Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonrigid PET motion compensation in the lower abdomen using simultaneous tagged-MRI and PET imaging.

PURPOSE We propose a novel approach for PET respiratory motion correction using tagged-MRI and simultaneous PET-MRI acquisitions. METHODS We use a tagged-MRI acquisition followed by motion tracking in the phase domain to estimate the nonrigid deformation of biological tissues during breathing. In order to accurately estimate motion even in the presence of noise and susceptibility artifacts, we regularize the traditional HARP tracking strategy using a quadratic roughness penalty on neighboring displacement vectors (R-HARP). We then incorporate the motion fields estimated with R-HARP in the system matrix of an MLEM PET reconstruction algorithm formulated both for sinogram and list-mode data representations. This approach allows reconstruction of all detected coincidences in a single image while modeling the effect of motion both in the emission and the attenuation maps. At present, tagged-MRI does not allow estimation of motion in the lungs and our approach is therefore limited to motion correction in soft tissues. Since it is difficult to assess the accuracy of motion correction approaches in vivo, we evaluated the proposed approach in numerical simulations of simultaneous PET-MRI acquisitions using the NCAT phantom. We also assessed its practical feasibility in PET-MRI acquisitions of a small deformable phantom that mimics the complex deformation pattern of a lung that we imaged on a combined PET-MRI brain scanner. RESULTS Simulations showed that the R-HARP tracking strategy accurately estimated realistic respiratory motion fields for different levels of noise in the tagged-MRI simulation. In simulations of tumors exhibiting increased uptake, contrast estimation was 20% more accurate with motion correction than without. Signal-to-noise ratio (SNR) was more than 100% greater when performing motion-corrected reconstruction which included all counts, compared to when reconstructing only coincidences detected in the first of eight gated frames. These results were confirmed in our proof-of-principle PET-MRI acquisitions, indicating that our motion correction strategy is accurate, practically feasible, and is therefore ready to be tested in vivo. CONCLUSIONS This work shows that PET motion correction using motion fields measured with tagged-MRI in simultaneous PET-MRI acquisitions can be made practical for clinical application and that doing so has the potential to remove motion blur in whole-body PET studies of the torso.
Significance of the Lateral Thoracic Artery in Pectoralis Major Musculocutaneous Flap Reconstruction: Quantitative Assessment of Blood Circulation Using Indocyanine Green Angiography

Abstract Free tissue transfer is the preferred reconstruction option in most major head and neck reconstructions. The pectoralis major muscle musculocutaneous (PMMC) flap is commonly used in salvage of necrotic free flaps and is the first choice for patients who are not candidates for free flaps. The lateral thoracic artery (LTA), which is thought to contribute to blood perfusion of the inferior and lateral mammary area, is not preserved in a conventionally harvested PMMC flap. With regard to blood supply, it has been suggested that the LTA should be preserved, in addition to the pectoral branch of the thoracoacromial artery, when a skin island is designed in the lower chest to attain a pedicle length sufficient for head and neck reconstruction. However, an effect on hemodynamic improvement using the LTA has not been shown quantitatively. In this study, we examined 8 patients with oral cancer who underwent reconstruction procedures with a bipedicle PMMC flap that included the LTA, in addition to the thoracoacromial artery. Intraoperative indocyanine green angiography was performed to examine circulation to the PMMC flap with or without LTA clamping after harvesting. After image processing, data were analyzed using a new quantitative perfusion assessment system with parameters that we recently established for assessment of peripheral arterial disease of the lower limbs. All patients had good clinical courses with whole-flap survival, no vascular insufficiency of the skin island, and no fistula formation. Intraoperative indocyanine green angiography showed an increased inflow rate into the skin island in an LTA-declamped condition in all cases, implying that the preserved LTA increased the blood supply to skin islands in the pectoralis major muscle. We conclude that preserving the LTA in a PMMC flap can increase blood perfusion and stabilize the vascularity of the flap, making the reconstruction more effective and reliable than with use of a conventionally harvested flap. Therefore, it is worthwhile to preserve the LTA as a major contributor to a lateral and distal PMMC flap.
The Treatment of School Avoidance in Children and Adolescents With Psychiatric Illness.

BACKGROUND 5-10% of schoolchildren in Germany are absent from school without an excuse more than five times per year. We investigate the effectiveness of manual-based, multimodal cognitive behavioral therapy focusing on school-avoidant behavior and on the underlying mental disorders. METHODS 112 school avoiders were recruited from an outpatient child and adolescent psychiatric clinic and adaptively randomized into two treatment groups. The first group received manual-based multimodal treatment (MT), the second group treatment as usual (TAU) in the child and adolescent mental health care system. The primary outcome of the study was the percentage of classes attended in the five days prior to first measurement (before the intervention), as well as 6 and 12 months afterward. In each of these periods, school attendance was characterized as regular, partial, or none. Secondary outcomes were the severity of anxiety and depressive symptoms, self-efficacy, and quality of family life. RESULTS In both treatment arms, the percentage of regular school attenders rose to about 60% in 6 months, regardless of the intervention (MT 60.6%, TAU 58.3%; odds ratio [OR] for changes over baseline 6.94, 95% confidence interval [CI] 3.98-12.12, p< 0.001; OR for MT versus TAU 1.05, 95% CI 0.58-1.90, p = 0.875). The improvement persisted 12 months after inclusion. CONCLUSION In accordance with earlier studies, we found that manual-based multimodal treatment did not improve school avoidance to any greater extent than treatment as usual. Future studies should focus on the conditions for successful reintegration in school and on the differential indicators for outpatient versus inpatient treatment.
Quantification of bolus‐tracking MRI: Improved characterization of the tissue residue function using Tikhonov regularization

Quantification of cerebral blood flow (CBF) and the tissue residue function (R) using bolus‐tracking MRI requires deconvolution of the arterial input function (AIF). Currently, the most commonly used deconvolution method is singular value decomposition (SVD), which has been shown to produce accurate estimations of CBF. However, this method introduces unwanted oscillations in the time course of R, and there are situations in which the actual shape is of interest (e.g., in calculating flow heterogeneity and assessing bolus dispersion). In such cases, the conventional SVD method may no longer be suitable, and an alternative approach may be required. This work describes the implementation of Tikhonov regularization with the L‐curve criterion to quantify CBF and obtain a better characterization of R. The methodology is tested on simulated and patient data, and the results are compared to those found using the conventional SVD approach. Although both methods produce similar CBF values, the deconvolved R shape obtained using SVD is dominated by oscillations and fails to characterize the shape in the presence of dispersion. On the other hand, the use of the proposed regularization method improves the characterization of the tissue residue function. Magn Reson Med 50:1237–1247, 2003. © 2003 Wiley‐Liss, Inc.
Foxp3+ Regulatory T Cells Impede the Priming of Protective CD8+ T Cells

T cell activation is controlled by incompletely defined opposing stimulation and suppression signals that together sustain the balance between optimal host defense against infection and peripheral tolerance. In this article, we explore the impacts of Foxp3+ regulatory T cell (Treg) suppression in priming Ag-specific T cell activation under conditions of noninfection and infection. We find the transient ablation of Foxp3+ Tregs unleashes the robust expansion and activation of peptide-stimulated CD8+ T cells that provide protection against Listeria monocytogenes infection in an Ag-specific fashion. By contrast, Treg ablation had nonsignificant impacts on the CD8+ T cell response primed by infection with recombinant L. monocytogenes. Similarly, nonrecombinant L. monocytogenes administered with peptide stimulated the expansion and activation of CD8+ T cells that paralleled the response primed by Treg ablation. Interestingly, these adjuvant properties of L. monocytogenes did not require CD8+ T cell stimulation by IL-12 produced in response to infection, but instead were associated with sharp reductions in Foxp3+ Treg suppressive potency. Therefore, Foxp3+ Tregs impose critical barriers that, when overcome naturally during infection or artificially with ablation, allow the priming of protective Ag-specific CD8+ T cells.
A Corpus of Text Data and Gaze Fixations from Autistic and Non-Autistic Adults

The paper presents a corpus of text data and its corresponding gaze fixations obtained from autistic and non-autistic readers. The data was elicited through reading comprehension testing combined with eye-tracking recording. The corpus consists of 1034 content words tagged with their POS, syntactic role and three gaze-based measures corresponding to the autistic and control participants. The reading skills of the participants were measured through multiple-choice questions and, based on the answers given, they were divided into groups of skillful and less-skillful readers. This division of the groups informs researchers on whether particular fixations were elicited from skillful or less-skillful readers and allows a fair between-group comparison for two levels of reading ability. In addition to describing the process of data collection and corpus development, we present a study on the effect that word length has on reading in autism. The corpus is intended as a resource for investigating the particular linguistic constructions which pose reading difficulties for people with autism and hopefully, as a way to inform future text simplification research intended for this population.
Initiation of antiretroviral therapy leads to a rapid decline in cervical and vaginal HIV-1 shedding

Background:Antiretroviral therapy (ART) may decrease HIV-1 infectivity in women by reducing genital HIV-1 shedding. Objectives:To evaluate the time course and magnitude of decay in cervical and vaginal HIV-1 shedding as women initiate ART. Methods:This prospective, observational study of 20 antiretroviral-naive women initiating ART with stavudine, lamivudine, and nevirapine measured HIV-1 RNA in plasma, cervical secretions, and vaginal secretions. Qualitative polymerase chain reaction estimated HIV-1 DNA in cervical and vaginal samples. Perelson's two-phase viral decay model and non-linear random effects were used to compare RNA decay rates. Decreases in proviral DNA were evaluated using logistic regression and generalized estimating equations. Results:Significant decreases in the quantity of HIV-1 RNA were observed by day 2 in plasma (P < 0.001), day 2 in cervical secretions (P = 0.001), and day 4 in vaginal secretions (P < 0.001). Modeled initial and subsequent RNA decay rates in plasma, cervical secretions, and vaginal secretions were 0.6, 0.8, and 1.2 log10 virions/day, and 0.04, 0.05, and 0.06 log10 virions/day, respectively. The initial decay rate for vaginal HIV-1 RNA was more rapid than for plasma RNA (P = 0.02). Detection of HIV-1 DNA decreased significantly in vaginal secretions during the first week (P < 0.001). At day 28, 10 women had detectable HIV-1 RNA or proviral DNA in genital secretions. Conclusions:Genital HIV-1 shedding decreased rapidly after ART initiation, consistent with a rapid decrease in infectivity. However, incomplete viral suppression in half of these women may indicate an ongoing risk of transmission.
Patient Risk Factors’ Influence on Survival of Posterior Composites

This practice-based retrospective study evaluated the survival of resin composite restorations in posterior teeth, focusing on the influence of potential patient risk factors. In total, 306 posterior composite restorations placed in 44 adult patients were investigated after 10 to 18 yrs. The history of each restoration was extracted from the dental records, and a clinical evaluation was performed with those still in situ. The patient risk status was assessed for caries and “occlusal-stress” (bruxism-related). Statistical analysis was performed by the Kaplan–Meier method and Cox-regression multivariate analysis. In total, 30% of the restorations failed, of which 82% were found in patients with 1 or 2 risk factors. Secondary caries was the main reason of failure within caries-risk patients, whereas fracture was the main reason in “occlusal-stress-risk” patients. The patient variables gender and age did not significantly affect survival, but risk did (p < .001). Tooth type (p < .001), arch (p = .013), and pulpal vitality (p = .003) significantly affected restoration survival. Within the limits of this retrospective evaluation, the survival of restorations is affected by patient risk factors, which should be included in survival analyses of restorations.
Efficient power allocation strategy in multiuser MIMO broadcast channels

In this paper, sum rate optimization of multiuser multiple-input multiple-output broadcast (MU-MIMO) communication systems with perfect channel state information (CSI) at the base station is investigated. Since power allocation is a signomial optimization problem in the presence of multiuser interference (MUI), it is not a convex problem in general. Several optimal solutions proposed in the literature have exponential computational complexity, which is hard to implement for practice. We propose an iterative water-filling algorithm that takes advantage of the classical simple water-filling principle. The proposed algorithm reduces significantly the computational complexity compared with the methods in the literature only with a negligible performance degradation. In addition, the generalized eigenvalue technique for beamforming design is utilized in this paper for minimizing MUI, the number of users and the number of antennas of each user can be arbitrary. Simulations show that the sum rate of the proposed method is close to the sum capacity of the MU-MIMO broadcast channel, especially in low signal-to-noise ratio (SNR) region.
The International Journal of Biostatistics Comparison of Estimators for Measures of Linkage Disequilibrium

The measurement of biallelic pair-wise association called linkage disequilibrium (LD) is an important issue in order to understand the genomic architecture. A plethora of measures of association in two by two tables have been proposed in the literature. Beside the problem of choosing an appropriate measure, the problem of their estimation has been neglected in the literature. It needs to be emphasized that the definition of a measure and the choice of an estimator function for it are conceptually unrelated tasks. In this paper, we compare the performance of various estimators for the three popular LD measures D', r and Y in a simulation study for small to moderate samples sizes (N<=500). The usual frequency-plug-in estimators can lead to unreliable or undefined estimates. Estimators based on the computationally expensive volume measures have been proposed recently as a remedy to this well-known problem. We confirm that volume estimators have better expected mean square error than the naive plug-in estimators. But they are outperformed by estimators plugging-in easy to calculate non-informative Bayesian probability estimates into the theoretical formulae for the measures. Fully Bayesian estimators with non-informative Dirichlet priors have comparable accuracy but are computationally more expensive. We recommend the use of non-informative Bayesian plug-in estimators based on Jeffreys' prior, in particular when dealing with SNP array data where the occurrence of small table entries and table margins is likely.
History, Advances, and Challenges in Liquid Flow and Flow Boiling Heat Transfer in Microchannels: A Critical Review

As the scale of devices becomes small, thermal control and heat dissipation from these devices can be effectively accomplished through the implementation of microchannel passages. The small passages provide a high surface area to volume ratio that enables higher heat transfer rates. High performance microchannel heat exchangers are also attractive in applications where space and/or weight constraints dictate the size of a heat exchanger or where performance enhancement is desired. This survey article provides a historical perspective of the progress made in understanding the underlying mechanisms in single-phase liquid flow and two-phase flow boiling processes and their use in high heat flux removal applications. Future research directions for (i) further enhancing the single-phase heat transfer performance, and (ii) enabling practical implementation of flow boiling in microchannel heat exchangers, are outlined.Copyright © 2010 by ASME
Multiple bcl‐2/Ig gene rearrangements in persistent polyclonal B‐cell lymphocytosis

Persistent polyclonal B‐cell lymphocytosis is a benign lymphoproliferative disorder of unknown aetiology occurring exclusively in women, characterized by typical binucleated lymphocytes, polyclonal expansion of B cells and elevated serum IgM. Owing to the role of Bcl‐2 oncogene in inhibition of apoptosis, we have investigated the presence of the bcl‐2/Ig gene rearrangement. Bcl‐2/Ig gene rearrangement was determined by polymerase chain reaction targeting the usual breakpoint regions of the t(14;18). Bcl‐2/Ig gene rearrangement was identified in all six patients and, more importantly, multiple rearrangements were present in five patients. The frequency of the bcl‐2/Ig gene rearrangement is estimated to be of one translocation in 1 × 102 to 1 × 103 peripheral blood mononuclear cells. We conclude that persistent polyclonal B‐cell lymphocytosis is associated with bcl‐2/Ig gene rearrangement. These findings are of clinical importance because these patients may be misdiagnosed as having a leukaemic expression of non‐Hodgkin's lymphoma.
An Indicator to Measure Inequality in the Provision of Local Public Transport in Italy

An indicator measuring inequality in the provision of local public transport was constructed in order to compare service levels in 20 Italian regional capital cities and analyze emerging criticalities. The indicator aims at identifying the level of measurable rather than perceived public transport effectiveness. Consequently, measurable features such as network coverage (capillarity), frequency, extent of transit lanes, passenger information systems, are considered, whereas features closely tied to personal expectations and tastes (e.g. customer satisfaction/dissatisfaction) are excluded. The relevance of this method derives from the possibility of using this approach for the analysis of the sector of the LPT in other countries, allowing as a consequence, to compare the local transport sector between cities in different countries.
Traceability for Automated Production Systems: A Position Paper

Automated production systems are design-to-order, custom-built mechatronic systems that are intended to deliver automation capabilities to satisfy the stakeholder requirements in the manufacturing/production domain. Traceability has its research root in requirements engineering (RE) and is defined as "the ability to describe and follow the life of a requirement". Such descriptions and followings have mainly been scoped within a single software project's process and artifacts. We argue that, in the context of automated production systems, the scope of traceability shall go beyond the software engineering boundary into the environments which the software is operated. We outline in this position paper our aim to define a new form of the trace links and to explore the role of these links in the RE of automated production systems. In particular, we adapt a formal interaction-oriented RE framework that focuses on specifying the commitments of participants rather than the goals of each individual participant. We then integrate model checking into the framework to elaborate when, why, and how much traceability should be instrumented. We demonstrate our approach with a bench-scale automated production system where model-driven engineering practices such as constructing and evolving SysML models are adopted.
Nucleic Acid Quality Preservation by an Alcohol-based Fixative: Comparison With Frozen Tumors in a Routine Pathology Setting

Pathologic diagnosis requires tissue fixation for histologic and immunohistologic analysis, and formalin is routinely used for this. The disadvantage of this fixative is its inability to preserve nucleic acids. Pathologic tumor diagnosis requires extensive molecular analyses, for which formalin fixation may be not adequate. Recently, an alcohol-based fixative (molecular fixative, MF) was described that allows nucleic acid preservation as well as histologic and immunohistologic studies. Moreover, the MF fixation processing system (Xpress) is fast and is well adapted to a routine process. We evaluated RNA and DNA quality within 1 month and after 1 year for 10 breast carcinomas and 20 sarcomas fixed in MF in comparison with the corresponding frozen tumors. The quality of DNA extracted from the MF-fixed tissue was similar to that extracted from the frozen tumors. The quality of RNA extracted from the MF-fixed tissue was lower than that of frozen tumors; nevertheless, a majority of RNA integrity number (RIN) values were greater than 7. Gene expression quantification by real-time polymerase chain reaction gave comparable results between tumors fixed with MF and frozen tumors. Tissue fixation at 4°C with the MF improved the RNA quality measured by the RIN value. However, after storage for 1 year at room temperature, although DNA quality was preserved, RNA extracted from tissues fixed with the MF was degraded. Tissue fixation with the MF is an important improvement for molecular pathologic diagnosis, enabling a combination of routine pathologic diagnoses and current molecular diagnoses if they are carried out near the processing time.
Training Program Impacts and the Onset of the Great Recession

In the context of the Great Recession, we examine how the impacts of training shifted during a period when theory suggests they might have the greatest potential to improve individual and societal well-being. Using particularly rich data from the state of Missouri for participants in the WIA Adult and Dislocated Worker and the Trade Adjustment Assistance programs over the period 2007-2010, we estimate program impacts, comparing outcomes for participants receiving training in one of these programs with a comparison group of individuals seeking job search services through job offices, or those receiving Unemployment Insurance payments. Individuals who have the same demographic characteristics, prior employment and earnings histories, and local labor markets are matched to maximize the likelihood that the estimates reflect causal training impacts. Making comparisons of impacts before and after the onset of the recession allows us to test the claim that the net benefits of training increase during recessionary periods.