Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovery of a functional, contracted heme-binding motif within a multiheme cytochrome

Anaerobic ammonium-oxidizing (anammox) bacteria convert nitrite and ammonium via nitric oxide (NO) and hydrazine into dinitrogen gas by using a diverse array of proteins, including numerous c-type cytochromes. Many new catalytic and spectroscopic properties of c-type cytochromes have been unraveled by studies on the biochemical pathways underlying the anammox process. The unique anammox intermediate hydrazine is produced by a multiheme cytochrome c protein, hydrazine synthase, through the comproportionation of ammonium and NO and the input of three electrons. It is unclear how these electrons are delivered to hydrazine synthase. Here, we report the discovery of a functional tetraheme c-type cytochrome from the anammox bacterium Kuenenia stuttgartiensis with a naturally-occurring contracted Cys–Lys–Cys–His (CKCH) heme-binding motif, which is encoded in the hydrazine synthase gene cluster. The purified tetraheme protein (named KsTH) exchanged electrons with hydrazine synthase. Complementary spectroscopic techniques revealed that this protein harbors four low-spin hexa-coordinated hemes with His/Lys (heme 1), His/Cys (heme 2), and two His/His ligations (hemes 3 and 4). A genomic database search revealed that c-type cytochromes with a contracted CXCH heme-binding motif are present throughout the bacterial and archaeal domains in the tree of life, suggesting that this heme recognition site may be employed by many different groups of microorganisms.
The Outcome of TGFβ Antagonism in Metastatic Breast Cancer Models In Vivo Reflects a Complex Balance between Tumor-Suppressive and Proprogression Activities of TGFβ

Purpose: TGFβs are overexpressed in many advanced cancers and promote cancer progression through mechanisms that include suppression of immunosurveillance. Multiple strategies to antagonize the TGFβ pathway are in early-phase oncology trials. However, TGFβs also have tumor-suppressive activities early in tumorigenesis, and the extent to which these might be retained in advanced disease has not been fully explored. Experimental Design: A panel of 12 immunocompetent mouse allograft models of metastatic breast cancer was tested for the effect of neutralizing anti-TGFβ antibodies on lung metastatic burden. Extensive correlative biology analyses were performed to assess potential predictive biomarkers and probe underlying mechanisms. Results: Heterogeneous responses to anti-TGFβ treatment were observed, with 5 of 12 models (42%) showing suppression of metastasis, 4 of 12 (33%) showing no response, and 3 of 12 (25%) showing an undesirable stimulation (up to 9-fold) of metastasis. Inhibition of metastasis was immune-dependent, whereas stimulation of metastasis was immune-independent and targeted the tumor cell compartment, potentially affecting the cancer stem cell. Thus, the integrated outcome of TGFβ antagonism depends on a complex balance between enhancing effective antitumor immunity and disrupting persistent tumor-suppressive effects of TGFβ on the tumor cell. Applying transcriptomic signatures derived from treatment-naïve mouse primary tumors to human breast cancer datasets suggested that patients with breast cancer with high-grade, estrogen receptor–negative disease are most likely to benefit from anti-TGFβ therapy. Conclusions: Contrary to dogma, tumor-suppressive responses to TGFβ are retained in some advanced metastatic tumors. Safe deployment of TGFβ antagonists in the clinic will require good predictive biomarkers.
A novel, safe, fast and efficient treatment for Her2‐positive and negative bladder cancer utilizing an EGF‐anthrax toxin chimera

Bladder cancer is the sixth most common cancer in the United States, and it exhibits an alarming 70% recurrence rate. Thus, the development of more efficient antibladder cancer approaches is a high priority. Accordingly, this work provides the basis for a transformative anticancer strategy that takes advantage of the unique characteristics of the bladder. Unlike mucin‐shielded normal bladder cells, cancer cells are exposed to the bladder lumen and overexpress EGFR. Therefore, we used an EGF‐conjugated anthrax toxin that after targeting EGFR was internalized and triggered apoptosis in exposed bladder cancer cells. This unique agent presented advantages over other EGF‐based technologies and other toxin‐derivatives. In contrast to known agents, this EGF‐toxin conjugate promoted its own uptake via receptor microclustering even in the presence of Her2 and induced cell death with a LC50 < 1 nM. Furthermore, our data showed that exposures as short as ≈3 min were enough to commit human (T24), mouse (MB49) and canine (primary) bladder cancer cells to apoptosis. Exposure of tumor‐free mice and dogs with the agent resulted in no toxicity. In addition, the EGF‐toxin was able to eliminate cells from human patient tumor samples. Importantly, the administration of EGF‐toxin to dogs with spontaneous bladder cancer, who had failed or were not eligible for other therapies, resulted in ~30% average tumor reduction after one treatment cycle. Because of its in vitro and in vivo high efficiency, fast action (reducing treatment time from hours to minutes) and safety, we propose that this EGF–anthrax toxin conjugate provides the basis for new, transformative approaches against bladder cancer.
Health-Related Quality of Life Before and After Use of a Smartphone App for Adolescents and Young Adults With Cancer: Pre-Post Interventional Study

Background Adolescent and young adult (AYA) patients with cancer are a group with underexplored needs throughout treatment and in survivorship. This missing knowledge can influence their quality of life (QoL). Given this fact, we have developed a smartphone app based on a cocreation process and have an investigation of QoL among users planned as part of pilot testing this app. Future research is warranted to determine the effect of mobile health (mHealth) tools such as smartphone apps among the AYA cancer population. Objective The aim of this study was to investigate the feasibility of a smartphone app among AYA patients with cancer in active treatment and posttreatment, in a pilot test by measuring health-related QoL before and after the use of the app. Methods Participants were recruited via the youth support initiative and social organization for AYAs with cancer, Kræftværket, based at Rigshospitalet, University Hospital of Copenhagen, Denmark. Participants were evenly distributed in active treatment and posttreatment groups. After written informed consent, all participants were asked to use the app Kræftværket as they deemed appropriate over a 6-week period. The participants were asked to complete the 30-item European Organization for Research and Treatment of Cancer Quality of Life Questionnaire before and after the 6-week period. The collected QoL data were analyzed with t tests to determine differences between groups and from baseline. Results In total, we enrolled 20 participants, 10 in active treatment and 10 posttreatment (median time after treatment was 4 months) group. Median age of the participants was 25 years. No differences in QoL were seen at baseline (P=.65). The posttreatment group experienced a significant increase in overall QoL after the 6-week period (global QoL: baseline 62.5, SD 22.3; after 6 weeks 80.8, SD 9.7; P=.04). For the group in active treatment, the QoL remained stable throughout the 6 weeks. Conclusions This study shows the feasibility and possible effect on QoL associated with the use of an mHealth tool in AYA patients. mHealth support tools are warranted for this population.
CRISPR/CAS9 Gene-Editing Strategies in Cardiovascular Cells.

Cardiovascular diseases are among the main causes of morbidity and mortality in Western countries and considered as a leading public health issue. Therefore, there is a strong need for new disease models to support the development of novel therapeutics approaches. The successive improvement of genome editing tools with zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and more recently with clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) has enabled the generation of genetically modified cells and organisms with much greater efficiency and precision than before. The simplicity of CRISPR/Cas9 technology made it especially suited for different studies, both in vitro and in vivo, and has been used in multiple studies evaluating gene functions, disease modeling, transcriptional regulation, and testing of novel therapeutic approaches. Notably, with the parallel development of human induced pluripotent stem cells (hiPSCs), the generation of knockout and knockin human cell lines significantly increased our understanding of mutation impacts and physiopathological mechanisms within the cardiovascular domain. Here, we review the recent development of CRISPR-Cas9 genome editing, the alternative tools, the available strategies to conduct genome editing in cardiovascular cells with a focus on its use for correcting mutations in vitro and in vivo both in germ and somatic cells. We will also highlight that, despite its potential, CRISPR/Cas9 technology comes with important technical and ethical limitations. The development of CRISPR/Cas9 genome editing for cardiovascular diseases indeed requires to develop a specific strategy in order to optimize the design of the genome editing tools, the manipulation of DNA repair mechanisms, the packaging and delivery of the tools to the studied organism, and the assessment of their efficiency and safety.
Neutropenic complications in the PANTHER phase III study of adjuvant tailored dose-dense chemotherapy in early breast cancer

Abstract Introduction: Myelosuppresion is a common side effect of chemotherapy and granulocyte-colony stimulating factor (G-CSF) is often used to reduce the risk of neutropenic events. The purpose of this exploratory analysis was to investigate neutropenic complications in the phase III PANTHER trial of standard 3-weekly chemotherapy with 5-fluorouracil, epirubicin and cyclophosphamide plus docetaxel (FEC/D) versus bi-weekly tailored dose-dense EC/D adjuvant chemotherapy in breast cancer. Patients and methods: Febrile neutropenia, neutropenic infection and infection grade 3–4 according to CTC AE 3.0, were explored in relation to G-CSF use. Per cycle analysis was performed concerning dose reduction and dose delays in conjunction with G-CSF administration. Results: In the experimental group, 98.9% of patients received primary G-CSF support during EC and 97.4% during docetaxel, compared with 49.7% during FEC and 63.88% during docetaxel in the standard group. Overall, the use of G-CSF was associated with a lower risk for developing neutropenic events (OR 0.44, 95% CI 0.35–0.55, p < .001). Chemotherapy delays due to neutropenia and leukopenia were significantly decreased among patients that received G-CSF (OR 0.098, 95% CI 0.06–0.15 and OR 0.32, 95% CI 0.18–0.58, respectively). Discussion: In conclusion, G-CSF support reduces neutropenic events and permits increased relative dose intensity, which is essential for improved survival outcomes.
Model-based QTL detection is sensitive to slight modifications in model formulation

Classical crop models have been developed to predict crop yield and quality, and they are based on physiological and environmental inputs. After molecular discoveries, models should integrate genetic variation to allow predictions that are more genotype-dependent. An interesting approach, Quantitative Trait Locus (QTL)-based ecophysiological modeling, has shown promising results for the design of ideotypes that are adapted to biotic and abiotic stresses, but there are still limitations to attaining a fully integrated model. The aim of this case study is to clarify the impact of choosing different model equations (closely related and with different numbers of parameters) and optimization methods on the detection of QTLs controlling the parameters of crop growth. Different growth equations were parameterized based on a genetic population by following different approaches. The correlations between parameters were analyzed, and two different strategies were adopted to address the correlation issue. QTL analysis was performed on the optimized values of the parameters of the growth equations and on the observed dry mass (DM) data to validate the QTLs detected. Overall, models and strategies resulted in different QTLs being detected. Similar LOD profiles but with peaks of different heights were observed, some of which were significant, resulting in different numbers of QTLs. In some cases, peaks had slightly different positions or were absent. Even closely related growth models led to the detection of different QTLs. The goodness of fit and complexity of the growth models were found to be insufficient to select the best model. Calculating parameters independently of observed data may not be a good strategy, whereas setting parameters independent of the genotype is recommended. Given the large-scale global optimization problem and the strong correlations between parameters, the two algorithms tested showed poor performance. Currently, the lack of effective algorithms is the main obstacle to answering the question posed. The authors therefore suggest testing different model formulations and comparing the QTLs detected before choosing the best formulation to use in an ecophysiological modeling approach based on QTLs.
A gene-edited mouse model of limb-girdle muscular dystrophy 2C for testing exon skipping

ABSTRACT Limb-girdle muscular dystrophy type 2C is caused by autosomal recessive mutations in the γ-sarcoglycan (SGCG) gene. The most common SGCG mutation is a single nucleotide deletion from a stretch of five thymine residues in SGCG exon 6 (521ΔT). This founder mutation disrupts the transcript reading frame, abolishing protein expression. An antisense oligonucleotide exon-skipping method to reframe the human 521ΔT transcript requires skipping four exons to generate a functional, internally truncated protein. In vivo evaluation of this multi-exon skipping, antisense-mediated therapy requires a genetically appropriate mouse model. The human and mouse γ-sarcoglycan genes are highly homologous in sequence and gene structure, including the exon 6 region harboring the founder mutation. Herein, we describe a new mouse model of this form of limb-girdle muscular dystrophy generated using CRISPR/Cas9-mediated gene editing to introduce a single thymine deletion in murine exon 6, recreating the 521ΔT point mutation in Sgcg. These mice express the 521ΔT transcript, lack γ-sarcoglycan protein and exhibit a severe dystrophic phenotype. Phenotypic characterization demonstrated reduced muscle mass, increased sarcolemmal leak and fragility, and decreased muscle function, consistent with the human pathological findings. Furthermore, we showed that intramuscular administration of a murine-specific multiple exon-directed antisense oligonucleotide cocktail effectively corrected the 521ΔT reading frame. These data demonstrate a molecularly and pathologically suitable model for in vivo testing of a multi-exon skipping strategy to advance preclinical development of this genetic correction approach. Summary: The most common SGCG mutation that causes LGMD 2C has been modeled in mice using gene editing, providing a platform for preclinical evaluation of multi-exon antisense therapy.
Development and application of implementation tools for rehabilitation guidelines.

OBJECTIVE To describe a project to develop guideline implementation tools (GItools) for rehabilitation guidelines, and a collaboration between a guideline producer and a healthcare organization to implement guidelines into care pathways. DESIGN Descriptive case study. METHODS A national guideline organization in Finland launched a 3-year project in 2015 to implement rehabilitation recommendations. Usability of the GItools was evaluated and improved, based on literature, workshops and surveys. An implementation plan guided the production of the GItools. An implementation plan was developed to integrate the shoulder disorders guideline into a care pathway at Päijät-Häme district rehabilitation unit. The implementation plan was produced in 3 facilitated workshops, which included brainstorming, snowballing, prioritizing and short lectures. RESULTS Twenty implementation plans and 119 different GItools for 22 guidelines were developed. The GItools, in particular patient material, were perceived as useful for the facilitation of guideline implementation. Four seminars and 14 sessions of continuous medical education were arranged. A plan was developed and executed for the implementation of the shoulder disorders guideline. CONCLUSION It is feasible for a guideline producer to systematically include GItools into rehabilitation guidelines. This implementation project was an example of a successful collaboration between a guideline producer and a healthcare organization.
Heat-Dependent Desorption of Proanthocyanidins from Grape-Derived Cell Wall Material under Variable Ethanol Concentrations in Model Wine Systems

Desorption of proanthocyanidins (PA) from grape cell wall material (CWM) was investigated in solutions of varying ethanol concentrations and increasing temperature. The results reveal the reversibility of PA-CWM interactions and the role that temperature and ethanol concentration play in the extent of PA desorption. Sequentially raising temperature from 15 to 35 °C resulted in desorption of up to 48% of the initial adsorbed PA. A comparison to a phenolic extraction model showed significant differences between the predicted and actual amount of PA that desorbed from the CWM. This suggests that the initial conditions of temperature and ethanol concentration must be considered when estimating PA extraction in red wine production. Under typical winemaking conditions, a significant amount of PA may be irreversibly adsorbed if exposed to CWM at low temperature (i.e., cold soak). A compositional analysis suggests the selective desorption of large molecular weight PA from CWM under all experimental conditions. Additionally, a preferential desorption of skin-derived PA over seed-derived PA was noted in the absence of ethanol.
Uric acid levels in gestational hypertensive women predict preeclampsia and outcome of small-for-gestational-age infants

Abstract Objective This study aims to ascertain whether serum uric acid is a suitable predictor of preeclampsia and/or the delivery of small-for-gestational-age infants for women with gestational hypertension. Methods 364 singleton pregnant women with initial presentation of gestational hypertension were recruited and followed up until 6 weeks after delivery. Uric acid z score and binary logistic regression analysis were applied to establish the relationship between serum uric acid and the chance of progression to preeclampsia and giving birth to a small-for-gestational-age infant. Furthermore, receiver operating characteristic (ROC) analysis was used to evaluate the prediction value of serum uric acid. Results Uric acid z score and binary logistic regression analysis indicated that elevated serum uric acid increased the chances of gestational hypertension progression to preeclampsia and subsequent delivery of small-for-gestational-age infants. ROC analysis showed that serum uric acid at a cutoff value of 303μmol l-1, moderately predict the development of preeclampsia and the delivery of small-for-gestational age infants. The prediction values of preeclampsia were 90.7% sensitivity, 69.4% specificity, 97.7% negative predictor values and 34.0% positive predictor values, comparatively, the prediction value for small-for-gestational age infant was low. The ROC curve improved with 95.8% sensitivity, 86.7% specificity, 98.1% NPV, and 74.2% PPV in the Chinese Han women with early onset of gestational hypertension thus the diagnosis of gestational hypertension before 34 weeks. Conclusions Elevated serum uric acid in Chinese Han women with gestational hypertension indicated an increased risk of their progression to preeclampsia and the further delivering of small-for-gestational-age infants.
The simplified oral flucloxacillin absorption test: an accurate method to identify patients with inadequate oral flucloxacillin absorption.

BACKGROUND The preferred treatment for severe methicillin-sensitive Staphylococcus aureus infections is flucloxacillin, a small-spectrum antibiotic administered intravenously (IV) and orally. However, clinicians switch to the less preferred broad-spectrum antibiotics because of the variable absorption after oral administration of flucloxacillin. A classical oral absorption test (OAT) requires overnight fasting and interruption of IV therapy, and is laborious. In the current study, we investigated whether a simplified OAT can be utilized in a clinical setting to guide antibiotic treatment in patients with severe S. aureus infections. For this, OAT IV therapy is continued and oral dosing is performed after a one-hour fast and implemented after a small study. METHODS In 196 patients receiving IV flucloxacillin by continuous infusion, a classical OAT (test A) or simplified version of the OAT (test B) was performed. In both tests, 1 g oral flucloxacillin was given and serum samples were taken prior to intake and at one and two hours after administration. Flucloxacillin concentrations were determined by high-performance liquid chromatography. Adequate absorption was defined as an increase of flucloxacillin concentration of at least 10 mg/l after one or two hours compared to baseline. RESULTS In a sample of 196 patients (85 F/111 M), test A was performed in 28 patients, and test B in 168 patients. Age, gender, and baseline values of creatinine and albumin were similar in both groups. The maximal increase of flucloxacillin absorption was highly variable between patients. In 26 (13%) of the 196 patients, the flucloxacillin increase did not reach the value of 10 mg/l. The median (interquartile range, IQR) maximal increase of flucloxacillin absorption was 22.0 (15-31.25) mg/l for test A and 21.5 (13-32.25) mg/l for test B. There was no significant difference in maximal increase of flucloxacillin absorption between test A and B (p = 0.74), nor between males and females (p = 0.95). Age, creatinine, and albumin were not correlated with flucloxacillin levels. CONCLUSIONS The simplified version of the OAT is useful to identify patients with adequate oral flucloxacillin absorption, and to ensure the effective continuation of an oral small-spectrum treatment.
Association of Histologic Disease Activity With Progression of Nonalcoholic Fatty Liver Disease

Key Points Question In patients with nonalcoholic fatty liver disease who are not undergoing specific therapeutic interventions, what factors are associated with progression and regression of hepatic fibrosis? Findings In this cohort study of 446 patients, high baseline nonalcoholic fatty liver disease activity score and changes in the score were associated with concordant changes in fibrosis. Weight gain, high baseline aspartate aminotransferase level, and increases in the aspartate aminotransferase level were associated with fibrosis progression. Meaning These data may support the use of therapeutics targeting disease activity in nonalcoholic steatohepatitis and the use of short-term changes in the nonalcoholic fatty liver disease activity score as an end point in such clinical trials; in clinical practice, weight gain and an increasing aspartate aminotransferase level should increase suspicion of increasing fibrosis.