Miracle-dz/UniFAR-FTUs huggingface dataset:
A Tool-based Methodology for Software Portfolio Monitoring

We present a tool-based methodology for monitoring the development and maintenance performed on the software portfolio of a large company. The toolkit on which the methodology is based includes an extendable framework for software analysis and visualization that meets strong demands with respect to scalability and usability. The methodology consists of 3 nested iterations and is carried out by software engineers with very strong consultancy skills. The shortest iteration consists in applying the toolkit to the software portfolio to obtain and register basic facts such as metrics and dependencies. In the middle iteration, the engineers interpret and evaluate the newly registered facts. The findings are reported to IT management together with recommendations about how to react to the findings. In particular, one kind of recommendation is to carry out a Software Risk Assessment on a selected system or project. Finally, the longest iteration is the publication of an annual software report, which summarizes the monitoring results of the previous year.
A Tri-Band Antenna for Wireless Applications using Slot-Type SRR

─ A tri-band microstrip-fed slot antenna for WLAN/WiMAX applications is proposed and investigated. Three operating bands are obtained by inserting split ring resonator (SRR) slots for band-rejected design. An electromagnetic (EM) model of this antenna is simulated by Ansoft HFSS. The principle of operation and parametric of the proposed antenna are also provided. The measured -10 dB bandwidth for return loss is from 2.39 GHz − 2.48 GHz, 3 GHz − 3.7 GHz, and 5 GHz − 7 GHz, covering the WLAN (2.4/5.2/5.8) and WiMAX (3.5/5.5) bands. The proposed antenna achieves a stably omni-directional radiation pattern and acceptable gain at all three operating frequency bands. Index Terms – Slot antennas, SRR, tri-band antennas, and WiMAX/WLAN applications.
Engineering hybrid nano-devices powered by the F1-ATPase biomolecular motor

Hybrid nano-devices that encompass organic and inorganic components offer truly unique and flexible functionalities. With integrated biomolecules and active proteins, it is plausible to envision seamless interfacing with nastive biological environments. The ability to incorporate inorganic features not only enables the synthesis of complex systems, it provides a myriad of options in custom tailoring devices to pertinent biomedical applications as well. This is especially true with the advent of more advanced nano-fabrication technologies in recent years. F1-ATPase is a motor protein whose rotary motion has been well characterised [1,2]. The biomolecular motor hydrolyses ATP to generate forces compatible with currently fabricated nano-mechanical structures. We have fabricated and operated a hybrid organic-inorganic nano-device powered by the F1-ATPase biomolecular motor [3–5]. The scope of the hybrid device developments was manifold including the local movement of surrounding suspended particles by functional organic-inorganic devices and in other efforts, the capability of implementing control mechanisms [6]. In addition, a renewable biological fuel (ATP) source has recently been developed through sol–gel encapsulation of proteoliposomes in an effort towards creating a self-sustaining device. The following paper is a review of the knowledge that has transpired upon developing hybrid organic-inorganic nano-devices to hopefully elicit future advancements of bio-nano-systems.
Homology Modeling of the Calcium Sensing Receptor Extracellular Domain

The extracellular calcium-sensing receptor (CaR) on the parathyroid cell surface negatively regulates secretion of parathyroid hormone (PTH). CaR has an important rule in diseases. Cinacalcet hydrochloride, an allosteric agonist of this receptor was approved by FDA in 2004 for treatment of secondary hyperparathyroidism. Cinacalcet is indicated for the treatment of hypercalcemia in patients with parathyroid carcinoma or for secondary hyperparathyroidism in patients with chronic kidney disease who require dialysis. This drug is an allosteric agonist which is bind to transmembrane domain of CaR. Studies showed that the ligand binding region of CaR, as expected, is located at the amino-terminal domain (extracellular domain). There is no crystal structure or model is available for this domain of CaR so we constructed the model and found putative ligand binding site. This model will be useful for finding new CaR orthosteric ligands and designing new drugs.
Projected Future Vegetation Changes for the Northwest United States and Southwest Canada at a Fine Spatial Resolution Using a Dynamic Global Vegetation Model

Future climate change may significantly alter the distributions of many plant taxa. The effects of climate change may be particularly large in mountainous regions where climate can vary significantly with elevation. Understanding potential future vegetation changes in these regions requires methods that can resolve vegetation responses to climate change at fine spatial resolutions. We used LPJ, a dynamic global vegetation model, to assess potential future vegetation changes for a large topographically complex area of the northwest United States and southwest Canada (38.0–58.0°N latitude by 136.6–103.0°W longitude). LPJ is a process-based vegetation model that mechanistically simulates the effect of changing climate and atmospheric CO2 concentrations on vegetation. It was developed and has been mostly applied at spatial resolutions of 10-minutes or coarser. In this study, we used LPJ at a 30-second (~1-km) spatial resolution to simulate potential vegetation changes for 2070–2099. LPJ was run using downscaled future climate simulations from five coupled atmosphere-ocean general circulation models (CCSM3, CGCM3.1(T47), GISS-ER, MIROC3.2(medres), UKMO-HadCM3) produced using the A2 greenhouse gases emissions scenario. Under projected future climate and atmospheric CO2 concentrations, the simulated vegetation changes result in the contraction of alpine, shrub-steppe, and xeric shrub vegetation across the study area and the expansion of woodland and forest vegetation. Large areas of maritime cool forest and cold forest are simulated to persist under projected future conditions. The fine spatial-scale vegetation simulations resolve patterns of vegetation change that are not visible at coarser resolutions and these fine-scale patterns are particularly important for understanding potential future vegetation changes in topographically complex areas.
The Mechanical Design and Analysis of an Active Prosthetic Knee

In a world of war and turmoil in developing nations, land mines are becoming a concern, as millions of them are scattered in countries all over the world. Moreover, land mine prevention programs cannot clear land mine fields as fast as they are detonated each day. As a result, there are thousands that fall victim each year. There is immense demand for newer technologies to replace the aging prostheses used in these war torn nations. The active prosthetic knee (APK) design project is a novel design that utilizes simple, robust one degree of freedom (DOF) mechanics, while providing fully active knee torque control. The APK utilizes a high-speed brushed servomotor, providing the necessary torque and dynamics to provide the necessary gait characteristics of human locomotion. The main research contributions of this thesis are: 1) the mechanics and 2) the intelligence of the APK. This thesis investigates and highlights the prosthetic’s design process. The human biological system is studied and used as the design criteria when designing the device. Anthropometric data was used to determine the sizing and other physical properties. Moreover, Adaptive-Network-based Fuzzy-Interference Systems (ANFIS) and Fuzzy Interference Systems (FIS) are used to provide control to the APK. Finite element analysis (FEA) verifies the structural integrity of the APK. Four simulations are analyzed: equivalent stress, equivalent strain, shear stress and total deformation. These four simulations provide a mathematical interpretation of the physical system. We found that the first prototype, although a sound design, can be further improved to allow greater loading capabilities. Moreover, cyclical loading and total life cycles would also be significantly improved. A modular test stand is also designed and prototyped to allow APK testing. Since the APK prototype cannot be immediately placed on a human test subject, the test stand allows for experimentation in replicating human gait cycles.
Neoadjuvant chemotherapy versus primary debulking surgery in advanced epithelial ovarian cancer: A meta-analysis of peri-operative outcome

Objective To assess whether neoadjuvant chemotherapy (NACT) is superior to primary debulking surgery (PDS) with regard to optimal cytoreduction, peri-operative morbidity, mortality, and quality of life (QOL) in advanced epithelial ovarian cancer (EOC). Methods We searched the PubMed, Embase, Cochrane Central Register of Controlled Trials, Web of Science, Registers of Clinical Trials for randomized controlled trials (RCTs) comparing NACT to PDS in women with Federation of International Gynaecologists and Obstetricians stage Ⅲ-Ⅳ EOC. RevMan 5.3 software was utilized for statistical analysis. Results Four RCTs involving 1,607 women with advanced EOC were included. Compared with PDS, NACT provided a higher rate of complete cytoreduction (risk ratio [RR], 1.95; 95% confidence interval [CI], 1.33 to 2.87), optimal cytoreduction (RR: 1.61 [95%CI: 1.05 to 2.47]), but there was no significant difference in residual disease 0–1 cm (p = 0.49). NACT was associated with lower peri-operative morbidity with respect to infection (RR: 0.30 [95% CI: 0.16 to 0.56]), gastrointestinal fistula (RR: 0.24 [95% CI: 0.06 to 0.95]), any grade 3 or 4 adverse event (RR: 0.29 [95% CI: 0.11 to 0.78]), and less post-surgical death within 28 days (RR: 0.14 [95% CI: 0.04 to 0.49]). NACT provided better QOL in terms of fatigue (weight mean difference [WMD], -3.28; [95% CI: -3.99 to -2.57]), role functioning (WMD: 5.29 [95% CI: 4.44 to 6.14]), emotional functioning (WMD: 6.19 [95% CI: 5.57 to 6.82]), and cognitive functioning (WMD: 1.02 [95% CI: 0.43 to 1.61]) at 6-month follow-up compared with PDS. Conclusions NACT is associated with superior optimal cytoreduction, lower peri-operative morbidity as well as post-surgical mortality, and better QOL compared to initial surgery in patients with advanced EOC. Future research should focus on improving the efficacy of NACT.
Exergy and Pinch Analysis of Diesel Engine Bottoming Cycles with Ammonia-Water Mixtures as Working Fluid

In the present study, exergy and pinch analyses have been performed on ammonia-water and Rankine bottoming cycles for gas diesel engines. Gas diesel engines produce four waste heat streams at different temperature levels that can be used as heat sources by a bottoming cycle. The ammonia-water cycle has the potential to use these heat sources more efficiently than a Rankine cycle. The second law efficiency of the best ammonia-water cycle configuration is 43-48 % higher than the efficiency of a single-pressure Rankine cycle and 20-25 % higher than the efficiency of a dual-pressure Rankine cycle. This paper was presented at the ECOS’00 Conference in Enschede, July 5-7, 2000
Synaptic Membrane Synthesis in Rats Depends on Dietary Sufficiency of Vitamin C, Vitamin E, and Selenium: Relevance for Alzheimer’s Disease

Chronic consumption of a diet enriched with nutritional precursors of phospholipids, including uridine and the polyunsaturated fatty acids, docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), was shown previously to enhance levels of brain phospholipids and synaptic proteins in rodents. Vitamin C, vitamin E, and selenium may directly affect the breakdown or synthesis of membrane phospholipids. The present study investigated the necessity of antioxidants for the effectiveness of supplementation with uridine plus DHA and EPA (as fish oil) in rats. Rats were randomized to four treatment groups and received, for 6 weeks, one of four experimental diets, i.e., a diet low in antioxidants, a diet high in antioxidants, a diet low in antioxidants supplemented with DHA+EPA+uridine, or a diet high in antioxidants supplemented with DHA+EPA+uridine. On completion of dietary treatment, rats were sacrificed, and brain levels of phospholipids, synaptic proteins, and two enzymes involved in phospholipid synthesis (choline-phosphate cytidylyltransferase, PCYT1A, and choline/ethanolamine phosphotransferase, CEPT1) were analyzed. Levels of phospholipids, the pre- and post-synaptic proteins Synapsin-1 and PSD95, and the enzymes PCYT1A and CEPT1 were significantly enhanced by combined supplementation of DHA+EPA+uridine and antioxidants and not enhanced by supplementation of DHA+EPA+uridine with insufficient antioxidant levels. Our data suggest that dietary vitamin C, vitamin E, and selenium are essential for the phospholipid precursors’ effects on increasing levels of membrane phospholipids and synaptic proteins, the indirect indicators of synaptogenesis. Their concomitant supply may be relevant in Alzheimer’s disease patients, because the disease is characterized by synapse loss and lower plasma and brain levels of phospholipid precursors and antioxidants.
Adaptive estimation of high-dimensional signal-to-noise ratios

We consider the equivalent problems of estimating the residual variance, the proportion of explained variance $\eta$ and the signal strength in a high-dimensional linear regression model with Gaussian random design. Our aim is to understand the impact of not knowing the sparsity of the regression parameter and not knowing the distribution of the design on minimax estimation rates of $\eta$. Depending on the sparsity $k$ of the regression parameter, optimal estimators of $\eta$ either rely on estimating the regression parameter or are based on U-type statistics, and have minimax rates depending on $k$. In the important situation where $k$ is unknown, we build an adaptive procedure whose convergence rate simultaneously achieves the minimax risk over all $k$ up to a logarithmic loss which we prove to be non avoidable. Finally, the knowledge of the design distribution is shown to play a critical role. When the distribution of the design is unknown, consistent estimation of explained variance is indeed possible in much narrower regimes than for known design distribution.
Increased Circulating Endothelial Apoptotic Microparticle to Endothelial Progenitor Cell Ratio Is Associated with Subsequent Decline in Glomerular Filtration Rate in Hypertensive Patients

Background Recent research indicates hypertensive patients with microalbuminuria have decreased endothelial progenitor cells (EPCs) and increased levels of endothelial apoptotic microparticles (EMP). However, whether these changes are related to a subsequent decline in glomerular filtration rate (GFR) remains unclear. Methods and Results We enrolled totally 100 hypertensive out-patients with eGFR ≥30 mL/min/1.73 m2. The mean annual rate of GFR decline (△GFR/y) was −1.49±3.26 mL/min/1.73 m2 per year during the follow-up period (34±6 months). Flow cytometry was used to assess circulating EPC (CD34+/KDR+) and EMP levels (CD31+/annexin V+) in peripheral blood. The △GFR/y was correlated with the EMP to EPC ratio (r = −0.465, p<0.001), microalbuminuria (r = −0.329, p = 0.001), and the Framingham risk score (r = −0.245, p = 0.013). When we divided the patients into 4 groups according to the EMP to EPC ratio, there was an association between the EMP to EPC ratio and the ΔGFR/y (mean ΔGFR/y: 0.08±3.04 vs. −0.50±2.84 vs. −1.25±2.49 vs. −4.42±2.82, p<0.001). Multivariate analysis indicated that increased EMP to EPC ratio is an independent predictor of ΔeGFR/y. Conclusions An increased circulating EMP to EPC ratio is associated with subsequent decline in GFR in hypertensive patients, which suggests endothelial damage with reduced vascular repair capacity may contribute to further deterioration of renal function in patients with hypertension.
Short‐Term Exposure to Air Pollution and Biomarkers of Oxidative Stress: The Framingham Heart Study

Background Short‐term exposure to elevated air pollution has been associated with higher risk of acute cardiovascular diseases, with systemic oxidative stress induced by air pollution hypothesized as an important underlying mechanism. However, few community‐based studies have assessed this association. Methods and Results Two thousand thirty‐five Framingham Offspring Cohort participants living within 50 km of the Harvard Boston Supersite who were not current smokers were included. We assessed circulating biomarkers of oxidative stress including blood myeloperoxidase at the seventh examination (1998–2001) and urinary creatinine‐indexed 8‐epi‐prostaglandin F2α (8‐epi‐PGF 2α) at the seventh and eighth (2005–2008) examinations. We measured fine particulate matter (PM 2.5), black carbon, sulfate, nitrogen oxides, and ozone at the Supersite and calculated 1‐, 2‐, 3‐, 5‐, and 7‐day moving averages of each pollutant. Measured myeloperoxidase and 8‐epi‐PGF 2α were loge transformed. We used linear regression models and linear mixed‐effects models with random intercepts for myeloperoxidase and indexed 8‐epi‐PGF 2α, respectively. Models were adjusted for demographic variables, individual‐ and area‐level measures of socioeconomic position, clinical and lifestyle factors, weather, and temporal trend. We found positive associations of PM 2.5 and black carbon with myeloperoxidase across multiple moving averages. Additionally, 2‐ to 7‐day moving averages of PM 2.5 and sulfate were consistently positively associated with 8‐epi‐PGF 2α. Stronger positive associations of black carbon and sulfate with myeloperoxidase were observed among participants with diabetes than in those without. Conclusions Our community‐based investigation supports an association of select markers of ambient air pollution with circulating biomarkers of oxidative stress.
The Role of the Electronic Medical Record in the Intensive Care Unit Nurse's Detection of Patient Deterioration: A Qualitative Study

Failure to detect patient deterioration signals leads to longer stays in the hospital, worse functional outcomes, and higher hospital mortality rates. Surveillance, including ongoing acquisition, interpretation, and synthesis of patient data by the nurse, is essential for early risk detection. Electronic medical records promote accessibility and retrievability of patient data and can support patient surveillance. A secondary analysis was performed on interview data from 24 intensive care unit nurses, collected in a study that examined factors influencing nurse responses to alarms. Six themes describing nurses' use of electronic medical record information to understand the patients' norm and seven themes describing electronic medical record design issues were identified. Further work is needed on electronic medical record design to integrate documentation and information presentation with the nursing workflow. Organizations should involve bedside nurses in the design of handoff formats that provide key information common to all intensive care unit patient populations, as well as population-specific information.
SEM Based CARMA Time Series Modeling for Arbitrary N

ABSTRACT This article explains in detail the state space specification and estimation of first and higher-order autoregressive moving-average models in continuous time (CARMA) in an extended structural equation modeling (SEM) context for N = 1 as well as N > 1. To illustrate the approach, simulations will be presented in which a single panel model (T = 41 time points) is estimated for a sample of N = 1,000 individuals as well as for samples of N = 100 and N = 50 individuals, followed by estimating 100 separate models for each of the one-hundred N = 1 cases in the N = 100 sample. Furthermore, we will demonstrate how to test the difference between the full panel model and each N = 1 model by means of a subject-group-reproducibility test. Finally, the proposed analyses will be applied in an empirical example, in which the relationships between mood at work and mood at home are studied in a sample of N = 55 women. All analyses are carried out by ctsem, an R-package for continuous time modeling, interfacing to OpenMx.
The Schizotypal Ambivalence Scale as a Marker of Schizotypy

The present study examined the psychometric properties of the Schizotypal Ambivalence Scale (SAS) in a sample of 1798 young adults. The study also investigated the concurrent validity of the measure for identifying schizophrenic-like symptoms in a sample of 43 high scorers on the scale and 43 control participants. Previous findings indicated that high scores on the SAS were associated with schizophrenia-spectrum pathology in a sample of schizotypic young adults selected with other measures. However, this is the first study to assess schizophrenic-like psychopathology in a sample selected using the SAS. The SAS has good internal consistency (coefficient α = 0.84) and test-retest reliability (intraclass correlation = 0.74 across 9 weeks). As hypothesized, the ambivalence group exceeded the control group on interview ratings of schizotypal, schizoid, paranoid, psychotic-like, and negative symptoms, as well as exhibiting poorer overall functioning. The SAS seems to be a promising measure of schizotypy in young adults.
Geographic population structure in an outcrossing plant invasion after centuries of cultivation and recent founding events

We investigated the genetic diversity and origins of a long-term cultivar. Dyer’s woad has been used as a dye source for at least eight centuries in Eurasia. It was introduced to eastern USA in the 1600s, and is now considered invasive in the western USA. Our analysis of plants from the USA and Eurasia suggests that there are two distinct invasions in western USA that most likely originate from Switzerland, Ukraine and Germany. This information assists in finding effective biological control agents, and continued combination of ecological and molecular data helps bring us closer to sustainable management of plant invasions.
Inflammatory biomarkers as predictors of heart failure in women without obstructive coronary artery disease: A report from the NHLBI-sponsored Women’s Ischemia Syndrome Evaluation (WISE)

Background Women with signs and symptoms of ischemia, no obstructive coronary artery disease (CAD) and preserved left ventricular ejection fraction (EF) often have diastolic dysfunction and experience elevated rates of major adverse cardiac events (MACE), including heart failure (HF) hospitalization with preserved ejection fraction (HFpEF). We evaluated the predictive value of inflammatory biomarkers for long-term HF hospitalization and all-cause mortality in these women. Methods We performed a cross-sectional analysis to investigate the relationships between inflammatory biomarkers [serum interleukin-6 (IL-6), C-reactive protein (hs-CRP) and serum amyloid A (SAA)] and median of 6 years follow-up for all-cause mortality and HF hospitalization among women with signs and symptoms of ischemia, non-obstructive CAD and preserved EF. Multivariable Cox regression analysis tested associations between biomarker levels and adverse outcomes. Results Among 390 women, mean age 56 ± 11 years, median follow up of 6 years, we observed that there is continuous association between IL-6 level and HF hospitalization (adjusted hazard ratio [AHR] 2.5 [1.2–5.0], p = 0.02). In addition, we found significant association between IL-6, SAA levels and all-cause mortality AHR (1.8 [1.1–3.0], p = 0.01) (1.5 [1.0–2.1], p = 0.04), respectively. Conclusion In women with signs and symptoms of ischemia, non-obstructive CAD and preserved EF, elevated IL-6 predicted HF hospitalization and all-cause mortality, while SAA level was only associated with all-cause mortality. These results suggest that inflammation plays a role in the pathogenesis of development of HFpEF, as well all-cause mortality.