Miracle-dz/UniFAR-FTUs huggingface dataset:
CUX1—Transcriptional Master Regulator of Tumor Progression in Pancreatic Neuroendocrine Tumors

Recently, we identified the homeodomain transcription factor Cut homeobox 1 (CUX1) as mediator of tumour de-differentiation and metastatic behaviour in human insulinoma patients. In insulinomas, CUX1 enhanced tumour progression by stimulating proliferation and angiogenesis in vitro and in vivo. In patients with non-functional pancreatic neuroendocrine tumours (PanNET), however, the impact of CUX1 remains to be elucidated. Here, we analysed CUX1 expression in two large independent cohorts (n = 43 and n = 141 tissues) of non-functional treatment-naïve and pre-treated PanNET patients, as well as in the RIP1Tag2 mouse model of pancreatic neuroendocrine tumours. To further assess the functional role of CUX1, expression profiling of DNA damage-, proliferation- and apoptosis-associated genes was performed in CUX1-overexpressing Bon-1 cells. Validation of differentially regulated genes was performed in Bon-1 and QGP1 cells with knock-down and overexpression strategies. CUX1 expression assessed by a predefined immunoreactivity score (IRS) was significantly associated with shorter progression-free survival (PFS) of pre-treated PanNET patients (23 vs. 8 months; p = 0.005). In treatment-naïve patients, CUX1 was negatively correlated with grading and recurrence-free survival (mRFS of 39 versus 8 months; p = 0.022). In both groups, high CUX1 levels indicated a metastatic phenotype. Functionally, CUX1 upregulated expression of caspases and death associated protein kinase 1 (DAPK1), known as mediators of tumour progression and resistance to cytotoxic drugs. This was also confirmed in both cell lines and human tissues. In the RIP1Tag2 mouse model, CUX1 expression was associated with advanced tumour stage and resistance to apoptosis. In summary, we identified the transcription factor CUX1 as mediator of tumour progression in non-functional PanNET in vitro and in vivo, indicating that the CUX1-dependent signalling network is a promising target for future therapeutic intervention.
Chemical and Physical Properties of Soil Amended with Pecan Wood Chips

The pruning wood of pecan (Carya illinoinensis (Wangenh.) K. Koch) is often burned. Chipping and soil incorporation of pruning wood is becoming more popular as a result of environmental constraints on burning. The objective of our research was to determine how pecan wood incorporation into soil affects the soil chemical and physical properties. Pecan wood chips were incorporated into a silty clay soil at rates of 0, 4484, 8968, 13,452, and 17,936 kgha -1 in Summer 2002, 2003, and 2004. Some plots received nitrogen at a rate of 0, 15.2, 30.5, 45.7, and 61.0 kgha -1 to adjust the C : N ratio of trim- mings to 30 : 1. Ammonium sulfate, as a nitrogen source to balance the C : N ratio of pecan wood chips, reduced soil pH. However, the wood chip amendments alone did not reduce soil pH. Soil salinity (as determined by electrical conductivity) and bulk density were unaffected by wood chip incorporation regardless of application rate or number of applications. Incorporation of pecan chips had little effect on soil moisture content, but the soil had an inherently high waterholding capacity. Pecan wood chip incorporation significantly increased soil organic matter content and aggregate stability, particularly at the higher application rates and with repeated amendment. The incorporation of pecan pruning wood into the soil appears to improve soil tilth and aggregation while providing growers with an environmentally acceptable means of disposal.
Correlation of axial length and peripapillary retinal nerve fiber layer thickness measured by Cirrus HD optical coherence tomography in myopes

Purpose: To evaluate the RNFL thickness by optical coherence tomography (OCT) and correlate it with the axial length and refractive error in myopes. Methods: Patients with myopia −1D to −10D attending ophthalmology OPD at a tertiary hospital from October 2013 to April 2015 for evaluation underwent ophthalmic examination including refraction, axial length, and OCT RNFL thickness measurements. The patients were divided into two groups; group A included patients with AL ≤24 mm and group B AL >24 mm. Results: The study included 100 eyes with myopia ranging from −1D to −10D. The mean (±SD) age was 26.87 (±5.93) years with a range of 21–48 years and male: female ratio of 2:3. There was a statistically significant difference in the average peripapillary RNFL thickness between the two axial length groups (P = 0.01); RNFL thickness in group A being 91.40 (±10.17) and group B 86.06 (±10.09); and in the average RNFL thickness between the 3 degrees of myopia groups, with higher myopic group having thinner RNFL (P = 0.001). Conclusion: There is a significant decrease in RNFL thickness with an increase in the grade of myopia and axial length. This polar RNFL thinning could be wrongly attributed to glaucomatous change. We recommend careful interpretation of RNFL data in myopes with axial length >24 mm, when applying the current OCT nomograms.
Correlation and Reliability Analyses among the Upper Cervical Rotation-Flexion Test, Upper Cervical Flexion-Extension Test, and Upper Cervical Flexion Angle Measurement Using Radiography

(1) Background: The cervical rotation-flexion test is one method of measuring the range of motion of the upper cervical spine; however, this test has not been investigated in detail. The aim of this study was to investigate the reliability and concurrent validity of the upper cervical rotation-flexion test. (2) Methods: Twenty-five healthy individuals (13 women and 12 men) participated in this study. The participants underwent radiography, the upper cervical flexion-extension test, and the upper cervical rotation-flexion test in a sitting position while wearing a cervical goniometer to measure the upper cervical flexion angle. Three experienced physical therapists administered the upper cervical rotation-flexion test using the cervical device, twice for each participant. Inter-rater and intra-rater reliabilities were evaluated using the intraclass correlation coefficient (95% confidence interval). (3) Results: The inter-rater and intra-rater reliability values of the total scores were excellent. The results of the upper cervical rotation-flexion test significantly correlated with those of the radiographic evaluation of the upper cervical flexion angle (r = 0.80, p < 0.001) and those of the upper cervical flexion-extension test (r = 0.77, p < 0.001). Significant correlations among the three test results were observed. (4) Conclusions: The findings of this study suggest that the upper cervical rotation-flexion test is meaningful for independently measuring the upper cervical flexion angle.
Using a network modularity analysis to inform management of a rare endemic plant in the northern Great Plains, USA

Summary Analyses of flower-visitor interaction networks allow application of community-level information to conservation problems, but management recommendations that ensue from such analyses are not well characterized. Results of modularity analyses, which detect groups of species (modules) that interact more with each other than with species outside their module, may be particularly applicable to management concerns. We conducted modularity analyses of networks surrounding a rare endemic annual plant, Eriogonum visheri, at Badlands National Park, USA, in 2010 and 2011. Plant species visited were determined by pollen on insect bodies and by flower species upon which insects were captured. Roles within modules (network hub, module hub, connector and peripheral, in decreasing order of network structural importance) were determined for each species. Relationships demonstrated by the modularity analysis, in concert with knowledge of pollen species carried by insects, allowed us to infer effects of two invasive species on E. visheri. Sharing a module increased risk of interspecific pollen transfer to E. visheri. Control of invasive Salsola tragus, which shared a module with E. visheri, is therefore a prudent management objective, but lack of control of invasive Melilotus officinalis, which occupied a different module, is unlikely to negatively affect pollination of E. visheri. Eriogonum pauciflorum may occupy a key position in this network, supporting insects from the E. visheri module when E. visheri is less abundant. Year-to-year variation in species' roles suggests management decisions must be based on observations over several years. Information on pollen deposition on stigmas would greatly strengthen inferences made from the modularity analysis. Synthesis and applications: Assessing the consequences of pollination, whether at the community or individual level, is inherently time-consuming. A trade-off exists: rather than an estimate of fitness effects, the network approach provides a broad understanding of the relationships among insect visitors and other plant species that may affect the focal rare plant. Knowledge of such relationships allows managers to detect, target and prioritize control of only the important subset of invasive species present and identify other species that may augment a rare species' population stability, such as E. pauciflorum in our study.
The timing and extent of 'juvenile ovary' phase are highly variable during zebrafish testis differentiation

Gonad differentiation in male zebrafish involves a transformation from a ‘juvenile ovary’ to testis. In our study, this phenomenon was analysed using a stable transgenic line (vas::egfp) created by Krovel & Olsen (Mechanisms of Development, 116: 141–150, 2002). Our data obtained by histological and immunohistochemical methods show that the onset of enhanced green fluorescent protein (EGFP) expression marks the conversion of the bipotential gonad into a ‘juvenile ovary’, and its subsequent decrease in the males indicates transformation into a testis. Furthermore, during the ‘juvenile ovary’ stage, a high level of variation was observed among individuals not only in the starting point and duration of EGFP expression but also in its intensity. The intensity of reporter expression in the males ranged from a high level of expression – similar to that observed in females – to invisible expression and correlated with the number of oocytes, the shape of ‘juvenile ovary’ and its lumen. Therefore, the authors conclude that although all males develop ‘juvenile ovaries’, they differ vastly in the extent of their commitment toward femaleness during this stage before testis differentiation. The differentiating zebrafish testis shows morphological features similar to those of the transforming gonad of protogynous hermaphrodites, and therefore, it could be a good model for the study of the process of female-to-male sex change in adult teleosts.
A Green Approach towards Native Collagen Scaffolds: Environmental and Physicochemical Assessment

Native collagen scaffolds were prepared in this work, in which both materials and environmental approaches were considered with the aim of providing a global strategy towards more sustainable biomaterials. From the environmental perspective, it is worth mentioning that acid and enzymatic treatments have been avoided to extract collagen, allowing the reduction in the use of resources, in terms of chemicals, energy, and time, and leading to a low environmental load of this step in all the impact categories under analysis. With the incorporation of chitosan into the scaffold-forming formulations, physical interactions occurred between collagen and chitosan, but the native collagen structure was preserved, as observed by Fourier transform infrared (FTIR) and X-ray diffraction (XRD) analyses. The incorporation of chitosan also led to more homogenous porous microstructures, with higher elastic moduli and compression resistance for both dry and hydrated scaffolds. Furthermore, hydrated scaffolds preserved their size and shape after some compression cycles.
Circulating Insulin-like Growth Factor-I Concentrations and Risk of 30 Cancers: Prospective Analyses in UK Biobank

The results from this outcome-wide analysis are consistent with a positive association of IGF-I with cancers at several sites. Circulating insulin-like growth factor I (IGF-I) is positively associated with the risks of colorectal, breast, and prostate cancer, but evidence for other less common cancers is limited. In this study, we investigated associations between serum IGF-I concentrations and incidence of less common cancers in the UK Biobank study. To enable comparison of effect estimates, and as positive controls, both common and less common cancer sites (total 30) were included in an outcome-wide analysis. Data from 394,388 cancer-free participants in the UK Biobank study were analyzed. Multivariable adjusted Cox proportional hazards models were used to determine associations between baseline serum IGF-I concentrations and cancer incidence, using repeated IGF-I measurements from up to 14,149 participants to correct for regression dilution bias. Higher IGF-I concentration was associated with increased risks of thyroid cancer [HR per 5 nmol/L higher concentration 1.18; 95% confidence interval (CI), 1.01–1.37] in addition to colorectal (HR, 1.08; 95% CI, 1.03–1.13), breast (HR, 1.11; 95% CI, 1.07–1.15), and prostate cancer (HR, 1.08; 95% CI, 1.05–1.12), and reduced risks of ovarian and liver cancer. Mean follow-up was 6.9 years and the possibility that the observed associations may be influenced by reverse causality bias cannot be excluded. Additional nominally significant associations with malignant melanoma, multiple myeloma, oral cancer, and esophageal squamous cell carcinoma did not survive correction for multiple testing. Studies with longer follow-up and pooled analyses are needed to further assess how broad the role of IGF-I is in cancer development. Significance: The results from this outcome-wide analysis are consistent with a positive association of IGF-I with cancers at several sites.
Merkel Cell Polyomavirus T Antigens Induce Merkel Cell-Like Differentiation in GLI1-Expressing Epithelial Cells

Merkel cell carcinoma (MCC) is an aggressive skin cancer frequently caused by the Merkel cell polyomavirus (MCPyV). It is still under discussion, in which cells viral integration and MCC development occurs. Recently, we demonstrated that a virus-positive MCC derived from a trichoblastoma, an epithelial neoplasia bearing Merkel cell (MC) differentiation potential. Accordingly, we hypothesized that MC progenitors may represent an origin of MCPyV-positive MCC. To sustain this hypothesis, phenotypic comparison of trichoblastomas and physiologic human MC progenitors was conducted revealing GLI family zinc finger 1 (GLI1), Keratin 17 (KRT 17), and SRY-box transcription factor 9 (SOX9) expressions in both subsets. Furthermore, GLI1 expression in keratinocytes induced transcription of the MC marker SOX2 supporting a role of GLI1 in human MC differentiation. To assess a possible contribution of the MCPyV T antigens (TA) to the development of an MC-like phenotype, human keratinocytes were transduced with TA. While this led only to induction of KRT8, an early MC marker, combined GLI1 and TA expression gave rise to a more advanced MC phenotype with SOX2, KRT8, and KRT20 expression. Finally, we demonstrated MCPyV-large T antigens’ capacity to inhibit the degradation of the MC master regulator Atonal bHLH transcription factor 1 (ATOH1). In conclusion, our report suggests that MCPyV TA contribute to the acquisition of an MC-like phenotype in epithelial cells.
Peroxisomal proliferator‐activated receptor α‐b deficiency induces the reprogramming of nutrient metabolism in zebrafish

The pparab subtype in zebrafish is much more highly expressed in tissues with high oxidative activity than pparaa. The pparab deficiency in zebrafish reduces fatty acid β‐oxidation both in liver and muscle, illustrating its functional homology as a mammalian peroxisome proliferator‐activated receptor α (PPARα). pparab deficiency promotes metabolic reprogramming by increasing glucose utilization and inhibiting amino acid breakdown. The present study brings new insights into the comprehensive regulatory roles of PPARα in the cellular fuel selection and provides a valuable animal model for PPARα studies from a viewpoint of comparative physiology.
Application of Multiblock Analysis on Small Metabolomic Multi-Tissue Dataset

Data integration has been proven to provide valuable information. The information extracted using data integration in the form of multiblock analysis can pinpoint both common and unique trends in the different blocks. When working with small multiblock datasets the number of possible integration methods is drastically reduced. To investigate the application of multiblock analysis in cases where one has a few number of samples and a lack of statistical power, we studied a small metabolomic multiblock dataset containing six blocks (i.e., tissue types), only including common metabolites. We used a single model multiblock analysis method called the joint and unique multiblock analysis (JUMBA) and compared it to a commonly used method, concatenated principal component analysis (PCA). These methods were used to detect trends in the dataset and identify underlying factors responsible for metabolic variations. Using JUMBA, we were able to interpret the extracted components and link them to relevant biological properties. JUMBA shows how the observations are related to one another, the stability of these relationships, and to what extent each of the blocks contribute to the components. These results indicate that multiblock methods can be useful even with a small number of samples.
SOME AROMATIC AMINES AND RELATED COMPOUNDS VOLUME 127 IARC MONOGRAPHS ON THE IDENTIFICATION OF CARCINOGENIC HAZARDS TO HUMANS

On the basis of the recommendations of an independent Advisory Group of international experts, the IARC Monographs Programme evaluates agents that are suspected to cause cancer. Agents are recommended for evaluation when there is evidence that people may be exposed, and when there is also scientific evidence available to evaluate carcinogenicity. In 2019, an Advisory Group recommended a wide variety of agents or substances for a new or updated evaluation by the IARC Monographs Programme. These agents may have different impacts on public health. For example, air pollution has a high impact because everyone is exposed to air pollution at some level, even if exposure levels are generally low. In contrast, occupational exposures, such as those involved in firefighting, may be very high and can therefore have a marked public health impact even if fewer people are exposed through their work.
Analysis of the Statistical Distribution of Energization Overvoltages of EHV Cables and OHLs

Insulation levels of EHV systems have been determined based on the statistical distribution of switching overvoltages since 1970s when the statistical distribution was found for overhead lines. Responding to an increase in the planned and installed EHV cables, the authors have derived the statistical distribution of energization overvoltages for EHV cables and have made clear their characteristics compared with those of the overhead lines. This paper identifies the causes and physical meanings of the characteristics so that it becomes possible to use the obtained statistical distribution for the determination of insulation levels of cable systems.
VidCNN - Learning Blind Video Denoising

We propose a novel Convolutional Neural Network (CNN) for Video Denoising called VidCNN, which is capable to denoise videos without prior knowledge on the noise distribution (Blind). VidCNN is a ﬂexible model, since it tackles multiple noise types, artiﬁcial and real. The CNN architecture uses a combination of spatial and temporal ﬁltering, which learns how to spatially denoise the frames ﬁrst and how to combine their temporal information, handling camera and objects motion, brightness changes, low-light conditions and temporal inconsistencies at the same time. We demonstrate the importance of the data used for CNNs training, creating for this purpose a speciﬁc dataset for low-light conditions. We test VidCNN on videos commonly used for benchmarking and on self-collected data, achieving good results comparable with the state-of-the-art in video denoising. Our model can be easily adapted to different noise models, keeping the same temporal denoising network, maintaining performance in terms of accuracy and speed.
Evaluation of mobilization in operated case of fracture tibia

<p class="abstract"><strong>Background:</strong> In spite of all the advances optimal method of treatment, fractures of the tibia still pose a challenge to the orthopaedic surgeons and thus the management of the fractured tibia requires the widest experience, the greatest wisdom, and the nicest of the clinical judgement in order to choose the most appropriate treatment for particular pattern of injury. Therefore, in this study we evaluated the role of mobilization efficacy and results of nailing and plating compression in management of tibial fractures and its VAS scoring. </p><p class="abstract"><strong>Methods:</strong> This is a prospective study of fractures tibia in 150 cases aged from 18-60 years, out of which 109 (72.6%) were males. The left side was involved in 85(56.6%) patients and RTA was the major cause of the tibial fractures 98 (65.3%). Among the patients full weight bearing time was early (<3 weeks) with 90 (60%) and 60 (40%) patients within delay (>3 weeks) of surgery. <strong></strong></p><p class="abstract"><strong>Results:</strong> VAS score was significant better in early (<3 weeks) mobilization and in nailing treatment of tibial fractures in first month (7.8±074 and 7.6±0.81) and (2.1±0.8 and 1.8±0.65) at the final follow-up. Vas score correlation was significant with process and mobilization. </p><p class="abstract"><strong>Conclusions:</strong> We here conclude from our study that interlocking nailing appears to be promising method of treatment of unstable tibia fractures in adults without any external splintage after adequate stabilization and early weight bearing leading to excellent functional results in most of cases. </p>
Maturation temperature and rainfall influence seed dormancy characteristics of annual ryegrass (Lolium rigidum)

The role of temperature and rainfall during seed development in modulating subsequent seed dormancy status was studied for Lolium rigidum Gaud. (annual ryegrass). Climatic parameters relating to geographic origin were compared with annual ryegrass seed dormancy characteristics for seeds collected from 12 sites across the southern Western Australian cropping region. Seed germination was tested soon after collection and periodically during subsequent after-ripening. Temperature in the year of seed development and long-term rainfall patterns showed correlations with aspects of seed dormancy, particularly the proportion of seeds remaining dormant following 5 months of after-ripening. Consequently, for one population the temperature (warm/cool) and water supply (adequate/reduced) during seed development were manipulated to investigate the role of maternal environment in the quantity and dormancy characteristics of seeds produced. Seeds from plants grown at warm temperatures were fewer in number, weighed less, and were less dormant than those from plants grown at cool temperature. Seeds that developed under both cool temperature and reduced moisture conditions lost dormancy faster than seeds from well-watered plants. Seed maturation environment, particularly temperature, can have a significant effect on annual ryegrass seed numbers and seed dormancy characteristics.