Miracle-dz/UniFAR-FTUs huggingface dataset:
Single Amino Acids G196 and R198 in hr1 of Subgroup K Avian Leukosis Virus Glycoprotein Are Critical for Tva Receptor Binding

Avian leukosis viruses (ALVs), a type of retrovirus responsible for various tumor diseases in chickens, are divided into 11 subgroups: ALV-A to ALV-K. After the envelope glycoproteins of ALV interact with the cellular receptor to initiate viral invasion, alterations in a few amino acids of the viral glycoproteins or cell receptors may trigger changes in their conformation and binding affinity. To identify the functional determinants of the ALV-K envelope protein that binds to Tva (a recently identified cellular receptor of ALV-K), using the strategy of continuous, segment-by-segment substitution of the gp85-encoded surface glycoprotein (SU) of ALV-K GDFX0602 with ALV-E ev-1 (using Tvb as the receptor), a series of chimeric soluble gp85 proteins were expressed for co-immunoprecipitation (co-IP) analysis and a series of recombinant viruses with replication-competent avian retrovirus vectors containing Bryan polymerase (RCASBP) as their skeleton were created for transfecting to DF-1 cells and titer determination. The co-IP analysis, fluorescence-activated cell sorting, and virus titer measurements revealed that the substitution of residues 194–198, 206–216 of hr1, residues 251–256 between hr1 and hr2, and residues 269–280 of hr2 were identified to reduce the binding of gp85 to Tva. The substitution of residues 194–221 in hr1 nullified the infectiveness of these viruses, similar to the effect of single amino acid mutations in K251E and L252I located between hr1 and hr2; continuous amino acid mutations in hr2 could not produce the same effect despite reducing their infectiveness. Finally, single amino acid mutations G196A and R198H nearly abolished the binding of gp85 to Tva and nullified the infectiveness of these viruses to DF-1. This study paves the way for exploring the molecular mechanisms of the binding of Tva to ALV-K SU.
Coastal Image Captioning

ABSTRACT Yang, Q. ; Wang, G. ; Zhang, X. ; Grecos, C. , and Ren, P., 2020. Coastal image captioning. In: Jung, H. -S. ; Lee, S. ; Ryu, J.-H. , and Cui, T. (eds.), Advances in Geospatial Research of Coastal Environments. Journal of Coastal Research, Special Issue No. 102, pp. 145-150. Coconut Creek (Florida), ISSN 0749-0208. Coastal images convey immense semantic information of the corresponding coastal areas. This article presents a preliminary approach to coastal image captioning that describes salient semantic information of coastal images with accurate and meaningful sentences. Specifically, this article exploits a state-of-the-art method referred to as self-critical sequence training for coastal image captioning. Firstly, a convolutional neural network (CNN) produces fixed-length features from the coastal images. Secondly, the fixed-length features are fed into a long short-term memory (LSTM) to generate captions, i.e., the accurate and meaningful sentences. Finally, the LSTM is optimized in the context of reinforcement learning. Experimental evaluation on the Moye island remote sensing dataset validates the effectiveness.
Using The Cancer Genome Atlas as an Inquiry Tool in the Undergraduate Classroom

Undergraduate students in the biomedical sciences are often interested in future health-focused careers. This presents opportunities for instructors in genetics, molecular biology, and cancer biology to capture their attention using lab experiences built around clinically relevant data. As biomedical science in general becomes increasingly dependent on high-throughput data, well-established scientific databases such as The Cancer Genome Atlas (TCGA) have become publicly available tools for medically relevant inquiry. The best feature of this database is that it bridges the molecular features of cancer to human clinical outcomes—allowing students to see a direct connection between the molecular sciences and their future professions. We have developed and tested a learning module that leverages the power of TCGA datasets to engage students to use the data to generate and test hypotheses and to apply statistical tests to evaluate significance.
art.pics Database: An Open Access Database for Art Stimuli for Experimental Research

While art is omnipresent in human history, the neural mechanisms of how we perceive, value and differentiate art has only begun to be explored. Functional magnetic resonance imaging (fMRI) studies suggested that art acts as secondary reward, involving brain activity in the ventral striatum and prefrontal cortices similar to primary rewards such as food. However, potential similarities or unique characteristics of art-related neuroscience (or neuroesthetics) remain elusive, also because of a lack of adequate experimental tools: the available collections of art stimuli often lack standard image definitions and normative ratings. Therefore, we here provide a large set of well-characterized, novel art images for use as visual stimuli in psychological and neuroimaging research. The stimuli were created using a deep learning algorithm that applied different styles of popular paintings (based on artists such as Klimt or Hundertwasser) on ordinary animal, plant and object images which were drawn from established visual stimuli databases. The novel stimuli represent mundane items with artistic properties with proposed reduced dimensionality and complexity compared to paintings. In total, 2,332 novel stimuli are available open access as “art.pics” database at https://osf.io/BTWNQ/ with standard image characteristics that are comparable to other common visual stimuli material in terms of size, variable color distribution, complexity, intensity and valence, measured by image software analysis and by ratings derived from a human experimental validation study [n = 1,296 (684f), age 30.2 ± 8.8 y.o. ]. The experimental validation study further showed that the art.pics elicit a broad and significantly different variation in subjective value ratings (i.e., liking and wanting) as well as in recognizability, arousal and valence across different art styles and categories. Researchers are encouraged to study the perception, processing and valuation of art images based on the art.pics database which also enables real reward remuneration of the rated stimuli (as art prints) and a direct comparison to other rewards from e.g., food or money. Key Messages: We provide an open access, validated and large set of novel stimuli (n = 2,332) of standardized art images including normative rating data to be used for experimental research. Reward remuneration in experimental settings can be easily implemented for the art.pics by e.g., handing out the stimuli to the participants (as print on premium paper or in a digital format), as done in the presented validation task. Experimental validation showed that the art.pics’ images elicit a broad and significantly different variation in subjective value ratings (i.e., liking, wanting) across different art styles and categories, while size, color and complexity characteristics remained comparable to other visual stimuli databases.
Rumen-Reticular Temperature During Estrus and Ovulation Using Automated Activity Monitors in Dairy Cows

This study aimed to determine changes in rumen-reticular temperature (RRT) at estrus or ovulation and determine if these changes are associated with the intensity of estrous expression. Cows were equipped with an automated activity monitor (AAM) and a rumen-reticular bolus thermometer. A total of 190 estrus episodes were used where physical activity data was recorded using the AAM and ovulation was determined via ultrasonography of the ovaries at alert and twice daily, for a maximum of 60 h. Estrous expression was assessed using the maximum activity and duration in which activity remained above the AAM threshold; both characteristics were categorized using the median. Temperature data was collected for the duration of estrus, as well as for the interval of time where ovulation was determined to occur. Three measures of temperature were calculated: (1) positive area under the curve (AUC), (2) maximum positive temperature change (PTC), (3) maximum negative temperature change (NTC) at estrus (AUCE/ PTCE/ NTCE) and around ovulation (AUCO/PTCO/ NTCO). Both AUC and PTC were greater during estrus than around ovulation (2.7 ± 0.2 and 1.1 ± 0.3°C2 for AUCE and AUCO; 0.55 ± 0.03 and 0.26 ± 0.04°C for PTCE and PTCO, respectively). In contrast, NTC was lower around ovulation than estrus (−0.28 ± 0.05 and −0.60 ± 0.06°C for NTCE and NTCO). Cows with greater estrous expression had greater AUC and PTC during estrus than around ovulation, but cows with lesser estrous expression had similar AUC and PTC. Increases in AUC [High THI (Temperature Humidity Index): High activity: 4.7 ± 0.5, Low activity: 1.5 ± 0.4; Low THI: High activity: 3.1 ± 0.2, Low activity: 1.4 ± 0.2 °C2] and PTC (High THI: High activity: 0.79 ± 0.08, Low activity: 0.36 ± 0.07; Low THI: High activity: 0.60 ± 0.04, Low activity: 0.47 ± 0.04°C) associated with estrous expression were found to be greater on days with higher THI. Alerts created using standard deviations from the mean were unable to detect estrus or ovulation with acceptable precision. Further research is required to determine how changes in RRT can be used successfully to predict estrus and ovulation.
CdSe tetrapod synthesis using cetyltrimethylammonium bromide and heat transfer fluids

The synthesis of CdSe tetrapod-shaped quantum dots using phenyl-based heat transfer fluids as inexpensive alternatives to octadecene solvent was studied. The CdSe tetrapods were synthesized using the hot-injection method, in which the trioctylphosphine selenide precursor and the shape-inducing cetyltrimethylammonium bromide surfactant were injected into a cadmium oleate-containing solvent at 190 °C. At a synthesis temperature of 160 °C, the resulting quantum dot particles were found to grow more slowly in heat transfer fluids and pure phenyl-type solvents than in octadecene. With synthesis time, the selectivity to tetrapods increased, and the arms grew proportionally in width and length. The use of heat transfer fluids provides a convenient means to control growth of shaped nanoparticles.
My Brain Needs a Break: Kindergarteners’ Willpower Theories Are Related to Behavioral Self-Regulation

Is the way that kindergarteners view their willpower – as a limited or as a non-limited resource – related to their motivation and behavioral self-regulation? This study is the first to examine the structure of beliefs about willpower in relation to behavioral self-regulation by interviewing 147 kindergarteners (52% girls) aged 5 to 7 years (M = 6.47, SD = 0.39). A new instrument was developed to assess implicit theories about willpower for this specific age group. Results indicated that kindergarteners who think of their willpower as a non-limited resource showed better behavioral self-regulation than children who adopted a more limited theory, even when controlling for age and gender. This relation was especially pronounced in low achieving children. Mediation and moderation analyses showed that this relation was partly mediated through the children’s willingness to invest effort to reach a learning goal. Findings suggest that fostering metacognitive beliefs in children, such as the belief that willpower is a non-limited resource, may increase behavioral self-regulation for successful adjustment to the demands of kindergarten and school.
Electrophysiological Profile Remodeling via Selective Suppression of Voltage-Gated Currents by CLN1/PPT1 Overexpression in Human Neuronal-Like Cells

CLN1 disease (OMIM #256730) is an inherited neurological disorder of early childhood with epileptic seizures and premature death. It is associated with mutations in CLN1 coding for Palmitoyl-Protein Thioesterase 1 (PPT1), a lysosomal enzyme which affects the recycling and degradation of lipid-modified (S-acylated) proteins by removing palmitate residues. Transcriptomic evidence from a neuronal-like cellular model derived from differentiated SH-SY5Y cells disclosed the potential negative roles of CLN1 overexpression, affecting the elongation of neuronal processes and the expression of selected proteins of the synaptic region. Bioinformatic inquiries of transcriptomic data pinpointed a dysregulated expression of several genes coding for proteins related to voltage-gated ion channels, including subunits of calcium and potassium channels (VGCC and VGKC). In SH-SY5Y cells overexpressing CLN1 (SH-CLN1 cells), the resting potential and the membrane conductance in the range of voltages close to the resting potential were not affected. However, patch-clamp recordings indicated a reduction of Ba2+ currents through VGCC of SH-CLN1 cells; Ca2+ imaging revealed reduced Ca2+ influx in the same cellular setting. The results of the biochemical and morphological investigations of CACNA2D2/α2δ-2, an accessory subunit of VGCC, were in accordance with the downregulation of the corresponding gene and consistent with the hypothesis that a lower number of functional channels may reach the plasma membrane. The combined use of 4-AP and NS-1643, two drugs with opposing effects on Kv11 and Kv12 subfamilies of VGKC coded by the KCNH gene family, provides evidence for reduced functional Kv12 channels in SH-CLN1 cells, consistent with transcriptomic data indicating the downregulation of KCNH4. The lack of compelling evidence supporting the palmitoylation of many ion channels subunits investigated in this study stimulates inquiries about the role of PPT1 in the trafficking of channels to the plasma membrane. Altogether, these results indicate a reduction of functional voltage-gated ion channels in response to CLN1/PPT1 overexpression in differentiated SH-SY5Y cells and provide new insights into the altered neuronal excitability which may underlie the severe epileptic phenotype of CLN1 disease. It remains to be shown if remodeling of such functional channels on plasma membrane can occur as a downstream effect of CLN1 disease.
Electrospun PCL/PLA Scaffolds Are More Suitable Carriers of Placental Mesenchymal Stromal Cells Than Collagen/Elastin Scaffolds and Prevent Wound Contraction in a Mouse Model of Wound Healing

Mesenchymal stem/stromal cells (MSCs) exert beneficial effects during wound healing, and cell-seeded scaffolds are a promising method of application. Here, we compared the suitability of a clinically used collagen/elastin scaffold (Matriderm) with an electrospun Poly(ε-caprolactone)/poly(l-lactide) (PCL/PLA) scaffold as carriers for human amnion-derived MSCs (hAMSCs). We created an epidermal-like PCL/PLA scaffold and evaluated its microstructural, mechanical, and functional properties. Sequential spinning of different PCL/PLA concentrations resulted in a wide-meshed layer designed for cell-seeding and a dense-meshed layer for apical protection. The Matriderm and PCL/PLA scaffolds then were seeded with hAMSCs, with or without Matrigel coating. The quantity and quality of the adherent cells were evaluated in vitro. The results showed that hAMSCs adhered to and infiltrated both scaffold types but on day 3, more cells were observed on PCL/PLA than on Matriderm. Apoptosis and proliferation rates were similar for all carriers except the coated Matriderm, where apoptotic cells were significantly enhanced. On day 8, the number of cells decreased on all carrier types except the coated Matriderm, which had consistently low cell numbers. Uncoated Matriderm had the highest percentage of proliferative cells and lowest apoptosis rate of all carrier types. Each carrier also was topically applied to skin wound sites in a mouse model and analyzed in vivo over 14 days via optical imaging and histological methods, which showed detectable hAMSCs on all carrier types on day 8. On day 14, all wounds exhibited newly formed epidermis, and all carriers were well-integrated into the underlying dermis and showing signs of degradation. However, only wounds treated with uncoated PCL/PLA maintained a round appearance with minimal contraction. Overall, the results support a 3-day in vitro culture of scaffolds with hAMSCs before wound application. The PCL/PLA scaffold showed higher cell adherence than Matriderm, and the effect of the Matrigel coating was negligible, as all carrier types maintained sufficient numbers of transplanted cells in the wound area. The anti-contractive effects of the PCL/PLA scaffold offer potential new therapeutic approaches to wound care.
Test–Retest Reliability of Magnetoencephalography Resting-State Functional Connectivity in Schizophrenia

The reliability of magnetoencephalography (MEG) resting-state functional connectivity in schizophrenia (SZ) is unknown as previous research has focused on healthy controls (HC). Here, we examined reliability in 26 participants (13-SZ, 13-HC). Eyes opened and eyes closed resting-state data were collected on 4 separate occasions during 2 visits, 1 week apart. For source modeling, we used minimum norm software to apply dynamic statistical parametric mapping. Source analyses compared the following functional connectivity metrics from each data run: coherence (coh), imaginary coherence (imcoh), pairwise phase consistency (ppc), phase-locking value (plv), phase lag index (pli), weighted phase lag index (wpli), and weighted phase lag index debiased (wpli2). Intraclass correlation coefficients (ICCs) were calculated for whole brain, network, and network pair averages. For reliability, ICCs above 0.75 = excellent, above 0.60 = good, above 0.40 = fair, and below 0.40 = poor reliability. We found the reliability of these metrics varied greatly depending on frequency band, network, network pair, and participant group examined. Broadband (1–58 Hz) whole brain averages in both HC and SZ showed excellent reliability for wpli2, and good to fair reliability for ppc, plv, and coh. Broadband network averages showed excellent to good reliability across 1 hour and 1 week for coh, imcoh, ppc, plv, wpli within default mode, cognitive control, and visual networks in HC, while the same metrics had excellent to fair reliability in SZ. Regional network pair averages showed good to fair reliability for coh, ppc, plv within default mode, cognitive control and visual network pairs in HC and SZ. In general, HC had higher reliability compared to SZ, and the default mode, cognitive control, and visual networks had higher reliability compared to somatosensory and auditory networks. Similar reliability levels occurred for both eyes opened and eyes closed resting-states for most metrics. The functional connectivity metrics of coh, ppc, and plv performed best across 1 hour and 1 week in HC and SZ. We also found that SZ had reduced coh, plv, and ppc in the dmn average and pair values indicating dysconnectivity in SZ. These findings encourage collecting both eyes opened and eyes closed resting-state MEG, while demonstrating that clinical populations may differ in reliability.
A Novel G542X CFTR Rat Model of Cystic Fibrosis Is Sensitive to Nonsense Mediated Decay

Nonsense mutations that lead to the insertion of a premature termination codon (PTC) in the cystic fibrosis transmembrane conductance regulator (CFTR) transcript affect 11% of patients with cystic fibrosis (CF) worldwide and are associated with severe disease phenotype. While CF rat models have contributed significantly to our understanding of CF disease pathogenesis, there are currently no rat models available for studying CF nonsense mutations. Here we created and characterized the first homozygous CF rat model that bears the CFTR G542X nonsense mutation in the endogenous locus using CRISPR/Cas9 gene editing. In addition to displaying severe CF manifestations and developmental defects such as reduced growth, abnormal tooth enamel, and intestinal obstruction, CFTR G542X knockin rats demonstrated an absence of CFTR function in tracheal and intestinal sections as assessed by nasal potential difference and transepithelial short-circuit current measurements. Reduced CFTR mRNA levels in the model further suggested sensitivity to nonsense-mediated decay, a pathway elicited by the presence of PTCs that degrades the PTC-bearing transcripts and thus further diminishes the level of CFTR protein. Although functional restoration of CFTR was observed in G542X rat tracheal epithelial cells in response to single readthrough agent therapy, therapeutic efficacy was not observed in G542X knockin rats in vivo. The G542X rat model provides an invaluable tool for the identification and in vivo validation of potential therapies for CFTR nonsense mutations.
High‐Throughput Fabrication of Uniform and Homogenous MOF Coatings

We describe a novel method to produce monolithic, oriented, crystalline and highly porous coatings on solid substrates. By adopting the recently described liquid‐phase epitaxy (LPE) process developed to grow metal‐organic framework coatings (MOFs) on modified Au‐substrates to the spray method, we have prepared thick (μm) layers of several MOF types on modified Au‐substrates, including HKUST‐I and layer‐pillar MOFs. The spray method not only allows such SURMOFs to be grown much faster than with the LPE‐process but the dependence of layer thickness on the number of immersion cycles also provides valuable insights into the mechanism governing the layer‐by‐layer MOF formation process.
Selective Growth of Calcium Molybdate Whiskers by Rapid Cooling of a Sodium Chloride Flux

Long whiskers of calcium molybdate (CaMoO4) were selectively grown by rapid cooling of a NaCl flux. The crystal growth of CaMoO4 was conducted by heating a mixture of solute and flux at 900 °C for 10 h and then cooling to 500 °C at a rate of 270 °C·h-1 or quenching in a furnace with the electric power turned off. The obtained whiskers were colorless and transparent. Transmission electron microscopy images showed that the grown whiskers were of a very good crystallinity. The major constituents were homogeneously distributed throughout the whiskers. Sodium and chlorine atoms from the flux were not detected. Whiskers grown from the solutions were up to 5.2 mm long and 7 μm in diameter. The whiskers were cylindrical in shape with average aspect ratios ranging from 150 to 750, and they elongated dominantly in the 〈110〉 directions.