Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA-Topology Simplification by Topoisomerases

The topological properties of DNA molecules, supercoiling, knotting, and catenation, are intimately connected with essential biological processes, such as gene expression, replication, recombination, and chromosome segregation. Non-trivial DNA topologies present challenges to the molecular machines that process and maintain genomic information, for example, by creating unwanted DNA entanglements. At the same time, topological distortion can facilitate DNA-sequence recognition through localized duplex unwinding and longer-range loop-mediated interactions between the DNA sequences. Topoisomerases are a special class of essential enzymes that homeostatically manage DNA topology through the passage of DNA strands. The activities of these enzymes are generally investigated using circular DNA as a model system, in which case it is possible to directly assay the formation and relaxation of DNA supercoils and the formation/resolution of knots and catenanes. Some topoisomerases use ATP as an energy cofactor, whereas others act in an ATP-independent manner. The free energy of ATP hydrolysis can be used to drive negative and positive supercoiling or to specifically relax DNA topologies to levels below those that are expected at thermodynamic equilibrium. The latter activity, which is known as topology simplification, is thus far exclusively associated with type-II topoisomerases and it can be understood through insight into the detailed non-equilibrium behavior of type-II enzymes. We use a non-equilibrium topological-network approach, which stands in contrast to the equilibrium models that are conventionally used in the DNA-topology field, to gain insights into the rates that govern individual transitions between topological states. We anticipate that our quantitative approach will stimulate experimental work and the theoretical/computational modeling of topoisomerases and similar enzyme systems.
AFOROS: A Low-Cost Wi-Fi-Based Monitoring System for Estimating Occupancy of Public Spaces

Estimating the number of people present in a given venue in real-time is extremely useful from a security, management, and resource optimization perspective. This article presents the architecture of a system based on the use of Wi-Fi sensor devices that allows estimating, almost in real-time, the number of people attending an event that is taking place in a venue. The estimate is based on the analysis of the “probe request” messages periodically transmitted by smartphones to determine the existence of Wi-Fi access points in the vicinity. The method considers the MAC address randomization mechanisms introduced in recent years in smartphones, which prevents the estimation of the number of devices by simply counting different MAC addresses. To solve this difficulty, our Wi-Fi sensors analyze other fields present in the header of the IEEE 802.11 frames, the information elements, to extract a unique fingerprint from each smartphone. The designed system was tested in a set of real scenarios, obtaining an estimate of attendance at different public events with an accuracy close to 95%.
Comparison of Oncologic Outcomes of Dose-Dense Methotrexate, Vinblastine, Doxorubicin, and Cisplatin (ddMVAC) with Gemcitabine and Cisplatin (GC) as Neoadjuvant Chemotherapy for Muscle-Invasive Bladder Cancer: Systematic Review and Meta-Analysis

Simple Summary Currently, platinum-based neoadjuvant chemotherapy (NAC) is becoming a standard treatment for use in patients with muscle-invasive bladder cancer. However, comparisons of oncologic outcomes for the two most commonly used NAC regimens, ddMVAC (dose-dense methotrexate, vinblastine, doxorubicin, and cisplatin) and GC (gemcitabine and cisplatin), are controversial. We sought to compare the oncologic outcomes of these two regimens via a systematic review and meta-analysis of all the available studies published to date. Through this, we aimed to provide evidence on the optimal NAC regimen for use in muscle-invasive bladder cancer. Abstract Platinum-based neoadjuvant chemotherapy (NAC) is widely used for treating muscle-invasive bladder cancer (MIBC). A systematic review was performed following PRISMA guidelines. PubMed, Embase, and the Cochrane Library were searched up to December 2020. We conducted a meta-analysis to compare the oncologic outcomes of ddMVAC (dose-dense methotrexate, vinblastine, doxorubicin, and cisplatin) and GC (gemcitabine and cisplatin), which are the most widely used NAC regimens. Endpoints included pathologic complete response (pCR), pathologic downstaging (pDS), overall survival (OS), and cancer-specific survival (CSS). Five studies, with a total of 1206 patients, were included for meta-analysis. pCR was observed in 35.2% of the ddMVAC arm and in 25.1% of the GC arm, and pCR was significantly higher in ddMVAC than in GC (odds ratio (OR), 1.45; 95% confidence interval (CI), 1.11–1.89; p = 0.006). There was no significant difference in pDS (OR, 1.37; CI, 0.84–2.21; p = 0.20). OS was significantly higher in ddMVAC than in GC (hazard ratio, 2.16; CI, 1.42–3.29; p = 0.0004). Only one study reported CSS outcomes. The results of this analysis indicate that ddMVAC is superior to GC in terms of pCR and OS, suggesting that ddMVAC is more effective than GC in NAC for MIBC. However, this should be interpreted with caution because of the inherent limitations of retrospective studies.
Whole Exome Sequencing of Biliary Tubulopapillary Neoplasms Reveals Common Mutations in Chromatin Remodeling Genes

Simple Summary Intraductal tubulopapillary neoplasms (ITPN) have recently been described as rare precursor lesions of pancreatic ductal adenocarcinoma and cholangiocarcinoma. Despite a high number of associated invasive adenocarcinomas at the time of diagnosis, patients with ITPN tend to have a much better clinical outcome than those with classical pancreato-biliary adenocarcinoma. Furthermore, rare molecular studies of ITPN show an unexpected lack of hotspot mutations in common driver genes of pancreato-biliary adenocarcinoma, including KRAS. This article reports the first large comprehensive and comparative molecular study of pancreato-biliary ITPN. In the absence of KRAS mutations, we found a high genetic heterogeneity with enrichment in core signaling pathways, including putative actionable genomic targets in one-third of the cases. Whereas, pancreatic ITPN demonstrates a highly distinct genetic profile, differing from classical pancreatic carcinogenesis, biliary ITPN and classical cholangiocarcinoma share common alterations in key genes of the chromatin remodeling pathway, and therefore, appear more closely related than pancreatic ITPN and classical pancreatic ductal adenocarcinoma PDAC. Abstract The molecular carcinogenesis of intraductal tubulopapillary neoplasms (ITPN), recently described as rare neoplasms in the pancreato-biliary tract with a favorable prognosis despite a high incidence of associated pancreato-biliary adenocarcinoma, is still poorly understood. To identify driver genes, chromosomal gains and losses, mutational signatures, key signaling pathways, and potential therapeutic targets, the molecular profile of 11 biliary and 6 pancreatic ITPNs, associated with invasive adenocarcinoma in 14/17 cases, are studied by whole exome sequencing (WES). The WES of 17 ITPNs reveals common copy number variants (CNVs) broadly distributed across the genome, with recurrent chromosomal deletions primarily in 1p36 and 9p21 affecting the tumor suppressors CHD5 and CDKN2A, respectively, and gains in 1q affecting the prominent oncogene AKT3. The identified somatic nucleotide variants (SNVs) involve few core signaling pathways despite high genetic heterogeneity with diverse mutational spectra: Chromatin remodeling, the cell cycle, and DNA damage/repair. An OncoKB search identifies putative actionable genomic targets in 35% of the cases (6/17), including recurrent missense mutations of the FGFR2 gene in biliary ITPNs (2/11, 18%). Our results show that somatic SNV in classical cancer genes, typically associated with pancreato-biliary carcinogenesis, were absent (KRAS, IDH1/2, GNAS, and others) to rare (TP53 and SMAD4, 6%, respectively) in ITPNs. Mutational signature pattern analysis reveals a predominance of an age-related pattern. Our findings highlight that biliary ITPN and classical cholangiocarcinoma display commonalities, in particular mutations in genes of the chromatin remodeling pathway, and appear, therefore, more closely related than pancreatic ITPN and classical pancreatic ductal adenocarcinoma.
Wearables for Industrial Work Safety: A Survey

Today, ensuring work safety is considered to be one of the top priorities for various industries. Workplace injuries, illnesses, and deaths often entail substantial production and financial losses, governmental checks, series of dismissals, and loss of reputation. Wearable devices are one of the technologies that flourished with the fourth industrial revolution or Industry 4.0, allowing employers to monitor and maintain safety at workplaces. The purpose of this article is to systematize knowledge in the field of industrial wearables’ safety to assess the relevance of their use in enterprises as the technology maintaining occupational safety, to correlate the benefits and costs of their implementation, and, by identifying research gaps, to outline promising directions for future work in this area. We categorize industrial wearable functions into four classes (monitoring, supporting, training, and tracking) and provide a classification of the metrics collected by wearables to better understand the potential role of wearable technology in preserving workplace safety. Furthermore, we discuss key communication technologies and localization techniques utilized in wearable-based work safety solutions. Finally, we analyze the main challenges that need to be addressed to further enable and support the use of wearable devices for industrial work safety.
Effect of Epoxide Content on the Vulcanizate Structure of Silica-Filled Epoxidized Natural Rubber (ENR) Compounds

The demand for truck–bus radial (TBR) tires with enhanced fuel efficiency has grown in recent years. Many studies have investigated silica-filled natural rubber (NR) compounds to address these needs. However, silica-filled compounds offer inferior abrasion resistance compared to carbon black-filled compounds. Further, the use of NR as a base rubber can hinder silanization and coupling reactions due to interference by proteins and lipids. Improved silica dispersion be achieved without the use of a silane coupling agent by introducing epoxide groups to NR, which serve as silica-affinitive functional groups. Furthermore, the coupling reaction can be promoted by facilitating chemical interaction between the hydroxyl group of silica and the added epoxide groups. Thus, this study evaluated the properties of commercialized NR, ENR-25, and ENR-50 compounds with or without an added silane coupling agent, and the filler–rubber interaction was quantitatively calculated using vulcanizate structure analysis. The increased epoxide content, when the silane coupling agent was not used, improved silica dispersion, abrasion resistance, fuel efficiency, and wet grip. Once a basic level of silica dispersion was secured by using the silane coupling agent, both the abrasion resistance and wet grip improved with increasing epoxide content. Furthermore, the silane coupling agent could be partially replaced by ENR due to the high filler–rubber interaction between the ENR and silica. Therefore, epoxidation shows potential for resolving the issues associated with poor coupling reactions and abrasion resistance in silica-filled NR compounds.
Involvement of Neutrophils in Metastatic Evolution of Pancreatic Neuroendocrine Tumors

Simple Summary The neutrophil-to-lymphocytes (NLR) reflects the systemic inflammation. Based on a cohort of 144 patients treated for localized or metastatic well-differentiated pancreatic neuroendocrine tumors (pNET), we identified the NLR ≥ 4 to be associated with worse overall survival. Using MCP-Counter on a publicly available pNET RNA-sequencing dataset, we inferred the tumor microenvironment composition of 83 primary pNET and 30 liver metastasis. The neutrophils scores were statistically higher in liver metastasis relative to primary pancreatic tumors (p = 0.005). Gene set enrichment analysis further revealed activation of complement pathway signature in liver metastasis. Through combination of the neutrophil and complement pathway genes, we found that pNET can be classified into two clusters: Neu-Comp1 and Neu-Comp2. Notably, the Neu-Compt1 cluster was enriched in neutrophils and complement pathway signatures and was associated with liver metastasis. These data offer new insights into the role of inflammatory factors in the metastatic progression of the pNET. Abstract Well-differentiated pancreatic neuroendocrine tumors (pNET) have an unpredictable natural history. The identification of both blood and tumor immune features associated with patients’ outcomes remains limited. Herein, we evaluated the best prognostic value of the neutrophils-to-lymphocyte ratio (NLR) in a cohort of 144 pNETs. The NLR ≥ 4 was associated with worse overall survival in both univariate analysis (HR = 3.53, CI95% = 1.50–8.31, p = 0.004) and multivariate analysis (HR = 2.57, CI95% = 1.061–6.216, p = 0.036). The presence of synchronous liver metastasis was identified as a prognostic factor in multivariate analysis (HR = 3.35, CI95% = 1.411–7.973, p = 0.006). Interestingly, the absolute tumor-associated neutrophils count was higher in liver metastasis as compared to their paired primary tumor (p = 0.048). Deconvolution of immune cells from the transcriptome of 83 primary tumors and 30 liver metastases reveals enrichment for neutrophils in metastasis relative to primary tumors (p = 0.005), and this was associated with upregulation of the complement pathway (NES = 1.84, p < 0.0001). Combining neutrophils signature and complement pathway genes, unsupervised clustering identified two pNETs subgroups, namely Neu-Comp1 and Neu-Comp2. Characterized by neutrophils infiltration and activation of the complement pathway, Neu-Comp1 was highly enriched for metastatic liver samples as compared to Neu-Comp2 (p < 0.0001). These data suggest the possible link between liver metastasis, complement pathway activation, and neutrophils infiltration in well-differentiated pNET and open avenues for targeting complement pathways in these tumors.
Anti-Inflammatory and Anti-Diabetic Effect of Black Soybean Anthocyanins: Data from a Dual Cooperative Cellular System

Obesity is characterized by elevated infiltration of macrophages into adipose tissue, leading to the development of insulin resistance. The black soybean seed coat is a rich source of anthocyanins with antioxidative and anti-inflammatory activities. This study investigated the effects of black soybean anthocyanin extract (BSAn) on obesity-induced oxidative stress, the inflammatory response, and insulin resistance in a coculture system of hypertrophied 3T3-L1 adipocytes and RAW264 macrophages. Coculture of adipocytes with macrophages increased the production of reactive oxygen species and inflammatory mediators and cytokines (NO, MCP-1, PGE2, TNFα, and IL-6) and the release of free fatty acids but reduced anti-inflammatory adiponectin secretion. BSAn treatment (12.5, 25, 50, and 100 μg/mL) alleviated the coculture-induced changes (p < 0.001) and inhibited coculture-induced activation of JNK and ERK signaling (p < 0.01). BSAn also blocked the migration of RAW264.7 macrophages toward 3T3-L1 adipocytes. In addition, treatment with BSAn increased PPARγ expression and glucose uptake in response to insulin in hypertrophied 3T3-L1 adipocyte and RAW264.7 macrophage coculture (p < 0.01). These results demonstrate that BSAn attenuates inflammatory responses and improves adipocyte metabolic function in the coculture of hypertrophied 3T3-L1 adipocytes and RAW264.7 macrophages, suggesting the effectiveness of BSAn for obesity-induced insulin resistance.
Effect of Intermittent Theta Burst Stimulation on the Neural Processing of Emotional Stimuli in Healthy Volunteers

Background: Intermittent theta burst stimulation (iTBS) is a form of repetitive transcranial magnetic stimulation that has shown to be effective in treatment-resistant depression. Through studying the effect of iTBS on healthy subjects, we wished to attain a greater understanding of its impact on the brain. Our objective was to assess whether 10 iTBS sessions altered the neural processing of emotional stimuli, mood and brain anatomy in healthy subjects. Methods: In this double-blind randomized sham-controlled study, 30 subjects received either active iTBS treatment (10 sessions, two sessions a day) or sham treatment over the left dorsolateral prefrontal cortex. Assessments of mood, structural magnetic resonance imaging (MRI) and functional MRI (fMRI) were performed before and after iTBS sessions. During the fMRI, three different categories of stimuli were presented: positive, negative and neutral photographs. Results: This study showed that, during the presentation of negative stimuli (compared with neutral stimuli), 10 sessions of iTBS increased activity in the left anterior insula. However, iTBS did not induce any change in mood, regional gray matter volume or cortical thickness. Conclusions: iTBS modifies healthy subjects’ brain activity in a key region that processes emotional stimuli. (AFSSAPS: ID-RCB 2010A01032-37).
Effects of Vertical Temperature Gradient on the Growth Morphology and Properties of Single Domain YBCO Bulks Fabricated by a New Modified TSIG Technique

Single domain YBCO bulk superconductors have been fabricated with different vertical temperature gradients (VTG) by a modified top-seeded infiltration and growth (TSIG) process with a new solid phase (Y2O3+BaCuO2) and a new liquid phase (Y2O3+6CuO+10BaCuO2). It is found that the angle α (between the upper surface and interface of a- and c-growth sectors) is very sensitive to the VTG, which means that the growth rate in c-axis direction (Rc) can be changed by the VTG, according to tan α = Rc/Ra; Ra is the growth rate in the a-axis direction. It is also found that the 4-fold growth sectors did not cover the whole surface of the sample grown with a positive VTG, and the volume fraction of the single c-axis growth sector (Vfc) is 37.5% of the sample grown with a zero VTG, but it is reduced to 25% by a positive VTG, and enlarged to 53.6% by a negative VTG. The results of levitation force and trapped field of the samples show that a negative (or positive) VTG can improve (or reduce) levitation force and trapped.
Recent Advances on Detection of Insecticides Using Optical Sensors

Insecticides are enormously important to industry requirements and market demands in agriculture. Despite their usefulness, these insecticides can pose a dangerous risk to the safety of food, environment and all living things through various mechanisms of action. Concern about the environmental impact of repeated use of insecticides has prompted many researchers to develop rapid, economical, uncomplicated and user-friendly analytical method for the detection of insecticides. In this regards, optical sensors are considered as favorable methods for insecticides analysis because of their special features including rapid detection time, low cost, easy to use and high selectivity and sensitivity. In this review, current progresses of incorporation between recognition elements and optical sensors for insecticide detection are discussed and evaluated well, by categorizing it based on insecticide chemical classes, including the range of detection and limit of detection. Additionally, this review aims to provide powerful insights to researchers for the future development of optical sensors in the detection of insecticides.
Evaluation of Collagen Alterations in Early Precursor Lesions of High Grade Serous Ovarian Cancer by Second Harmonic Generation Microscopy and Mass Spectrometry

Simple Summary The collagen architecture in the extracellular matrix (ECM) is highly remodeled in high grade serous ovarian cancer (HGSOC). Many of these tumors begin in the fallopian tubes (FT) before metastasizing to the ovaries and it is important to study ECM alterations in carcinogenesis. Here, we used Second Harmonic Generation (SHG) microscopy to classify changes in the collagen fiber morphology in normal FT, and precursor pure p53 signatures and serous tubal intraepithelial carcinoma (STICs) in tissues with no HGSOC. Using a machine learning approach based on image features, we were able to discriminate the tissue groups with good classification accuracy. We additionally performed mass spectrometry analysis of normal and HGSOC tissues to associate the differential expression of collagen isoforms with fiber morphology alterations. This work provides new insights into ECM remodeling in early stage HGSOC and suggests the combined use of SHG microscopy and mass spectrometry as a new diagnostic/prognostic approach. Abstract Background: The collagen architecture in high grade serous ovarian cancer (HGSOC) is highly remodeled compared to the normal ovary and the fallopian tubes (FT). We previously used Second Harmonic Generation (SHG) microscopy and machine learning to classify the changes in collagen fiber morphology occurring in serous tubal intraepithelial carcinoma (STIC) lesions that are concurrent with HGSOC. We now extend these studies to examine collagen remodeling in pure p53 signatures, STICs and normal regions in tissues that have no concurrent HGSOC. This is an important distinction as high-grade disease can result in distant collagen changes through a field effect mechanism. Methods: We trained a linear discriminant model based on SHG texture and image features as a classifier to discriminate the tissue groups. We additionally performed mass spectrometry analysis of normal and HGSOC tissues to associate the differential expression of collagen isoforms with collagen fiber morphology alterations. Results: We quantified the differences in the collagen architecture between normal tissue and the precursors with good classification accuracy. Through proteomic analysis, we identified the downregulation of single α-chains including those for Col I and III, where these results are consistent with our previous SHG-based supramolecular analyses. Conclusion: This work provides new insights into ECM remodeling in early ovarian cancer and suggests the combined use of SHG microscopy and mass spectrometry as a new diagnostic/prognostic approach.