Miracle-dz/UniFAR-FTUs huggingface dataset:
Manganese concentration mapping in the rat brain with MRI, PET, and autoradiography

Purpose: Mn2+ is used as a contrast agent and marker for neuronal activity with magnetic resonance imaging (MRI) in rats and mice, but its accumulation is generally not assessed quantitatively. In this work, nonradioactive Mn and 52Mn are injected simultaneously in rats, and imaged with MRI, positron emission tomography (PET) and autoradiography (AR). Mn distributions are compared between modalities, to assess the potential and limitations on quantification of Mn with MRI, and to investigate the potential of multimodal measurement of Mn accumulation. Methods: MRI (in vivo), PET (in vivo and post mortem), and AR (ex vivo) were acquired of rat brains, for which animals received simultaneous intraperitoneal (IP) or intracerebrovertricular (ICV)‐targeted injections containing the positron‐emitting radionuclide 52Mn and additional nonradioactive MnCl2, which acts as an MRI contrast agent. Pre and postinjection MR images were fit for the longitudinal relaxation rate (R1), coregistered, and subtracted to generate R1 difference maps, which are expected to be proportional to change in Mn concentration in tissue. AR and PET images were coregistered to smoothed R1 difference maps. Results: Similar spatial distributions were seen across modalities, with Mn accumulation in the colliculus, near the injection site, and in the 4th ventricle. There was no 52Mn accumulation measurable with PET in the brain after IP injection. In areas of very highly localized and concentrated 52Mn accumulation in PET or AR, consistent increases of R1 were not seen with MRI. Scatter plots of corresponding voxel R1 difference and PET or AR signal intensity were generated and fit with least squares linear models within anatomical regions. Linear correlations were observed, particularly in regions away from very highly localized and concentrated Mn accumulation at the injection site and the 4th ventricle. Accounting for radioactive decay of 52Mn, the MnCl2 longitudinal relaxivity was between 4.0 and 5.1 s−1/mM, which is within 22% of the in vitro relaxivity. Conclusions: This proof‐of‐concept study demonstrates that MR has strong potential for quantitative assessment of Mn accumulation in the brain, although local discrepancies from linear correlation suggest limitations to this use of MR in areas of inflammation or very high concentrations of Mn. These discrepancies also suggest that a combination of modalities may have additional utility for discriminating between different pools of Mn accumulation in tissue.
Pain and Discomfort Associated With Initial Alignment with Three Different Archwires-A Clinical Study

6; pain is known to be influenced by psychological, sociocultural, and environmental factors, making objective evaluation difficult. The experience of pain is measured indirectly, and the visual analog scale (VAS) is the most reliable method of measuring pain perception. 7-10 Nonlinear relationships have been shown between pain experienced after initial archwire placement and archwire material and age; social class; degree of force applied; dental arch relationships; and dental crowding. 11-15 It is not surprising that the use of preemptive and postoperative analgesia has been shown to reduce pain scores. 8 The present study is intended to test whether any significant difference in the pain and discomfort experience could be found during initial alignment with three initial archwires ,i.e. 0.0175 multisranded stainless steel archwire, 0.018 Cu-Niti and 0.018 Niti. Ideally, archwires are designed to move teeth with light and continuous forces. Such force reduces the potential for patient discomfort, tissue hyalinization and undermining resorption. When force is applied, the archwire should behave elastically over a period of weeks to months. Keeping these wire characteristics in mind, research work was pursued by orthodontists. AIMS AND OBJECTIVES: 1 To investigate the amount of pain and discomfort experienced by the patient during the alignment phase of treatment.
Hematopoietic stem cell transplantation‐associated thrombotic microangiopathy accompanied by renal arteriolar C4d deposition

HSCT‐associated thrombotic microangiopathy (TA‐TMA) is a severe complication with a poor prognosis. Recently, it has been reported that complement system dysregulation, such as CFH autoantibodies and deletions CFH‐related genes 3 and 1, induced TA‐TMA. In addition, C4d‐positive renal arterioles are both a good marker of complement system activation and a useful diagnostic tool for TA‐TMA. Because dysregulation of the complement system is associated with TA‐TMA, the complement system might be a therapeutic target, such as eculizumab, a terminal complement inhibitor. Herein, we describe an eight‐yr‐old boy who developed TA‐TMA accompanied by severe renal dysfunction. His renal specimen showed diffuse C4d deposition in the renal arterioles, which is consistent with TA‐TMA. Although the patient gradually improved without eculizumab, renal arteriolar C4d staining in sample with TA‐TMA shows the complement system activation and may guide the target therapy using the eculizumab.
Average glandular dose coefficients for pendant‐geometry breast CT using realistic breast phantoms

Purpose: To design volume‐specific breast phantoms from breast CT (bCT) data sets and estimate the associated normalized mean glandular dose coefficients for breast CT using Monte Carlo methods. Methods: A large cohort of bCT data sets (N = 215) was used to evaluate breast volume into quintiles (plus the top 5%). The average radius profile was then determined for each of the six volume‐specific groups and used to both fabricate physical phantoms and generate mathematical phantoms (V1‐V6; “V” denotes classification by volume). The MCNP6 Monte Carlo code was used to model a prototype bCT system fabricated at our institution; and this model was validated against physical measurements in the fabricated phantoms. The mathematical phantoms were used to simulate normalized mean glandular dose coefficients for both monoenergetic source photons “DgNCT(E)” (8–70 keV in 1 keV intervals) and polyenergetic x‐ray beams “pDgNCT” (35–70 kV in 1 kV intervals). The Monte Carlo code was used to study the influence of breast size (V1 vs. V5) and glandular fraction (6.4% vs. 45.8%) on glandular dose. The pDgNCT coefficients estimated for the V1, V3, and V5 phantoms were also compared to those generated using simple, cylindrical phantoms with equivalent volume and two geometrical constraints including; (a) cylinder radius determined at the breast phantom chest wall “Rcw”; and (b) cylinder radius determined at the breast phantom center‐of‐mass “RCOM”. Results: Satisfactory agreement was observed for dose estimations using MCNP6 compared with both physical measurements in the V1, V3, and V5 phantoms (R2 = 0.995) and reference bCT dose coefficients using simple phantoms (R2 = 0.999). For a 49 kV spectrum with 1.5 mm Al filtration, differences in glandular fraction [6.5% (5th percentile) vs. 45.8% (95th percentile)] had a 13.2% influence on pDgNCT for the V3 phantom, and differences in breast size (V1 vs. V5) had a 16.6% influence on pDgNCT for a breast composed of 17% (median) fibroglandular tissue. For cylindrical phantoms with a radius of RCOM, the differences were 1.5%, 0.1%, and 2.1% compared with the V1, V3, and V5 phantoms, respectively. Conclusion: Breast phantoms were designed using a large cohort of bCT data sets across a range of six breast sizes. These phantoms were then fabricated and used for the estimation of glandular dose in breast CT. The mathematical phantoms and associated glandular dose coefficients for a range of breast sizes (V1–V6) and glandular fractions (5th to 95th percentiles) are available for interested users.
Comparison of image intensity, local, and multi‐atlas priors in brain tissue classification

Purpose: Automated and accurate tissue classification in three‐dimensional brain magnetic resonance images is essential in volumetric morphometry or as a preprocessing step for diagnosing brain diseases. However, noise, intensity in homogeneity, and partial volume effects limit the classification accuracy of existing methods. This paper provides a comparative study on the contributions of three commonly used image information priors for tissue classification in normal brains: image intensity, local, and multi‐atlas priors. Methods: We compared the effectiveness of the three priors by comparing the four methods modeling them: K‐Means (KM), KM combined with a Markov Random Field (KM‐MRF), multi‐atlas segmentation (MAS), and the combination of KM, MRF, and MAS (KM‐MRF‐MAS). The key parameters and factors in each of the four methods are analyzed, and the performance of all the models is compared quantitatively and qualitatively on both simulated and real data. Results: The KM‐MRF‐MAS model that combines the three image information priors performs best. Conclusions: The image intensity prior is insufficient to generate reasonable results for a few images. Introducing local and multi‐atlas priors results in improved brain tissue classification. This study provides a general guide on what image information priors can be used for effective brain tissue classification.
Automatic segmentation of the clinical target volume and organs at risk in the planning CT for rectal cancer using deep dilated convolutional neural networks

Purpose: Delineation of the clinical target volume (CTV) and organs at risk (OARs) is very important for radiotherapy but is time‐consuming and prone to inter‐observer variation. Here, we proposed a novel deep dilated convolutional neural network (DDCNN)‐based method for fast and consistent auto‐segmentation of these structures. Methods: Our DDCNN method was an end‐to‐end architecture enabling fast training and testing. Specifically, it employed a novel multiple‐scale convolutional architecture to extract multiple‐scale context features in the early layers, which contain the original information on fine texture and boundaries and which are very useful for accurate auto‐segmentation. In addition, it enlarged the receptive fields of dilated convolutions at the end of networks to capture complementary context features. Then, it replaced the fully connected layers with fully convolutional layers to achieve pixel‐wise segmentation. We used data from 278 patients with rectal cancer for evaluation. The CTV and OARs were delineated and validated by senior radiation oncologists in the planning computed tomography (CT) images. A total of 218 patients chosen randomly were used for training, and the remaining 60 for validation. The Dice similarity coefficient (DSC) was used to measure segmentation accuracy. Results: Performance was evaluated on segmentation of the CTV and OARs. In addition, the performance of DDCNN was compared with that of U‐Net. The proposed DDCNN method outperformed the U‐Net for all segmentations, and the average DSC value of DDCNN was 3.8% higher than that of U‐Net. Mean DSC values of DDCNN were 87.7% for the CTV, 93.4% for the bladder, 92.1% for the left femoral head, 92.3% for the right femoral head, 65.3% for the intestine, and 61.8% for the colon. The test time was 45 s per patient for segmentation of all the CTV, bladder, left and right femoral heads, colon, and intestine. We also assessed our approaches and results with those in the literature: our system showed superior performance and faster speed. Conclusions: These data suggest that DDCNN can be used to segment the CTV and OARs accurately and efficiently. It was invariant to the body size, body shape, and age of the patients. DDCNN could improve the consistency of contouring and streamline radiotherapy workflows.
Haploidentical hematopoietic stem cell transplantation with post‐transplant high‐dose cyclophosphamide in high‐risk children: A single‐center study

Recently, haploidentical transplantations have been performed with unmanipulated BM or PBSC. This approach is becoming more widely adopted with the use of PTCY. However, there is limited evidence about this approach in children. We present 15 children who received 16 haploidentical HSCT with unmanipulated BM or PBSC using PTCY for GVHD prophylaxis. Post‐transplant CY(50 mg/kg IV) was given on the third and fifth day, and CsA or tacrolimus with MMF or MP was also used for GVHD prophylaxis. All patients engrafted at a median of 16 and 18 days for neutrophil and thrombocyte recovery, respectively. Grades II–III acute GVHD developed in seven patients, and mild chronic GVHD was found in two patients. Two patients died within the first 100 days due to sepsis (TRM 12.5%). Eleven patients are currently alive, with a median follow‐up of 12 months (range 6–22 months). The 12‐month OS and DFS were 75 ± 10.8% and 68.8 ± 11.6%, respectively. Our results with these high‐risk patients are encouraging for haploidentical HSCT in pediatric patients. Future studies should continue to assess haploidentical HSCT, including comparison of other modalities, in a primary pediatric population.
Development of a dual‐energy computed tomography quality control program: Characterization of scanner response and definition of relevant parameters for a fast‐kVp switching dual‐energy computed tomography system

PURPOSE A prototype QC phantom system and analysis process were developed to characterize the spectral capabilities of a fast kV-switching dual-energy computed tomography (DECT) scanner. This work addresses the current lack of quantitative oversight for this technology, with the goal of identifying relevant scan parameters and test metrics instrumental to the development of a dual-energy quality control (DEQC). METHODS A prototype elliptical phantom (effective diameter: 35 cm) was designed with multiple material inserts for DECT imaging. Inserts included tissue equivalent and material rods (including iodine and calcium at varying concentrations). The phantom was scanned on a fast kV-switching DECT system using 16 dual-energy acquisitions (CTDIvol range: 10.3-62 mGy) with varying pitch, rotation time, and tube current. The circular head phantom (22 cm diameter) was scanned using a similar protocol (12 acquisitions; CTDIvol range: 36.7-132.6 mGy). All acquisitions were reconstructed at 50, 70, 110, and 140 keV and using a water-iodine material basis pair. The images were evaluated for iodine quantification accuracy, stability of monoenergetic reconstruction CT number, noise, and positional constancy. Variance component analysis was used to identify technique parameters that drove deviations in test metrics. Variances were compared to thresholds derived from manufacturer tolerances to determine technique parameters that had a nominally significant effect on test metrics. RESULTS Iodine quantification error was largely unaffected by any of the technique parameters investigated. Monoenergetic HU stability was found to be affected by mAs, with a threshold under which spectral separation was unsuccessful, diminishing the utility of DECT imaging. Noise was found to be affected by CTDIvol in the DEQC body phantom, and CTDIvol and mA in the DEQC head phantom. Positional constancy was found to be affected by mAs in the DEQC body phantom and mA in the DEQC head phantom. CONCLUSION A streamlined scan protocol was developed to further investigate the effects of CTDIvol and rotation time while limiting data collection to the DEQC body phantom. Further data collection will be pursued to determine baseline values and statistically based failure thresholds for the validation of long-term DECT scanner performance.
Analytic formulation of the 6-3 fully-parallel manipulator's singularity determination

When a parallel manipulator reaches a singular configuration (singularity), the end effect (platform) pose cannot be controlled any longer, and infinite active forces must be applied in the actuated joints to balance the loads exerted on the platform. Therefore, these singularities must be avoided during motion. The first step to avoid them is to locate all the platform poses (singularity locus) making the manipulator singular. Hence, the availability of a singularity locus equation, explicitly relating the manipulator geometric parameters to the singular platform poses, greatly facilitates the design process of the manipulator. The problem of determining the platform poses, that make the 6-3 fully-parallel manipulator (6-3 FPM) singular, will be addressed. A simple singularity condition will be written. This singularity condition consists in equating to zero the mixed product of three vectors, that are easy to be identified on the manipulator, and it is geometrically interpretable. The presented singularity condition will be transformed into an equation (singularity locus equation) explicitly containing the geometric parameters of the manipulator and the platform pose parameters making the 6-3 FPM singular. Eventually, the singularity locus equation will be reduced to a polynomial equation by using the Rodrigues parameters to parameterize the platform orientation. This polynomial equation is cubic in the platform position parameters and one of sixth degree in the Rodrigues parameters.
The predictive value of resistive index obtained by Doppler ultrasonography early after renal transplantation on long‐term allograft function

DUSG is a useful diagnostic tool for the follow‐up of renal transplant recipients. The measurement of intrarenal arterial RI by DUSG has been proven to predict short‐term AF. The aim of the study was to evaluate the predictive value of DUSG performed during the early after RTx on long‐term AF. Seventy patients were enrolled into study. DUSG was performed at third and seventh days after RTx. Patients were divided into two groups according to rate of recovery of graft function as patients with normal graft function and abnormal graft function. Although the RI values were correlated with the AF early after transplantation, they were not correlated with long‐term AF. However, the rate of recovery of graft function at early period after RTx was correlated with creatinine level at first year and with glomerular filtration rate at first year and last visit. Although the RI has no predictive value for long‐term AF, the rate of recovery of graft function at early post‐transplantation period has predictive value for long‐term AF; patients with higher RI values early after RTx should be followed carefully for the development of chronic allograft injury.
The fallacy of thresholds used in defining response and remission in depression rating scales

Response and remission are determined by the proportion of people who fall below a threshold score on depression rating scales. This calculation implies a possibility of false positives (FP) and false negatives (FN) depending on sensitivity and specificity of the threshold used, but also on response and remission rates. A simulation illustrates the methodological consequences of this phenomenon in a comparative trial where response and remission rates differ between groups: the probability of being misclassified differs between groups, and measures of association (relative risk and odds ratio) are biased. Alternatives are proposed to cope with this misclassification bias. Copyright © 2013 John Wiley & Sons, Ltd.
Depression following Traumatic Brain Injury Associated with Isolated Growth Hormone Deficiency: Two Case Reports

Background: Depression can be a sequela of a medical condition like traumatic brain injury (TBI), but the relationship between brain trauma and depression has not been recognized until recently. Eight to 15% of adults who sustain a TBI have severe and isolated growth hormone deficiency (GHD). It has been shown that GHD in adults is associated with changes in body composition, impairment of quality of life, and depression. Methods and Results: At the time of evaluation, two adult subjects who suffered TBI several years ago presented with isolated GHD together with depression. Prior to trauma, neither subject had psychiatric or endocrine morbidity. These case reports focus on opportunities and difficulties in deciding how best to treat them. Conclusions: Both depression and TBI are highly ranked in the list of burden of disease. The mechanism of depression in GH-deficient adults who have sustained a TBI should be clarified and the efficacy and tolerability of GH replacement therapy versus placebo versus antidepressant drugs should be assessed.
Improving the diagnostic criteria for alcohol use disorders through survey methodology and cognitive interviewing

This study aims to identify problems in the structure and wording of questions designed to operationalize four DSM‐IV diagnostic criteria for alcohol use disorders (AUDs): (1) use of alcohol in hazardous situations (hazard); (2) tolerance; (3) use of alcohol in larger amounts/longer periods than intended (larger/longer); (4) unsuccessful attempts to cut down or control alcohol use (quit/cut down). Ten experts appraised the questions related to these criteria in the WMH‐CIDI according to a standardized checklist. These experts identified three main problems: (1) the double‐barrelled nature of some of the questions; (2) definitional issues; and (3) unclear thresholds for criterion endorsement. Cognitive interviews of 100 young adult drinkers aged 18–24 were then conducted. The double‐barrelled nature of the DSM‐IV criteria led to their subsequent over‐ or under‐endorsement. Key terms in the questions under investigation were defined inconsistently. There was also a large amount of variability in the thresholds at which larger/longer and quit/cut down were endorsed. Many of these problems could be linked back to the DSM‐IV text. The findings raise questions as to the validity of AUD diagnoses when established via structured diagnostic interview. Further research should focus on testing alternative structure and wording of key AUD criteria to ensure accurate operationalizations of these criteria in structured diagnostic interviews. Copyright © 2014 John Wiley & Sons, Ltd.
A method to learn hand grasping posture from noisy sensing information

In this paper, we propose a new method to learn a multi-fingered hand grasping posture with little knowledge about the task and few sensing capabilities. The developed model is composed of two stages. The first is dedicated to the finger inverse kinematics learning in order to provide the fingertip-desired position. This function is fulfilled by modular neural network architecture. Following the concept of reinforcement learning, a second neural model dealing with noisy sensing information is used to search the space of hand configuration. Simulation results show a good learning of grasping postures with five fingers and different noise levels.