Miracle-dz/UniFAR-FTUs huggingface dataset:
Probiotics Clostridium butyricum and Bacillus subtilis ameliorate intestinal tumorigenesis.

AIMS To investigate the antitumor effects of probiotics Clostridium butyricum and Bacillus subtilis on colorectal cancer (CRC) progression. MATERIALS & METHODS The effects of C. butyricum and B. subtilis on CRC cells were studied. Male C57BL/6 mice with 1,2-dimethylhydrazine dihydrochloride (DMH)-induced CRC were intervened by these two probiotics and the antitumor effects were examined by comparing the tumor incidence and detecting the inflammatory and immune-related markers. RESULTS & CONCLUSIONS C. butyricum and B. subtilis inhibited the proliferation of CRC cells, caused cell cycle arrest and promoted apoptosis. In vivo, these two probiotics inhibited the development of DMH-induced CRC. The molecular mechanism involved reduced inflammation and improved immune homeostasis. This work establishes a basis for the protective role of probiotics B. subtilis and C. butyricum in intestinal tumorigenesis.
Effect of Methomyl on the Phenobarbital and Benzo [ a ] Pyrene Induced Hepatic Microsomal Mixed Function Oxidase System in Rats

Methomyl (Lannate) is a pesticide widely used to control of insects in grape gardens. Methomyl treatment induces significant alteration in mixed function oxidase system. The present work was designed to study the inhibitory effect of methomyl on different forms of cytochrome P450 induced by phenobarbital (CYP 2B1, 2B2 and 3A) and benzo[a]pyrene induced (CYP 1A1). Adult male rats were divided into 8 groups of 6 animals each. Microsomes were isolated by calcium precipitation. The levels of electron transport components, CYP 450, cytochrome b5, and cytochrome c-reductase were determined using extinction coefficients. Activities of drug-metabolizing enzymes were assayed. Inducers like phenobarbital, benzo[a]pyrene, showed significant induction of mixed function oxidase in rat. The methomyl treatment (4mg/kg) of inducer-(Phenobarbital, benzop [a] pyrene) pretreated rat caused a significant decrease in electron transport components and activities of drugmetabolizing enzymes when compared with treatment of inducer alone. Induction of mixed function oxidase enzymes due to phenobarbital was also altered by the pretreatment of methomyl. Benzo[a]pyrene treatment of methomyl pretreated rats showed significant decreased levels of electron transport components and drug metabolizing enzymes as compared to benzo[a]pyrene treatment alone. These results indicate that the susceptibility of phenobarbital and benzo[a]pyrene induced cytochrome P450 isoform (CYP 2B1, 2B2, 3A; and CYP 1A1) to methomyl and also affected in the induction pattern of some of the inducers with respect to CYP 450 isoforms.
The Role of Vitamin K in Bone Remodeling and Osteoporosis

Vitamin K is an essential fat soluble vitamin involved in the regulation of normal coagulation. However, growing evidence highlights that this molecule appears to be also implicated in the regulation of other important biological functions such as bone mineralization, calcium homeostasis, apoptosis, cell growth and signal transduction. In particular, many studies have focused their attention on the protective effects of vitamin K on bone tissue in the outlook of its use in the prevention and treatment of osteoporosis in post-menopausal women. The objective of the present paper is to review data of the literature regarding the metabolic effects of Vitamin K in bone tissue and its clinical role in the prevention and treatment of osteoporosis.
Structural analysis of plasmid and chromosomal loci involved in site-specific excision and integration of the SLP1 element of Streptomyces coelicolor

SLP1int (integrated [int] form of Streptomyces lividans plasmid 1 [SLP1]) is a Streptomyces coelicolor A3(2) transmissible sequence capable of autonomous replication as well as site-specific integration into and excision from the S. coelicolor chromosome. We report here that the plasmid and chromosomal loci involved in the integration of SLP1 and the two loci at which the recombination occurs during excision all share at least 111 base pairs of a 112-base-pair DNA sequence. Recombinational cross-over during integration or excision occurred nonrandomly within the common att sequence at or near a 25-base-pair inverted repeat. We suggest that chromosomally integrated plasmidogenic segments such as SLP1int may be involved in the acquisition and structural organization of genes encoding the diverse metabolic capabilities observed in different streptomycetes.
Ty1‐fused protein‐body formation for spatial organization of metabolic pathways in Saccharomyces cerevisiae

Metabolite production through a multistep metabolic pathway can often be increased by efficient substrate channeling created by spatial sequestration of the metabolic reactions. Here, Tya, a structural component in the Ty1 retrotransposon element that forms virus‐like particles (VLPs) in Saccharomyces cerevisiae, was used to spatially organize enzymes involved in a metabolic pathway into a multi‐enzyme protein body in yeast. As a proof of principle, Tya fusion to three key enzymes involved in biosynthesis of the isoprenoids farnesene and farnesol was tested to assess its potential to improve productivity. The Tya‐fusion protein resulted in three and fourfold increases in farnesene and farnesol production, respectively, as compared with that observed in a non‐fused control. Specifically, two‐phase partitioning fed‐batch fermentations of S. cerevisiae ATCC200589 overexpressing Tya‐fused enzymes (tHmg1, IspA, and α‐farnesene synthase) yielded 930 ± 40 mg/L of farnesene after 7 days. Additionally, we observed that the Tya‐fusion proteins tended to partition into particulate fractions upon 100,000g ultracentrifugation, suggesting the formation of large aggregates of protein bodies, with their particulate structure also observed by transmission electron microscopy. The dramatic increase in the biosynthetic productivity of metabolites via use of a Tya‐fusion protein suggested that this approach might be useful for the creation of multi‐enzyme complexes to improve metabolic engineering in yeast.
Clinical respiratory motion correction software (reconstruct, register and averaged-RRA), for 18F-FDG-PET-CT: phantom validation, practical implications and patient evaluation.

OBJECTIVE On fluorine-18 fludeoxyglucose (18F-FDG) positron emission tomography (PET) CT of pulmonary or hepatic lesions, standard uptake value (SUV) is often underestimated due to patient breathing. The aim of this study is to validate, on phantom and patient data, a motion correction algorithm [reconstruct, register and averaged (RRA)] implemented on a PET-CT system. METHODS Three phantoms containing five spheres filled with 18F-FDG and suspended in a water or Styrofoam®18F-FDG-filled tank to create different contrasts and attenuation environment were acquired on a Discovery GE710. The spheres were animated with a 2-cm longitudinal respiratory-based movement. Respiratory-gated (RRA) and ungated PET images were compared with static reference images (without movement). The optimal acquisition time, number of phases and the best phase within the respiratory cycle were investigated. The impact of irregular motion was also investigated. Quantification impact was computed on each sphere. Quantification improvement on 28 lung lesions was also investigated. RESULTS Phantoms: 4 min was required to obtain a stable quantification with the RRA method. The reference phase and the number of phases used for RRA did not affect the quantification which was similar on static acquisitions but different on ungated images. The results showed that the maximum standard uptake value (SUVmax) restoration is majored for the smallest spheres (≤2.1 ml). PATIENTS SUVmax on RRA and ungated acquisitions were statistically different to the SUVmax on whole-body images (p = 0.05) but not different from each other (mean SUVmax: 7.0 ± 7.8 vs 6.9 ± 7.8, p = 0.23 on RRA and ungated images, respectively). We observed a statistically significant correlation between SUV restoration and lesion displacement, with a real SUV quantitation improvement for lesion with movement >1.2 mm. CONCLUSION According to the results obtained using phantoms, RRA method is promising, showing a real impact on the lesion quantification on phantom data. With regard to the patient study, our results showed a trend towards an increase in the SUVs and a decrease in the volume between the ungated and RRA data. We also noticed a statistically significant correlation between the quantitative restoration obtained with RRA compared with ungated data and lesion displacement, indicating that the RRA approach should be reserved to patients with small lesions or nodes moving with a displacement larger than 1.2 cm. Advances in knowledge: This article investigates the performances of motion correction software recently introduced in PET. The conclusion revealed that such respiratory motion correction approach shows a real impact on the lesion quantification but must be reserved to the patient for whom lesion displacement was confirmed and high enough to clearly impact lesion evaluation.
Hippocampal and amygdala volumes in children and adults with childhood maltreatment‐related posttraumatic stress disorder: A meta‐analysis

Little work has directly examined the course of hippocampal volume in children and adults with childhood maltreatment‐related posttraumatic stress disorder (PTSD). Data from adults suggest that hippocampal volume deficits are associated with PTSD, whereas findings from children with PTSD generally show no hippocampal volume deficits in PTSD. Additionally, the role of the amygdala in emotional response makes it a possible region for investigation in children and adults with childhood maltreatment‐related PTSD. The objectives of this study were 2‐fold: (1) to meta‐analytically determine whether hippocampal and amygdala volumes in children and adults with PTSD from childhood maltreatment differ from those in healthy controls, and (2) to use cross‐sectional findings performed with meta‐analyses as a proxy for longitudinal studies to estimate the course of hippocampal and amygdala volumes in child and adult subjects with PTSD from childhood maltreatment. Using electronic databases, we identified articles containing hippocampal and amygdala data for children with PTSD and adults with PTSD from childhood maltreatment. Data were extracted and effect sizes were calculated using Comprehensive Meta‐Analysis Version 2.0. Reduced bilateral hippocampal volume was found in adults with childhood maltreatment‐related PTSD compared with healthy controls, but this deficit was not seen in children with maltreatment‐related PTSD, suggesting hippocampal volume deficits from childhood maltreatment may not be apparent until adulthood. Greater left than right hippocampal volume was found in the adult healthy control group but not in the PTSD group. Amygdala volume in children with maltreatment‐related PTSD did not differ from that in healthy controls. Hippocampal volume is normal in children with maltreatment‐related PTSD but not in adults with PTSD from childhood maltreatment, suggesting an initially volumetrically normal hippocampus with subsequent abnormal volumetric development occurring after trauma exposure. However, longitudinal studies are needed to support these preliminary findings. © 2008 Wiley‐Liss, Inc.
Quantitative DNA methylation analysis of genes coding for kallikrein-related peptidases 6 and 10 as biomarkers for prostate cancer

DNA methylation plays an important role in carcinogenesis and is being recognized as a promising diagnostic and prognostic biomarker for a variety of malignancies including Prostate cancer (PCa). The human kallikrein-related peptidases (KLKs) have emerged as an important family of cancer biomarkers, with KLK3, encoding for Prostate Specific Antigen, being most recognized. However, few studies have examined the epigenetic regulation of KLKs and its implications to PCa. To assess the biological effect of DNA methylation on KLK6 and KLK10 expression, we treated PC3 and 22RV1 PCa cells with a demethylating drug, 5-aza-2′deoxycytidine, and observed increased expression of both KLKs, establishing that DNA methylation plays a role in regulating gene expression. Subsequently, we have quantified KLK6 and KLK10 DNA methylation levels in two independent cohorts of PCa patients operated by radical prostatectomy between 2007–2011 (Cohort I, n = 150) and 1998–2001 (Cohort II, n = 124). In Cohort I, DNA methylation levels of both KLKs were significantly higher in cancerous tissue vs. normal. Further, we evaluated the relationship between DNA methylation and clinicopathological parameters. KLK6 DNA methylation was significantly associated with pathological stage only in Cohort I while KLK10 DNA methylation was significantly associated with pathological stage in both cohorts. In Cohort II, low KLK10 DNA methylation was associated with biochemical recurrence in univariate and multivariate analyses. A similar trend for KLK6 DNA methylation was observed. The results suggest that KLK6 and KLK10 DNA methylation distinguishes organ confined from locally invasive PCa and may have prognostic value.
Performance Characterization of SPEC CPU2006 Benchmarks on Intel and AMD Platform

For understanding the performance differences caused by different computer architectures and optimization technologies, the paper characterizes performance of SPEC CPU2006 benchmarks both on Intel and AMD platform. Using the performance events collected by Performance Monitor Unit, we compare their performance differences and analyze the causes from the features of architectures and the optimization technologies. Our results and analysis help the programmers better understand the memory performance and branch prediction performance which are caused by architectures and guide them in the optimization. The analysis also help the processor architects better balance among the key architecture factors such as memory disambiguation and hardware prefetch when doing architecture design decision.
Methods in translation science.

BACKGROUND The gap between research findings and practice has been, and continues to be, a concern for the international community. A number of descriptive studies have elucidated barriers and facilitators of evidence-based practice in nursing. It is argued that it is now time to use findings from these studies to design and test interventions that explicitly target barriers to the use of evidence in practice rather than doing further research to describe generic barriers and facilitators to evidence-based practice. This article discusses research methods to advance our knowledge regarding the efficacy of translating research into practice (TRIP) interventions that promote and hasten adoption of evidence in practice. APPROACH Published research is reviewed and used as exemplars of translation studies. The benefits and challenges in studying natural experiments are addressed as are the benefits and challenges in conducting TRIP studies using experimental designs. DISCUSSION The article discusses factors such as sample attainment, unit of analysis, intervention characteristics, outcome measurement, and sustainability. Although there are a myriad of initiatives aimed at increasing use of evidence in practice, there is little systematic evidence of the effectiveness of these initiatives. In order to advance knowledge, translation research needs more experimental studies that test TRIP interventions through, for example, partnership models.
Protection of Endothelial Survival by Peroxisome Proliferator-Activated Receptor-&dgr; Mediated 14-3-3 Upregulation

Objective—To determine the role of prostacyclin (PGI2) in protecting endothelial cells (ECs) from apoptosis and elucidate the protective mechanism. Methods and Results—To evaluate the effect of PGI2 on EC survival, we treated ECs with Ad-COX1/PGIS (Ad-COPI), which augmented selectively PGI2 production or carbaprostacyclin (cPGI2) followed by H2O2 for 4 hours. Ad-COPI inhibited annexin V–positive cells and blocked caspase 3 activation. cPGI2 inhibited apoptosis in a concentration-dependent manner. L-165041 had a similar effect, suggesting the involvement of peroxisome proliferator-activated receptor-&dgr; (PPAR&dgr;). ECs expressed functional PPAR&dgr;. PPAR&dgr; overexpression enhanced whereas PPAR&dgr; knockdown by small interfering RNA abrogated the antiapoptotic action of cPGI2 and L-165041. Our results show for the first time that PGI2 stimulated 14-3-3ϵ expression via PPAR&dgr; activation. cPGI2 and L-165041 induced binding oaf PPAR&dgr; to PPAR response elements located between −1426 and −1477 of 14-3-3ϵ promoter region, thereby activating 14-3-3ϵ promoter activity and protein expression. Upregulation of 14-3-3ϵ proteins resulted in an increase in Bad binding to 14-3-3ϵ and a reduction in Bad translocation to mitochondria. Conclusions—PGI2 protects ECs from H2O2-induced apoptosis by inducing PPAR&dgr; binding to 14-3-3ϵ promoter, thereby upregulating 14-3-3ϵ protein expression. Elevated 14-3-3ϵ augments Bad sequestration and prevents Bad-triggered apoptosis.
The effect of meat products enriched with plant sterols and minerals on serum lipids and blood pressure

The purpose of the study was to investigate the effect of non-esterified plant sterol-enriched and mineral-enriched low-fat and low-salted meat products compared with control meat products, on serum total and lipoprotein lipids and blood pressure in subjects with mildly to moderately elevated serum cholesterol concentration. A randomised, placebo-controlled, single-blind, repeated measure design was used. Altogether 21 volunteers completed the study. The study began with a pre-trial period of 1–2 weeks, which was followed by three different test periods in the following order: meat products enriched with plant sterols (1.2 g/day), potassium, calcium and magnesium (MP1); meat products with no added plant sterols and minerals (control); and meat products with plant sterols (2.1 g/day), potassium, calcium and magnesium (MP2). Each test period lasted for 3 weeks. During the MP2 period, the serum total and low-density lipoprotein cholesterol concentration decreased 4.9±7.5% (P<0.05) and 4.6±11.3% (not significant), respectively, compared with the control period. No differences in the high-density lipoprotein cholesterol and total triglyceride concentrations or in systolic blood pressure and diastolic blood pressure were found among the test periods. In conclusion, the present study showed that frankfurters and cold cuts enriched with plant sterols from tall oil, potassium, calcium and magnesium, as part of habitual Finnish diet reduced the serum total cholesterol concentration in hypercholesterolemic subjects when the intake of sitosterols was 2.1 g/day, but not with the lower dose.
Plasmonic axicon micro-lenses for chemical sensing

We report on the fabrication of plasmonic hybrid sensors made of a micro-axicon dielectric lens and a single metallic nanoparticle. The dielectric lens produces a Bessel-like beam of light at its apex under plane wave excitation confining light in a narrow and intense beam with a low divergence. This Bessel-like beam can be used to optimize efficiently the excitation of a plasmonic nano-object and the collection of its far-field collected signal. This hybrid structure using the optical properties of a single metallic nanoparticle can act as a highly sensitive nanosensor.
Excitement Up! Price Down! Measuring Emotions in Dutch Auctions

Recently, Internet auction sites have begun to compete in emotions by advertising the fun and excitement that bidders may experience during auction participation. The implicit conjecture inherent in these advertisements is that consumers derive a hedonic value from auction participation that makes exciting auctions more attractive and possibly induces bidders to stay active longer in the auction. We test this conjecture in a controlled economic laboratory experiment in which we also measure bidders' physiological arousal in terms of heart rate and skin conductivity as proxies for their excitement during auction participation. In particular, we conduct a series of descending price (Dutch) auctions with different clock speeds and find that in fast Dutch auctions bidders (1) are more excited and (2) stay longer in the bidding process. Moreover, the unpleasant event of losing a Dutch auction is experienced more strongly than the rewarding event of winning. Our results show that bidders' excitement is directly reflected in final prices, indicating that Internet auction site sponsors should carefully consider how the emotions elicited on their platforms affect bidding behavior.
A critical appraisal of a meta‐analysis comparing transcatheter closure of PFO versus medical therapy

We read “ A Meta-Analysis of Transcatheter Closure of Patent Foramen Ovale Versus Medical Therapy for Prevention of Recurrent Thromboembolic Events in patients with Cryptogenic Cerebrovascular Events” by Pineda et al., [1] with great interest. However, I have strong reservations regarding statistical technique used and classification of end points thus the conclusion reached by this study. First of all, the end points in all three trials reported hazard ratio. The meta-analysis reports odds ratio. The meta-analysis of trials reporting hazard ratios should have reported pooled hazard ratio as recommended by Cochrane Handbook for Systematic Reviews of Interventions [2]. The data reported in all three trials were time-to-event data so the best or better meta-analysisstatistical technique is generic inverse variance method, which should have been used as done by another metaanalysis published on the same topic [3]. We are surprised to see that the authors of this article stratified the data from the RESEPCT trial into transient ischemic attack (TIA) and cerebrovascular accidents (CVA). When the first sentence of the paragraph subtitled Primary End point in the RESPECT study states “A total of 25 primary end-point events occurred all of which were nonfatal ischemic strokes [4]. ” Yet, the authors abstracted on the Panel A composite of TIA and CVA as 15 and 21 in device closure and medical therapy, respectively. Obviously, the authors of this meta-analysis reported more events than actually reported by the study itself. Likewise, the RESPECT trial clearly reports no events of TIA but yet the authors report TIA as 6 and 5 in closure and medical therapy, respectively, with regards to the RESPECT trial. If authors could clarify the reader about the discrepancies, we would greatly appreciate that.
Alterations in perivascular innervation function in mesenteric arteries from offspring of diabetic rats

We have reported that exposure to a diabetic intrauterine environment during pregnancy increases blood pressure in adult offspring, but the mechanisms involved are not completely understood. This study was designed to analyse a possible role of perivascular sympathetic and nitrergic innervation in the superior mesenteric artery (SMA) in this effect.