Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematics, population genetics, and taxonomy, and their importance for tracking avifaunal change

The process of evolutionary divergence produces a continuum of differentiation from populations to subspecies to species to genera, and so forth. The fields of population genetics and systematics study patterns and processes from opposite ends of this divergence continuum, and taxonomy describes, names, and classifies the results of these studies. New methods of assessing population characteristics in phenotype and genotype, and new analytical methods, are improving our ability to determine where populations lie along the divergence continuum and their relationships and degrees of uniqueness. New techniques are also enabling us to more fully describe avian diversity, but genomic techniques in particular are furthering our understanding of how lineages responded to past climatic changes. As we learn more about evolutionary histories of lineages at the species level and below, we are finding that we need to pay more attention to important components of biodiversity (e.g., evolutionarily significant units, subspecies, and some phylogenetic species). We still have much work to do in fully describing extant avian diversity so that we know which populations we should be tracking when monitoring change. To enable future retrospective studies, we should include a specimen component in our monitoring programs, because archived, physical specimens prove invaluable for understanding recent historical changes in birds and our shared environments.
Microfluidic protein isolation and sample preparation for high-resolution cryo-EM

Significance The recent improvements in cryogenic electron microscopy (cryo-EM) caused a revolution in structural biology. However, 1) protein isolation and 2) sample preparation methods lag behind, and cryo-EM is performed at far from full efficiency. Here, we present a microfluidic method for the rapid isolation of a target protein from minimal amounts of cell lysate and for its direct preparation for high-resolution cryo-EM. Our technology opens more avenues for structural biology: High-throughput structure determination of proteins in a multitude of conditions, ultrafast isolation and structure determination of sensitive proteins, and the analysis of proteins that cannot be produced in sufficient amounts using conventional approaches. High-resolution structural information is essential to understand protein function. Protein-structure determination needs a considerable amount of protein, which can be challenging to produce, often involving harsh and lengthy procedures. In contrast, the several thousand to a few million protein particles required for structure determination by cryogenic electron microscopy (cryo-EM) can be provided by miniaturized systems. Here, we present a microfluidic method for the rapid isolation of a target protein and its direct preparation for cryo-EM. Less than 1 μL of cell lysate is required as starting material to solve the atomic structure of the untagged, endogenous human 20S proteasome. Our work paves the way for high-throughput structure determination of proteins from minimal amounts of cell lysate and opens more opportunities for the isolation of sensitive, endogenous protein complexes.
Delay Information in Virtual Queues: A Large-Scale Field Experiment on a Ride-Sharing Platform

The growing adoption of virtual queues in the service and retail industries has been greatly accelerated by COVID-19 due to the requirement of social distancing. In collaboration with a major ride-sharing platform, we study how the wait time information (WTI) given by the service provider impacts customers' abandonment behavior in virtual queues; the study was conducted through a large-scale randomized field experiment that included 1,425,745 rides: one-third of the rides received a neutral WTI, one-third received a more optimistic WTI shorter than the neutral WTI (hence less frequent updates), and one-third received a pessimistic WTI (hence more frequent updates). We find both the magnitude of the initial WTI and the update frequency of the WTI have a significant impact on customer abandonment. Specifically, when adjusting the initial WTI by 1 minute, it did not impact customer abandonment. We show that this may be because the magnitude effect of the initial WTI is cancelled out by the opposite update-frequency effect. However, when adjusting the WTI by more than 1 minute, the magnitude effect becomes dominant: when comparing the pessimistic WTI of 4 minutes with the neutral initial WTI of 2 minutes, 5 minutes with 3 minutes, and 8 minutes with 5 minutes, customers’ likelihood to abandon increases by 6.2%, 14.1%, and 19.6%, respectively. Similar but opposite effects are found when comparing the optimistic WTI with the neutral WTI. We discuss how firms can use our findings and insights to design and operate better virtual queues.
Reduced Expression of C-class Genes Is Associated with the Multiple-petal Phenotype in Nelumbo nucifera

The sacred lotus (Nelumbo nucifera) is an aquatic basal eudicot that is widely cultivated for food, medicine, and ornamental use. Ornamental lotus cultivars form flowers of various colors and shapes. The ABCE model for flower development has been proposed for model core eudicots such as Arabidopsis and snapdragon, but little is known about the molecular mechanisms of floral organ specification and development in N. nucifera. Here, we identified ABCE-class genes in the N. nucifera genome and compared their gene structures and spatial expression patterns in floral organs between singleand double-petalled flower-type lotus cultivars. Two lotus homologs of the C-class gene AGAMOUS (NnAG1, NnAG2) in a double-petal flower cultivar had intact transcripts, suggesting that loss of function of AG is not the cause of the double-petal phenotype in N. nucifera. NnAG1 and NnAG2 expression were specifically observed in stamens and carpels of a singlepetalled flower cultivar, but were slightly reduced in the double-petalled flower cultivar. In situ hybridization analysis further revealed that these two C-class homologs are specifically expressed in inner whorls such as stamens and carpels in a single-petal flower cultivar, but the signals are diminished in doubleand proliferating-petalled cultivars. These findings suggest that down-regulation of C-class genes is responsible for the multiple-petal phenotype in N. nucifera.
The Effect of Magnetic Treated Water and Foliar Nanofertilizer on the Active Ingredient of Fenugreek (Trigonellafoenum-graecum)

Afak district center of Al-Diwaniyah Governorate was chosen as a site for carrying out the study during the growing season 2018-2019 corresponding to 11/15/2018 using the method of cultivating potatoes for fenugreek seeds with the aim of determining the effect of magnetic treated irrigation water with differenttensiones (0, 750, 1500, and 3000) guass and spraying concentrations of foliarnanofertilizer(0) and recommended (1) and twice the recom mended (2)) g. L-1. In the indicators of the active substance of fenugreek plant, fenugreek seeds were sown in pots, at the rate of 10 seeds per pot, on 15/11/2018. After five days had passed, the germination was obtained at 100% for all the seeds sowing, and then watering operations for fenugreek plants with magnetic treated water were applied according to the strengths to be tested hidden Forced to treat irrigation water one month after the date of planting. Fenugreek plants were also sprayed with different concentrations of foliar nanofertilizer for the first time on 25/12/2018 and the second time on 15/1/2019. The indicators studied on fenugreek plant included indicators of ratios of the chemical component of fenugreek seeds [Trigonelline (%),Choline (%), Rhaponticin, Diosgenin (%) and Fenugreekine (%)]The results showed the significant effect of treated water on recording the highest averages of the studied plant indicators compared to the indicators caused by magnetic untreated water (comparison) as well as the significant moral superiority of magnetic treated water of 750 guass in recording the highest averages for the ratio of active ingredient Choline (%), Rhaponticin (%), and Trigonelline (%)with magnetic treated water at 1500 guass, as well as Diosgenin (%) and Fenugreekine (%) which significantly outperformed with treated water strongly 3000 gauss.
Bispecific antibody approach for EGFR-directed blockade of the CD47-SIRPα “don’t eat me” immune checkpoint promotes neutrophil-mediated trogoptosis and enhances antigen cross-presentation

ABSTRACT Cancer cells overexpress CD47 to subvert phagocytic elimination and evade immunogenic processing of cancer antigens. Moreover, CD47 overexpression inhibits the antibody-dependent cellular phagocytosis (ADCP) and cytotoxicity (ADCC) activities of therapeutic anticancer antibodies. Consequently, CD47-blocking antibodies have been developed to overcome the immunoevasive activities of cancer cell-expressed CD47. However, the wide-spread expression of CD47 on normal cells forms a massive “antigen sink” that potentially limits sufficient tumor accretion of these antibodies. Additionally, a generalized blockade of CD47-SIRPα interaction may ultimately lead to unintended cross-presentation of self-antigens potentially promoting autoimmunity. To address these issues, we constructed a bispecific antibody, designated bsAb CD47xEGFR-IgG1, that blocks cancer cell surface-expressed CD47 in an EGFR-directed manner. BsAb CD47xEGFR-IgG1 selectively induced phagocytic removal of EGFRpos/CD47pos cancer cells and endowed neutrophils with capacity to kill these cancer cells by trogoptosis; an alternate form of ADCC that disrupts the target cell membrane. Importantly, bsAb CD47xEGFR-IgG1 selectively enhanced phagocytosis and immunogenic processing of EGFRpos/CD47pos cancers cells ectopically expressing viral protein CMVpp65. In conclusion, bsAb CD47xEGFR-IgG1 may be useful to reduce on-target/off-tumor effects of CD47-blocking approaches, enhance cancer cell elimination by trogoptosis, and promote adaptive anticancer immune responses.
Anomaly detection for aircraft electrical generator using machine learning in a functional data framework

To reduce the number of aircrafts on ground, the electrical design engineers are interested in predicting the oil temperature of the generator during a flight. Changes on the temperature value may indicate an incorrect functioning of the generator. An abnormal behavior can be identified by using machine learning algorithms trained on flights free from any anomalies to predict the generator oil temperature. These predictions can then be compared to the observed values, here the sensor data collected from the aircraft during flight. If the observed value is far from the predicted value, a failure warning is raised and a maintenance action shall be performed.In this paper, we build a digital twin of the electrical generator which predicts the oil generator temperature at a given time thanks to the history of features. We compare several machine learning algorithms and the most promising appears to be a neural network which was implemented as part of the electrical generator digital twin.The digital twin is tested by using real flight data containing generator failures and it is verified that the algorithm is able to detect an anomaly prior to the failure events (early failure detection).
In silico Prediction and Cytotoxicity Evaluation of siRNAs Targeting Conserved Regions of MERS-CoV in Cell Culture

The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was isolated in 2012 and is well known to cause the respiratory syndrome. The orf1ab gene is known to mediate MERS-CoV replication. In this study, we have discussed the in silico prediction of potential siRNAs targeting MERS-CoV-orf1ab gene for antiviral therapeutics. To identify the potential siRNAs, various factors were considered. We have excluded the siRNAs with off-target effects and potential binding with human mRNAs. By using available softwares, total twenty-one functional, off-target reduced potential siRNA were selected from four hundred and sixty-two siRNAs based on greater potency and specificity. We have tested only seven siRNAs initially to evaluate their performance by reverse transfection approach by lipofectamine mediated delivery in Vero cells. The evaluation results showed no cytotoxicity at various concentrations of siRNAs used. The results obtained in this study provided preliminary information about the cytotoxicity which will help us to further evaluate siRNAs in other cell cultures to find out the replication inhibition efficiency of MERS-CoV. Finally, it is concluded that the in silico prediction and designing resulted in filtration and selection of potential siRNAs with high accuracy, efficiency, and strength which can be further utilized for the development of oligonucleotide-based therapeutics.
Comparative Population Structure in Species of Bats Differing in Ecology and Morphology in the Andaman Islands, India

Gene flow results from movement between populations, homogenising gene pools and impacting genetic variation and evolution. Growing evidence suggests that movement of individuals among populations may be more strongly determined by ecological traits. We compared genetic and morphometric differentiation in four species of bats — Eonycteris spelaea, Cynopterus sphinx, Rhinolophus affinis and Hipposideros pomona — which differ in their flight capability and roosting requirement to understand their effects in shaping genetic structure. Hypervariable region I of the mitochondrial control region was amplified from 40 E. spelaea, 28 C. sphinx, 44 R. affinis and 57 H. pomona sampled from locations spread across the Andaman archipelago. Populations of E. spelaea were nearly panmictic; R. affinis were differentiated into two clusters, and H. pomona were differentiated into three clusters. Consistent genetic and morphometric clusters were obtained for C. sphinx and the genetic break for C. sphinx occurs between Middle and South Andaman Islands, coincided with the Jarawa Tribal Reserve. In conclusion, poorly-dispersing, caveroosting species show high population structure, but when flight capability is very well-developed, the effect of disjunct roost availability is offset. The genetic structure of C. sphinx where we expected panmixia, is possibly confounded by the colonization history of its two genetic lineages and its habitat use which may prevent significant gene flow between the two lineages.
Accuracy in clinical examinations for the diagnosis of vulvovaginitis by CANDIDA SPP. and IN VITRO susceptibility to the main antifungals

Vulvovaginal candidiasis (VVC) is a common infection. This work aims to determine the positive predictive value (PPV) of the clinical diagnosis of VVC and to characterize Candida species isolated from the vaginal mucosa. This cross-sectional study was conducted from February 2016 to February 2017 at the Gynecology and Obstetrics Outpatient Clinic of the Hospital das Clínicas, in Goiânia, Goiás State, Brazil. The study included samples of vaginal secretion from 55 women who complained of vaginal discharge and itching as their main symptoms. The PPV of the clinical diagnosis of VVC was estimated in comparison to the laboratory culture method. The phenotypic methods and molecular tests were performed to identify Candida spp. In vitro susceptibility of Candida spp. isolates to fluconazole, itraconazole, clotrimazole, nystatin, and amphotericin B was determined using the broth microdilution assay. Yeast growth using the enzymes protease, phospholipase, and hemolysin was carried out in media containing respectively bovine albumin, egg yolk, and sheep erythrocytes. A PPV of 61.8% (34/55) was determined. Among the 55 vulvovaginal samples collected, we identified 36 isolates in which C. albicans was the most common species. High resistance to fluconazole and low minimal inhibitory concentration (MIC) values for clotrimazole, nystatin and amphotericin B were observed. All isolates were proteinase and hemolysin producers, while seven strains were phospholipase negative. The clinical diagnosis of VVC presented a moderate PPV, which meant that cultures had to be conducted in the laboratory to confirm infection. The high resistance to fluconazole and itraconazole indicated the importance of the in vitro susceptibility test.
Detection Systems in Immunohistochemistry

Immunohistochemistry (IHC) is a process of selectively imaging antigens in cells or tissue sections by exploiting antibody specificity. This technique is widely used in diagnostic pathology and research experiments for tracking specific molecular markers characteristic of a particular cell type or cellular events such as cancerous cell development, cell proliferation, or apoptosis. Visualizing the target antigen following an antibody-antigen interaction is accomplished by different detection systems. In the simplest instance, primary antibody directly conjugated to an enzyme is responsible for both specifically binding to the antigen and catalyz-ing a color-producing reaction. Alternatively, complex detection systems could be designed to profoundly improve minimal detection level of the antigen. During the past years, there has been a considerable improvement in designing and introduction of new and highly sensitive detection systems. The choice of an IHC detection system is a compromise of a variety of variables including desired sensitivity, cost, and the time needed for an IHC staining to be performed. This chapter covers the immunohistochemistry detection systems with emphasis on their principle, history, advantages, and limitations and delineates factors needed to be considered for choosing an appropriate detection system for IHC applications.
The Regulatory Role Of Matrix Metalloproteinases In T Cell Activation

Indiana University-Purdue University Indianapolis (IUPUI)%%%%Introduction: Matrix metalloproteinases (MMPs) are known for their role in extracellular matrix remodeling, but their role in regulating intracellular immune cell function is unknown. We reported that MMP inhibition down regulated T cell proliferation in response to alloantigens and autoantigens; but the direct role of MMP involvement in T cell activation has not been reported. Methods: MMP deficient or MMP sufficient wild-type CD4+ or CD8+ T cells from C57BL/6 mice were treated with SB-3CT, a specific inhibitor of MMP2 and MMP9, stimulated with anti-CD3 Ab, alone, or with IL-2 or CD28. Cellular activation and cytokine profiles were examined. A mouse model of antigen specific T cell mediated lung injury was used to examine MMP inhibition in antigen-specific T cell mediated lung injury. Results: SB-3CT (1-25μM) induced dose-dependent reductions in anti-CD3 Ab-induced proliferation (p<0.0001). Compared to wild-type, MMP9-/- CD4+ and CD8+ T cells proliferated 80-85% less (p<0.001) in response to anti-CD3 Ab. Compared to untreated or wild-type cells, anti-CD3 Ab-induced calcium flux was enhanced in SB-3CT-treated or MMP9-/- CD4+ and CD8+ T cells. Cytokine transcripts for IL-2, TNF-α and IFN-γ were reduced in both CD4+ and CD8+ MMP9-/- T cells, as well as in SB3CT treated CD4+ T cells. MMP inhibition dampened antigen-specific T cell mediated lung injury. Conclusions: Although known to be functional extracellularly, the current data suggest that MMPs function inside the cell to regulate intracellular signaling events involved in T cell activation. T cell targeted MMP inhibition may provide a novel approach of immune regulation in the treatment of T cell-mediated diseases. - David S. Wilkes, M.D., Chair.
Aerosol scattering and mass concentration for different aerosol types

m 2 g -1 and the later values between 2.5 - 3 m 2 g -1 . The difference is more visible as the aerosol load increases and so do PM10 and σ550. During the continental polluted period (likely a mixture with desert dust aerosols) the mass scattering efficiency values exhibited higher variability and range from 1 up to 3 m 2 g -1 . The mass scattering efficiencies for the
Mitigating the effects of geomagnetically induced currents in the power network

: Geomagnetically induced currents (GICs) in long high-voltage transmission lines cause half-cycle saturation of transformers, malfunction of protective relays, reactive power loss, and voltage instability. This study describes the design for a GIC effects mitigation device (GEMD) that can be installed at a power system autotransformer common node connection to block the flow of GIC DC flux at the cores of the autotransformers. The devices consist of variable resistors, which are controlled by a wide-area method based on particle swarm optimisation algorithm. The effectiveness of the proposed protective electrical devices is investigated and validated through simulation studies under many operational cases. The test results obtained from 648 cases verify the high performance of GEMD. The proposed method can mitigate the reactive power loss due to GIC in the power system with average improvements by 7.9 and 7.09% over resistive and capacitive blocking devices, respectively.
Effect of different dietary proteins and fats on the digestive enzymes activities in the common carp fingerlings (Cyprinus carpio L.) reared in floating cages

The digestive enzyme activities of the common carp fed with different diets of protein sources were investigated during 150 days trial in order to obtain a theoretical basis for artificial diet preparation for the culture of carp fingerlings (Cyprinus carpio L.). The results showed that the fish at treatment 3 (protein 13.82%, fat 4.76% and carbohydrate 67.81%) had high levels of alkaline protease activity. Acid protease activity was high at the treatment 1 (protein 23.68%, fat 16.28% and carbohydrate 43.68%) (p<0.05). In general, the acid protease activity was higher than alkaline protease during the course of the study. Amylase activity reached a highest value in fish fed with none animal protein sources (treatment 3). Lipase activity showed a high level in fish fed with high lipid contents (treatment 1).
Cysteine oxidation triggers amyloid fibril formation of the tumor suppressor p16INK4A

Accumulation of the CDK4/6 inhibitor p16INK4A in response to oncogenic transformation leads to cell cycle arrest and senescence and is therefore frequently lost in cancer. p16INK4A is also known to accumulate under conditions of oxidative stress and thus could potentially be regulated by the reversible oxidation of cysteines (redox signaling). Indeed, oxidation of the single cysteine in p16INK4A in human cells occurs under relatively mild oxidizing conditions and leads to disulfide-dependent dimerization. p16INK4A is an all alpha-helical protein, but here we report that upon cysteine-dependent dimerization, p16INK4A undergoes a dramatic structural rearrangement and forms aggregates that have the typical features of amyloid fibrils, including binding of diagnostic dyes, presence of cross-β sheet structure, and typical dimensions found in electron microscopy. p16INK4A amyloid formation abolishes its function as a CDK4/6 inhibitor. Collectively, these observations mechanistically link the cellular redox state to the inactivation of p16INK4A through the formation of amyloid fibrils.