Miracle-dz/UniFAR-FTUs huggingface dataset:
The use of F-FDG PET/CT in testicular cancer

Testicular germ cell tumors are one of the most common neoplasms in young men. After inguinal orchiectomy is performed, treatment options range from active surveillance to chemotherapy, radiation therapy or retroperitoneal lymphadenectomy. For the accurate use of the different treatment options, precise imaging techniques are necessary to reduce side effects of the aggressive therapies but also to avoid undertreatment exposing the patient to the risk of recurrence. F-FDG PET/CT is already recommended in the European guidelines for the follow up of seminomas under certain conditions but conventional primary staging or restaging is still performed with CT or MRI. Recently, the importance of F-FDG PET/CT in this context has become an interesting topic of academic discussion and subject of various clinical trials which are reviewed in the following.
Preventive Effect of Lactobacillus fermentum CQPC03 on Activated Carbon-Induced Constipation in ICR Mice

Background and objectives: Paocai (pickled cabbage), which is fermented by lactic acid bacteria, is a traditional Chinese food. The microorganisms of Paocai were isolated and identified, and the constipation inhibition effect of one of the isolated Lactobacillus was investigated. Materials and Methods: The 16S rDNA technology was used for microbial identification. A mouse constipation model was established using activated carbon. After intragastric administration of Lactobacillus (109 CFU/mL), the mice were dissected to prepare pathological sections of the small intestine. Serum indicators were detected using kits, and the expression of small intestine-related mRNAs was detected by qPCR assay. Results: One strain of Lactobacillus was identified and named Lactobacillus fermentum CQPC03 (LF-CQPC03). Body weight and activated carbon propulsion rate were all higher in mice intragastrically administered with LF-CQPC03 compared with the control group, while the time to the first black stool in treated mice was lower than that in the control group. Serum assays showed that gastrin (Gas), endothelin (ET), and acetylcholinesterase (AchE) levels were significantly higher in the LF-CQPC03-treated mice than in the control group, while somatostatin (SS) levels were significantly lower than in the control mice. Mouse small intestine tissue showed that c-Kit, stem cell factor (SCF), and glial cell-derived neurotrophic factor (GDNF) mRNA expression levels were significantly higher in the LF-CQPC03 treated mice than in control mice, while transient receptor potential cation channel subfamily V member 1 (TRPV1) and inducible nitric oxide synthase (iNOS) expression levels were significantly lower in the LF-CQPC03 treated mice than in control mice. Conclusions: There is a better effect with high-dose LF-CQPC03, compared to the lower dose (LF-CQPC03-L), showing good probiotic potential, as well as development and application value.
Augmenting Microsoft's HoloLens with vuforia tracking for neuronavigation

Major hurdles for Microsoft's HoloLens as a tool in medicine have been accessing tracking data, as well as a relatively high-localisation error of the displayed information; cumulatively resulting in its limited use and minimal quantification. The following work investigates the augmentation of HoloLens with the proprietary image processing SDK Vuforia, allowing integration of data from its front-facing RGB camera to provide more spatially stable holograms for neuronavigational use. Continuous camera tracking was able to maintain hologram registration with a mean perceived drift of 1.41 mm, as well as a mean sub 2-mm surface point localisation accuracy of 53%, all while allowing the researcher to walk about a test area. This represents a 68% improvement for the later and a 34% improvement for the former compared with a typical HoloLens deployment used as a control. Both represent a significant improvement on hologram stability given the current state-of-the-art, and to the best of the authors knowledge are the first example of quantified measurements when augmenting hologram stability using data from the RGB sensor.
Neonatal abstinence syndrome - a better way.

The excellent practice point published in the June 2018 issue of Paediatrics & Child Health strongly advocates that rooming in with mother should become the normative way to manage infants at risk of neonatal abstinence syndrome. This stands in sharp contrast to the ‘usual’ pattern of practice where infants exhibiting signs of neonatal abstinence syndrome (NAS) are transferred to an neonatal intensive care unit (NICU) or ‘observational nursery’, as occurs in approximately 90% of Canadian hospitals as revealed by a national survey of practice published in 2017 (1). In Vancouver, we have been employing a ‘rooming in’ model of care at BC Women’s Hospital since 2001, when we dedicated an entire postpartum ward for the care of mothers and infants with opiate exposure at risk of NAS. NICU or intermediate nursery admission only happens if there are medical problems requiring other interventions such as respiratory support, NG feeding or IV antibiotics. We have demonstrated convincingly that this model significantly reduces the proportion of infants needing treatment with morphine, reduces the number of days they need treatment AND significantly increases the odds of breastfeeding and discharge in the custody of their mother (2,3). Our rooming in model of care has never employed the Finnegan numerical scoring system in the original or modified form, as we were very concerned that it would lead to over treatment. We opted instead for a variation of the ‘Eat/Sleep/Console’ model of observation espoused by Grossman et al. in their recently published article (4), which convincingly shows that use of the Finnegan scoring system leads to over treatment. The ideal model of care for infants with neonatal abstinence syndrome is still evolving, but on balance of best evidence we should 1) bypass NICU and have the baby ‘room in’ with mother as the default strategy and 2) avoid the use of the Finnegan scoring system. Based on our 17 year experience with approximately 1,500 infants here in Vancouver, everyone will be happier!
A comparison of NCT, Goldman application tonometry values with and without fluorescein

Purpose The aim of the study was to statistically compare intraocular pressure (IOP) values measured using noncontact tonometer (NCT), Goldmann applanation tonometry (GAT) with fluorescein (fGAT), and GAT without fluorescein (nGAT). The study was also performed to test whether the values obtained using each technique change in accordance with the central corneal thickness (CCT) and refractive and keratometric values. Study design This study was a prospective study of 188 eyes of 94 healthy volunteers. Methods: IOP was measured using fGAT, nGAT and NCT. CCT, refractive values, and keratometric values were measured, and the correlations and differences in the IOP for each tonometer were investigated. Results The mean IOP values obtained with the NCT, nGAT, and fGAT were 17.5±3.7, 12.3±2.7, and 12.5±2 mmHg. The mean CCT was 538.2±34.4 µm, the mean refractive value was 0.9±1.2 D, and the mean keratometric value was 43.5±1.5 D. NCT was positively correlated with fGAT and GAT values and was significantly higher than both the values. There were no differences between fGAT and GAT values. No correlation was observed between the CCT and keratometric and refractive values and the difference between NCT and nGAT or fGAT. Conclusion Differences in the measurements obtained using nGAT and fGAT were insignificant (P>0.05). Both values were positively correlated with NCT measurements (r =0.354, P<0.05) and were independent of CCT, keratometry, and refraction values. nGAT appears to be suitable for use in routine clinic practice.
Calibration and validation of an activated sludge model for membrane bioreactor wastewater treatment plants

ABSTRACT A mathematical model to simulate the biological processes occurring in a membrane bioreactor (MBR) is presented. The model accounts for different MBR technical features by introducing specific permeability parameters for the applied membrane system. The model considers for the heterotrophic storage process and the formation of soluble microbial products. The introduction of an inhibition coefficient influencing the anoxic kinetics enables the model to simulate the particular operating conditions of the plant, such as a high or low dissolved oxygen concentration in the denitrification tank. The model was applied at the MBR wastewater treatment plant of Vila Nova do Ceira (Portugal) which uses a classic pre-denitrification cycle. Data for calibration and validation were sampled at the same wastewater treatment plant. Calibration was achieved by varying the kinetic parameters of the model to match the simulation results to the experimental data. The values of the kinetic parameters were similar to those found in the literature. The validation was performed by two different methodologies to analyse the model response to diverse operating conditions, and to evaluate the resilience of the MBR. Calibration and validation results were evaluated with mean average error, root mean square error and fractional mean bias as performance indexes. In most cases, these indexes confirmed the high accuracy of the model. Overall, the results of the calibration and validation steps enriched the proposed model by providing an effective biological description of the processes characterizing the MBR. Thus, the model is a reliable tool for the management and designing of MBR. GRAPHICAL ABSTRACT
On the Importance of Strong Baselines in Bayesian Deep Learning

Like all sub-fields of machine learning Bayesian Deep Learning is driven by empirical validation of its theoretical proposals. Given the many aspects of an experiment it is always possible that minor or even major experimental flaws can slip by both authors and reviewers. One of the most popular experiments used to evaluate approximate inference techniques is the regression experiment on UCI datasets. However, in this experiment, models which have been trained to convergence have often been compared with baselines trained only for a fixed number of iterations. We find that a well-established baseline, Monte Carlo dropout, when evaluated under the same experimental settings shows significant improvements. In fact, the baseline outperforms or performs competitively with methods that claimed to be superior to the very same baseline method when they were introduced. Hence, by exposing this flaw in experimental procedure, we highlight the importance of using identical experimental setups to evaluate, compare, and benchmark methods in Bayesian Deep Learning.
Lack of correlation between serum 25(OH)D level and endoscopy-based chronic rhinosinusitis in Korean adults.

BACKGROUND Several previous studies have shown that serum 25(OH)D deficiency is associated with increased risk of chronic rhinosinusitis (CRS) in adults and also correlated with disease severity. We aimed to investigate the correlation between serum 25(OH)D level and endoscopy-based CRS in adults using the Korean National Health and Nutrition Examination Survey. METHODS The data were based on the Korean National Health and Nutrition Examination Survey from 2008 to 2011. Diagnosis of endoscopy-based CRS was based on endoscopic findings of mucopurulent rhinorrhea in the middle meatus or nasal polyps, with nasal symptoms satisfying symptom-based CRS based on European Position Paper on Rhinosinusitis and Nasal Polyps 2012 criteria. Nasal symptoms included nasal obstruction, anterior/posterior nasal drip, facial pain, and the loss of smell. Serum 25(OH) D level was defined as deficient (less than 20 ng/mL), insufficient (20â€"29.9 ng/mL), or sufficient (less than or equal to 30 ng/mL). RESULTS The serum 25(OH)D level in the CRS group was 19.293 'plus or minus' 7.035 ng/mL, which was higher than that of the control group (18.057 'plus or minus' 6.56 ng/mL, p = 0.0072). Among symptom combinations of endoscopy-based CRS, some combinations with mucopurulent rhinorrhea at the middle meatus were significantly related to normal serum 25(OH)D level. CONCLUSION Low serum 25(OH)D level might not be associated with increased prevalence of CRS in Korean adults; rather, patients with CRS showed higher serum 25(OH)D levels than the control group. Thus, these results, contradicting those of previous studies, should be further verified in other countries to investigate the role of the serum 25(OH)D in CRS.
Cellular density‐dependent increases in HIF‐1α compete with c‐Myc to down‐regulate human EP4 receptor promoter activity through Sp‐1‐binding region

The up‐regulated expression of E‐type prostanoid (EP) 4 receptors has been implicated in carcinogenesis; however, the expression of EP4 receptors has also been reported to be weaker in tumor tissues than in normal tissues. Indeed, EP4 receptors have been suggested to play a role in the maintenance of colorectal homeostasis. This study aimed to examine the underlying mechanisms/reasons for why inconsistent findings have been reported regarding EP4 receptor expression levels in homeostasis and carcinogenesis by focusing on cellular densities. Thus, the human colon cancer HCA‐7 cells, which retain some functional features of normal epithelia, and luciferase reporter genes containing wild‐type or mutated EP4 receptor promoters were used for elucidating the cellular density‐dependent mechanisms about the regulation of EP4 receptor expression. In silico analysis was also utilized for confirming the relevance of the findings with respect to colon cancer development. We here demonstrated that the expression of EP4 receptors was up‐regulated by c‐Myc by binding to Sp‐1 under low cellular density conditions, but was down‐regulated under high cellular density conditions via the increase in the expression levels of HIF‐1α protein, which may pull out c‐Myc and Sp‐1 from DNA‐binding. The tightly regulated EP4 receptor expression mechanism may be a critical system for maintaining homeostasis in normal colorectal epithelial cells. Therefore, once the system is altered, possibly due to the transient overexpression of EP4 receptors, it may result in aberrant cellular proliferation and transformation to cancerous phenotypes. However, at the point, EP4 receptors themselves and their mediated homeostasis would be no longer required.
Approximate Eigenvalue Decompositions of Linear Transformations with a Few Householder Reflectors

The ability to decompose a signal in an orthonormal basis (a set of orthogonal components, each normalized to have unit length) using a fast numerical procedure rests at the heart of many signal processing methods and applications. The classic examples are the Fourier and wavelet transforms that enjoy numerically efficient implementations (FFT and FWT, respectively). Unfortunately, orthonormal transformations are in general unstructured, and therefore they do not enjoy low computational complexity properties. In this paper, based on Householder reflectors, we introduce a class of orthonormal matrices that are numerically efficient to manipulate: we control the complexity of matrix-vector multiplications with these matrices using a given parameter. We provide numerical algorithms that approximate any orthonormal or symmetric transform with a new orthonormal or symmetric structure made up of products of a given number of Householder reflectors. We show analyses and numerical evidence to highlight the accuracy of the proposed approximations and provide an application to the case of learning fast Mahanalobis distance metric transformations.
A Natural Language Programming Approach for Requirements-Based Security Testing

To facilitate communication among stakeholders, software security requirements are typically written in natural language and capture both positive requirements (i.e., what the system is supposed to do to ensure security) and negative requirements (i.e., undesirable behavior undermining security). In this paper, we tackle the problem of automatically generating executable security test cases from security requirements in natural language (NL). More precisely, since existing approaches for the generation of test cases from NL requirements verify only positive requirements, we focus on the problem of generating test cases from negative requirements. We propose, apply and assess Misuse Case Programming (MCP), an approach that automatically generates security test cases from misuse case specifications (i.e., use case specifications capturing the behavior of malicious users). MCP relies on natural language processing techniques to extract the concepts (e.g., inputs and activities) appearing in requirements specifications and generates executable test cases by matching the extracted concepts to the members of a provided test driver API. MCP has been evaluated in an industrial case study, which provides initial evidence of the feasibility and benefits of the approach.
Influence of DOAC Stop on coagulation assays in samples from patients on rivaroxaban or apixaban

Direct oral anticoagulants (DOACs) require no laboratory monitoring, but they interfere with almost all clotting tests to a varying degree, depending on the DOAC, assay principles and reagents used. DOAC Stop (Haematex Research, Sydney, Australia) has recently been shown to adsorb DOACs from spiked and patient plasmas. The aim of our work was to investigate the DOAC Stop effect on a range of haemostasis assays on plasmas collected from patients on rivaroxaban or apixaban, to see whether it removes the effect of these drugs to enable more accurate interpretation of coagulation assays.
Dynamic prediction of childhood high blood pressure in a population-based birth cohort: a model development study

Objectives To develop a dynamic prediction model for high blood pressure at the age of 9–10 years that could be applied at any age between birth and the age of 6 years in community-based child healthcare. Design, setting and participants Data were used from 5359 children in a population-based prospective cohort study in Rotterdam, the Netherlands. Outcome measure High blood pressure was defined as systolic and/or diastolic blood pressure ≥95th percentile for gender, age and height. Using multivariable pooled logistic regression, the predictive value of characteristics at birth, and of longitudinal information on the body mass index (BMI) of the child until the age of 6 years, was assessed. Internal validation was performed using bootstrapping. Results 227 children (4.2%) had high blood pressure at the age of 9–10 years. Final predictors were maternal hypertensive disease during pregnancy, maternal educational level, maternal prepregnancy BMI, child ethnicity, birth weight SD score (SDS) and the most recent BMI SDS. After internal validation, the area under the receiver operating characteristic curve ranged from 0.65 (prediction at age 3 years) to 0.73 (prediction at age 5–6 years). Conclusions This prediction model may help to monitor the risk of developing high blood pressure in childhood which may allow for early targeted primordial prevention of cardiovascular disease.
Mature outcomes and prognostic indices in diffuse large B‐cell lymphoma in Malawi: a prospective cohort

Outcomes for diffuse large B‐cell lymphoma (DLBCL) in sub‐Saharan Africa (SSA) are poorly described. We report mature data from one of the first prospective SSA cohorts. Patients aged ≥18 years with DLBCL were enrolled in Malawi 2013–2017. Participants were treated with CHOP (cyclophosphamide, doxorubicin, vincristine, prednisone) chemotherapy and concurrent antiretroviral therapy (ART) if positive for human immunodeficiency virus (HIV+). Eighty‐six participants (mean age 47 years, standard deviation 13) were enrolled: 54 (63%) were male and 51 (59%) were HIV+, of whom 34 (67%) were on ART at DLBCL diagnosis. Median CD4 count was 0·113 cells × 109/l (interquartile range [IQR] 0·062–0·227) and 25 (49%) had HIV viral load <400 copies/μl. Participants received median six cycles CHOP (IQR 4–6). No patients were lost to follow‐up and the 2‐year overall survival was 38% (95% confidence interval 28–49). In multivariable analyses, Eastern Cooperative Oncology Group performance status (PS) ≥2 and lactate dehydrogenase (LDH) >2× upper limit of normal (ULN) were associated with mortality. HIV status was not associated with mortality. A simplified prognostic model of LDH >2× ULN and PS ≥2 performed at least as well as the age‐adjusted International Prognostic Index. DLBCL can be successfully treated in SSA and outcomes did not differ by HIV status. A simplified prognostic model prognosticates well and may be easier to use in resource‐limited settings but requires validation.
Optimizing Hemp Fiber Production for High Performance Composite Applications

Hemp is a sustainable and environmental friendly crop that can provide valuable raw materials to a large number of industrial applications. Traditionally harvested at full flowering for textile destinations, nowadays hemp is mainly harvested at seed maturity for dual-purpose applications and has a great potential as multipurpose crop. However, the European hemp fiber market is stagnating if compared to the growing market of hemp seeds and phytocannabinoids. To support a sustainable growth of the hemp fiber market, agronomic techniques as well as genotypes and post-harvest processing should be optimized to preserve fiber quality during grain ripening, enabling industrial processing and maintaining, or even increasing, actual fiber applications and improving high-added value applications. In this paper, the effect of genotypes, harvest times, retting methods and processing on the yield and quality of long hemp for wet spun yarns was investigated. Conventional green-stem varieties were compared with yellow-stem ones on two harvesting times: at full flower and seed maturity. Scutching was performed on un-retted stems and dew-retted stems, the un-retted scutched fiber bundles were then bio-degummed before hackling. Both scutching and hackling was performed on flax machines. Quality of hackled hemp, with particular reference to its suitability for high performance composites production, was assessed. The results of fiber extraction indicate that yellow-stem varieties are characterized by higher scutching efficiency than green-stem varieties. Composites strength at breaking point, measured on specimens produced with the Impregnated Fiber Bundle Test, was lower with hemp obtained from stems harvested at seed maturity than at full flowering. On average, back-calculated fiber properties, from hackled hemp-epoxy composites, proved the suitability of long hemp fiber bundles for high performance composites applications, having properties comparable to those of high quality long flax. Highlights: - The trait yellow stem in hemp is an indicator of processability. - Yellow stem varieties have finer hackled fiber bundles. - Controlled dew retting increased yield of hackled fiber compared to bio-degumming. - Retting influenced fiber and composite mechanical properties. - Hemp can achieve properties comparable to high quality long flax for high performance composites.