Miracle-dz/UniFAR-FTUs huggingface dataset:
THINGSvision: A Python Toolbox for Streamlining the Extraction of Activations From Deep Neural Networks

Over the past decade, deep neural network (DNN) models have received a lot of attention due to their near-human object classification performance and their excellent prediction of signals recorded from biological visual systems. To better understand the function of these networks and relate them to hypotheses about brain activity and behavior, researchers need to extract the activations to images across different DNN layers. The abundance of different DNN variants, however, can often be unwieldy, and the task of extracting DNN activations from different layers may be non-trivial and error-prone for someone without a strong computational background. Thus, researchers in the fields of cognitive science and computational neuroscience would benefit from a library or package that supports a user in the extraction task. THINGSvision is a new Python module that aims at closing this gap by providing a simple and unified tool for extracting layer activations for a wide range of pretrained and randomly-initialized neural network architectures, even for users with little to no programming experience. We demonstrate the general utility of THINGsvision by relating extracted DNN activations to a number of functional MRI and behavioral datasets using representational similarity analysis, which can be performed as an integral part of the toolbox. Together, THINGSvision enables researchers across diverse fields to extract features in a streamlined manner for their custom image dataset, thereby improving the ease of relating DNNs, brain activity, and behavior, and improving the reproducibility of findings in these research fields.
Bone marrow haemophagocytosis indicates severe infection with severe acute respiratory syndrome coronavirus 2

Haemophagocytosis in the bone marrow of patients who have succumbed to coronavirus disease 19 (COVID‐19) has not been widely studied. The aims of the present study were to perform morphological analyses and morphometry of haemophagocytosis in the bone marrow of patients with severe COVID‐19, and to correlate the findings with the clinical course of the disease.
Light pollution is the fastest growing potential threat to firefly conservation in the Atlantic Forest hotspot

In addition to being threatened by habitat loss derived from deforestation and urbanisation, fireflies are further deeply impacted by light pollution, which impairs their unique use of light signals to communicate and track females. The impact of stressors that can lead to declines in firefly populations is poorly known in the southern hemisphere, including the Atlantic Forest where they are especially diverse, associated with lack of knowledge about their distributions. Here, we model the potential distribution of the tracker ghost firefly Amydetes fastigiata and investigate whether light pollution, urbanisation and deforestation are increasing over time in this area. We found that light pollution is the stressor with the most prominent increase rates over its distribution. Light pollution is significantly increasing in extent and intensity over time, outpassing urbanisation and deforestation which increased at lower rates. Protected areas successfully buffer effects of urbanisation and deforestation, but are incapable to halt the spread of light pollution. Increasing light pollution is especially concerning due to the spotlighting behaviour of A. fastigiata to track females through the night, which is imperilled by overshadowing lights. Light pollution trends are increasing fast and should be considered as a significant stressor even within protected areas – which calls for a reform in regional conservation policies and designation of new areas to be prioritised. We presented a framework for the evaluation of threat rates based on species distribution models that can foster future research and assess vulnerabilities of important species facing global change.
Moths are strongly attracted to ultraviolet and blue radiation

We carried out three choice experiments with 6116 nocturnal lepidopteran individuals (95 species, 7 families, 32 075 counts), each replicated 105 times during the seasons of 2 years. Moths were released indoors at the centre of a 10 × 10 m area with different lamps placed at each corner. In experiment 1, lamps emitted ultraviolet (UV) (peak at 365 nm), blue (450 nm), green (520 nm) or cool white (450 and 520 nm) radiation. In experiment 2, UV was replaced by red (640 nm). In experiment 3, we used UV and three mixed radiation lamps of different emission intensities (365–520 nm). We applied a linear mixed effect model to test for differences in attraction to the light sources. Among all counts, 12.2% (males) and 9.2% (females) were attracted to a lamp. Among the lamp counts, 84% were made at the UV lamp in experiment 1. In experiment 2, 63% of the counts were made at the blue lamp. In experiment 3, most counts were made at the strongest mixed radiation lamp (31%), and the UV lamp (28%). Patterns were generally similar across Lepidopteran families, and for both sexes. Moths are clearly preferentially attracted to short‐wave radiation. Even small quantities of UV radiation, emitted, for example, by metal halide lamps and certain mercury vapour tubes, will disproportionately contribute to light pollution. Since blue light also attracts moths strongly, lamps with a low proportion of blue light should be given priority in lighting planning.
Case Report: Administration of Amniotic Fluid-Derived Nanoparticles in Three Severely Ill COVID-19 Patients

Rationale/Objectives: A human coronavirus (HCoV-19) has caused the novel coronavirus disease (COVID-19) outbreak worldwide. There is an urgent need to develop new interventions to suppress the excessive immune response, protect alveolar function, and repair lung and systemic organ damage. Zofin (previously known as Organicell Flow) is a novel therapeutic that is derived from the soluble and nanoparticle fraction (extracellular vesicles and exosomes) of human amniotic fluid. Here within, we present the clinical outcomes after Zofin treatment in three critically ill patients suffering from severe, multi-organ complications induced by COVID-19 infection. All patients were diagnosed with COVID-19, developed respiratory failure, and were hospitalized for more than 40 days. Methods: Zofin was administered to patients concurrently with ongoing medical care who were monitored for 28-days post-therapy. SOFA score assessment, chest X-rays, and inflammatory biomarker testing was performed. Main Results: There were no adverse events associated with the therapy. The patients showed improvements in ICU clinical status and experienced respiratory improvements. Acute delirium experienced by patients completely resolved and inflammatory biomarkers improved. Conclusions: Primary outcomes demonstrate the therapy was safe, accessible, and feasible. This is the first demonstration of human amniotic fluid-derived nanoparticles as a safe and potentially efficacious therapeutic treatment for respiratory failure induced by COVID-19 infection.
Rescue and Conservation of Male Adult Alpacas (Vicugna pacos) Based on Spermatogonial Stem Cell Biotechnology Using Atomized Black Maca as a Supplement of Cryopreservation Medium

This is the first time that testicular tissue (n = 44) and isolated testicular cells (n = 51) were cryopreserved from alpaca testes 24 h postmortem. For this purpose, internally designed freezing media and cryopreservation protocols were used. Testicular tissue fragments (25 mg) and isolated testicular cells were frozen in MTDB (trehalose and black maca), MTD (trehalose), MSDB (sucrose and black maca), and MSD (sucrose) media. Isolated spermatogonial cells were cryopreserved in two ways, before and after proliferation in vitro. After cryopreservation, the percentage of cell viability in Group 1 (>50% of cell viability) by trypan blue did not show differences within each group (p > 0.05) but showed significant differences when comparing fragments with isolated cells (p < 0.05). Spermatogonial stem cells (SSC) were identified by flow cytometry as strong Dolichos biflorus agglutinin (sDBA) and mitochondrial activity of SSC as strongly positive for MitoSense (sMitoSense+) in intact mitochondria cells, weakly positive for MitoSense (wMitoSense+) in early apoptosis, and necrosis with 7-Aminoactinomycin-D positive (7-AAD). After freezing, in Group 1M (≥30% sMitoSense+), the fragments did not show differences between the media (p > 0.05), but in the isolated cells frozen in MSDB medium, 63.68 ± 8.90% (p < 0.05). In Group 2M (<30% sMitoSense+), necrosis (7AAD+) in MSDB medium was 27.03 ± 5.80%, and necrosis in isolated cells was 14.05 ± 9.3% with significant differences between these groups (p < 0.05); in sMitoSense+, the isolated cells (34.40 ± 23%) had a higher percentage than the fragments (12.4 ± 5.2) (p < 0.05). On the other hand, MSDB and MSD media were significantly higher for isolated cells than for fragments in sDBA+ (p < 0.05). On the other hand, the SSC (sDBA+) had significant differences (p < 0.05) between fresh cells 7.43 ± 1.3% (sDBA+) compared with those cryopreserved in MSDB medium 1.46 ± 0.34% (sDBA+). Additionally, the proliferated and cryopreserved SSC 6.29 ± 1.17% (sDBA+) did not show significant differences concerning the fresh cells (p > 0.05). In conclusion, the black maca showed antioxidant properties when it was included in the freezing medium and, therefore, improved the SSC's conservation of the alpaca. Furthermore, the proliferation of isolated cells in vitro produces a higher amount of SSC after thawing them for further preclinical or clinical work.
Detecting SARS-CoV-2 in the Breath of COVID-19 Patients

In the COVID-19 outbreak year 2020, a consensus was reached on the fact that SARS-CoV-2 spreads through aerosols. However, finding an efficient method to detect viruses in aerosols to monitor the risk of similar infections and enact effective control remains a great challenge. Our study aimed to build a swirling aerosol collection (SAC) device to collect viral particles in exhaled breath and subsequently detect SARS-CoV-2 using reverse transcription polymerase chain reaction (RT-PCR). Laboratory tests of the SAC device using aerosolized SARS-CoV-2 pseudovirus indicated that the SAC device can produce a positive result in only 10 s, with a collection distance to the source of 10 cm in a biosafety chamber, when the release rate of the pseudovirus source was 1,000,000 copies/h. Subsequent clinical trials of the device showed three positives and 14 negatives out of 27 patients in agreement with pharyngeal swabs, and 10 patients obtained opposite results, while no positive results were found in a healthy control group (n = 12). Based on standard curve calibration, several thousand viruses per minute were observed in the tested exhalations. Furthermore, referring to the average tidal volume data of adults, it was estimated that an exhaled SARS-CoV-2 concentration of approximately one copy/mL is detectable for COVID-19 patients. This study validates the original concept of breath detection of SARS-CoV-2 using SAC combined with RT-PCR.
Meaning-Centered Coping in the Era of COVID-19: Direct and Moderating Effects on Depression, Anxiety, and Stress

The COVID-19 pandemic has subjected most of the world’s population to unprecedented situations, like national lockdowns, health hazards, social isolation and economic harm. Such a scenario calls for urgent measures not only to palliate it but also, to better cope with it. According to existential positive psychology, well-being does not simply represent a lack of stress and negative emotions but highlights their importance by incorporating an adaptive relationship with them. Thus, suffering can be mitigated (and transformed into growth) by, among other factors, adopting an attitude of positive reframing, maintaining hope, existential courage, life appreciation, engagement in meaningful activities, and prosociality. The conglomerate of these elements has been recently denominated as meaning-centered coping. In this study, we evaluated the protective role of this type of coping on mental health. A sample of 12,243 participants from 30 countries across all continents completed measures of Meaning-Centered Coping Scale (MCCS), depression, stress, anxiety and stressful COVID-19 related conditions they experienced. Results indicated that meaning-centered coping was strongly associated with diminished symptoms of stress, anxiety, and depression. Moreover, it moderated various relationships between vulnerability factors and markers of psychological distress, especially in the case of depression. These findings call for attention to meaning-centered coping approaches in the context of hardship, such as the current COVID-19 health crisis. In these difficult times, decision-makers and health organizations may integrate these approaches into their guidelines.
Visual Search in 3D: Effects of Monoscopic and Stereoscopic Cues to Depth on the Validity of Feature Integration Theory and Perceptual Load Theory

Previous research has successfully used feature integration theory to operationalise the predictions of Perceptual Load Theory, while simultaneously testing the predictions of both models. Building on this work, we test the extent to which these models hold up in a 3D world. In two experiments, participants responded to a target stimulus within an array of shapes whose apparent depth was manipulated using a combination of monoscopic and stereoscopic cues. The search task was designed to test the predictions of (a) feature integration theory, as the target was identified by a single feature or a conjunction of features and embedded in search arrays of varying size, and (b) perceptual load theory, as the task included congruent and incongruent distractors presented alongside search tasks imposing high or low perceptual load. Findings from both experiments upheld the predictions of feature integration theory, regardless of 2D/3D condition. Longer search times in conditions with a combination of monoscopic and stereoscopic depth cues suggests that binding features into three-dimensional objects requires greater attentional effort. This additional effort should have implications for perceptual load theory, yet our findings did not uphold its predictions; the effect of incongruent distractors did not differ between conjunction search trials (conceptualised as high perceptual load) and feature search trials (low perceptual load). Individual differences in susceptibility to the effects of perceptual load were evident and likely explain the absence of load effects. Overall, our findings suggest that feature integration theory may be useful for predicting attentional performance in a 3D world.
Transcriptome Analysis Identifies Candidate Genes and Signaling Pathways Associated With Feed Efficiency in Xiayan Chicken

Feed efficiency is an important economic factor in poultry production, and the rate of feed efficiency is generally evaluated using residual feed intake (RFI). The molecular regulatory mechanisms of RFI remain unknown. Therefore, the objective of this study was to identify candidate genes and signaling pathways related to RFI using RNA-sequencing for low RFI (LRFI) and high RFI (HRFI) in the Xiayan chicken, a native chicken of the Guangxi province. Chickens were divided into four groups based on FE and sex: LRFI and HRFI for males and females, respectively. We identified a total of 1,015 and 742 differentially expressed genes associated with RFI in males and females, respectively. The 32 and 7 Gene Ontology (GO) enrichment terms, respectively, identified in males and females chiefly involved carbohydrate, amino acid, and energy metabolism. Additionally, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 11 and 5 significantly enriched signaling pathways, including those for nutrient metabolism, insulin signaling, and MAPK signaling, respectively. Protein–protein interaction (PPI) network analysis showed that the pathways involving CAT, ACSL1, ECI2, ABCD2, ACOX1, PCK1, HSPA2, and HSP90AA1 may have an effect on feed efficiency, and these genes are mainly involved in the biological processes of fat metabolism and heat stress. Gene set enrichment analysis indicated that the increased expression of genes in LRFI chickens was related to intestinal microvilli structure and function, and to the fat metabolism process in males. In females, the highly expressed set of genes in the LRFI group was primarily associated with nervous system and cell development. Our findings provide further insight into RFI regulation mechanisms in chickens.
Macroeconomic Uncertainty and Crude Oil Futures Volatility–Evidence from China Crude Oil Futures Market

This paper investigates whether the macroeconomic uncertainty factors can explain and forecast China’s INE crude oil futures market volatility. We use the GARCH-MIDAS model to investigate the explaining and predicting power of the macroeconomic uncertainties. We considered various geopolitical risk (GPR) indices, economic policy uncertainty (EPU) indices, and infectious disease pandemic (IDEMV) indices in our model. The empirical results suggest that the geopolitical risk, the geopolitical act risk, the global economic policy uncertainty, the economic policy uncertainty from the United Kingdom, and the economic policy uncertainty from Japan comprehensively integrate the information contained in the rest factors, and have superior predictive powers for INE crude oil future volatility. These findings highlight the importance of the impact of macroeconomic uncertainty factors has on the crude oil futures market, and indicate that the macroeconomic uncertainties need to be considered when explaining and forecasting crude oil futures market volatility.
The Prognostic Significance of ZNF384 Fusions in Adult Ph-Negative B-Cell Precursor Acute Lymphoblastic Leukemia: A Comprehensive Cohort Study From a Single Chinese Center

Novel recurrent fusion gene types such as zinc finger protein 384 (ZNF384) fusions have been identified in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) with the application of next-generation sequencing technologies. However, the comprehensive large-scale clinical cohort study for clarifying their prognostic significance remains scarce to date. A total of 242 consecutive adult Ph-negative BCP-ALL patients treated in our institute were retrospectively screened ZNF384 fusions at diagnosis by multiplex real time quantitative PCR. ZNF384 fusions were identified in 47 patients (19.4%) and all belonged to B-other ALL (having no high hyperdiploid karyotype, BCR-ABL1, TCF3-PBX1, ETV6-RUNX1, or MLL rearrangement). In the whole cohort, patients with ZNF384 fusions had significantly higher 3-year relapse-free-survival (RFS) and tended to have a higher 3-year overall survival (OS) than those with no ZNF384 fusions (80.1% vs. 52.5%, P = 0.013; 67.6% vs. 54.0%, P = 0.10). For patients receiving chemotherapy alone and received allogeneic-hematologic stem cell transplantation (allo-HSCT) were censored at the time of transplantation, patients with ZNF384 fusions had both similar RFS and similar OS to B-other ALL patients with no ZNF384 fusions (RFS: P =0.94 and 0.30; OS: P =0.94 and 0.51). For patients receiving transplantation, those with ZNF384 fusions had significantly higher 3-year RFS than B-other ALL patients with no ZNF384 fusions and their OS were similar (P = 0.022 and 0.24). Only two of 31 patients with ZNF384 fusions and receiving allo-HSCT relapsed, individually occurred 66.8 and 69.8 months after transplantation. Therefore, ZNF384 fusion is common in adult BCP-ALL, which may define a new group from BCP-ALL containing no classical fusion transcript with better prognosis through receiving allo-HSCT.
Prostac: A New Composite Score With Potential Predictive Value in Prostate Cancer

Prostate cancer (PCa) is the most commonly diagnosed solid organ cancer in men worldwide. Current diagnosis of PCa includes use of initial prostate specific antigen assay which has a high false positive rate, low specificity, and low sensitivity. The side effects of unnecessary prostate biopsies that healthy men are subjected to, often result in unintended health complications. New PCa biomarkers are being discovered to address this unmet need. Here, we report on the creation of a composite score (Prostac) based on three recently discovered PCa biomarkers, Plasmacytoma Variant Translocation 1 (PVT1) exons 4A, 4B, and 9. Statistical analysis of copy numbers derived from a real-time quantitative polymerase chain (qPCR) reaction - based assay, showed these PCa biomarkers to be linearly separable and significantly over expressed in PCa epithelial cells. We train a supervised learning algorithm using support vector machines to generate a classification hyperplane from which a user-friendly composite score is developed. Cross validation of Prostac using data from prostate epithelial cells (RWPE1) and PCa cells (MDA PCa 2b) accurately classified 100% of PCa cells. Creation of the Prostac score lays the groundwork for clinical trial of its use in PCa diagnosis.
A Novel c-MET-Targeting Antibody-Drug Conjugate for Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer-associated death in the United States and has a 5-year survival rate of <4%. Although much effort has been invested in the research and development of pancreatic cancer drugs over the past 30 years, due to the lack of effective targetable carcinogenic drivers, no new targeted therapies that can improve patient prognosis have been approved for clinical use. SHR-A1403 is a new c-mesenchymal-epithelial transition factor (c-MET) antibody-drug conjugate that can be used for the targeted treatment of PDAC with high c-MET expression. This study reports for the first time the application prospects of SHR-A1403 in preclinical models of PDAC. SHR-A1403 significantly inhibited the proliferation, migration, and invasion of pancreatic cancer cells and induced cell cycle arrest and apoptosis. These changes were caused by inhibition of intracellular cholesterol biosynthesis by SHR-A1403. Therefore, targeting c-MET through SHR-A1403 showed strong preclinical anti-tumour efficacy in pancreatic cancer. Our work suggests the potential application of c-MET-targeted antibody-drug conjugate treatment for PDAC in clinical practise.
Interannual Nearshore Habitat Use of Young of the Year White Sharks Off Southern California

Young-of-the-year (YOY) and juvenile-stage white sharks may use southern California nearshore beach habitats more extensively than previously known, within meters of some of the most heavily used beaches in the world. Such knowledge forms a critical component of species management and conservation plans, in addition to public safety and risk mitigation planning. We used data derived from a combination of satellite tag locations (13 animals over 3 years) and passive acoustic monitoring (34 animals over 8 years) to examine the occurrence, relative abundance, and residency patterns of YOY white sharks in southern California waters. Our results suggest that southern California contains spatiotemporally dynamic centers of primary nursery habitat. Tagged YOY white sharks formed loose aggregations at “hotspot” locations that were interannually variable, where individuals exhibited temporal fidelity, higher levels of residency, and spatially restricted movements, with multiple YOY individuals simultaneously displaying this behavior. While models of biotic and abiotic variables suggested relative abundance of tagged sharks may be predicted by sea surface temperature, salinity and productivity (chlorophyll-A), these predictors were not consistent across all years of the study. Thus, novel approaches that incorporate technologies to derive high resolution environmental data, paired with more comprehensive telemetry datasets are therefore required to better understand the extrinsic factors that drive habitat selection and residency patterns in juvenile white sharks.