Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamics of molecular fluctuations in gene regulatory networks

The components that are central to cellular processing are proteins, whose production is regulated by other proteins known as transcription factors. Proteins are products of genes that regulate the expression of one another, thereby forming large gene regulatory networks that perform specific cellular functions. The complex connectivity between genes of a network could result in various behaviours that are interesting. The assumption then is that tracking subnetwork behaviour helps understand the characteristics of the larger networks they are embedded in. For example, the structure of a subnetwork could say a lot about its biological role. Theoretical models of such systems and their deterministic dynamical properties have been the focus of study in the past. However, the dynamics of transcriptional control involves small numbers of molecules and result in significant fluctuations in protein and mRNA concentrations. Hence the recent shift in focus has been towards stochastic modelling approaches. Experimentally, the issues regarding average molecular numbers over a cell population draw our attention towards single-cell techniques where these fluctuations in the numbers are captured. On understanding the fluctuation properties of the smaller networks, one could study or design a combination of these networks leading to more complex regulatory networks. The objective of this thesis is to characterize small subnetworks of genes, based on the properties of their internal fluctuations. The correlations between these intrinsic fluctuations then offer, via the fluctuation dissipation relation, the possibility of capturing the system’s response to external perturbations, and hence the nature of the regulatory activity itself. Therefore we do a stochastic analysis and derive time-dependent noise correlation functions between molecular species of the networks, and using these functions we study simple networks by varying three of its factors. One is the type of regulatory activity that is present between two genes or proteins, whose correlations we are interested in. We show that the regulatory mechanism of activation, repression either by monomers or dimers, produces different correlations. We also study the dependence of the correlations on the values of the rate constants for the ingredient processes. We demonstrate the influence of various rate constants on the protein correlations. Finally, we analyze regulatory networks of different motifs such as cascades and feedforward loops and explore the extent to which fluctuation correlations report on the network structure. The distinct correlated fluctuations could then possibly be used as signatures for identifying the regulatory mechanism present between two genes of a network. To that end, in this thesis we present analytical and numerical results on features such as the magnitudes and time delays in dynamic correlations between proteins within smaller networks, and the dependence of these features on rate constants and regulatory and network mechanisms.
Multicenter comparative multimodality surveillance of women at genetic-familial high risk for breast cancer (HIBCRIT study): interim results.

PURPOSE To prospectively compare clinical breast examination (CBE), mammography, ultrasonography (US), and contrast material-enhanced magnetic resonance (MR) imaging for screening women at genetic-familial high risk for breast cancer and report interim results, with pathologic findings as standard. MATERIALS AND METHODS Institutional review board of each center approved the research; informed written consent was obtained. CBE, mammography, US, and MR imaging were performed for yearly screening of BRCA1 or BRCA2 mutation carriers, first-degree relatives of BRCA1 or BRCA2 mutation carriers, or women enrolled because of a strong family history of breast or ovarian cancer (three or more events in first- or second-degree relatives in either maternal or paternal line; these included breast cancer in women younger than 60 years, ovarian cancer at any age, and male breast cancer at any age). RESULTS Two hundred seventy-eight women (mean age, 46 years +/- 12 [standard deviation]) were enrolled. Breast cancer was found in 11 of 278 women at first round and seven of 99 at second round (14 invasive, four intraductal; eight were <or=10 mm in diameter). Detection rate per year was 4.8% (18 of 377) overall; 4.3% (11 of 258) in BRCA1 or BRCA2 mutation carriers and first-degree relatives of BRCA1 or BRCA2 mutation carriers versus 5.9% (seven of 119) in women enrolled because of strong family history; and 5.3% (nine of 169) in women with previous personal breast and/or ovarian cancer versus 4.3% (nine of 208) in those without. In six (33%) of 18 patients, cancer was detected only with MR imaging. Sensitivity was as follows: CBE, 50% (95% confidence interval [CI]: 29%, 71%); mammography, 59% (95% CI: 36%, 78%); US, 65% (95% CI: 41%, 83%); and MR imaging, 94% (95% CI: 82%, 99%). Positive predictive value was as follows: CBE, 82% (95% CI: 52%, 95%); mammography, 77% (95% CI: 50%, 92%); US, 65% (95% CI: 41%, 83%); and MR imaging, 63% (95% CI: 43%, 79%). CONCLUSION Addition of MR imaging to the screening regimen for high-risk women may enable detection of otherwise unsuspected breast cancers.
Endogenous Gibbon Ape Leukemia Virus Identified in a Rodent (Melomys burtoni subsp.) from Wallacea (Indonesia)

ABSTRACT Gibbon ape leukemia virus (GALV) and koala retrovirus (KoRV) most likely originated from a cross-species transmission of an ancestral retrovirus into koalas and gibbons via one or more intermediate as-yet-unknown hosts. A virus highly similar to GALV has been identified in an Australian native rodent (Melomys burtoni) after extensive screening of Australian wildlife. GALV-like viruses have also been discovered in several Southeast Asian species, although screening has not been extensive and viruses discovered to date are only distantly related to GALV. We therefore screened 26 Southeast Asian rodent species for KoRV- and GALV-like sequences, using hybridization capture and high-throughput sequencing, in the attempt to identify potential GALV and KoRV hosts. Only the individuals belonging to a newly discovered subspecies of Melomys burtoni from Indonesia were positive, yielding an endogenous provirus very closely related to a strain of GALV. The sequence of the critical receptor domain for GALV infection in the Indonesian M. burtoni subsp. was consistent with the susceptibility of the species to GALV infection. The second record of a GALV in M. burtoni provides further evidence that M. burtoni, and potentially other lineages within the widespread subfamily Murinae, may play a role in the spread of GALV-like viruses. The discovery of a GALV in the most western part of the Australo-Papuan distribution of M. burtoni, specifically in a transitional zone between Asia and Australia (Wallacea), may be relevant to the cross-species transmission to gibbons in Southeast Asia and broadens the known distribution of GALVs in wild rodents. IMPORTANCE Gibbon ape leukemia virus (GALV) and the koala retrovirus (KoRV) are very closely related, yet their hosts neither are closely related nor overlap geographically. Direct cross-species infection between koalas and gibbons is unlikely. Therefore, GALV and KoRV may have arisen via a cross-species transfer from an intermediate host whose range overlaps those of both gibbons and koalas. Using hybridization capture and high-throughput sequencing, we have screened a wide range of rodent candidate hosts from Southeast Asia for KoRV- and GALV-like sequences. Only a Melomys burtoni subspecies from Wallacea (Indonesia) was positive for GALV. We report the genome sequence of this newly identified GALV, the critical domain for infection of its potential cellular receptor, and its phylogenetic relationships with the other previously characterized GALVs. We hypothesize that Melomys burtoni, and potentially related lineages with an Australo-Papuan distribution, may have played a key role in cross-species transmission to other taxa.
The combination of cognitive testing and an informant questionnaire in screening for dementia.

AIM A cognitive test and an informant report questionnaire were used together to investigate whether their combined use could improve the accuracy of detecting dementia in a memory clinic, compared with either test used alone. METHOD The subjects were 323 patients assessed at a memory clinic. The Mini-Mental State Examination and the short form of the Informant Questionnaire on Cognitive Decline in the Elderly were used. A method of combining the test scores developed by Mackinnon and Mulligan [Am J Psychiatry 1998; 155: 1529-35] was used. Dementia was diagnosed according to Diagnostic and Statistical Manual of Mental Disorders, Third Edition-Revised criteria. RESULTS Logistic regression analysis showed that the combination of the Mini-Mental State Examination and the Informant Questionnaire on Cognitive Decline in the Elderly produced a slightly more accurate prediction of dementia caseness than either test used alone. Using receiver operating characteristic analysis the performance of the combination of the tests according to a weighted sum rule was compared with the performance of either test used alone. This way of combining the tests resulted in a more accurate screening for dementia than when the Informant Questionnaire on Cognitive Decline in the Elderly was used alone. The area under the receiver operating characteristic curve for the Mini-Mental State Examination combined with the Informant Questionnaire on Cognitive Decline in the Elderly was 0.89 compared with 0.82 for the Informant Questionnaire on Cognitive Decline in the Elderly alone (chi-square = 10.63; P = 0.0011). However, there was no improvement in screening performance when the combination of Mini-Mental State Examination and Informant Questionnaire on Cognitive Decline in the Elderly was compared with the Mini-Mental State Examination used alone (area under the receiver operating characteristic curve = 0.89 versus 0.86; chi-square = 3.54; P = 0.060). CONCLUSION The combination of cognitive testing and an informant report according to a weighted sum rule in this population did not result in any advantage over the use of the Mini-Mental State Examination alone. The mixed results of this study contrast with those of Mackinnon and Mulligan.
Improved sparse representation based super-resolution

In this paper, super-resolution image is obtained from a single low-resolution image using dictionary learning approach. The original image is blurred and downsampled to the low-resolution image, and has to find the value which is lost during downsampling and trained with patches. Each patches of low-resolution image use that value of their respective high-resolution image during training of dictionary. The Hilbert phase congruency which provides more features and good edges and applied to each patches. Then, LR and HR patches of the dictionary are used to generate the high-resolution image patch. In our approach, which results in good quality HR image and having better PSNR values than the other similar SR methods.
Development and demographic parameters of the carob moth Apomyelois ceratoniae on four diet regimes

The carob moth, Apomyelois ceratoniae (Zeller) (Lepidoptera Pyralidae), is a serious pest of pomegranate in Iran and a well known pest of many fruits from a wide range of plant families as well as dried fruits during storage. Development and demographic parameters of A. ceratoniae were studied in a growth chamber at temperature of 30 ± 1 °C, relative humidity of 75 ± 5% and a photoperiod of 16:8 (L:D) on fruits of pomegranate, pistachio, fig, and date. The results indicated that mean generation times were 42.38 ± 0.47, 45.24 ± 0.42, 57.83 ± 1.19 and, 89.55 ± 1.48 days on pomegranate, pistachio, fig and, date, respectively. The gross fecundity rate on pistachio was higher than those on three other diets. The net reproductive rate (Ro) was calculated to be lowest on date (3.64 ± 0.59) and highest on pistachio (45.74 ± 4.17). The net reproductive rates on four diets differed significantly. The highest and lowest amounts of the intrinsic rate of increase (rm) were observed on pomegranate (0.107 ± 0.013) and date (0.018 ± 0.002), respectively. The rm values were significantly different among four diets. The highest estimated doubling time was 37.46 ± 5.82 days on date. Our findings showed that the reproduction and population growth parameters of the carob moth on fruits of pomegranate and pistachio were higher than those obtained on fig and date.
Adjunctive nutraceuticals with standard pharmacotherapies in bipolar disorder: a systematic review of clinical trials

Sarris J, Mischoulon D, Schweitzer I. Adjunctive nutraceuticals with standard pharmacotherapies in bipolar disorder: a systematic review of clinical trials. Bipolar Disord 2011: 13: 454–465. © 2011 The Authors. Journal compilation © 2011 John Wiley & Sons A/S.
Analysis of the Effect of DNA Purification on Detection of Human Papillomavirus in Oral Rinse Samples by PCR

ABSTRACT Human papillomavirus (HPV) has recently been associated with oral cancers. To prepare for a study of the natural history of oral HPV infection, the effect of the DNA purification method on HPV genomic DNA detection in Scope mouthwash oral rinse samples and the reproducibility of HPV detection in rinse samples collected 7 days apart were investigated. The study was conducted with a population at high risk for oral HPV infection: human immunodeficiency virus-infected men with CD4-cell counts <200. Five DNA purification methods were compared among equal aliquots of oral rinse samples collected from a subset of individuals. The purification methods included (i) proteinase K digestion (PKD) and heat inactivation; (ii) PKD and ethanol precipitation (EP); (iii) PKD, phenol-chloroform extraction, and EP; (iv) use of the Puregene DNA purification kit; and (v) use of the QIAamp DNA Blood Midi kit. HPV was detected by PCR amplification with PGMY09 and PGMY11 L1 primer pools and by use of a Roche linear array. Puregene-purified samples had higher human DNA yields and purities, and Puregene purification detected the greatest number of HPV-positive subjects and total HPV infections in comparison to the numbers detected by all other methods. The total number of HPV infections and HPV prevalence estimates were also higher for Puregene-processed oral rinse samples when a fixed volume (10 μl) rather than a fixed cell number (∼50,000 cells) was used for PCR amplification. A good concordance was observed for oral HPV infection status (agreement, 80%; kappa value, = 0.60) and type-specific infection (agreement, 98%; kappa value, 0.57) in matched oral rinse samples. The method of DNA purification significantly affects the detection of HPV genomic DNA from oral rinse samples and may result in exposure misclassification that could contribute to the inconsistent associations reported in the literature.
Analysis of oral skills development in the most used English language textbooks in the second year of baccalaureate in Spain

espanolEste trabajo examina como se implementa la competencia oral en los libros de texto mas usados en el ultimo ano de Bachillerato en Espana. Usando una herramienta validada en un estudio anterior (Bueno-Alastuey and Luque Agullo, 2015a), se analizaron cinco libros de texto. Los resultados muestran la misma proporcion de tareas dedicadas al desarrollo de destrezas orales y escritas, un nivel B1 segun el Marco de Referencia Europeo (CEFR), y un acercamiento metodologico enmarcado en las corrientes pedagogicas actuales. Estos resultados sugieren que los libros de texto siguen las directrices europeas en cuanto al desarrollo de las destrezas orales, ignorando el enfasis en los aspectos escritos del examen de acceso a la Universidad. EnglishThis paper examines oral/aural competence in the most commonly used coursebooks in the second year of Baccalaureate in Spain. Using a checklist created and validated in a former pilot analysis (Bueno-Alastuey and Luque Agullo, 2015a), five textbooks were analysed. Results showed that the proportion of tasks1 devoted to oral/aural and written skills was similar, that the level introduced was B1 according to the Common European Framework for Languages (CEFR), and that the methodological approach used was consistent with current pedagogical schemes. This suggests that Spanish coursebooks are following the CEFR requirements on oral/aural aspects, overlooking the written focus of the University Entrance exam
Fiber Endface Fabry–Perot Microsensor With Distinct Response to Vapors of Different Chlorinated Organic Solvents

A Fabry-Perot optical sensing microresonator, fabricated by direct laser writing on the endface of a standard telecom fiber, is demonstrated as a microsensor for the specific detection of common chlorinated organic solvent vapors. The device operates within the 1550-nm spectral region, while the spectra recorded in the reflection mode correlate to the refractive index and absorption changes due to the different vapors trapped inside the microcavity. The operation of the microresonator sensing probe is explained in terms of standard physisorption and molecule packing mechanisms of organic vapors onto the porous sites of the photopolymerized reflection surface. The sensing of traces of three different chlorinated organic solvents vapors at concentrations down to 4 ppm and their discrimination through their spectral and temporal evolution is demonstrated and discussed, while the chlorinated volatile organic compound identification potential is also considered.
Semantic-aware Grad-GAN for Virtual-to-Real Urban Scene Adaption

Recent advances in vision tasks (e.g., segmentation) highly depend on the availability of large-scale real-world image annotations obtained by cumbersome human labors. Moreover, the perception performance often drops significantly for new scenarios, due to the poor generalization capability of models trained on limited and biased annotations. In this work, we resort to transfer knowledge from automatically rendered scene annotations in virtual-world to facilitate real-world visual tasks. Although virtual-world annotations can be ideally diverse and unlimited, the discrepant data distributions between virtual and real-world make it challenging for knowledge transferring. We thus propose a novel Semantic-aware Grad-GAN (SG-GAN) to perform virtual-to-real domain adaption with the ability of retaining vital semantic information. Beyond the simple holistic color/texture transformation achieved by prior works, SG-GAN successfully personalizes the appearance adaption for each semantic region in order to preserve their key characteristic for better recognition. It presents two main contributions to traditional GANs: 1) a soft gradient-sensitive objective for keeping semantic boundaries; 2) a semantic-aware discriminator for validating the fidelity of personalized adaptions with respect to each semantic region. Qualitative and quantitative experiments demonstrate the superiority of our SG-GAN in scene adaption over state-of-the-art GANs. Further evaluations on semantic segmentation on Cityscapes show using adapted virtual images by SG-GAN dramatically improves segmentation performance than original virtual data. We release our code at this https URL.
A unique homodimeric NAD+‐linked isocitrate dehydrogenase from the smallest autotrophic eukaryote Ostreococcus tauri

In eukaryotes, NAD+‐dependent isocitrate dehydrogenase (IDH) is strictly mitochondrial and is a key enzyme in the Krebs cycle. To date, all known NAD+‐specific IDHs (NAD‐IDHs) in the mitochondria are believed to be heteromeric in solution. Here, a unique homodimeric NAD‐IDH from Ostreococcus tauri (OtIDH), the smallest autotrophic picoeukaryote, was unveiled. Active OtIDH has a molecular weight of ~93 kDa with each subunit of 46.7 kDa. In the presence of Mn2+ and Mg2+, OtIDH displayed 42‐fold and 51‐fold preference for NAD+ over NADP+, respectively. Interestingly, OtIDH exhibited a sigmoidal kinetic behavior in response to isocitrate unlike other homodimeric homologs, and a remarkably high affinity for isocitrate (S0.5 < 10 μM) unlike other hetero‐oligomeric homologs. Furthermore, its coenzyme specificity can be completely converted from NAD+ (ancient trait) to NADP+ (adaptive trait) by rational mutagenesis based on the evolutionary trace. Mutants D344R and D344R/ M345H displayed a 15‐fold and 72‐fold preference for NADP+ over NAD+, respectively, indicating that D344 and M345 are the determinants of NAD+ specificity. These findings also suggest that OtIDH may be an ancestral form of type II IDHs (all reported members are NADP+‐linked enzymes) and may have evolved into NADP+‐dependent IDH for adaptation to the increased demand of NADPH under carbon starvation. —Tang, W.G. , Song, P., Cao, Z.Y. , Wang, P., Zhu, G. ‐P. A unique homodimeric NAD+‐linked IDH from the smallest autotrophic eukaryote Ostreococcus tauri. FASEB J. 29, 2462‐2472 (2015). www.fasebj. org
Cyclooxygenase-2 promoter 765C increase of digestive tract cancer risk in the Chinese population: a meta-analysis.

BACKGROUND To evaluate relationship between the cyclooxygenase-2 promoter 765G/C polymorphism and digestive cancer risk in China. MATERIALS AND METHODS A literature search through February 2014 was performed using PubMed, Chinese Biomedical Literature Database (CBM) and China National Knowledge Infrastructure (CNKI) databases, and a meta-analysis was performed with RevMan 5.2 software for odds ratios and 95%CIs. RESULTS In total, 9 articles with 3,263 cases and 4,858 controls were included in this meta-analysis.The pooled OR (95%CIs) in the co-dominant model (GC vs GG) was 1.56 [1.19, 2.06], and in the dominant model ((CC+GC) vs GG), the pooled OR was 1.59 [1.21, 2.09] in overall cancers. In the subgroup analysis, stratified by cancer type, significant associations were found that the-765C allele had increased pancreatic cancer and gastric risk. No significant liver cancer and colorectal cancer risk of COX-2 -765G/C polymorphism was found. CONCLUSIONS These findings suggest that COX-2-765*C is related to cancer susceptibility and may increase gastric and pancreatic cancer risk.
Red mold dioscorea-induced G2/M arrest and apoptosis in human oral cancer cells.

BACKGROUND Monascus-fermented products are among the most commonly used traditional food supplements. Dioscorea is known to exhibit anticancer properties. In this study the effects of the ethanol extract of red mold dioscorea (RMDE) on cell proliferation, cell cycle and apoptosis in human oral cancer cells were investigated. RESULTS RMDE exercised growth inhibition on squamous cell carcinoma-25 (SCC-25) cells. RMDE-mediated G2/M phase arrest was associated with the down-regulation of NF-κB, resulting in the inhibition of cyclin B1 and CDK1 expression; this may be the mechanism by which RMDE inhibits cancer cells. Furthermore, the proapoptotic activity of RMDE was revealed by the Annexin V-FITC/PI double-staining assay. In addition, the proapoptotic effect of RMDE was evident by the inhibition of Bax expression in the mitochondria, resulting in the activation of caspase-9 and caspase-3 and subsequent triggering of the mitochondrial apoptotic pathway. RMDE also enhanced caspase-8 activity, indicating the involvement of the death receptor pathway in RMDE-mediated SCC-25 cell apoptosis. CONCLUSION RMDE treatment inhibited the growth of SCC-25 cells by arresting cell cycle at the G2/M phase and induced apoptosis in a time- and dose-dependent manner. Therefore RMDE may be a good candidate for development as a dietary supplement against oral cancer.