Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of estradiol on transcriptional profiles in atherosclerotic iliac arteries in ovariectomized cynomolgus macaques

ObjectiveThis study aimed to assess the in vivo effects of estradiol treatment on arterial gene expression in atherosclerotic postmenopausal female monkeys. MethodsEight ovariectomized cynomolgus monkeys were fed atherogenic diets for 6.5 years. The left iliac artery was biopsied before randomization to the estradiol group (human equivalent dose of 1 mg/d, n = 4) or the vehicle group (n = 4) for 8 months. The right iliac artery was obtained at necropsy. Transcriptional profiles in pretreatment versus posttreatment iliac arteries were compared to assess the responses of atherosclerotic arteries to estradiol. ResultsIliac artery plaque size did not differ between the estradiol group and the placebo group at baseline or during the treatment period. Nevertheless, estradiol treatment was associated with increased expression of 106 genes and decreased expression of 26 genes in the iliac arteries. Estradiol treatment increased the expression of extracellular matrix genes, including the &agr;1 chain of type I collagen, the &agr;2 chain of type VI collagen, and fibulin 2, suggestive of an increase in the proportion or phenotype of smooth muscles or fibroblasts in lesions. Also increased were components of the insulin-like growth factor pathway (insulin-like growth factor 1, insulin-like growth factor binding protein 4, and insulin-like growth factor binding protein 5) and the Wnt signaling pathway (secreted frizzled-related protein 2, secreted frizzled-related protein 4, low-density lipoprotein receptor–related protein 6, and Wnt1-inducible signaling pathway protein 2). ConclusionsEstradiol treatment of monkeys with established atherosclerosis affected iliac artery gene expression, suggesting changes in the cellular composition of lesions. Moreover, it is probable that the presence of atherosclerotic plaque affected the gene expression responses of arteries to estrogen.
Microstructure and mechanical properties of biomedical alloys produced by Rapid Manufacturing techniques

Rapid Manufacturing (RM) technologies as Electron Beam Melting (EBM) and Selective Laser Melting (SLM) are able to produce fully dense parts from pre-alloyed powders in a layer-wise way. Moreover, they are able to create tailored surfaces with interconnected porosity. Applied to biomedical prostheses, such porosity can favour cell adhesion and osteointegration. The most important intrinsic characteristic of RM techniques is the large undercooling the parts undergo during the process. This undercooling results in peculiar, very fine, metastable microstructures, associated to peculiar mechanical behaviour. Metastable microstructures can change on post-melting operations, making the materials match the standard requirements and gain interesting properties.
Experimental validation of the usability of Wi-Fi over redundant paths for streaming phasor data

Applications performing streaming of phasor-measurement data require low latency and losses from the communication network. Traditionally, such requirements are realized through wired infrastructure. Recently, wireless infrastructure has gained attention due to its low-cost and ease of deployment, but its poor quality-of-service is a strong deterrent for use in mission-critical applications. Recent studies have used measurements to explore the use of packet replication over redundant Wi-Fi paths, for obtaining the desired loss performance without hampering the end-to-end latency. However, these studies are done in a controlled, laboratory environment and do not reflect the real, in-field performance. In this paper, we perform extensive measurements using two co-located directional Wi-Fi links in a real-life setting, to experimentally validate the use of packet replication over Wi-Fi for streaming phasor data. In the setting that we evaluated, we find that the two channels are not fail-independent but the performance achieved with replication is very close to what it would be if they were to be independent. From the loss and latency statistics after replication, we conclude that replicating the phasor data over redundant Wi-Fi paths is a viable option for achieving the desired quality-of-service.
Managing Maintenance Knowledge in the Context of Large Engineering Projects: Theory and Case Study

Tenix Defence, one of Australia's largest defence contractors, depends on winning bids and managing contracts for long-lifecycle engineering projects. The ability to capture, manage and deliver project knowledge in explicit formats is crucial to its success. Tenix is moving from a paradigm of traditional paper documents to electronically managing and automating structured knowledge artefacts in a knowledge management framework based on Karl Popper's (1973) three worlds of knowledge. The new technology captures the authors' implicit knowledge that was inevitably lost when working with paper documents and also moves aspects of personal cognition from the subjective and personal World 2 into the objective, virtual and persistent World 3.
Evaluation of injuries caused by anthropic action in snakes from Brazil

Abstract Human behavior toward wild animals is defined by cultural influences and often is affected by lack of knowledge, mainly in situations of confrontation. The present study was conducted between 2008 and 2013, involving analysis of snakes that had suffered injuries belonging to the reptile collections of Centro Universitario de Lavras and Universidade Federal de Juiz de Fora. The injuries were classified according to location on the body. Among the 449 specimens analyzed, 245 specimens showed injury to some part of the body. The nonvenomous snakes were the most representative and had a higher rate of injury (66.3%) than the venomous ones (18.2%). The body region where the greatest percentage of injuries was recorded was the anterior (39.6%), followed by the middle (36.5%) and posterior (8.4%). We believe this fact may have resulted due the lack of knowledge on how to differentiate species. Studies of the relationship between schooling level and contact with environmental education activities demonstrate reduction of attacks on these animals. This fact indicates that the preservation of many species is related to awareness and education of the population.Keywords: conservation of natural resources, environmental education, injuries, snakes.
Concentration-dependent effects of a selective estrogen receptor modulator raloxifene on proliferation and apoptosis in human uterine leiomyoma cells cultured in vitro.

BACKGROUND This study was conducted to elucidate the effects of raloxifene on proliferation and apoptosis in cultured human uterine leiomyoma cells. METHODS The monolayer cultures were treated with graded concentrations (10(-9), 10(-8) and 10(-7) M) of raloxifene and 10(-7) M 17beta-estradiol (E(2)). Cell viability, percentage of proliferating cell nuclear antigen (PCNA)-positive cells, percentage of terminal deoxynucleotidyl transferase-mediated 2'-deoxyuridine 5'-triphosphate nick-end labelling (TUNEL)-positive cells and the expression of PCNA and Bcl-2 proteins were assessed by 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxylphenyl)-2-(4-sulphophenyl)-2H-tetraz olium assay, immunocytochemistry, TUNEL assay and western blot analysis, respectively. RESULTS Compared with untreated cultures, the number of viable cultured cells, percentage of PCNA-positive cells and PCNA protein expression were significantly decreased by treatment with 10(-9) M raloxifene, but increased by treatment with either 10(-8) M or 10(-7) M raloxifene. In contrast, the percentage of TUNEL-positive cells was significantly increased and Bcl-2 protein expression was significantly decreased by treatment with 10(-9) M raloxifene, whereas they were not affected by treatment with either 10(-8) or 10(-7) M raloxifene. CONCLUSIONS In cultured leiomyoma cells, low concentration (10(-9) M) of raloxifene may inhibit the growth of leiomyoma cells, whereas high concentrations (10(-8) M, 10(-7) M) of raloxifene may promote their growth.
The Impact of Classifier Configuration and Classifier Combination on Bug Localization

Bug localization is the task of determining which source code entities are relevant to a bug report. Manual bug localization is labor intensive since developers must consider thousands of source code entities. Current research builds bug localization classifiers, based on information retrieval models, to locate entities that are textually similar to the bug report. Current research, however, does not consider the effect of classifier configuration, i.e., all the parameter values that specify the behavior of a classifier. As such, the effect of each parameter or which parameter values lead to the best performance is unknown. In this paper, we empirically investigate the effectiveness of a large space of classifier configurations, 3,172 in total. Further, we introduce a framework for combining the results of multiple classifier configurations since classifier combination has shown promise in other domains. Through a detailed case study on over 8,000 bug reports from three large-scale projects, we make two main contributions. First, we show that the parameters of a classifier have a significant impact on its performance. Second, we show that combining multiple classifiers--whether those classifiers are hand-picked or randomly chosen relative to intelligently defined subspaces of classifiers--improves the performance of even the best individual classifiers.
Bayesian dynamic modeling for monthly Indian summer monsoon rainfall using El Niño–Southern Oscillation (ENSO) and Equatorial Indian Ocean Oscillation (EQUINOO)

There is an established evidence of climatic teleconnection between El Nino–Southern Oscillation (ENSO) and Indian summer monsoon rainfall (ISMR) during June through September. Against the long-recognized negative correlation between ISMR and ENSO, unusual experiences of some recent years motivate the search for some other causal climatic variable, influencing the rainfall over the Indian subcontinent. Influence of recently identified Equatorial Indian Ocean Oscillation (EQUINOO, atmospheric part of Indian Ocean Dipole mode) is being investigated in this regard. However, the dynamic nature of cause-effect relationship burdens a robust and consistent prediction. In this study, (1) a Bayesian dynamic linear model (BDLM) is proposed to capture the dynamic relationship between large-scale circulation indices and monthly variation of ISMR and (2) EQUINOO is used along with ENSO information to establish their concurrent effect on monthly variation of ISMR. This large-scale circulation information is used in the form of corresponding indices as exogenous input to BDLM, to predict the monthly ISMR. It is shown that the Indian monthly rainfall can be modeled in a better way using these two climatic variables concurrently (correlation coefficient between observed and predicted rainfall is 0.82), especially in those years when negative correlation between ENSO and ISMR is not well reflected (i.e., 1997, 2002, etc.). Apart from the efficacy of capturing the dynamic relationship by BDLM, this study further establishes that monthly variation of ISMR is influenced by the concurrent effects of ENSO and EQUINOO.
Growth of a nation part II: impact of recipient obesity on whole‐organ pancreas transplantation

Fridell JA, Mangus RS, Taber TE, Goble ML, Milgrom ML, Good J, Vetor R, Powelson JA. Growth of a nation part II: impact of recipient obesity on whole‐organ pancreas transplantation. Clin Transplant 2011: 25: E366–E374. © 2011 John Wiley & Sons A/S.
The integration of HPV-18 DNA in cervical carcinoma.

AIMS: Little information is available on the patterns of integration into the host chromosomal DNA of cervical carcinomas of human papillomavirus type 18 (HPV-18) DNA, which is associated with up to 20% of these carcinomas. Because integration of the viral genome may be extremely important in the pathogenesis of cervical carcinoma, the aim of this study was to investigate which regions of HPV-18 DNA are integrated into the cellular DNA of cervical carcinomas. METHODS: Southern analysis using four subgenomic probes covering the entire HPV-18 genome was used to map viral DNA integrated within cellular DNA. The polymerase chain reaction (PCR) was used to confirm the presence of specific regions of the viral genome. RESULTS: In all 11 carcinomas there was a single major HPV-18 DNA integrant, retaining approximately 4000 bp of HPV-18 DNA, indicating that approximately half of the virus genome had been lost upon integration. Southern analysis suggested strongly that the viral breakpoint was within the E1/E2 gene boundary, with concomitant loss of part or all of the E2 ORF (open reading frame), all of the E4, E5, and L2 ORFs and part of the L1 ORF. These data were supported by the PCR results, which confirmed that the region of integrated HPV-18 DNA from nucleotides 6558 to 162 was present in all the carcinoma samples studied. Assuming that no genomic rearrangements, deletions, or insertions had occurred, 4131 bp of integrated HPV-18 DNA could be accounted for in eight cervical carcinoma samples. The results of Southern analysis also suggested that integration of HPV-18 DNA may have occurred at a specific host chromosomal site. CONCLUSIONS: Broadly, the viral sequences retained upon HPV-18 integration resemble those found when HPV-16 is integrated. However, it appears that the HPV-18 E2 region is more consistently deleted.
Hepatitis C Recurrence after Orthotopic Liver Transplantation: Mechanisms and Management

Chronic Hepatitis C (HCV) infection is the leading indication for orthotopic liver transplantation and recurrence is nearly universal. Chronic HCV infection is frequently established through evasion of the innate immune system. Priming of adaptive immune responses modulate the severity and rate of fibrosis progression. Those with demonstrable viremia entering the transplant period uniformly suffer recurrence post-transplant. Progression to cirrhosis is accelerated post-transplant secondary to systemic immunosuppression. In addition, a number of factors, including donor, host, and viral characteristics, influence severity and rate of fibrosis progression. Interferon-based therapy, the previous standard of care, in those with advanced cirrhosis or post-transplant has been limited by a number of issues. These include a relative lack of efficacy and poor tolerability with higher incidence of infection and anemia. Recently, approval of direct acting antivirals have ushered in a new era in HCV therapeutics and have applicability in these special populations. Their use immediately prior to or post-transplant is expected to improve both morbidity and mortality.
Pharmacogenomic Research in South Africa: Lessons Learned and Future Opportunities in the Rainbow Nation

South Africa, like many other developing countries, stands to benefit from novel diagnostics and drugs developed by pharmacogenomics guidance due to high prevalence of disease burden in the region. This includes both communicable (e.g., HIV/AIDS and tuberculosis) and non-communicable (e.g., diabetes and cardiovascular) diseases. For example, although only 0.7% of the world’s population lives in South Africa, the country carries 17% of the global HIV/AIDS burden and 5% of the global tuberculosis burden. Nobel Peace Prize Laureate Archbishop Emeritus Desmond Tutu has coined the term Rainbow Nation, referring to a land of wealth in its many diverse peoples and cultures. It is now timely and necessary to reflect on how best to approach new genomics biotechnologies in a manner that carefully considers the public health needs and extant disease burden in the region. The aim of this paper is to document and review the advances in pharmacogenomics in South Africa and importantly, to evaluate the direction that future research should take. Previous research has shown that the populations in South Africa exhibit unique allele frequencies and novel genetic variation in pharmacogenetically relevant genes, often differing from other African and global populations. The high level of genetic diversity, low linkage disequilibrium and the presence of rare variants in these populations question the feasibility of the use of current commercially available genotyping platforms, and may partially account for genotype-phenotype discordance observed in past studies. However, the employment of high throughput technologies for genomic research, within the context of large clinical trials, combined with interdisciplinary studies and appropriate regulatory guidelines, should aid in acceleration of pharmacogenomic discoveries in high priority therapeutic areas in South Africa. Finally, we suggest that projects such as the H3Africa Initiative, the SAHGP and PGENI should play an integral role in the coordination of genomic research in South Africa, but also other African countries, by providing infrastructure and capital to local researchers, as well as providing aid in addressing the computational and statistical bottlenecks encountered at present.
The split Levinson algorithm

The classical Levinson algorithm for computing the predictor polynomial relative to a real positive definite Toeplitz matrix is shown to be redundant in complexity. It can be broken down into two simpler algorithms, either of which needs only to be processed. This result can be interpreted in the framework of the theory of orthogonal polynomials on the real line as follows: the symmetric and antisymmetric parts of the predictors relative to the sequence of Toeplitz matrices constitute two families of polynomials orthogonal on the interval [- 1,1] with respect to some even weight functions. It turns out that the recurrence relations for these orthogonal polynomials can be used efficiently to compute the desired predictor. The resulting "split Levinson algorithm" requires roughly one-half the number of multiplications and the same number of additions as the classical Levinson algorithm. A simple derivation of Cybenko's method for computing the Pisarenko frequencies is obtained from the recurrence relations underlying the split Levinson algorithm.
Multimodal alignment of scholarly documents and their presentations

We present a multimodal system for aligning scholarly docu- ments to corresponding presentations in a fine-grained man- ner (i.e., per presentation slide and per paper section). Our method improves upon a state-of-the-art baseline that em- ploys only textual similarity. Based on an analysis of base- line errors, we propose a three-pronged alignment system that combines textual, image, and ordering information to establish alignment. Our results show a statistically sig- nificant improvement of 25%, confirming the importance of visual content in improving alignment accuracy.
Deterministic Annealing for Multiple-Instance Learning

In this paper we demonstrate how deterministic annealing can be applied to different SVM formulations of the multiple-instance learning (MIL) problem. Our results show that we find better local minima compared to the heuristic methods those problems are usually solved with. However this does not always translate into a better test error suggesting an inadequacy of the objective function. Based on this finding we propose a new objective function which together with the deterministic annealing algorithm finds better local minima and achieves better performance on a set of benchmark datasets. Furthermore the results also show how the structure of MIL datasets influence the performance of MIL algorithms and we discuss how future benchmark datasets for the MIL problem should be designed.
May–July precipitation reconstruction from oak tree‐rings for Bohemia (Czech Republic) since AD 1040

This contribution presents a near‐millennium‐long reconstruction of May–July (MJJ) precipitation for Bohemia, the western part of the recent Czech Republic. A well‐replicated chronology of oak (Quercus spp.) tree‐ring width (TRW) measurements covering the 1040–2013 period was employed as a high‐resolution hydroclimatic proxy. Standardized TRW indices were calibrated to selected grid points from the CRU precipitation database, covering the geographical distribution of the oak data used. The oak TRW chronology explains 34% of MJJ precipitation variability during the 1901–1980 period used for calibration. Although the relationship between oak TRW and target data was relatively stable for this period, the coherence drops significantly beyond it. However, two independent verification periods reveal highly positive reduction of error (RE) and coefficient of efficiency (CE) statistics. Less formal verification based on direct comparison with 14 European proxy‐based reconstructions further suggests relatively good agreement in the temporal occurrence of above/below mean late spring–early summer precipitation totals, especially in the 16th–17th centuries. The new MJJ precipitation reconstruction is restricted to inter‐annual and inter‐decadal variability, which is in line with our understanding of natural precipitation variability. Reconstruction reveals two long periods of low precipitation variability, in the 13th–14th centuries and 1630s–1850s. It also demonstrates that precipitation anomalies of larger amplitude and longer duration occurred in the earlier part of the last millennium than those found in the instrumental period. Negative trends in soil moisture content and gradual changes in annual precipitation distribution leading to higher extremity of precipitation regime may be responsible for the lower sensitivity of oaks to precipitation after the 1980s. The new reconstruction does not indicate any exceptional recent decline in MJJ precipitation.
TV Tip‐Over Morbidity and Mortality in Children *

Abstract: Twenty‐eight non‐fatal cases of TV related injuries were noted in San Diego in the 2 years prior to September 2008. We reviewed the scene, witness reports, past history, and autopsy findings from three fatal cases and distinguished them from abusive head trauma. The recent literature was also reviewed. Our fatal cases resulted from TVs falling on small children and causing severe head injury. The literature review showed increasing injuries and deaths relating to TV tip‐over, TV stands and dressers. Most of the fatalities were head injuries in small children. The reporting methods may not be complete or accurate. Some authors in the literature review suggested preventive measures so as to decrease these injuries. Forensic scientists should become familiar with these injuries and measures so that they may communicate effectively with their communities.
word2vec or JoBimText?: A Comparison for Lexical Expansion of Hindi Words

Exploration of distributional semantics for NLP tasks in Indian languages has been scarce. This work carries out a comparative analysis of two recent and high performing distributional semantics techniques namely word2vec and JoBimText. The task of lexical expansion of words in Hindi is considered for the analysis. A manual similarity assessment of the lexical expansions of words is employed for evaluation of the techniques. It can be observed that word2vec framework performs better than the JoBimText for various corpus sizes. Analysis of the results also presents insights on performance of the systems on various word types.