Miracle-dz/UniFAR-FTUs huggingface dataset:
Gastrointestinal stromal tumors of the rectum: Clinical, pathologic, immunohistochemical characteristics and prognostic analysis

Objective. To describe the clinical, pathological and immunohistochemical characteristics of rectal gastrointestinal stromal tumors (GISTs) and to correlate them with clinical outcomes. Material and methods. A retrospective review of 29 patients with surgically treated rectal GISTs during the period from 1997 to 2005 was undertaken. The NIH (National Institute of Health Consensus) criteria were applied. Results. All the rectal GISTs in our series originated in the lower half of the rectum and patients underwent primary surgery for complete resections; High-risk, intermediate-risk, low-risk and very low-risk GISTs were found in 11, 6, 5 and 7 patients, respectively. Necrosis, adjacent (mucosal or serosa) invasion and marked pleomorphisms were found in 10, 7 and 20 patients, respectively. Positive expression of CD117, CD34, SMA and S-100 was found in 28, 28, 7 and 3 patients, respectively. Twelve patients had recurrence or metastasis within the median disease-free survival time of 41 months. Among the patients who underwent local resections, the recurrence rate for low-risk and very low-risk GISTs was only 1/10; for intermediate-risk and high-risk GISTs, the recurrence rate after local resections was 3/4, which was higher than the recurrence and metastasis rate of 8/13 after laparotomy. Of the 12 patients with adverse outcomes, 4 patients underwent secondary complete resections; however, all 4 patients had further recurrences. On univariate analysis, risk classification (p=0.0002), necrosis (p=0.0205), adjacent invasion (p=0.0090) and marked pleomorphism (p=0.0480) were significant predictors of disease-free survival. In the Cox regression model, only the risk classification (p=0.012) was found to be an independent factor. Conclusions. We found that rectal GISTs arise predominantly in the lower half of the rectum and have high CD117 and CD34 expression. Local resection may be a good choice for very-low-risk and low-risk GISTs, but aggressive surgery may be more beneficial for high-risk and intermediate-risk GISTs. For patients with disease recurrence, the results of secondary surgery were poor. Only the NIH risk classification proved to be an independent prognostic factor for rectal GISTs, whereas the proof for other factors was insufficient.
Molecular and Cellular Pathobiology 18 F-Fluorodeoxy-glucose Positron Emission Tomography Marks MYC-Overexpressing Human Basal-Like Breast Cancers

In contrast to normal cells, cancer cells avidly take up glucose andmetabolize it to lactate even when oxygen is abundant, a phenomenon referred to as the Warburg effect. This fundamental alteration in glucose metabolism in cancer cells enables their specific detection by positron emission tomography (PET) following i.v. injection of the glucose analogue F-fluorodeoxy-glucose (FDG). However, this useful imaging technique is limited by the fact that not all cancers avidly take up FDG. To identify molecular determinants of FDG retention, we interrogated the transcriptomes of human-cancer cell lines and primary tumors for metabolic pathways associated with FDG radiotracer uptake. From ninety-five metabolic pathways that were interrogated, the glycolysis, and several glycolysis-related pathways (pentose phosphate, carbon fixation, aminoacyl-tRNA biosynthesis, one-carbon-pool by folate) showed the greatest transcriptional enrichment. This "FDG signature" predicted FDG uptake in breast cancer cell lines and overlapped with established gene expression signatures for the "basal-like" breast cancer subtype and MYC-induced tumorigenesis in mice. Human breast cancers with nuclear MYC staining and high RNA expression of MYC target genes showed high FDG-PET uptake (P < 0.005). Presence of the FDG signature was similarly associated with MYC gene copy gain, increased MYC transcript levels, and elevated expression of metabolic MYC target genes in a human breast cancer genomic dataset. Together, our findings link clinical observations of glucose uptake with a pathologic and molecular subtype of human breast cancer. Furthermore, they suggest related approaches to derive molecular determinants of radiotracer retention for other PET-imaging probes. Cancer Res; 71(15); 5164–74. 2011 AACR.
Inferring Latent States and Refining Force Estimates via Hierarchical Dirichlet Process Modeling in Single Particle Tracking Experiments

Understanding the basis for intracellular motion is critical as the field moves toward a deeper understanding of the relation between Brownian forces, molecular crowding, and anisotropic (or isotropic) energetic forcing. Effective forces and other parameters used to summarize molecular motion change over time in live cells due to latent state changes, e.g., changes induced by dynamic micro-environments, photobleaching, and other heterogeneity inherent in biological processes. This study discusses limitations in currently popular analysis methods (e.g., mean square displacement-based analyses) and how new techniques can be used to systematically analyze Single Particle Tracking (SPT) data experiencing abrupt state changes in time or space. The approach is to track GFP tagged chromatids in metaphase in live yeast cells and quantitatively probe the effective forces resulting from dynamic interactions that reflect the sum of a number of physical phenomena. State changes can be induced by various sources including: microtubule dynamics exerting force through the centromere, thermal polymer fluctuations, and DNA-based molecular machines including polymerases and protein exchange complexes such as chaperones and chromatin remodeling complexes. Simulations aiming to show the relevance of the approach to more general SPT data analyses are also studied. Refined force estimates are obtained by adopting and modifying a nonparametric Bayesian modeling technique, the Hierarchical Dirichlet Process Switching Linear Dynamical System (HDP-SLDS), for SPT applications. The HDP-SLDS method shows promise in systematically identifying dynamical regime changes induced by unobserved state changes when the number of underlying states is unknown in advance (a common problem in SPT applications). We expand on the relevance of the HDP-SLDS approach, review the relevant background of Hierarchical Dirichlet Processes, show how to map discrete time HDP-SLDS models to classic SPT models, and discuss limitations of the approach. In addition, we demonstrate new computational techniques for tuning hyperparameters and for checking the statistical consistency of model assumptions directly against individual experimental trajectories; the techniques circumvent the need for “ground-truth” and/or subjective information.
COPD and Sleep Apnea Syndrome – Impact and Interaction of Coexisting Disease

COPD includes heterogeneous lesions that variably affect the airways, lung parenchyma and systemic structures. COPD is caused by various pathogenic mechanisms and does not present a uniform histological substrate. Patients with this disease present with different clinical features: non-exacerbator with emphysema or chronic bronchitis; mixed COPD-asthma; exacerbator with emphysema and exacerbator with chronic bronchitis (Miravitlles et al., 2013). In addition to affecting the lungs, the disease presents significant systemic consequences including skeletal muscle dysfunction, nutritional disorders and weight loss (Andreassen &
Long-term consequences of flooding: a case study of the 2011 Queensland floods

Free to read on publisher website Devastating floods in southeast Queensland in 2011 were the combination of flash flooding in the Lockyer Valley with riverine flooding in the Brisbane metropolitan area. While there is considerable information about the immediate impact on those affected, there is less understanding of the long-term health effects that follow such events. This study explored the perceptions of health effects and support received by people affected by the 2011 southeast Queensland flood six years after the event. A cross-sectional survey of 327 people was conducted in areas affected by the floods. The questionnaire sought information about the ongoing social, economic, demographic and self-declared physical and mental health effects. The data were analysed through comparison of those unaffected with those directly affected by the floods. Residents whose households were flooded were more likely to score their health negatively than non-affected residents and had higher reported rates of trauma, injury and mental illness. Twenty-six per cent of this group reported that they still experience some adverse health effects from the floods. Managing the long-term health implications of a flood-affected population is an important public policy task. Dissatisfaction with recovery operations and perceived injustices associated with insurance and compensation arrangements may aggravate health consequences. Early recognition and intervention may assist with reducing secondary effects.
Self-assembly of the general membrane-remodeling protein PVAP into sevenfold virus-associated pyramids

Significance The Sulfolobus islandicus rod-shaped virus 2 (SIRV2) has developed unique mechanisms to penetrate the plasma membrane and S-layer of its host Sulfolobus islandicus in order to leave the cell after replication. SIRV2 encodes the 10-kDa protein PVAP, which assembles into sevenfold symmetric virus-associated pyramids (VAPs) in the host cell plasma membrane. Toward the end of the viral replication cycle, these VAPs open to form pores through the plasma membrane and S-layer, allowing viral egress. Here we show that PVAP inserts spontaneously and forms VAPs in any kind of biological membrane. By electron cryotomography we have obtained a 3D map of the VAP and present a model describing the assembly of PVAP into VAPs. Our findings open new avenues for a large variety of biotechnological applications. Viruses have developed a wide range of strategies to escape from the host cells in which they replicate. For egress some archaeal viruses use a pyramidal structure with sevenfold rotational symmetry. Virus-associated pyramids (VAPs) assemble in the host cell membrane from the virus-encoded protein PVAP and open at the end of the infection cycle. We characterize this unusual supramolecular assembly using a combination of genetic, biochemical, and electron microscopic techniques. By whole-cell electron cryotomography, we monitored morphological changes in virus-infected host cells. Subtomogram averaging reveals the VAP structure. By heterologous expression of PVAP in cells from all three domains of life, we demonstrate that the protein integrates indiscriminately into virtually any biological membrane, where it forms sevenfold pyramids. We identify the protein domains essential for VAP formation in PVAP truncation mutants by their ability to remodel the cell membrane. Self-assembly of PVAP into pyramids requires at least two different, in-plane and out-of-plane, protein interactions. Our findings allow us to propose a model describing how PVAP arranges to form sevenfold pyramids and suggest how this small, robust protein may be used as a general membrane-remodeling system.
The Real-Time Optimisation of DNO Owned Storage Devices on the LV Network for Peak Reduction

Energy storage is a potential alternative to conventional network reinforcement of the low voltage (LV) distribution network to ensure the grid’s infrastructure remains within its operating constraints. This paper presents a study on the control of such storage devices, owned by distribution network operators. A deterministic model predictive control (MPC) controller and a stochastic receding horizon controller (SRHC) are presented, where the objective is to achieve the greatest peak reduction in demand, for a given storage device specification, taking into account the high level of uncertainty in the prediction of LV demand. The algorithms presented in this paper are compared to a standard set-point controller and bench marked against a control algorithm with a perfect forecast. A specific case study, using storage on the LV network, is presented, and the results of each algorithm are compared. A comprehensive analysis is then carried out simulating a large number of LV networks of varying numbers of households. The results show that the performance of each algorithm is dependent on the number of aggregated households. However, on a typical aggregation, the novel SRHC algorithm presented in this paper is shown to outperform each of the comparable storage control techniques.
Full Body Virtual Autopsies using a State-of-the-art Volume Rendering Pipeline

This paper presents a procedure for virtual autopsies based on interactive 3D visualizations of large scale, high resolution data from CT-scans of human cadavers. The procedure is described using examples from forensic medicine and the added value and future potential of virtual autopsies is shown from a medical and forensic perspective. Based on the technical demands of the procedure state-of-the-art volume rendering techniques are applied and refined to enable real-time, full body virtual autopsies involving gigabyte sized data on standard GPUs. The techniques applied include transfer function based data reduction using level-of-detail selection and multi-resolution rendering techniques. The paper also describes a data management component for large, out-of-core data sets and an extension to the GPU-based raycaster for efficient dual TF rendering. Detailed benchmarks of the pipeline are presented using data sets from forensic cases
Knowledge‐based treatment planning for adolescent early intervention of mental healthcare: a hybrid case‐based reasoning approach

Abstract: Treatment planning is a crucial and complex task in the social services industry. There is an increasing need for knowledge‐based systems for supporting caseworkers in the decision‐making of treatment planning. This paper presents a hybrid case‐based reasoning approach for building a knowledge‐based treatment planning system for adolescent early intervention of mental healthcare. The hybrid case‐based reasoning approach combines aspects of case‐based reasoning, rule‐based reasoning and fuzzy theory. The knowledge base of case‐based reasoning is a case base of client records consisting of documented experience while that for rule‐based reasoning is a set of IF–THEN rules based on the experience of social service professionals. Fuzzy theory is adopted to deal with the uncertain nature of treatment planning. A prototype system has been implemented in a social services company and its performance is evaluated by a group of caseworkers. The results indicate that hybrid case‐based reasoning has an enhanced performance and the knowledge‐based treatment planning system enables caseworkers to construct more efficient treatment planning in less cost and less time.
An experimental setup for in-circuit optimization of broadband automotive power-line communications

In this paper, an experimental setup for broadband automotive power-line communications is presented. Modular prototyping equipment is used to construct both a transmitting and receiving node on the wiring harness of a motorcar. Initial characterizing measurements are used to choose typical point-to-point communication paths. Some benchmarking results at 1 Mbps (4-FSK) and 5 Mbps (2-FSK) are also presented. This experimental setup is intended to study the suitability of various modulation techniques and frequency bands. Gathered data is also intended to help trade off performance against complexity/cost.
PP2A1 Binding, Cell Transducing and Apoptotic Properties of Vpr77–92: A New Functional Domain of HIV-1 Vpr Proteins

Background The hallmark of HIV-1 pathogenesis is the progressive CD4+ T cell depletion and high propensity of CD4+ T cells to apoptosis. HIV-1 viral protein R (Vpr) is a major pro-apoptotic gene product. A first Vpr-mediated apoptotic mechanism that requires a physical interaction of HIV-1 Vpr71-82 mitochondriotoxic domain containing the conserved sequence 71-HFRIGCRHSRIG-82 with the Adenine Nucleotide Translocator (ANT) has been characterized. The family of Ser/Thr protein phosphatase PP2A interacts with several viral proteins to regulate cell growth and apoptotic pathways. Previous studies based on yeast two hybrid assays and mutational experiments indicated that PP2A1 is involved in the induction of G2 arrest by HIV-1 Vpr. Principal Findings Experiments combining pull-down, cell penetration and apoptosis analyses in distinct human cells indicate that the PP2A1 binding sequence from Vpr77–92 is a new cell penetrating apoptotic sequence. We also found that the I84P mutation or the IIQ/VTR83–85 and T89A substitutions in the Vpr77–92 sequence prevent PP2A1 binding, cell penetration and apoptosis. In addition the double R77A and R80A mutation known to inactivate the mitochondriotoxic Vpr71–82 domain, has no effect on the biological properties of the Vpr77–92 domain. Conclusion Together our data provide evidence for the first time that the Vpr77–92 sequence delineates a biological active domain of Vpr with PP2A1 binding and pro-apopototic capacities and, it is conceivable that this cell penetrating sequence may account for the Vpr internalization in uninfected cells. Finally, our data also implicate the existence of two partially overlapping pro-apoptotic domains in the Vpr C-terminal part, a redundancy that represents a new approach to address the question of biological relevance of HIV-1 Vpr. In this context, future studies will be required to determine the functional relevance of the Vpr77–92 domain in full length Vpr protein and also in entire HIV provirus.
Controls on Mid‐ocean Ridge Normal Fault Seismicity Across Spreading Rates From Rate‐and‐State Friction Models

Recent seismic and geodetic observations have led to a growing realization that a significant amount of fault slip at plate boundaries occurs aseismically and that the amount of aseismic slip varies across tectonic settings. Seismic moment release rates measured along the fast‐spreading East Pacific Rise suggest that the majority of fault slip occurs aseismically. By contrast, at the slow‐spreading Mid‐Atlantic Ridge seismic slip may represent up to 60% of total fault displacement. In this study, we use rate‐and‐state friction models to quantify the seismic coupling coefficient, defined as the fraction of total fault slip that occurs seismically, on mid‐ocean ridge normal faults and investigate controls on fault behavior that might produce variations in coupling observed at oceanic spreading centers. We find that the seismic coupling coefficient scales with the ratio of the downdip width of the seismogenic area (W) to the critical earthquake nucleation size (h*). At mid‐ocean ridges, W is expected to increase with decreasing spreading rate. Thus, the relationship between seismic coupling and W/h* predicted from our models explains the first‐order variations in seismic coupling coefficient as a function of spreading rate.
Characterization of Canadian High Arctic glacier surface albedo from MODIS C6 data, 2001–2016

Inter-annual variations and longer-term trends in the annual mass balance of glaciers in Canada's Queen Elizabeth Islands (QEI) are largely attributable to changes in summer melt. The largest source of melt energy in the QEI in summer is net shortwave radiation, which is modulated by changes in glacier surface albedo. We used measurements from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensors to investigate large scale spatial patterns and temporal trends and variability in the summer surface albedo of QEI glaciers and their relationship to observed changes in glacier surface temperature from 2001 to 2016. Mean summer black-sky shortwave broadband albedo (BSA) decreased at a rate of 0.029 ± 0.025 decade -1 over that period. Larger reductions in BSA occurred in July (−0.050 ± 0.031 decade -1 ). No change in BSA was observed in either June or August. Most of the decrease in BSA, which was greatest at lower elevations around the margins of the ice masses, occurred between 2007 and 2012 when mean summer BSA was anomalously low. The First Principal Component of the 16-year record of mean summer BSA was well correlated with the mean summer North Atlantic Oscillation Index, except in 2006, 2010, and 2016. During this 16-year period, the mean summer LST increased by 0.046 ± 0.036 °C yr -1 and the BSA record was negatively correlated (−0.64, p < 0.01) with the LST record, indicative of a positive ice-albedo feedback that would increase rates of mass loss from the QEI glaciers.
Regional regularization of the electrocardiographic inverse problem: a model study using spherical geometry

This study examines the use of a new regularization scheme, called regional regularization, for solving the electrocardiographic inverse problem. Previous work has shown that different time frames in the cardiac cycle require varying degrees of regularization. This reflects differences in potential magnitudes, gradients, signal-to-noise ratio (SNR), and locations of electrical activity. One might expect, therefore, that a single regularization parameter and a uniform level of regularization may also be insufficient for a single potential map of a single time frame because in one map there are regions of high and low potentials and potential gradients. Regional regularization is a class of methods that subdivides a given potential map into functional "regions" based on the spatial characteristics of the potential ("spatial frequencies"). These individual regions are regularized separately and recombined into a complete map. This paper examines the hypothesis that such regionally regularized maps are more accurate than if all regions were taken together and solved with an averaged level of regularization. In a homogeneous concentric spheres model, Legendre polynomials are used to decompose a torso potential map into a set of submaps, each with a different degree of spatial variation. The original torso map is contaminated with data noise, or geometrical error or both, and regional regularization improves the epicardial potential reconstruction by up to 25% [relative error (RE)]. Regional regularization also improves the reconstructed location of peaks. A practical goal is to extend the application of this method to the realistic torso geometry, but because Legendre decomposition is limited to geometries with spherical symmetry, other methods of map decomposition must be found. Singular value decomposition (SVD) is used to decompose the maps into component parts. Its individual submaps also have different levels of spatial variation; moreover, it is generalizable to any vector, does not require spherical symmetry, and is extremely efficient numerically. Using SVD decomposition for regional regularization, significant improvement was achieved in the map quality in the presence of data noise.
Long-Term Associations of Justice Sensitivity, Rejection Sensitivity, and Depressive Symptoms in Children and Adolescents

Depressive symptoms have been related to anxious rejection sensitivity, but little is known about relations with angry rejection sensitivity and justice sensitivity. We measured rejection sensitivity, justice sensitivity, and depressive symptoms in 1,665 9-to-21-year olds at two points of measurement. Participants with high T1 levels of depressive symptoms reported higher anxious and angry rejection sensitivity and higher justice sensitivity than controls at T1 and T2. T1 rejection, but not justice sensitivity predicted T2 depressive symptoms; high victim justice sensitivity, however, added to the stabilization of depressive symptoms. T1 depressive symptoms positively predicted T2 anxious and angry rejection and victim justice sensitivity. Hence, sensitivity toward negative social cues may be cause and consequence of depressive symptoms and requires consideration in cognitive-behavioral treatment of depression.