Miracle-dz/UniFAR-FTUs huggingface dataset:
Software evolution and time series volatility: an empirical exploration

The paper presents the first empirical study to examine econometric time series volatility modeling in the software evolution context. The econometric volatility concept is related to the conditional variance of a time series rather than the conditional mean targeted in conventional regression analysis. The software evolution context is motivated by relating these variance characteristics to the proximity of operating system releases, the theoretical hypothesis being that volatile characteristics increase nearby new milestone releases. The empirical experiment is done with a case study of FreeBSD. The analysis is carried out with 12 time series related to bug tracking, development activity, and communication. A historical period from 1995 to 2011 is covered under a daily sampling frequency. According to the results the time series dataset contains visible volatility characteristics, but these cannot be explained by the time windows around the six observed major FreeBSD releases. The paper consequently contributes to the software evolution research field with new methodological ideas, as well as with both positive and negative empirical results.
Modulation of Autophagy-Like Processes by Tumor Viruses

Autophagy is an intracellular degradation pathway for long-lived proteins and organelles. This process is activated above basal levels upon cell intrinsic or environmental stress and dysregulation of autophagy has been linked to various human diseases, including those caused by viral infection. Many viruses have evolved strategies to directly interfere with autophagy, presumably to facilitate their replication or to escape immune detection. However, in some cases, modulation of autophagy appears to be a consequence of the virus disturbing the cell’s metabolic signaling networks. Here, we summarize recent advances in research at the interface of autophagy and viral infection, paying special attention to strategies that human tumor viruses have evolved.
Structure of defective DNA molecules in Epstein-Barr virus preparations from P3HR-1 cells

Epstein-Barr virus (EBV), isolated from P3HR-1 cells, induces early antigen and viral capsid antigen upon infection of human B-lymphoblasts. The strong early antigen- and viral capsid antigen-inducing activity is only observed in P3HR-1 virus preparations harboring particles with defective genomes, suggesting that this biological activity is directly associated with the defective DNA population. After infection of EBV genome-carrying Raji or EBV genome-negative BJAB cells, defective genomes of P3HR-1 EBV DNA are replicated in excess, depending on the multiplicity of infecting EBV particles. Hybridization of the DNA from such infected cells with 32P-labeled EBV DNA after HindIII cleavage reveals six hypermolar fragments. Mapping of these fragments shows that they form one defective genome unit containing four nonadjacent regions (alpha, beta, gamma, and delta) of the nondefective P3HR-1 EBV DNA. Two of the segments (alpha and beta) contain ca. 17 and 13 megadaltons, respectively, from the terminal regions of the P3HR-1 genome, whereas the two smaller segments (gamma and delta) contain ca. 3.7 and 3.0 megadaltons, respectively, originating from the central portion of the genome. In the defective molecule, the regions gamma and delta are present in the opposite orientation compared with nondefective P3HR-1 EBV DNA. Tandem concatemers are formed by fusion of the alpha and beta regions. Our model suggests that tandem concatemers of three defective genome units can be packaged into virions in P3HR-1 cells.
An Elevation of Serum Ferritin Level Might Increase Clinical Risk for the Persistence of Patent Ductus Arteriosus, Sepsis and Bronchopulmonary Dysplasia in Erythropoietin-Treated Very-Low-Birth-Weight Infants

Background: The substantial risk of iron overload is not routinely monitored in most of the neonatal intensive care units (NICUs) in Japan; however, blood transfusion is an essential strategy for successfully treating preterm low-birth-weight infants. Objective: The aim of this study was to investigate the iron status and clinical features of infants with a birth weight of <1,500 g, i.e. very-low-birth-weight infants (VLBWIs). Methods: This prospective observational study enrolled 176 (82.6%) patients from a total of 213 VLBWIs admitted to our NICU from 2009 to 2014. Clinical information was collected including maternal records and infant morbidity and treatment. Management strategies including enteral iron supplementation, erythropoietin administration and blood transfusion were allowed according to the consensus in Japan. The hematological status was surveyed from birth to 12 postnatal weeks of age. The iron status was determined according to serum iron, unbound iron-binding capacity and serum ferritin. The definition of hyperferritinemia was set as a value of ≥500 ng/ml. Results: Twenty-four (13.6%) infants displayed hyperferritinemia. A multiple logistic analysis selected 3 associated factors of hyperferritinemia: surgical ligation for patent ductus arteriosus, sepsis and moderate or severe states of bronchopulmonary dysplasia. We also verified that the value of ferritin was significantly correlated with those of aspartate transaminase, creatine kinase and C-reactive protein according to a multilinear regression analysis. After excluding the ferritin data of these outliers, we did not observe any factors associated with hyperferritinemia. Conclusions: Hyperferritinemia might be associated with oxygen radical diseases and susceptibility to infection.
Effects of blend composition and dynamic vulcanization on the morphology and dynamic viscoelastic properties of PP/EPDM blends

Received 30 October 2007; accepted 30 January 2008DOI 10.1002/app.28158Published online 15 April 2008 in Wiley InterScience (www.interscience.wiley.com). ABSTRACT: The morphology and dynamic viscoelasticproperties of isotactic polypropylene (PP) blended withoil-free/oil-extended ethylene–propylene–diene (EPDM)rubbers were studied. Unvulcanized and dynamically vul-canized blends with the compositions PP/EPDM 5 50/50and 5 30/70 were investigated. The morphology wasobserved by phase contrasted atomic force microscopy.The dynamic viscoelastic properties were determined witha rheometer of plate–plate conﬁguration. It was shownthat the rheological behavior was strongly affected by boththe composition and the morphology of the blends. Signiﬁ-cant improvement in the ﬂowability of the dynamicallyvulcanized blends was observed when oil-extended EPDMwas used instead of the oil-free version. It was demon-strated that the rheological properties are mostly con-trolled by the elastomer phase at low frequencies, while inthe high-frequency range the inﬂuence of PP becomesdominant. The peculiarities in the rheological behavior ofthe thermoplastic elastomers (uncured blends, TPE) andthermoplastic dynamic vulcanizates (TPV, dynamicallycured blends) containing oil-extended EPDMs were tracedto a limited compatibility between the PP and EPDM com-ponents in the melt.
Atherosclerotic Carotid Vulnerable Plaque and Subsequent Stroke: A High-Resolution MRI Study

Background: High-resolution contrast-enhanced magnetic resonance imaging (CEMRI) has been proven to be an effective tool for the identification of carotid atherosclerotic vulnerable plaque, such as a large lipid core and thin fibrous cap. The aim of this study was to evaluate the relationship between carotid plaque characteristics and the types of stroke in patients who had carotid artery (CA) stenosis ≥50%. Methods: 102 consecutive subjects (mean age 67.2 ± 10.2 years; 73 males) who initially had ischemic stroke or asymptomatic CA stenosis from 50 to 100% diagnosed by ultrasound were included in this study. Carotid CEMRI, brain MRI and magnetic resonance angiography were performed to understand the infarct patterns and to exclude intracranial artery stenosis. The modified American Heart Association (AHA) plaque classification was used in our study. Results: Our study demonstrated that 45 patients had CA stroke, and 55 patients had lacunar and asymptomatic lesions. The majority of patients had AHA classification type IV–V and VI which presented as vulnerable plaques. Of 63 patients with mild to moderate stenosis (≤70%), 44 (69.8%) had type IV–V vulnerable plaques, which was significantly higher than those of patients with severe stenosis (>70%; p < 0.001). In CA stroke, the number of patients with a thin or ruptured fibrous cap was twice that of those with a thick and intact fibrous cap. Conclusions: CEMRI may have important applications in clinical risk evaluations in CA atherosclerosis. Physicians ought to recognize that different types of stroke should be identified by brain MRI detection before invasive therapies.
Incidence rates of stroke in the eighties: the end of the decline in stroke?

Has the decline in the incidence of stroke ended? If so, why? These questions are addressed in the May issue of Stroke in the study of Broderick et al, based on the trends in stroke incidence in Rochester, Minnesota, between 1950-1954 and 1980-1984. The incidence of stroke for men in that community declined until 1975-1979 and then increased in 1980-1984, while for women the incidence rates appeared to "bottom out" around 1970-1974 and increased in 1980-1984. The apparent increase between 1975 and 1979 occurred in every 10-year age group from 45 to older than 85 years. However, by 1980-1984, approximately half of the incident strokes occurred among individuals 75 years of age or older. The mortality and case-fatality rates following a stroke continued to decline, which is consistent with trends in stroke mortality in the United States and many other countries. The first question to be resolved is whether the trends to 1980-1984 are an artifact of caseascertainment, criteria of diagnosis, changes in the characteristics of the population at risk, or, possibly, errors in the measurement of the size of the population at risk. The cases were all collected in the same way, reviewed by the same nurse-abstractor, and had criteria of diagnoses that were consistent over time. It is extremely unlikely that between 1975-1979 and 1980-1984 there was a substantial change in the ascertainment of stroke cases within this community. It is possible that strokes diagnosed in the 1950-1954 period were missed, but if this were the case, the trends to 1975-1979 would not have shown the decline in the incidence rates. The selected increase in the use of CT scans in the 1970s and 1980s could have resulted in a greater ascertainment of strokes, but the authors wisely excluded strokes diagnosed only on the basis of CT scan or autopsy findings, without prior clinical evidence of stroke. They believe, however, that the use of CT scans may have increased physicians'
Optimal swim speeds for traversing velocity barriers: an analysis of volitional high-speed swimming behavior of migratory fishes

SUMMARY Migrating fish traversing velocity barriers are often forced to swim at speeds greater than their maximum sustained speed (Ums). Failure to select an appropriate swim speed under these conditions can prevent fish from successfully negotiating otherwise passable barriers. I propose a new model of a distance-maximizing strategy for fishes traversing velocity barriers, derived from the relationships between swim speed and fatigue time in both prolonged and sprint modes. The model predicts that fish will maximize traversed distance by swimming at a constant groundspeed against a range of flow velocities, and this groundspeed is equal to the negative inverse of the slope of the swim speed–fatigue time relationship for each mode. At a predictable flow velocity, they should switch from the optimal groundspeed for prolonged mode to that for sprint mode. Data from six migratory fish species (anadromous clupeids: American shad Alosa sapidissima, alewife A. pseudoharengus and blueback herring A. aestivalis; amphidromous: striped bass Morone saxatilis; and potomodromous species: walleye (previously known as Stizostedion vitrium) and white sucker Catostomus commersonii) were used to explore the ability of fish to approximate the predicted distance-maximizing behaviors, as well as the consequences of deviating from the optima. Fish volitionally sprinted up an open-channel flume against fixed flow velocities of 1.5–4.5 m s-1, providing data on swim speeds and fatigue times, as well as their groundspeeds. Only anadromous clupeids selected the appropriate distance-maximizing groundspeed at both prolonged and sprint modes. The other three species maintained groundspeeds appropriate to the prolonged mode, even when they should have switched to the sprint optima. Because of this, these species failed to maximize distance of ascent. The observed behavioral variability has important implications both for distributional limits and fishway design.
Fano Multiple-Symbol Differential Detectors for Differential Unitary Space–Time Modulation

We present a class of suboptimal multiple-symbol differential detectors (MSDDs) for differential unitary space-time (ST) codes in a time-selective Rayleigh flat-fading channel. These noncoherent detectors, termed Fano ST-MSDDs, employ the well-known Fano algorithm as their decoding engines. Their bit-error rate (BER) performance is excellent, as there is no irreducible error floor, even at very high fade rates. Compared with the sphere decoder, which is optimal, our best detector, termed an on-demand bi-Fano ST-MSDD, suffers only a 0.3 dB degradation in power efficiency. However, its computational complexity, as a function of the signal-to-noise ratio (SNR), is consistently lower than that of the sphere decoder and does not experience the exponential growth in complexity in the latter when the SNR decreases. It can thus be concluded that the Fano algorithm is a powerful detection strategy for differential ST codes in fading channels. Our main contribution is in making the modifications and improvements to the Fano algorithm that enables this realization. The innovations include the bi-Fano, edge-bi-Fano, and on-demand bi-Fano search strategies, as well as a new dynamic threshold adjustment scheme for avoiding unnecessary back-and-forth node evaluations during backtracking
Integrable lattices and their sublattices : From the discrete Moutard (discrete Cauchy-Riemann) 4-point equation to the self-adjoint 5-point scheme

We present the sublattice approach, a procedure to generate, from a given integrable lattice, a sublattice which inherits its integrability features. We consider, as illustrative example of this approach, the discrete Moutard 4-point equation and its sublattice, the self-adjoint 5-point scheme on the star of the square lattice, which are relevant in the theory of the integrable discrete geometries and in the theory of discrete holomorphic and harmonic functions (in this last context, the discrete Moutard equation is called discrete Cauchy-Riemann equation). Therefore an integrable, at one energy, discretization of elliptic two-dimensional operators is considered. We use the sublattice point of view to derive, from the Darboux transformations and superposition formulas of the discrete Moutard equation, the Darboux transformations and superposition formulas of the self-adjoint 5-point scheme. We also construct, from algebro-geometric solutions of the discrete Moutard equation, algebro-geometric solutions of.
How Does Consensus Scoring Work for Virtual Library Screening? An Idealized Computer Experiment

It has been reported recently that consensus scoring, which combines multiple scoring functions in binding affinity estimation, leads to higher hit-rates in virtual library screening studies. This method seems quite independent to the target receptor, the docking program, or even the scoring functions under investigation. Here we present an idealized computer experiment to explore how consensus scoring works. A hypothetical set of 5000 compounds is used to represent a chemical library under screening. The binding affinities of all its member compounds are assigned by mimicking a real situation. Based on the assumption that the error of a scoring function is a random number in a normal distribution, the predicted binding affinities were generated by adding such a random number to the "observed" binding affinities. The relationship between the hit-rates and the number of scoring functions employed in scoring was then investigated. The performance of several typical ranking strategies for a consensus scoring procedure was also explored. Our results demonstrate that consensus scoring outperforms any single scoring for a simple statistical reason: the mean value of repeated samplings tends to be closer to the true value. Our results also suggest that a moderate number of scoring functions, three or four, are sufficient for the purpose of consensus scoring. As for the ranking strategy, both the rank-by-number and the rank-by-rank strategy work more effectively than the rank-by-vote strategy.
Human Papillomavirus Genotype Distribution in Czech Women and Men with Diseases Etiologically Linked to HPV

Background The HPV prevalence and genotype distribution are important for the estimation of the impact of HPV-based cervical cancer screening and HPV vaccination on the incidence of diseases etiologically linked to HPVs. The HPV genotype distribution varies across different geographical regions. Therefore, we investigated the type-specific HPV prevalence in Czech women and men with anogenital diseases. Methods We analyzed 157 squamous cell carcinoma samples, 695 precancerous lesion samples and 64 cervical, vulvar and anal condylomata acuminate samples. HPV detection and typing were performed by PCR with GP5+/6+ primers, reverse line blot assay and sequencing. Results Thirty different HPV genotypes were detected in our study, HPV 16 being the most prevalent type both in precancerous lesions (45%) and squamous cell carcinomas (59%). In benign lesions, HPV 6 (72%) was the most common type. Altogether, 61% of carcinoma samples and 43% of precancerous lesion samples contained HPV 16 and/or 18. The presence of HPV types related to the vaccinal ones (HPV 31, 45, 33, 52, 58) were detected in 16% of carcinoma samples and 18% of precancerous lesion samples. HPV 16 and/or 18 were present in 76% of cervical cancer samples, 33% of CIN1, 43% CIN2 and 71% of CIN3 samples. HPV types 6 and/or 11 were detected in 84% samples of condylomata acuminate samples. Conclusions The prevalence of vaccinal and related HPV types in patients with HPV-associated diseases in the Czech Republic is very high. We may assume that the implementation of routine vaccination against HPV would greatly reduce the burden of HPV-associated diseases in the Czech Republic.
Molecular cloning of ovine connexin44 and temporal expression of gap junction proteins in a lens cell culture.

PURPOSE The lens plasma membranes of several mammalian species have been shown to contain three different connexin proteins. The goal of this study was to clone the sheep homologue of rat connexin46 identified as sheep connexin44 and to determine the temporal changes in the expression of the three sheep connexin proteins in a lens primary cell culture system. METHODS A sheep genomic library was screened with a rat lens connexin46 cDNA probe. Lens junctional protein and mRNA levels were determined in a sheep primary cell culture system by Western and Northern blot analyses, respectively. RESULTS Sheep connexin44, the homologue of rat lens connexin46, was identified as a single-copy gene with a predicted molecular weight of 43,989 Daltons that is contained within a single exon. Northern blot analysis detected a 2.2-kb connexin44 transcript in RNA isolated from lens but not that isolated from heart, kidney, liver, or lung. During the in vitro differentiation of lens epithelial cells from 5 to 20 days in culture, connexin43 mRNA levels declined approximately 75%, whereas connexin49 RNA levels increased approximately 24 fold. The 40% decrease in the level of connexin43 protein and the 21-fold increase in the level of connexin49 protein did not directly correlate with the changes in mRNA levels encoding these proteins during this same period. Although detectable, the amount of connexin44 mRNA and protein remained low throughout the 20-day period during which lens cells were grown in culture. Neither mRNA nor protein encoding MP20 or MP26 transcripts could be detected in even the oldest 20-day lens cultures. CONCLUSIONS Steady state mRNA levels of sheep connexin43 and connexin49 do not appear to be the only factor regulating the expression of these genes during in vitro differentiation of lens cells in culture. Although a decreased level of expression of connexin43 was accompanied by an increased level of expression of connexin49 over the 20-day period in culture, connexin44 mRNA and protein levels remained low throughout this 20-day period. Overall, these results suggest that these junctional proteins have a unique temporal pattern of expression during differentiation, and this lens primary cell culture system provides a valuable tool to better understand this process.
Lipid profile of healthy adult Nigerians in Port Harcourt, Nigeria.

BACKGROUND Hyperlipidaemia is a major cardiovascular risk factor for coronary artery disease, atherosclerosis, hypertension and stroke. It is thought that serum cholesterol levels are low in Nigerians as shown by results of a population survey done over twenty years ago. In addition the last national non communicable disease survey recorded a low prevalence of Hyperlipidaemia (4.0%) in Nigeria. With increasing urbanisation and socioeconomic improvement, changing population dynamics is expected to influence disease pattern and noncommunicable diseases are expected to rise. Thus there is a need to screen healthy adults for their lipid pattern in Port Harcourt a city with high population dynamics where such studies have not been previously reported. METHOD A prospective descriptive population survey was carried out among healthy adults residing in Port Harcourt. A total of ninety two adults were screened after obtaining informed consent. Weight, height, blood pressure, fasting blood sugar and fasting lipid profile were measured. Results were analysed using simple statistical methods. RESULTS A total of ninety two subjects were recruited into the study. Fourty seven (51.1%) of the subjects were males while fourty five (48.9%) were females. The age range of subjects was 24-59 years with mean of 38.84 +/- 8.36 years. The mean BMI was 28.76 +/- 5.91 Kg/m2. There was no significant statistical difference between the mean BMI for males and females. The mean fasting blood sugar, mean total cholesterol and mean LDL cholesterol were 4.45 +/- 0.89 mmol/L, 4.76 +/- 1.06 mmol/L and 3.65 +/- 0.89 mmol/L. The mean total triglyceride was 1.02 +/- 0.30 mmol/L while the mean HDL was 0.90 +/- 0.25 mmol/L. There was an increase in total cholesterol with increasing age and an increase in total cholesterol and LDL cholesterol with increasing social class. Subjects with total cholesterol above 6.5 mmol/L constituted 31.52% of study subjects. Subjects with BMI between 25-29 Kg/m2 made up 43.48% of subjects while 33.69% of subjects had BMI above 30 Kg/m2. CONCLUSION A high mean total and LDL cholesterol values were observed among healthy adults in Port Harcourt. The prevalence of obesity was also found to be high. There is a need for public health action to address these findings especially as high serum cholesterol levels have a direct correlation with coronary artery disease. Further large scale urban survey of non communicable diseases in the country is therefore necessary at this time.