Miracle-dz/UniFAR-FTUs huggingface dataset:
Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana

Photosynthesis is one of the most important biological processes on the earth. So far, though the molecular mechanisms underlying photosynthesis is well understood, however, the regulatory networks of photosynthesis are poorly studied. Given the current interest in improving photosynthetic efficiency for greater crop yield, elucidating the detailed regulatory networks controlling the construction and maintenance of photosynthetic machinery is not only scientifically significant but also holding great potential in agricultural application. In this study, we first identified transcription factors (TFs) related to photosynthesis through the TRAP approach using position weight matrix information. Then, for TFs related to photosynthesis, interactions between them and their targets were also determined by the ARACNE approach. Finally, a gene regulatory network was established by combining TF-targets information generated by these two approaches. Topological analysis of the regulatory network suggested that (a) the regulatory network of photosynthesis has a property of “small world”; (b) there is substantial coordination mediated by transcription factors between different components in photosynthesis.
Dependable Horizontal Scaling Based on Probabilistic Model Checking

The focus of this work is the on-demand resource provisioning in cloud computing, which is commonly referredto as cloud elasticity. Although a lot of effort has been invested in developing systems and mechanisms that enable elasticity, the elasticity decision policies tend to be designed without quantifying or guaranteeing the quality of their operation. We present an approach towards the development of more formalized and dependable elasticity policies. We make two distinct contributions. First, we propose an extensible approach to enforcing elasticity through the dynamic instantiation and online quantitative verification of Markov Decision Processes(MDP) using probabilistic model checking. Second, various concrete elasticity models and elasticity policies are studied. We evaluate the decision policies using traces from a realNoSQL database cluster under constantly evolving externalload. We reason about the behaviour of different modelling and elasticity policy options and we show that our proposal can improve upon the state-of-the-art in significantly decreasing under-provisioning while avoiding over-provisioning.
Chronos and KAIROS: MOSFIRE observations of post-starburst galaxies in z ∼ 1 clusters and groups

We present an exploration of ∼500 spectroscopically confirmed galaxies in and around two large-scale structures (LSSs) at z ∼ 1 drawn from the Observations of Redshift Evolution in Large Scale Environments survey, an ongoing, wide-field photometric and spectroscopic campaign targeting a large ensemble of LSSs at 0.6 < z < 1.3. A sub-sample of these galaxies (∼150) was targeted for the initial phase of a near-infrared MOSFIRE spectroscopic campaign investigating the differences in selections of galaxies that had recently ended a burst of star formation and/or had rapidly quenched (i.e. post-starburst/K+A galaxies). Selection with MOSFIRE utilizing the H α and [N II] emission features resulted in a post-starburst sample more than double that selected by traditional z ∼ 1 (observed-frame optical) methods even after the removal of the relatively large fraction of dusty starburst galaxies selected through traditional methods. While the traditional post-starburst fraction increased with increasing global density, the MOSFIRE-selected post-starburst fraction was found to be constant across field, group, and cluster environments. However, this fraction computed relative to the number of star-forming galaxies was observed to elevate in the cluster environment. Post-starbursts selected with MOSFIRE exhibited moderately strong [O II] emission originating from activity other than star formation. Such galaxies, termed K+A with ImposteR [O II]-derived Star formation (KAIROS) galaxies, were found to be younger than and likely undergoing feedback absent or diminished in their optically selected counterparts. A comparison between the environments of the two types of post-starbursts suggested a picture in which the evolution of a post-starburst galaxy is considerably different in cluster environments than in the more rarefied environments of a group or the field.
Transcriptional Profiling of the Developing Rat Brain Reveals That the Most Dramatic Regional Differentiation in Gene Expression Occurs Postpartum

Neural development involves the expression of ensembles of regulatory genes that control the coordinate and region-specific expression of a host of other genes, resulting in the unique structure, connectivity, and function of each brain region. Although the role of some specific genes in neural development has been studied in detail, we have no global view of the orchestration of spatial and temporal aspects of gene expression across multiple regions of the developing brain. To this end, we used transcriptional profiling to examine expression levels of 9955 genes in the hypothalamus, hippocampus, and frontal cortex across seven stages of postnatal development and up to four stages of prenatal development in individual male rats (six per group). The results reveal dramatic changes across development in >97% of the neurally expressed genes. They also uncover a surprising degree of regional differentiation occurring after birth and through the first 2 weeks of life. Cluster analysis identifies 20 clusters of transcripts enriched in genes related to particular functions, such as DNA metabolism, nuclear function, synaptic vesicle transport, myelination, and neuropeptide hormone activity. Thus, groups of genes with related functions change in the brain at specific times, possibly marking critical periods for each function. These findings can broadly serve as a backdrop for studying the role of individual genes in neural development. They also underscore the importance of early postnatal life in the rat, which corresponds to late gestation in the human, as a critical late phase of neural organization and differentiation, even in subcortical regions.
Hepatotoxicity, Nephrotoxicity and Oxidative Stress in Rat Testis Following Exposure to Haloxyfop-p-methyl Ester, an Aryloxyphenoxypropionate Herbicide

Haloxyfop-p-methyl ester (HPME) ((R)-2-{4-[3-chloro-5-(trifluoromethyl)-2-pyridyloxy]phenoxy}propionic acid), is a selective aryloxyphenoxypropionate (AOPP) herbicide. It exerts phytotoxicity through inhibition of lipid metabolism and induction of oxidative stress in susceptible plants. This study investigated the toxicological potentials of HPME in rats. Twenty-four male Wistar rats (170–210 g) were randomized into four groups (I–IV). Group I (control) received 1 mL of distilled water, while animals in Groups II, III and IV received 6.75, 13.5 and 27 mg/kg body weight HPME, respectively, for 21 days. There was a significant (p < 0.05) increase in renal and hepatic function biomarkers (urea, creatinine, total bilirubin, ALP, ALT, AST) in the plasma of treated animals compared to control. Levels of testicular antioxidants, ascorbic acid and glutathione, and activities of glutathione-S-transferase, superoxide dismutase and catalase were reduced significantly after 21 days of HPME administration in a dose-dependent manner. The testicular malondialdehyde level increased significantly in the HPME-treated rats relative to the control. A significant decrease in testicular lactate dehydrogenase, acid phosphatase and γ-glutamyl transferase was also observed in HPME-treated animals. Testicular histology revealed severe interstitial edema and sections of seminiferous tubules with necrotic and eroded germinal epithelium in the HPME-treated rats. Overall, data from this study suggest that HPME altered hepatic and renal function and induced oxidative stress and morphological changes in the testis of rats.
Framework for Knowledge-Based Integrative Analysis of Microarray Data

The whole genome DNA microarrays make it possible to monitor the expression of nearly all the genes in an organism and have been widely used in scientific and industrial fields. The challenges no longer lie in obtaining the data, but rather in interpreting the results to reveal the mechanisms of biological significance. A recent established method GSEA [1] assesses whether priori defined gene sets shows statistically significant, concordant differences between two biological states. This knowledge-based modular level analysis method proved to be superior to traditional single gene-based method [2], which is also demonstrated by several improvements base on the concept of GSEA. However, GSEA was designed to work on a ranked list of genes [3], so knowledge-based analysis of other data types remains a challenge. In this study, we have proposed a framework for gene set analysis of three major data types, ranked genes, clustered genes and signature genes. More interestingly, we further extended these methods to de novo motif discovery in almost the same framework. Analysis on real microarray data showed that results of biological significance could be recovered. The R scripts for Knowledge-based Integrative Analysis of Microarray data (KIAM) are available upon request from the authors.
Ifosfamide in Urologic Cancer

The therapeutic activity of ifosfamide in urologic tumors has been reviewed. Ifosfamide has definite activity in nephroblastoma, where it represents the treatment of choice for children who are not cured by front-line chemotherapy, and for the adults who are diagnosed with this uncommon disease. Definite therapeutic activity has also been shown in patients with urothelial tract malignancies and it represents a major option for patients failing first-line cisplatin-based chemotherapy. However, promising results have been achieved in chemo-naïve patients in combination with taxanes or gemcitabine, though at the price of relevant toxicity. A modest activity has been shown by ifosfamide in renal cancer (including the sarcomatoid variant) and in hormone-refractory prostate cancer, which unfortunately respond poorly to cytotoxic chemotherapy. No results of ifosfamide in penile carcinoma are available so far.
Stroke-Related Changes in Neuromuscular Fatigue of the Hip Flexors and Functional Implications

ObjectiveThe aim of this study was to compare stroke-related changes in hip flexor neuromuscular fatigue of the paretic leg during a sustained isometric submaximal contraction with those of the nonparetic leg and controls and to correlate fatigue with clinical measures of function. DesignHip torques were measured during a fatiguing hip flexion contraction at 20% of the hip flexion maximal voluntary contraction in the paretic and nonparetic legs of 13 people with chronic stroke and 10 age-matched controls. In addition, the participants with stroke performed a fatiguing contraction of the paretic leg at the absolute torque equivalent to 20% maximal voluntary contraction of the nonparetic leg and were tested for self-selected walking speed (10-m Walk Test) and balance (Berg). ResultsWhen matching the nonparetic target torque, the paretic hip flexors had a shorter time to task failure compared with the nonparetic leg and controls (P < 0.05). The time to failure of the paretic leg was inversely correlated with the reduction of hip flexion maximal voluntary contraction torque. Self-selected walking speed was correlated with declines in torque and steadiness. Berg-Balance scores were inversely correlated with the force fluctuation amplitude. ConclusionsFatigue and precision of contraction are correlated with walking function and balance after stroke.
Increasing stroke incidence and prevalence of risk factors in a low-income Chinese population

Objective: We investigated secular trends in incidence of first-ever stroke and the prevalence of stroke risk factors within the same population in rural China. Methods: In 1985, 15,438 residents from a township of Tianjin, China, were recruited to the Tianjin Brain Study, a population-based stroke surveillance study. Stroke events and all deaths were registered annually. Because imaging technology was first available in 1992, we analyzed the incidence of first-ever stroke over 3 study periods—1992–1998, 1999–2005, and 2006–2012—from 1992 to 2012. Risk factor surveys were conducted in 1991 and 2011. Results: The age-standardized incidence of first-ever stroke per 100,000 person-years increased rapidly from 124.5 in 1992–1998 to 190.0 in 1999–2005 and to 318.2 in 2006–2012; incidence increased annually by 6.5% overall and by 12% among men aged 45–64 years (p < 0.05). From 1992 to 2012, the age at first-ever stroke in men was earlier by 3.3 years overall, but a similar trend was not observed in women. Concurrently, the prevalence of high fasting glucose and alcohol consumption increased significantly in both men and women, especially in men aged <45 years; the prevalence of obesity and high fasting glucose increased by 8.8-fold and 11-fold, respectively, from 1992 to 2012. Conclusions: The incidence of stroke in rural China increased rapidly, particularly among middle-aged adults, along with a concurrent increase in risk factor prevalence. These findings suggest that without controlling these risk factors, stroke incidence will continue to increase over future decades in China.
Prior Expectation Mediates Neural Adaptation to Repeated Sounds in the Auditory Cortex: An MEG Study

Repetition suppression, the phenomenon that the second presentation of a stimulus attenuates neural activity, is typically viewed as an automatic consequence of repeated stimulus presentation. However, a recent neuroimaging study has suggested that repetition suppression may be driven by top-down expectations. Here we examined whether and when repetition suppression can be modulated by top-down expectation. Participants listened to auditory stimuli in blocks where tone repetitions were either expected or unexpected, while we recorded ongoing neural activity using magnetoencephalography. We found robust repetition suppression in the auditory cortex for repeated tones. Interestingly, this reduction was significantly larger for expected than unexpected repetitions, both in terms of evoked activity and gamma-band synchrony. These findings indicate a role of top-down expectation in generating repetition suppression and are in line with predictive coding models of perception, in which the difference between expected and actual input is propagated from lower to higher cortical areas.
Ancient mtDNA Analysis of Early 16th Century Caribbean Cattle Provides Insight into Founding Populations of New World Creole Cattle Breeds

The Columbian Exchange resulted in a widespread movement of humans, plants and animals between the Old and New Worlds. The late 15th to early 16th century transfer of cattle from the Iberian Peninsula and Canary Islands to the Caribbean laid the foundation for the development of American creole cattle (Bos taurus) breeds. Genetic analyses of modern cattle from the Americas reveal a mixed ancestry of European, African and Indian origins. Recent debate in the genetic literature centers on the ‘African’ haplogroup T1 and its subhaplogroups, alternatively tying their origins to the initial Spanish herds, and/or from subsequent movements of taurine cattle through the African slave trade. We examine this problem through ancient DNA analysis of early 16th century cattle bone from Sevilla la Nueva, the first Spanish colony in Jamaica. In spite of poor DNA preservation, both T3 and T1 haplogroups were identified in the cattle remains, confirming the presence of T1 in the earliest Spanish herds. The absence, however, of “African-derived American” haplotypes (AA/T1c1a1) in the Sevilla la Nueva sample, leaves open the origins of this sub-haplogroup in contemporary Caribbean cattle.
A Spectrum Sensing Prototype for TV White Space in China

TV white space (TVWS) has been considered a favorable spectrum for sharing with other spectrum deficient technologies. There are three popular TV standards in China: the Digital Terrestrial Multimedia Broadcast (DTMB), China Multimedia Mobile Broadcasting (CMMB) and PAL-D/K (Phase Alternating Line -D/K). In this paper we present a prototype platform for experimental spectrum sensing, which is developed in-house to test TVWS spectrum sharing for all the three popular TV standards. We discuss the details on the prototype architecture, the spectrum sensing algorithms and the testing setup in this paper. The performance results show that the developed prototype platform can detect the signals from all the three TV standards robustly and efficiently.
Iranian Journal of Basic Medical Sciences Anti-inflammatory Effect of Yu-ping-feng-san via Tgf-β1 Signaling Suppression in Rat Model of Copd

Original article Objective(s): Yu-Ping-Feng-San (YPFS) is a classical traditional Chinese medicine that is widely used for treatment of the diseases in respiratory systems, including chronic obstructive pulmonary disease (COPD) recognized as chronic inflammatory disease. However, the molecular mechanism remains unclear. Here we detected the factors involved in transforming growth factor beta 1 (TGF-β1)/Smad2 signaling pathway and inflammatory cytokines, to clarify whether YPFS could attenuate inflammatory response dependent on TGF-β1/Smad2 signaling in COPD rats or cigarette smoke extract (CSE)-treated human bronchial epithelial (Beas-2B) cells. Materials and Methods: The COPD rat model was established by exposure to cigarette smoke and intratracheal instillation of lipopolysaccharide, YPFS was administered to the animals. The efficacy of YPFS was evaluated by comparing the severity of pulmonary pathological damage, pro-inflammation cytokines, collagen related genes and the activation of TGF-β1/Smad2 signaling pathway. Furthermore, CSE-treated cells were employed to confirm whether the effect of YPFS was dependent on the TGF-β1/Smad2 signaling via knockdown Smad2 (Si-RNA), or pretreatment with the inhibitor of TGF-β1. Results: Administration of YPFS effectively alleviated injury of lung, suppressed releasing of pro-inflammatory cytokines and collagen deposition in COPD animals (P<0.05), whereas exogenous TGF-β1 promoted releasing of IL-1β, IL-6, TNFα (P<0.05). Administration YPFS reduced inflammatory response significantly, also down-regulated TGF-β1/Smad2 signaling in vivo and in vitro. Unexpectedly, knockdown Smad2 or inhibition of TGF-β1 abolished anti-inflammatory effect of YPFS in CSE-treated cells. Conclusion: YPFS accomplished anti-inflammatory effects mainly by suppressing phosphorylation of Smad2, TGF-β1/Smad2 signaling pathway was required for YPFS-mediated anti-inflammation in COPD rats or CSE-treated Beas-2B cells.
Transient and Long-Term Changes in Seismic Response of the Natural Resources Building, Olympia, Washington, due to Earthquake Shaking

The Natural Resources Building (NRB) in Olympia, Washington, was shaken by three earthquakes (Mw = 5.8, 6.8, and 5.0) between 1999 and 2001. Building motions were recorded on digital accelerographs, providing important digital recordings of repeated strong shaking in a building. The NRB has 5-stories above grade with 3 sub-grade levels and a ductile steel-frame elongated in the E-W direction. The upper two floors extend significantly beyond the lower 3 on the southern and eastern sides. N-S motions dominate the fundamental modal vibrations of the building system. In the 1999 Satsop M5.8 earthquake, the frequency of this fundamental system mode was 1.3 Hz during motions of 10% g. The frequency dropped to 0.7 Hz during the 2001 M6.8 Nisqually strong motions. Moreover, the Nisqually recordings reveal both numerous high-frequency transients of up to 0.18 g, several of which are visible on widely spaced sensors, and long-term tilts of some of the sensors. The weaker 2001 M5.0 Satsop earthquake motions showed the frequency remained depressed at less than 1 Hz for the eastern side of the structure, although the western side had recovered to 1.3 Hz. An ambient noise survey in 2008 showed the fundamental frequency of N/S vibrations remains about 1.0 Hz for the eastern side of the building and 1.3 Hz for the western side. These results suggest that in the Nisqually earthquake, the east side of the NRB suffered a permanent reduction in fundamental mode frequency of 37% due to loss of system stiffness by undetermined mechanism.
The effect of in-office vital bleaching and patient perception of the shade change.

OBJECTIVES This study aimed to evaluate the degree of colour change after an in-office vital tooth bleaching procedure with a 35% hydrogen peroxide gel using a spectrophotometer. The study also determined the patients' perceptions of the colour change and assessed the post operative sensitivity during the first week of the intervention. METHODS The maxillary teeth (from 15 to 25) of 22 patients comprising of 11 males and 11 females were bleached with a 35% hydrogen peroxide (HP) gel in a single visit treatment procedure (Yotuel Special, Biocosmetics Laboratories, Spain). Colour readings of the two maxillary central incisors were obtained using a spectrophotometer (CM-2600d Konica, Minolta) before and after the bleaching procedure. All the patients were requested to complete a form regarding post-operative tooth sensitivity and to record their perceptions toward the success of the bleaching treatment. RESULTS The quantitative effect of the bleaching material on tooth colour showed an increase in the L* values and a decrease in the a* and b* values. The changes were significant (Wilcoxon Signed Rank Sum Test; p < 0.05) from baseline until one month, except for the b* values one month after the bleaching procedure which were only significant at p < or = 0.1. The median overall colour change (deltaE) between baseline and after the bleaching procedure was 3.56. The mean value of the patients' colour perception was found to be 2.14 immediately after bleaching on a 3 point visual analogue scale. A Spearman correlation test showed a positive relationship between the deltaE values immediately and one week after bleaching and a weak relationship one week and one month after the bleaching procedure. There was a significant consistency in the patients' colour perception data immediately and one week after the bleaching process and a weak relationship between the deltaE values and the patients' colour perception one month after bleaching. Ten out of the twenty two patients experienced tooth sensitivity on the first day, immediately after the bleaching procedure. However only five patients experienced sensitivity on the second day, four patients on the third day and only one patient experienced sensitivity on the fourth and the fifth days after bleaching which was described as mild. CONCLUSIONS Yotuel Special 35% HP was able to bleach the patients' teeth with a perceptive colour change noticeable by the patients; however colour regression was evident quantitatively from the first week. Tooth sensitivity was a temporary side effect. The material cost is reasonable, it was easy to use and the procedure is not dependant on light activation. CLINICAL IMPLICATIONS A single application of this product may not be sufficient to give patients the bright smile they desire. However it is important to monitor the rebound effect after this procedure. Patients may experience some tooth sensitivity after the use of this bleaching material but the sensitivity is of a transient nature.