Miracle-dz/UniFAR-FTUs huggingface dataset:
Respiratory motion‐resolved, self‐gated 4D‐MRI using rotating cartesian k‐space (ROCK)

Purpose To propose and validate a respiratory motion resolved, self‐gated (SG) 4D‐MRI technique to assess patient‐specific breathing motion of abdominal organs for radiation treatment planning. Methods The proposed 4D‐MRI technique was based on the balanced steady‐state free‐precession (bSSFP) technique and 3D k‐space encoding. A novel rotating cartesian k‐space (ROCK) reordering method was designed which incorporates repeatedly sampled k‐space centerline as the SG motion surrogate and allows for retrospective k‐space data binning into different respiratory positions based on the amplitude of the surrogate. The multiple respiratory‐resolved 3D k‐space data were subsequently reconstructed using a joint parallel imaging and compressed sensing method with spatial and temporal regularization. The proposed 4D‐MRI technique was validated using a custom‐made dynamic motion phantom and was tested in six healthy volunteers, in whom quantitative diaphragm and kidney motion measurements based on 4D‐MRI images were compared with those based on 2D‐CINE images. Results The 5‐minute 4D‐MRI scan offers high‐quality volumetric images in 1.2 × 1.2 × 1.6 mm3 and eight respiratory positions, with good soft‐tissue contrast. In phantom experiments with triangular motion waveform, the motion amplitude measurements based on 4D‐MRI were 11.89% smaller than the ground truth, whereas a −12.5% difference was expected due to data binning effects. In healthy volunteers, the difference between the measurements based on 4D‐MRI and the ones based on 2D‐CINE were 6.2 ± 4.5% for the diaphragm, 8.2 ± 4.9% and 8.9 ± 5.1% for the right and left kidney. Conclusion The proposed 4D‐MRI technique could provide high‐resolution, high‐quality, respiratory motion‐resolved 4D images with good soft‐tissue contrast and are free of the “stitching” artifacts usually seen on 4D‐CT and 4D‐MRI based on resorting 2D‐CINE. It could be used to visualize and quantify abdominal organ motion for MRI‐based radiation treatment planning.
Burden of rheumatoid arthritis in the Nordic region, 1990–2015: a comparative analysis using the Global Burden of Disease Study 2015

Objective: To report mortality and disability due to rheumatoid arthritis (RA) in the Nordic region (Denmark, Finland, Greenland, Iceland, Norway, and Sweden) using data from the Global Burden of Disease Study (GBD) 2015. Method: Using the results of GBD 2015, we present rates and trends in prevalence, mortality, years of life lost, years lived with disability (YLD), and disability-adjusted life-years (DALYs) of RA in the Nordic region during 1990–2015. Results: In 2015, the age-standardized prevalence of RA was higher in the Nordic region than the global level (0.44%, 95% uncertainty interval 0.40–0.48%, vs 0.35%, 0.32–0.38%). For women (men), DALYs increased by 2.4% (12.9%), from 29 263 (10 909) in 1990 to 29 966 (12 311) in 2015. The burden of RA as a proportion of total DALYs in women (men) increased from 0.90% (0.29%) in 1990 to 0.94% (0.36%) in 2015. Age-standardized DALY rates declined in all countries except Denmark and Greenland between 1990 and 2015. Of 315 conditions studied, RA was ranked as the 16th (37th) leading cause of YLD in women (men) in the region. Of 195 countries studied, Greenland, Finland, Denmark, Norway, Sweden, and Iceland had the 7th, 11th, 28th, 38th, 48th, and 78th highest age-standardized YLD rates for RA, respectively. Conclusions: The prevalence of RA in the Nordic region is higher than the global average. Current trends in population growth and ageing suggest a potential increase in RA burden in the coming decades in the region that should be considered in healthcare resources allocation.
Natural language processing to ascertain two key variables from operative reports in ophthalmology

Antibiotic prophylaxis is critical to ophthalmology and other surgical specialties. We performed natural language processing (NLP) of 743 838 operative notes recorded for 315 246 surgeries to ascertain two variables needed to study the comparative effectiveness of antibiotic prophylaxis in cataract surgery. The first key variable was an exposure variable, intracameral antibiotic injection. The second was an intraoperative complication, posterior capsular rupture (PCR), which functioned as a potential confounder. To help other researchers use NLP in their settings, we describe our NLP protocol and lessons learned.
Low childhood subjective social status and telomere length in adulthood: The role of attachment orientations

Low subjective social status (SSS) in childhood places one at greater risk of a number of health problems in adulthood. Theoretical and empirical evidence indicates that exposure to supportive parenting may buffer the negative effects of low childhood SSS on adult health. Given the importance of supportive caregivers and close others for the development of attachment orientations throughout the lifespan, attachment theory may be important for understanding why some individuals are resilient to the negative effects of low childhood SSS on adult health while others are not. We examined if attachment anxiety and attachment avoidance altered the association between childhood subjective social status (SSS) and length of telomeres in white blood cells in adulthood. Shorter telomere length is associated with increased risk of age-related diseases including cancer, type 2 diabetes, and cardiovascular disease. Participants (N = 128) completed self-report measures of childhood SSS and attachment orientations, as well as a blood draw. We found that among those with low childhood SSS, low attachment anxiety was associated with longer telomere length in white blood cells in comparison to high attachment anxiety controlling for participant age, sex, race, body mass index, and adult SSS. Among those with high childhood SSS, low attachment anxiety was associated with a slight decrease in telomere length. Attachment avoidance was unrelated to length of telomeres. Such findings provide further evidence for the role that close relationships may have on buffering SSS related health disparities.
Anticipatory Emotion in Schizophrenia

While people with schizophrenia report experiencing as much emotion in the presence of emotionally evocative stimuli as do people without schizophrenia, evidence suggests that they have deficits in the anticipation of positive emotion. However, little is known about the anticipation of negative emotion in schizophrenia, thus leaving open whether anticipation deficits are more general. We sought to assess anticipation of positive and negative stimuli across multiple methods of measurement. We measured reported experience and emotion-modulated startle response in people with (n = 27) and without (n = 27) schizophrenia as they anticipated and subsequently viewed evocative pictures. People with schizophrenia showed an overall dampened response during the anticipation of positive and negative stimuli, suggesting a more general deficit in anticipatory emotional responses. Moreover, anticipatory responses were related to symptoms and functioning in people with schizophrenia. Together, these findings point to important new directions for understanding emotion deficits in schizophrenia
Functional clues from the crystal structure of an orphan periplasmic ligand‐binding protein from Treponema pallidum

The spirochete Treponema pallidum is the causative agent of syphilis, a sexually transmitted infection of major global importance. Other closely related subspecies of Treponema also are the etiological agents of the endemic treponematoses, such as yaws, pinta, and bejel. The inability of T. pallidum and its close relatives to be cultured in vitro has prompted efforts to characterize T. pallidum's proteins structurally and biophysically, particularly those potentially relevant to treponemal membrane biology, with the goal of possibly revealing the functions of those proteins. This report describes the structure of the treponemal protein Tp0737; this polypeptide has a fold characteristic of a class of periplasmic ligand‐binding proteins associated with ABC‐type transporters. Although no ligand for the protein was observed in electron‐density maps, and thus the nature of the native ligand remains obscure, the structural data described herein provide a foundation for further efforts to elucidate the ligand and thus the function of this protein in T. pallidum.
Transport capabilities of environmental Pseudomonads for sulfur compounds

Sulfur is an essential element in plant rhizospheres and microbial activity plays a key role in increasing the biological availability of sulfur in soil environments. To better understand the mechanisms facilitating the exchange of sulfur‐containing molecules in soil, we profiled the binding specificities of eight previously uncharacterized ABC transporter solute‐binding proteins from plant‐associated Pseudomonads. A high‐throughput screening procedure indicated eighteen significant organosulfur binding ligands, with at least one high‐quality screening hit for each protein target. Calorimetric and spectroscopic methods were used to validate the best ligand assignments and catalog the thermodynamic properties of the protein‐ligand interactions. Two novel high‐affinity ligand‐binding activities were identified and quantified in this set of solute‐binding proteins. Bacteria were cultured in minimal media with screening library components supplied as the sole sulfur sources, demonstrating that these organosulfur compounds can be metabolized and confirming the relevance of ligand assignments. These results expand the set of experimentally validated ligands amenable to transport by this ABC transporter family and demonstrate the complex range of protein‐ligand interactions that can be accomplished by solute‐binding proteins. Characterizing new nutrient import pathways provides insight into Pseudomonad metabolic capabilities which can be used to further interrogate bacterial survival and participation in soil and rhizosphere communities.
Main and interactive effects of emotion dysregulation and HIV symptom severity on quality of life among persons living with HIV/AIDS

ABSTRACT HIV symptoms are associated with a poorer quality of life (QOL) among persons living with HIV/AIDS (PLWHA). Yet, there is little understanding of emotional factors that impact the relation between HIV symptom severity and QOL. The present study examined the main and interactive effects of emotion dysregulation and HIV symptom severity on multiple indices of QOL, including physical (impact of physical problems related to HIV), psychological (frequency of negative feelings), independence (necessity of medical treatment to function in daily life), social (feelings of acceptance), environmental (satisfaction with living conditions and medical care), and spiritual (fear of the future and death) among a sample of 74 PLWHA. Participants (72.9% male; mean age = 48.24, SD = 7.85) were recruited from AIDS Service Organizations in the United States. Results indicated that higher HIV symptom severity is significantly associated with lower physical and independence QOL, whereas higher emotion dysregulation is significantly associated with lower scores on all measured aspects of QOL. Additionally, results indicated that the interaction of emotion dysregulation and HIV symptom severity was significantly associated with both physical and environmental QOL. The form of the observed significant interactions indicated that HIV symptom severity was related to poorer QOL among those with lower (versus higher) emotion dysregulation. The present findings indicate that emotion dysregulation is related to QOL among PLWHA and may interact with HIV symptom severity to negatively impact certain aspects of QOL. Given the profound impact that HIV has on QOL, this finding is important in understanding these relations mechanistically, and may be important in the development of novel psychological treatment strategies.
Output-optimal Parallel Algorithms for Similarity Joins

Parallel join algorithms have received much attention in recent years, due to the rapid development of massively parallel systems such as MapReduce and Spark. In the database theory community, most efforts have been focused on studying worst-optimal algorithms. However, the worst-case optimality of these join algorithms relies on the hard instances having very large output sizes. In the case of a two-relation join, the hard instance is just a Cartesian product, with an output size that is quadratic in the input size. In practice, however, the output size is usually much smaller. One recent parallel join algorithm by Beame et al.[8] has achieved output-optimality, i.e., its cost is optimal in terms of both the input size and the output size, but their algorithm only works for a 2-relation equi-join, and has some imperfections. In this paper, we first improve their algorithm to true optimality. Then we design output-optimal algorithms for a large class of similarity joins. Finally, we present a lower bound, which essentially eliminates the possibility of having output-optimal algorithms for any join on more than two relations.
Autocrine release of angiopoietin-2 mediates cerebrovascular disintegration in Moyamoya disease

Moyamoya disease is a rare steno-occlusive cerebrovascular disorder often resulting in hemorrhagic and ischemic strokes. Although sharing the same ischemic stimulus with atherosclerotic cerebrovascular disease, Moyamoya disease is characterized by a highly instable cerebrovascular system which is prone to rupture due to pathological neovascularization. To understand the molecular mechanisms underlying this instability, angiopoietin-2 gene expression was analyzed in middle cerebral artery lesions obtained from Moyamoya disease and atherosclerotic cerebrovascular disease patients. Angiopoietin-2 was significantly up-regulated in Moyamoya vessels, while serum concentrations of soluble angiopoietins were not changed. For further evaluations, cerebral endothelial cells incubated with serum from these patients in vitro were applied. In contrast to atherosclerotic cerebrovascular disease serum, Moyamoya disease serum induced an angiopoietin-2 overexpression and secretion, accompanied by loss of endothelial integrity. These effects were absent or inverse in endothelial cells of non-brain origin suggesting brain endothelium specificity. The destabilizing effects on brain endothelial cells to Moyamoya disease serum were partially suppressed by the inhibition of angiopoietin-2. Our findings define brain endothelial cells as the potential source of vessel-destabilizing factors inducing the high plasticity state and disintegration in Moyamoya disease in an autocrine manner. We also provide new insights into Moyamoya disease pathophysiology that may be helpful for preventive treatment strategies in future.
The True North Strong and Free? Opportunities for Improving Canadian Mental Health Care and Education by Adopting the WHO’s ICD-11 Classification

A majority of Canadian mental health care professionals rely on the Diagnostic and Statistical Manual of Mental Disorders (DSM) to inform their diagnostic formulations. The American nosology is taught across Canada in undergraduate and graduate programs, including in residencies in psychiatry and clinical psychology. The DSM rose to prominence in Canada and elsewhere with the introduction of the DSM-III, which offered the first glimpse of a scientifically informed classification and provided clinical researchers with a reliable way to form homogeneous participant groups. However, the DSM has become so entrenched in our way of conceptualising psychopathology that despite well-documented concerns about the reliability, validity, and safety of its latest revision, Canadian clinicians appear to accept without question that it is the only viable system of classification for the purposes of clinical care as well as medical and allied health care professional education. Canadians actually have an excellent alternative, the World Health Organization’s (WHO’s) International Classification of Diseases and Related Health Problems (ICD), which is currently being revised and comprehensively field-tested in multiple languages for an anticipated approval by the World Health Assembly in 2018. The purpose of the present perspective is to highlight several important distinctions between the DSM-5 and the forthcoming ICD-11 to argue for adoption of the ICD in Canada for teaching, training, clinical practice, and research. The choice of a classification system has important implications for patient care, health policy, and other civil and forensic decisions. Unfortunately, the current state of knowledge about mental disorders does not permit a fully scientifically validated or etiologically grounded approach to classification. Until such a time that we are able to reliably categorise disorders according to, for example, specific biomarkers, psychiatric diagnosis must rely on descriptive phenomenological nosologies such as the DSM-5 and ICD-11 to accomplish the pragmatic tasks of compiling health statistics, making treatment decisions, communicating effectively, and allocating resources. We argue that Canadians should be using and teaching the ICD-11, particularly in light of emerging evidence that it is a valid, reliable, safe, and clinically useful classification. Importantly, the ICD, unlike the DSM, is a nosology conceived and developed for the betterment of public health that is available to users at minimal cost.
Chronic stress exposure following photothrombotic stroke is associated with increased levels of Amyloid beta accumulation and altered oligomerisation at sites of thalamic secondary neurodegeneration in mice

Exposure to severe stress following stroke is recognised to complicate the recovery process. We have identified that stress can exacerbate the severity of post-stroke secondary neurodegeneration in the thalamus. In this study, we investigated whether exposure to stress could influence the accumulation of the neurotoxic protein Amyloid-β. Using an experimental model of focal cortical ischemia in adult mice combined with exposure to chronic restraint stress, we examined changes within the contra- and ipsilateral thalamus at six weeks post-stroke using Western blotting and immunohistochemical approaches. Western blotting analysis indicated that stroke was associated with a significant enhancement of the 25 and 50 kDa oligomers within the ipsilateral hemisphere and the 20 kDa oligomer within the contralateral hemisphere. Stroked animals exposed to stress exhibited an additional increase in multiple forms of Amyloid-beta oligomers. Immunohistochemistry analysis confirmed that stroke was associated with a significant accumulation of Amyloid-beta within the thalami of both hemispheres, an effect that was exacerbated in stroke animals exposed to stress. Given that Amyloid-beta oligomers, most notably the 30–40 and 50 kDa oligomers, are recognised to correlate with accelerated cognitive decline, our results suggest that monitoring stress levels in patients recovering from stroke may merit consideration in the future.
Interactive ray tracing

We examine a rendering system that interactively ray traces an image on a conventional multiprocessor. The implementation is “brute force” in that it explicitly traces rays through every screen pixel, yet pays careful attention to system resources for acceleration. The design of the system is described, along with issues related to material models, lighting and shadows, and frameless rendering. The system is demonstrated for several different types of input scenes. CR Categories: I.3. 0 [Computer Graphics]: General; I.3. 6 [Computer Graphics]: Methodology and Techniques.
Gliadel for brain metastasis

With therapies for systemic malignancy improving, life expectancy for cancer patients is becoming increasingly dependent on control of brain metastatic disease. Despite improvements in surgical and radiotherapy modalities for control of brain metastasis, the prognosis for patients with brain metastases is poor. The development of controlled release polymers has lead to novel new therapies for malignant brain tumors consisting of direct surgical delivery of chemotherapy agents to the tumor bed and sustained chemotherapy release over a prolonged period of time. Although there is a large body of literature in support of BCNU polymer wafer for primary brain malignancy and experimental brain metastases, clinical studies evaluating the BCNU polymer wafer for brain metastatic disease are relatively sparse. In this review, we discuss the role of the BCNU polymer wafer for brain metastasis focusing specifically on rationale for use of locally delivered sustained release polymers, history of the BCNU polymer wafer, and emerging studies examining the role of the BCNU polymer wafer for metastatic brain tumors.
Inhibition of x‐box binding protein 1 reduces tunicamycin‐induced apoptosis in aged murine macrophages

Endoplasmic reticulum (ER) stress is induced by the accumulation of unfolded and misfolded proteins in the ER. Although apoptosis induced by ER stress has been implicated in several aging‐associated diseases, such as atherosclerosis, it is unclear how aging modifies ER stress response in macrophages. To decipher this relationship, we assessed apoptosis in macrophages isolated from young (1.5–2 months) and aged (16–18 months) mice and exposed the cells to the ER stress inducer tunicamycin. We found that aged macrophages exhibited more apoptosis than young macrophages, which was accompanied by reduced activation of phosphorylated inositol‐requiring enzyme‐1 (p‐IRE1α), one of the three key ER stress signal transducers. Reduced gene expression of x‐box binding protein 1 (XBP1), a downstream effector of IRE1α, enhanced p‐IRE1α levels and reduced apoptosis in aged, but not young macrophages treated with tunicamycin. These findings delineate a novel, age‐dependent interaction by which macrophages undergo apoptosis upon ER stress, and suggest an important protective role of IRE1α in aging‐associated ER stress‐induced apoptosis. This novel pathway may not only be important in our understanding of longevity, but may also have important implications for pathogenesis and potential treatment of aging‐associated diseases in general.
Absence of cell surface expression of human ACE leads to perinatal death

Renal tubular dysgenesis (RTD) is a recessive autosomal disease characterized most often by perinatal death. It is due to the inactivation of any of the major genes of the renin-angiotensin system (RAS), one of which is the angiotensin I-converting enzyme (ACE). ACE is present as a tissue-bound enzyme and circulates in plasma after its solubilization. In this report, we present the effect of different ACE mutations associated with RTD on ACE intracellular trafficking, secretion and enzymatic activity. One truncated mutant, R762X, responsible for neonatal death was found to be an enzymatically active, secreted form, not inserted in the plasma membrane. In contrast, another mutant, R1180P, was compatible with life after transient neonatal renal insufficiency. This mutant was located at the plasma membrane and rapidly secreted. These results highlight the importance of tissue-bound ACE versus circulating ACE and show that the total absence of cell surface expression of ACE is incompatible with life. In addition, two missense mutants (W594R and R828H) and two truncated mutants (Q1136X and G1145AX) were also studied. These mutants were neither inserted in the plasma membrane nor secreted. Finally, the structural implications of these ACE mutations were examined by molecular modelling, which suggested some important structural alterations such as disruption of intra-molecular non-covalent interactions (e.g. salt bridges).