Miracle-dz/UniFAR-FTUs huggingface dataset:
Tree recruitment is determined by stand structure and shade tolerance with uncertain role of climate and water relations

Abstract Tree regeneration is a key process for long‐term forest dynamics, determining changes in species composition and shaping successional trajectories. While tree regeneration is a highly stochastic process, tree regeneration studies often cover narrow environmental gradients only, focusing on specific forest types or species in distinct regions. Thus, the larger‐scale effects of temperature, water availability, and stand structure on tree regeneration are poorly understood. We investigated these effects in respect of tree recruitment (in‐growth) along wide environmental gradients using forest inventory data from Flanders (Belgium), northwestern Germany, and Switzerland covering more than 40 tree species. We employed generalized linear mixed models to capture the abundance of tree recruitment in response to basal area, stem density, shade casting ability of a forest stand as well as site‐specific degree‐day sum (temperature), water balance, and plant‐available water holding capacity. We grouped tree species to facilitate comparisons between species with different levels of tolerance to shade and drought. Basal area and shade casting ability of the overstory had generally a negative impact on tree recruitment, but the effects differed between levels of shade tolerance of tree recruitment in all study regions. Recruitment rates of very shade‐tolerant species were positively affected by shade casting ability. Stem density and summer warmth (degree‐day sum) had similar effects on all tree species and successional strategies. Water‐related variables revealed a high degree of uncertainty and did not allow for general conclusions. All variables had similar effects independent of the varying diameter thresholds for tree recruitment in the different data sets. Synthesis: Shade tolerance and stand structure are the main drivers of tree recruitment along wide environmental gradients in temperate forests. Higher temperature generally increases tree recruitment rates, but the role of water relations and drought tolerance remains uncertain for tree recruitment on cross‐regional scales.
Monocytes Contribute to IFN-β Production via the MyD88-Dependent Pathway and Cytotoxic T-Cell Responses against Mucosal Respiratory Syncytial Virus Infection

Respiratory syncytial virus (RSV) is the leading cause of respiratory viral infection in infants and children. However, little is known about the contribution of monocytes to antiviral responses against RSV infection. We identified the IFN-β production of monocytes using IFN-β/YFP reporter mice. The kinetic analysis of IFN-β-producing cells in in vivo RSV-infected lung cells indicated that monocytes are recruited to the inflamed lung during the early phase of infection. These cells produced IFN-β via the myeloid differentiation factor 88-mediated pathway, rather than the TLR7- or mitochondrial antiviral signaling protein-mediated pathway. In addition, monocyte-ablated mice exhibited decreased numbers of IFN-γ-producing and RSV Ag-specific CD8+ T cells. Collectively, these data indicate that monocytes play pivotal roles in cytotoxic T-cell responses and act as type I IFN producers during RSV infection.
Comparing of two dimensional and three dimensional fully convolutional networks for radiotherapy dose prediction in left-sided breast cancer

Fully convolutional networks were developed for predicting optimal dose distributions for patients with left-sided breast cancer and compared the prediction accuracy between two-dimensional and three-dimensional networks. Sixty cases treated with volumetric modulated arc radiotherapy were analyzed. Among them, 50 cases were randomly chosen to conform the training set, and the remaining 10 were to construct the test set. Two U-Net fully convolutional networks predicted the dose distributions, with two-dimensional and three-dimensional convolution kernels, respectively. Computed tomography images, delineated regions of interest, or their combination were considered as input data. The accuracy of predicted results was evaluated against the clinical dose. Most types of input data retrieved a similar dose to the ground truth for organs at risk (p > 0.05). Overall, the two-dimensional model had higher performance than the three-dimensional model (p < 0.05). Moreover, the two-dimensional region of interest input provided the best prediction results regarding the planning target volume mean percentage difference (2.40 ± 0.18%), heart mean percentage difference (4.28 ± 2.02%), and the gamma index at 80% of the prescription dose are with tolerances of 3 mm and 3% (0.85 ± 0.03), whereas the two-dimensional combined input provided the best prediction regarding ipsilateral lung mean percentage difference (4.16 ± 1.48%), lung mean percentage difference (2.41 ± 0.95%), spinal cord mean percentage difference (0.67 ± 0.40%), and 80% Dice similarity coefficient (0.94 ± 0.01). Statistically, the two-dimensional combined inputs achieved higher prediction accuracy regarding 80% Dice similarity coefficient than the two-dimensional region of interest input (0.94 ± 0.01 vs 0.92 ± 0.01, p < 0.05). The two-dimensional data model retrieves higher performance than its three-dimensional counterpart for dose prediction, especially when using region of interest and combined inputs.
Multilevel profiling of situation and dialogue-based deep networks for movie genre classification using movie trailers

Automated movie genre classification has emerged as an active and essential area of research and exploration. Short duration movie trailers provide useful insights about the movie as video content consists of the cognitive and the affective level features. Previous approaches were focused upon either cognitive or affective content analysis. In this paper, we propose a novel multi-modality: situation, dialogue, and metadata-based movie genre classification framework that takes both cognition and affect-based features into consideration. A pre-features fusion-based framework that takes into account: situation-based features from a regular snapshot of a trailer that includes nouns and verbs providing the useful affect-based mapping with the corresponding genres, dialogue (speech) based feature from audio, metadata which together provides the relevant information for cognitive and affect based video analysis. We also develop the English movie trailer dataset (EMTD), which contains 2000 Hollywood movie trailers belonging to five popular genres: Action, Romance, Comedy, Horror, and Science Fiction, and perform cross-validation on the standard LMTD-9 dataset for validating the proposed framework. The results demonstrate that the proposed methodology for movie genre classification has performed excellently as depicted by the F1 scores, precision, recall, and area under the precision-recall curves.
Just What do You Think You're Doing, Dave?' A Checklist for Responsible Data Use in NLP

A key part of the NLP ethics movement is responsible use of data, but exactly what that means or how it can be best achieved remain unclear. This position paper discusses the core legal and ethical principles for collection and sharing of textual data, and the tensions between them. We propose a potential checklist for responsible data (re-)use that could both standardise the peer review of conference submissions, as well as enable a more in-depth view of published research across the community. Our proposal aims to contribute to the development of a consistent standard for data (re-)use, embraced across NLP conferences.
Habitat‐linked genetic structure for white‐crowned sparrow (Zonotrichia leucophrys): Local factors shape population genetic structure

Abstract Ecological, environmental, and geographic factors all influence genetic structure. Species with broad distributions are ideal systems because they cover a range of ecological and environmental conditions allowing us to test which components predict genetic structure. This study presents a novel, broad geographic approach using molecular markers, morphology, and habitat modeling to investigate rangewide and local barriers causing contemporary genetic differentiation within the geographical range of three white‐crowned sparrow (Zonotrichia leucophrys) subspecies: Z. l. gambelii, Z. l. oriantha, and Z. l. pugetensis. Three types of genetic markers showed geographic distance between sampling sites, elevation, and ecosystem type are key factors contributing to population genetic structure. Microsatellite markers revealed white‐crowned sparrows do not group by subspecies, but instead indicated four groupings at a rangewide scale and two groupings based on coniferous and deciduous ecosystems at a local scale. Our analyses of morphological variation also revealed habitat differences; sparrows from deciduous ecosystems are larger than individuals from coniferous ecosystems based on principal component analyses. Habitat modeling showed isolation by distance was prevalent in describing genetic structure, but isolation by resistance also had a small but significant influence. Not only do these findings have implications concerning the accuracy of subspecies delineations, they also highlight the critical role of local factors such as habitat in shaping contemporary population genetic structure of species with high dispersal ability.
Pore-Forming Toxins During Bacterial Infection: Molecular Mechanisms and Potential Therapeutic Targets

Abstract Bacterial infections are predominantly treated with antibiotics, and resistance to antibiotics is becoming an increasing threat to our health. Pore-forming toxins (PFTs) are virulence factors secreted by many pathogenic bacterial strains, both in acute and chronic infections. They are special membrane-targeting proteins that exert toxic effects by forming pores in the cell membrane. Recent studies have elucidated the structure of PFTs and the detailed molecular mechanisms of their pathogenicity. Here, we discuss recent findings that highlight the regulatory mechanisms and important roles of two types of PFTs, α-PFTs and β-PFTs, in mediating the virulence of bacteria, and the therapeutic potential of targeting PFTs for antibacterial treatment. Therapeutic strategies based on PFTs are highly specific and may alleviate the issue of increasing resistance to antibiotics.
Mitofusin-2 Promotes the Epithelial-Mesenchymal Transition-Induced Cervical Cancer Progression

High expression of mitofusin-2 (MFN2), a mitochondrial fusion protein, has been frequently associated with poor prognosis of patients with cervical cancer. Here, we aimed to identify the function of MFN2 in cervical cancer to understand its influence on disease prognosis. To this end, from cervical adenocarcinoma, we performed an MTT assay and quantitative RT-PCR (qRT-PCR) analysis to assess the effects of MFN2 on the proliferation and of HeLa cells. Then, colony-formation ability and tumorigenesis were evaluated using a tumor xenograft mouse model. The migration ability related to MFN2 was also measured using a wound healing assay. Consequently, epithelial-mesenchymal transition (EMT) of MFN2-knockdowned HeLa cells originating from adenocarcinoma. markers related to MFN2 were assessed by qRT-PCR. Clinical data were analyzed using cBioPortal and The Cancer Genome Atlas. We found that MFN2 knockdown reduced the proliferation, colony formation ability, migration, and in vivo tumorigenesis of HeLa cells. Primarily, migration of MFN2-knockdowned HeLa cells decreased through the suppression of EMT. Thus, we concluded that MFN2 facilitates cancer progression and in vivo tumorigenesis in HeLa cells. These findings suggest that MFN2 could be a novel target to regulate the EMT program and tumorigenic potential in HeLa cells and might serve as a therapeutic target for cervical cancer. Taken together, this study is expected to contribute to the treatment of patients with cervical cancer.
Development of the Binary and Ternary Atorvastatin Solid Dispersions: In Vitro and In Vivo Investigations

The object of this study was to prepare binary and ternary solid dispersions of atorvastatin (ATR) by the melting method using PEGs and poloxamer 188 (P188) as the carriers, singly and in combination with each other. Dissolution behavior, solubility studies, X-ray diffractometry, differential scanning calorimetry, and Fourier transform infrared spectroscopy were studied. Furthermore, antihyperlipidemic activities of formulations were compared to each other by serum lipid analyses in hyperlipidemic rats. Based on the results, the highest dissolution efficiency (DE30 = 83%) was obtained by binary systems consisted of ATR and P188. Also, no additional improvement was observed in dissolution properties of ternary solid dispersion formulations. Solubility studies showed enhancement of ATR phase solubility in water and a buffer solution containing P188 or PEG 10000. Furthermore, saturated solubility of ATR in the buffer solution improved more than twofold in the optimized ternary dispersion system. No crystalline changes occurred in PEG-based formulations; meanwhile, partial amorphization happened in the ATR-P188 combination. Finally, the in vivo study in hyperlipidemic rats exhibited a rapid decrease in the lipid profile of all formulations compared to ATR (after 7 days). Moreover, reduction of serum triglycerides and total cholesterol on the 14th day in the ATR group (p value < 0.01) was less than solid dispersion or physical mixing preparations (p value < 0.001). These findings proved the appropriate influence of using PEG and P188 in solid dispersion systems for the improvement of the therapeutic efficiency of ATR.
An Energy Conserving Vlasov Solver That Tolerates Coarse Velocity Space Resolutions: Simulation of MMS Reconnection Events

Vlasov solvers that operate on a phase‐space grid are highly accurate but also numerically demanding. Coarse velocity space resolutions, which are largely unproblematic in particle‐in‐cell (PIC) simulations, can lead to numerical heating or oscillations in continuum Vlasov methods. To address this issue, we present a new dual Vlasov solver which is based on an established positivity preserving advection scheme for the update of the distribution function and an energy conserving partial differential equation solver for the kinetic update of mean velocity and temperature. The solvers work together via moment fitting during which the maximum entropy part of the distribution function is replaced by the solution from the partial differential equation solver. This numerical scheme makes continuum Vlasov methods competitive with PIC methods concerning computational cost and enables us to model large scale reconnection in Earth's magnetosphere with a fully kinetic continuum method. The simulation results agree well with measurements by the MMS spacecraft.
Cleaved Delta like 1 intracellular domain regulates neural development via Notch signal-dependent and -independent pathways

ABSTRACT Notch-Delta signaling regulates many developmental processes, including tissue homeostasis and maintenance of stem cells. Upon interaction of juxtaposed cells via Notch and Delta proteins, intracellular domains of both transmembrane proteins are cleaved and translocate to the nucleus. Notch intracellular domain activates target gene expression; however, the role of the Delta intracellular domain remains elusive. Here, we show the biological function of Delta like 1 intracellular domain (D1ICD) by modulating its production. We find that the sustained production of D1ICD abrogates cell proliferation but enhances neurogenesis in the developing dorsal root ganglia (DRG), whereas inhibition of D1ICD production promotes cell proliferation and gliogenesis. D1ICD acts as an integral component of lateral inhibition mechanism by inhibiting Notch activity. In addition, D1ICD promotes neurogenesis in a Notch signaling-independent manner. We show that D1ICD binds to Erk1/2 in neural crest stem cells and inhibits the phosphorylation of Erk1/2. In summary, our results indicate that D1ICD regulates DRG development by modulating not only Notch signaling but also the MAP kinase pathway.
Influence of Parenting Style on Body Mass Index, Physical Activity, and Sedentary Time

The purpose of the current study was to determine the influence of parenting style on body mass index (BMI) percentile, physical activity (PA), and sedentary time (ST) in children. Accelerometers were used to assess PA and ST in 152 fifth-grade children. Parenting style was assessed by the child participants’ responses to modified questions from the Parenting Style Inventory II and dichotomized as authoritative or non-authoritative. Multiple linear regression analyses were utilized to identify significant predictors of outcomes of interest. Parenting style did not predict ST or any intensity of PA; however, BMI percentile and gender were significant predictors of moderate-intensity PA, vigorous-intensity PA, and moderate-to-vigorous intensity PA (P < .01). BMI percentile was predicted to be lower in females with authoritative mothers (P < .01). While authoritative and non-authoritative parenting style did not predict objectively measured PA or ST in early adolescents, authoritative parenting style did predict BMI percentile in female participants.
A Reflection on How Carcinoma-Associated Fibroblasts Were Recognized as Active Participants of Epithelial Tumorigenesis

Today's view of cancer as a systemic disease was facilitated by studies accentuating the local as well as the systemic role that non-tumorigenic cells, such as carcinoma-associated fibroblasts, play in cancer onset, development, and progression. The study highlighted in this Cancer Research Landmark was instrumental for supporting the idea that cancer is a full-body disease that depends on reciprocal interactions between cancer cells and the tumor microenvironment. Fibroblasts are mesenchymal cells of the connective tissue and are responsible for maintaining tissue homeostasis. Importantly, contractile myofibroblastic activation and immunoregulatory fibroblastic nemosis (the process of mesenchymal cell activation, followed by death, associated with release of proinflammatory molecules) constitute two functional aspects of fibroblasts that are essential for organogenesis as well as for modulating wound healing. Yet, in epithelial cancers, fibroblastic cell functions are chronically misregulated. The study by Olumi and colleagues published in Cancer Research in 1999 exemplifies how normal fibroblasts play a tumor-suppressive role and how modulating fibroblastic activity provides carcinoma-associated fibroblasts with tumor-promoting functions, similar to the needed “second hit” in a tumor suppressor gene. The emphasis on tumor/fibroblast interactions has provided a new framework for thinking about tumorigenesis as well as new targets for therapeutic intervention. See related article by Olumi and colleagues, Cancer Res 1999;59:5002–11
HN1L promotes stem cell‐like properties by regulating TGF‐β signaling pathway through targeting FOXP2 in prostate cancer

Dysregulated hematological and neurological expressed 1‐like (HN1L) has been implicated in carcinogenesis of difference cancers, including hepatocellular carcinoma and breast cancer. However, the role of HN1L in the progression of prostate cancer (PCA) remains unknown. Therefore, we aimed to investigate the role of HN1L in stemness and progression of PCA. The expression of HN1L in PCA tissues and cells was determined by quantitative reverse‐transcription polymerase chain reaction (qRT‐PCR), western blot analysis, and/or immunohistochemistry (IHC). CD133+ cells were sorted from PCA cells using magnetic fluorescence cell sorting technology and were considered as cancer stem cells (CSCs). Sphere formation assays, transwell assays, and animal experiments were conducted to assess cell stemness, migration, invasion, and in vivo tumorigenesis, respectively. The results showed that HN1L expression was higher in PCA tissues and cells as compared with normal tissues and cells, as well as in CD133+ cells as compared with CD133− cells. HN1L knockdown significantly decreased the expression levels of CSC markers including OCT4 (POU class 5 homeobox 1), CD44, and SRY‐box transcription factor 2, inhibited cell migration, invasion, and tumorigenesis and decreased the number of tumor spheroids and CD133+ cell population. Furthermore, we found that HN1L could bind to forkhead box P2 (FOXP2) and positively regulated transforming growth factor‐β (TGF‐β) expression via upregulation of FOXP2. In addition, the overexpression of TGF‐β in HN1L‐knockdown PCA cells increased the number of tumor spheroids and CD133+ cell population, as well as enhanced cell migration and invasion. Collectively, this study demonstrates that HN1L promotes stem cell‐like properties and cancer progression by targeting FOXP2 through TGF‐β signaling pathway in PCA.
Early Diastolic Longitudinal Strain Rate at MRI and Outcomes in Heart Failure with Preserved Ejection Fraction.

Background Assessment of subclinical myocardial dysfunction by using feature tracking has shown promise in prognosis evaluation of heart failure with preserved ejection fraction (HFpEF). Global early diastolic longitudinal strain rate (eGLSR) can identify earlier diastolic dysfunction; however, limited data are available on its prognostic value in HFpEF. Purpose To evaluate the association between left ventricular (LV) eGLSR and primary composite outcomes (all-cause death or heart failure hospitalization) in patients with HFpEF. Materials and Methods In this retrospective study, consecutive patients with HFpEF (included from January 2010 to March 2013) underwent cardiovascular MRI. The correlation between eGLSR and variables was assessed by using linear regression. The association between eGLSR (obtained with use of feature tracking) and outcomes was analyzed by using Cox proportional regression. Results A total of 186 patients with HFpEF (mean age ± standard deviation, 59 years ± 12; 77 women) were included. The eGLSR was weakly correlated with LV end-diastole volume index (Pearson correlation coefficient [r] = -0.35; P < .001), heart rate (r = 0.35; P < .001), and LV ejection fraction (r = 0.30; P < .001) and moderately correlated with LV end-systole volume index (r = -0.41; P < .001). At a median follow-up of 9.2 years (interquartile range, 8.7-10.0 years), 72 patients experienced primary composite outcomes. Impaired eGLSR, defined as an eGLSR of less than 0.57 per second, was associated with a greater rate of heart failure hospitalization or all-cause death (hazard ratio, 2.0 [95% CI: 1.1, 3.7]; P = .02) after adjusting for multiple clinical and imaging-based variables. Conclusion Left ventricular global early diastolic longitudinal strain rate obtained from cardiovascular MRI feature tracking was independently associated with adverse outcomes in patients with heart failure with preserved ejection fraction. © RSNA, 2021 Online supplemental material is available for this article.