a lack of techniques for the rapid and accurate determination of wood quality for charcoal production with good energy characteristics. The association of NIR spectroscopy and important charcoal parameters allows the prediction of these characteristics. This is a fast method that does not require sample preparation before the reading. The spectral readings were performed with solid and ground samples, and presented the second best representation of the evaluated parameters. Data went was adjusted to correct for variations that could occur during the spectra reading. The treatment with the best results was the normal transformation of variation. The evaluated spectra were able to explain 77% of the data for the variable gravimetric yield, 88% for volatile materials content and 86% for fixed carbon content.
The New Perception of the Other in Chipilo, Mexico

espanolEl presente trabajo etnografico se enfoca en Chipilo, comunidad inmigrante bilingue de origen italiano en Mexico, que ha logrado conservar su dialecto y cultura por mas de seis generaciones gracias a un fuerte sentido y orgullo de la identidad etnica. Los cambios socioeconomicos y el aumento de las uniones mixtas de los ultimos veinte anos han repercutido en el proceso de construccion identitaria. Partiendo del analisis de los rasgos que tipicamente han definido la identidad y la alteridad, se examina la nueva percepcion del “otro” desde la perspectiva interna de la comunidad. Los datos con base en un corpus de entrevistas evidencian una representacion discursiva de la “otredad” distinta en virtud de nuevos elementos que establecen una nueva diferenciacion entre grupos dentro de la misma comunidad. EnglishThis ethnographic work focuses on Chipilo, a bilingual immigrant community of Italian origin in Mexico that has managed to maintain its dialect and culture for more than six generations thanks to a strong sense and pride of its ethnic identity. Socioeconomic changes and increase in mixed marriages during the last twenty years have affected the process of identity construction. Starting with an analysis of the characteristics that have typically come to define identity and otherness, we examine the new perception of “the other” from the internal perspective of the community. Data derived from a corpus of interviews provide grounds to claim the emergence of a different discourse representation of “otherness” among groups within the same community.
Biodegradation of Triphenyltin by Marine Bacteria

Twenty-two surface sediment samples were col­ lected from Visakhapatnam harbour, east coast of India, and anahsed for monophenyltin (MPT), diphenyltin (DPT), rnphenyltin (TPT), total bacteria, and TPT tolerant bacteria. Concentrations of MPT, DPT and TPT varied between 1-26, 3—28. and 0.31-145 ng Sn g 1 dry wt, respectively. Phenyltin concentrations were influenced by ship related activities, agricultural waste and sewage. These phenyltin concentra­ tions indicate sediments are contaminated. Abundance of TPT tolerant bacteria was strongly influenced by the levels of phenyltins.
Wearable Optical Fiber Sensor Based on a Bend Singlemode-Multimode-Singlemode Fiber Structure for Respiration Monitoring

Respiration rate (RR) is an important information related to human physiological health. A wearable optical fiber sensor for respiration monitoring based on a bend singlemode-multimode-singlemode (SMS) fiber structure, which is highly sensitive to bend, is firstly proposed and experimentally demonstrated. The sensor fastened by an elastic belt on the abdomen of a person will acquire the respiration signal when the person breaths, which will introduce front and back movement of the abdomen, and thus bend of SMS fiber structure. Short-time Fourier transform (STFT) method is employed for signal processing to extract characteristic information of both the time and frequency domain of the measured waveform, which provides accurate RR measurement. Six different SMS fiber sensors have been tested by six individuals and the experimental results demonstrated that the RR signals can be effectively monitored among different individuals, where an average Pearson Correlation Coefficient of 0.88 of the respiration signal has been achieved, which agrees very well with that of commercial belt respiration sensor. The proposed technique can provide a new wearable and portable solution for monitoring of respiratory with advantage of easy fabrication and robust to environment.
High Speed and Low Digital Resources Implementation of Hodgkin-Huxley Neuronal Model Using Base-2 Functions

Neurons are the basic blocks in the Central Nervous System (CNS). Simulation and hardware realization of these blocks are vital in neuromorphic engineering. This paper presents a set of multiplierless mathematical equations based on $2^{X}$ terms to achieve a low-cost, high-speed, and high-accuracy digital implementation of Hodgkin-Huxley (HH) neuron model. The HH model is the most complicated and high-accuracy among the mathematical neuron models. The proposed model can reproduce spiking behaviors of the original HH model with high precision. To validate the mathematical simulation results, the proposed model has been synthesized and implemented on Field-Programmable Gate Array (FPGA) development board. Hardware synthesis and physical implementations reveal that the biological behavior of different spiking patterns can be reproduced with higher performance and significantly lower implementation costs compared with the original HH model. Also, in this approach the maximum frequency of 200 MHz is achievable which is valuable in comparison with other similar works.
Quantifying uncertainties in the discharge distribution over the river Rhine branches using expert elicitation

For flood protection it is essential to have accurate estimates of river water levels. In a bifurcating river system, the uncertainty of the discharge distribution over the down­ stream branches has a main impact on the river water level uncertainty. Sources of uncertainty within the discharge distribution are manifold: e.g. wind, river geometry, main channel and floodplain roughness, primary defense and regulation structures. This study aims to quantify these uncertainty in the discharge distribution at the Pannerdense Kop, the major bifurcation of the Dutch Rhine river. Seven experts were interviewed and quantified both the uncertainty in the discharge distribution per individual source of uncertainty as well as the total amount of uncertainty. The experts state that the geometry, main channel and floodplain roughness are the most important sources of uncertainty. The 90% confidence interval of the discharge distribu­ tion was quantified as 571 m3/s, which is around 4% of the upstream discharge.
Characterisation of pulpal responses to bacterial challenge and novel sntimicrobials for management of bacterial contamination of infected pulps.

Dental pain from pulpal infection and inflammation are the common cause of dental emergencies. Therefore, evaluation of modalities to treat them would be beneficial. This work aims to characterise and validate the previously developed ex vivo pulp infection model and make it reliable and reproducible in terms of quantifying cell viability, area of bacterial colonisation and expression of inflammatory markers. The method developed and used in this work demonstrated that SAG infection reduced cell viability and IL-10 levels. SAG infection also Increased area of SAG colonisation of pulp,expression of IL-β, TNF-a and IL-18 in a time depended manner compared to uninfected control pulp. These findings were consistent with clinical observations, making it a reliable model for the observed characteristics. There were differences in the response to two SAG strains, with similar overall trends, but with greater response to S. constellatus.Differences in response to the two strains was confirmed by evaluating the effect of the SAG supernatants using the model. The response observed confirmed the deleterious effects of the supernatant on cell viability, and increase in expression of inflammatory markers, with a greater response of pulp observed to S. constellatus. Analysing the supernatants of SAG strains revealed the difference could be due to hyaluronidase produced by S. constellatus.Triclosan’s anti-microbial and anti-inflammatory effect in the treatment of pulpal infection was demonstrated using the SAG model through increased cell viability, reduced area of colonisation and inflammatory marker expression levels form triclosan treatment. Triclosan showed no anti-hyaluronisase activity.A poly-microbial infection model was developed with E. faecalis and S. anginosus on tooth slices. It was observed that E. faecalis perpetuated S. anginosus growth in mixed culture and caused greater cell-death compared to S. anginosus mono-infection. The proportion of E.faecalis and its affinity to blood vessels could influence the response of the model.
Languages and Sociolinguistics of the Caucasus

This chapter provides a sociolinguistic account of the languages of the Caucasus, including figures for speakers and their geographical distribution, language vitality, the official status of the languages, orthography, and writing practices. The chapter discusses language repertoires typical of different areas in the Caucasus, and their change over the 20th century. As a showcase, it provides an overview of traditional multilingualism in Daghestan, the most linguistically dense are in the Caucasus. It discusses various patterns of interethnic communication, including lingua franca and asymmetrical bilingualism. We show that bilingualism was gendered, and how Russian was spreading in the area as a new lingua franca. The chapter surveys the outcomes of language contact, covering both lexical borrowing (including main references to etymological research) and providing examples of structural convergence, with a special focus on the area of the highest language density in the Caucasus, Dagestan. Data in the chapter are based both on official sources (censuses), on information provided by experts and on the authors’ own work in the field.
Cloning and Expression Levels of TFAM and TFB2M Genes and their Correlation with Meat and Carcass Quality Traits in Jiaxing Black Pig

Abstract The coding sequences (CDS) of TFAM and TFB2M genes from Jiaxing Black Pig (JBP) were first obtained by RT-PCR and DNA-seq in the present study. Sequence analyses showed that the TFAM gene contains a 741-bp CDS region encoding 246 amino acids sharing a 100% homology with the sequence on NCBI, while TFB2M gene contains a CDS region of 1176 bp encoding 391 amino acids with two missense mutations. The results of quantitative Real-Time PCR for TFAM and TFB2M revealed that transcripts of the genes were both presented at the highest levels in spleen tissue followed by liver tissue, while the least levels in longissimus dorsi muscle (LDM), and obviously the higher levels in two adipose tissues than those in LDM tissue (P<0.01). Meanwhile, a total of forty-two JBPs were employed in this experiment to investigate the effect of these two genes on the carcass, meat quality traits and flavor substances such as fatty acids, intramuscular fat (IMF) in LDM. As expected, some strong correlations of gene expression abundance of TFAM and TFB2M mRNA in particular tissues such as liver and LDM with carcass and meat quality traits including marbling score, as well as the content of saturated fatty acid (SFA), in JBP were found.
MORPhA Scale: Behavioral and electroencephalographic validation of a rodent anesthesia scale

Degree of anesthesia in laboratory rodents is normally evaluated by testing loss of reflexes. While these are useful endpoint assessments, they are of limited application to study induction/reversal kinetics or factors affecting individual susceptibility (e.g. sex or age). We developed and validated a grading system for a temporal follow up of anesthesia. The Minho Objective Rodent Phenotypical Anesthesia (MORPhA) scale was tested in mice and rats anaesthetized with a mixture of ketamine/dexmedetomidine (ket/dex - 3 doses). The scale comprises 12 behavioral readouts organized in 5 stages – (i) normal/(ii) hindered voluntary movement, elicited response to (iii) non-noxious/(iv) noxious stimuli and (v) absence of response – evaluated at regular time points. Progression across stages was monitored by electroencephalography (EEG) in rats during anesthesia induction and reversal (atipamezole) and during induction with a second anesthetic drug (pentobarbital). Higher anesthetic doses decreased the time to reach higher levels of anesthesia during progression, while increasing the time to regain waking behavior during reversal, in mice and in rats. A regular decrease in high frequencies (low and high gamma) power was observed as the MORPhA score increased during anesthesia induction, while the opposite pattern was observed during emergence from anesthesia through reversion of dex effect. The devised anesthetic scale is of simple application and provides a semi-quantifiable readout of anesthesia induction/reversal.
An Alternate to Survey Methods to Measure Work from Home

During unprecedented times like COVID-19, when social distancing is a new normal,knowing the jobs that can be performed from homeis useful for policymakers and researchers. A most common way to estimate jobs that can be performed from home is by carrying out surveys, but this method is time and cost-intensive. Moreover, using US-based O*NET surveys to estimate work from home (WFH) index in a home country, other than the US, can potentially lead to large measurement errors. In this paper,we proposearatingbasedmethodology to estimatethe WFH index. Theratings are provided foroccupation-wise work activitiesaccording to their likelihood of getting performed from home by experts. This method is time and cost-effective and can easily be replicated in any country accounting forindigenous reality. Using tools like Inter-Rater Reliability (IRR), which is extensively used in psychology literature, we attempt to create a robust index of WFH for India.
Using expressed behaviour of coho salmon (
 
 Oncorhynchus kisutch
 
 ) to evaluate the vulnerability of upriver migrants under future hydrological regimes: Management implications and conservation planning

Globally, river systems have been extensively modified through alterations in riverscapes and flow regimes, reducing their capacity to absorb geophysical and environmental changes. In western North America and elsewhere, alterations in natural flow regimes and swimways through dams, levees, and floodplain development, work in concert with fire regime, forest management practices, as well as agriculture and urban development, to change recovery trajectories of river systems. Hydroregime scenarios for coho salmon, Oncorhynchus kisutch (Walbaum, 1792), were investigated in Washington and Oregon, USA, where long‐term records of discharge, water temperature, and upstream fish passage are available. This novel approach combines hydrological and ecological data in a single visualization, providing empirical foundations for understanding upstream behavioural movement and tolerances of native fishes. The timing of coho salmon movement with respect to temperature and discharge were compared with scenarios representing possible future hydrological conditions associated with a changing climate. This approach provides a framework for the study of future hydrological alterations in other locations, and can inform local and regional conservation planning, particularly in view of water management policy. Management implications and recommendations for action that may expand the capacity of riverscapes to absorb perturbations are discussed.
Stochastic AUC optimization with general loss

Recently, there is considerable work on developing efficient stochastic optimization algorithms for AUC maximization. However, most of them focus on the least square loss which may be not the best option in practice. The main difficulty for dealing with the general convex loss is the pairwise nonlinearity w.r. t. the sampling distribution generating the data. In this paper, we use Bernstein polynomials to uniformly approximate the general losses which are able to decouple the pairwise nonlinearity. In particular, we show that this reduction for AUC maximization with a general loss is equivalent to a weakly convex (nonconvex) min-max formulation. Then, we develop a novel SGD algorithm for AUC maximization with per-iteration cost linearly w.r. t. the data dimension, making it amenable for streaming data analysis. Despite its non-convexity, we prove its global convergence by exploring the appealing convexity-preserving property of Bernstein polynomials and the intrinsic structure of the min-max formulation. Experiments are performed to validate the effectiveness of the proposed approach.