Miracle-dz/UniFAR-FTUs huggingface dataset:
Perceived Duration: The Interplay of Top-Down Attention and Task-Relevant Information

Perception of time is susceptible to distortions; among other factors, it has been suggested that the perceived duration of a stimulus is affected by the observer’s expectations. It has been hypothesized that the duration of an oddball stimulus is overestimated because it is unexpected, whereas repeated stimuli have a shorter perceived duration because they are expected. However, recent findings suggest instead that fulfilled expectations about a stimulus elicit an increase in perceived duration, and that the oddball effect occurs because the oddball is a target stimulus, not because it is unexpected. Therefore, it has been suggested that top-down attention is sometimes sufficient to explain this effect, and sometimes only necessary, with an additional contribution from saliency. However, how the expectedness of a target stimulus and its salient features affect its perceived duration is still an open question. In the present study, participants’ expectations about and the saliency of target stimuli were orthogonally manipulated with stimuli presented on a short (Experiment 1) or long (Experiment 2) temporal scale. Four repetitive standard stimuli preceded each target stimulus in a task in which participants judged whether the target was longer or shorter in duration than the standards. Engagement of top-down attention to target stimuli increased their perceived duration to the same extent irrespective of their expectedness. A small but significant additional contribution to this effect from the saliency of target stimuli was dependent on the temporal scale of stimulus presentation. In Experiment 1, saliency only significantly increased perceived duration in the case of expected target stimuli. In contrast, in Experiment 2, saliency exerted a significant effect on the overestimation elicited by unexpected target stimuli, but the contribution of this variable was eliminated in the case of expected target stimuli. These findings point to top-down attention as the primary cognitive mechanism underlying the perceptual extraction and processing of task-relevant information, which may be strongly correlated with perceived duration. Furthermore, the scalar properties of timing were observed, favoring the pacemaker-accumulator model of timing as the underlying timing mechanism.
webCEMiTool: Co-expression Modular Analysis Made Easy

Co-expression analysis has been widely used to elucidate the functional architecture of genes under different biological processes. Such analysis, however, requires substantial knowledge about programming languages and/or bioinformatics skills. We present webCEMiTool,1 a unique online tool that performs comprehensive modular analyses in a fully automated manner. The webCEMiTool not only identifies co-expression gene modules but also performs several functional analyses on them. In addition, webCEMiTool integrates transcriptomic data with interactome information (i.e., protein-protein interactions) and identifies potential hubs on each network. The tool generates user-friendly html reports that allow users to search for specific genes in each module, as well as check if a module contains genes overrepresented in specific pathways or altered in a specific sample phenotype. We used webCEMiTool to perform a modular analysis of single-cell RNA-seq data of human cells infected with either Zika virus or dengue virus.
The Effects of Body Mass on Immune Cell Concentrations of Mammals

Theory predicts that body mass should affect the way organisms evolve and use immune defenses. We investigated the relationship between body mass and blood neutrophil and lymphocyte concentrations among more than 250 terrestrial mammalian species. We tested whether existing theories (e.g., protecton theory, immune system complexity, and rate of metabolism) accurately predicted the scaling of immune cell concentrations. We also evaluated the predictive power of body mass for these leukocyte concentrations compared to sociality, diet, life history, and phylogenetic relatedness. Phylogeny explained >70% of variation in both lymphocytes and neutrophils, and body mass appeared more informative than other interspecific trait variation. In the best-fit mass-only model, neutrophils scaled hypermetrically (b=0.11) with body mass, whereas lymphocytes scaled just shallow of isometrically. Extrapolating to total cell numbers, this exponent means that an African elephant circulates 13.3 million times the neutrophils of a house mouse, whereas their masses differ by only 250,000-fold. We hypothesize that such high neutrophil numbers might offset the (i) higher overall parasite exposure that large animals face and/or (ii) the higher relative replication capacities of pathogens to host cells.
Müzik Öğretmenliği Lisans Programı Öğrencilerinin Müzik Performans Kaygı Düzeyleri (Ankara-Gazi Üniversitesi Örneği)

Bu calismanin amaci Gazi Universitesi, Muzik Ogretmenligi Ana Bilim Dali ogrencilerinin muzik performans kaygi duzeylerini belirlemektir. Bu amac dogrultusunda, ogrencilerin muzik performans kaygi duzeylerinin negatif performans algisi, psikolojik savunmasizlik, somatik kaygi, kisisel denetim ve fizyolojik savunmasizlik acisindan degerlendirilmesi hedeflenmistir. Arastirma verilerini toplamak amaciyla lisans programinda ogrenim goren 110 ogrenciye ulasilmistir. Veri toplama araci olarak 2004’de Kenny tarafindan gelistirilen ve 2013’te Tokinan tarafindan Turkce’ye uyarlanan “Kenny Muzik Performans Kaygisi Envanteri” kullanilmistir. Envanter 25 maddeden olusmaktadir. Envanterin maddeleri negatif performans algisi, psikolojik savunmasizlik, somatik kaygi, kisisel denetim ve fizyolojik savunmasizlik olarak toplam bes faktorde dagilmaktadir. Verilerin analizi icin ogrencilerin muzik performans kaygisi toplam puanlari ve alt faktorleri toplam puanlari hesaplanmistir. Alt boyutlarin frekans ve yuzde degerleri de ayrica tablolar halinde verilmistir. Arastirma sonucunda Ankara Gazi Universitesi Gazi Egitim Fakultesi Muzik Egitimi Ana Bilim Dali’nda 2016-2017 ogretim yilinda ogrenim gormekte olan ogrencilerin muzik performansi ile ilgili orta duzeyde kaygi duydugu ortaya cikmistir. Alt boyutlar icerisinde kaygi duzeyinin en yuksek goruldugu boyut kisisel denetimdir. Ardindan fizyolojik savunmasizlik alt boyutunda dile getirilmis olunan kas gerginligi ile ortaya cikan kaygi durumu ikinci sirada yer almaktadir. Mesleki muzik egitimi alan ogretmen adaylarinda ortaya cikan muzik performansi icin kaygi durumunda erken mudahalede bulunulmasi onerilmistir.
Mechanisms of Immune Control of Mucosal HSV Infection: A Guide to Rational Vaccine Design

Herpes Simplex Virus (HSV) is a highly prevalent sexually transmitted infection that aside from causing cold sores and genital lesions, causes complications in the immunocompromised and has facilitated a large proportion of HIV acquisition globally. Despite decades of research, there is no prophylactic HSV vaccine ready for use in humans, leaving many questioning whether a prophylactic vaccine is an achievable goal. A previous HSV vaccine trial did have partial success in decreasing acquisition of HSV2–promising evidence that vaccines can prevent acquisition. However, there is still an incomplete understanding of the immune response pathways elicited by HSV after initial mucosal infection and how best to replicate these responses with a vaccine, such that acquisition and colonization of the dorsal root ganglia could be prevented. Another factor to consider in the rational design of an HSV vaccine is adjuvant choice. Understanding the immune responses elicited by different adjuvants and whether lasting humoral and cell-mediated responses are induced is important, especially when studies of past trial vaccines found that a sufficiently protective cell-mediated response was lacking. In this review, we discuss what is known of the immune control involved in initial herpes lesions and reactivation, including the importance of CD4 and CD8 T cells, and the interplay between innate and adaptive immunity in response to primary infection, specifically focusing on the viral relay involved. Additionally, a summary of previous and current vaccine trials, including the components used, immune responses elicited and the feasibility of prophylactic vaccines looking forward, will also be discussed.
Norepinephrine Induces PTSD-Like Memory Impairments via Regulation of the β-Adrenoceptor-cAMP/PKA and CaMK II/PKC Systems in the Basolateral Amygdala

Glucocorticoids (GCs) can modulate the memory enhancement process during stressful events, and this modulation requires arousal-induced norepinephrine (NE) activation in the basolateral amygdale (BLA). Our previous study found that an intrahippocampal infusion of propranolol dose-dependently induced post-traumatic stress disorder (PTSD)-like memory impairments. To explore the role of the noradrenergic system of the BLA in PTSD-like memory impairment, we injected various doses of NE into the BLA. We found that only a specific quantity of NE (0.3 μg) could induce PTSD-like memory impairments, accompanied by a reduction in phosphorylation of GluR1 at Ser845 and Ser831. Moreover, this phenomenon could be blocked by a protein kinase A (PKA) inhibitor or calcium/calmodulin-dependent protein kinase II (CaMK II) inhibitor. These findings demonstrate that NE could induce PTSD-like memory impairments via regulation of the β-adrenoceptor receptor (β-AR)-3′,5′-cyclic monophosphate (cAMP)/PKA and CaMK II/PKC signaling pathways.
Interferometric Observations of Magnetic Fields in Forming Stars

The magnetic field is a key ingredient in the recipe of star formation. Over the past two decades, millimeter and submillimeter interferometers have made major strides in unveiling the role of the magnetic field in star formation at progressively smaller spatial scales. From the kiloparsec scale of molecular clouds down to the inner few hundred au immediately surrounding forming stars, the polarization at millimeter and submillimeter wavelengths is dominated by polarized thermal dust emission, where the dust grains are aligned relative to the magnetic field. Interferometric studies have focused on this dust polarization and occasionally on the polarization of spectral-line emission. We review the current state of the field of magnetized star formation in the context of several questions that continue to motivate the studies of high- and low-mass star formation. By aggregating and analyzing the results from individual studies, we come to several conclusions: (1) Magnetic fields and outflows from low-mass protostellar cores are randomly aligned, suggesting that the magnetic field at ~1000 au scales is not the dominant factor in setting the angular momentum of embedded disks and outflows. (2) Recent measurements of the thermal and dynamic properties in high-mass star-forming regions reveal small virial parameters, challenging the assumption of equilibrium star formation. However, we estimate that a magnetic field strength of a fraction of a mG to several mG in these objects could bring the dense gas close to a state of equilibrium. Finally, (3) We find that the small number of sources with hourglass-shaped magnetic field morphologies at 0.01 -- 0.1 pc scales cannot be explained purely by projection effects, suggesting that while it does occur occasionally, magnetically dominated core collapse is not the predominant mode of low- or high-mass star formation. [Abridged]
Genotyping of Diacylglycerol Acyltransferase 2 Gene in Holstein Cattle Population

This study was conducted to describe the single nucleotide polymorphism (SNPs) within exon 8 and its intron 9 flanking region within bovine Diacylglycerol Acyltransferase 2 (DGAT2) gene and the possible association of these SNPs with the milk productive traits. Blood samples were collected from randomly selected Holstein cattle. Genomic DNA was extracted, and a pair of specific PCR primers was designed to amplify a segment that consists of partial exon 8/partial intron 9 of DGAT2 gene. SSCP experiments were optimized and performed for each amplified PCR fragment. Each set of SSCP resolved bands was sequenced and analyzed. Four SSCP patterns representing four genotypes (BD, BB, CD, and AD) were detected with four alleles. Several novel genetic polymorphisms were discovered. Three SNPs (157 C/A, 158 T/G, and 159 G/A) were found in genotype BD, while one SNP (94 G/T, 153 C/A, 154 T/A) were found in the genotypes BB, CD, and AD, respectively. The only non-synonymous SNP was found in genotype CD (344 D/Y), and the effect of this missense mutation on the protein three-dimensional structure was visualized. The sequence homology between the bovine DGAT2 gene and other species was also analyzed. The significance of the correlation of each genotype with the productive traits of milk was observed. The Holstein cattle with BD genotype produced significantly more milk for all studied 90 days of lactation, with a significant effect on fat for only the last 30 days of lactation, whereas there was no effect on protein and lactose percentage for the entire lactation period. The results suggest a novel association between bovine DGAT2 genetic variability and the milk yield in Holstein cattle. This opens interesting prospects for future DGAT2 based selection programs and preservation strategies.
Carcass traits and meat quality of steers on pasture submitted to different dietary supplementation

This study aimed at evaluating carcass traits and meat quality of Nellore steers on pasture submitted to different dietary supplementation strategies. The 32 Nellore animals tested (8 ± 0.6 months) were raised under rotational grazing on Brachiaria brizantha cv. Piatã (syn. Urochloa brizantha cv. Piatã) pasture and distributed in four treatments: supply of mineral salt ad libitum in the growth and finishing phases (MSGF); concentrate supplementation only during the growth phase (CG); concentrate supplementation only during the finishing phase (CF) and concentrate supplementation the growth and finishing phases (CGF). The concentrated supplement was supplied at 0.5% of body weight and mineral ad libitum. The steers were slaughtered when more than 50% of the lot of each treatment reached 450 kg body weight. The mean the hot and cold carcass weight and subcutaneous fat thickness did not differ between treatments (P > 0.05). The calves the treatment CF and CGF showed a larger rib-eye area and higher ether extract levels in the Longissimus dorsi muscle than in MSGF and CG (P < 0.05). Mean shearing force was similar between treatments (P > 0.05). The use of feeding strategies on pasture with concentrate supplementation in the growth and finishing phases of Nellore cattle anticipates slaughter in 92 days and produces carcasses and meat with satisfactory traits.
Isolation and Molecular Identification of Halophilic Microorganisms from Around Saghand Uranium Mine, Saghand Desert, Iran

Abstract Halophiles are a group of microorganisms found in salty environments such as marine ecosystems, salty meat, salt evaporation ponds, and salt mines. The present study aimed to investigate the diversity of halophilic microorganisms in Saghand Desert (Yazd Province, Iran). To this end, water, soil, and salt crystal samples were taken from Saghand Desert. In order to isolate and culture bacteria and archaea, they were separately inoculated in solid 10% Halophiles Moderate (HM) medium and 23% Modified Growth Medium (MGM). After incubation at 37 °C, all obtained halophilic isolates were analyzed in terms of phenotypic, microscopic, and biochemical characteristics. After eliminating repetitive strains, 26 isolates from each representative sample were selected for DNA extraction and molecular studies. Phylogenetic analysis showed that archaeal isolates belonged to genera Natrinema and Haloarcula and bacterial isolates were from genera Halomonas, Bacillus, Staphylococcus, and Gracilibacillus. The isolation of these genera from many regions of Iran and their enzymatic activity indicate the high biodiversity of these microorganisms in Iran and their potentials for use in biotechnology, which should be considered by industries more seriously.
Investigating the Role of Neuraminidase Activity in the Co-pathogenesis of Mycoplasma gallisepticum and Low Pathogenic Avian Influenza A Virus

The avian pathogen Mycoplasma gallisepticum, the etiologic agent of chronic respiratory disease in chickens, exhibits enhanced pathogenesis in the presence of a co-pathogen such as low-pathogenic avian influenza virus (LPAIV). M. gallisepticum Rlow can utilize α-2,3 linked sialic acids, abundant in the avian respiratory tract, to bind host cells in vitro. To further investigate the intricacies of this co-pathogenesis, chickens were monoor co-infected with either virulent M. gallisepticum strain Rlow, attenuated M. gallisepticum neuraminidase mutant P1C5 and Mycoplasma specific lipoprotein A mutant P1H9, or LPAIV H3N8 (A/duck/Ukraine/1963). These chickens were then assessed for tracheal histopathology, pathogen load, and transcriptomic host response to infection using RNA-sequencing. Chickens co-infected with M. gallisepticum Rlow followed by H3N8 exhibited significantly more severe tracheal lesions and mucosal thickening in response to infection than chickens infected with H3N8 alone. Viral load was also significantly increased in this group over chickens who were infected first with H3N8 and subsequently with M. gallisepticum Rlow. The attenuated M. gallisepticum mutants P1C5 and P1H9, previously shown to be cleared 14 days post-infection, were able to persist 6 to 7 days post-infection in the presence and absence of co-infection Jessica A. Canter, University of Connecticut, 2019 with H3N8. P1H9 was able to persist to 14 days post-infection only in the presence of H3N8. The transcriptional response to monoand co-infection with M. gallisepticum and LPAIV highlighted the involvement of differential expression of genes such as TLR4, TLR15, TLR21, IL-1β, IRF4, MMP1, and MMP9. Pathway and gene ontology analysis of these differentially expressed genes suggests that co-infection with virulent M. gallisepticum and LPAIV induces a downregulation of ciliary activity in vivo and alters the multiple immune-related signaling cascades. Although H3N8 is susceptible to neuraminidase inhibition by oseltamivir in vitro, this antiviral treatment was not effective in vivo at reducing H3N8 load in the trachea of co-infected chickens. These data indicate that the co-pathogenesis of LPAIV and M. gallisepticum is not strictly neuraminidase-dependent and warrants further experimental understanding. Investigating the Role of Neuraminidase Activity in the Co-pathogenesis of Mycoplasma gallisepticum and Low Pathogenic Avian Influenza A Virus
Factors underlying masking release by voice-gender differences and spatial separation cues in multi-talker listening environments in listeners with and without hearing loss

Voice-gender differences and spatial separation are important cues for auditory object segregation. The goal of this study was to investigate the relationship of voice-gender difference benefit to the breadth of binaural pitch fusion, the perceptual integration of dichotic stimuli that evoke different pitches across ears, and the relationship of spatial separation benefit to localization acuity, the ability to identify the direction of a sound source. Twelve bilateral hearing aid (HA) users (age from 30 to 75 years) and eleven normal hearing (NH) listeners (age from 36 to 67 years) were tested in the following three experiments. First, speech-on-speech masking performance was measured as the threshold target-to-masker ratio (TMR) needed to understand a target talker in the presence of either same- or different-gender masker talkers. These target-masker gender combinations were tested with two spatial configurations (maskers co-located or 60° symmetrically spatially separated from the target) in both monaural and binaural listening conditions. Second, binaural pitch fusion range measurements were conducted using harmonic tone complexes around a 200-Hz fundamental frequency. Third, absolute localization acuity was measured using broadband (125–8000 Hz) noise and one-third octave noise bands centered at 500 and 3000 Hz. Voice-gender differences between target and maskers improved TMR thresholds for both listener groups in the binaural condition as well as both monaural (left ear and right ear) conditions, with greater benefit in co-located than spatially separated conditions. Voice-gender difference benefit was correlated with the breadth of binaural pitch fusion in the binaural condition, but not the monaural conditions, ruling out a role of monaural abilities in the relationship between binaural fusion and voice-gender difference benefits. Spatial separation benefit was not significantly correlated with absolute localization acuity. In addition, greater spatial separation benefit was observed in NH listeners than in bilateral HA users, indicating a decreased ability of HA users to benefit from spatial release from masking (SRM). These findings suggest that sharp binaural pitch fusion may be important for maximal speech perception in multi-talker environments for both NH listeners and bilateral HA users.
High-dose vitamin C suppresses the invasion and metastasis of breast cancer cells via inhibiting epithelial-mesenchymal transition

Purpose Vitamin C (VC) is a kind of essential nutrient in the body regarded as a canonical antioxidant during the past hundred years. However, the anti-cancer effect of VC is controversial. Our study is trying to clarify the relationship between VC dosage and breast cancer metastasis. Methods Human breast cancer cell lines Bcap37 and MDA-MB-453 were treated with VC at three different concentrations (low-dose, 0.01 mM; medium-dose, 0.1 mM; high-dose, 2 mM). Wound healing assays were conducted for migration assay; transwell tests were performed to detect the ability of cell invasion. The protein levels were evaluated by Western blot analysis or immunohistochemistry. Tumor xenografts in nude mice were built to test the effects of VC on breast cancer cell proliferation and metastasis. Results 0.01 and 0.1 mM VC promoted cell migration and invasion when compared with the control group, but 2 mM VC significantly suppressed cell migration and invasion of breast cancer cell lines. High-dose VC increased E-cadherin and reduced Vimentin, indicating that high-dose VC suppressed epithelial-mesenchymal transition (EMT) in breast cancer cells. Besides, high-dose VC inhibited cell invasion promoted by TGF-β1 in breast cancer cells. Meanwhile, high-dose VC reversed the suppression of E-cadherin and enhancement of Vimentin induced by TGF-β1 in breast cancer cells. Furthermore, high-dose VC significantly inhibited breast cancer metastasis in vivo. Conclusion High-dose VC inhibits cell migration and invasion of breast cancer cell lines through suppressing EMT. Thus, it may be considered as an anticancer drug candidate for breast cancer patients.