Miracle-dz/UniFAR-FTUs huggingface dataset:
Software engineering: an unconsummated marriage

When the first conference on “Software Engineering” was held, under NATO sponsorship three decades ago in Munich, the vast majority of Engineers ignored it. Electrical Engineers were obviously interested in building computers, but they regarded programming those computers as something to be done by others, often scientists who wanted the numerical results, or mathematicians who were interested in numerical methods. Programming was not viewed as engineering, but as a trivial task, akin to using a calculator. An engineer might have to perform such a task in order to get numerical results needed for some other task, but their real job was the other task.
Correction: An Immeasurable Crisis? A Criticism of the Millennium Development Goals and Why They Cannot Be Measured

0704 May 2006 | Volume 3 | Issue 5 | e223 | e224 | e225 Correction: Large-Scale Evidence for the Effect of the COLIA1 Sp1 Polymorphism on Osteoporosis Outcomes: The GENOMOS Study Stuart H. Ralston, André G. Uitterlinden, Maria Luisa Brandi, Susana Balcells, Bente L. Langdahl, Paul Lips, Roman Lorenc, Barbara Obermayer-Pietsch, Serena Scollen, Mariona Bustamante, Lise Bjerre Husted, Alisoun H. Carey, Adolfo Diez-Perez, Alison M. Dunning, Alberto Falchetti, Elzbieta Karczmarewicz, Marcin Kruk, Johannes P. T. M. van Leeuwen, Joyce B. J. van Meurs, Jon Mangion, Fiona E. A. McGuigan, Leonardo Mellibovsky, Francesca del Monte, Huibert A. P. Pols, Jonathan Reeve, David M. Reid, Wilfried Renner, Fernando Rivadeneira, Natasja M. van Schoor, Rachael E. Sherlock, John P. A. Ioannidis, for the GENOMOS investigators DOI: 10.1371/journal.pmed. 0030090 In PLoS Medicine, volume 3, issue 4: Among the listed additional authors, J. da Silva, J. Bruges Armas, and A. Lopes Vaz are from Portugal. This correction note may be found online at DOI: 10.1371/journal.pmed. 0030223. Published May 30, 2006. Citation: Correction: Large-scale evidence for the effect of the COLIA1 Sp1 polymorphism on osteoporosis outcomes: The GENOMOS study. PLoS Med 3(4): e223.
Thomas Vicary and the Anatomie of Mans Body

Dysfunction of prefrontal cortex in schizophrenia includes changes in GABAergic mRNAs, including decreased expression of GAD1, encoding the 67 kDa glutamate decarboxylase (GAD67) GABA synthesis enzyme. The underlying molecular mechanisms remain unclear. Alterations in DNA methylation as an epigenetic regulator of gene expression are thought to play a role but this hypothesis is difficult to test because no techniques are available to extract DNA from GAD1 expressing neurons efficiently from human postmortem brain. Here, we present an alternative approach that is based on immunoprecipitation of mononucleosomes with anti-methyl-histone antibodies differentiating between sites of potential gene expression as opposed to repressive or silenced chromatin. Methylation patterns of CpG dinucleotides at the GAD1 proximal promoter and intron 2 were determined for each of the two chromatin fractions separately, using a case-control design for 14 schizophrenia subjects affected by a decrease in prefrontal GAD1 mRNA levels. In controls, the methylation frequencies at CpG dinucleotides, while overall higher in repressive as compared to open chromatin, did not exceed 5% at the proximal GAD1 promoter and 30% within intron 2. Subjects with schizophrenia showed a significant, on average 8-fold deficit in repressive chromatin-associated DNA methylation at the promoter. These results suggest that chromatin remodeling mechanisms are involved in dysregulated GABAergic gene expression in schizophrenia.
Inhibition of Restenosis With &bgr;-Emitting Radiotherapy: Report of the Proliferation Reduction With Vascular Energy Trial (PREVENT)

BackgroundIntracoronary &ggr;- and &bgr;-radiation have reduced restenosis in animal models. In the clinical setting, the effectiveness of &bgr;-emitters has not been studied in a broad spectrum of patients, particularly those receiving stents. Methods and ResultsA prospective, randomized, sham-controlled study of intracoronary radiotherapy with the &bgr;-emitting 32P source wire, using a centering catheter and automated source delivery unit, was conducted. A total of 105 patients with de novo (70%) or restenotic (30%) lesions who were treated by stenting (61%) or balloon angioplasty (39%) received 0 (control), 16, 20, or 24 Gy to a depth of 1 mm in the artery wall. Angiography at 6 months showed a target site late loss index of 11±36% in radiotherapy patients versus 55±30% in controls (P <0.0001). A low late loss index was seen in stented and balloon-treated patients and was similar across the 16, 20, and 24 Gy radiotherapy groups. Restenosis (≥50%) rates were significantly lower in radiotherapy patients at the target site (8% versus 39%;P =0.012) and at target site plus adjacent segments (22% versus 50%;P =0.018). Target lesion revascularization was needed in 5 radiotherapy patients (6%) and 6 controls (24%;P <0.05). Stenosis adjacent to the target site and late thrombotic events reduced the overall clinical benefit of radiotherapy. Conclusions&bgr;-radiotherapy with a centered 32P source is safe and highly effective in inhibiting restenosis at the target site after stent or balloon angioplasty. However, minimizing edge narrowing and late thrombotic events must be accomplished to maximize the clinical benefit of this modality.
Validation of the Symptom Screening in Pediatrics Tool in Children Receiving Cancer Treatments

Abstract Background The objective was to evaluate the reliability and validity of the self-report Symptom Screening in Pediatrics Tool (SSPedi) from the perspective of children with cancer and pediatric hematopoietic stem cell transplant (HSCT) recipients. Methods In this multicenter study, respondents were children age eight to 18 years who had cancer or had received HSCT, and their parents. Two different child respondent populations were targeted. More symptomatic respondents were receiving active treatment for cancer, admitted to the hospital, and expected to be in the hospital three days later. Less symptomatic respondents were in maintenance therapy for acute lymphoblastic leukemia or had completed cancer therapy. Children completed SSPedi and then responded to validated self-report measures of mucositis, nausea, pain, and global quality of life. Children in the more symptomatic group repeated SSPedi and a global symptom change scale three days later. Parent proxy-report was optional. Reliability was evaluated using intraclass correlations while convergent validity was evaluated using Spearman correlations. Results Of 502 children enrolled, 302 were in the more symptomatic group and 200 were in the less symptomatic group. Intraclass correlation coefficients were 0.88 (95% confidence interval [CI] = 0.82 to 0.92) for test-retest reliability and 0.76 (95% CI = 0.71 to 0.80) for inter-rater reliability. The mean difference in SSPedi scores between more and less symptomatic groups was 7.8 (95% CI = 6.4 to 9.2). SSPedi was responsive to change in global symptoms. All hypothesized relationships among measures were observed. Conclusions SSPedi is a self-report symptom bother tool for children with cancer and HSCT recipients that is reliable, valid, and responsive to change. SSPedi can be used for clinical and research purposes. Future work should focus on integration into care delivery.
Persevering toward What? Investigating the Relationship between Ninth-grade Students’ Achievement Goals and Perseverant Actions on an Algebraic Task

Perseverance is vital for the process of learning mathematics with understanding. To do so, students must wrestle with obstacles and amend their problem-solving plan when necessary. I collected qualitative data to investigate the nature of perseverance for 11 ninth-grade algebra students working on a challenging task for which they affirmed interest. Employing analytical frameworks of achievement goal perceptions and subsequent perseverant actions, the findings inform three distinct profiles of in-the-moment perseverance states. These profiles suggest that perseverant actions are not always aligned with students’ goals of meaning-making. Although students may report being motivated by building conceptual understanding, they may not fully grasp what it means to achieve such mastery goals. I provide suggestions for teachers to further encourage the development of more perseverant learners.
Comorbidity and survival of Danish breast cancer patients from 2000–2011: a population-based cohort study

Objective Previous studies have suggested that breast cancer survival in Denmark has improved, primarily in cancer patients without comorbidity. We therefore conducted a population-based cohort study to examine recent temporal changes in survival and mortality among breast cancer patients with different extents of comorbidity. Methods We used population-based medical and administrative registries to identify breast cancer patients diagnosed between 2000 and 2011 in the Central Denmark Region. We defined comorbid diseases according to the Charlson Comorbidity Index (CCI), including a history of hospitalization for comorbid disease up to 10 years before breast cancer diagnosis. We studied the impact of comorbidities on overall 1- and 5-year survival in different calendar time periods, using a hybrid analysis for survival prediction in the most recent calendar periods. Results We included 9,329 breast cancer patients. The proportion of patients within different comorbidity categories remained stable from 2000 to 2011. One-year survival improved from 91% in 2000–2002 to 95% in 2009–2011, while 5-year survival improved from 72% to a predicted 78%. During the entire study period, comorbidity was a strong predictor of the survival of breast cancer patients. However, we observed improvements over time in 1- and 5-year survival for all comorbidity groups. During the 12-year study period, the estimated 5-year survival for patients with a high comorbidity disease burden (CCI score ≥3) increased from 25% to a predicted 50%, and their 5-year age-adjusted mortality hazard ratio (HR) fell from 4.0 (95% confidence interval [CI]: 3.0, 5.4) to 2.7 (95% CI: 2.0, 3.6), respectively, compared with patients with no comorbid disease. Conclusion Survival of breast cancer patients diagnosed in the Central Denmark Region improved from 2000 to 2011, regardless of the extent of comorbid disease.
Comparison of Physical and Software-Implemented Fault Injection Techniques

This paper addresses the issue of characterizing the respective impact of fault injection techniques. Three physical techniques and one software-implemented technique that have been used to assess the fault tolerance features of the MARS fault-tolerant distributed real-time system are compared and analyzed. After a short summary of the fault tolerance features of the MARS architecture and especially of the error detection mechanisms that were used to compare the erroneous behaviors induced by the fault injection techniques considered, we describe the common distributed testbed and test scenario implemented to perform a coherent set of fault injection campaigns. The main features of the four fault injection techniques considered are then briefly described and the results obtained are finally presented and discussed. Emphasis is put on the analysis of the specific impact and merit of each injection technique.
Optimal Denial-of-Service Attack Scheduling With Energy Constraint

Security of Cyber-Physical Systems (CPS) has gained increasing attention in recent years. Most existing works mainly investigate the system performance given some attacking patterns. In this technical note, we investigate how an attacker should schedule its Denial-of-Service (DoS) attacks to degrade the system performance. Specifically, we consider the scenario where a sensor sends its data to a remote estimator through a wireless channel, while an energy-constrained attacker decides whether to jam the channel at each sampling time. We construct optimal attack schedules to maximize the expected average estimation error at the remote estimator. We also provide the optimal attack schedules when a special intrusion detection system (IDS) at the estimator is given. We further discuss the optimal attack schedules when the sensor has energy constraint. Numerical examples are presented to demonstrate the effectiveness of the proposed optimal attack schedules.
Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines

Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.
Induction chemotherapy for the treatment of non-endemic locally advanced nasopharyngeal carcinoma

Background The role of induction chemotherapy is less clear in non-endemic locally advanced nanopharyngeal carcinomas (NPC). Results With a total of 233 eligible patients and a median follow-up of 36 months, 3-year overall survival (OS), local recurrence-free survival (LRFS), distant metastasis-free survival (DMFS), disease free survival (DFS) were 84.5%, 94.9%, 78.6% and 69.2%, respectively. The overall failure rate was 21.0% and distant metastasis occurred in 17.2% patients. Multivariate analyses showed that retropharyngeal and bilateral neck lymph node metastasis were significant prognostic factors for DFS and OS. Moreover, patients receiving both GP (gemcitabine+cisplatin) and TP (docetaxel+cisplatin) regimes had significantly higher DFS and OS compared with PF (cisplatin+5-FU) regime. GP regimes lead to significantly improved OS than TP/PF in some subgroup of patients. No severe toxicities were observed. Materials and Methods We retrospectively analyzed stage III-IVb NPC patients treated between Jan 2006 and Dec 2014, with induction chemotherapy followed by concurrent chemoradiation (IC-CCRT). Statistical analyses were performed on survival and failure patterns. Conclusions These results suggested IC-CCRT was safe and effective for NPCs from non-endemic region. The choice of induction regimen appeared to affect patient outcomes.
Accelerating evolutionary algorithms with Gaussian process fitness function models

We present an overview of evolutionary algorithms that use empirical models of the fitness function to accelerate convergence, distinguishing between evolution control and the surrogate approach. We describe the Gaussian process model and propose using it as an inexpensive fitness function surrogate. Implementation issues such as efficient and numerically stable computation, exploration versus exploitation, local modeling, multiple objectives and constraints, and failed evaluations are addressed. Our resulting Gaussian process optimization procedure clearly outperforms other evolutionary strategies on standard test functions as well as on a real-world problem: the optimization of stationary gas turbine compressor profiles.
Bmc Public Health Does a Self-referral Counselling Program Reach Doctors in Need of Help? a Comparison with the General Norwegian Doctor Workforce

Background: Doctors have a relatively high degree of emotional distress, but seek help to a lesser degree and at a later stage than other academic groups. This can be deleterious for themselves and for their patients. Prevention programs have therefore been developed but it is unclear to what extent they reach doctors in need of help. This study describes doctors who participated in a self-referrral, easily accessible, stress relieving, counselling program in Norway, and compares them with a nationwide sample of Norwegian doctors.
Omeprazole- and Esomeprazole-associated Hypomagnesaemia: Data Mining of the Public Version of the FDA Adverse Event Reporting System

Objective: Case reports showing that proton-pump inhibitors (PPIs), omeprazole and esomeprazole, can cause hypomagnesaemia have been accumulating since 2006. In this study, the reports submitted to the Adverse Event Reporting System (AERS) of the US Food and Drug Administration (FDA) were evaluated to assess omeprazole and esomeprazole in terms of susceptibility to hypomagnesaemia. Methods: After a revision of arbitrary drug names and the deletion of duplicated submissions, the reports involving omeprazole and esomeprazole were analyzed. Standardized official pharmacovigilance tools were used for the quantitative detection of a signal, i.e., an association between a drug and an adverse drug event, including the proportional reporting ratio, the reporting odds ratio, the information component given by a Bayesian confidence propagation neural network, and the empirical Bayes geometric mean. Results: A total of 22,017,956 co-occurrences were found in 1,644,220 reports from 2004 to 2009, where a co-occurrence was a pair of a drug and an adverse drug event. In total, 818 and 743 adverse drug events were listed as omeprazole- and esomeprazole-associated, with hypomagnesaemia ranking 85th and 135th, respectively. Although both PPIs were associated with hypomagnesaemia, the statistical metrics suggested that the association was more noteworthy for omeprazole. Conclusion: The data obtained in this study do not provide sufficient evidence to recommend systematic monitoring of magnesium levels in plasma, but chronic exposure to a PPI can lead to severe hypomagnesaemia.
Possible Precision of Statistical Insulation Test Methods

The report deals with insulation test methods where voltages of constant shape but different amplitudes are applied to a test object to determine the voltage which corresponds to a certain probability of flashover. A hypothetical test method is considered which gives the minimum statistical error in the determination of that voltage for any given number of voltage applications. It is shown that some existinig test methods give nearly this result. There is therefore no need for further development of such methods. Present methods to determine voltages corresponding to low probability of flashover are criticized.
Analyticity of Entropy Rate of Hidden Markov Chains With Continuous Alphabet

We first prove that under certain mild assumptions, the entropy rate of a hidden Markov chain, observed when passing a finite-state stationary Markov chain through a discrete-time continuous-output channel, is analytic with respect to the input Markov chain parameters. We then further prove, under strengthened assumptions on the channel, that the entropy rate is jointly analytic as a function of both the input Markov chain parameters and the channel parameters. In particular, the main theorems establish the analyticity of the entropy rate for two representative channels: 1) Cauchy and 2) Gaussian. The analyticity results obtained are expected to be helpful in computation/estimation of entropy rate of hidden Markov chains and capacity of finite-state channels with continuous output alphabet.
Olympic Weightlifting Training Causes Different Knee Muscle–Coactivation Adaptations Compared with Traditional Weight Training

Abstract Arabatzi, F and Kellis, E. Olympic weightlifting training causes different knee muscle–coactivation adaptations compared with traditional weight training. J Strength Cond Res 26(8): 2192–2201, 2012—The purpose of this study was to compare the effects of an Olympic weightlifting (OL) and traditional weight (TW) training program on muscle coactivation around the knee joint during vertical jump tests. Twenty-six men were assigned randomly to 3 groups: the OL (n = 9), the TW (n = 9), and Control (C) groups (n = 8). The experimental groups trained 3 d·wk−1 for 8 weeks. Electromyographic (EMG) activity from the rectus femoris and biceps femoris, sagittal kinematics, vertical stiffness, maximum height, and power were collected during the squat jump, countermovement jump (CMJ), and drop jump (DJ), before and after training. Knee muscle coactivation index (CI) was calculated for different phases of each jump by dividing the antagonist EMG activity by the agonist. Analysis of variance showed that the CI recorded during the preactivation and eccentric phases of all the jumps increased in both training groups. The OL group showed a higher stiffness and jump height adaptation than the TW group did (p < 0.05). Further, the OL showed a decrease or maintenance of the CI recorded during the propulsion phase of the CMJ and DJs, which is in contrast to the increase in the CI observed after TW training (p < 0.05). The results indicated that the altered muscle activation patterns about the knee, coupled with changes of leg stiffness, differ between the 2 programs. The OL program improves jump performance via a constant CI, whereas the TW training caused an increased CI, probably to enhance joint stability.
A Modal Logic for Fusing Partial Belief of Multiple Reasoners

We present PLn, a multi-agent epistemic logic in which each agent can perform uncertain (possibilistic) reasoning. The original feature of this logic is the presence of a distributed belief operator, with the purpose of merging the belief of different agents. Unlike the corresponding operator in the categorical (non-uncertain) case, our distributed belief operator accumulates support for the same fact coming from different agents. This means that opinions shared by different agents can be combined into a stronger distributed belief. This feature is useful in problems like pooling expert opinions and combining information from multiple unreliable sources. We provide a possible worlds semantics and an axiomatic calculus for our logic, and prove soundness, completeness and decidability results. We hint at some possible applications of PLn in the conclusions