Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical learning in computed tomography image estimation

PURPOSE There is increasing interest in computed tomography (CT) image estimations from magnetic resonance (MR) images. The estimated CT images can be utilized for attenuation correction, patient positioning, and dose planning in diagnostic and radiotherapy workflows. This study aims to introduce a novel statistical learning approach for improving CT estimation from MR images and to compare the performance of our method with the existing model-based CT image estimation methods. METHODS The statistical learning approach proposed here consists of two stages. At the training stage, prior knowledge about tissue types from CT images was used together with a Gaussian mixture model (GMM) to explore CT image estimations from MR images. Since the prior knowledge is not available at the prediction stage, a classifier based on RUSBoost algorithm was trained to estimate the tissue types from MR images. For a new patient, the trained classifier and GMMs were used to predict CT image from MR images. The classifier and GMMs were validated by using voxel-level tenfold cross-validation and patient-level leave-one-out cross-validation, respectively. RESULTS The proposed approach has outperformance in CT estimation quality in comparison with the existing model-based methods, especially on bone tissues. Our method improved CT image estimation by 5% and 23% on the whole brain and bone tissues, respectively. CONCLUSIONS Evaluation of our method shows that it is a promising method to generate CT image substitutes for the implementation of fully MR-based radiotherapy and PET/MRI applications.
A Weighted Histogram-Based Tone Mapping Algorithm for CT Images

Computed Tomography (CT) images have a high dynamic range, which makes visualization challenging. Histogram equalization methods either use spatially invariant weights or limited kernel size due to the complexity of pairwise contribution calculation. We present a weighted histogram equalization-based tone mapping algorithm which utilizes Fast Fourier Transform for distance-dependent contribution calculation and distance-based weights. The weights follow power-law without distance-based cut-off. The resulting images have good local contrast without noticeable artefacts. The results are compared to eight popular tone mapping operators.
Assessment of General Public’s Knowledge and Opinions towards Antibiotic Use and Bacterial Resistance: A Cross-Sectional Study in an Urban Setting, Rufisque, Senegal

Background: Bacterial resistance is a major public health problem worldwide. One solution to this scourge is to sensitize the general public on rational use of antibiotics. Our goal was to assess people’s knowledge and opinions about antibiotic use and bacterial resistance in an urban setting. Method: We performed a cross-sectional study. A convenience sampling was done. A questionnaire was administered to 400 persons during face-to-face interviews. Results: Most respondents thought that antibiotics are effective against colds/flu (69.8%), cough (72.3%) and sore throat (64.4%). At the same time, 42.8% stated that antibiotic therapy can be stopped as soon as the symptoms disappear. Only 8.8% and 41.8% of people knew that handwashing and vaccination prevented bacterial resistance. Globally, 7% of people had a good knowledge. Socio-demographic variables were not associated with the level of knowledge. The main sources of information were entourage and pharmacy staff. Regarding the opinions, 78.3% of surveyed participants the people thought that that people overuse antibiotics. Additionally, 28% said that they have no role to play against bacterial resistance. Conclusion: People living in an urban setting had a low knowledge about antibiotic use and bacterial resistance. There is a need to implement awareness campaigns. Further studies on population practices toward antibiotic use are necessary.
Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network

Co-expression network analysis provides useful information for studying gene regulation in biological processes. Examining condition-specific patterns of co-expression can provide insights into the underlying cellular processes activated in a particular condition. One challenge in this type of analysis is that the sample sizes in each condition are usually small, making the statistical inference of co-expression patterns highly underpowered. A joint network construction that borrows information from related structures across conditions has the potential to improve the power of the analysis. One possible approach to constructing the co-expression network is to use the Gaussian graphical model. Though several methods are available for joint estimation of multiple graphical models, they do not fully account for the heterogeneity between samples and between co-expression patterns introduced by condition specificity. Here we develop the condition-adaptive fused graphical lasso (CFGL), a data-driven approach to incorporate condition specificity in the estimation of co-expression networks. We show that this method improves the accuracy with which networks are learned. The application of this method on a rat multi-tissue dataset and The Cancer Genome Atlas (TCGA) breast cancer dataset provides interesting biological insights. In both analyses, we identify numerous modules enriched for Gene Ontology functions and observe that the modules that are upregulated in a particular condition are often involved in condition-specific activities. Interestingly, we observe that the genes strongly associated with survival time in the TCGA dataset are less likely to be network hubs, suggesting that genes associated with cancer progression are likely to govern specific functions, rather than regulating a large number of biological processes. Additionally, we observed that the tumor-specific hub genes tend to have few shared edges with normal tissue, revealing tumor-specific regulatory mechanism. Author summary Gene co-expression networks provide insights into the mechanism of cellular activity and gene regulation. Condition-specific mechanisms may be identified by constructing and comparing co-expression networks of multiple conditions. We propose a novel statistical method to jointly construct co-expression networks for gene expression profiles from multiple conditions. By using a data-driven approach to capture condition-specific co-expression patterns, this method is effective in identifying both co-expression patterns that are specific to a condition and that are common across conditions. The application of this method on real datasets reveals interesting biological insights.
Arterial stiffness and hypertension status in Afro-Caribbean men

Objective: African ancestry individuals are at high risk for hypertensive cardiovascular disease (CVD) and could benefit from early detection of arterial stiffening. We tested the association between the 2017 ACC/AHA hypertension categorizations, which include new blood pressure (BP) cutoffs and a definition for elevated BP, and arterial stiffness in 772 Afro-Caribbean men aged 50+ years (mean 64 years). Methods: Arterial stiffness was assessed by brachial–ankle pulse-wave velocity (PWV) using a waveform analyzer. Hypertension groups were based on the 2017 ACC/AHA guidelines and by pharmacologic control status. Multiple linear/logistic regression was used to determine the association of PWV with BP and hypertension. Results: Mean (SD) PWV was 1609 (298) cm/s and was independently correlated with age, SBP, pulse, diabetes, height, and alcohol intake (all P < 0.02). After adjusting for these, in men aged at least 65 years, those with stage 1 or uncontrolled stage 2 hypertension had significantly greater PWV than all other groups (all P < 0.05). Men with controlled hypertension had similar PWV to those with elevated BP (P = 0.7); however, this was significantly greater than men with normal BP (all P < 0.05). Patterns were similar, but with smaller effect sizes, in men aged less than 65 years (all P < 0.05 except controlled hypertension versus elevated or normal BP were not significant). Conclusion: In these high-risk Afro-Caribbeans: stage 1 hypertension is associated with increased PWV, which supports the new guidelines; and, pharmacologic control appears to partially protect men from increased PWV. Longitudinal studies are needed to determine optimal PWV and timing of antihypertensive treatment for preventing future CVD.
A widely used sampling device in colorectal cancer screening programmes allows for large-scale microbiome studies

We read with interest the article by Passamonti et al ,1 reporting the performance of two different faecal immunochemical tests (FITs) highlighting the importance of standardisation and validation of screening methodologies. Conventionally, laboratory-based FIT is the preferred approach in testing for occult blood in faeces, which includes colorectal cancer screening programmes.2–4 The potential of preserving stable faecal samples in a widely used FIT buffer for microbiome research would enable prospective microbiome studies in generally healthy subjects undergoing colorectal cancer screening. For this purpose, we evaluated faecal sample stability in the commonly used OC-Sensor (Eiken Chemical, Tokyo, Japan) under various storage conditions. Faecal samples from five healthy adult individuals were used for the analysis and exposed to 16 different conditions: immediately frozen at −86°C (with FIT (wFIT)/without FIT (woFIT)); immediately frozen at −20°C (wFIT/woFIT); wFIT stored at 4°C for 1, 2, 7, 14 days; stored at 20°C for 1, 2, 7, 14 days; stored at 30°C for 1, 2, 7 days and lastly stored at 4°C for 2 days and at 20°C for additional 2 days. Shotgun metagenomic analysis was performed by Illumina 2500, while taxonomic compositions were determined by 16S rRNA analysis employing Illumina MiSeq and Ion Torrent PGM. Our first attempt to extract DNA from wFIT samples failed due to low amount of DNA obtained. Thus, lyophilisation for all of the wFIT samples, except for woFIT samples, was applied, increasing the yield of DNA up to 30 times. As shown by the figure 1, the Shannon index in both platforms displayed a clear pattern of …
Health-Related Quality of Life and Survival Outcomes of Pediatric Patients With Nonmetastatic Osteosarcoma Treated in Countries With Different Resources

Purpose Health-related quality of life (HRQOL) improves throughout treatment of patients with nonmetastatic osteosarcoma. We compared HRQOL for patients in the United States and Chile treated on an international trial (OS99) with polychemotherapy and surgery, and we assessed the relationships among HRQOL measures, event-free survival (EFS), and overall survival (OS). Materials and Methods Patients with newly diagnosed, localized osteosarcoma and their parents completed three HRQOL instruments (PedsQL v.4, PedsQL Cancer v.3, and Symptom Distress Scale [SDS]). Data were collected at four time points throughout therapy. Repeated measures models were used to investigate the effect of treatment site on instrument scores. The log-rank test examined the impact of treatment site on survival outcomes, and Cox proportional hazards regression models evaluated baseline HRQOL measures as predictors of EFS and OS. Results Of 71 eligible patients, 66 (93%) participated in the HRQOL studies in the United States (n = 44) and Chile (n = 22). The median age was 13.4 years (range, 5 to 23 years). Clinical characteristics were similar between treatment sites. US patients reported better scores for physical (P = .030), emotional (P = .027), and school functioning (P < .001). Chilean patients reported poorer scores for worry (P < .001) and nausea (P = .007). Patient and parent nausea scores were similar between patients treated in the United States and Chile by the end of therapy. Differences in symptom distress were not observed between the countries. Neither HRQOL measures nor treatment site were associated with EFS or OS. Conclusion Although significant differences in HRQOL were observed between countries, outcomes were similar, and HRQOL measures were not associated with prognosis.
Improvement of membranous nephropathy by inhibition of miR‐193a to affect podocytosis via targeting WT1

The objective of this paper was to explore the role and molecular mechanism of miR‐193a in membranous nephropathy (MN). Experimental rats and podocytes were randomly divided into four groups: control, MN, miR‐NC, and miR‐193a inhibitor groups. The relative mRNA level of miR‐193a was determined. The mRNA level and protein expression of PODXL, NPHS1, and Notch1 were determined by real‐time polymerase chain reaction (RT‐PCR) and Western blot analysis, respectively. The mRNA level and protein expression of WT1 in podocytes were also determined by RT‐PCR and Western blot analysis. The relative mRNA level of miR‐193a in the MN group was significantly higher than that in the control group, and inhibition of miR‐193a inhibited the increase successfully. Inhibition of miR‐193a inhibited renal injury, podocyte injury, and tissue cell apoptosis resulting from MN. The expression of PODXL, NPHS1, and Notch1 was decreased in the MN group, while the expression was increased in the miR‐193a inhibitor group. WT1 was verified as a target gene of miR‐193a and the expression of WT1 increased after inhibition of miR‐193a. Inhibition of miR‐193a by targeting WT1 could inhibit renal function injury, renal tissue cell apoptosis, and podocytosis.
Theta Bursts Precede, and Spindles Follow, Cortical and Thalamic Downstates in Human NREM Sleep

Since their discovery, slow oscillations have been observed to group spindles during non-REM sleep. Previous studies assert that the slow-oscillation downstate (DS) is preceded by slow spindles (10–12 Hz) and followed by fast spindles (12–16 Hz). Here, using both direct transcortical recordings in patients with intractable epilepsy (n = 10, 8 female), as well as scalp EEG recordings from a healthy cohort (n = 3, 1 female), we find in multiple cortical areas that both slow and fast spindles follow the DS. Although discrete oscillations do precede DSs, they are theta bursts (TBs) centered at 5–8 Hz. TBs were more pronounced for DSs in NREM stage 2 (N2) sleep compared with N3. TB with similar properties occur in the thalamus, but unlike spindles they have no clear temporal relationship with cortical TB. These differences in corticothalamic dynamics, as well as differences between spindles and theta in coupling high-frequency content, are consistent with NREM theta having separate generative mechanisms from spindles. The final inhibitory cycle of the TB coincides with the DS peak, suggesting that in N2, TB may help trigger the DS. Since the transition to N1 is marked by the appearance of theta, and the transition to N2 by the appearance of DS and thus spindles, a role of TB in triggering DS could help explain the sequence of electrophysiological events characterizing sleep. Finally, the coordinated appearance of spindles and DSs are implicated in memory consolidation processes, and the current findings redefine their temporal coupling with theta during NREM sleep. SIGNIFICANCE STATEMENT Sleep is characterized by large slow waves which modulate brain activity. Prominent among these are downstates (DSs), periods of a few tenths of a second when most cells stop firing, and spindles, oscillations at ∼12 times a second lasting for ∼a second. In this study, we provide the first detailed description of another kind of sleep wave: theta bursts (TBs), a brief oscillation at ∼six cycles per second. We show, recording during natural sleep directly from the human cortex and thalamus, as well as on the scalp, that TBs precede, and spindles follow DSs. TBs may help trigger DSs in some circumstances, and could organize cortical and thalamic activity so that memories can be consolidated during sleep.
Effect of liraglutide on ambulatory blood pressure in patients with hypertension and type 2 diabetes: A randomized, double‐blind, placebo‐controlled trial

To assess the effect of liraglutide on 24‐hour ambulatory blood pressure and heart rate in patients with hypertension (pre‐ and stage 1 hypertension) and inadequately controlled Type 2 diabetes (glycated haemoglobin 7%–10% [53‐86 mmol/mol]).
Tailoring emergent spin phenomena in Dirac material heterostructures

Dirac material–based heterostructures reveal enhanced spin-orbit coupling with an emerging spin texture. Dirac materials such as graphene and topological insulators (TIs) are known to have unique electronic and spintronic properties. We combine graphene with TIs in van der Waals heterostructures to demonstrate the emergence of a strong proximity-induced spin-orbit coupling in graphene. By performing spin transport and precession measurements supported by ab initio simulations, we discover a strong tunability and suppression of the spin signal and spin lifetime due to the hybridization of graphene and TI electronic bands. The enhanced spin-orbit coupling strength is estimated to be nearly an order of magnitude higher than in pristine graphene. These findings in graphene-TI heterostructures could open interesting opportunities for exploring exotic physical phenomena and new device functionalities governed by topological proximity effects.
Dichoptic Attentive Motion Tracking is Biased Toward the Nonamblyopic Eye in Strabismic Amblyopia.

Purpose To determine whether attention is biased toward the nonamblyopic eye under binocular viewing conditions in adults with anisometropic or strabismic amblyopia. We first determined whether attention could be allocated preferentially to one eye in visually normal observers performing a dichoptic attentive motion tracking task. We then assessed dichoptic attentive motion tracking in amblyopia. Methods Participants performed a multiple-object tracking task under the following three viewing conditions: target dots to the dominant eye and distractor dots to the nondominant eye (DE condition), vice versa (NDE condition), or all dots to both eyes (binocular condition). Interocular attentional asymmetry scores were computed as the difference in accuracy between DE and NDE conditions. An interocular contrast difference favoring the amblyopic eye was used for all conditions to neutralize amblyopic eye suppression. To test for confounding effects of suppression, participants completed a separate dot enumeration task under dichoptic presentation conditions to obtain an interocular enumeration asymmetry score. Results Participants with normal vision demonstrated similar accuracy between the DE and NDE conditions and exhibited slightly impaired performance under dichoptic compared with binocular viewing conditions. Participants with strabismic/mixed amblyopia had significantly higher interocular attentional asymmetry than participants with normal vision or with anisometropic amblyopia, whereby attention was biased toward the nonamblyopic eye. The latter two groups did not exhibit a bias in interocular attention. No interocular asymmetries for the enumeration task were observed for any group. Conclusions A nonamblyopic eye bias in the interocular allocation of attention may contribute to the binocular vision impairments caused by strabismic amblyopia.
Do day-3 embryo grade predict day-5 blastocyst transfer outcomes in patients with good prognosis?

Abstract The main aim was to investigate whether or not day-3 embryo grade could predict day-5 blastocyst transfer outcomes in patients with good prognosis. This study included 233 elective single blastocyst transfers (eSBT) by D5 selection with conventional morphology (CM) and 121 elective single blastocyst transfers (eSBT) by D5 selection with time-lapse monitoring system (TL) from October 2016 to October 2017. All the patients were submitted to controlled ovarian stimulation (COS) with long-term protocol and transferred for the first time. The main outcome measures were clinical pregnancy rates (CPR) and ongoing pregnancy (OPR). Our results suggested that CPR (58.04 versus 57.89 versus 55.56%; p = .957) and OPR (66.07 versus 65.79 versus 64.44%; p = .981) were comparable among day 3 grades I, grades II, and grades III groups. We also observed that the TL group showed a slightly better CPR and OPR than CM group (p > .05). Our findings suggested that good or poor embryos at day-3 were not predictive of the outcomes of good-quality blastocysts in a good-prognosis population. It needed to be emphasized that time-lapse monitoring might be useful for elective single blastocyst transfer.
Arterial Stiffening with Ultrafast Ultrasound Imaging Gives New Insight into Arterial Phenotype of Vascular Ehlers-Danlos Mouse Models

Abstract Objective Vascular Ehlers–Danlos syndrome (vEDS) is associated with arterial ruptures due to a mutant gene encoding collagen type III (Col-III). To better understand the role of Col-III, we aimed at evaluating aortic stiffness and dynamic stiffening in vEDS mouse models, with either a quantitative (col3KO mice) or a qualitative Col-III defect (col3KI mice). Materials and Methods Abdominal aortic wall pulse wave velocities (PWV) in col3KO and col3KI mice were compared to their respective wild type (WT) littermates using a 15 MHz ultrafast ultrasonic transducer. A carotid catheter continuously monitored pressure changes due to phenylephrine injections. PWV1, generated at diastolic blood pressure (DBP), and PWV2, at systolic blood pressure (SBP) were recorded. Difference between PWV2 and PWV1 (Delta-PWV) normalized by the pulse pressure (PP), corresponding to the aortic stiffening over the cardiac cycle, were compared between mutant and WT mice, as well as the regression slope of PWV as a function of pressure. Results Delta-PWV/PP was lower in col3KO (p = 0.033) and col3KI mice (p < 0.001) vs. WT-mice regardless of the pressure level. The slope of PWV1 with DBP increase showed a lower arterial stiffness in mutant mice vs. controls in both models. This difference was amplified when evaluating stiffness at systolic blood pressure levels with PWV2. Conclusion In both vEDS mouse models, aortic stiffening was reduced, mainly driven by a lower stiffness at systolic blood pressure. Defective Col-III may be responsible for this, as it is utilized when pressure rises. These pre-clinical data could explain vascular fragility observed in vEDS patients.
The long-term impact of employment bans on the economic integration of refugees

Temporary employment bans for asylum seekers have lasting negative consequences for their economic integration. Many European countries impose employment bans that prevent asylum seekers from entering the local labor market for a certain waiting period upon arrival. We provide evidence on the long-term effects of these employment bans on the subsequent economic integration of refugees. We leverage a natural experiment in Germany, where a court ruling prompted a reduction in the length of the employment ban. We find that, 5 years after the waiting period was reduced, employment rates were about 20 percentage points lower for refugees who, upon arrival, had to wait for an additional 7 months before they were allowed to enter the labor market. It took up to 10 years for this employment gap to disappear. Our findings suggest that longer employment bans considerably slowed down the economic integration of refugees and reduced their motivation to integrate early on after arrival. A marginal social cost analysis for the study sample suggests that this employment ban cost German taxpayers about 40 million euros per year, on average, in terms of welfare expenditures and foregone tax revenues from unemployed refugees.