Miracle-dz/UniFAR-FTUs huggingface dataset:
Human BCR/ABL1 induces chronic myeloid leukemia-like disease in zebrafish

Chronic myeloid leukemia (CML) is induced by the BCR/ABL1 oncogene, which encodes a protein tyrosine kinase. We examined the effect of direct overexpression of the human p210BCR/ABL1 oncoprotein in zebrafish. Humanized p210BCR/ABL1 protein was detectable in Tg(hsp70: p210BCR/ABL1) transgenic zebrafish embryos and adult kidney marrow. Transgenic zebrafish developed CML, which could be induced via cells transplanted into recipients. The expression of human BCR/ABL1 promoted myeloid lineages in Tg(hsp70:p210BCR/ABL1) transgenic embryos. A total of 77 of 101 (76.24%) Tg(hsp70:p210BCR/ABL1) adult transgenic zebrafish (age 6 months-1 year) developed CML. CML in zebrafish showed a triphasic phenotype, similar to that in humans, involving a chronic phase predominantly characterized by neutrophils in various degrees of maturation, an accelerated phase with an increase in blasts and immature myeloid elements, and a blast phase with >90% blasts in both the peripheral blood and kidney marrow. Tyrosine kinase inhibitors, as the standard drug treatment for human CML, effectively reduced the expanded myeloid population in Tg(hsp70:p210BCR/ABL1) transgenic embryos. Moreover, we screened a library of 171 compounds and identified ten new drugs against BCR/ABL1 kinase-dependent or -independent pathways that could also reduce lcp1+ myeloid cell numbers in Tg(hsp70:p210BCR/ABL1) transgenic embryos. In summary, we generated the first humanized zebrafish CML model that recapitulates many characteristics of human CML. This novel in vivo model will help to elucidate the mechanisms of CML disease progression and allow high-throughput drug screening of possible treatments for this disease.
Zebrafish Wtx is a negative regulator of Wnt signaling but is dispensable for embryonic development and organ homeostasis

The X‐chromosomally linked gene WTX is a human disease gene and a member of the AMER family. Mutations in WTX are found in Wilms tumor, a form of pediatric kidney cancer and in patients suffering from OSCS (Osteopathia striata with cranial sclerosis), a sclerosing bone disorder. Functional data suggest WTX to be an inhibitor of the Wnt/β‐catenin signaling pathway. Deletion of Wtx in mouse leads to perinatal death, impeding the analysis of its physiological role.
Study on the Synthetic Characteristics of Biomass-Derived Isosorbide-Based Poly(arylene ether ketone)s for Sustainable Super Engineering Plastic

Demand for the development of novel polymers derived from biomass that can replace petroleum resources has been increasing. In this study, biomass-derived isosorbide was used as a monomer in the polymerization of poly(arylene ether ketone)s, and its synthetic characteristics were investigated. As a phase-transfer catalyst, crown ether has increased the weight-average molecular weight of polymers over 100 kg/mol by improving the reaction efficiency of isosorbide and minimizing the effect of moisture. By controlling the experimental parameters such as halogen monomer, polymerization solvent, time, and temperature, the optimal conditions were found to be fluorine-type monomer, dimethyl sulfoxide, 24 h, and 155 °C, respectively. Biomass contents from isosorbide-based polymers were determined by nuclear magnetic resonance and accelerator mass spectroscopy. The synthesized polymer resulted in a high molecular weight that enabled the preparation of transparent polymer films by the solution casting method despite its weak thermal degradation stability compared to aromatic polysulfone. The melt injection molding process was enabled by the addition of plasticizer. The tensile properties were comparable or superior to those of commercial petrochemical specimens of similar molecular weight. Interestingly, the prepared specimens exhibited a significantly lower coefficient of thermal expansion at high temperatures over 150 °C compared to polysulfone.
Point‐of‐care analyses of blood samples from intraosseous access in pre‐hospital critical care

Intraosseous (IO) access is used for fluid and medication administration in emergency situations when difficulties with vascular access are encountered. IO access would be readily available to take samples for point‐of‐care (POC) analysis, but there is scarce evidence about the reliability of POC analysis of IO samples among emergency patients. The aim of this study was to evaluate the feasibility and reliability of POC analysis of IO samples in critically ill pre‐hospital patients.
A Targeted Mass Spectrometry Strategy for Developing Proteomic Biomarkers: A Case Study of Epithelial Ovarian Cancer*

The discovery of protein biomarkers is hampered by the limited availability of assays needed for the reproducible quantification of proteins in complex biological matrices such as blood plasma. Here, we describe a biomarker development strategy based on large scale targeted proteomics measurements including a rigorous experimental design and data analysis. Applied to epithelial ovarian cancer, we identified a five-protein biomarker signature that in combination with CA125 increased sensitivity in detecting epithelial ovarian cancer compared to CA125 alone. Graphical Abstract Highlights Rigorous experimental design and data analysis for large-scale SRM studies. Plasma-based biomarker signature combined with CA125 for ovarian cancer detection. Broadly applicable strategy for the development of diagnostic biomarker assays. Protein biomarkers for epithelial ovarian cancer are critical for the early detection of the cancer to improve patient prognosis and for the clinical management of the disease to monitor treatment response and to detect recurrences. Unfortunately, the discovery of protein biomarkers is hampered by the limited availability of reliable and sensitive assays needed for the reproducible quantification of proteins in complex biological matrices such as blood plasma. In recent years, targeted mass spectrometry, exemplified by selected reaction monitoring (SRM) has emerged as a method, capable of overcoming this limitation. Here, we present a comprehensive SRM-based strategy for developing plasma-based protein biomarkers for epithelial ovarian cancer and illustrate how the SRM platform, when combined with rigorous experimental design and statistical analysis, can result in detection of predictive analytes. Our biomarker development strategy first involved a discovery-driven proteomic effort to derive potential N-glycoprotein biomarker candidates for plasma-based detection of human ovarian cancer from a genetically engineered mouse model of endometrioid ovarian cancer, which accurately recapitulates the human disease. Next, 65 candidate markers selected from proteins of different abundance in the discovery dataset were reproducibly quantified with SRM assays across a large cohort of over 200 plasma samples from ovarian cancer patients and healthy controls. Finally, these measurements were used to derive a 5-protein signature for distinguishing individuals with epithelial ovarian cancer from healthy controls. The sensitivity of the candidate biomarker signature in combination with CA125 ELISA-based measurements currently used in clinic, exceeded that of CA125 ELISA-based measurements alone. The SRM-based strategy in this study is broadly applicable. It can be used in any study that requires accurate and reproducible quantification of selected proteins in a high-throughput and multiplexed fashion.
Derivo Embolization Device for the Treatment of Intracranial Aneurysms.

Background and Purpose- Flow diverter technology improvements are necessary to provide safe and good results and enable the treatment of a larger variety of aneurysms. We report a nationwide experience with the Derivo Embolization Device in the treatment of intracranial aneurysms. Methods- BRAIDED (Brazilian Registry of Aneurysms Assigned to Intervention With the Derivo Embolization Device) is a multicenter, prospective, interventional, single-arm trial of the Derivo Embolization Device for the treatment of intracranial aneurysms. The primary effectiveness end point was total aneurysm occlusion at 6- and 12-month angiographies. The secondary safety end point was the absence of serious adverse events during follow-up. Univariable and multivariable logistic regression was performed to identify predictors of aneurysm persistence, periprocedural complications, and adverse events during follow-up. Results- Between December 2016 and October 2018, 146 patients harboring 183 intracranial aneurysms were treated in 151 interventions at 7 centers. Derivo Embolization Device placement was technically successful in all patients. Most aneurysms (86.9%) were located at the internal carotid artery, and the mean diameter was 6.7 mm. At 6 months, 113 of 140 (80.7%) aneurysms met the study's primary end point, and 74 of 83 (89.2%) met the study's primary end point at 12 months. Saccular morphology of the aneurysm (odds ratio, 5.66; 95% CI, 1.01-31.77) and the presence of a branch arising from the sac (odds ratio, 6.36; 95% CI, 2.11-22.36) predicted persistence. A long duration of follow-up (odds ratio, 0.86; 95% CI, 0.78-0.95) predicted total occlusion. Of the 146 enrolled patients, 138 (94.5%) were treated without serious adverse events during follow-up. In the multivariable analysis, aneurysms located at a sidewall were less likely to experience these events than those located at bifurcations (odds ratio, 0.07; 95% CI, 0.01-0.51). Conclusions- The Derivo Embolization Device is a safe and effective treatment for intracranial aneurysms. Clinical Trial Registration- URL: http://plataformabrasil.saude. gov.br/login.jsf . Unique identifier: CAAE 77089717.7. 1001.5125.
Validating a New Tablet-Based Tool in the Determination of Cochlear Implant Angular Insertion Depth.

OBJECTIVE The objective of this study is to determine the reliability of a new tablet-based software that utilizes postoperative computed tomography to determine angular insertion depth (AID), cochlear duct length (CDL), and the cochlear place frequency of individual electrodes in cochlear implant recipients. PATIENTS Twenty adult cochlear implant recipients with lateral-wall electrode arrays of varying lengths were included in the study. INTERVENTION Cochlear and electrode array measurements were made by 2 otolaryngologists using a tablet-based software. The user manually identifies the modiolus, round window, and each electrode contact to calculate AID. The user also manually identifies cochlear landmarks to calculate the CDL. The AID and CDL are applied to the Greenwood function to obtain an estimate of the cochlear place frequency for each electrode. MAIN OUTCOME MEASURE(S) The primary outcome measure was the reliability of the instrument, as assessed with intra and interrater reliability of measured AID and CDL. The resultant differences in the estimated cochlear place frequency of the most apical electrode were also evaluated. RESULTS A broad range of AIDs were observed (390°-659°). Intraclass correlation coefficients for intra (0.991) and interrater reliability (0.980) of AID of the most apical electrode contact were excellent. Intra (0.820) and interrater reliability (0.784) of CDL were also excellent. The estimated cochlear place frequency for the most apical electrode differed by an average of 6.7% (0-18.7%) across the 2 raters. CONCLUSION There is excellent agreement amongst clinicians in the determination of AID and CDL, resulting in small changes in estimated cochlear place frequency of the most apical electrode using this new software.
Characterization of temperature‐dependent hemin uptake receptors HupA and HvtA in Vibrio vulnificus

The Gram‐negative pathogen Vibrio vulnificus produces several iron‐sequestration systems including a hemin uptake system in response to iron limitation as a means to acquire this essential element. Strains of this organism are capable of causing serious septicemia in humans and eels, where hemin is abundant and an advantageous source of iron. Vibrio vulnificus hemin uptake systems consist of HupA, a well studied outer membrane protein, and a recently identified HvtA protein receptor. In this study, we confirmed that the expression of the hvtA gene is iron‐regulated in a fur‐dependent manner. When analyzed for virulence in a hemin‐overloaded murine model system, the hupA gene was more important for establishing infection than the hvtA gene. Transcriptional profiling of these genes using strains of two different biotypes, biotype 1 (human pathogen) and biotype 2 (eel pathogen), showed that the expression of the two receptors was also regulated in response to temperature. The expression of hupA was highly induced in elevated temperatures in the human pathogenic strain when tested in iron‐depleted conditions. Conversely, hvtA expression was induced significantly in the eel pathogenic strain at a lower temperature, a condition where the hupA locus was relatively repressed. Our results indicate that although both hupA and hvtA are involved for optimal hemin uptake in V. vulnificus, their expression is dually regulated by the environmental cues of iron concentration and temperature. Together, these data suggest that the virulence genes hupA and hvtA are tightly regulated and strictly induced during iron limitation combined with the physiological temperature of the host organism.
A tailored approach towards informing relatives at risk of inherited cardiac conditions: study protocol for a randomised controlled trial

Introduction In current practice, probands are asked to inform relatives about the possibility of predictive DNA testing when a pathogenic variant causing an inherited cardiac condition (ICC) is identified. Previous research on the uptake of genetic counselling and predictive DNA testing in relatives suggests that not all relatives are sufficiently informed. We developed a randomised controlled trial to evaluate the effectiveness of a tailored approach in which probands decide together with the genetic counsellor which relatives they inform themselves and which relatives they prefer to have informed by the genetic counsellor. Here, we present the study protocol of this randomised controlled trial. Methods A multicentre randomised controlled trial with parallel-group design will be conducted in which an intervention group receiving the tailored approach will be compared with a control group receiving usual care. Adult probands diagnosed with an ICC in whom a likely pathogenic or pathogenic variant is identified will be randomly assigned to the intervention or control group (total sample: n=85 probands). Primary outcomes are uptake of genetic counselling and predictive DNA testing by relatives (total sample: n=340 relatives). Secondary outcomes are appreciation of the approach used and impact on familial and psychological functioning, which will be assessed using questionnaires. Relatives who attend genetic counselling will be asked to fill out a questionnaire as well. Ethics and dissemination Ethical approval was obtained from the Medical Ethical Committee of the Amsterdam University Medical Centres (MEC 2017-145), the Netherlands. All participants will provide informed consent prior to participation in the study. Results of the study on primary and secondary outcome measures will be published in peer-reviewed journals. Trial registration number NTR6657; Pre-results.
Misidentification of MLL3 and other mutations in cancer due to highly homologous genomic regions

Abstract The MLL3 gene has been shown to be recurrently mutated in many malignancies including in families with acute myeloid leukemia. We demonstrate that many MLL3 variant calls made by exome sequencing are false positives due to misalignment to homologous regions, including a region on chr21, and can only be validated by long-range PCR. Numerous other recurrently mutated genes reported in COSMIC and TCGA databases have pseudogenes and cannot also be validated by conventional short read-based sequencing approaches. Genome-wide identification of pseudogene regions demonstrates that frequency of these homologous regions is increased with sequencing read lengths below 200 bps. To enable identification of poor quality sequencing variants in prospective studies, we generated novel genome-wide maps of regions with poor mappability that can be used in variant calling algorithms. Taken together, our findings reveal that pseudogene regions are a source of false-positive mutations in cancers
Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of their CD Spectra.

While successful in the structural determination of ordered biomolecules, the spectroscopic investigation of oligopeptides in solution is hindered by their complex and rapidly changing conformational ensemble. The measured circular dichroism (CD) spectrum of an oligopeptide is an ensemble average over all microstates, severely limiting its interpretation, in contrast to ordered biomolecules. Spectral deconvolution methods to estimate the secondary structure contributions in the ensemble are still mostly based on databases of larger ordered proteins. Here we establish how the interpretation of CD spectra of oligopeptides can be enhanced by the ability to compute the same observable from a set of atomic coordinates. Focusing on two representative oligopeptides featuring a known propensity towards an α-helical and β-hairpin motif, respectively, we compare and cross-validate the structural information coming from: deconvolution of the experimental CD spectra, sequence-based de novo structure prediction and molecular dynamics simulations based on enhanced sampling methods. We find that small conformational variations can give rise to significant changes in the CD signals. While for the simpler conformational landscape of the α-helical peptide de novo structure prediction can already give reasonable agreement with the experiment, an extended ensemble of conformers needs to be considered for the β-hairpin sequence.
Implementation of the Symptom Navi © Programme for cancer patients in the Swiss outpatient setting: a study protocol for a cluster randomised pilot study (Symptom Navi© Pilot Study)

Introduction Self-management interventions show promising results on symptom outcomes and self-management behaviours. The Symptom Navi© Programme (SN©P) is a nurse-led intervention supporting patients’ symptom self-management during anticancer treatment. It consists of written patient information (Symptom Navi© Flyers (SN©Flyers)), semistructured consultations and a training manual for nurses. Methods and analysis This pilot study will evaluate the implementation of the SN©P based on the Reach Effectiveness—Adoption Implementation Maintenance framework at Swiss outpatient cancer centres. We will use a cluster-randomised design and randomise the nine participating centres to the intervention or usual care group. We expect to include 140 adult cancer patients receiving first-line systemic anticancer treatment. Trained nurses at the intervention clusters will provide at least two semistructured consultations with the involvement of SN©Flyers. Outcomes include patients’ accrual and retention rates, patient-reported interference of symptoms with daily functions, symptom burden, perceived self-efficacy, quality of nursing care, nurse-reported facilitators and barriers of adopting the programme, nurses’ fidelity of providing the intervention as intended, and patients’ safety (patients timely reporting of severe symptoms). We will use validated questionnaires for patient-reported outcomes, focus group interviews with nurses and individual interviews with oncologists. Linear mixed models will be used to analyse patient-reported outcomes. Focus group and individual interviews will be analysed by thematic analysis. Ethics and dissemination The Symptom Navi© Pilot Study has been reviewed and approved by Swiss Ethic Committee Bern (KEK-BE: 2017–00020). Results of the study will be disseminated in peer-reviewed journal and at scientific conferences. Trial registration number NCT03649984; Pre-results.
Adaptable Scripting in Computer-Supported Collaborative Learning to Foster Knowledge and Skill Acquisition

Collaboration scripts have repeatedly been implemented in CSCL with the aim of improving individual acquisition of domain-specific knowledge and domain-general skills. However, it is a delicate compromise between taking the "freedom from" (i.e., constraining the learners' efforts to self-regulate their learning) and providing the "freedom to" learners (i.e., enabling them to collaborate on a higher level) when implementing CSCL scripts. The study reported here aimed to answer the question whether adaptable scripting would be an effective approach to realize flexibility in scripted CSCL. 54 university students participated in this study which compared three experimental conditions (unscripted CSCL, CSCL with a non-adaptable script, CSCL with an adaptable script). Results showed that the adaptable script improved individual knowledge and skill acquisition compared to the other two conditions.
Effective hematopoietic stem cell-based gene therapy in a murine model of hereditary pulmonary alveolar proteinosis

Hereditary pulmonary alveolar proteinosis due to GM-CSF receptor deficiency (herPAP) constitutes a life-threatening lung disease characterized by alveolar deposition of surfactant protein secondary to defective alveolar macrophage function. As current therapeutic options are primarily symptomatic, we have explored the potential of hematopoietic stem cell-based gene therapy. Using Csf2rb−/− mice, a model closely reflecting the human herPAP disease phenotype, we here demonstrate robust pulmonary engraftment of an alveolar macrophage population following intravenous transplantation of lentivirally corrected hematopoietic stem and progenitor cells. Engraftment was associated with marked improvement of critical herPAP disease parameters, including bronchoalveolar fluid protein, cholesterol and cytokine levels, pulmonary density on computed tomography scans, pulmonary deposition of Periodic Acid-Schiff+ material as well as respiratory mechanics. These effects were stable for at least nine months. With respect to engraftment and alveolar macrophage differentiation kinetics, we demonstrate the rapid development of CD11c+/SiglecF+ cells in the lungs from a CD11c–/SiglecF+ progenitor population within four weeks after transplantation. Based on these data, we suggest hematopoietic stem cell-based gene therapy as an effective and cause-directed treatment approach for herPAP.
Interactions of nanomaterials with ion channels and related mechanisms

The pharmacological potential of nanotechnology, especially in drug delivery and bioengineering, has developed rapidly in recent decades. Ion channels, which are easily targeted by external agents, such as nanomaterials (NMs) and synthetic drugs, due to their unique structures, have attracted increasing attention in the fields of nanotechnology and pharmacology for the treatment of ion channel‐related diseases. NMs have significant effects on ion channels, and these effects are manifested in many ways, including changes in ion currents, kinetic characteristics and channel distribution. Subsequently, intracellular ion homeostasis, signalling pathways, and intracellular ion stores are affected, leading to the initiation of a range of biological processes. However, the effect of the interactions of NMs with ion channels is an interesting topic that remains obscure. In this review, we have summarized the recent research progress on the direct and indirect interactions between NMs and ion channels and discussed the related molecular mechanisms, which are crucial to the further development of ion channel‐related nanotechnological applications.