Miracle-dz/UniFAR-FTUs huggingface dataset:
Cost-Effectiveness of Routine Screening for Autoimmune Encephalitis in Patients With First-Episode Psychosis in the United States.

OBJECTIVE Autoimmune encephalitis (AE) is a highly treatable neurologic condition that can cause psychosis. Screening for AE is not currently recommended in routine workup for first-episode psychosis (FEP), owing partly to the high cost of testing for AE-associated neuronal autoantibodies. METHODS This study used a decision-analytic model to estimate the cost-effectiveness of routine serum screening for AE compared with clinically targeted screening in patients with FEP. Model parameters drawn from prior published literature included the prevalence of neuronal autoantibodies in FEP (4.5%), serum autoantibody panel cost (US $291), remission probability with antipsychotics (0.58), and remission probability with immunotherapy for patients diagnosed with AE (0.85). Outcomes included quality-adjusted life-years (QALYs), costs, and incremental cost-effectiveness ratios (ICERs), assessed over a 5-year horizon from the US health care sector and societal perspectives. ICER thresholds of $50,000/QALY to $150,000/QALY were used to define cost-effectiveness. The analysis was conducted between June 2018 and January 2020. RESULTS Routine screening led to mean QALY gains of 0.008 among all patients and 0.174 among the subgroup of patients with neuronal autoantibodies. Mean costs increased by $780 from a societal perspective and $1,150 from a health care sector perspective, resulting in ICERs of $99,330/QALY and $147,460/QALY, respectively. Incorporating joint input data uncertainty, the likelihood routine screening has an ICER ≤ $150,000/QALY was 55% from a societal perspective and 37% from a health care sector perspective. The model parameter with the greatest contribution to overall uncertainty was the effectiveness of immunotherapy relative to antipsychotics. CONCLUSIONS Routine screening for AE in patients with FEP may be cost-effective in the United States. As further immunotherapy effectiveness data become available, a more definitive recommendation to perform routine screening could be warranted.
FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs

Abstract The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation, of mammalian genomes for the last 20 years. To share these resources with the research community, the FANTOM web-interfaces and databases are being regularly updated, enhanced and expanded with new data types. In recent years, the FANTOM Consortium's efforts have been mainly focused on creating new non-coding RNA datasets and resources. The existing FANTOM5 human and mouse miRNA atlas was supplemented with rat, dog, and chicken datasets. The sixth (latest) edition of the FANTOM project was launched to assess the function of human long non-coding RNAs (lncRNAs). From its creation until 2020, FANTOM6 has contributed to the research community a large dataset generated from the knock-down of 285 lncRNAs in human dermal fibroblasts; this is followed with extensive expression profiling and cellular phenotyping. Other updates to the FANTOM resource includes the reprocessing of the miRNA and promoter atlases of human, mouse and chicken with the latest reference genome assemblies. To facilitate the use and accessibility of all above resources we further enhanced FANTOM data viewers and web interfaces. The updated FANTOM web resource is publicly available at https://fantom.gsc. riken.jp/.
Active Optical Fibers and Components for Fiber Lasers Emitting in the 2-μm Spectral Range

Laser sources emitting in the infrared range at around 2 µm are attracting great interest for a variety of applications like processing of transparent thermoplastic polymers in industry as well as plenty of applications in medicine, spectroscopy, gas sensing, nonlinear frequency conversion to the mid-infrared, to mention a few. Of late, fiber lasers compared to other kinds of lasers benefit from their all-fiber design, leading to a compact, robust, and well thermally manageable device. Particularly, thulium- and holmium-doped fiber lasers are the first choice in fiber lasers emitting light around 2 µm. In this paper, we give an overview of our recent results in the research on thulium- and holmium-doped optical fibers, fiber lasers, and related research topics in the 2-µm spectral range. In particular, we present, to our knowledge, the first results of improvement of pump absorption in double-clad fibers thanks to the fiber twist frozen during drawing. Finally, a brief demonstration of material processing by thulium all-fiber laser operating at 2 µm is presented.
Neurogenic rosacea in Korea

Rosacea with severe neurological symptoms such as burning and stinging is often not treated effectively by conventional therapies. The aim of this study was to investigate the clinical characteristics of Korean rosacea patients with prominent neurological symptoms. The demographic features, medical history, clinical manifestations and treatment modalities of 17 neurogenic rosacea patients who had prominent neurological symptoms and 106 erythematotelangiectatic rosacea (ETR) patients as a control group were investigated. All 17 neurogenic rosacea patients had severe persistent erythema with burning/stinging sensation limited to both cheeks. Among these patients, 94.1% were female (16/17). Heat stimuli (58.8%, 10/17) and stress (52.9%, 9/17) were major aggravating factors. Fourteen of 17 patients (82.3%) improved after receiving anticonvulsants and antidepressants. In conclusion, rosacea patients with severe neurological symptoms show distinct clinical manifestations and should be classified separately, and a different therapeutic approach is necessary for them.
Counterfactual thoughts distinguish benign and malicious envy.

When people encounter others surpassing them in terms of an important quality, possession, or achievement, they often think about what might have happened differently so that they would have obtained a better outcome. Such upward counterfactual thoughts have been shown to contribute to the intensity of envy. We investigated whether specific counterfactual thoughts distinguish different forms of envy, namely benign envy, which entails upward motivation, and malicious envy-which entails hostility. A meta-analysis of 8 studies (1 preregistered, N = 1,264) of a first line of research supports that recalled episodes of benign versus malicious envy are characterized by more additive, self-focused counterfactuals or by more other-focused counterfactuals, respectively. Furthermore, a meta-analysis of 6 studies (1 preregistered, N = 1,299) of a second line of research supports that eliciting these counterfactuals promotes the corresponding form of envy. In line with functional accounts of counterfactual thinking and envy, the results highlight cognitive processes that underlie functionally diverging pathways of envious responding. (PsycInfo Database Record (c) 2020 APA, all rights reserved).
Comparison of Prostate MRI Lesion Segmentation Agreement Between Multiple Radiologists and a Fully Automatic Deep Learning System

Abstract Purpose A recently developed deep learning model (U-Net) approximated the clinical performance of radiologists in the prediction of clinically significant prostate cancer (sPC) from prostate MRI. Here, we compare the agreement between lesion segmentations by U-Net with manual lesion segmentations performed by different radiologists. Materials and Methods 165 patients with suspicion for sPC underwent targeted and systematic fusion biopsy following 3 Tesla multiparametric MRI (mpMRI). Five sets of segmentations were generated retrospectively: segmentations of clinical lesions, independent segmentations by three radiologists, and fully automated bi-parametric U-Net segmentations. Per-lesion agreement was calculated for each rater by averaging Dice coefficients with all overlapping lesions from other raters. Agreement was compared using descriptive statistics and linear mixed models. Results The mean Dice coefficient for manual segmentations showed only moderate agreement at 0.48–0.52, reflecting the difficult visual task of determining the outline of otherwise jointly detected lesions. U-net segmentations were significantly smaller than manual segmentations (p < 0.0001) and exhibited a lower mean Dice coefficient of 0.22, which was significantly lower compared to manual segmentations (all p < 0.0001). These differences remained after correction for lesion size and were unaffected between sPC and non-sPC lesions and between peripheral and transition zone lesions. Conclusion Knowledge of the order of agreement of manual segmentations of different radiologists is important to set the expectation value for artificial intelligence (AI) systems in the task of prostate MRI lesion segmentation. Perfect agreement (Dice coefficient of one) should not be expected for AI. Lower Dice coefficients of U-Net compared to manual segmentations are only partially explained by smaller segmentation sizes and may result from a focus on the lesion core and a small relative lesion center shift. Although it is primarily important that AI detects sPC correctly, the Dice coefficient for overlapping lesions from multiple raters can be used as a secondary measure for segmentation quality in future studies. Key Points: Intermediate human Dice coefficients reflect the difficulty of outlining jointly detected lesions. Lower Dice coefficients of deep learning motivate further research to approximate human perception. Comparable predictive performance of deep learning appears independent of Dice agreement. Dice agreement independent of significant cancer presence indicates indistinguishability of some benign imaging findings. Improving DWI to T2 registration may improve the observed U-Net Dice coefficients. Citation Format Schelb P, Tavakoli AA, Tubtawee T et al. Comparison of Prostate MRI Lesion Segmentation Agreement Between Multiple Radiologists and a Fully Automatic Deep Learning System. Fortschr Röntgenstr 2021; 193: 559 – 573
Characterisation of patients with idiopathic olfactory dysfunction and plan for clinical follow-up.

INTRODUCTION Characterisation and management of olfactory dysfunction (OD) can be challenging, especially in patients diagnosed with idiopathic OD. This group of patients is at risk of developing neurodegenerative diseases such as Parkinson's disease, wherefore appropriate guidelines for management of OD are needed. We aimed to identify and characterise patients suffering from idiopathic hyposmia/anosmia. METHODS This prospective study included 515 consecutive patients referred to the Flavour Clinic, Holstebro, Denmark. Patients with idiopathic, sino-nasal or post-infectious OD were compared with regards to symptoms and clinical findings including endoscopy of the upper airways, sino-nasal CT, allergy testing, and olfactory and gustatory assessment. RESULTS Patients with idiopathic OD were older and a preponderance of females was observed compared with the sino-nasal group (p = 0.0302, and p = 0.0549, respectively). The OD group had a lower prevalence of allergy and longer symptom duration than both the sino-nasal and the post-infectious groups (p Less than 0.0001 and p = 0.0014; p less than 0.0001 and p less than 0.0001, respectively). CONCLUSIONS Patients suffering from idiopathic OD were predominantly females with a long symptom duration. Only few of these patients suffered from allergies or sino-nasal pathologies. Patient history, the Sino-Nasal Outcome Test and threshold discrimination identification scores from the Extended Sniffin Sticks test are the most valuable clinical tools for diagnosing the aetiology behind OD. An ideal workup for idiopathic OD is presented. FUNDING none. TRIAL REGISTRATION not relevant.
Personality and Stigma in Lung Cancer Patients.

BACKGROUND Stigma in lung cancer has been associated with diagnostic and treatment delay and with poor outcomes. Personality has impact on the perception of someone's life situation and interacts with psychosocial variables and coping strategies. The vulnerability to stigma is still under-researched. The aim of this study was to investigate this vulnerability by examining the associations between stigma and personality dimensions (i.e., temperament and character traits). SUBJECTS AND METHODS Seventy six (76) inpatients of the two teaching hospitals with the diagnosis of non-small-cell lung cancer were consecutively included in the study. Patients were assessed with self-reporting scales: Cataldo Lung Cancer Stigma Scale (CLCSS) and Temperament and Character Inventory (TCI). Sociodemographic and clinical data were also collected. RESULTS Personality dimensions Self-directedness and Persistence showed to be significant predictors of stigma in the linear regression (R=0.519; F=3.104; P=0.007). Stigma and personality dimensions were not associated with age, gender, tumor stage and smoking status. CONCLUSION Stigma is associated with particular character (i.e., Self-directedness) and temperament (i.e., Persistence) dimensions. Given the negative clinical outcomes of stigma in lung cancer patients, personality should be taken into account during screening and treatment planning phases.
Choosing an Effective and Safe Direct Aspiration Setup for Tortuous Anatomy in Acute Ischemic Stroke: In vitro Study in a Physiological Flow Model

Abstract Purpose A direct aspiration first pass technique (ADAPT) is an effective thrombectomy option in patients with acute ischemic stroke. Balloon guide catheters (BGC) seem to improve the efficacy of stent retrievers and ADAPT. The last generation 6F aspiration catheters require 9F BGCs, which are rigid devices that are challenging to position in a tortuous anatomy. In this experimental study the efficacy of 6F ADAPT alone and 5F ADAPT combined with 8F BGC was evaluated. Materials and Methods Either a fibrin rich (white) clot or an RBC rich (red) clot was placed in the M1 segment of a transparent silicon phantom. Physiological hemodynamic conditions were maintained. The clots were retrieved by 6F aspiration catheter via 8F long sheath or 5F aspiration catheter via a flexible 8F BGC. Thrombectomy was performed under direct visual control. The primary endpoints were the number of passes and the number of distal emboli. Results Ten experiments were made with each clot model and thrombectomy technique (n = 40). Full recanalization could be achieved in every experiment. First pass mTICI 3 could be achieved by 6F ADAPT in 80 % of red clots and 90 % of white clots. Distal emboli were caused in 10 % and 20 %, respectively. When using 5F ADAPT combined with BGC, a first pass mTICI 3 rate of 90 % in red clots and 100 % in white clots could be achieved. A 10 % rate of distal emboli occurred in both groups. In almost all experiments (both techniques), the thrombi clogged the aspiration catheter. No statistically significant differences could be found between the techniques and clot models. Conclusion 6F ADAPT without BGC was as effective as 5F ADAPT combined with a flexible 8F BGC, with both techniques showing high first-pass recanalization rates and low distal emboli rates. Especially in the case of a tortuous anatomy, these setups should be considered as alternatives to a rigid 9F BGC. The thrombus compositions seemed to be irrelevant in this setting. Key Points: 6F ADAPT with no BGC and 5F ADAPT with BGC were very effective and performed equally. Both techniques should be considered in tortuous anatomy. In this setting the clot composition showed no effect on the recanalization rate. Citation Format Madjidyar J, Nerkada L, Larsen N et al. Choosing an Effective and Safe Direct Aspiration Setup for Tortuous Anatomy in Acute Ischemic Stroke: In vitro Study in a Physiological Flow Model. Fortschr Röntgenstr 2021; 193: 544 – 550
A Deep Learning-Based Automated CT Segmentation of Prostate Cancer Anatomy for Radiation Therapy Planning-A Retrospective Multicenter Study

A commercial deep learning (DL)-based automated segmentation tool (AST) for computed tomography (CT) is evaluated for accuracy and efficiency gain within prostate cancer patients. Thirty patients from six clinics were reviewed with manual- (MC), automated- (AC) and automated and edited (AEC) contouring methods. In the AEC group, created contours (prostate, seminal vesicles, bladder, rectum, femoral heads and penile bulb) were edited, whereas the MC group included empty datasets for MC. In one clinic, lymph node CTV delineations were evaluated for interobserver variability. Compared to MC, the mean time saved using the AST was 12 min for the whole data set (46%) and 12 min for the lymph node CTV (60%), respectively. The delineation consistency between MC and AEC groups according to the Dice similarity coefficient (DSC) improved from 0.78 to 0.94 for the whole data set and from 0.76 to 0.91 for the lymph nodes. The mean DSCs between MC and AC for all six clinics were 0.82 for prostate, 0.72 for seminal vesicles, 0.93 for bladder, 0.84 for rectum, 0.69 for femoral heads and 0.51 for penile bulb. This study proves that using a general DL-based AST for CT images saves time and improves consistency.
Longitudinal dynamics of intact HIV proviral DNA and outgrowth virus frequencies in a cohort of ART-treated individuals.

BACKGROUND The replication-competent HIV reservoir is the major barrier to cure. The quantitative viral outgrowth assay (QVOA), the gold-standard method to quantify replication competent HIV, is resource-intensive which limits its application in large clinical trials. The Intact Proviral DNA Assay (IPDA) requires minimal cell input relative to QVOA and quantifies both defective and intact proviral HIV DNA, the latter potentially serving as a surrogate marker for replication-competent provirus. However, there is limited cross-sectional and longitudinal data on the relationship between IPDA and QVOA measurements. METHODS QVOA and IPDA measurements were performed on 155 resting CD4 T cell (rCD4) samples from 83 ART-suppressed HIV+ participants. Longitudinal QVOA and IPDA measurements were performed on rCD4 from 29 of these participants. RESULTS Frequencies of intact, defective, and total proviruses were positively associated with frequencies of replication-competent HIV. Longitudinally, decreases in intact proviral frequencies were strikingly similar to that of replication-competent virus in most participants. In contrast, defective proviral DNA frequencies appeared relatively stable over time in most individuals. CONCLUSIONS Changes in frequencies of IPDA-derived intact proviral DNA and replication-competent HIV measured by QVOA are similar. The IPDA is a promising high-throughput approach to estimate changes in the frequency of the replication-competent reservoir.
An empirical comparison of univariate versus multivariate methods for the analysis of brain-behavior mapping

Lesion symptom mapping (LSM) tools are used on brain injury data to identify the neural structures critical for a given behavior or symptom. Univariate lesion-symptom mapping (ULSM) methods provide statistical comparisons of behavioral test scores in patients with and without a lesion on a voxel by voxel basis. More recently, multivariate lesion-symptom mapping (MLSM) methods have been developed that consider the effects of all lesioned voxels in one model simultaneously. However, very little work has been done to empirically compare the advantages and disadvantages of these two different methods. In the current study, we provide a needed systematic comparison of 5 ULSM and 8 MLSM methods, using both synthetic and real data to identify the potential strengths and weaknesses of both approaches. We tested power and spatial precision of each LSM method for both single and dual (network type) anatomical target simulations across anatomical target location, sample size, noise level, and lesion smoothing. Additionally, we performed false positive simulations to identify the characteristics associated with each method’s spurious findings. Simulations showed no clear superiority of either ULSM or MLSM methods overall, but rather highlighted specific advantages of different methods. No single method produced a thresholded LSM map that exclusively delineated brain regions associated with the target behavior. Thus, different LSM methods are indicated, depending on the particular study design, specific hypotheses, and sample size. Overall, we recommend the use of both ULSM and MLSM methods in tandem to enhance confidence in the results: Brain foci identified as significant across both types of methods are unlikely to be spurious and can be confidently reported as robust results.
Monte Carlo Modeling of Shortwave-Infrared Fluorescence Photon Migration in Voxelized Media for the Detection of Breast Cancer

Recent progress regarding shortwave-infrared (SWIR) molecular imaging technology has inspired another modality of noninvasive diagnosis for early breast cancer detection in which previous mammography or sonography would be compensated. Although a SWIR fluorescence image of a small breast cancer of several millimeters was obtained from experiments with small animals, detailed numerical analyses before clinical application were required, since various parameters such as size as well as body hair differed between humans and small experimental animals. In this study, the feasibility of SWIR was compared against visible (VIS) and near-infrared (NIR) region, using the Monte Carlo simulation in voxelized media. In this model, due to the implementation of the excitation gradient, fluorescence is based on rational mechanisms, whereas fluorescence within breast cancer is spatially proportional to excitation intensity. The fluence map of SWIR simulation with excitation gradient indicated signals near the upper surface of the cancer, and stronger than those of the NIR. Furthermore, there was a dependency on the fluence signal distribution on the contour of the breast tissue, as well as the internal structure, due to the implementation of digital anatomical data for the Visible Human Project. The fluorescence signal was observed to become weaker in all regions including the VIS, the NIR, and the SWIR region, when fluorescence-labeled cancer either became smaller or was embedded in a deeper area. However, fluorescence in SWIR alone from a cancer of 4 mm diameter was judged to be detectable at a depth of 1.4 cm.
First autochthonous human West Nile virus infections in the Netherlands, July to August 2020

In October 2020, the first case of autochthonous West Nile virus neuroinvasive disease was diagnosed in the Netherlands with a presumed infection in the last week of August. Investigations revealed five more cases of local West Nile virus (WNV) infection. The cases resided in a region where WNV was detected in a bird and mosquitoes in August 2020. Molecular analysis was successful for two cases and identified the presence of WNV lineage 2.