Miracle-dz/UniFAR-FTUs huggingface dataset:
Conserved and Differential Features of TNF Superfamily Ligand Expression on APC Subsets over the Course of a Chronic Viral Infection in Mice

There is currently much interest in how different APC subsets shape the immune response. We recently described a division of labor between classical dendritic cells (cDC) and inflammatory monocyte-derived APC in provision of costimulatory ligands to T cells early during chronic lymphocytic choriomeningitis clone 13 (LCMV 13) infection in mice. At day 2 of LCMV 13 infection, cDC preferentially express CD80 and CD86, whereas TNF superfamily ligands GITRL, 4-1BBL, CD70, and OX40L are preferentially induced by type I IFN on inflammatory monocyte-derived APC, with minimal expression on cDC. In this study, we further investigate the expression of TNF and B7 family ligands on APC over the course of LCMV 13 infection. OX40L and 4-1BBL remain above baseline through the chronic stage of infection, with predominant expression on inflammatory APC compared with cDC in the spleen, partially blocked by anti–IFN-γR Ab pretreatment. Conversely, CD70, like GITRL, returns to baseline on the APC within a few days postinfection. In the lung, TNF family ligands were also preferentially expressed on inflammatory monocyte-derived APC. CD86 was generally higher on cDC than inflammatory APC in the spleen, but in the lung CD86 was highest on inflammatory APC. Moreover, in the spleen, CD80 levels on different APC subsets fluctuated over the course of the infection. We also show that LPS induction of TNF superfamily ligands is largely mediated through type I IFN. This study highlights the importance of IFNs and monocyte-derived APC in TNF superfamily ligand expression in both secondary lymphoid organs and tissues during chronic viral infection.
Relation between the asymmetric ring current effect and the anti-sunward auroral currents, as deduced from CHAMP observations

Abstract. During magnetically active periods the storm-time disturbance signal on the ground commonly develops an azimuthal asymmetry. Negative deflections of the magnetic horizontal ( H ) component are enhanced in the 18:00 local time sector and smallest in the morning sector. This is commonly attributed to the asymmetric ring current effect. In this study we investigate the average characteristics of anti-sunward net currents that are not closing in the ionosphere. Their intensity is growing proportionally with the amount of solar wind input to the magnetosphere. There is almost twice as much current flowing across the polar region in the winter hemisphere as on the summer side. This seasonal dependence is more pronounced in the dusk sector than in the dawn sector. Event studies reveal that anti-sunward currents are closely related to the main phase of a magnetic storm. Since the asymmetry of storm-time disturbances also builds up during the main phase, we suggest a relation between these two phenomena. From a statistical study of ground-based disturbance levels during magnetically active periods, we obtain support for our suggestion. We propose a new 3D current system responsible for the zonally asymmetric storm-time disturbance signal that does not involve the ring current. The high-latitude anti-sunward currents are connected at their noon and midnight ends to field-aligned currents that lead the currents to the outer magnetosphere. The auroral net current branch on the morning side is closed along the dawn flank near the magnetopause, and the evening side currents flow along the dusk flank magnetosphere. Regardless through which loop the current is flowing, near-Earth storm-time disturbance levels will in both cases be reduced in the morning sector and enhanced in the evening.
MRI brain tumor segmentation: A forthright image processing approach

Brain tumor is a collection of cells that grow in an abnormal and uncontrollable way. It may affect the regular function of the brain since it grows inside the skull region. As a brain tumor can be possibly led to cancer, early detection in Computed Tomography (CT) or Magnetic Resonance Imaging (MRI) scanned images are crucial. Thus, this paper proposed a forthright image processing approach towards detection and localization of brain tumor region The approach consists of a few stages such as pre-processing, edge detection and segmentation. The pre-processing stage converts the original image into a greyscale image, and noise removal if necessary. Next, the image is enhanced using image enhancement techniques. It is then followed by edge detection using Sobel and Canny algorithms. Finally, the segmentation is applied to highlight the tumor with morphological operations towards the affected region in the MRI images. The in-depth analysis is measured using a confusion matrix. From the results, it signifies that the proposed approach is capable to provide decent segmentation of brain tumor from various MRI brain images.
Mutational landscape and in silico structure models of SARS-CoV-2 Spike Receptor Binding Domain reveal key molecular determinants for virus-host interaction

Protein-protein interactions between virus and host are crucial for infection. SARS-CoV-2, the causative agent of COVID-19 pandemic is an RNA virus prone to mutations. Formation of a stable binding interface between the Spike (S) protein Receptor Binding Domain (RBD) of SARS-CoV-2 and Angiotensin-Converting Enzyme 2 (ACE2) of host actuates viral entry. Yet, how this binding interface evolves as virus acquires mutations during pandemic remains elusive. Here, using a high fidelity bioinformatics pipeline, we analysed 31,403 SARS-CoV-2 genomes across the globe, and identified 444 non-synonymous mutations that cause 49 distinct amino acid substitutions in the RBD. Molecular phylogenetic analysis suggested independent emergence of these RBD mutants during pandemic. In silico structure modelling of interfaces induced by mutations on residues which directly engage ACE2 or lie in the near vicinity revealed molecular rearrangements and binding energies unique to each RBD mutant. Comparative structure analysis using binding interface from mouse that prevents SARS-CoV-2 entry uncovered minimal molecular determinants in RBD necessary for the formation of stable interface. We identified that interfacial interaction involving amino acid residues N487 and G496 on either ends of the binding scaffold are indispensable to anchor RBD and are well conserved in all SARS-like corona viruses. All other interactions appear to be required to locally remodel binding interface with varying affinities and thus may decide extent of viral transmission and disease outcome. Together, our findings propose the modalities and variations in RBD-ACE2 interface formation exploited by SARS-CoV-2 for endurance. Importance COVID-19, so far the worst hit pandemic to mankind, started in January 2020 and is still prevailing globally. Our study identified key molecular arrangements in RBD-ACE2 interface that help virus to tolerate mutations and prevail. In addition, RBD mutations identified in this study can serve as a molecular directory for experimental biologists to perform functional validation experiments. The minimal molecular requirements for the formation of RBD-ACE2 interface predicted using in silico structure models may help precisely design neutralizing antibodies, vaccines and therapeutics. Our study also proposes the significance of understanding evolution of protein interfaces during pandemic.
Lactarius Subg. Lactarius (Russulaceae) in Indian Himalaya: Two New Species with Morphology and Phylogenetic Inferences

Abstract - The present paper deals with two novel species in Lactarius subg. Lactarius collected from western Himalaya (India): Lactarius indozonarius sp. nov. and Lactarius thindii sp. nov. Morphological descriptions, illustrations and nrITS-based phylogenetic analyses of these species are presented.
Detection, Classification, and Location of Seismovolcanic Signals with Multicomponent Seismic Data: Example from the Piton de La Fournaise Volcano (La Réunion, France)

We apply three different methods based on the analysis of the multicomponent seismic data to detect seismovolcanic tremors and other seismovolcanic signals, to propose an approach to classify them, and to locate their sources. We use continuous seismograms recorded during 1 year by 21 stations at the Piton de la Fournaise volcano (La Réunion, France). The first method allows the detection of seismovolcanic signals based on stability in time of the intercomponent cross‐correlation function. Two other methods based on the simultaneous analysis of the whole network can be used to detect seismovolcanic signals and to locate their sources. In the first network‐based method, the seismic wavefield is analyzed by calculating the width of the network covariance matrix eigenvalue distribution.The second network‐based method consists in performing the 3‐D backprojection of the interstation cross correlations in order to calculate the network response function. Simultaneous analysis of the parameters measured by the three different methods can be used to classify different types of seismovolcanic tremors. Our results demonstrate that all three methods efficiently detect seismovolcanic tremors accompanying the 2010 eruptions and the preceding pre‐eruptive seismic swarms. Furthermore, Methods 2 and 3 based on simultaneous analysis of the whole network detect a large number of volcanic earthquakes. Our location results show that each seismovolcanic tremor is located in a distinct regionof the volcano, close to the eruptive site at a shallow depth, and the preceding seismic crisis is located deeper at about the sea level under the summit crater.
Individual‐based models of community assembly: Neighbourhood competition drives phylogenetic community structure

It is now commonplace for community ecologists to infer assembly processes from the evolutionary relatedness of co‐occurring species. Such inferences, however, have typically depended on assembly theories that assume competitive equilibrium and that are species based. In reality, all natural communities are dynamic, particularly during the course of succession, and the ecological interactions which drive phylogenetic community structure actually occur among neighbouring individuals rather than species. To bridge this gap between theory and reality, we examine how colonisation, competition, and consequent replacement of individuals translate into phylogenetic community structure by using an individual‐based model. The model we use assumes a trade‐off between competition and colonisation abilities and that the points where species fall on the trade‐off curve are phylogenetically conserved. We find that the phylogenetic alpha diversity of a given community will be equal to or greater than the null expectation generated by randomly drawing individuals from communities at the same time step (i.e. phylogenetic overdispersion). This pattern results from the combination of interspecific differences in colonisation ability and neighbourhood competition that lead to individuals being regularly distributed in two‐dimensional space. We also show that phylogenetic beta diversity increases with increasing temporal differences between two communities. However, when this positive relationship is analysed only among the communities at close time steps, it becomes insignificant as they approach competitive equilibrium. We find similar patterns for functional alpha and beta diversity when phylogeny is replaced with functional traits. Synthesis. Though questions concerning community assembly have often been spatially framed, our model shows that the span of the time frame can also affect, or even reverse, inferences about assembly processes. Our model also implies that a shift in the frame of reference from species to individuals brings a new perspective to community assembly. Careful consideration of non‐equilibrium and individual‐level aspects provides better insights into the consequences of the evolutionary and functional similarities of individuals on community assembly.
Chemistry education student response toward general biology course: A descriptive study

Chemistry and biology are interrelated branches of science, but students majoring in Chemistry Education are often considered as less ability to understand several biological concepts. The aim of this study was to obtain the information about the response of Chemistry Education students on General Biology course. The research was a descriptive study conducted in August to December 2017 in which the subjects were twenty-four first-semester students of Chemistry Education who take General Biology course at Faculty of Tarbiyah and Teaching Sciences, State Islamic Institute Batusangkar, West Sumatera. The instrument used was the questionnaire of student responses on General Biology course. The analysis used was descriptive statistical analysis by using percentage. The best response of students on General Biology course is on assessment transparency aspect, while the lowest response is on lecture attractiveness aspect. The conclusion, the response of Chemistry Education student who has taken General Biology course in State Islamic Institute Batusangkar on the criteria good. Although from Chemistry Education Program, most students give positive responses to General Biology course. Information obtained from this study can be used as a basis for improving the quality of General Biology course, especially in Chemistry Education Program.
ForecastTB—An R Package as a Test-Bench for Time Series Forecasting—Application of Wind Speed and Solar Radiation Modeling

This paper introduces an R package ForecastTB that can be used to compare the accuracy of different forecasting methods as related to the characteristics of a time series dataset. The ForecastTB is a plug-and-play structured module, and several forecasting methods can be included with simple instructions. The proposed test-bench is not limited to the default forecasting and error metric functions, and users are able to append, remove, or choose the desired methods as per requirements. Besides, several plotting functions and statistical performance metrics are provided to visualize the comparative performance and accuracy of different forecasting methods. Furthermore, this paper presents real application examples with natural time series datasets (i.e., wind speed and solar radiation) to exhibit the features of the ForecastTB package to evaluate forecasting comparison analysis as affected by the characteristics of a dataset. Modeling results indicated the applicability and robustness of the proposed R package ForecastTB for time series forecasting.
My Professor Cares: Experimental Evidence on the Role of Faculty Engagement

We provide experimental evidence on the impact of specific faculty behaviors aimed at increasing student success for college students from historically underrepresented groups. The intervention was developed after conducting in-person focus groups and a pilot experiment. We find significant positive treatment effects across a multitude of short- and longer-run outcomes. Specifically, underrep-resented students in the treatment report more positive perceptions of the professor and earned higher course grades. These positive effects persisted over the next several years, with students in the treatment more likely to persist in college, resulting in increased credit accumulation and degree completion. (JEL I22, I23, I28, J15, J44)
How Are Fenebahçe’s And Beşiktaş’s Stock Returns Reacted To The Match-Fixing Announcement?

Bu calisma, sike iddiasi oncesi ve sonrasi donemlerde Besiktas ve Fenerbahce Spor kuluplerinin UEFA Avrupa Liginde yakaladiklari basarilarinin pay piyasalarindaki performanslarini karsilastirmayi amaclamaktadir. Calismada iki ayri donem incelenmistir; Besiktas icin sike oncesi donem 2010-2011 sezonunu ve sike sonrasi donem 2011-2012 sezonu olarak belirlenmistir. Fenerbahce icin ise sike oncesi donem 2009-2010 ve sike sonrasi donem ise 2012-2013 sezonu olarak belirlenmistir. Calismada Olay calismasi metodu kullanarak play-off maclarinda basarili olup grup maclarina gecen takimlarin bu basarisinin gunluk hisse senedi getirisi uzerindeki etkisi incelenmistir. Takimlarin grup maclarina yukseldiginin ilan edilmesi her iki takiminda hisse senedi hareketlerini pozitif etkilemistir. Diger taraftan sike sonrasi donemde hem Besiktas hem de Fenerbahce hisse senetlerinin getirileri grup maclarina yukseldikleri duruma ragmen negatif etkilenmistir. Calismada dikkat ceken sonuclardan birisi de Fenerbahce hisse senedi getirilerinin Besiktas hisse senedi getirilerine gore daha sert bir negatif etki ile karsilasmasidir.
Data‐driven framework for the prediction of cutting force in turning

Cutting force is one of the most important parameters for assessing power consumption and tool wear. This work attempts to utilise the concept of data analytics for collecting and building a data warehouse in a cloud-based platform called Central Database Repository (CDR), which can share the information about the machining forces in turning operations directly to the process planner or shop floor operator. The estimation of cutting force is accomplished based on the input of process parameters. CDR uses multiple-linear regression on the data collected and stored in the data bank. Uncertainties in machining operations are taken care of in a separate cloud-based platform known as mini-repository. This study estimates the interval of cutting force with a certain level of confidence and a new concept of dynamic reliability is attached to it. The information from the CDR can be accessed from anywhere across the globe. There is a provision to update the database based on the feedback and filter out unnecessary data by evaluating Cook's distance. The proposed framework is explained through illustrative case studies.
An interface between spatial memory and scene perception in posterior cerebral cortex

Here, we report a new link between the spatial-memory and scene-perception systems of the human brain. Using fine-grained individual-subject fMRI, we describe three cortical areas, each lying immediately anterior to a region of the scene perception network, that are selectively activated when recalling familiar places. Network analyses show that these regions constitute a distinct functional network and interface with memory systems during naturalistic scene understanding. These regions may bridge perception and memory, supporting visually-guided navigation.
Content and Antimicrobial Activities of Bingol Royal Jelly

Ari sutu (AS), amino asitler, proteinler, karbohidratlar, lipitler, mineral tuzlari ve vitaminleri iceren cesitli biyoaktif maddelerden olusan kralice bal arisi larvalarinin (Apis mellifera) ozel besleyicisidir. AS icerigi, flora turlerine ve iklim kosullarina gore arilarin genotipine bagli olarak degisir ve bu, AS'nin biyolojik aktivitelerini etkiler. Son yillarda, literaturde ilaca (antibiyotik) direncli patojenik bakteri miktarinda asiri miktarda artisa rastlanmaktadir. Antibiyotik direncinin artmasinin ana nedenleri, antibiyotik kullaniminin kotuye kullanilmasina bagli olabilir. Bu durum antibiyotik direncinde ek bir birikmeyi onlemek icin ari urunleri gibi antibiyotik ozellik tasiyan maddelerin diger secenekler olarak incelenmesinin onemini ortaya koymaktadir. Bingol AS'nin (BAS) kimyasal icerigi ve antimikrobiyal aktivitesi bugune kadar arastirilmamistir. Bu calisma ile BAS’in icerigi ve antimikrobiyal aktivitelerinin arastirilmasi amaclanmistir. Sonuclar BAS’in, antimikrobial ve antioksidan ozelliklerine katkida bulunan apigenin, quercetin, naringenin, gallik asit, kafeik asit gibi major flavonoidler ve fenolikler icerdigini gostermistir. Ayni zamanda BAS’in iceriginde linoleik asit ve propionik asit gibi bazi orta ve kisa zincirli yag asitlerinin varligi da gosterilmistir. BAS ayrica eser elementlerin ve mineralin bircogunu icermektedir. Kimyasal icerige ek olarak, BAS’in antimikrobiyal aktivitesi de patojenlere karsi arastirilmis ve Salmonella typhimurium (8.64 mm), Escherichia coli (9.1 mm) ve Staphylococcus aureus'a (10.73 mm) karsi antimikrobiyal aktivite gostermistir.
Trace Metal Fractional Solubility in Size‐Segregated Aerosols From the Tropical Eastern Atlantic Ocean

Soluble and total trace metals were measured in four size fractionated aerosol samples collected over the tropical eastern Atlantic Ocean. In samples that were dominated by Saharan dust, the size distributions of total iron, aluminum, titanium, manganese, cobalt, and thorium were very similar to one another and to the size distributions of soluble manganese, cobalt, and thorium. Finer particle sizes (< ~3 μm) showed enhanced soluble concentrations of iron, aluminum, and titanium, possibly as a result of interactions with acidic sulfate aerosol during atmospheric transport. The difference in fine particle solubility between these two groups of elements might be related to the hyperbolic increase in the fractional solubility of iron, and a number of other elements, during the atmospheric transport of Saharan dust, which is not observed for manganese and its associated elements. In comparison to elements whose solubility varies during atmospheric transport, the stability of thorium fractional solubility should reduce uncertainties in the use of dissolved concentrations of this element in seawater as a proxy for dust deposition, although this topic requires further work.
“Elethia” And “A Sudden Trip Home in Spring”: Alice Walker’s Womanist Response to the Issues of Black People

Alice Walker Annelerimizin Bahcesinin Arayisinda (1983) adli eserinde acikladigi kadincilik teorisiyle siyah feminizme yeni bir boyut getirmistir. Amaci; irk, toplumsal cinsiyet ve etnik farkliliklara bakmaksizin mucadelesini dunyadaki tum insanlari kapsayarak evrensellige erismektir. Bunun icin, Walker’a gore, insanlarin tarihini, ana soyunu ve onlara mucadele etmeleri icin ilham veren siyahi ve siyahi olmayan yazarlarin eserlerini kabullenip bilmesi gerekir. Walker, Kadinin Hasi Kolay Ezilmez (1981) baslikli eserindeki “Elethia” ve “Ilkbahar’da Eve Ani Yolculuk” baslikli iki oykusunde kadinci anlayisini temsil etmektedir. Walker’in kadin sorunsalina iliskin evrimlesen durusunu yansittigi icin adi gecen oykuler calismada incelenmektedir. “Elethia” ’nin baslik karakteri ve “Ilkbahar’da Eve Ani Yolculuk” oykusundeki Sarah sorunlariyla yuzlesir ve onlarla nasil savasabilecegini anlar. Boylece, calisma, Walker’in secilen oykulerini inceleyerek, yazarin Elethia ve Sarah adli karakterleriyle irkci ve cinsiyetci toplumda siyahilere kadinci bir cikar yol sundugunu gostermektedir.
Development, sensory profile and physicochemical properties of jabuticaba nectar
 with lyophilized jussara pulp

Jabuticaba and jussara are both fruits from the Brazilian Atlantic Forest and endangered plant species due to their unsustainable exploitation. In order to protect these plants, it is important to develop products made with these fruits. We have developed a ready-to-drink jabuticaba nectar with the addition of lyophilized jussara pulp (LJP) applying sensory tests, such as acceptance test and Check-All-That-Apply (CATA). Optimal sensory conditions ranged between 150 g L-1 and 200 g L-1 for sucrose concentration and between 450 mL L-1 and 550 mL L-1 for jabuticaba pulp concentration. Just-about-right scale showed that the ideal concentration of LJP used as a natural color additive was 7.2 g L-1 (R2=0.99902). Affective test showed that nectars added with LJP had higher acceptance means than samples without the colorant (P 0.05). Jabuticaba nectar added with LJP presented high acceptance among consumers (P<0.05), indicating commercial potential for this product.