Miracle-dz/UniFAR-FTUs huggingface dataset:
Immune Modulation Therapy and Imaging: Workshop Report

A workshop at the National Cancer Institute on May 2, 2016, considered the current state of imaging in assessment of immunotherapy. Immunotherapy has shown some remarkable and prolonged responses in the treatment of tumors. However, responses are variable and frequently delayed, complicating the evaluation of new immunotherapy agents and customizing treatment for individual patients. Early anatomic imaging may show that a tumor has increased in size, but this could represent pseudoprogression. On the basis of imaging, clinicians must decide if they should stop, pause, or continue treatment. Other imaging technologies and approaches are being developed to improve the measurement of response in patients receiving immunotherapy. Imaging methods that are being evaluated include radiomic methods using CT, MRI, and 18F-FDG PET, as well as new radiolabeled small molecules, antibodies, and antibody fragments to image the tumor microenvironment, immune status, and changes over the course of therapy. Current studies of immunotherapy can take advantage of these available imaging options to explore and validate their use. Collection of CT, PET, and MR images along with outcomes from trials is critical to develop improved methods of assessment.
Test–Retest Reproducibility for the Tau PET Imaging Agent Flortaucipir F 18

Alzheimer disease (AD) is characterized by β-amyloid (Aβ) plaques and tau neurofibrillary tangles. There are several PET imaging biomarkers for Aβ including 11C-PiB and 18F-florbetapir. Recently, PET tracers for tau neurofibrillary tangles have become available and have shown utility in detection and monitoring of neurofibrillary pathology over time. Flortaucipir F 18 is one such tracer. Initial clinical studies indicated greater tau binding in AD and mild cognitive impairment patients than in controls in a pattern consistent with tau pathology observed at autopsy. However, little is known about the reproducibility of such findings. To our knowledge, this study reports the first data regarding test–retest reproducibility of flortaucipir F 18 PET. Methods: Twenty-one subjects who completed the study (5 healthy controls, 6 mild cognitive impairment, and 10 AD) received 370 MBq of flortaucipir F 18 and were imaged for 20 min beginning 80 min after injection and again at 110 min after injection. Follow-up (retest) imaging occurred between 48 h and 4 wk after initial imaging. Images were spatially normalized to Montreal Neurological Institute template space. SUVRs were calculated using AAL (Automated Anatomical Labeling atlas) volumes of interest (VOIs) for parietal, temporal, occipital, anterior, and posterior hippocampal, parahippocampal, and fusiform regions, as well as a posterior neocortical VOI composed of average values from parietal, temporal, and occipital areas. Further, a VOI derived by discriminant analysis that maximally separated diagnostic groups (multiblock barycentric discriminant analysis [MUBADA]) was used. All VOIs were referenced to a subsection of cerebellar gray matter (cere-crus) as well as a parametrically derived white matter–based reference region (parametric estimate of reference signal intensity [PERSI]). t test, correlation analyses, and intraclass correlation coefficient were used to explore test–retest performance. Results: Test–retest analyses demonstrated low variability in flortaucipir F 18 SUVR. The SD of mean percentage change between test and retest using the PERSI reference region was 2.22% for a large posterior neocortical VOI, 1.84% for MUBADA, 1.46% for frontal, 1.98% for temporal, 2.28% for parietal, and 3.27% for occipital VOIs. Further, significant correlations (R2 > 0.85; P < 0.001) were observed for all regions, and intraclass correlation coefficient values (test–retest consistency) were greater than 0.92 for all regions. Conclusion: Significant test–retest reproducibility for flortaucipir F 18 was found across neocortical and mesial temporal lobe structures. These preliminary data suggest that flortaucipir F 18 tau imaging could be used to examine changes in tau burden over time.
Sensitivity and Isoform Specificity of 18F-Fluorofuranylnorprogesterone for Measuring Progesterone Receptor Protein Response to Estradiol Challenge in Breast Cancer

The purpose of this study was to evaluate the ability of 21-18F-fluoro-16α,17α-[(R)-(1′-α-furylmethylidene)dioxy]-19-norpregn-4-ene-3,20-dione (18F-FFNP) to measure alterations in progesterone receptor (PR) protein level and isoform expression in response to 17β-estradiol (E2) challenge. Methods: T47D human breast cancer cells and female mice bearing T47D tumor xenografts were treated with E2 to increase PR expression. 18F-FFNP uptake was measured using cell uptake and tissue biodistribution assays. MDA-MB-231 breast cancer clonal cell lines were generated that express the A or B isoform of human PR. PR protein levels, transcriptional function, and subcellular localization were determined. In vitro 18F-FFNP binding was measured via saturation and competitive binding curves. In vivo 18F-FFNP uptake was measured using tumor xenografts and PET. Statistical significance was determined using ANOVA and t tests. Results: After 48 and 72 h of E2, 18F-FFNP uptake in T47D cells was maximally increased compared with both vehicle and 24 h of E2 treatment (P < 0.0001 vs. ethanol; P = 0.02 and P = 0.0002 vs. 24 h for 48 and 72 h, respectively). T47D tumor xenografts in mice treated with 72 h of E2 had maximal 18F-FFNP uptake compared with ethanol-treated mice (percentage injected dose per gram: 11.3 ± 1.4 vs. 5.2 ± 0.81, P = 0.002). Corresponding tumor-to-muscle uptake ratios were 4.1 ± 0.6, 3.9 ± 0.5, and 2.3 ± 0.4 for 48 h of E2, 72 h of E2, and ethanol-treated mice, respectively. There was no significant preferential 18F-FFNP binding or uptake by PR-A versus PR-B in the PR isoform–specific cell lines and tumor xenografts. Conclusion: 18F-FFNP is capable of measuring estrogen-induced shifts in total PR expression in human breast cancer cells and tumor xenografts, with equivalent isoform binding.
On creation of reference image for degraded documents binarisation

In degraded document image processing, a reference image is required for quantitative evaluation. Most of the papers found in the literature rely on creating reference images based on manual processing which is often subjective and prone to error. This paper proposes a method for creating reference image for degraded documents binarisation. Another standard approach towards automated creation of reference image is majority voting. The reference image produced by the majority voting scheme, does not discriminate the wrong estimation of threshold from the correct one by considering the possibility of strong bias due to poor estimation of threshold by some methods for a particular image. This leads to bad estimation of threshold for reference image. The proposed method overcomes the biasness of majority voting to a great extent by discarding some of the binarisation algorithms participating in the creation of the final reference image. This method gives a partially automated approach in calculating a threshold for the reference image depending on the type of degradation present in the input image. Experimental verification on standard benchmark images illustrates the effectiveness of the proposed method over majority voting approach.
Family contact and health status among older adults with serious mental illnesses.

OBJECTIVES The purpose of this study was to explore the amount of family contact among older persons with serious mental illnesses (SMI), and to examine its relationship to health and mental health. METHODS An analysis of baseline data was conducted from a treatment study including 180 adults age 50 and older. The amount of family contact was examined with descriptive statistics. Differences in health and mental health were examined between participants with low, moderate, or high levels of family contact. Analyses also compared these groups on health and mental health functioning, controlling for psychiatric symptoms and the number and severity of medical diseases, respectively. RESULTS Over three-quarters of respondents (77.8%) reported speaking on the phone with a relative and two-thirds (67.2%) reported seeing a relative at least once during the past month. Older adults who lived with a family member had more severe mood symptoms and poorer mental health functioning. Those who lived with family or had moderate levels of family contact had more comorbid diseases and more disease severity than those with less family contact. These relationships remained significant after controlling for medical conditions or psychiatric symptoms. CONCLUSIONS AND IMPLICATIONS FOR PRACTICE The majority of older persons have regular family contact and those with the highest levels of family contact appear to have more compromised physical and mental health. Study findings provide new knowledge for practitioners regarding the importance of using family interventions to target physical health and mental illness management for older consumers who may need assistance to access medical care and treatment. Further research on the role of families in psychiatric and physical health management will provide a foundation for family interventions aimed at supporting community living among older adults.
Psychological distress, associated factors and coping strategies among female student nurses in the Nurses' Training School Galle

Objectives To assess the prevalence, describe selected factors associated with status of psychological distress and coping strategies among female student nurses in the Nurses‟ Training School (NTS) Galle. Methods A descriptive cross-sectional study was carried out among 525 female student nurses in the NTS Galle in 2009. A self -administered questionnaire (SAQ) identified work and non-work related factors. The validated General Health Questionnaire- 30 (GHQ-30) Sinhala version was used for the assessment of the status of psychological distress, with a score of ≥6 confirming psychological distress. Problem-focused and emotion-focused coping strategies for stress were identified using a SAQ. Logistic regression analysis was applied and results were expressed as odds ratios (OR) and 95% confidence intervals (95% CI). Results The prevalence of psychological distress among student nurses was 46.6% (n=239). Among work related factors, dissatisfaction about the training environment, boredom at work and fear of failure in examinations were significantly associated with psychological distress among them (p Conclusions The proportion of female student nurses with psychological distress was high. Programmes to improve life skills, specially coping strategies and provision of professional counseling services are recommended. Key words : Student nurses; Psychological distress; Coping strategies; Sri Lanka DOI: http://dx.doi.org/10.4038/jccpsl.v16i1.3868 Journal of the College of Community Physicians of Sri Lanka Vol.16(1) 2011, p23-29
Environmentally Dependent Density–Distance Relationship of Dispersing Culex tarsalis in a Southern California Desert Region

Abstract The direct inclusion of environmental factors into the empirical model that describes a density–distance relationship (DDR) is demonstrated on dispersal data obtained in a capture–mark–release–recapture experiment (CMRR) with Culex tarsalis conducted around the community of Mecca, CA. Empirical parameters of standard (environmentally independent) DDR were expressed as linear functions of environmental variables: relative orientation (azimuthal deviation of north) of release point (relative to recapture point) and proportions of habitat types surrounding each recapture point. The yielded regression model (R2 = 0.5373, after optimization on the best subset of linear terms) suggests that spatial density of recaptured individuals after 12 days of a CMRR experiment significantly depended on 1) distance from release point, 2) orientation of recapture points in relation to release point (preferring dispersal toward the south, probably due to wind drift and position of periodically flooded habitats suitable for species egg clutches), and 3) habitat spectrum in surroundings of recapture points (increasing and decreasing population density in desert and urban environment, respectively).
Hospital Costs and Excess Bed Capacity: A Statistical Analysis

The present paper develops and estimates a cost model for U.S. hospitals which enables us to analyze the cost of excess bed capacity. A new estimate is worth making for at least two reasons. First, recent changes in the economic environment in which hospitals operate has caused their utilization rates in the U.S. to fall sharply over the past decade, making previous estimates inaccurate. Second, the present paper employs econometric techniques of cost estimation not previously applied to this problem, with estimation based on all U.S. short-term community hospitals from 1979 through 1989. Our results, based on conservative estimates of the average optimal occupancy rate, indicate an annual cost of excess bed capacity (in current dollars) of $13.2 billion in 1989, $18.4 billion in 1991, and over $20 billion in 1993.
Co-decision matrix framework for name entity recognition in biomedical text

As a new branch of data mining and knowledge discovery, the research of biomedical text mining has a rapid progress currently. Biomedical named entity (BNE) recognition is a basic technique in the biomedical knowledge discovery and its performance has direct effects on further discovery and processing in biomedical texts. In this paper, we present an improved method based on co-decision matrix framework for Biomedical Named Entity Recognition (BNER). The relativity between classifiers is utilised by using co-decision matrix to exchange decision information among classifiers. The experiments are carried on GENIA corpus with the best result of 75.9% F-score. Experimental results show that the proposed method, co-decision matrix framework, can yield promising performances.
A simple algorithm for identifying integrons and gene cassettes in bacteria on next generation sequencing data

In 21st century, antibiotic resistance is a crucial phenomenon in contemporary medicine and has revealed the serious threat to public health. Integrons are mobile DNA units to capture and incorporate gene cassettes by site-specific recombination, particularly those responsible for antibiotic resistance. Meanwhile, integrons has been reported that it could play an important role in transfer of resistance to multiple drugs. In this paper, we propose a simple and efficient method to identify integrons from raw reads produced by next generation sequencing technology and detect the drug-resistant gene from gene cassettes incorporated by the integrons. In the case study, it shows that the proposed method is able to identify the integron and find the resistance genes of Acinetobacter baumannii, TYTH-1.
The development and evaluation of a manualised participatory HIV/AIDS risk reduction programme (Sex and Risk) for tertiary level learners: a pilot study

This paper reports on a pilot study of the development and evaluation (using outcome and process measures) of a manualised participatory risk reduction programme, aimed at reducing high-risk sexual behaviour amongst tertiary level learners, called 'Sex and Risk' (S&R), at the University of Durban-Westville 1 in South Africa. The programme was grounded in a focused ethnographic study of the risk behaviours and life context of tertiary level learners at this institution, as well as informed by literature on successful behavioural risk reduction programmes on Western and African populations. Significantly, the S&R programme was shown to facilitate greater awareness in males of how social influences inform high-risk sexual behaviour. This greater awareness did not, however, translate into greater self-efficacy in relation to negotiating safer sexual relationships for either males or females and was attributed to the dominant social norms, which promote and sustain gender inequity that places the sexual health of young women and men at risk. Given that the S&R programme operates largely at the level of the individual, although it does address the subjective aspects of social influences on behaviour, these findings highlight the need for proximal situation-centred interventions, which promote more egalitarian social norms in sexual relationships, to accompany such curriculum interventions at tertiary institutions.
Intermediation: a new concept for medical data exchanges

With the development of the Information and Communication Technologies, the exchanges of data between Healthcare Professionals are modified. Hospitals and Private Clinics are installing their Hospital Information Systems, while the General Practitioners are computing their patients records. Therefore the environment is suitable for the installation and diffusion of telematics services allowing better exchanges of information between the physicians of a geographical sector. The Intermediation platform was developed to provide an asynchronous n to n communication. It ensures several functions such as: movements of the patients (in/out/inside) the hospital, management and mailing of letters and reports, specific information about the treatments or data concerning the hospital structure. On the other hand, the G.P.s can send medical records to their hospital correspondents. This platform has been used in the town of Armentieres in the city of Lille (North of France). It is currently routinely used to accelerate and secure data exchanges between all the physicians working in this area.
MIL: a data discretisation approach

Data discretisation is an important step in the process of machine learning, since it is easier for classifiers to deal with discrete attributes rather than continuous attributes. Over the years, several methods of performing discretisation such as Boolean reasoning, equal frequency binning, entropy have been proposed, explored, and implemented. In this article, a simple supervised discretisation approach called minimum information loss (MIL) is introduced. The prime goal of MIL is to maximise classification accuracy of classifier, minimising loss of information while discretisation of continuous attributes. The performance of the suggested approach is compared with the supervised discretisation algorithms: selective pseudo iterative deletion 4.7 (SPID4.7) and minimum description length principle (MDLP), using four state-of-the-art rule inductive algorithms – neural network, C4.5, Naive-Bayes, and CN2. The empirical results show that the presented approach performs better in several cases in comparison to the other two algorithms.
Annotation tools for syntax and named entities in the National Corpus of Polish

The ongoing National Corpus of Polish project assumes several levels of linguistic annotation. We present the technical environment and methodological background developed for the three upper annotation levels: the levels of syntactic words, syntactic groups and named entities. We show how knowledge-based platforms Spejd and Sprout are used for the automatic pre-annotation of the corpus and discuss some particular problems faced during the preparation of the parser grammar, which contains over 1,000 rules and is one of the largest chunking grammars for Polish. We also show how the tree editor TrEd has been customised for manual post-editing of annotations and for further revision of discrepancies. Our XML format converters and customised archiving repository ensure an automatic data flow and efficient corpus file management. We discuss the inter-annotator agreement in the manually annotated data, and present the first results of a CRF classifier trained on these data.
Quality of life of people living with HIV/AIDS and on highly active antiretroviral therapy in Ethiopia

The Amharic version of the Short Form-36 Health Survey (SF-36) was used to measure quality of life among patients on highly active antiretroviral therapy (HAART) at selected governmental hospitals in central and southern Ethiopia. The study was cross-sectional and used SF-36-specific software for automatic scoring of the form's scales and dimensions. Pearson bivariate correlations showed moderate correlation between the SF-36 scales, ranging from 0.2673 between ‘general health’ and ‘vitality,’ to 0.8583 between ‘role physical’ and ‘role emotional. ’ Cronbach's-αwas >0.70 for six out of eight multi-item scales, with values ranging from 0.6500 to 0.8860 for all scales, thus indicating good internal reliability of the Amharic version of the SF-36. The independent variables shown to positively affect mean scores were: duration of treatment, CD4 cell count, and adherence to doses of antiretrovirals. Participants treated for >12 months had higher mean scores for all domains than those who had been treated for ≤12 months. Likewise, those with a CD4 cell count >200 cells/mm3 had better mean scores for all scales except ‘social functioning’ and ‘mental health’ than those with counts ≤200. Participants adhering to treatment (in the last 15 days, according to self-report) had better mean scores for all scales except ‘role physical,’ ‘bodily pain’ and ‘vitality’ in comparison to those who were not adherent. The findings suggest that the Amharic version of the SF-36 is a valid and reliable health survey instrument for use in Ethiopia to assess the quality of life of people living with HIV/AIDS on HAART.
Strategic positioning for real-estate management in Australia: implementing e-business for competitive advantage

Many initiatives that create additional value in real estate transactions, derive from effective web presence and virtual searching facilities. Recent research takes a strategic view, and utilises a structured approach of translating the impact of the internet as an enabling technology on business strategy, business model development and business infrastructure, stating that companies need to tailor their deployment of internet technology to their particular strategies. This research describes such deployment from a strategic positioning perspective and via a competitive positioning matrix. Dimensions of interactiveness with customers, and the flexibility/complexity and innovation of the website environment/infrastructure that supports and complements the real estate interaction and/or transaction are considered, and a preferred competitive positioning model is derived, along with a preferred expansion path. An e-business model for a regional real estate organisation in Australia demonstrates how the competitive positioning model may be deployed as the driver for building competitive advantage.
Architecture for deploying e-business: business processes, web services-business interactions manager, and information systems

The aim of e-business applications is to make businesses agile by supporting dynamic internal and external boundary-crossing business processes. This study defines a three-level architecture for developing e-business. The architecture includes (L1) business processes as front-end components; (L2) a business interactions manager (BIM) as a middle component; and (L3) disparate information systems (i.e., the information systems of enterprise, partners, suppliers, and customers) as back-end components. It specifies the requirements for the implementing technology platform to adopt it to a web services-oriented architecture (WSOA). Finally, the WSOA is used as a methodology for deploying e-business through steady instantiation for each business interactions category.