Miracle-dz/UniFAR-FTUs huggingface dataset:
The homologous regulators ANR of Pseudomonas aeruginosa and FNR of Escherichia coli have overlapping but distinct specificities for anaerobically inducible promoters.

The anaerobic transcriptional regulator ANR induces the arginine deiminase and denitrification pathways in Pseudomonas aeruginosa during oxygen limitation. The homologous activator FNR of Escherichia coli, when introduced into an anr mutant of P. aeruginosa, could functionally replace ANR for anaerobic growth on nitrate but not for anaerobic induction of arginine deiminase. In an FNR-positive E. coli strain, the ANR-dependent promoter of the arcDABC operon, which encodes the enzymes of the arginine deiminase pathway, was not expressed. To analyse systematically these distinct induction patterns, a lacZ promoter-probe, broad-host-range plasmid containing various -40 regions (the ANR/FNR recognition sequences) and -10 promoter sequences was constructed. These constructs were tested in P. aeruginosa and in E. coli expressing either ANR or FNR. In conjunction with the consensus -10 hexamer of E. coli sigma 70 RNA polymerase (TATAAT), the consensus FNR site (TTGAT . ATCAA) was recognized efficiently by ANR and FNR in both hosts. By contrast, when promoters contained the Arc box (TTGAC . ATCAG), which is found in the arcDABC promoter, or a symmetrical mutant FNR site (CTGAT . ATCAG), ANR was a more effective activator than was FNR. Conversely, an extended 22 bp, fully symmetrical FNR site allowed better activation with FNR than with ANR. Combination of the arc promoter -10 sequence (CCTAAT) with the Arc box or the consensus FNR site resulted in good ANR-dependent expression in P. aeruginosa but gave practically no expression in E. coli, suggesting that RNA polymerase of P. aeruginosa differs from the E. coli enzyme in -10 recognition specificity. In conclusion, ANR and FNR are able to activate the RNA polymerases of P. aeruginosa and E. coli when the -40 and -10 promoter elements ae identical or close to the E. coli consensus sequences.
The Linearized Alternating Direction Method of Multipliers for Dantzig Selector

The Dantzig selector was recently proposed to perform variable selection and model fitting in the linear regression model. It can be solved numerically by the alternating direction method of multipliers (ADM); and in this paper, we show that the application of ADM to the Dantzig selector can be speeded up significantly if one of its resulting subproblems at each iteration is linearized. The resulting linearized ADM for the Dantzig selector is shown to be efficient for solving both synthetic and real world data sets.
Optical fiber Fabry-Pérot sensor fabrication based on focused ion beam post-processing

A combination of focused ion beam milling and chemical etching is proposed for the creation of Fabry-Pérot cavities in microwires. Both simple cavities and cantilevers are created on 15 μm-diameter microwires and characterized in temperature. The cantilever structure shows sensitivity to vibration and is capable of measuring frequencies in the range 1 Hz – 40 kHz.
Centralized and decentralized approaches to smart charging of plug-in Vehicles

A large penetration of electric and plug-in hybrid electric vehicles would likely result in increased system peaks and overloading of power system assets if the charging of vehicles is left uncontrolled. In this paper we propose both a centralized and a decentralized smart-charging scheme which seek to minimize system-wide generation costs while respecting grid constraints. Under the centralized scheme, vehicles' batteries are aggregated to virtual storage resources at each network node, which are optimally dispatched with a multiperiod Optimal Power Flow. On the other hand, under the decentralized scheme, price profiles broadcasted to vehicles day-ahead are determined so that the optimal response of individual vehicles to this tariff achieves the goal of cost minimization. Two alternative tariffs are explored, one where the same price profile applies system-wide, and another where different prices can be defined at different nodes. Results show that compared with uncontrolled charging, these smart-charging schemes successfully avoid asset overloading, displace most charging to valley hours and reduce generation costs. Moreover they are robust in the face of forecast errors in vehicle behavior.
What Factors Affect People's Stickiness on the Social Network Site? The Case of Facebook in Taiwan

With the rapid growth of population of Internet, social network site has become a communicable platform that people share some information themselves or connecting whit friends, such as MySpace, Facebook, Twitter. This study uses TRA and TAM as basic model, and combined with the Social Identity Theory to explore what factors affect internet users to stick on the social network site. The study adopts the Facebook as experiment platform, and collects 318 Taiwanese samples from internet. After the analysis of structural equation model, main results are the followings: (1)Users’ social identity, perceived usefulness, perceived entertainment, attitude toward a social network site will significantly and positively affect their stickiness on a social network site; (2)Users’ perceived usefulness, perceived ease of use, perceived entertainment will significantly and positively affect their attitude toward a social network site; (3)Users’ social identity will affect their perceived usefulness and perceived entertainment toward a social network site.
In vivo enzymatic modulation of IgG glycosylation inhibits autoimmune disease in an IgG subclass-dependent manner

IgG antibodies are potent inducers of proinflammatory responses. During autoimmune diseases such as arthritis and systemic lupus erythematosus, IgG autoantibodies are responsible for the chronic inflammation and destruction of healthy tissues by cross-linking Fc receptors on innate immune effector cells. The sugar moiety attached to the asparagine-297 residue in the constant domain of the antibody is critical for the overall structure and function of the molecule. Removal of this sugar domain leads to the loss of the proinflammatory activity, suggesting that in vivo modulation of antibody glycosylation might be a strategy to interfere with autoimmune processes. In this work, we investigated whether removal of the majority of the IgG-associated sugar domain by endoglycosidase S (EndoS) from Streptococcus pyogenes is able to interfere with autoimmune inflammation. We demonstrate that EndoS injection efficiently removes the IgG-associated sugar domain in vivo and interferes with autoantibody-mediated proinflammatory processes in a variety of autoimmune models. Importantly, however, we observed a differential impact of EndoS-mediated sugar side chain hydrolysis on IgG activity depending on the individual IgG subclass.
Leishmania amazonensis Amastigotes Trigger Neutrophil Activation but Resist Neutrophil Microbicidal Mechanisms

ABSTRACT Neutrophils are the first cells to infiltrate to the site of Leishmania promastigote infection, and these cells help to reduce parasite burden shortly after infection is initiated. Several clinical reports indicate that neutrophil recruitment is sustained over the course of leishmaniasis, and amastigote-laden neutrophils have been isolated from chronically infected patients and experimentally infected animals. The goal of this study was to compare how thioglycolate-elicited murine neutrophils respond to L. amazonensis metacyclic promastigotes and amastigotes derived from axenic cultures or from the lesions of infected mice. Neutrophils efficiently internalized both amastigote and promastigote forms of the parasite, and phagocytosis was enhanced in lipopolysaccharide (LPS)-activated neutrophils or when parasites were opsonized in serum from infected mice. Parasite uptake resulted in neutrophil activation, oxidative burst, and accelerated neutrophil death. While promastigotes triggered the release of tumor necrosis factor alpha (TNF-α), uptake of amastigotes preferentially resulted in the secretion of interleukin-10 (IL-10) from neutrophils. Finally, the majority of promastigotes were killed by neutrophils, while axenic culture- and lesion-derived amastigotes were highly resistant to neutrophil microbicidal mechanisms. This study indicates that neutrophils exhibit distinct responses to promastigote and amastigote infection. Our findings have important implications for determining the impact of sustained neutrophil recruitment and amastigote-neutrophil interactions during the late phase of cutaneous leishmaniasis.
Autoregressive order selection in missing data problems

Maximum likelihood presents a useful solution for the estimation of the parameters of time series models when data are missing. The highest autoregressive (AR) model order that can be computed without numerical problems is limited and depends on the missing fraction. Order selection will be necessary to obtain a good AR model. The best criterion to select an AR order with an accurate spectral estimate is slightly different from the criterion for contiguous data. The penalty for the selection of additional parameters depends on the missing fraction. The resulting maximum likelihood algorithm can give very accurate spectra, sometimes even if less than 1% of the data remains.
A Scalable Probabilistic Classifier for Language Modeling

We present a novel probabilistic classifier, which scales well to problems that involve a large number of classes and require training on large datasets. A prominent example of such a problem is language modeling. Our classifier is based on the assumption that each feature is associated with a predictive strength, which quantifies how well the feature can predict the class by itself. The predictions of individual features can then be combined according to their predictive strength, resulting in a model, whose parameters can be reliably and efficiently estimated. We show that a generative language model based on our classifier consistently matches modified Kneser-Ney smoothing and can outperform it if sufficiently rich features are incorporated.
Creep – fatigue damage accumulation and interaction diagram based on metallographic interpretation of mechanisms

Abstract The deleterious effect of creep damage upon fatigue endurance in elevated temperature low cycle fatigue is well established and has become known as the ‘creep – fatigue interaction’. This has been identified as a narrow region where a transgranular crack becomes intergranular as creep damage develops. In other cases transgranular fatigue cracks and intergranular creep cavitation damage to some extent can take place separately (‘competitive’ mode) so that interaction is less pronounced. These phenomena have been incorporated into ‘damage interaction diagrams’ which feature in many high temperature Code cases (ASME, R5, RCC-MR etc.). Fractional creep and fatigue damage are considered separately, and failure is conceded when their sum is unity (‘additive’ mode). For some materials the sum is set to a value <1. It appears that purely empirical arguments have been used to arrive at total damage values <1. It is shown that such deviations from linearity can be simply predicted, assuming that creep damage accumulates uniformly during a given test. For maximum interaction, the resulting assessment curve is shown to pass through the points (total fatigue damage = 0.4; total creep damage = 0.4), or very nearly. The influence of fatigue upon creep damage is less well known. Examples are provided, and when included in the calculation, produce a more damaging curve passing through the point (0.33, 0.33). By use of ‘interaction coefficients’ less damaging curves for the ‘competitive’ model can be produced. The calculation may be simplified by use of an effective fatigue damage cycle number for use as a reference. Based on metallographic examples from power plant operation and laboratory testing, the ‘competitive’, ‘additive’ and ‘true interaction’ modes of creep and fatigue damage are identified. These can be related to practical applications of base load operation, fast start-up and shut-down procedures, slow start-up and shut-down procedures etc. Components might operate under base load conditions (creep) followed by temperature cycling (fatigue). These sequential events may not be interactive (as has been demonstrated in the laboratory) and thus use of the current assessment diagram would be pessimistic. Comment is made on a proposed damage diagram for the advanced ferritic steels, which is highly conservative and does not reflect their good performance in service and laboratory tests.
Degree and Reciprocity of Self-Disclosure in Online Forums

Cyberspace has become a common social environment in which people interact and operate in many ways. The purpose of the present study was to investigate the occurrence and reciprocity of self-disclosure, two subjects that are extensively studied in face-to-face interactions but only to a limited degree in virtual, computer-mediated, textual communication. Data was based on 240 first messages in a thread, sampled in equal numbers from six Internet forums (three discussion and three support groups), and written in equal numbers by each gender, and 240 first responses to them (a total of 480 forum messages). Trained, expert judges blindly rated each message on the degree to which it disclosed personal information, thoughts, and feelings. Linguistic parameters (total number of words and number of first-voice words) were also used as dependent variables. Results showed the following: (a) self-disclosure in support forums was much higher than in discussion forums, in terms of both total number and type of disclosure; (b) messages in support forums were longer and included more first-voice words than in discussion forums; (c) there were no gender differences interacting with level of self-disclosure; (d) reciprocity of self-disclosure was evident, yielding positive correlations between the measures of self-disclosure in messages and responses to them; (e) some differences appeared in level of reciprocity of self-disclosure between male and female participants, with female respondents tending to be more reciprocal than male respondents. The implications of these results are discussed in light of growing social interactions online, and possible applications are suggested.
Optical properties of polystyrene from the near-infrared to the x-ray region and convergence of optical sum rules

Optical properties of polystyrene in the form of thin films were determined for photon energies between 0.6 and 82 eV from transmission measurements. The results for k, the extinction coefficient, were combined with previous experimental results in the soft and hard x-ray regions up to 8050 eV. Analyses were made on several sum rules for the optical properties in this unusually wide energy range, including a sum rule for the refractive index n, derived recently by Altarelli et al. Redistribution of the oscillator strength corresponding to 2.7% of the total electrons was found between the valence and core excitations of carbon. Using the complex dielectric function and the energy-loss function obtained, the average photoexcitation energy and the average energy loss for fast-charged particles over the entire oscillator strength distribution were evaluated to be 25.1 and 36.8 eV, respectively.
Middle-Down Mass Spectrometry Enables Characterization of Branched Ubiquitin Chains

Protein ubiquitylation, one of the most prevalent post-translational modifications in eukaryotes, is involved in regulating nearly every cellular signaling pathway. The vast functional range of ubiquitylation has largely been attributed to the formation of a diverse array of polymeric ubiquitin (polyUb) chains. Methods that enable the characterization of these diverse chains are necessary to fully understand how differences in structure relate to function. Here, we describe a method for the detection of enzymatically derived branched polyUb conjugates in which a single Ub subunit is modified by two Ub molecules at distinct lysine residues. Using a middle-down mass spectrometry approach in which restricted trypsin-mediated digestion is coupled with mass spectrometric analysis, we characterize the polyUb chains produced by bacterial effector E3 ligases NleL (non-Lee-encoded effector ligase from enterohemorrhagic Escherichia coli O157:H7) and IpaH9.8 (from Shigella flexneri). Because Ub is largely intact after minimal trypsinolysis, multiple modifications on a single Ub moiety can be detected. Analysis of NleL- and IpaH9.8-derived polyUb chains reveals branch points are present in approximately 10% of the overall chain population. When unanchored, well-defined polyUb chains are added to reaction mixtures containing NleL, longer chains are more likely to be modified internally, forming branch points rather than extending from the end of the chain. These results suggest that middle-down mass spectrometry can be used to assess the extent to which branched polyUb chains are formed by various enzymatic systems and potentially evaluate the presence of these atypical conjugates in cell and tissue extracts.
Development of a powerful tool for nanostructuring and multiphoton imaging with nanojoule femtosecond laser pulses

An integrated tool combining control and diagnostic for nanoprocessing of bio-compatible and biological materials and also allowing multiphoton large area laser scanning microscopy has been developed. The device is based on an customized inverted microscope integrating a motorized open x,y stage with a very high precision and repeatability, a piezoelectric z axe. A strong development in hardware and software has been made for the control of the process. Imaging of large area by images reconstruction using a high resolution CCD camera for the machining and perforation of biological materials and non-biological materials on scales in the sub-micrometer range is possible. This tool can also be used as a laser scanning microscope of a large area using a PMT detector. This multi-function compact device is of prime interest and can be considered as a novel tool for nanoprocessing in material science, nanobiotechnology, nanomedicine. Further progress in telecommunications, optics, electronics, biomaterials, medicine, and transport strongly depends on the availability of reliable and rapid processing techniques. Laser-based micro-nano technology holds great promises and the evolution will be dictated by the development of inexpensive yet precise processing tools that can develop and structure materials with a high degree of controllability, accuracy, and reduced residual damage. Applications in biomedicine include, for example, optoporation, cells nanodrilling, nanocutting transfection of cells, deactivation of cell organelles or investigation of cell dynamics but also potentially useful in material science for the manufacture of waveguides, gratings, micro fluidic devices, nanocontainers, data storage, nanolithography, nanomarking,.
Assembly of a Chromosomal Replication Machine: Two DNA Polymerases, a Clamp Loader, and Sliding Clamps in One Holoenzyme Particle.

The Escherichia coli replicase, DNA polymerase III holoenzyme, derives its processivity from the β subunit sliding clamp that encircles DNA and tethers the replicase to the template. The β dimer is assembled around DNA by the γ complex clamp loader in an ATP-dependent reaction. In this report, the essential contact between the clamp loader and β is identified as mediated through the δ subunit of the γ complex. The δ subunit appears to contact the face of the β dimer ring that contains the two C termini. Surprisingly, ATP is required for the γ complex to bind β, but not for δ to bind β. This indicates that δ is buried in the γ complex and suggests a role for ATP in exposing δ for interaction with β. A protease protection assay has been developed to specifically probe the δ subunit within the γ complex. The results of the assay are consistent with an ATP-induced conformational change in the γ complex that alters the state of the δ subunit within it. The implication of these key features to the clamp loading mechanism of the γ complex is discussed.
Computational Issues in Biomedical Nanometrics and Nano-Materials

Biomedical Nanotechnology is an emerging area of great scientific and technological opportunity. It is widely recognized as one of the most potentially beneficial applications of nanotechnology to industry and society to date. Work in this area has a number of computational aspects: information technology based tools and measurement techniques are used to study biosystems with micro- and nano-scale physics and chemistry, and computational methods are helping to generate remarkable new insights into how biological systems function, how metabolic processes interrelate, and how new molecular scale machines can operate. This paper reviews current advances in computational algorithms and tools applied to biomedical nanometrics and nano-materials. We categorize algorithms into three general areas, describe representative methods, and conclude with several promising directions of future investigation.
Activation of the Vibrio cholerae SOS Response Is Not Required for Intestinal Cholera Toxin Production or Colonization

ABSTRACT Cholera toxin, one of the main virulence factors of Vibrio cholerae, is encoded in the genome of CTXφ, a V. cholerae-specific lysogenic filamentous bacteriophage. Although the genes encoding cholera toxin, ctxAB, are known to have their own promoter, the toxin genes can also be transcribed from an upstream CTXφ promoter, PrstA. The V. cholerae SOS response to DNA damage induces the CTX prophage by stimulating gene expression initiating from PrstA. Here, we investigated whether ctxA mRNA levels increase along with the levels of the transcripts for the other CTXφ genes following stimulation of the V. cholerae SOS response. Treatment of V. cholerae with the SOS-inducing agent mitomycin C increased the level of ctxA mRNA approximately sevenfold, apparently by augmenting the activity of PrstA. However, using suckling mice as a model host, we found that intraintestinal ctxA transcription does not depend on PrstA. In fact, the suckling mouse intestine does not appear to be a potent inducer of the V. cholerae SOS response. Furthermore, alleviation of LexA-mediated repression of the V. cholerae SOS regulon was not required for V. cholerae growth in the suckling mouse intestine. Our observations suggest that pathogenicity of V. cholerae does not depend on its SOS response.
Integrating flash-based SSDs into the storage stack

Over the past few years, hybrid storage architectures that use high-performance SSDs in concert with high-density HDDs have received significant interest from both industry and academia, due to their capability to improve performance while reducing capital and operating costs. These hybrid architectures differ in their approach to integrating SSDs into the traditional HDD-based storage stack. Of several such possible integrations, two have seen widespread adoption: Caching and Dynamic Storage Tiering. Although the effectiveness of these architectures under certain workloads is well understood, a systematic side-by-side analysis of these approaches remains difficult due to the range of design alternatives and configuration parameters involved. Such a study is required now more than ever to be able to design effective hybrid storage solutions for deployment in increasingly virtualized modern storage installations that blend several workloads into a single stream. In this paper, we first present our extensions to the Loris storage stack that transform it into a framework for designing hybrid storage systems. We then illustrate the flexibility of the framework by designing several Caching and DST-based hybrid systems. Following this, we present a systematic side-by-side analysis of these systems under a range of individual workload types and offer insights into the advantages and disadvantages of each architecture. Finally, we discuss the ramifications of our findings on the design of future hybrid storage systems in the light of recent changes in hardware landscape and application workloads.