Miracle-dz/UniFAR-FTUs huggingface dataset:
Issues and challenges with integrating patient-reported outcomes in clinical trials supported by the National Cancer Institute-sponsored clinical trials networks.

PURPOSE The objective of this report is to provide a historical overview of and the issues and challenges inherent in the incorporation of patient-reported outcomes (PROs) into multinational cancer clinical trials in the cancer cooperative groups. METHODS An online survey of 12 cancer cooperative groups from the United States, Canada, and Europe was conducted between June and August of 2006. Each of the cooperative groups designated one respondent, who was a member of one of the PRO committees within the cooperative group. RESULTS There was a 100% response rate, and all of the cancer clinical trial cooperative groups reported conducting PRO research. PRO research has been conducted in the cancer cooperative groups for an average of 15 years (range, 6 to 30 years), and all groups had multidisciplinary committees focused on the design of PRO end points and the choice of appropriate PRO measures for cancer clinical trials. The cooperative groups reported that 5% to 50% of cancer treatment trials and an estimated 50% to 75% of cancer control trials contained PRO primary and secondary end points. There was considerable heterogeneity among the cooperative groups with respect to the formal and informal policies and procedures or cooperative group culture towards PROs, investigator training/mentorship, and resource availability for the measurement and conduct of PRO research within the individual cooperatives. CONCLUSION The challenges faced by the cooperative groups to the incorporation of PROs into cancer clinical trials are varied. Some common opportunities for improvement include the adoption of standardized training/mentorship mechanisms for investigators for the conduct of PRO assessments and data collection and the development of minimal criteria for PRO measure acceptability. A positive cultural shift has occurred in most of the cooperative groups related to the incorporation of PROs in clinical trials; however, financial and other resource barriers remain and need to be addressed.
Paper-STATE-SPACE DIGITAL PID CONTROLLER DESIGN FOR MULTIVARIABLE ANALOG SYSTEMS WITH MULTIPLE TIME DELAYS

This paper presents a discrete-time state-space methodology for optimal design of digital PID controllers for multivariable analog systems with multiple time delays. The multiple time-delayed multivariable analog systems are formulated in a state-space generic form so that the exact discrete-time state-space model can be constructed. Then, the optimal digital PID controller is designed via a state-feedback and state-feedforward LQR approach. The developed PID controller can be applied to a general time-delayed multivariable analog system represented by a semi-proper or strictly proper transfer function matrix. Illustrative examples are given to compare the performance of the proposed approach with alternative techniques.
Stochastic Model Driven Capacity Planning for an Infrastructure-as-a-Service Cloud

From an enterprise perspective, one key motivation to transform the traditional IT management into Cloud is the cost reduction of the hosted services. In an Infrastructure-as-a-Service (IaaS) Cloud, virtual machine (VM) instances share the physical machines (PMs) in the provider's data center. With large number of PMs, providers can maintain low cost of service downtime at the expense of higher infrastructure and other operational costs (e.g., power consumption and cooling costs). Hence, determining the optimal PM capacity requirements that minimize the overall cost is of interest. In this paper, we show how a cost analysis and optimization framework can be developed using stochastic availability and performance models of an IaaS Cloud. Specifically, we study two cost minimization problems to address the capacity planning in an IaaS Cloud: (1) what is the optimal number of PMs that minimizes the total cost of ownership for a given downtime requirement set by service level agreements? and, (2) is it more economical to use cheaper but less reliable PMs or to use costlier but more reliable PMs for insuring the same availability characteristics? We use simulated annealing, a well-known stochastic search algorithm, to solve these optimization problems. Results from our analysis show that the optimal solutions are found within reasonable time.
Analysis of the indentation size effect on the hardness of alumina ceramics using different models

The Vickers hardness of slip-cast high purity alumina ceramics is determined as a function of the indentation load. The results show that the measured hardness depends crucially on the load, which indicates the influence of the indentation size effect (ISE). The load dependence of hardness is analyzed by using the traditional Meyer Law ; a proportional specimen resistance (PSR) model and a modified proportional specimen resistance (MPSR) model. The best correlation between measured values and used models is achieved by using a modified PSR model.
Vector-Valued Image Processing by Parallel Level Sets

Vector-valued images such as RGB color images or multimodal medical images show a strong interchannel correlation, which is not exploited by most image processing tools. We propose a new notion of treating vector-valued images which is based on the angle between the spatial gradients of their channels. Through minimizing a cost functional that penalizes large angles, images with parallel level sets can be obtained. After formally introducing this idea and the corresponding cost functionals, we discuss their Gâteaux derivatives that lead to a diffusion-like gradient descent scheme. We illustrate the properties of this cost functional by several examples in denoising and demosaicking of RGB color images. They show that parallel level sets are a suitable concept for color image enhancement. Demosaicking with parallel level sets gives visually perfect results for low noise levels. Furthermore, the proposed functional yields sharper images than the other approaches in comparison.
Becoming Food Aware in Hospital: A Narrative Review to Advance the Culture of Nutrition Care in Hospitals

The Nutrition Care in Canadian Hospitals (2010–2013) study identified the prevalence of malnutrition on admission to medical and surgical wards as 45%. Nutrition practices in the eighteen hospitals, including diagnosis, treatment and monitoring of malnourished patients, were ad hoc. This lack of a systematic approach has demonstrated the need for the development of improved processes and knowledge translation of practices aimed to advance the culture of nutrition care in hospitals. A narrative review was conducted to identify literature that focused on improved care processes and strategies to promote the nutrition care culture. The key finding was that a multi-level approach is needed to address this complex issue. The organization, staff, patients and their families need to be part of the solution to hospital malnutrition. A variety of strategies to promote the change in nutrition culture have been proposed in the literature, and these are summarized as examples for others to consider. Examples of strategies at the organizational level include developing policies to support change, use of a screening tool, protecting mealtimes, investing in food and additional personnel (healthcare aides, practical nurses and/or diet technicians) to assist patients at mealtimes. Training for hospital staff raises awareness of the issue, but also helps them to identify their role and how it can be modified to improve nutrition care. Patients and families need to be aware of the importance of food to their recovery and how they can advocate for their needs while in hospital, as well as post-hospitalization. It is anticipated that a multi-level approach that promotes being “food aware” for all involved will help hospitals to achieve patient-centred care with respect to nutrition.
Understanding the Relationship Between Environmental Energy Availability and Bird Species Richness in Kenya Using Remote Sensing and Ancillary Data

The energy hypothesis predicts that, in regions of roughly equal area, energy flux per unit of area should be the prime determinant of species richness. In the case of plants, primary production represents realized energy capture. Poten- tial evapotranspiration is a measure of community energy use and it is related to terrestrial primary productivity. The best correlate of the latter on regional scale is the Advanced Very High Resolution Radiometer (AVHRR) derived Normalized Difference Vegetation Index (NDVI). I examined the relationship between bird species richness and measures of available environmental energy (interannual maximum average NDVI and mean annual potential evapotranspiration) at a quarter degree scale (55 x 55 km). Statistical analyses revealed higher interannual maximum average NDVI results in higher bird species richness, whereas mean annual potential evapotranspiration correlated negatively with species richness. Under- standing these relationships can help in estimating changes in bird species richness in response to global climatic change.
Case Studies Synthesis: Brief Experience and Challenges for the Future

Synthesis of case studies is different from synthesis of purely quantitative studies, for example, in that sampling and analysis in primary studies have been carried out differently, and that primary results are of a different nature. The objective of this research is to identify what challenges should be considered when choosing and using a method for synthesis of case studies. We collected experience from independent synthesis of two published case studies (on trust in outsourcing) by two teams, one team applied cross-case analysis, the other team applied thematic synthesis. The two teams reached both supporting and complimentary conclusions. Identified challenges relate to the goals and research questions of the cases to be synthesized, the number of case studies, temporal and spatial variations, and access to raw data.
TreeDom: a graphical web tool for analysing domain architecture evolution

UNLABELLED We present TreeDom, a web tool for graphically analysing the evolutionary history of domains in multi-domain proteins. Individual domains on the same protein chain may have distinct evolutionary histories, which is important to grasp in order to understand protein function. For instance, it may be important to know whether a domain was duplicated recently or long ago, to know the origin of inserted domains, or to know the pattern of domain loss within a protein family. TreeDom uses the Pfam database as the source of domain annotations, and displays these on a sequence tree. An advantage of TreeDom is that the user can limit the analysis to N sequences that are most similar to a query, or provide a list of sequence IDs to include. Using the Pfam alignment of the selected sequences, a tree is built and displayed together with the domain architecture of each sequence.Availablility and implementation: http://TreeDom.sbc. su.se CONTACT Erik.Sonnhammer@scilifelab.se.
Choreography for the Grid: towards fitting BPEL to the resource framework

The inherent heterogeneity of the Grid demands the ability to specify choreographies in a portable manner. This ensures that a choreography once specified can be deployed and executed in every workflow system within a Grid environment. It is likely that the Business Process Execution Language (BPEL) will have the corresponding broad support in the industry. In order to become first class citizens in the Grid, choreographies have to comply with the resource framework. We therefore suggest steps to make BPEL compliant with the resource framework. As a result, features of BPEL such as extended transactions will be available in a Grid environment. Copyright © 2005 John Wiley & Sons, Ltd.
Improving Walking, Muscle Strength, and Balance in the Elderly with an Exergame Using Kinect: A Randomized Controlled Trial.

BACKGROUND Many issues prevent elderly individuals from exercising in daily life. There is a need for a system that allows elderly individuals to engage in exercise regularly at a low cost. We developed an exergame that uses a Kinect(®) sensor (Microsoft Corp., Redmond, WA) and conducted a randomized controlled trial of the effects of using this exergame on muscle strength and balance in healthy elderly individuals. SUBJECTS AND METHODS We enrolled 57 healthy elderly individuals and randomly divided them into an intervention group (n=29) and a control group (n=28) using a table of random numbers. All participants underwent gait analyses and were examined using the Berg Balance Scale (BBS), Functional Reach Test (FRT), and the 30-second chair-stand (CS-30) test before the intervention. Participants in the intervention group played the exergame once or twice a week, up to a total of 24 times. The tests were repeated after intervention, and the scores were compared with those obtained before intervention. RESULTS Our results indicated that walking, muscle strength, and motor function improved in participants in the intervention group. Decreased double standing time (P=0.03), minimum foot clearance (P=0.04), BBS scores (P<0.01), CS-30 scores (P<0.01), and FRT scores (P<0.01) significantly improved in the intervention group compared with values in the control group. CONCLUSIONS The Kinect-based exergame developed in this study was found to be effective in improving walking, muscular strength, and balance in elderly people.
Terahertz quantum cascade laser coupled with high efficiency to the low loss optical modes of cylindrical hollow-core waveguides

We demonstrate that azimuthally polarized micro-ring THz quantum-cascade lasers can be coupled to hollow metallic waveguides with efficiencies ≥96% and perfectly matched with the TE01 waveguide mode, giving attenuation losses < 3dB/m. The use of Ag coated-flexible pipe waveguides allows propagation of either vertically polarized or azimuthally polarized QCL beams with propagation losses as low as 2.1-4.4 dB/m and bending losses lower than 1.2 dB.
ptimal manipulator design for a cucumber arvesting robot

This paper presents a procedure and the results of an optimal design of the kinematic structure of a manipulator to be used for autonomous cucumber harvesting in greenhouses. The design objective included the time needed to perform a collision-free motion from an initial position to the target position as well as a dexterity measure to allow for motion corrections in the neighborhood of the fruits. The optimisation problem was solved using the DIRECT algorithm implemented in the Tomlab package. A four link PPRR type manipulator was found to be most suitable. For cucumber harvesting four degrees-of-freedom, i.e. three
Prediction of lateral lymph node metastasis in lower rectal cancer: analysis of paraffin-embedded sections.

OBJECTIVE In the surgical treatment for lower rectal cancer, preoperative selection of patients at high risk for lateral lymph node metastasis is important, since lateral lymph node dissection might impair genitourinary functions. We examined whether the status of lateral lymph node metastasis can be predicted from the lymph node size. METHODS The subjects were 533 (35 positive and 498 negative) lateral lymph nodes from 47 patients with lower rectal cancer who underwent curative resection with lateral lymph node dissection. The sizes of the lateral lymph nodes immediately after removal and those in paraffin-embedded sections were compared for 108 lateral lymph nodes from 13 patients. In addition, receiver-operating characteristic curves were generated for the 533 paraffin-embedded lateral lymph nodes from the 47 patients to determine the optimal cut-off size for discriminating between positive and negative lateral lymph nodes. RESULTS Irrespective of the presence/absence of metastasis and the long-/short-axis diameter, a positive relationship was noted between the sizes of the lateral lymph nodes measured immediately after removal and those measured on paraffin-embedded sections (P< 0.01). The area under the curve for the short-axis diameter differed little from that for the long-axis diameter (0.77 vs. 0.76, P =0.80). The optimal cut-off values of the short- and long-axis diameter extrapolated to the living body were 5.4 and 8.4 mm, respectively, with an accuracy of 72.8% for the short-axis diameter and 71.9% for the long-axis diameter. CONCLUSIONS Prediction of the status of lateral lymph node metastasis from the lymph node size (long-/short-axis diameter) may be a simple and reliable method. The optimal cut-off diameter should be validated in prospective imaging studies.
Uptake of novel statistical methods for early-phase clinical studies in the UK public sector

Background In recent years, the success rate of confirmatory studies has been poor resulting in more emphasis on the conduct of exploratory studies. As one possibility to improve decision-making during the early stages of development, adaptive and Bayesian methods have been recommended. Purpose To investigate the current practice in designing early-phase studies in UK public sector research institutions and the use of adaptive and Bayesian methods in particular and to determine factors that hinder the penetration of methodological advances into practice. Methods A questionnaire was sent to all UK clinical trials units (CTUs) to gauge their involvement in early-phase studies and to learn about the designs used in these studies. Follow-up visits to units conducting early-phase studies with round-table discussions around the methods used and the obstacles faced when using adaptive methods were undertaken. Results More than half of the CTUs are involved in early-phase studies, but conservatism in the methods used in these studies is present. Reasons for novel methodology not being used include a lack of expertise, incompatible funding and unit structure, and a lack of software. Limitations Information is collected from UK CTUs, which undertake a large portion (but not all) publicly funded trials. Conclusions The use of adaptive and Bayesian methods for early-phase clinical studies in the UK public sector is at present limited. Various different initiatives aim to support and facilitate the use of these methods, however, so that an increased use of these methods can be anticipated in the future.
Quality of Service (QoS) Contract Specification, Establishment, and Monitoring for Service Level Management

This paper describes an approach and the architecture of Quality of Service (QoS) contract specification, establishment, and monitoring for Service Level Management (SLM). Contract is an essential concept in SLM. The service consumer side and the service provider side must share common understanding of QoS characteristics and agree on the common language for specifying desired QoS parameters in the form of QoS contracts. A service consumer must also negotiate with a service provider to establish mutually agreed QoS contracts for an interactive session. The service provider must consider QoS contracts already agreed upon with existing consumers and system resource conditions in establishing a new QoS contract. Similarly, a service consumer must be prepared in revising its contract with the service provider as conditions change over time. Once a QoS contract is established, SLM must provide monitoring to make sure that the service is provided at agreed QoS parameter range. If necessary, SLM must activate adaptation mechanisms to bring the service quality to the desired level. A case study is presented to validate the QoS contract management design approach and architecture for SLM.
Experiences of route and task-based walking in a university community: qualitative perspectives in a randomized control trial.

BACKGROUND This study explored the experiences of university employees recruited to a 10-week randomized controlled trial (n = 64). The trial compared "walking routes" with "walking-while-working" on daily step totals, showing that, compared with controls, interventions resulted in around 1000 extra steps per day. METHODS A subsample of 15 academic and administrative employees from intervention groups completed interviews at the end of intervention. Interviews were transcribed verbatim and subject to inductive coding within the major themes of benefits/positives and problems/barriers. FINDINGS Both interventions benefited employee health and work productivity but were difficult to implement in the workplace. Involvement in walking routes was challenged by the difficulties of managing time pressures, and individuals assigned to walking-while-working had to deal with local management subcultures favoring physical presence and inactivity. CONCLUSIONS Findings highlight the need for further research, advocate the value of walking at work, and provide insights into the challenges that face staff in workplace interventions.
Cerebrospinal fluid acetylcholinesterase in patients with dementia associated with schizophrenia or chronic alcoholism

Cerebrospinal fluid (CSF) acetylcholinesterase (AChE) was determined for 11 chronic schizophrenic patients with dementia, 9 patients with dementia associated with alcoholism and 8 age‐equivalent control subjects. The AChE levels in both patient groups were unrelated to the degree of cognitive decline and they were in the same range as in the control group. In schizophrenic patients no relationship was found between CSF AChE and the severity of psychotic symptoms. Our results suggest that dementia may occur in these patient groups without CSF AChE involvement.
Immunotherapy of metastatic renal cell carcinoma with tumor lysate-pulsed autologous dendritic cells.

PURPOSE We wanted to evaluate feasibility and safety of dendritic cell-based immunotherapy in patients with metastatic renal cell carcinoma (RCC). EXPERIMENTAL DESIGN Patients with metastatic RCC (n = 35) received vaccinations (i.v. or i.d.) of CD83+ autologous monocyte-derived dendritic cells (moDCs). MoDCs were loaded with lysate of cultured autologous or allogeneic permanent tumor cells (A-498) as well as keyhole limpet hemocyanin as control and helper antigen. Maturation of moDCs was induced by a combination of tumor necrosis factor alpha, interleukin 1 beta, interleukin 6, and prostaglandin E2. RESULTS Treatment was associated with transient flu-like symptoms. In 2 of 27 evaluable patients, any evidence of disease disappeared (complete response). In both cases, metastatic tissue had been the source of tumor antigen. One patient had an objective partial response. Seven patients had stable disease, the remaining 17 patients had progressive disease. In 11 of 11 patients evaluated, moDCs induced strong immune responses against keyhole limpet hemocyanin. In 5 of 6 patients tested, enhanced immune responses against oncofetal antigen (immature laminin receptor; OFA/LRP) could also be detected. The strongest responses against OFA/LRP were detectable in 2 patients with complete response and partial response, respectively. At the time of submission, mean follow up is 32 months and 8 patients are currently alive. CONCLUSIONS Our data indicate that moDC-based vaccination is well tolerated and has immunological as well as clinical effects in patients with metastatic RCC. OFA/LRP might be an attractive candidate antigen for DC-based immunotherapy of RCC.
Characterization and cleaning control of optical coatings by using a goniometric light scatter instrument with sample imaging ability

The principle of a new scattering measurement system including a mobile lighting and a fixed CCD array is described. This new system allows a spatially resolved light scattering characterization. Moreover it is possible to separate localized defects contribution from the local roughness measurement. The comprehensive characterization of optical coatings can be performed with this set-up, and some examples will be given.