Miracle-dz/UniFAR-FTUs huggingface dataset:
Transvaginal three-dimensional ultrasound for preoperative assessment of myometrial invasion in patients with endometrial cancer: a systematic review and meta-analysis.

AIM The aim of this meta-analysis is to evaluate the diagnostic accuracy of three-dimensional transvaginal ultrasound subjective assessment (3D-TVS) in the preoperative detection of deep myometrial invasion (MI) in patients with endometrial cancer, using definitive frozen section diagnosis after surgery as the reference standard. MATERIAL AND METHODS A search for studies evaluating the role of 3D-TVS for assessing myometrial invasion in endometrial cancer from January 1990 to Novem-ber 2020 was performed in PubMed/MEDLINE and Web of Science. The Quality Assessment of Diagnostic Accuracy Studies 2 evaluated the quality of the studies (QUADAS-2). All analyses were performed using MIDAS and METANDI commands. RESULTS Nine studies comprising 581 women were included. The mean prevalence of deep MI was 39.8%. QUADAS as-sessment showed that most studies had a high risk for the patient selection domain. Overall, the pooled estimated sensitivity, specificity, positive likelihood and negative likelihood ratio of 3D-TVS for detecting deep MI were 84% (95% CI, 73-90%), 82% (95% CI, 75-88%), 5 (95% CI, 3.1-7.1) and 0.20 95% CI, 0.11-0.35). respectively. CONCLUSIONS 3D-TVS has an accept-able diagnostic performance for detecting MI in women with endometrial cancer.
Next-Generation Sequencing of 487 Esophageal Adenocarcinomas Reveals Independently Prognostic Genomic Driver Alterations and Pathways

Purpose: To delineate recurrent oncogenic driver alterations and dysregulated pathways in esophageal adenocarcinoma and to assess their prognostic value. Experimental Design: We analyzed a large cohort of patients with lower esophageal and junctional adenocarcinoma, prospectively sequenced by MSK-IMPACT with high-quality clinical annotation. Patients were subdivided according to treatment intent, curative versus palliative, which closely mirrored clinical staging. Genomic features, alterations, and pathways were examined for association with overall survival using Cox proportional hazard models, adjusted for relevant clinicopathologic factors knowable at the time of diagnosis. Results: Analysis of 487 patients revealed 16 oncogenic driver alterations, mostly amplifications, present in ≥5% of patients. Patients in the palliative-intent cohort, compared with those in the curative-intent cohort, were more likely to have metastatic disease, ERBB2 amplifications, Cell-cycle and RTK–RAS pathway alterations, as well as a higher fraction of genome altered and rate of whole-genome doubling. In multivariable analyses, CDKN2A alterations, SMAD4 alterations, KRAS amplifications, Cell-cycle and TGFβ pathways, and overall number of oncogenic drivers were independently associated with worse overall survival. ERBB2 amplification was associated with improved survival, presumably due to trastuzumab therapy. Conclusions: Our study suggests that higher levels of genomic instability are associated with more advanced disease in esophageal adenocarcinoma. Furthermore, CDKN2A, KRAS, and SMAD4 represent prognostic biomarkers, given their strong association with poor survival.
Transport mechanisms at the malaria parasite-host cell interface

Obligate intracellular malaria parasites reside within a vacuolar compartment generated during invasion which is the principal interface between pathogen and host. To subvert their host cell and support their metabolism, these parasites coordinate a range of transport activities at this membrane interface that are critically important to parasite survival and virulence, including nutrient import, waste efflux, effector protein export, and uptake of host cell cytosol. Here, we review our current understanding of the transport mechanisms acting at the malaria parasite vacuole during the blood and liver-stages of development with a particular focus on recent advances in our understanding of effector protein translocation into the host cell by the Plasmodium Translocon of EXported proteins (PTEX) and small molecule transport by the PTEX membrane-spanning pore EXP2. Comparison to Toxoplasma gondii and other related apicomplexans is provided to highlight how similar and divergent mechanisms are employed to fulfill analogous transport activities.
Novel Human-Derived RET Fusion NSCLC Cell Lines Have Heterogeneous Responses to RET Inhibitors and Differential Regulation of Downstream Signaling

Rearranged during transfection (RET) rearrangements occur in 1% to 2% of lung adenocarcinomas as well as other malignancies and are now established targets for tyrosine kinase inhibitors. We developed three novel RET fusion–positive (RET+) patient–derived cancer cell lines, CUTO22 [kinesin 5B (KIF5B)–RET fusion], CUTO32 (KIF5B-RET fusion), and CUTO42 (echinoderm microtubule-associated protein-like 4–RET fusion), to study RET signaling and response to therapy. We confirmed each of our cell lines expresses the RET fusion protein and assessed their sensitivity to RET inhibitors. We found that the CUTO22 and CUTO42 cell lines were sensitive to multiple RET inhibitors, whereas the CUTO32 cell line was >10-fold more resistant to three RET inhibitors. We discovered that our RET+ cell lines had differential regulation of the mitogen-activated protein kinase and phosphoinositide 3-kinase/protein kinase B (AKT) pathways. After inhibition of RET, the CUTO42 cells had robust inhibition of phosphorylated AKT (pAKT), whereas CUTO22 and CUTO32 cells had sustained AKT activation. Next, we performed a drug screen, which revealed that the CUTO32 cells were sensitive (<1 nM IC50) to inhibition of two cell cycle–regulating proteins, polo-like kinase 1 and Aurora kinase A. Finally, we show that two of these cell lines, CUTO32 and CUTO42, successfully establish xenografted tumors in nude mice. We demonstrated that the RET inhibitor BLU-667 was effective at inhibiting tumor growth in CUTO42 tumors but had a much less profound effect in CUTO32 tumors, consistent with our in vitro experiments. These data highlight the utility of new RET+ models to elucidate differences in response to tyrosine kinase inhibitors and downstream signaling regulation. Our RET+ cell lines effectively recapitulate the interpatient heterogeneity observed in response to RET inhibitors and reveal opportunities for alternative or combination therapies. SIGNIFICANCE STATEMENT We have derived and characterized three novel rearranged during transfection (RET) fusion non-small cell lung cancer cell lines and demonstrated that they have differential responses to RET inhibition as well as regulation of downstream signaling, an area that has previously been limited by a lack of diverse cell line modes with endogenous RET fusions. These data offer important insight into regulation of response to RET tyrosine kinase inhibitors and other potential therapeutic targets.
Use of Patient Abdominal Compression Device Reduces Staff Musculoskeletal Pain Associated With Supporting Colonoscopy

Supplemental Digital Content is Available in the Text. Work-related musculoskeletal disorders occur frequently among the endoscopy staff, and patient-handling duties involved with colonoscopy—applying manual pressure and repositioning patients—are particularly physically demanding. This study explored whether the use of a lower abdominal compression device (ColoWrap), previously shown to reduce the need for manual pressure and patient repositioning, would diminish the frequency of staff-reported musculoskeletal pain. A randomized, blinded, sham-controlled clinical trial was performed at the University of North Carolina Hospitals. Three hundred fifty patients had either ColoWrap or a sham device applied before colonoscopy. The primary outcome was the frequency of staff-reported musculoskeletal pain after assisting with colonoscopy. In the intention-to-treat analysis, which included procedures in which ColoWrap was removed, there was no statistical difference in the frequency of staff-reported pain in the control versus ColoWrap arm (4.6% vs. 3.4% of procedures, p = .59). However, when ColoWrap was used as directed (e.g., remained in place for the duration of the procedure), the frequency of staff-reported musculoskeletal pain was significantly reduced (4.6% vs. 0.7% of procedures, p = 0.04). Use of ColoWrap as directed was also found to be independently associated with reduced odds of staff-reported pain relative to the sham arm (OR = 0.12; 95% CI [0.02, 0.95]). When used as directed, ColoWrap reduced the frequency of musculoskeletal pain experienced related to assisting with colonoscopy and may reduce the risk of musculoskeletal disorders and injuries among the endoscopy staff.
A Raf-like kinase is required for smoke-induced seed dormancy in Arabidopsis thaliana

Significance Seed dormancy is an important developmental trait for plants, which ensures seed germination under more favorable spatiotemporal environments. A smoke compound, 3,4,5-trimethylfuran-2(5H)-one, which is called TMB for short, has been identified to inhibit seed germination in a still elusive way. Here, we presented several lines of evidence that TMB inhibits seed germination through the induction of physiological dormancy. Furthermore, by isolating TMB-resistant Arabidopsis mutants, we demonstrated that TMB RESISTANT1, encoding a Raf-like kinase, is critically required for the TMB-induced seed dormancy. These results suggest the presence of a smoke sensory pathway that takes part in the multiple layers of the dormancy regulatory network in higher plants. Plants sense and integrate diverse stimuli to determine the timing for germination. A smoke compound, 3,4,5-trimethylfuran-2(5H)-one (trimethylbutenolide, TMB), has been identified to inhibit the seed germination of higher plants. To understand the mode of action, we examined various physiological and molecular aspects of the TMB-dependent inhibition of seed germination in Arabidopsis thaliana. The results indicated that the effect of TMB is due to the enhanced physiological dormancy, which is modulated by other dormancy regulatory cues such as after-ripening, stratification, and ABA/GA signaling. In addition, gene expression profiling showed that TMB caused genome-wide transcriptional changes, altering the expression of a series of dormancy-related genes. Based on the TMB-responsive physiological contexts in Arabidopsis, we performed mutant screening to isolate genetic components that underpin the TMB-induced seed dormancy. As a result, the TMB-RESISTANT1 (TES1) gene in Arabidopsis, encoding a B2 group Raf-like kinase, was identified. Phenotypic analysis of the tes1 mutant implicated that TES1 has a critical role in the TMB-responsive gene expression and the inhibition of seed germination. Taken together, we propose that plants have been equipped with a TMB sensory pathway through which the TMB induces the seed dormancy in a TES1-dependent way.
Consensus Statement on preoperative diagnosis of ovarian tumors

The European Society of Gynaecological Oncology (ESGO), the International Society of Ultrasound in Obstetrics and Gynecology (ISUOG), the International Ovarian Tumour Analysis (IOTA) group and the European Society for Gynaecological Endoscopy (ESGE) jointly developed clinically relevant and evidence-based statements on the preoperative diagnosis of ovarian tumors, including imaging techniques, biomarkers and prediction models. assessment of different neoplasias in the adnexa, assessment of different neoplasias in the adnexa masses, assessment of different neoplasias in the adnexa model, benign ovarian masses, benign ovarian tumours, beta-human chorionic gonadotropin, biomarker, borderline tumours, carbohydrate antigen 19.9, carbohydrate antigen 125, carcinoembryonic antigen, cell-free deoxyribonucleic acid, circulating cancer cells, circulating cell-free deoxyribonucleic acid, circulating free deoxyribonucleic acid, circulating tumour cells, circulating tumour deoxyribonucleic acid, clinical routine, computed tomography, consensus statement, daily practice, diagnosis, diagnostic performance, diagnostic models, diffusion-weighted imaging, diffusion-weighted magnetic resonance imaging, dynamic contrast-enhanced magnetic resonance imaging, expert ultrasound examiners, ﬁrst line test, functional sequences, gynecology imaging reporting and data system, human epididymis protein, imaging, imaging methods, immunohistochemical diagnosis, inhibin, international ovarian tumor analysis, international ovarian tumor analysis methods, international ovarian tumor analysis rules, intraoperative ultrasound, investigations, logistic regression 1 test, logistic regression 2 test, magnetic resonance imaging, malignant ovarian masses, malignant ovarian tumours, marker, maximum standardized uptake value, molecular biology, molecular marker, morphological scoring system, multivariate analysis, ovarian cancer, ovarian masses, ovarian tumours, ovary, positron emission tomography, positron emission tomography-computed tomography, pre-operative characterization, pre-operative diagnosis, prognostic factor, prognostic value, protein biomarker, risk factors, risk of malignancy score, risk of malignancy index, risk of ovarian malignancy algorithm, scoring system, screening test, secondary metastatic tumours, second line test, simple rules, simple rules risk, simple rules risk model, single protein biomarker, standardized uptake value, suspected malignancy, suspected metastatic tumour, test performances, threshold risk, transabdominal ultrasound, transvaginal ultrasound, tumour markers, ultrasonography,
5,6‐Dihydroxyindole Chemistry: Unexplored Opportunities Beyond Eumelanin

5,6-Dihydroxyindoles, the key building blocks of eumelanin biopolymers, hold promise as versatile molecular systems for the design and development of new functional aromatic scaffolds, biomimetic polymers, and nanomaterials with tailored optical and electronic properties. During the past decade, research into the photophysics, synthesis, π electron manipulation, and reaction behavior of 5,6-dihydroxyindoles has expanded beyond the traditional boundaries of biology and medicine to involve physicists, organic chemists, and materials scientists. This review presents the latest advances in 5,6-dihydroxyindole chemistry from a new perspective. Touching only upon themes at the periphery of eumelanin research, it seeks rather to throw light on the chemical and photophysical features of this peculiar π electron system as an unexplored conceptual and practical platform on which synthetic creativity and rational design might generate a range of chemically diverse molecular scaffolds.
Electrocoalescence of water drop pairs in oil

In an emulsion in an ac field, charges induced on the drops will make adjacent drops align with the field and attract each other. Coalescence of water droplet pairs in naphtenic oil subjected to an ac electric field of varying frequency, shape and amplitude was studied with high-speed optical and electrical techniques. The coalescence is a very rapid process. At the moment of drop impact a current pulse was observed. Different possible coalescence mechanisms are suggested and discussed.
In-Situ Clean-Up and OPLC Fractionation of Chamomile Flower Extract to Search Active Components by Bioautography

Bioassay-guided isolation of antibacterial components of chamomile flower methanol extract was performed by overpressured layer chromatography (OPLC) with on-line detection, fractionation combined with sample clean-up in-situ in the adsorbent bed after off-line sample application. The antibacterial effect of the eluted fractions and of those compounds remaining on the adsorbent layer after separation was tested with direct bioautography (DB) against the bioluminescent Pseudomonas savastanoi pv. maculicola and Vibrio fischeri. The fractions with high biological activity were analyzed by solid phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS) and liquid chromatography and tandem mass spectrometry (LC-MS/MS). Two active uneluted compounds were characterized by off-line OPLC-MS using a thin-layer chromatography (TLC)-MS interface. Mainly, essential oil components, coumarins, flavonoids, phenolic acids, and fatty acids were identified in the active fractions.
Narrow Polydispersity Polystyrene by a Free-Radical Polymerization Process-Rate Enhancement

It is shown that the rate of polymerization of nitrixide-mediated stable free radical polymerization processes for styrene-based polymers and copolymers can be dramatically increased by the addition of camphorsulphonic acid (CSA). Very narrow polydispersity resins are obtained with CSA concentrations of 0.02 M or less, while larger amounts of CSA result in slight increases in polydispersity
BioNetApp: An interactive visual data analysis platform for molecular expressions

Motivation Systems biology faces two key challenges when dealing with large amounts of disparate data produced by different experiments: the integration of results across different experiments, and the extraction of meaningful information from the data produced by these experiments. An ongoing challenge is to provide better tools that can mine data patterns that could not have been discovered through simple visualization. Such mining capabilities also need to be coupled with intuitive visualization to portray those findings. We introduce a software toolbox entitled BioNetApp to mine these patterns and visualize them across all experiments. Results BioNetApp is an interactive visual data mining software for analyzing high-volume molecular expression data obtained from multiple ‘omics experiments. By integrating visualization, statistical methods, and data mining techniques, BioNetApp can perform interactive correlative and comparative analysis along time-course studies of molecular expression data. Correlation analysis provides several visualization features such as Kamada-Kawai, Fruchterman-Reingold Spring embedding network layouts, in addition to single circle, multiple circle and heatmap layouts, whereas comparative analysis presents expression-data distributions across samples, groups, and time points with boxplot display, outlier detection, and data curve fitting. BioNetApp also provides data clustering based on molecular concentrations using Self Organizing Maps (SOM), K-Means, K-Medoids, and Farthest First algorithms. Conclusion BioNetApp has been utilized in a metabolomics study to investigate the metabolite abundance changes in alcohol induced fatty liver, where pair-wise analyses of metabolome concentration revealed correlation networks and interesting patterns in the metabolomics dataset. This study case demonstrates the effectiveness of the BioNetApp software as an interactive visual analysis tool for molecular expression data in systems biology. The BioNetApp software is freely available under GNU GPL license and can be downloaded (including the case-study data and user-manual) at: https://doi.org/10.5281/zenodo.2563129.
Recovery of Ionic Liquids from Wastewater by Nanofiltration

In this study, the possibility to recover ionic liquids from their respective wastewater by nanofiltration was tested in two case studies. The experiments were performed using a commercial dead-end stirred cell and/or a cross-flow cell especially developed for this purpose. Hydrophilic ionic liquids are being presently used for the dissolution of cellulose and its further regeneration by water addition. Wastewater containing a mixture of 1-butyl-3-methylimidazolium chloride (IM14 Cl) and 1-butyl-3-methylimidazolium acetate (IM14 1COO) was treated by nanofiltration and the ionic liquids were recovered as an aqueous solution which is also almost free of undesired by-products. On the contrary, hydrophobic ionic liquids are commonly used in biphasic systems to perform either enzymatic or whole-cell biotransformations. Wastewater containing hydrophobic ionic liquids derived from the conversion of 2-octanone to 2-octanol was also tested, and the ionic liquids used can be recovered as a separate phase by concentrating them beyond the solubility limit. The effect of other wastewater components on the recovery was also investigated with the ionic liquid 1-hexyl-3-methylimidazolium bis (trifluoromethylsulfonyl) amide, IM16 (CF3SO2)2N. Furthermore, using model solutions of 1-hexyl-1-methylpyrrolidinium bis (trifluoromethylsulfonyl) amide, Pyr16 (CF3SO2)2N, it could be evidenced that the formation of a new phase of ionic liquid during the concentration process follows a nucleation-growth mechanism. In this case, up to 69% of the ionic liquid originally present in the feed was separated. Additionally, the effective recovery rate was duplicated up to 33% by using a coalescence filter. Some suggestions to increase both theoretical and effective recovery rates are also discussed.
Molecular weight‐intrinsic viscosity relationship and molecular weight distribution of low pressure polyethylenes

Molecular weights of low pressure polyethylene fractions were measured by an ebulliometric method and an osmotic pressure method. The results can be correlated by an equation, [η] = 5.10 × 10−4M0.725, with the intrinsic viscosity measured at 130°C. in Tetralin, for a molecular weight greater than 3750. All three types of polymer fractions, Ziegler-type low pressure polyethylene, Phillips low pressure polyethylene, and polymethylene from the decomposition of diazomethane, conform to the above correlation. The molecular weight distributions of two samples of Ziegler type polyethylene and one sample of Phillips' Marlex 50 were determined. All three distributions were found to be very broad and contained large amounts of low molecular weight materials.
A Catalytic Reaction Inside a Single‐Walled Carbon Nanotube

More than fifteen years after their discovery, single-walled carbon nanotubes (SWCNTs) are still attracting much interest for their novel electronic and structural properties. The interior space of the SWCNTs can be utilized for encapsulation of molecules. This opens the pathway for the exploration of a new chemistry within the confined one-dimensional nanospace inside the tubes. The first example was the encapsulation of fullerenes. Later on fullerene-filled SWCNTs were transformed into double-walled carbon nanotubes (DWCNTs). This demonstrated the non-catalytic growth of the secondary SWCNTs based on the coalescence of adjacent fullerenes tightly encapsulated within the primary SWCNTs. In turn, attempts to fill SWCNTs with other fullerenes, atoms, and molecules have been intensively explored. Very recently, organic molecules encapsulated in SWCNTs have been reported. Owing to their large variety with diverse chemical properties, the incorporated organic molecules can tune the properties of the SWCNTs. Aside from being a tuning material for the SWCNT properties, the encapsulated molecules themselves may well exhibit novel structural and chemical properties in the confined nanospaces. It is therefore
FACILE PREPARATION AND CHARACTERIZATION OF GRAPHENE NANOSHEET/POLYANILINE NANOFIBER THERMOELECTRIC COMPOSITES

Graphene nanosheet (GNs)/polyaniline (PANI) nanofiber composites were prepared by oxidative polymerization of aniline in a GNs dispersed 1 mol/L HCl solution. The phase composition of the composites was analyzed by Fourier Transform Infrared Spectroscopy and X-ray Diffraction. The thermoelectric properties of the composite powders, after cold pressing into pellets, were measured at room temperature. As the content of GNs increased from 0 to 40 wt. %, the electrical conductivity and Seebeck coefficient of the composite pellets increased simultaneously; especially the electrical conductivity increased dramatically from 15.4 to 120.1 S/cm. The highest power factor (~ 394.4 × 10-8 Wm-1K-2) was obtained from the 40 wt. % GNs/PANI composite sample, which is ~200 times as high as that of HCl-doped PANI.
Chemistry Of Photofrin II And Some New Photosensitizers

The biological activity of a series of porphyrin dimers and trimers with ester and ether linkages, related to Photofrin II and some new photosensitizers with better optical properties are discussed. The structure and biological activity of a large number of photosensitizers, recently reported in the literature, are also reviewed.