Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutational Analysis of the Sir3 BAH Domain Reveals Multiple Points of Interaction with Nucleosomes

ABSTRACT Sir3, a component of the transcriptional silencing complex in the yeast Saccharomyces cerevisiae, has an N-terminal BAH domain that is crucial for the protein's silencing function. Previous work has shown that the N-terminal alanine residue of Sir3 (Ala2) and its acetylation play an important role in silencing. Here we show that the silencing defects of Sir3 Ala2 mutants can be suppressed by mutations in histones H3 and H4, specifically, by H3 D77N and H4 H75Y mutations. Additionally, a mutational analysis demonstrates that three separate regions of the Sir3 BAH domain are important for its role in silencing. Many of these BAH mutations also can be suppressed by the H3 D77N and H4 H75Y mutations. In agreement with the results of others, in vitro experiments show that the Sir3 BAH domain can interact with partially purified nucleosomes. The silencing-defective BAH mutants are defective for this interaction. These results, together with the previously characterized interaction between the C-terminal region of Sir3 and the histone H3/H4 tails, suggest that Sir3 utilizes multiple domains to interact with nucleosomes.
THE USE OF CITATION DATA IN WRITING THE HISTORY OF SCIENCE

Abstract : A study is reported which tested the hypothesis that citation indexes are useful heuristic tools for the historian. In this approach, the history of science is regarded as a chronological sequence of events in which each new discovery is dependent upon earlier discoveries. Models of history were constructed consisting of chronological maps or topological network diagrams. Two such models were used here. The first is based on the events in the history of DNA as described by Dr. Isaac Asimov in the Genetic Code. The second is based on the bibliographic citation data contained in the documents which are the original published studies of events represented in the Asimov book. The interdependencies of linkages among 40 major events (nodes) included in both network diagrams were mapped and compared. The study confirmed 65% (28 of 43) of the historical dependencies in the Asimov network by corresponding linkages established by citations. In addition, 31 citation connections were found which did not correspond to any historical dependencies noted in The Genetic Code.
Resource Allocation for Frequency-Selective Fading, Multi-Carrier Systems with Fairness Constraints

We consider the problem of fair resource allocation for multi-carrier systems. Opportunistic scheduling exploits the time-varying, location-dependent channel conditions to achieve multi-user diversity. Previous work in this area has focused on the single-user scheduling in single-carrier systems over a narrowband flat-fading channel, where only one node is scheduled at a time. In wideband multi-carrier systems, multiple nodes can be scheduled concurrently over multiple narrowband channels. In this paper, we analyze proportional fair scheduling (PFS) in multi-carrier systems over a wideband frequency-selective channel. In particular, we first derive analytical expressions for the throughput of opportunistic scheduling under proportional fairness constraints in a frequency-selective channel, for both single-user and multi-user systems. Furthermore, we provide closed-form expression to quantify the throughput benefit of the multi-user PFS over the single-user PFS in frequency-selective systems. This research is an extension of our previous theoretical work on opportunistic scheduling over flat-fading channel in narrowband single-carrier systems.
Modeling Data and Knowledge in the EON Guideline Architecture

Compared to guideline representation formalisms, data and knowledge modeling for clinical guidelines is a relatively neglected area. Yet it has enormous impact on the format and expressiveness of decision criteria that can be written, on the inferences that can be made from patient data, on the ease with which guidelines can be formalized, and on the method of integrating guideline-based decision-support services into implementation sites' information systems. We clarify the respective roles that data and knowledge modeling play in providing patient-specific decision support based on clinical guidelines. We show, in the context of the EON guideline architecture, how we use the Protégé-2000 knowledge-engineering environment to build (1) a patient-data information model, (2) a medical-specialty model, and (3) a guideline model that formalizes the knowledge needed to generate recommendations regarding clinical decisions and actions. We show how the use of such models allows development of alternative decision-criteria languages and allows systematic mapping of the data required for guideline execution from patient data contained in electronic medical record systems.
Distribution of Antimicrobial Resistance and Virulence Genes in Enterococcus spp. and Characterization of Isolates from Broiler Chickens

ABSTRACT Enterococci are now frequent causative agents of nosocomial infections. In this study, we analyzed the frequency and distribution of antibiotic resistance and virulence genotypes of Enterococcus isolates from broiler chickens. Fecal and cecal samples from nine commercial poultry farms were collected to quantify total enterococci. Sixty-nine presumptive enterococci were isolated and identified by API 20 Strep, and their susceptibilities to antibiotics were determined. Genotypes were assessed through the use of a novel DNA microarray carrying 70 taxonomic, 17 virulence, and 174 antibiotic resistance gene probes. Total enterococcal counts were different from farm to farm and between sample sources (P < 0.01). Fifty-one (74%) of the isolates were identified as E. faecium, whereas nine (13%), seven (10%), and two (3%) isolates were identified as E. hirae, E. faecalis, and E. gallinarum, respectively. Multiple-antibiotic resistance was evident in E. faecium and E. faecalis isolates. The most common multiple-antibiotic resistance phenotype was Bac Ery Tyl Lin Str Gen Tet Cip. Genes conferring resistance to aminoglycoside (aac, aacA-aphD, aadB, aphA, sat4), macrolide (ermA, ermB, ermAM, msrC), tetracycline (tetL, tetM, tetO), streptogramin (satG_vatE8), bacitracin (bcrR), and lincosamide (linB) antibiotics were detected in corresponding phenotypes. A range of 9 to 12 different virulence genes was found in E. faecalis, including ace, agg, agrBEfs (agrB gene of E. faecalis), cad1, the cAM373 and cCF10 genes, cob, cpd1, cylAB, efaAEfs, and gelE. All seven E. faecalis isolates were found to carry the gelE gene and to hydrolize gelatin and bile salts. Results from this study showed the presence of enterococci of public and environmental health concerns in broiler chicken farms and demonstrated the utility of a microarray to quickly and reliably analyze resistance and virulence genotypes of Enterococcus spp.
Evaluation approaches of sludge ultrasonic pretreatment efficiency: a review

Ultrasonic irradiation (US) is a feasible and promising mechanical disruption technique for sludge disintegration, biodegradability acceleration, and anaerobic digestion enhancement. It is clear that many processing factors significantly affect cavitation and consequently the efficiency of sludge pretreatment. Therefore, assessment, comparison, and selection of optimal ultrasonic conditions for actual application of sludge pretreatment are sorely necessary. The objective of this work is to present an extensive review of evaluation approaches of sludge ultrasonic pretreatment efficiency based on physical, chemical, and biological properties of sludge.
Side-channel Analysis of Lightweight Ciphers: Current Status and Future Directions

Side-channel attacks represent a powerful category of attacks against cryptographic devices. Still, side-channel analysis for lightweight ciphers is much less investigated than for instance for AES. Although in­ tuition may lead to the conclusion that lightweight ciphers are weaker in terms of side-channel resistance, that remains to be confirmed and quan­ tified. In this paper, we consider various side-channel analysis metrics which should provide an insight on the resistance of lightweight ciphers against side-channel attacks. In particular, for the non-profiled scenario we use the confusion coefficient and empirical correlation power analysis. Furthermore, we conduct a profiled side-channel analysis using various machine learning attacks on PRESENT and AES. Our results show that the difference between AES and lightweight ciphers is smaller than one would expect. Interestingly, we observe that the studied 4-bit S-boxes have different side-channel resiliences, where the difference in the 8-bit ones is only theoretically present.
Development of an enzyme-linked immunosorbent assay (ELISA) for quantification of skeletal muscle calpastatin.

An indirect antibody ELISA was developed for rapid and sensitive quantification of skeletal muscle calpastatin. Polyclonal antibodies were raised in rabbits against recombinant calpastatin, corresponding to domains 2, 3, and 4 of bovine skeletal muscle calpastatin. Western blot analysis revealed that these antibodies specifically recognize an immunoreactive calpastatin protein of approximately 130 kDa in prerigor skeletal muscle extracts. The intensity of the immunoreactive bands corresponds qualitatively with assayable calpastatin activity. For ELISA development, optimum dilutions of sample, primary anti-calpastatin antibody, and peroxidase-conjugated secondary antibody were determined by titration. A dilution optimum for coating of Immulon 4 (Dynatech) plates was observed when heated muscle extracts were diluted to 2 to 4 micrograms of protein/mL and incubated for 2 h at 37 degrees C. Optimum primary (30 micrograms IgG/mL) and secondary (Sigma A-6154; 1:1000 dilution) antibody incubations were for 1 h at 37 degrees C. Tetramethylbenzidine was used as substrate and A450 of the stopped reaction product was recorded in an automated plate reader. Calpastatin ELISA results were linearly related to calpastatin activity (calpain inhibitory activity) of heated longissimus muscle homogenates from prerigor lamb (r2 = .89; n = 40) and beef aged for 24 or 48 h (r2 = .90; n = 47). Intra-assay CV was < 5% (n = 8) and inter-assay CV was < 6% (n = 5). This assay offers advantages of speed, simplicity, and sensitivity over conventional methodology for calpastatin quantification.
A Tool Supporting the Extraction of Angling Effort Data from Remote Camera Images

Estimating angling effort on more than a few lakes can be prohibitively expensive using creel surveys and often requires finer-scale angler distribution data than aerial surveys can provide. An alternate method uses remote cameras to capture images of lakes at hourly intervals over long time periods. Technicians then visually analyze the thousands of generated images for features of interest (e.g., angler counts and environmental conditions) and use those data to estimate angling effort. The problem is that the visual analysis step is time-consuming, expensive, and difficult to validate. Consequently, we elicited the strategies and best practices technicians used when analyzing images and identified bottlenecks. We then designed software, called Timelapse to better support image analysis. In use for several years, Timelapse has proven a cost-effective method of estimating angling effort in British Columbia's small lakes fisheries; it significantly eases a technician's workflow and doubles the number of im.
Crucial role of membrane type 1 matrix metalloproteinase (MT1- MMP) in RhoA/Rac1-dependent signaling pathways in thrombin- stimulated endothelial cells.

AIM Thrombin induces vascular responses including the promotion of tissue factor (TF) and plasminogen activator inhibitor-1 (PAI-1) protein expression, which is modulated by small GTPases RhoA and Rac1, Ca(2+) signaling and reactive oxygen species (ROS). Recent studies have shown that membrane type 1 matrix metalloproteinase (MT1-MMP) functions not only as a protease but also as a signaling molecule. In this study, we hypothesized that MT1-MMP may mediate RhoA and Rac1 activation and their downstream events in thrombin-stimulated endothelial cells. METHODS We used cultured human aortic endothelial cells (HAECs). MT1-MMP was silenced by small interfering RNA (siRNA). RhoA was inhibited by C3 exoenzyme, whereas adenovirus-mediated gene transfection of dominant negative RhoA and Rac1 was used for the inhibition of RhoA and Rac1. RhoA and Rac1 activation was determined by pull-down assays. Intracellular Ca(2+) concentrations ([Ca(2+)](i)) were fluorescently measured by fura-2 assay. NADPH oxidase activity was determined by lucigenin-enhanced chemiluminescence. RESULTS Inhibition of RhoA attenuated thrombin-triggered [Ca(2+)](i) increase and TF and PAI-1 expression in HAECs, whereas thrombin-triggered ROS generation and TF and PAI-1 expression were blocked by inhibition of Rac1. Silencing of MT1-MMP attenuated thrombin-triggered RhoA and Rac1 activation, resulting in the attenuation of downstream events including Ca(2+) signaling, NADPH oxidase activity, ROS generation, and TF and PAI-1 expression. CONCLUSIONS The present study shows that MT1-MMP mediates the RhoA/Ca(2+) and Rac1/NADPH oxidase-dependent signaling pathways in thrombin-induced vascular responses.
Mesoscale structure in a coastal front: a case study

Between 31 March and 03 April 2004, a heavy rainstorm moved through the southern part of the northeast United States, extending from Connecticut eastward into Rhode Island and northward into Massachusetts, Vermont, and New Hampshire. This event caused extreme precipitation totals of over three inches throughout the region, with some areas receiving in excess of seven inches of precipitation as shown in Figure 1.
The SAMI Galaxy Survey: revising the fraction of slow rotators in IFS galaxy surveys

The fraction of galaxies supported by internal rotation compared to galaxies stabilized by internal pressure provides a strong constraint on galaxy formation models. In integral field spectroscopy surveys, this fraction is biased because survey instruments typically only trace the inner parts of the most massive galaxies. We present aperture corrections for the two most widely used stellar kinematic quantities V/σ and λ_R (spin parameter proxy). Our demonstration involves integral field data from the SAMI (Sydney-AAO Multi-object Integral-field spectrograph) Galaxy Survey and the ATLAS^(3D) survey. We find a tight relation for both V/σ and λ_R when measured in different apertures that can be used as a linear transformation as a function of radius, i.e. a first-order aperture correction. In degraded seeing, however, the aperture corrections are more significant as the steeper inner profile is more strongly affected by the point spread function than the outskirts. We find that V/σ and λ_R radial growth curves are well approximated by second-order polynomials. By only fitting the inner profile (0.5R_e), we successfully recover the profile out to one R_e if a constraint between the linear and quadratic parameter in the fit is applied. However, the aperture corrections for V/σ and λ_R derived by extrapolating the profiles perform as well as applying a first-order correction. With our aperture-corrected λ_R measurements, we find that the fraction of slow rotating galaxies increases with stellar mass. For galaxies with log M*/M⊙ > 11, the fraction of slow rotators is 35.9 ± 4.3 per cent, but is underestimated if galaxies without coverage beyond one Re are not included in the sample (24.2 ± 5.3 per cent). With measurements out to the largest aperture radius, the slow rotator fraction is similar as compared to using aperture-corrected values (38.3 ± 4.4 per cent). Thus, aperture effects can significantly bias stellar kinematic integral field spectrograph studies, but this bias can now be removed with the method outlined here.
Quality Metric Development Framework (qMDF)

Several object-oriented metrics have been developed and used in conjunction with the quality models to predict the overall quality of software. However, it may not be enough to propose metrics. The fundamental question may be of their validity, utility and reliability. It may be much significant to be sure that these metrics are really useful and for that their construct validity must be assured. Thereby, good quality metrics must be developed using a foolproof and sound framework / model. A critical review of literature on the attempts in this regard reveals that there is no standard framework or model available for such an important activity. This study presents a framework for the quality metric development called Metric Development Framework (qMDF), which is prescriptive in nature. qMDF is a general framework but it has been established specially with ideas of object-oriented metrics. qMDF has been implemented to develop a good quality design metric, as a validation of proposed framework. Finally, it is defended that adaptation of qMDF by metric developers would yield good quality metrics, while ensuring their construct validity, utility, reliability and reduced developmental effort.
Olfactory Mucosal Autografts and Rehabilitation for Chronic Traumatic Spinal Cord Injury

Background/objective . Basic science advances in spinal cord injury (SCI) are leading to novel clinical approaches. The authors report a prospective, uncontrolled pilot study of the safety and outcomes of implanting olfactory mucosal autografts (OMA) in 20 patients with chronic, sensorimotor complete or motor complete SCI. Methods. Seven paraplegic and 13 tetraplegic subjects (17 men and 3 women; 19-37 years old) who sustained a traumatic SCI 18 to 189 months previously (mean = 49 months) were enrolled. Preoperative rehabilitation that emphasized lower extremity stepping using either overground walking training or a robotic weight-supported treadmill training was provided for 25 to 39 hours per week for a median of 4 months at 3 sites. No change in ASIA Impairment Scale (AIS) motor scores for the lower extremities or AIS grades of completeness was found. OMAs were transplanted into 1.3- to 4-cm lesions at C4-T12 neurological levels after partial scar removal. Therapy was continued postoperatively. Preoperative and postoperative assessments included AIS scores and classification, electromyography (EMG) of attempted voluntary contractions, somatosensory evoked potentials (SSEP), urodynamic studies with sphincter EMG, spinal cord magnetic resonance imaging (MRI), and otolaryngology and psychology evaluations. The Functional Independence Measure (FIM) and Walking Index for Spinal Cord Injury (WISCI) were obtained in 13 patients. Results. All patients survived and recovered olfaction. One patient was rehospitalized for aseptic meningitis. Minor adverse events occurred in 4 others. The mean duration of follow-up was 27.7 months (range = 12-45 months). By MRI, the lesion site was filled in all patients with no neoplastic overgrowth or syringomyelia. AIS grades improved in 11 of 20 patients, 6 (A → C), 3 (B → C), and 2 (A → B), and declined in 1 (B → A). Improvements included new voluntary EMG responses (15 patients) and SSEPs (4 patients). Scores improved in the FIM and WISCI (13/13 tested), and urodynamic responses improved in 5 patients. Conclusion. OMA is feasible, relatively safe, and possibly beneficial in people with chronic SCI when combined with postoperative rehabilitation. Future controlled trials may need to include a lengthy and intensive rehabilitation arm as a control.
Determinants of Protein Abundance and Translation Efficiency in S. cerevisiae

The translation efficiency of most Saccharomyces cerevisiae genes remains fairly constant across poor and rich growth media. This observation has led us to revisit the available data and to examine the potential utility of a protein abundance predictor in reinterpreting existing mRNA expression data. Our predictor is based on large-scale data of mRNA levels, the tRNA adaptation index, and the evolutionary rate. It attains a correlation of 0.76 with experimentally determined protein abundance levels on unseen data and successfully cross-predicts protein abundance levels in another yeast species (Schizosaccharomyces pombe). The predicted abundance levels of proteins in known S. cerevisiae complexes, and of interacting proteins, are significantly more coherent than their corresponding mRNA expression levels. Analysis of gene expression measurement experiments using the predicted protein abundance levels yields new insights that are not readily discernable when clustering the corresponding mRNA expression levels. Comparing protein abundance levels across poor and rich media, we find a general trend for homeostatic regulation where transcription and translation change in a reciprocal manner. This phenomenon is more prominent near origins of replications. Our analysis shows that in parallel to the adaptation occurring at the tRNA level via the codon bias, proteins do undergo a complementary adaptation at the amino acid level to further increase their abundance.
Topical Dermal Application of Essential Oils Attenuates the Severity of Adjuvant Arthritis in Lewis Rats

This study was aimed at examining the effect of an ointment containing essential oils (EO) on the severity of adjuvant arthritis (AA), an experimental model of human rheumatoid arthritis (RA), in Lewis rats and to define the underlying mechanisms. At the onset of AA, the rats received topical application twice daily of an ointment containing 20% EO or placebo ointment. The synovial fluid (SF) and synovium‐infiltrating cells (SIC) of rats were tested for pro‐inflammatory cytokines TNF‐α and IL‐1β. The hind paws and skin were examined histologically. The activity/level of matrix metalloproteinases (MMPs) and anti‐mycobacterial heat‐shock protein 65 (Bhsp65) antibodies were tested. Arthritic rats treated with ointment containing EO developed less severe clinical arthritis compared with the controls, and this activity was attributable to EO and not to the carrier oil. The levels of TNF‐α and IL‐1β, and the activity of MMPs in SF and SIC‐lysate were significantly reduced in EO‐treated arthritic rats compared with the controls. However, the levels of anti‐Bhsp65 antibodies were unaffected by treatment. Thus, topical dermal delivery of EO‐containing ointment down‐modulates the severity of AA in Lewis rats by inhibiting defined mediators of inflammation. Such ointments should be tested in patients with RA and other arthritic conditions. Copyright © 2011 John Wiley & Sons, Ltd.
Ultra-intense laser-driven target normal sheath radiation in the terahertz region

Ultra-intense radiation in the terahertz (THz) regime emitted from the rear side of laser-irradiated solid target is experimentally investigated using a 20 TW fs laser system. The THz radiation emitted in a conical angle around 45 degrees is of radially polarized and has its duration of tens of ps. The waveform, angular distribution, polarization and laser intensity dependence of the observed radiation are in good agreement with those predicted for the radiation from deceleration of >sub-MeV electrons passing through the sheath electric field behind the target.
Information Retrieval on the web and its evaluation

Internet is one of the main sources of information for millions of people. One can find information related to practically all matters on internet. Moreover if we want to retrieve information about some particular topic we may find thousands of Web Pages related to that topic. But our main concern is to find relevant Web Pages from among that collection. So in this paper I have discussed that how information is retrieved from the web and the efforts required for retrieving this information in terms of system and users efforts.