Miracle-dz/UniFAR-FTUs huggingface dataset:
Different techniques to study rumen fermentation characteristics of maturing grass and grass silage.

Grass samples were harvested during the 1993 growing season after a precut on April 27, 1993 and were stored frozen or left to ensile in 30-L buckets. Effects on chemical composition and fermentation kinetics of the maturation of the grass and of ensiling were investigated. Chemical composition and fermentation kinetics were determined using the gas production technique, in vitro techniques, and the nylon bag technique. Two silage samples were also investigated in vivo. Maturation caused a decrease in crude protein content and organic matter degradability and an increase in neutral detergent fiber, acid detergent fiber, and lignin contents. Degradation rates were highest for the youngest samples and decreased as grass and silage matured. This result could be observed from the first derivative of the cumulative gas production curves (i.e., the rate of gas production) and from the gas production parameters. The rate of degradation of the nonsoluble fraction of the young samples, determined using the gas production technique, was relatively higher in rumen fluid from a cow fed silage from grass cut at a young stage. More mature samples were degraded relatively faster in rumen fluid from a cow fed mature grass silage, suggesting a specific adaptation of the rumen microorganisms to the grass properties. There was a good relationship among the second phase of gas production (i.e., fermentation of the nonsoluble fraction), maturity of the grass and grass silage samples, degradability determined with the Tilley and Terry technique, and degradability determined after 46 h of incubation in rumen fluid. Results obtained with both of the different in vitro techniques and the nylon bag technique were confirmed by the in vivo experiments involving the two silage samples.
Cardiovascular-Kidney Interactions in Health and Disease Role of fibroblast growth factor-binding protein in the pathogenesis of HIV-associated hemolytic uremic syndrome

Ray, Patricio E. , Elena Tassi, Xue-Hui Liu, and Anton Wellstein. Role of fibroblast growth factor-binding protein in the pathogenesis of HIV-associated hemolytic uremic syndrome. Am J Physiol Regul Integr Comp Physiol 290: R105–R113, 2006; doi:10.1152/ajpregu.00492. 2005. —A characteristic finding of childhood HIV-associated hemolytic uremic syndrome (HIV-HUS) is the presence of endothelial injury and microcystic tubular dilation, leading to a rapid progression of the renal disease. We have previously shown that a secreted fibroblast growth factor-binding protein (FGFBP) is upregulated in kidneys from children affected with HIV-HUS and HIV nephropathy. Here, we sought to determine the potential role of FGF-BP in the pathogenesis of HIV-HUS. By immunohistochemical and in situ hybridization studies, we observed FGF-BP protein and mRNA upregulation in regenerating renal tubular epithelial cells from kidneys of HIV-Tg26 mice with late-stage renal disease, that is, associated with the development of microcystic tubular dilatation and accumulation of FGF-2. Moreover, FGF-BP increased the FGF-2dependent growth and survival of cultured primary human renal glomerular endothelial cells and enhanced FGF-2-induced MAPK/ ERK2 activation, as well as the proliferation of immortalized GM7373 endothelial cells. We propose that HIV-Tg26 mice are a clinically relevant model system to study the role of FGF-BP in the pathogenesis of HIV-associated renal diseases. Furthermore, the upregulation of FGF-BP by regenerating renal tubular epithelial cells may provide a mechanism by which the regenerative and angiogenic activity of FGF-2 in renal capillaries can be modulated in children with HIV-HUS and other renal disease.
The role of plant-based diets in the treatment and prevention of coronary artery disease.

Correspondence and requests for reprints to Christopher D. Gardner, PhD, Stanford Center for Research in Disease Prevention, 730 Welch Road, Suite B, Palo Alto, CA 94304-1583, USA. Tel: +1 650 725-2751; fax: +1 723 7018 email: cgardner@stanford.edu Introduction The impact of nutrition on coronary artery disease Ž . CAD and cardiovascular health includes effects on serum lipids, blood pressure, blood glucose homeostasis, antioxidant status, homocysteine, endothelial function, and fibrinolytic activity. A long and growing list of dietary components with varying levels of supportive evidence is thought to affect these CAD risk factors. An older, shorter list of these dietary components would have included some specific fatty acids 1 , fiber 2 , cholesterol 3 , sodium 4 , and antioxidant vitamins like E and C 5 7 . But a more current list would also include isoflavones from soybeans 8 , allicin from garlic 9,10 , plant sterols from vegetable and seed oils 11 , specific amino acids such as arginine 12 , B vitamins such as folate, B6, and B12 13 15 , minerals such as selenium, potassium, and magnesium 16 , and an expanded group of antioxidants such as flavonoids 17 and carotenoids 18,19 , The lists above of specific CAD risk factors and dietary components are not intended to be exhaustive, but make the point that the impact of nutrition on CAD is complex. Consequently, advising CAD patients and the general public about the practical implementation of nutrition in the treatment and prevention of heart disease can be challenging.
The Bromodomain Protein Brd4 Stimulates G1 Gene Transcription and Promotes Progression to S Phase*

Brd4 is a bromodomain protein that binds to acetylated chromatin. It regulates cell growth, although the underlying mechanism has remained elusive. Brd4 has also been shown to control transcription of viral genes, whereas its role in transcription of cellular genes has not been fully elucidated. Here we addressed the role of Brd4 in cell growth and transcription using a small hairpin (sh) RNA approach. The Brd4 shRNA vector stably knocked down Brd4 protein expression by ∼90% in NIH3T3 cells and mouse embryonic fibroblasts. Brd4 knockdown cells were growth impaired and grew more slowly than control cells. When synchronized by serum starvation and released, Brd4 knockdown cells were arrested at G1, whereas control cells progressed to S phase. In microarray analysis, although numerous genes were up-regulated during G1 in control cells, many of these G1 genes were not up-regulated in Brd4 knockdown cells. Reintroduction of Brd4 rescued expression of these G1 genes in Brd4 knockdown cells, allowing cells to progress toward S phase. Chromatin immunoprecipitation analysis showed that Brd4 was recruited to the promoters of these G1 genes during G0-G1 progression. Furthermore, Brd4 recruitment coincided with increased binding of Cdk9, a component of P-TEFb and RNA polymerase II to these genes. Brd4 recruitment was low to absent at genes not affected by Brd4 shRNA. The results indicate that Brd4 stimulates G1 gene expression by binding to multiple G1 gene promoters in a cell cycle-dependent manner.
Induction of apoptosis by idarubicin: how important is the plasma peak?

OBJECTIVES It is still not clear whether a high plasma peak or a prolonged plasma presence of the drug is optimal for chemotherapy with anthracyclines. A high plasma peak seems to correlate with the liberation of oxygen radicals and cumulative delayed cardiotoxicity, and therefore, should be avoided. On the other hand, its role in attaining the desired therapeutic effect, i.e. induction of apoptosis in tumor cells, has not been clearly elucidated. METHODS Idarubicin is the only anthracycline that can be applied orally. We measured the DNA-binding of idarubicin and idarubicinol and the induced apoptosis in the human promyelocytic HL-60 leukemia cell line. Various pharmacokinetic profiles, with and without clinically relevant peak concentrations, were simulated in vitro. RESULTS The concentration necessary for maximal DNA-binding and subsequent induction of apoptosis was 1.5 microg/ml for 20 minutes which is well above the plasma concentration achievable in therapy. A plateau of apoptosis was observed after 90 minutes of incubation; a prolongation above 90 minutes did not increase the rate of apoptosis. We simulated a bolus application and a continuous infusion using two different pharmacokinetic profiles of idarubicin with comparable AUCs (area under the time curve). After 48 hours of total incubation, the viability of HL-60 cells was 56.88% with profile 1 (50 ng/ml idarubicin for 2 hours) and 83.00% with profile 2 (4.25 ng/ml for 24 hours). CONCLUSIONS Although these in vitro experiments are not directly applicable to the clinical situation, they do indicate that a prolongation of the application time up to at least 90 minutes, either by continuous infusion or by oral application, may be acceptable as a method of increasing apoptosis. On the other hand, the plasma peak seems to be an important factor for the induction of apoptosis. Further studies are in progress to define the minimal plasma peak necessary to induce a maximum of apoptosis.
Broadband passive harmonic mode locking in a dispersion-managed Er-doped fiber laser

We report on an Erbium-doped fiber laser operated at harmonic mode locking (HML) state with broadband spectrum. Stable pulse train emitted from the light source can continuously vary from 2nd to 17th order with spectrum bandwidth beyond 50 nm. The bandwidth can be up to 57 nm at 10th order HML. The pulse duration is measured to be 966 fs by an autocorrelator, and the corresponding time band product is 6.7, indicating high chirped pulse profile. In addition, stable states of noise-like pulse, domain wall, bound solitons could be also observed.
Phase III trial of nanoparticle albumin-bound paclitaxel compared with polyethylated castor oil-based paclitaxel in women with breast cancer.

PURPOSE ABI-007, the first biologically interactive albumin-bound paclitaxel in a nanameter particle, free of solvents, was compared with polyethylated castor oil-based standard paclitaxel in patients with metastatic breast cancer (MBC). This phase III study was performed to confirm preclinical studies demonstrating superior efficacy and reduced toxicity of ABI-007 compared with standard paclitaxel. PATIENTS AND METHODS Patients were randomly assigned to 3-week cycles of either ABI-007 260 mg/m(2) intravenously without premedication (n = 229) or standard paclitaxel 175 mg/m(2) intravenously with premedication (n = 225). RESULTS ABI-007 demonstrated significantly higher response rates compared with standard paclitaxel (33% v 19%, respectively; P = .001) and significantly longer time to tumor progression (23.0 v 16.9 weeks, respectively; hazard ratio = 0.75; P = .006). The incidence of grade 4 neutropenia was significantly lower for ABI-007 compared with standard paclitaxel (9% v 22%, respectively; P < .001) despite a 49% higher paclitaxel dose. Febrile neutropenia was uncommon (< 2%), and the incidence did not differ between the two study arms. Grade 3 sensory neuropathy was more common in the ABI-007 arm than in the standard paclitaxel arm (10% v 2%, respectively; P < .001) but was easily managed and improved rapidly (median, 22 days). No hypersensitivity reactions occurred with ABI-007 despite the absence of premedication and shorter administration time. CONCLUSION ABI-007 demonstrated greater efficacy and a favorable safety profile compared with standard paclitaxel in this patient population. The improved therapeutic index and elimination of corticosteroid premedication required for solvent-based taxanes make the novel albumin-bound paclitaxel ABI-007 an important advance in the treatment of MBC.
Novel combination therapy for the eradication of Helicobacter pylori infection in a mouse model

Abstract Objective. To investigate the combination therapy, consisting of hyperimmune bovine colostrum, N-acetyl cysteine, zinc and amoxicillin on the eradication of Helicobacter pylori in a mouse model. Material and methods. C57BL/6 female mice (6 weeks of age) were inoculated with 0.1 ml of 1 × 109 H. pylori via a single oro-gastric gavage and were left infected for 4 weeks. Mice (n = 9/group) were randomly allocated to receive by oral gavage (0.1 ml) HNZ (hyperimmune bovine colostrum + N-acetyl cysteine + zinc), HNZA (HNZ + amoxicillin; A), HNZA2 (2× amoxicillin; A2), HNZA5 (5× amoxicillin; A5), triple therapy (TT) or saline twice daily for 10 days. Bacterial load was assessed by culture. Gastric emptying was assessed by 13C-octanoic acid breath test. Results. Mice receiving HNZ, HNZA, and HNZA2 have a 22%, 44% and 67% eradication rate, respectively. Eradication rate was 100% with HNZA5, TT and those animals receiving A5 alone. In H. pylori infected mice there was an increased gastric emptying time by 7.9, 3.7, 10.1 and 7.7 min for the TT, HNZ, HNZA2, and HNZA5, respectively, compared to saline. Conclusions. HNZ with the addition of a high dose of amoxicillin is effective at eradicating H. pylori in vivo as HNZA1 and HNZA2 did not give raise to eradication. The potency of the novel anti-H. pylori combination therapy may be due to the delayed gastric emptying.
ParC subunit of DNA topoisomerase IV of Streptococcus pneumoniae is a primary target of fluoroquinolones and cooperates with DNA gyrase A subunit in forming resistance phenotype

The genes encoding the ParC and ParE subunits of topoisomerase IV of Streptococcus pneumoniae, together with the region encoding amino acids 46 to 172 (residue numbers are as in Escherichia coli) of the pneumococcal GyrA subunit, were partially characterized. The gyrA gene maps to a physical location distant from the gyrB and parC loci on the chromosome, whereas parC is closely linked to parE. Ciprofloxacin-resistant (Cpr) clinical isolates of S. pneumoniae had mutations affecting amino acid residues of the quinolone resistance-determining region of ParC (low-level Cpr) or in both quinolone resistance-determining regions of ParC and GyrA (high-level Cpr). Mutations were found in residue positions equivalent to the serine at position 83 and the aspartic acid at position 87 of the E. coli GyrA subunit. Transformation experiments suggest that ParC is the primary target of ciprofloxacin. Mutation in parC appears to be a prerequisite before mutations in gyrA can influence resistance levels.
Growth of Phase Pure Yttrium Iron Garnet Thin Films on Silicon: The Effect of Substrate and Postdeposition Annealing Temperatures

Growth of phase pure yttrium iron garnet (YIG) on silicon is a challenging task due to the complexity of the Y-Fe-O phase diagram, and the lattice mismatch between Si and YIG. In this paper, we report the effect of deposition and post-deposition annealing (PDA) temperatures on the structure and the magnetic properties of YIG deposited on silicon using pulsed laser deposition. Both temperatures are found to be important for growing phase pure YIG on silicon. Non-garnet phases or mixed Fe valence states are observed in films when deposited or PDA at too high temperatures, whereas partially amorphous thin films are obtained when deposited or PDA at too low temperatures. YIG thin films with bulk-like structure and saturation magnetization are obtained for films deposited at 400 °C and PDA at 800 °C-850 °C, respectively.
Distributed Data Aggregation Technology for Real-Time DDoS Attacks Detection

The information technology has revolutionized almost every facet of our lives. Government, commercial, and educational organizations depend on computers and Internet to such an extent that day-to-day operations are significantly hindered when the networks are “down” (Gordon, Loeb, Lucyshyn & Richardson, 2005). The prosperity of the Internet also attracted abusers and attackers motivated for personal, financial, or even political reasons. What attackers aim at currently is beyond obtaining unauthorized network accesses or stealing private information, there have been attacks on Internet infrastructures (Chakrabarti & Manimaran, 2002; Moore, Voelker & Savage, 2001; Naoumov & Ross, 2006). Distributed Denial of Services (DDoS) attacks is one of such attacks that can lead to enormous destruction, as different infrastructure components of the Internet have implicit trust relationship with each other (Mirkovic & Reiher, 2004; Specht & Lee, 2004). The DDoS attacker often exploits the huge resource asymmetry between the Internet and the victim systems (Chen, Hwang & Ku, 2007; Douligeris & Mitrokosta, 2003). A comprehensive solution to DDoS attacks requires covering global effects over a wide area of autonomous system (AS) domains on the Internet (Mirkovic & Reiher, 2005). Timely detection of the ongoing attacks is the prerequisite of any effective defense scheme (Carl, Kesidis, Brooks & Rai, 2006). It is highly desirable to detect DDoS attacks at very early stage, instead of waiting for the flood to become widespread. It is mandatory for the detection systems to collect real time traffic data from widely deployed traffic monitors and construct the spatiotemporal pattern of anomaly propagation inside the network. This chapter will introduce a novel distributed real time data aggregation technique named Change Aggregation Tree (CAT). The CAT system adopts a hierarchical architecture to simplify the alert correlation and global detection procedures. At intra-domain level, each individual router, which plays the role of traffic monitor, periodically report the local traffic status to the CAT server in the AS. At the inter-domain layer, CAT servers share local detected anomaly patterns with peers located in other ASes, where the potential attack victim is located.
Tumor cell invasion of basement membrane in vitro is regulated by amino acids.

Because most cancer deaths result from disseminated disease, understanding the regulation of tumor invasion and metastasis is a central theme in tumor cell biology. Interactions between extracellular matrices (ECM) and cellular microenvironment play a crucial role in this process. We have tested selected amino acids and polyamines for their ability to regulate RL95-2 cell invasion through both intact human amniotic basement membrane and a novel human ECM (Amgel). Three major systems for neutral amino acid transport, systems L, A, and ASC, are operational in these neoplastic cells. Amino acids entering the cell via transport system A or N, i.e., (methyl amino)-isobutyrate (MeAIB) or Asn, markedly enhanced invasiveness of these human adenocarcinoma cells as measured by a standard 72-hr amnion or Amgel invasion assay. Addition of 2-amino-2-norborane carboxylic acid (BCH; 1 mM), a model substrate of the L transport system, caused a significant decrease in invasive activity when tested in the Amgel assay. Interestingly, Val lowers steady-state levels of MeAIB uptake and blocks the increase in cell invasion elicited by MeAIB. At the same time, these amino acids do not influence cell proliferation activity. Neither the charged amino acid Lys or Asp (not transported by A/N/L systems) nor the polyamines putrescine, spermidine, or spermine modulate invasiveness under similar experimental conditions. Moreover, the observed time-dependent stimulation of system A activity (cellular influx of MeAIB) by substrate depletion is prevented by the addition of actinomycin D (5 microM) or cycloheximide (100 microM), suggesting the involvement of de novo RNA and protein synthesis events in these processes. MeAIB treatment of tumor cells selectively increased the activities of key invasion-associated type IV collagenases/gelatinases. These results indicate that in the absence of defined regulators (growth factors or hormones), certain amino acids may contribute to the epigenetic control of human tumor cell invasion and, by extension, metastasis. We propose that amino acids, acting via specific signaling pathways, modulate phenotypic cell behavior by modulating the levels of key regulatory enzymatic proteins.
High IL‐13 production by human neonatal T cells: neonate immune system regulator?

Neonates are highly susceptible to diseases and display biased type 2 immune responses, although no skewing to type 2 cytokines has been reported. In view of the emerging importance of IL‐13 in type 2 inflammatory responses and clinical allergy, we analyzed IL‐13 production by neonatal T cells. We found that, mainly CD8 T cells produced high levels of IL‐13, while producing low levels ofIL‐4, IL‐10 and IFN‐γ, upon primary and secondary stimulation. Our results point towards a possible immunoregulatory role of CD8 T cells in neonate responses. Moreover, they suggest that the abundance of IL‐13 in the neonate immune system might account for the type 2 bias in neonates, providing a basis for the high disease susceptibility of newborns, for instance to allergic diseases.
Continuous improvement of a document treatment chain using reinforcement learning

We tackle the problem of continuous improvement of a treatment chain which extracts events from open-source documents. We use the human operators' corrections to allow the treatment chain to learn from its errors, and self-improve generally. We apply reinforcement learning (specifically Q-learning) to this problem, where the actions are the services of a treatment chain for the extraction of information. The objective is to use the user feedback to allow the system to learn the ideal configuration of the services (order, gazetteers, and extraction rules) based on the characteristics of the documents treated (language, type, etc.). We carry out the first experiments with automatically generated feedback data, and the results are encouraging.
Optimization of double-sampled PWM used within power supplies

The emergence of high-frequency high-voltage power semiconductor devices allows the re-design of AC power supplies for operation at higher pulse frequencies with benefits in reduced loss and improved reliability. Conventional PWM algorithms face a hard limit of the minimum pulse width in certain operation points. This paper discusses and proposes a set of new PWM algorithms able to operate the power stage at higher switching frequency without minimum pulse occurrences. These PWM algorithms follow the Staircase PWM algorithm and use optimization at the pulse level. The implementation of such a non-conventional complex PWM structure is possible in modern FPGA System-on-Chip devices.
Interaction of a rat lung lectin with the exopolysaccharides of Pseudomonas aeruginosa

The specific interaction between the exopolysaccharide purified from a number of Pseudomonas aeruginosa isolates from cystic fibrosis patients and a rat lung heparin-lectin was assayed. The polysaccharide prepared from Homma serotypes M, B, I, and G did not act as hapten inhibitors of lectin activity, whereas the polymers prepared from ca. 80% of strains that did not type with Homma serum did act as hapten inhibitors. Inhibition was shown not to be due to lipopolysaccharide. The infrared spectrums of both inhibitory and noninhibitory polymers appeared very similar, although small amounts of glucose and an unidentified amino sugar were found only in the nontypable strains. This evidence suggests that rat lung lectin recognizes and distinguishes a specific type of alginate-like polymer prevalent on the Homma nontypable P. aeruginosa.
etermination of the metabolizable energy content of common eedstuffs in meat-type growing ducks

A trial was conducted using 275 growing Cherry Valley ducks to determine the apparent (AMEn) and true (TMEn) metabolizable energy corrected for nitrogen of maize, broken rice, rice bran, wheat bran, cassava meal, soybean meal and two fish meals with 550 g (low protein) and 600 g (high protein) crude protein (CP)/kg. The design was completely randomized with 5 pens replicates of 5 birds each per ingredient. Five extra pens were used to measure endogenous energy loss. Trial was conducted within 14 days with the last 4 days for feeding and excreta collection to measure the AMEn and TMEn. The AMEn were 14.65, 14.63, 12.33, 12.15, 13.38, 11.25, 11.85, and 11.92 MJ/kg dry matter for maize, broken rice, rice bran, wheat bran, cassava meal, soybean meal and low and high CP fish meals, respectively. The TMEn values were 0.76–1.47% higher than the AMEn values. © 2011 Elsevier B.V. All rights reserved.