Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene fusion analysis in renal cell carcinoma by FusionPlex RNA‐sequencing and correlations of molecular findings with clinicopathological features

Translocation renal cell carcinoma (tRCC) affects younger patients and often presents as advanced disease. Accurate diagnosis is required to guide clinical management. Here we evaluate the RNA‐sequencing FusionPlex platform with a 115‐gene panel including TFE3 and TFEB for tRCC diagnosis and correlate molecular findings with clinicopathological features. We reviewed 996 consecutive RCC cases from our institution over the preceding 7 years and retrieved 17 cases with histological and immunohistochemical features highly suggestive of either TFE3 (n = 16) or TFEB (n = 1). Moderate to strong labeling for TFE3 was present in 15 cases; two cases with weak TFE3 expression were melan‐A or cathepsin‐K positive. RNA‐sequencing detected gene rearrangements in eight cases: PRCC‐TFE3 (3), ASPSCR1‐TFE3 (2), LUC7L3‐TFE3 (1), SFPQ‐TFE3 (1), and a novel SETD1B‐TFE3 (1). FISH assays of 11 tumors verified six positive cases concordant with FusionPlex analysis results. Two other cases were confirmed by RT‐PCR. FusionPlex was superior to FISH by providing precise breakpoints for tRCC‐related genes in a single assay and allowing identification of both known and novel fusion partners, thereby facilitating clinicopathological correlations as fusion partners can influence tumor appearance, immunophenotype, and behavior. Cases with partner genes PRCC and novel partner SETD1B were associated with prominent papillary architecture while cases with partner genes ASPSCR1 and LUC7L3 were associated with a predominantly nested/alveolar pattern. The case with SFPQ‐TFE3 fusion was characterized by biphasic morphology mimicking TFEB‐like translocation RCC. We recommend FusionPlex analysis of RCC in patients under age 50 or when the histologic appearance suggests tRCC.
Response of Drosophila epithelial cell and tissue shape to external forces in vivo

ABSTRACT How actomyosin generates forces at epithelial adherens junctions has been extensively studied. However, less is known about how a balance between internal and external forces establishes epithelial cell, tissue and organ shape. We used the Drosophila egg chamber to investigate how contractility at adherens junctions in the follicle epithelium is modulated to accommodate and resist forces arising from the growing germ line. We found that between stages 6 and 9, adherens junction tension in the post-mitotic epithelium decreases, suggesting that the junctional network relaxes to accommodate germline growth. At that time, a prominent medial Myosin II network coupled to corrugating adherens junctions develops. Local enrichment of medial Myosin II in main body follicle cells resists germline-derived forces, thus constraining apical areas and, consequently, cuboidal cell shapes at stage 9. At the tissue and organ level, local reinforcement of medial junction architecture ensures the timely contact of main body cells with the expanding oocyte and imposes circumferential constraints on the germ line guiding egg elongation. Our study provides insight into how adherens junction tension promotes cell and tissue shape transitions while integrating the growth and shape of an internally enclosed structure in vivo. Summary: The Drosophila follicle epithelium uses strategies of relaxation and contractility at adherens junctions to balance cell and tissue shape with germline growth and curvature.
Brazilian Green Propolis Rescues Oxidative Stress-Induced Mislocalization of Claudin-1 in Human Keratinocyte-Derived HaCaT Cells

Claudin-1 (CLDN1) is expressed in the tight junction (TJ) of the skin granular layer and acts as a physiological barrier for the paracellular transport of ions and nonionic molecules. Ultraviolet (UV) and oxidative stress may disrupt the TJ barrier, but the mechanism of and protective agents against this effect have not been clarified. We found that UVB and hydrogen peroxide (H2O2) caused the internalization of CLDN1 and increased the paracellular permeability of lucifer yellow, a fluorescent marker, in human keratinocyte-derived HaCaT cells. Therefore, the mechanism of mislocalization of CLDN1 and the protective effect of an ethanol extract of Brazilian green propolis (EBGP) were investigated. The UVB- and H2O2-induced decreases in CLDN1 localization were rescued by EBGP. H2O2 decreased the phosphorylation level of CLDN1, which was also rescued by EBGP. Wild-type CLDN1 was distributed in the cytosol after treatment with H2O2, whereas T191E, its H2O2-insensitive phosphorylation-mimicking mutant, was localized at the TJ. Both protein kinase C activator and protein phosphatase 2A inhibitor rescued the H2O2-induced decrease in CLDN1 localization. The tight junctional localization of CLDN1 and paracellular permeability showed a negative correlation. Our results indicate that UVB and H2O2 could induce the elevation of paracellular permeability mediated by the dephosphorylation and mislocalization of CLDN1 in HaCaT cells, which was rescued by EBGP. EBGP and its components may be useful in preventing the destruction of the TJ barrier through UV and oxidative stress.
Targeting CDK9 for treatment of colorectal cancer

Colorectal cancer (CRC) remains one of the most lethal human malignancies, and pursuit of new therapeutic targets for treatment has been a major research focus. Cyclin‐dependent kinase 9 (CDK9), which plays a crucial role in transcription, has emerged as a target for cancer treatment. CDKI‐73, one of the most potent and pharmacologically superior CDK9 inhibitors, has demonstrated excellent anti‐tumour efficacy against several types of cancers. In this study, we evaluated its therapeutic potential against CRC. CDKI‐73 elicited high cytotoxicity against all colon cancer cell lines tested. Cell cycle and apoptosis analysis in HCT 116 and HT29 cells revealed that CDKI‐73 induced cell death without accumulation of DNA at any phase of the cell cycle. Moreover, it caused depolarisation of mitochondrial membrane, leading to caspase‐independent apoptosis. Knockdown by shRNA demonstrated the CDK9‐targeted mechanism of CDKI‐73, which also affected the Mnk/eIF4E signalling axis. In addition, RT‐qPCR analysis showed that CDKI‐73 down‐regulated multiple pro‐survival factors at the mRNA level. Its in vivo anti‐tumour efficacy was further evaluated in Balb/c nude mice bearing HCT 116 xenograft tumours. CDKI‐73 significantly inhibited tumour growth (***P < 0.001) without overt toxicity. Analysis of the tumour tissues collected from the xenografted animals confirmed that the in vivo anti‐tumour efficacy was associated with CDK9 targeting of CDKI‐73. Overall, this study provides compelling evidence that CDKI‐73 is a promising drug candidate for treating colorectal cancer.
Probing disrupted neurodevelopment in autism using human stem cell‐derived neurons and organoids: An outlook into future diagnostics and drug development

Autism spectrum disorders (ASDs) represent a spectrum of neurodevelopmental disorders characterized by impaired social interaction, repetitive or restrictive behaviors, and problems with speech. According to a recent report by the Centers for Disease Control and Prevention, one in 68 children in the US is diagnosed with ASDs. Although ASD‐related diagnostics and the knowledge of ASD‐associated genetic abnormalities have improved in recent years, our understanding of the cellular and molecular pathways disrupted in ASD remains very limited. As a result, no specific therapies or medications are available for individuals with ASDs. In this review, we describe the neurodevelopmental processes that are likely affected in the brains of individuals with ASDs and discuss how patient‐specific stem cell‐derived neurons and organoids can be used for investigating these processes at the cellular and molecular levels. Finally, we propose a discovery pipeline to be used in the future for identifying the cellular and molecular deficits and developing novel personalized therapies for individuals with idiopathic ASDs.
Right Ventricular Oxygen Delivery as a Determinant of Right Ventricular Functional Reserve during Exercise in Juvenile Swine with Chronic Pulmonary Hypertension.

AIMS Assessing right ventricular (RV) functional reserve is important for determining clinical status and prognosis in patients with pulmonary hypertension (PH). In this study, we aim to establish RV-oxygen (O2) deliveryas a determinant for RV-functional reserve during exercise in swine with chronic PH. METHODS AND RESULTS Chronic PH was induced by pulmonary vein banding (PVB), with sham operation serving as control. RV function and RV-O2delivery were measured over time in chronically instrumented swine, up to 12 weeks after PVB at rest and during exercise. At rest, RV afterload (pulmonary artery pressure and Ea) and contractility (Ees and dP/dtmax) were higher in PH compared with control with preserved cardiac index and RV-O2delivery. However, RV-functional reserve, as measured by the exercise-induced relative change (Δ) in cardiac index, dP/dtmax, and Ees,was decreased in PH, and RV-pulmonary arterial coupling was lower both at rest and during exercise in PH. Furthermore, the increase in RV-O2deliverywas attenuated in PH during exercise principally due to a lower systolic coronary blood flow in combination with an attenuated increase in aorta pressure while arterial O2content was not significantly altered in PH. Moreover, RV-O2delivery reserve correlated with RV-functional reserve, Dcardiac index (R2=0.85), DdP/dtmax(R2=0.49), and DEes (R2=0.70), all P<0.05. CONCLUSION The inability to sufficiently increase RV-O2supply to meet the increased O2demand during exercise is principally due to the reduced RV-perfusion relative to healthy control values and likely contributes to impaired RV-contractile function and thereby to the limited exercise capacity that is commonly observed in patients with PH.
Activation of the Transcription of BrGA20ox3 by a BrTCP21 Transcription Factor Is Associated with Gibberellin-Delayed Leaf Senescence in Chinese Flowering Cabbage during Storage

Several lines of evidence have implicated the involvement of the phytohormone gibberellin (GA) in modulating leaf senescence in plants. However, upstream transcription factors (TFs) that regulate GA biosynthesis in association with GA-mediated leaf senescence remain elusive. In the current study, we report the possible involvement of a TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) TF BrTCP21 in GA-delayed leaf senescence in Chinese flowering cabbage. Exogenous GA3 treatment maintained a higher value of maximum PSII quantum yield (Fv/Fm) and total chlorophyll content, accompanied by the repression of the expression of senescence-associated genes and chlorophyll catabolic genes, which led to the delay of leaf senescence. A class I member of TCP TFs BrTCP21, was further isolated and characterized. The transcript level of BrTCP21 was low in senescing leaves, and decreased following leaf senescence, while GA3 could keep a higher expression level of BrTCP21. BrTCP21 was further found to be a nuclear protein and exhibit trans-activation ability through transient-expression analysis in tobacco leaves. Intriguingly, the electrophoretic mobility shift assay (EMSA) and transient expression assay illustrated that BrTCP21 bound to the promoter region of a GA biosynthetic gene BrGA20ox3, and activated its transcription. Collectively, these observations reveal that BrTCP21 is associated with GA-delayed leaf senescence, at least partly through the activation of the GA biosynthetic pathway. These findings expand our knowledge on the transcriptional mechanism of GA-mediated leaf senescence.
Predicting Transitioning Walking Gaits: Hip and Knee Joint Trajectories From the Motion of Walking Canes

In recent years, wearable exoskeletons and powered prosthetics have been considered key elements to remedy mobility loss. One of the main challenges pertaining to this field is the prediction of the wearer’s desired motion. In this paper, we perform a human locomotion analysis, and we investigate the accuracy of predicting the angular position of the lower limb joints from the motion of walking canes. Nine healthy subjects took part of this study and performed a locomotor task that comprised straight walking on flat ground, stair ascent, and upright resting posture. Recurrent Neural Networks and polynomial fitting using Least Squares were used to model dynamic and static non-linear mappings, respectively, between the motion of a cane and its contra-lateral leg joints. A successful prediction of both the hip and knee joints was achieved using information from the cane only, and significant improvement of the prediction error was realized through the addition of data from the arm joints. Overall, Recurrent Neural Networks outperformed Least Squares for both joints’ angular position prediction. When using the cane only, the static maps were able to predict steady behaviour but failed in predicting transitioning, as opposed to RNN, which was able to capture both steady behaviour and transitions.
Virtual Point Removal for Large-Scale 3D Point Clouds with Multiple Glass Planes

Large-scale 3D point clouds (LS3DPCs) captured by terrestrial LiDAR scanners often include virtual points which are generated by glass reflection. The virtual points may degrade the performance of various computer vision techniques when applied to LS3DPCs. In this paper, we propose a virtual point removal algorithm for LS3DPCs with multiple glass planes. We first estimate multiple glass regions by modeling the reliability with respect to each glass plane, respectively, such that the regions are assigned high reliability when they have multiple echo pulses for each emitted laser pulse. Then we detect each point whether it is a virtual point or not. For a given point, we recursively traverse all the possible trajectories of reflection, and select the optimal trajectory which provides a point with a similar geometric feature to a given point at the symmetric location. We evaluate the performance of the proposed algorithm on various LS3DPC models with diverse numbers of glass planes. Experimental results show that the proposed algorithm estimates multiple glass regions faithfully and detects the virtual points successfully. Moreover, we also show that the proposed algorithm yields a much better performance of reflection artifact removal compared with the existing method qualitatively and quantitatively.
Thulium laser to manage a difficult biliary lithiasis: a first case report

The thulium laser, a new therapeutic laser, has recently been introduced in the field of endoscopy to overcome the limitations of classic thermoablative therapies, particularly in terms of the precision of the technique and the risks associated with the procedure [1]. Although its main use is for hemostasis and ablation of lesions in the upper gastrointestinal tract, the thulium laser can be used in many other clinical situations [2]. In the present case, we report a new endoscopic application of the thulium laser, not yet described in the available international literature. A 61-year-old woman presented to our center for a difficult lithiasis of the common bile duct associated with Mirizzi type II syndrome (cholecystocholedochal fistula). Two previous endoscopic treatments had been unsuccessful. The patient’s past medical history included chronic ischemic heart disease, arterial hypertension, and severe obesity. At cholangiography two biliary stones in the main bile duct were reported, the distal one located at the origin of the cystic duct. Several standard attempts to remove the stones using a 15-mm Fogarty biliary balloon (Cook Medical Inc., Bloomington, Indiana, USA) and a 7-Fr Dormia basket (Cook Medical) failed. Reviewing available literature on laser applications in endoscopy [1–3], we decided to use thulium laser lithotripsy (coagulation set-up: 20W ablation/1W coagulation, 365 micron fiber, 7 minutes application; Quanta System Srl., Milan, Italy) through SpyGlass cholangioscopy (Boston Scientific Corporation, Marlborough, Massachusetts, USA) (▶Video 1). We decided to complete the lithotripsy using a mechanical lithotripter (Cook Medical) with Dormia basket. Unfortunately, this strategy failed and the Dormia basket was blocked by the fragmented stones in the common bile duct. Lithotripsy was completed using a thulium laser to free the Dormia basket. As a precaution, we positioned a 7-Fr nasobiliary tube for 24 hours. No adverse events occurred and the patient was discharged after removal of the nasobiliary tube. To our knowledge, this is the first case of biliary stone lithotripsy using a thulium laser. The technique seems to be safe, and faster and more effective than standard holmium laser lithotripsy [3].
Developmental programming: Contribution of Epigenetic Enzymes to Antral Follicular Defects in the Sheep Model of PCOS.

Prenatal testosterone (T) treated sheep, similar to PCOS women, manifest oligo- / anovulation, hyperandrogenism, and polyfollicular ovary. The polyfollicular ovarian morphology, a result of persistence of antral follicles, arises in part by transcriptional changes in key mediators of follicular development that in turn are driven by epigenetic mechanisms. We hypothesized that prenatal T excess induces, in cell-specific manner, transcriptional changes in key mediators of follicular development associated with relevant changes in epigenetic machinery. Expression levels of key mediators of follicular development, DNA methyltransferases, and histone de- / methylases and de- / acetylases were determined in laser capture microdissection isolated antral follicular granulosa and theca and ovarian stromal cells from 21 months-of-age control and prenatal T-treated (100mg im. twice weekly from gestational day 30 to 90; term: 147 days) sheep. Changes in histone methylation was determined by immunofluorescence. Prenatal T-treatment induced 1) cell-specific changes in gene expression of key mediators of follicular development and steroidogenesis; 2) granulosa, theca and stromal cell specific changes in DNA methyltransferases and histone de- / methylases and deacetylases and 3) increases in histone 3 trimethylation at lysine 9 in granulosa and histone 3 dimethylation at lysine 4 in theca cells. The pattern of histone methylation was consistent with the expression profile of histone de- / methylases in the respective cells. These findings suggest that changes in expression of key genes involved in the development of polyfollicular phenotype in prenatal T-treated sheep are mediated at least in part by cell specific changes in epigenetic modifying enzymes.
Toxicological Studies of Czech Beers and Their Constituents

Background: Czech beers are unique because they are brewed using specific technology at a particular latitude and for being entirely produced in the area of the Czech Republic. The purpose of this work is the evaluation of toxicological effects of a variety of freeze-dried Czech beers, their raw materials (malts, hops and yeast) and processed-beer (wort, hopped wort and young beer). Methods: In vivo assays to evaluate the safety and protective effects in the Drosophila melanogaster eukaryotic system, and the in vitro evaluations of chemopreventive and DNA damage activity using the HL-60 tumour human cell line were carried out. Results: The safe effects for all the analysed substances and general protective effects against H2O2 were shown both at the individual and genomic level in the Drosophila animal model, with some exceptions. Moreover, all the substances were able to inhibit the tumour cell growth and to induce DNA damage in the HL-60 cells at different levels (proapoptotic, single/double strands breaks and methylation status). Conclusions: The promising effects shown by freeze-dried Czech beers due to their safety, protection against a toxin, chemopreventive potential and the induction of DNA damage in tumour cells, allow the proposition of Czech beer as a beverage with nutraceutic potential.
Three-dimensional evaluation of mandibular volume in patients with cleft lip and palate during the deciduous dentition period.

OBJECTIVES To examine the relationship between mandibular volume and craniofacial morphology in patients with cleft lip and palate using cone beam computed tomography (CBCT) and to compare these findings with control (noncleft) patients undergoing CBCT for other purposes during the deciduous dentition period. MATERIALS AND METHODS Eighty-four patients were categorized into the unilateral cleft lip and alveolus (UCLA) group (n = 25; mean age, 4.60 ± 0.40 years), unilateral cleft lip and palate (UCLP) group (n = 23; mean age, 4.52 ± 0.39 years), bilateral cleft lip and palate (BCLP) group (n = 22; mean age, 4.54 ± 0.37 years), and control group without cleft (n = 14; mean age, 5.19 ± 0.52 years). Mandibular volume and craniofacial cephalometric measurements were obtained using CBCT. All measurements were assessed by analysis of covariance (ANCOVA) using Bonferroni post hoc pairwise comparison tests. RESULTS ANCOVA revealed no statistically significant differences in mandibular volume among the groups. SNA° and ANB° were significantly larger in the UCLA and BCLP groups than in the control group. SN-MP° was smallest in the UCLA group. Co-A in the UCLP group was shorter than in the UCLA and BCLP groups. Go-Gn was shortest in the UCLP and BCLP groups compared with the control group. CONCLUSIONS Three-dimensional evaluation of craniofacial morphology using CBCT can provide valuable information on malocclusion and other dentoskeletal problems among patients with CLP.
Timing of respiratory virus molecular testing in emergency departments and its association with patient care outcomes: a retrospective observational study across six Australian hospitals

Objective A rapid molecular diagnostic test (RMDT) offers a fast and accurate detection of respiratory viruses, but its impact on the timeliness of care in the emergency department (ED) may depend on the timing of the test. The aim of the study was to determine if the timing of respiratory virus testing using a RMDT in the ED had an association with patient care outcomes. Design Retrospective observational study. Setting Linked ED and laboratory data from six EDs in New South Wales, Australia. Participants Adult patients presenting to EDs during the 2017 influenza season and tested for respiratory viruses using a RMDT. The timing of respiratory virus testing was defined as the time from a patient’s ED arrival to time of sample receipt at the hospital laboratory. Outcome measures ED length of stay (LOS), >4 hour ED LOS and having a pending RMDT result at ED disposition. Results A total of 2168 patients were included. The median timing of respiratory virus testing was 224 min (IQR, 133–349). Every 30 min increase in the timing of respiratory virus testing was associated with a 24.0 min increase in the median ED LOS (95% CI, 21.8–26.1; p<0.001), a 51% increase in the likelihood of staying >4 hours in ED (OR, 1.51; 95% CI, 1.41 to 1.63; p<0.001) and a 4% increase in the likelihood of having a pending RMDT result at ED disposition (OR, 1.04; 95% CI, 1.02 to 1.05; p<0.001) after adjustment for confounders. Conclusion The timing of respiratory virus molecular testing in EDs was significantly associated with a range of outcome indicators. Results suggest the potential to maximise the benefits of RMDT by introducing an early diagnostic protocol such as triage-initiated testing.