Miracle-dz/UniFAR-FTUs huggingface dataset:
GOA? - Use of Gene Ontology Annotation (GOA) for biological interpretation of '-omics' data and for validation of automatic annotation tools

The number of large-scale experimental datasets generated from high-throughput technologies has grown rapidly. Biological knowledge resources such as the Gene Ontology Annotation (GOA) database, which provides high-quality functional annotation to proteins within the UniProt Knowledgebase, can play an important role in the analysis of such data. The integration of GOA with analytical tools has proved to aid the clustering, annotation and biological interpretation of such large expression datasets. GOA is also useful in the development and validation of automated annotation tools, in particular text-mining systems. The increasing interest in GOA highlights the great potential of this freely available resource to assist both the biological research and bioinformatics communities.
Frequency estimation of narrow band signals in Gaussian noise via Unscented Kalman Filter

In this paper the problem of frequency estimation of a harmonic signal embedded in noise is studied. We consider three frequency trackers, two in an input/output description and one in state space form, namely: the Notch Filter (NF), the Funnel Filter (FF) and the Cartesian Filter (CF). With the first two models, the estimation is carried on with prediction error minimization technique, whereas the Extended Kalman Filter (EKF) and the Unscented Kalman Filter (UKF) are used in the third model. The estimation methods are compared each other by introducing two standard step profiles and evaluating the quality of estimation by means of two indices based on the achieved quality in the tracking of such profiles. From this analysis, it turns out that the CF with UKF outperforms the other techniques from all considered viewpoints: steady-state variance, convergence time and robustness to large frequency variations.
LAPS: Layout-Aware Path Selection for Post-Silicon Timing Characterization

Process variation has become prominent in the advanced CMOS technology, making the timing of fabricated circuits more uncertain. In this paper, we propose a Layout-Aware Path Selection (LAPS) technique to accurately estimate the circuit timing variation from a small set of paths. Three features of paths are considered during the path selection. Experiments conducted on benchmark circuits with process variation simulated with VARIUS show that, by selecting only hundreds of paths, the fitting errors of timing distribution are kept below 5.3% when both spatial correlated and spatial uncorrelated process variations exist. key words: process variation, timing variation, sample, path selection, least square
Can the Risk of Medical Expenditure Explainthe Wealth Trajectories of Elderly Singles?

In this article, I analyze the role of precautionary savings as a determinant of the wealth holdings of elderly singles. The novel aspect of the analysis is that the distribution of medical expenditure is allowed to be individual-specific, and the variance of medical expenditure is estimated for each individual using repeated observations on medical expenditure. To address the measurement error problem in medical expenditure, I use an instrumental variable estimator. I construct a simple life-cycle model and show that the coefficient of relative risk aversion can be identified from a log-linearized Euler equation for wealth, using the variation in the risk of medical expenditure. The results imply that precautionary savings can account for up to 56% of the wealth holdings of elderly singles. This means lowering the risk exposure of medical expenses at older ages could significantly alter the retirement asset draw-down rates and strategies.
Prolonged exclusive breastfeeding reduces autoimmune diabetes incidence and increases regulatory T‐cell frequency in bio‐breeding diabetes‐prone rats

Previously, we reported that exclusive breastfeeding delayed and partially protected bio‐breeding diabetes‐prone (BBDP) rats from spontaneous autoimmune diabetes development. To investigate whether this protection results from modulation of the (mucosal) immune system, the present study was designed to analyse the effect of nutrition early in life on the immune status of BBDP rats.
Cellular (FLICE) like inhibitory protein (cFLIP) expression in diffuse large B‐cell lymphoma identifies a poor prognostic subset, but fails to predict the molecular subtype

Immunohistochemistry can sub‐classify diffuse large B‐cell lymphoma (DLBCL) into germinal centre B‐cell like (GCB) and non‐GCB subtypes. The latter consists predominately of the activated B‐cell like subgroup in which nuclear factor kappa‐B activation is its characteristic. Expression of cellular caspase 8 (FLICE)‐like inhibitory protein (cFLIP), a caspase 8 homologue, is regulated by nuclear factor kappa‐B signalling, and it is the main inhibitor of Fas ligand activated apoptosis. To determine if cFLIP expression was confined to non‐GCB subtype, we studied 66 cases of DLBCL. cFLIP expression showed no significant correlation to DLBCL subtypes (GCB or non‐GCB) but was associated with a worse clinical outcome. For cFLIP positive and negative patients, the five‐year event free survival was 20 and 31%, respectively (p = 0.049), and the five‐year overall survival was 20 and 57%, respectively (p = 0.041). Copyright © 2011 John Wiley & Sons, Ltd.
The effects of a supplement of dietary fibre on faecal excretion by human subjects

1. Four human subjects on strictly controlled diets were given a fibre supplement, 25 g Ispaghula husk (Isogel)/d, for 3 weeks. 2. Replicate diets and faeces were collected during two 5 d balance periods. The first period served as control for the second which occurred after the supplement had been fed for 2 weeks. 3. Diets and faeces were analysed for total solids, gross energy, total nitrogen, fat, available and unavailable carbohydrates. 4. Three of the four subjects showed a considerable increase in faecal bulk; total faecal weight was more than doubled in two subjects. In two subjects the increase was brought about mainly by extra fibre in the faeces accompanied by a higher proporation of faecal water whereas in one subject it was also an increased excretion of nutrients. One subject showed very little change in faecal bulk. 5. High values for the apparent digestibility of fibre were found during the control period; from 0.70 to 0.80. There was more variation during the experimental period when apparent digestibility of total fibre ranged from 0.47 to 0.82. Values arrived at for the minimum apparent digestibility of the fibre supplement were generally high; one subject appeared to digest Isogel completely. Isogel was degraded preferentially to the food-derived fibre; in particular, cellulose in the faeces was increased during the experimental period. 6. Only one subject showed distinct decreases in the apparent digestibility of energy, N and fat in the diet. The results do not therefore agree with the generally held view that increased fibre in the diet decreases the apparent digestibility of the other nutrients.
Nonlinear system identification using deep belief network based on PLSR

Deep learning has been successfully applied into pattern recognition due to its deep architecture and effective unsupervised learning, and deep belief network (DBN) is a popular model based on deep learning technique. In this paper, a DBN identification model based on partial least square regression (PLSR), named PLSR-DBN, is proposed for nonlinear system identification. In order to improve the identification accuracy, PLSR is introduced into the supervised fine-tuning of DBN to elimate the overfitting and local minimum resulted from gradients-based learning, and contrastive divergence (CD) algorithm is used in unsupervised pre-training. Finally, the proposed PLSR-DBN is tested on a benchmark nonlinear system. The experiment results show that the proposed PLSR-DBN has a better performance on nonlinear system identification than other similar methods.
Continuous delivery of endogenous inhibitors from poly(lactic-co-glycolic acid) polymeric microspheres inhibits glioma tumor growth.

PURPOSE There is an urgent need for modalities that can localize and prolong the administration of the antitumor agents, particularly antiangiogenic, to achieve long-term tumor inhibition. However, one of the major obstacles is designing a device in which the biological activity of sensitive endogenous inhibitors is retained. We have designed a biodegradable polymeric device, which provides a unique and practical means of localizing and continuously delivering hemopexin (PEX) or platelet factor 4 fragment (PF-4/CTF) at the tumor site while maintaining their biological activity. The potential and efficacy of this system is shown in vitro and in vivo in a human glioma mouse model. EXPERIMENTAL DESIGN Polymeric microspheres made of poly(lactic-co-glycolic acid) (PLGA) were loaded with very low amounts of PEX and PF-4/CTF. The release profiles of these factors from PLGA and their biological activity were confirmed in vitro using proliferation assays done on endothelial and tumor cells. Tumor inhibition using this system was studied in nude mice bearing a human s.c. glioma. RESULTS PEX and PF-4/CTF released in vitro from PLGA microspheres were biologically active and significantly inhibited the proliferation of human umbilical vein endothelial cells, bovine capillary endothelial cells, and U87-MG cells. A single local s.c. injection of PLGA microspheres loaded with low amounts of PEX or PF-4/CTF resulted in an 88% and 95% reduction in glioma tumor volume 30 days post-treatment. Immunohistochemical analysis of the treated tumors showed a marked decrease in tumor vessel density compared with untreated tumors. CONCLUSION Our findings show that polymeric microspheres are a very promising approach to locally and efficiently deliver endogenous inhibitors to the tumor site leading to a significant inhibition of the tumor.
Beam Dump of SPIRAL2 Facility: Residual Dose Rate Calculations and Impact of the Computational Approaches

The SPIRAL2 facility will produce 5 mA of deuterons at 40 MeV. The work presented here focuses on predicting the residual dose rates that can be expected in the beam dump room of this facility during beam-off phases as consequence of the deuteron stopping. The effect of different transport and activation computational approaches on the dose rates calculations is assessed.
Z Score Prediction Model for Assessment of Bone Mineral Content in Pediatric Diseases *

The objective of this study was to develop an anthropometry‐based prediction model for the assessment of bone mineral content (BMC) in children. Dual‐energy X‐ray absorptiometry (DXA) was used to measure whole‐body BMC in a heterogeneous cohort of 982 healthy children, aged 5–18 years, from three ethnic groups (407 European‐ American [EA], 285 black, and 290 Mexican‐American [MA]). The best model was based on log transformations of BMC and height, adjusted for age, gender, and ethnicity. The mean ± SD for the measured/predicted ln ratio was 1.000 ± 0.017 for the calibration population. The model was verified in a second independent group of 588 healthy children (measured/predicted ln ratio = 1.000 ± 0.018). For clinical use, the ratio values were converted to a standardized Z score scale. The whole‐body BMC status of 106 children with various diseases (42 cystic fibrosis [CF], 29 juvenile dermatomyositis [JDM], 15 liver disease [LD], 6 Rett syndrome [RS], and 14 human immunodeficiency virus [HIV]) was evaluated. Thirty‐nine patients had Z scores less than −1.5, which suggest low bone mineral mass. Furthermore, 22 of these patients had severe abnormalities as indicated by Z scores less than −2.5. These preliminary findings indicate that the prediction model should prove useful in determining potential bone mineral deficits in individual pediatric patients.
Role for Neuronal Nitric-Oxide Synthase in Cannabinoid-Induced Neurogenesis

Cannabinoids, acting through the CB1 cannabinoid receptor (CB1R), protect the brain against ischemia and related forms of injury. This may involve inhibiting the neurotoxicity of endogenous excitatory amino acids and downstream effectors, such as nitric oxide (NO). Cannabinoids also stimulate neurogenesis in the adult brain through activation of CB1R. Because NO has been implicated in neurogenesis, we investigated whether cannabinoid-induced neurogenesis, like cannabinoid neuroprotection, might be mediated through alterations in NO production. Accordingly, we measured neurogenesis in dentate gyrus (DG) and subventricular zone (SVZ) of CB1R-knockout (KO) and wild-type mice, some of whom were treated with the cannabinoid agonist R(+)-Win 55212-2 [(+)-[2,3-dihydro-5-methyl-3-[(morpholinyl)methyl]pyrrolo[1,2,3-de]-1,4-benzoxazin-yl]-(1-naphthalenyl)methanone] or the NO synthase (NOS) inhibitor 7-nitroindazole (7-NI). NOS activity was increased by ∼25%, whereas bromodeoxyuridine (BrdU) labeling of newborn cells in DG and SVZ was reduced by ∼50% in CB1R-KO compared with wild-type mice. 7-NI increased BrdU labeling in both DG and SVZ and to a greater extent in CB1R-KO than in wild-type mice. In addition, R(+)-Win 55212-2 and 7-NI enhanced BrdU incorporation into neuron-enriched cerebral cortical cultures to a similar maximal extent and in nonadditive fashion, consistent with a shared mechanism of action. Double-label confocal microscopy showed coexpression of BrdU and the neuronal lineage marker doublecortin (Dcx) in DG and SVZ of untreated and 7-NI-treated CB1R-KO mice, and 7-NI increased the number of Dcx- and BrdU/Dcx-immunoreactive cells in SVZ and DG. Thus, cannabinoids appear to stimulate adult neurogenesis by opposing the antineurogenic effect of NO.
The Effectiveness of Women’s Agricultural Education Programs: A Survey from Annie’s Project

This study determined the effectiveness of ‘Annie’s Project—Education for Farm Women’ in improving women’s skill sets. Illinois farm women who participated in Annie’s Project were given a pre–test or baseline survey which measured farming practices in the five areas of risk (production, marketing, financial, legal and human resource). The women were later resurveyed. The main methodology to measure improvement in skill is calculated by the difference in the percentage of ‘yes’ responses from the baseline to the post–test. Results suggest an overall increase of 10.92 percent with the largest improvement occurring in the financial area of risk. In general, the differences in ‘yes’ responses were found to be significantly different from zero. Regression analysis was also performed to determine whether socio–economic variables, such as marital status and farm size, play a role in the difference in the percentages of ‘yes’ responses.
Analysis of modulated Ho2PdSi3 crystal structure at Pd K and Ho L absorption edges using resonant elastic X-scattering

Replacing Si atoms with a transition metal in rare earth disilicides results in a family of intermetallic compounds with a variety of complex magnetic phase transitions. In particular, the family R2PdSi3 shows interesting magnetic behavior arising from the electronic interaction of the R element with the transition metal in the Si network, inducing the specific structure of the related phase. Within this series, the highest degree of superstructural order was reported for the investigated representative Ho2PdSi3, although several competing superstructures have been proposed in literature. The diffraction anomalous fine structure (DAFS) method is highly sensitive to the local structure of chosen atoms at specific positions within the unit cell of a crystalline phase. In combination with x-ray absorption fine structure (XAFS), this sophisticated synchrotron method has been applied in the present work to several selected reflections, i.a. a satellite reflection. Extensive electronic modeling was used to test the most relevant structure proposals. The 2×2×8 ? > superstructure has been strongly confirmed, although a small amount of disorder in the modulation is very probable.
Smart Crawler: Using Committee Machines for\\Web Pages Continuous Classification

The speed of information publishing in WWW is unprecedented. The individuals and organizations struggle to be up to date and find relevant knowledge from a tsunami of news, videos, posts, and comments. In the other hand, these contents (mostly bound to HTML pages) are unstructured and not explicitly classified. In this context, machine-learning techniques can be very handy to automatic separate useful information from irrelevant noise. The present paper describes a novel approach for Web Pages crawling. The Smart Crawler employs two techniques for improving the information classification: massive Web page crawling and continuous classification through committee machines. These ideas are implemented using Big Data and cloud-ready technologies, whose the cornerstone is a framework that enables memory-intensive processing, high scalability, and streaming processing. The results indicates a significant classification capability and that the classification rate can scale linearly according to the size of the dataset.
Metabolite profiling and quantitative genetics of natural variation for flavonoids in Arabidopsis

Little is known about the range and the genetic bases of naturally occurring variation for flavonoids. Using Arabidopsis thaliana seed as a model, the flavonoid content of 41 accessions and two recombinant inbred line (RIL) sets derived from divergent accessions (Cvi-0×Col-0 and Bay-0×Shahdara) were analysed. These accessions and RILs showed mainly quantitative rather than qualitative changes. To dissect the genetic architecture underlying these differences, a quantitative trait locus (QTL) analysis was performed on the two segregating populations. Twenty-two flavonoid QTLs were detected that accounted for 11–64% of the observed trait variations, only one QTL being common to both RIL sets. Sixteen of these QTLs were confirmed and coarsely mapped using heterogeneous inbred families (HIFs). Three genes, namely TRANSPARENT TESTA (TT)7, TT15, and MYB12, were proposed to underlie their variations since the corresponding mutants and QTLs displayed similar specific flavonoid changes. Interestingly, most loci did not co-localize with any gene known to be involved in flavonoid metabolism. This latter result shows that novel functions have yet to be characterized and paves the way for their isolation.
Public Opinion Mining on Social Media: A Case Study of Twitter Opinion on Nuclear Power

Social media, including micro-blogs such as Twitter, have become main channels to communicate and share public social opinion among people. The opinion on nuclear power is an important social issue because nuclear plant construction needs national consensus. This paper proposes an opinion mining approach to monitor public sentiments on nuclear related issues using tweets on Twitter. The proposed process consists on (1) crawling related tweets, (2) text preparation, (3) sentiment dictionary construction, and (4) sentimental scoring. Based on experiment using nuclear related tweets in Korean between 2009 and 2013, we verify the usefulness on the proposed approach and confirm the changes on national opinion on nuclear generation depending on critical events such as Fukushima Daiichi nuclear disaster.
Tieg3/Klf11 induces apoptosis in OLI‐neu cells and enhances the TGF‐β signaling pathway by transcriptional repression of Smad7

TGF‐β signaling is indispensible for development of the nervous system since it regulates ontogenetic cell death. The recently identified TGF‐β‐inducible zinc finger protein Tieg3/Klf11 belongs to the family of Sp1/Klf‐like transcription factors and shares all structural and functional features with other Tieg proteins. Using the established TGF‐β‐responsive oligodendroglial cell line OLI‐neu, we analyzed the role of Tieg3/Klf11 in TGF‐β signaling. In this report, we show that Tieg3/Klf 11 mimics TGF‐β effects by inducing apoptotic cell death accompanied by activation of caspase‐3. Moreover, we demonstrate that Tieg3/Klf11 enhances TGF‐β signaling by transcriptional repression of the inhibitory Smad7 and, thereby, disrupts the negative feedback loop of the TGF‐β signaling pathway. Loss of the N‐terminal repression domains of Tieg3/Klf11 abrogates the pro‐apoptotic nature of this transcription factor and abolishes the enhancement of Smad‐mediated TGF‐β responses. In conclusion, we provide evidence that the recently identified transcription factor Tieg3/Klf11 is a downstream mediator of TGF‐β‐induced apoptosis in the oligodendroglial cell line OLI‐neu. Since other signaling molecules are able to initiate transcription of members of the Tieg family, the ability of Tieg3/Klf11 to modulate TGF‐β signaling by transcriptional inhibition of Smad7 might be an important clue for the understanding of the crosstalk between different signaling pathways. J. Cell. Biochem. 104: 850–861, 2008. © 2008 Wiley‐Liss, Inc.
Interferon inhibition of thymidine incorporation into DNA through effects on thymidine transport and uptake

Replenishment of medium after 72 hr of growth of HeLa‐S3 cells in dense suspension cultures increased [3H]‐thymidine uptake into cells and incorporation into DNA, with the levels reaching a peak ∼ 12 hr following medium change; β interferon inhibits the enhanced uptake of [3H]‐thymidine and labeling of DNA in a dose‐dependent manner. Some reduction in these processes is observed at a concentration as low as 1 u/ml, and ∼ 75% inhibition at 640 u/ml. Kinetic analysis has revealed that the rate of labeling of the acid‐soluble pool with [3H]‐thymidine, measured either at 22°C, or 37°C, is reduced in interferon‐treated (640 u/ml, 24 hr) HeLa‐S3 cells. At 22°C, the initial rate of thymidine transport at a high (500 μM) thymidine concentration, determined within the first 30 sec of [3H]‐thymidine addition was depressed by 44% in interferon‐treated HeLa cells. At 37°C, labeled precursors accumulate in acid‐soluble material for ∼ 8 min after the addition of [3H]‐thymidine, after which an apparent equilibrium level is attained. At this temperature, the rate of thymidine uptake and the apparent equilibrium level attained were depressed by 70% in interferon‐treated HeLa cells. The reduced incorporation of [3H]‐thymidine into DNA in interferon‐treated HeLa‐S3 cells can be largely explained by interferon inhibition of thymidine transport and phosphorylation.
Efficient E. coli expression systems for the production of recombinant β-mannanases and other bacterial extracellular enzymes

Two Escherichia coli expression systems based on T7 RNA polymerase promoter (pET system) and tac promoter (pFLAG system) have been used for the production and secretion of recombinant b-mannanases from Bacillus sp. Both E. coli OmpA signal peptide and native Bacillus signal peptide could be used efficiently for the secretion of recombinant enzymes into periplasmic space and culture media. The genes could be induced for over-expression with 0.1 - 1 mM isopropyl-β-D- 1-thiogalactopyranoside (IPTG) when the OD600 of the culture broth reached 0.6-1.5. The recombinant enzymes could be harvested from whole cell lysate, perimplasmic extract, or culture broth after induction for 4 - 20 hours. Since the enzyme is C-terminally tagged with hexahistidine, the recombinant enzymes could be conveniently purified to apparent homogeneity by one-step immobilized-metal affinity chromatography (IMAC) using Ni-NTA resins. The characteristics of purified recombinant b-mannanases from B. licheniformis and B. subtilis, which share 78% amino acid identity, are slightly different. These systems should be applicable for the production of various recombinant bacterial extracellular enzymes.