Miracle-dz/UniFAR-FTUs huggingface dataset:
Treatment planning methodology for the Miami Multichannel Applicator following the American Brachytherapy Society recently published guidelines: the Lahey Clinic experience

The objective of this study was to develop a standardized procedure from simulation to treatment delivery for the multichannel Miami applicator, in order to increase planning consistency and reduce errors. A plan is generated prior to the 1st treatment using the CT images acquired with the applicator in place, and used for all 3 fractions. To confirm the application placement before each treatment fraction, an AP image is acquired and compared with the AP baseline image taken at simulation. A preplanning table is generated using the EBRT doses and is used to compute the maximum allowable D2cc for bladder, rectum, and sigmoid, and the mean allowable dose for the upper vaginal wall per HDR brachytherapy fraction. These data are used to establish the criteria for treatment planning dose optimization. A step‐by‐step treatment planning approach was developed to ensure appropriate coverage for the tumor (D90>100% prescribed dose of 700 cGy/fraction) and the uninvolved vaginal surface (dose for the entire treatment length > 600 cGy/fraction), while keeping the organs at risk below the tolerance doses. The equivalent dose 2 Gy (EQD2) tolerances for the critical structures are based on the American Brachytherapy Society (ABS) recently published guidelines. An independent second check is performed before the 1st treatment using an in‐house Excel spreadsheet. This methodology was successfully applied for our first few cases. For these patients: the cumulative tumor dose was 74–79 EQD2 Gy10 (ABS recommended range 70–85); tumor D90 was >100% of prescribed dose (range 101%–105%); cumulative D2cc for bladder, rectum, and sigmoid were lower than the tolerances of 90, 75, and 75 EQD2 Gy3, respectively; cumulative upper vaginal wall mean dose was below the tolerance of 120 EQD2 Gy3; the second check agreement was within 5%. By using a standardized procedure the planning consistency was increased and all dosimetric criteria were met. PACS numbers: 87.55‐x, 87.56 bg
Longitudinal change of biomarkers in cognitive decline.

OBJECTIVE To delineate the trajectories of Aβ42 level in cerebrospinal fluid (CSF), fludeoxyglucose F18 (FDG) uptake using positron emission tomography, and hippocampal volume using magnetic resonance imaging and their relative associations with cognitive change at different stages in aging and Alzheimer disease (AD). DESIGN Cohort study. SETTING The 59 study sites for the Alzheimer's Disease Neuroimaging Initiative. PARTICIPANTS A total of 819 participants 55 to 90 years of age with normal cognition, mild cognitive impairment, and AD who were followed up during the period from 2005 to 2007. MAIN OUTCOME MEASURES Rates of change in level of Aβ42 in CSF, FDG uptake, hippocampal volume, and the Alzheimer Disease's Assessment Scale-cognitive subscale score during up to 36 months of follow-up by diagnostic group as well as prediction of cognitive change by each biomarker. RESULTS Reductions in the level of Aβ42 in CSF were numerically greater in participants with normal cognition than in participants with mild cognitive impairment or AD; whereas both glucose metabolic decline and hippocampal atrophy were significantly slower in participants with normal cognition than in participants with mild cognitive impairment or AD. Positive APOE4 status accelerated hippocampal atrophic changes in participants with mild cognitive impairment or AD, but did not modify rates of change in level of Aβ42 in CSF or FDG uptake. The Alzheimer Disease's Assessment Scale-cognitive subscale scores were related only to the baseline level of Aβ42 in CSF and the baseline FDG uptake in participants with normal cognition, which were about equally associated with change in FDG uptake and hippocampal volume in participants with mild cognitive impairment and best modeled by change in FDG uptake in participants with AD. CONCLUSION Trajectories of Aβ42 level in CSF, FDG uptake, and hippocampal volume vary across different cognitive stages. The longitudinal patterns support a hypothetical sequence of AD pathology in which amyloid deposition is an early event before hypometabolism or hippocampal atrophy, suggesting that biomarker prediction for cognitive change is stage dependent.
Neurochemical and behavioural indices of exercise reward are independent of exercise controllability

Brain reward circuits are implicated in stress‐related psychiatric disorders. Exercise reduces the incidence of stress‐related disorders, but the contribution of exercise reward to stress resistance is unknown. Exercise‐induced stress resistance is independent of exercise controllability; both voluntary running (VR) and forced running (FR) protect rats against the anxiety‐like and depression‐like behavioural consequences of stress. Voluntary exercise is a natural reward, but whether rats find FR rewarding is unknown. Moreover, the contribution of dopamine (DA) and striatal reward circuits to exercise reward is not well characterized. Adult, male rats were assigned to locked wheels, VR, or FR groups. FR rats were forced to run in a pattern resembling the natural wheel running behavior of rats. Both VR and FR increased the reward‐related plasticity marker ΔFosB in the dorsal striatum and nucleus accumbens, and increased the activity of DA neurons in the lateral ventral tegmental area, as revealed by immunohistochemistry for tyrosine hydroxylase and pCREB. Both VR and FR rats developed conditioned place preference (CPP) to the side of a CPP chamber paired with exercise. Re‐exposure to the exercise‐paired side of the CPP chamber elicited conditioned increases in cfos mRNA in direct‐pathway (dynorphin‐positive) neurons in the dorsal striatum and nucleus accumbens in both VR and FR rats, and in tyrosine hydroxylase‐positive neurons in the lateral ventral tegmental area of VR rats only. The results suggest that the rewarding effects of exercise are independent of exercise controllability and provide insight into the DA and striatal circuitries involved in exercise reward and exercise‐induced stress resistance.
Interactive 3D Visualization for Theoretical Virtual Observatories

Virtual Observatories (VOs) are online hubs of scientific knowledge. They encompass a collection of platforms dedicated to the storage and dissemination of astronomical data, from simple data archives to e-research platforms offering advanced tools for data exploration and analysis. Whilst the more mature platforms within VOs primarily serve the observational community, there are also services fulfilling a similar role for theoretical data. Scientific visualization can be an effective tool for analysis and exploration of datasets made accessible through web platforms for theoretical data, which often contain spatial dimensions and properties inherently suitable for visualization via e.g. mock imaging in 2d or volume rendering in 3d. We analyze the current state of 3d visualization for big theoretical astronomical datasets through scientific web portals and virtual observatory services. We discuss some of the challenges for interactive 3d visualization and how it can augment the workflow of users in a virtual observatory context. Finally we showcase a lightweight client-server visualization tool for particle-based datasets allowing quantitative visualization via data filtering, highlighting two example use cases within the Theoretical Astrophysical Observatory.
Experiences and issues of using cellular automata for assisting urban and regional planning in China

ABSTRACT Since the late 1990s, there are growing studies on the development of cellular automata (CA) as a simulation tool for assisting urban and regional planning in China. Rapid urban development is the main reason that this country has become one of the best places to test the methodology of CA and analyze the effectiveness of using these models. This paper attempts to summarize the experiences and issues of using CA to solve various environmental and planning problems in China. The analysis is based on the literature review using the search engines of ISI Web of Science and Google Scholar. These experiences could be important for those who want to apply CA in developing countries. For example, which environmental and ecological problems can be solved by using this bottom-up approach? What are the data inputs to these models and how can they be calibrated? Our analyses indicate that CA have the great potential to support land-use planning and policy analysis for fast-growing regions. Some specific features of using CA in China are also identified in the literature review, including delineation of urban growth boundary, prevention of illegal development and formulating zoning schemes. The CA studies in this fast-growing country provided valuable experiences for other developing countries to solve a series of simulation and planning problems by using this bottom-up approach.
Erlotinib in the treatment of recurrent or metastatic cutaneous squamous cell carcinoma: A single‐arm phase 2 clinical trial

Cutaneous squamous cell carcinoma (CSCC) is a very common malignancy in which most patients present with localized disease. Recurrent and metastatic disease is rare, and there is no standard therapy. These tumors frequently overexpress the epidermal growth factor receptor (EGFR). We conducted a phase 2 trial to determine the response rate to therapy with erlotinib, an EGFR tyrosine kinase inhibitor, in patients with locoregionally recurrent or metastatic CSCC that was not amenable to curative treatment (NCT01198028).
Will climate change drive 21st century burn rates in Canadian boreal forest outside of its natural variability: collating global climate model experiments with sedimentary charcoal data.

Natural ecosystems have developed within ranges of conditions that can serve as references for setting conservation targets or assessing the current ecological integrity of managed ecosystems. Because of their climate determinism, forest fires are likely to have consequences that could exacerbate biophysical and socioeconomical vulnerabilities in the context of climate change. We evaluated future trends in fire activity under climate change in the eastern Canadian boreal forest and investigated whether these changes were included in the variability observed during the last 7000 years from sedimentary charcoal records from three lakes. Prediction of future annual area burned was made using simulated Monthly Drought Code data collected from an ensemble of 19 global climate model experiments. The increase in burn rate that is predicted for the end of the 21st century (0.45% year–1 with 95% confidence interval (0.32, 0.59) falls well within the long‐term past variability (0.37 to 0.90% year–1). Although our results suggest that the predicted change in burn rates per se will not move this ecosystem to new conditions, the effects of increasing fire incidence cumulated with current rates of clear‐cutting or other low‐retention types of harvesting, which still prevail in this region, remain preoccupying.
Development of Subunit Vaccines That Provide High-Level Protection and Sterilizing Immunity against Acute Inhalational Melioidosis

ABSTRACT Burkholderia pseudomallei, the etiologic agent of melioidosis, causes severe disease in humans and animals. Diagnosis and treatment of melioidosis can be challenging, and no licensed vaccines currently exist. Several studies have shown that this pathogen expresses a variety of structurally conserved protective antigens that include cell surface polysaccharides and cell-associated and cell-secreted proteins. Based on those findings, such antigens have become important components of the subunit vaccine candidates that we are currently developing. In the present study, the 6-deoxyheptan capsular polysaccharide (CPS) from B. pseudomallei was purified, chemically activated, and covalently linked to recombinant CRM197 diphtheria toxin mutant (CRM197) to produce CPS-CRM197. Additionally, tandem nickel-cobalt affinity chromatography was used to prepare highly purified recombinant B. pseudomallei Hcp1 and TssM proteins. Immunization of C57BL/6 mice with CPS-CRM197 produced high-titer IgG and opsonizing antibody responses against the CPS component of the glycoconjugate, while immunization with Hcp1 and TssM produced high-titer IgG and robust gamma interferon-secreting T cell responses against the proteins. Extending upon these studies, we found that when mice were vaccinated with a combination of CPS-CRM197 and Hcp1, 100% of the mice survived a lethal inhalational challenge with B. pseudomallei. Remarkably, 70% of the survivors had no culturable bacteria in their lungs, livers, or spleens, indicating that the vaccine formulation had generated sterilizing immune responses. Collectively, these studies help to better establish surrogates of antigen-induced immunity against B. pseudomallei as well as provide valuable insights toward the development of a safe, affordable, and effective melioidosis vaccine.
Transarterial Chemoembolization (TACE) plus Sorafenib Versus TACE for Intermediate or Advanced Stage Hepatocellular Carcinoma: A Meta-Analysis

Background Sorafenib is used in patients with intermediate or advanced stage hepatocellular carcinoma (HCC) before or after of transarterial chemoembolization (TACE). However, the survival outcomes of TACE combined with sorafenib versus TACE alone remain controversial. Thus, we conducted a meta-analysis to evaluate the efficacy and safety of the combination therapy of TACE plus sorafenib in patients with intermediate or advanced stage of HCC. Methods Pubmed and Embase databases were systematically reviewed for studies published up to November 2013, that compared TACE alone or in combination with sorafenib. Pooled hazard ratios (HRs) with 95% confidence intervals (95%CIs) were calculated for overall survival (OS), time to progression (TTP), objective response rate (ORR), and progression free survival (PFS) using random-effects or fixed-effects model, depending on the heterogeneity between the included studies. Results Six studies published from 2011 to 2013, with a total of 1254 patients, were included in this meta-analysis. The pooled results showed that TACE combined with sorafenib significantly improved OS (HR = 0.65; 95% CI: 0.47–0.89, P = 0.007), TTP (HR = 0.68; 95% CI: 0.52–0.87, P = 0.003), ORR (HR = 1.06; 95% CI: 1.01–1.12, P = 0.021), but did not affect PFS (HR = 0.84; 95% CI: 0.62–1.14, P = 0.267). The incidence of grade III/IV adverse reaction was higher in the TACE plus sorafenib group than in the TACE group. Conclusions The meta-analysis confirmed that the combination therapy of TACE plus sorafenib in patients with intermediate or advanced stage of HCC, can improve the OS, TTP, and ORR. This combination therapy was also associated with a significantly increased risk of adverse reactions.
Melissa officinalis L: A Review Study With an Antioxidant Prospective

Melissa officinalis is a plant cultivated in some parts of Iran. The leaves of lemon balm, Melissa officinalis L (Lamiaceae), are used in Iranian folk medicine for their digestive, carminative, antispasmodic, sedative, analgesic, tonic, and diuretic properties, as well as for functional gastrointestinal disorders. This review article was aimed not only to introduce Melissa officinalis (its growth condition, its chemical compounds, and its traditional usages) but also to overview its antioxidant properties in detail. This review was carried out by searching studies in PubMed, Medline, Web of Science, and IranMedex databases up to 2016. The search terms used were “Melissa officinalis L,” “antioxidant properties,” oxidative stress,” “oxidative damage”, “ROS. ” Articles whose full texts were not available were excluded from the study. In this study, firstly, traditional usage of this herb was reviewed, including antimicrobial activity (antiparasitic, antibacterial, antiviral, etc), antispasmodic, and insomnia properties. Then, its antioxidant properties were overviewed. Various studies have shown that Melissa officinalis L possesses high amount of antioxidant activity through its chemical compounds including high amount of flavonoids, rosmaric acid, gallic acid, phenolic contents. Many studies confirmed the antioxidative effects of Melissa officinalis; thus, its effect in preventing and treating oxidative stress-related diseases might be reliable.
Best practices: Restorative complications

Metal clamps damage tooth structure or porcelain surfaces of crowns Prevention and management The use of light cured provisional material can reduce the potential of metal rubber dam clamps to cause iatrogenic damage (Liebenberg, 1995). Prior to clamp placement, a small amount of composite based material may be added to the metal prongs of the clamp. Alternatively instead of metal clamps, the use of plastic rubber dam clamps is less likely to damage tooth structure or existing restorations (Madison, Jordan, and Krell, 1986).
Prevalence of depressive and anxiety disorders and validation of the Hospital Anxiety and Depression Scale as a screening tool in axial spondyloarthritis patients

To determine the prevalence of anxiety and depression in axial spondyloarthritis (SpA) patients by a psychiatrist using the Chinese‐bilingual Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders, fourth edition patient research version (CB‐SCID‐I/P), and to examine the effectiveness of the Hospital Anxiety and Depression Scale (HADS) as a screening tool.
We Want to Know: Eliciting Hospitalized Patients’ Perspectives on Breakdowns in Care

BACKGROUND: There is increasing recognition that patients have critical insights into care experiences, including breakdowns in care. Harnessing patient perspectives for hospital improvement requires an in‐depth understanding of the types of breakdowns patients identify and the impact of these events. METHODS: We interviewed a broad sample of patients during hospitalization and postdischarge to elicit patient perspectives on breakdowns in care. Through an iterative process, we developed a categorization of patient‐perceived breakdowns called the Patient Experience Coding Tool. RESULTS: Of 979 interviewees, 386 (39.4%) believed they had experienced at least one breakdown in care. The most common reported breakdowns involved information exchange (n = 158, 16.1%), medications (n = 120, 12.3%), delays in admission (n = 90, 9.2%), team communication (n = 65, 6.6%), providers’ manner (n = 62, 6.3%), and discharge (n = 56, 5.7%). Of the 386 interviewees who reported a breakdown, 140 (36.3%) perceived associated harm. Patient‐perceived harms included physical (eg, pain), emotional (eg, distress, worry), damage to relationship with providers, need for additional care or prolonged hospital stay, and life disruption. We found higher rates of reporting breakdowns among younger (<60 years old) patients (45.4% vs 34.5%, P < 0.001), those with at least some college education (46.8% vs 32.7%, P < 0.001), and those with another person (family or friend) present during the interview or interviewed in lieu of the patient (53.4% vs 37.8%, P = 0.002). CONCLUSIONS: When asked directly, almost 4 out of 10 hospitalized patients reported a breakdown in their care. Patient‐perceived breakdowns in care are frequently associated with perceived harm, illustrating the importance of detecting and addressing these events.
Initial Observations of Lingual Movement Characteristics of Children With Cerebral Palsy.

Purpose This preliminary study compared the speech motor control of the tongue and jaw between children with cerebral palsy (CP) and their typically developing (TD) peers. Method Tongue tip and jaw movements of 4 boys with spastic CP and 4 age- and sex-matched TD peers were recorded using an electromagnetic articulograph during 10 repetitions of "Dad told stories today. " The duration, path distance, average speed, and speech movement stability of the movements were calculated for each repetition. Results The children with CP had longer durations than their TD peers. Children with CP had longer path distances and faster average speed as compared with their TD peers for both articulators. The TD group but not the CP group had longer path distances and faster average speeds for the tongue than the jaw. The CP group had reduced speech movement stability for the tongue as compared with their TD peers, but both groups had similar speech movement stability for the jaw. Conclusions Children with CP had impaired speech motor control of the tongue and jaw as compared with their TD peers, and these speech motor control deficits were more pronounced in the tongue tip than the jaw.
Rates and Predictors of Conversion to Schizophrenia or Bipolar Disorder Following Substance-Induced Psychosis.

OBJECTIVE The authors investigated the rates of conversion to schizophrenia and bipolar disorder after a substance-induced psychosis, as well as risk factors for conversion. METHOD All patient information was extracted from the Danish Civil Registration System and the Psychiatric Central Research Register. The study population included all persons who received a diagnosis of substance-induced psychosis between 1994 and 2014 (N=6,788); patients were followed until first occurrence of schizophrenia or bipolar disorder or until death, emigration, or August 2014. The Kaplan-Meier method was used to obtain cumulative probabilities for the conversion from a substance-induced psychosis to schizophrenia or bipolar disorder. Cox proportional hazards regression models were used to calculate hazard ratios for all covariates. RESULTS Overall, 32.2% (95% CI=29.7-34.9) of patients with a substance-induced psychosis converted to either bipolar or schizophrenia-spectrum disorders. The highest conversion rate was found for cannabis-induced psychosis, with 47.4% (95% CI=42.7-52.3) converting to either schizophrenia or bipolar disorder. Young age was associated with a higher risk of converting to schizophrenia. Self-harm after a substance-induced psychosis was significantly linked to a higher risk of converting to both schizophrenia and bipolar disorder. Half the cases of conversion to schizophrenia occurred within 3.1 years after a substance-induced psychosis, and half the cases of conversion to bipolar disorder occurred within 4.4 years. CONCLUSIONS Substance-induced psychosis is strongly associated with the development of severe mental illness, and a long follow-up period is needed to identify the majority of cases.