Miracle-dz/UniFAR-FTUs huggingface dataset:
Consideration of optimal isodose surface selection for target coverage in micro-multileaf collimator-based stereotactic radiotherapy for large cystic brain metastases: comparison of 90%, 80% and 70% isodose surface-based planning.

OBJECTIVE This study aims to compare dynamic conformal arc (DCA) plans based on different-percentage isodose surfaces (IDSs), normalised to 100% at the isocentre, for target coverage (TC; dose prescription) in stereotactic radiotherapy for large cystic brain metastases. METHODS The DCA plans were generated for 15 targets (5 spherical models and 10 metastatic brain lesions) based on 90%, 80% and 70% IDSs for dose prescription to attain ≥99% TC values using the Novalis Tx platform. These plans were optimised mainly by leaf margin and/or collimator angle adjustment, while similar arc arrangements were used. RESULTS TC values were equivalent among the three plans. Conformity index values were similar between the 80% and 70% plans, while they were worse in the 90% plans. Mean doses (D(mean)) of the interior 3 mm rind structure were highest in the 70% plans, followed by the 80% plans and lowest in the 90% plans. D(mean) of the exterior 3 mm rind structure and the ratio of 50%/100% isodose volumes (Paddick's gradient index values) were highest in the 90% plans, followed by 80% and lowest in the 70% plans. CONCLUSIONS These results suggest that the 70% IDS plans might be beneficial for both tumour control and reducing toxicity to surrounding normal tissue if appropriate dose conformity and precise treatment set-up are ensured. The 90% IDS plans are unfavourable in view of inferior dose gradient outside the target and should be limited to cases in which the target dose homogeneity is given the highest priority.
Probabilistic record linkage and a method to calculate the positive predictive value.

BACKGROUND Computerized record linkage is commonly used in cohort studies to ascertain the study outcome, and as such its accuracy classifying the outcome can be described using the standard epidemiological terms of sensitivity and positive predictive value (PPV). METHOD We describe a 'duplicate method' to calculate the PPV of record linkage when each record can only be involved in one match (e.g. linking population files to death files). The method does not require a validation subset of records from both files with detailed personal information (e.g. name and address), and is therefore ideal for linkage projects using anonymous data. The duplicate method assumes that the number of records from one file with zero, one, two, etc., links from the other file is distributed in a manner predicted by combinatorial probabilities. Having made this assumption, the number of false positive links, and hence the PPV, are estimable. We demonstrate this duplicate method using output from anonymous and probabilistic record linkage of census and mortality records in New Zealand. RESULTS The PPV estimates conform to the pattern expected based on the underlying theory of probabilistic record linkage, and were robust to sensitivity analyses. We encourage other researchers to further assess the accuracy of this method.
Fat-derived Factor Omentin Stimulates Endothelial Cell Function and Ischemia-induced Revascularization via Endothelial Nitric Oxide Synthase-dependent Mechanism*

Obesity-related diseases are associated with vascular dysfunction and impaired revascularization. Omentin is a fat-derived secreted protein, which is down-regulated in association with obese complications. Here, we investigated whether omentin modulates endothelial cell function and revascularization processes in vitro and in vivo. Systemic delivery of an adenoviral vector expressing omentin (Ad-omentin) enhanced blood flow recovery and capillary density in ischemic limbs of wild-type mice in vivo, which were accompanied by increased phosphorylation of Akt and endothelial nitric oxide synthase (eNOS). In cultured human umbilical vein endothelial cells (HUVECs), a physiological concentration of recombinant omentin protein increased differentiation into vascular-like structures and decreased apoptotic activity under conditions of serum starvation. Treatment with omentin protein stimulated the phosphorylation of Akt and eNOS in HUVECs. Inhibition of Akt signaling by treatment with dominant-negative Akt or LY294002 blocked the stimulatory effects of omentin on differentiation and survival of HUVECs and reversed omentin-stimulated eNOS phosphorylation. Pretreatment with the NOS inhibitor also reduced the omentin-induced increase in HUVEC differentiation and survival. Omentin protein also stimulated the phosphorylation of AMP-activated protein kinase in HUVECs. Transduction with dominant-negative AMP-activated protein kinase diminished omentin-induced phosphorylation of Akt and omentin-stimulated increase in HUVEC differentiation and survival. Of importance, in contrast to wild-type mice, systemic administration of Ad-omentin did not affect blood flow in ischemic muscle in eNOS-deficient mice in vivo. These data indicate that omentin promotes endothelial cell function and revascularization in response to ischemia through its ability to stimulate an Akt-eNOS signaling pathway.
A longitudinal, HIV care continuum: 10-year restricted mean time in each care continuum stage after enrollment in care, by history of IDU

Objectives:We present a novel, patient-centric, longitudinal summary of patient progress through the HIV care continuum. Using this new approach, we compare person-time spent alive, in care, on antiretroviral therapy (ART), and virally suppressed among people who inject drugs (PWID) and those who do not (non-IDU). Design:Prospective clinical observational cohort study. Methods:We followed ART-naive patients with detectable HIV viral loads who enrolled in the Johns Hopkins HIV Clinical Cohort from enrollment until the occurrence of several care continuum-related milestones, including ART initiation and viral suppression, and until several care continuum-related failures, including loss to clinic and death. We added and subtracted cumulative incidence curves to estimate the proportion of the cohort in each of seven continuum stages across the 10 years following enrollment in clinical care. Results:PWID composed 32% of the study sample (n = 1443). Over 10 years following enrollment in care, PWID and non-IDU spent only 23 and 37%, respectively, of person-time in care, on ART, and virally suppressed. PWID lost 8.9 more months of life compared with non-IDU and spent an additional 5.0 months on ART but not virally suppressed, and an additional 5.5 months in care but not on ART. There were not meaningful improvements in the 5-year restricted mean person-time differences comparing PWID to non-IDU across enrollment cohorts (2000–2003, 2004–2007, 2008–2014). Conclusion:Efforts to increase viral suppression among PWID should focus on increasing ART initiation and improving adherence to therapy.
Observation of extreme sensitivity to induced molecular coherence in stimulated Raman scattering.

We have detected molecular coherence lasting nearly nine times the collisional dephasing time in a Raman generator. Two laser pulses, separated in time, pumped a common set of hydrogen molecules, producing two Stokes pulses whose relative phase was measured interferometrically. By making repeated measurements, the probability distribution of the relative phase was obtained. The variance of this phase distribution is a direct measure of the memory of the molecular coherence induced by the first scattering process. A one-dimensional theoretical model is developed which implies that the technique is capable of measuring a level of molecular coherence equivalent to between 15 and 50 phonons (delocalized vibrational quanta) in the most strongly excited mode
Impaired conscious access and abnormal attentional amplification in schizophrenia

1. Cognitive Neuroimaging Unit, CEA DSV/I2BM, INSERM, Université Paris-Sud, Université Paris-Saclay, NeuroSpin center, 91191 Gif/Yvette, France 2. Sorbonne Universités, UPMC Univ Paris 06, IFD, 4 place Jussieu, 75252 PARIS cedex 05, France 3. AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Psychiatrie d'Adultes, 75013 Paris, France. 4. Inserm, CNRS, APHP, Institut du Cerveau et de la Moelle (ICM), Hôpital PitiéSalpêtrière, Sorbonne Universités, UPMC Univ Paris 06, 75013 Paris, France. 5. Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France. 6. Collège de France, 11 Place Marcelin Berthelot, 75005 Paris, France
Family caregivers' reactions and coping for persons with brain injury

Background : This study was a follow-up of a previous study on the empowerment of families caring for Chinese persons with brain injury. Objective : The present study examined, in a qualitative way, the impact of brain injury on the family and the complex array of factors that appears to be related to effective family coping and their independence. The reactions of families under stress and their coping strategies are summarized. Individual families' differences in terms of an empowerment framework are discussed for possible guidance in family intervention. Method : Individual families were interviewed using open-ended questions, their responses and the verbatim transcripts of long interviews performed with selected families were examined. Results : A total of 50 family members were successfully recruited for interview. They were found to show typical coping strategies, including shock and uncertainty, which are suggested to be relating closely to the nature of brain injury and the difficulties in managing it. The physical and psychological burdens involved in caring for members with brain injury were also reflected. Content analysis of the long interviews of four selected families showed that it was not every family that coped well. Possible factors leading to better adjustment, such as clear personal expectations, a desire to master the situation, strong motivation, flexibility to adjust life goals and awareness of one's own powerless state are proposed. Conclusion : The results indicated that family coping varies with individual families and should be explored further for the development of intervention guidelines.
Analysis of Idiopathic Scoliosis Progression by Using Numerical Simulation

Study Design. The mechanisms of idiopathic scoliosis progression were investigated through a patient-specific numerical model. Objective. To explore the combined effect of gravity, the decrease of intervertebral discs’ stiffness and the anterior spinal growth on scoliosis progression, by using a numerical simulation, to better understand mechanisms of scoliosis progression. Summary of Background Data. Eighteen adolescents (12 girls, 6 boys) with an average age of 10.5 years (range, 7–13) were divided into 2 groups: 12 mild scoliotic patients with thoracolumbar curves and 6 asymptomatic subjects. Methods. Accurate 3-dimensional reconstructions of the spine were performed from biplanar radiographs. A patient-specific validated finite element model was used. Four configurations were simulated for each patient: the first configuration with the spine under gravity, the second one under gravity with a decrease of disc’s mechanical stiffness, the third one under gravity with anterior vertebral growth, and the last one with combination of the 3 previous configurations. Results. Gravity loads resulted mainly in a vertebral lateral deviation of the curve without axial rotation for all patients with mild scoliosis. Anterior vertebral growth with gravity induced both lateral deviation and axial rotation. This phenomenon was amplified when the mechanical properties of discs were decreased. None of these simulations initiated a scoliosis-like deformity for asymptomatic subjects. Conclusion. For preexisting spinal curvature, an anterior spinal growth combined with gravity and a decrease of disc’s mechanical stiffness could lead to a progression of scoliosis. Biomechanical factors could be secondary after initial deformation.
Seasonal variation and environmental predictors of exhaled nitric oxide in children with asthma

The fraction of exhaled nitric oxide (FeNO), a measure of airway inflammation, shows promise as a noninvasive tool to guide asthma management, but there is a paucity of longitudinal data about seasonal variation and environmental predictors of FeNO in children. The objective of this project was to evaluate how environmental factors affect FeNO concentrations over a 12‐month study period among children with doctor diagnosed asthma. We conducted a prospective cohort study of 225 tobacco‐smoke exposed children age 6–12 years with doctor‐diagnosed asthma including measures of FeNO, medication use, settled indoor allergens (dust mite, cat, dog, and cockroach), and tobacco smoke exposure. Baseline geometric mean FeNO was 12.4 ppb (range 1.9–60.9 ppb). In multivariable analyses, higher baseline FeNO levels, atopy, and fall season were associated with increased FeNO levels, measured 6 and 12 months after study initiation, whereas inhaled steroid use, summer season, and increasing nicotine exposure were associated with lower FeNO levels. In secondary analyses of allergen sensitization, only sensitization to dust mite and cat were associated with increased FeNO levels. Our data demonstrate that FeNO levels over a year long period reflected baseline FeNO levels, allergen sensitization, season, and inhaled steroid use in children with asthma. These results indicate that FeNO levels are responsive to common environmental triggers as well as therapy for asthma in children. Clinicians and researchers may need to consider an individual's baseline FeNO levels to manage children with asthma. Pediatr Pulmonol. 2008; 43:576–583. © 2008 Wiley‐Liss, Inc.
The structures of thymidine kinase from Herpes simplex virus type 1 in complex with substrates and a substrate analogue

Thymidine kinase from Herpes simplex virus type 1 (TK) was crystallized in an N‐terminally truncated but fully active form. The structures of TK complexed with ADP at the ATP‐site and deoxythymidine‐5′‐monophosphate (dTMP), deoxythymidine (dT), or idoxuridine‐5′‐phosphate (5‐iodo‐dUMP) at the substrate‐site were refined to 2.75 Å, 2.8 Å, and 3.0 Å resolution, respectively. TK catalyzes the phosphorylation of dT resulting in an ester, and the phosphorylation of dTMP giving rise to an anhydride. The presented TK structures indicate that there are only small differences between these two modes of action. Glu83 serves as a general base in the ester reaction. Arg163 parks at an internal aspartate during ester formation and binds the α‐phosphate of dTMP during anhydride formation. The bound deoxythymidine leaves a 35 Å3 cavity at position 5 of the base and two sequestered water molecules at position 2. Cavity and water molecules reduce the substrate specificity to such an extent that TK can phosphorylate various substrate analogues useful in pharmaceutical applications. TK is structurally homologous to the well‐known nucleoside monophosphate kinases but contains large additional peptide segments.
Intrahepatic PD-1/PD-L1 Up-regulation Closely Correlates with Inflammation and Virus Replication in Patients with Chronic HBV Infection

Chronic hepatitis B was characterized by fluctuant immune response to infected hepatocytes resulting in hepatic inflammation and virus persistence. Recently, Programmed Death-1 (PD-1) and its ligand PD-L1 have been demonstrated to play an essential role in balancing antiviral immunity and inflammation in the livers of acute hepatitis B patients, significantly influencing disease outcome. PD-1 up-regulation in peripheral T cells is associated with immune dysfunction in chronic hepatitis B patients. However, the effect of PD-1/PD-L1 on hepatic damage and chronic infective status is still unknown in patients with chronic HBV infection. Here, we report up-regulation of PD-1 and PD-L1 in liver biopsies from 32 chronic HBV patients compared to 4 healthy donors. PD-1/PD-L1 up-regulation was significantly associated with hepatic inflammation and ALT elevation. Moreover, appropriate up-regulation but not overexpression of PD-L1 in the active phase of chronic hepatitis B as well as lower expression of PD-L1 in the inactive phase in liver residential antigen presenting cells (including Kupffer cells and sinusoidal endothelial cells) may contribute to viral inhibition. Our data suggest that the intrahepatic interaction of PD-1 and PD-L1 might play an important role in balancing the immune response to HBV and immune-mediated liver damage in chronic HBV infection.
The (Potential) Benefits of Campaigning via Social Network Sites

Social network sites (SNS) have become very popular, especially among adolescents and young adults. Consequently, politicians started to use them for their campaigns. This paper examines how this personalized soft campaigning strategy worked in the 2006 Dutch elections and how interaction with potential voters can influence the evaluation of the candidates. The first question is answered by a web survey among active users of Hyves, the largest Dutch SNS. The second question is answered by a web experiment on a fictive candidate. The survey showed that SNS provide an opportunity to reach individuals less interested in politics. Viewing a candidate's profile further strengthened existing attitudes. However, the politicians did not fully use the interactive features of SNS during the 2006 campaign. The web experiment showed that politicians who react on the comments of users were perceived more favorable. This effect was stronger for right-wing politicians and left-wing voters.
Degradation of Endocytosed Epidermal Growth Factor and Virally Ubiquitinated Major Histocompatibility Complex Class I Is Independent of Mammalian ESCRTII*

Models for protein sorting at multivesicular bodies in the endocytic pathway of mammalian cells have relied largely on data obtained from yeast. These data suggest the essential role of four ESCRT complexes in multivesicular body protein sorting. However, the putative mammalian ESCRTII complex (hVps25p, hVps22p, and hVps36p) has no proven functional role in endosomal transport. We have characterized the human ESCRTII complex and investigated its function in endosomal trafficking. The human ESCRTII proteins interact with one another, with hVps20p (a component of ESCRTIII), and with their yeast homologues. Our interaction data from yeast two-hybrid studies along with experiments with purified proteins suggest an essential role for the N-terminal domain of hVps22p in the formation of a heterotetrameric ESCRTII complex. Although human ESCRTII is found in the cytoplasm and in the nucleus, it can be recruited to endosomes upon overexpression of dominant-negative hVps4Bp. Interestingly, we find that small interference RNA depletion of mammalian ESCRTII does not affect degradation of epidermal growth factor, a known cargo of the multivesicular body protein sorting pathway. We also show that depletion of the deubiquitinating enzymes AMSH (associated molecule with the SH3 domain of STAM (signal transducing adaptor molecule)) and UBPY (ubiquitin isopeptidase Y) have opposite effects on epidermal growth factor degradation, with UBPY depletion causing dramatic swelling of endosomes. Down-regulation of another cargo, the major histocompatibility complex class I in cells expressing the Kaposi sarcoma-associated herpesvirus protein K3, is unaffected in ESCRTII-depleted cells. Our data suggest that mammalian ESCRTII may be redundant, cargo-specific, or not required for protein sorting at the multivesicular body.
Regional Development, World System's Taxonomies and Inequality: A MESO-Domain Approach

Limited research has been done about the applicability of World-Systems Theory (WST) on meso-sociological domains. This paper discusses the theoretical framework of the WST spatial divisions, applies it in subnational geographic domains, and examines the phenomenon of spatial income inequality across the Illinoisi¯ counties. We argue that the Human Development Index (HDI) could serve as a suitable classification measure of WST regional taxonomies. Our findings indicate equivalence of structural classification between local and global geographical domains at the state of Illinois. Also our analysis on spatial inequality supports the findings of vanguard studies of the field suggesting a negative association between rurality and development, as well as an inverse relationship between rurality and income inequality at a county level.
The Interaction of Population Growth and Environmental Quality

An important question for policy is whether holding constant per capita income and other relevant factors population pressures have a significant effect upon environmental degradation. The authors examine the effect of population pressures upon deforestation in 64 developing countries in an attempt to provide relevant empirical findings. Data on deforestation were drawn from the Food and Agriculture Organizations Production Yearbook. Results suggest that a relationship exists between per capita income and deforestation and that for Africa rural population density shifts the relationship upward. The increase in the rate of deforestation levels off as income increases. The rate of growth in per capita income also has a significant negative impact upon deforestation although the magnitude of the effect is small. The authors close in stressing that reducing the rate of population growth is not necessarily the best way to reduce the rate of deforestation. Deforestation in developing countries is really a problem of market failure. Since property rights are often neither defined nor enforced there is essentially no private cost of deforestation. With no long-term stake in the land people have no incentive to use land efficiently. This situation must be addressed in conjunction with the problems of poverty and population growth.
Age and individual variability in performance during sleep restriction

The effect of sleep loss on reaction time (RT) performance varies as a function of age, with RTs of older subjects typically showing less decrement (relative to rested baseline) than those of younger subjects. In the current paper, we examined the nature of this relationship in a 7‐day sleep restriction study. The number of repeated measures made it possible to model both intra‐individual trajectories over days and individual differences in these trajectories. Results revealed (a) consistent individual differences in RT patterns over time after controlling for experimental design effects; (b) less cumulative RT decline among older individuals regardless of the degree of sleep restriction; and (c) consistent individual variability in performance patterns even after accounting for the effects of age.