Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloning and characterization of the Vibrio cholerae genes encoding the utilization of iron from haemin and haemoglobin

Vibrio cholerae can utilize haemin or haemoglobin as its sole source of iron. Four haem utilization mutants of a classical strain of V. cholerae were isolated. These mutations were complemented with pHUT1, a cosmid clone isolated from a library of wild‐type CA401 DNA. Two independent Tn5 insertions into the cloned sequence disrupted function in all of the complemented mutants. Escherichia coli 1017 transformed with pHUT1 failed to utilize haemin as an iron source; a second plasmid containing a different cloned fragment of V. cholerae DNA (pHUT3) was required in addition to pHUT1 to reconstitute the system in E. coli. Minicell analysis and SDS‐PAGE of protein fractions indicate that pHUT10 (a subclone of p>HUT1) encodes a 26 kDa inner membrane protein, and pHUT3 encodes a 77 kDa outer membrane protein. Loss of either protein by Tn5 mutagenesis abolishes haem utilization in E. coli. An E. coli hemA mutant that cannot synthesize porphyrins was transformed with the recombinant plasmids to determine whether the plasmids encoded the ability to transport the porphyrin as well as the iron. The transformants grew aerobically in media containing haemin, whereas the parental strain was unable to grow under these conditions. This indicates that V. cholerae haem‐iron utilization genes allow transport of the entire haem moiety into the cell.
TRENDS IN THE MEASUREMENT OF ALPHA DIVERSITY IN THE LAST TWO DECADES

Claudia E. Moreno. Doctor in Ecology and Natural Resources Management, Instituto de Ecología, A.C. (IE), Mexico. Professor, Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Hidalgo (CIBUAEH). Address: A. P. 69-1, Pachuca, Hidalgo, Mexico C.P. 42001. email: cmoreno@uaeh.edu. mx Iriana Zuria. Ph.D. in Ecology, University of Maryland, USA. Professor, CIB-UAEH, Mexico. N. Marcela García-Zenteno. Biologist, UAEH. Former Student, CIB-UAEH, Mexico.
Molecular Mechanics of Chitin-Protein Interface

Chitin and protein are two main building blocks for many natural biomaterials. The interaction between chitin and protein critically determines the properties of the composite biological materials. As living organisms usually encounter complex ambient conditions like water, pH and ions are critical factors towards the structural integrity of biomaterials. It is therefore essential to study the chitin-protein interface under different environmental conditions. Here, an atomistic model consisting of a chitin substrate and a protein filament is constructed, which is regarded as a representative of the chitin-protein interface existing in many chitin-based biomaterials. Based on this model, the mechanical properties of chitin-protein interface under different moisture and pH values are investigated through molecular dynamics simulations. The results reveal a weakening effect of water towards the chitin-protein interface, as well as acidity, i.e. the protonated protein forms a stronger adhesion to chitin than that in the alkaline environment. In addition, the effect from side-chain of protein is studied and it is found that certain kinds of amino acid can form hydrophobic connections to chitin surface, which means that these peptides partly dodge the weakening effect of water. Our observation indicates that terminuses and side-chains in protein are of importance in forming interfacial hydrogen bonds. From our full atomistic models, we can observe some molecular mechanisms about how protein interacts with chitin in different conditions, which may spotlight the engineering on biomaterials with similar interfaces.
2‐Benzazepine Nitrones Protect Dopaminergic Neurons against 6‐Hydroxydopamine‐Induced Oxidative Toxicity

A number of C‐3 spirocyclic 2‐benzazepine analogs of α‐phenyl‐N‐tert‐butyl nitrone (PBN) were synthesized and tested for their activity in protecting rat brain mitochondria and dopaminergic (DA) neurons against 6‐hydroxydopamine (6‐OHDA), a toxin inducing destruction of the DA nigro‐striatal pathway in rodent models of Parkinson's disease. The newly synthesized nitrone derivatives were firstly investigated for their activity in decreasing the level of hydroxyl radicals generated during 6‐OHDA oxidation, and inhibit lipid peroxidation (TBARS assay) and protein carbonyl content (PCC) in rat brain mitochondria. Most of the studied 2‐benzazepine nitrones showed inhibitory potencies in both TBARS and PCC assays at least two magnitude orders higher than that of PBN. The data obtained usefully complemented the known structure–activity relationships. In particular, 5 and 10, bearing C‐3 spiro cyclopentyl and tetrahydropyranyl moieties, respectively, at 8 µM concentration proved to be significantly more effective than PBN in protecting cultured DA neurons exposed to 6‐OHDA, which alone causes about 45% cell loss in 24 h. In addition, we found that 5 inhibited butyrylcholinesterase with an IC50 value of 16.8 µM, which would enhance its potential as neuroprotective agent in Alzheimer's neurodegeneration. These findings extend the utility of benzazepine‐based PBN analogs in the treatment of age‐related free radical‐mediated disorders.
A Framework for Ranking Cloud Security Services

Although the use of Cloud services is proliferating, the notion of Cloud security remains ambiguous. This typically arises from two causes, namely (a) the limited awareness about security details by the average Cloud customer which results in the customers being unable to clearly express their security requirements, or (b) the lack of interfaces/tools that can meaningfully capture the customer requirements. In general, the Cloud customers are only able to provide qualitative requirements due to their inability to express precise security requirements. Nevertheless, Cloud customers still need to assess and benchmark various security services provided by different providers in order to select the most suitable Cloud provider that can satisfy their "imprecise and uncertain" security requirements. This paper proposes a methodology for enhancing the security aspects of Cloud services by quantitatively comparing the customer security requirements with the security offered by Cloud providers. The novelty of our approach is based on the usage of a fuzzy logic schema to manage the uncertainty of those qualitative requirements. We validate our framework by applying it to real-world data that leverages the standardized Cloud service level agreements structure proposed in the ISO/IEC 19086 standard.
Performance of Massive MIMO Uplink With Zero-Forcing Receivers Under Delayed Channels

In this paper, we analyze the performance of the uplink communication of massive multicell multiple-input multiple-output (MIMO) systems under the effects of pilot contamination and delayed channels because of terminal mobility. The base stations (BSs) estimate the channels through the uplink training and then use zero-forcing (ZF) processing to decode the transmit signals from the users. The probability density function (pdf) of the signal-to-interference-plus-noise ratio (SINR) is derived for any finite number of antennas. From this pdf, we derive an achievable ergodic rate with a finite number of BS antennas in closed form. Insights into the impact of the Doppler shift (due to terminal mobility) at the low signal-to-noise ratio (SNR) regimes are exposed. In addition, the effects on the outage probability are investigated. Furthermore, the power scaling law and the asymptotic performance result by infinitely increasing the numbers of antennas and terminals (while their ratio is fixed) are provided. The numerical results demonstrate the performance loss for various Doppler shifts. Among the interesting observations revealed is that massive MIMO is favorable even under channel aging conditions.
Molybdenum-containing nitrite reductases: Spectroscopic characterization and redox mechanism

ABSTRACT Objectives: This review summarizes the spectroscopic results, which will provide useful suggestions for future research. In addition, the fields that urgently need more information are also advised. Background: Nitrite-NO-cGMP has been considered as an important signaling pathway of NO in human cells. To date, all the four known human molybdenum-containing enzymes, xanthine oxidase, aldehyde oxidase, sulfite oxidase, and mitochondrial amidoxime-reducing component, have been shown to function as nitrite reductases under hypoxia by biochemical, cellular, or animal studies. Various spectroscopic techniques have been applied to investigate the structure and catalytic mechanism of these enzymes for more than 20 years. Methods: We summarize the published data on the applications of UV-vis and EPR spectroscopies, and X-ray crystallography in studying nitrite reductase activity of the four human molybdenum-containing enzymes. Results: UV-vis has provided useful information on the redox active centers of these enzymes. The utilization of EPR spectroscopy has been critical in determining the coordination and redox status of the Mo center during catalysis. Despite the lack of substrate-bound crystal structures of these nitrite reductases, valuable structural information has been obtained by X-ray crystallography. Conclusions: To fully understand the catalytic mechanisms of these physiologically/pathologically important nitrite reductases, structural studies on substrate-redox center interaction are needed.
The Comparative THD Analysis of Neutral Clamped Multilevel Z-Source Inverter using Novel PWM Control Techniques

A multilevel inverter is a power electronic device made to synthesize a desired AC voltage from several levels of DC voltages. These types of inverters are suitable in various high voltage and high power application due to their ability to synthesize waveforms with better harmonic spectrum and faithful output. Multilevel inverters through a single X-shaped LC impedance network is an important development in recent years. The power quality improvement is achieved by reducing the harmonics present at the output voltage of the inverter. The total harmonics distortion (THD) values of the output voltages of the inverter are measured and compared. This paper presents the comparative analysis of several multicarrier PWM techniques, which is effectively used for harmonic mitigation in the proposed neutral clamped multilevel Z-Source inverter and this work is compared with conventional three level inverter by using MATLAB-SIMULINK.
Self-configuration from a Machine-Learning Perspective

The goal of machine learning is to provide solutions which are trained by data or by experience coming from the environment. Many training algorithms exist and some brilliant successes were achieved. But even in structured environments for machine learning (e.g. data mining or board games), most applications beyond the level of toy problems need careful hand-tuning or human ingenuity (i.e. detection of interesting patterns) or both. We discuss several aspects how self-configuration can help to alleviate these problems. One aspect is the self-configuration by tuning of algorithms, where recent advances have been made in the area of SPO (Sequen- tial Parameter Optimization). Another aspect is the self-configuration by pattern detection or feature construction. Forming multiple features (e.g. random boolean functions) and using algorithms (e.g. random forests) which easily digest many fea- tures can largely increase learning speed. However, a full-fledged theory of feature construction is not yet available and forms a current barrier in machine learning. We discuss several ideas for systematic inclusion of feature construction. This may lead to partly self-configuring machine learning solutions which show robustness, flexibility, and fast learning in potentially changing environments.
Allergy and Sensitization during Childhood Associated with Prenatal and Lactational Exposure to Marine Pollutants

Background Breast-feeding may affect the risk of developing allergy during childhood and may also cause exposure to immunotoxicants, such as polychlorinated biphenyls (PCBs), which are of concern as marine pollutants in the Faroe Islands and the Arctic region. Objectives The objective was to assess whether sensitization and development of allergic disease is associated with duration of breast-feeding and prenatal or postnatal exposures to PCBs and methylmercury. Methods A cohort of 656 singleton births was formed in the Faroe Islands during 1999–2001. Duration of breast-feeding and history of asthma and atopic dermatitis were recorded at clinical examinations at 5 and 7 years of age. PCB and mercury concentrations were determined in blood samples obtained at parturition and at follow-up. Serum from 464 children (71%) at 7 years of age was analyzed for total immunoglobulin E (IgE) and grass-specific IgE. Results The total IgE concentration in serum at 7 years of age was positively associated both with the concomitant serum PCB concentration and with the duration of breast-feeding. However, the effect only of the latter was substantially attenuated in a multivariate analysis. A raised grass-specific IgE concentration compatible with sensitization was positively associated with the duration of breast-feeding and inversely associated with prenatal methylmercury exposure. However, a history of asthma or atopic dermatitis was not associated with the duration of breast-feeding, although children with atopic dermatitis had lower prenatal PCB exposures than did nonallergic children. Conclusions These findings suggest that developmental exposure to immunotoxicants may both increase and decrease the risk of allergic disease and that associations between breast-feeding and subsequent allergic disease in children may, at least in part, reflect lactational exposure to immunotoxic food contaminants.
Quantum Interactive Proofs with Short Messages

This paper considers three variants of quantum interactive proof systems in which short (meaning logarithmic-length) messages are exchanged between the prover and verifier. The first variant is one in which the verifier sends a short message to the prover, and the prover responds with an ordinary, or polynomial-length, message; the second variant is one in which any number of messages can be exchanged, but where the combined length of all the messages is logarithmic; and the third variant is one in which the verifier sends polynomially many random bits to the prover, who responds with a short quantum message. We prove that in all of these cases the short messages can be eliminated without changing the power of the model, so the first variant has the expressive power of QMA and the second and third variants have the expressive power of BQP. These facts are proved through the use of quantum state tomography, along with the finite quantum de Finetti theorem for the first variant.
Content-Based Features in the Composer Identication Problem CS 229 Final Project

Classification of digital music (also called Music Information Retrieval, or MIR), is a long-standing problem in machine learning, one with many potential real world applications. For example, providing accurate recommendations is extremely important to online music websites (Pandora, iTunes Genius, etc.) as this is the primary means by which users discover new music. Many classification schemes have therefore been proposed, with some attempting to group music according to characteristics like mood and genre, and others attempting to identify the particular artist or composer who created the work. Due to the complex nature of audio waveforms, however, nearly all music classification algorithms begin with a feature extraction step. Raw digital audio is essentially unusable for direct training on a learning algorithm; therefore, it is first necessary to process the data and distill key identifying features from the audio clips. Until recently, researchers were getting very good results using only relatively low-level signal features of the audio [5]. However, after the discovery of a design flaw now known as the “album effect”, the performance of such classifiers has dropped dramatically [1]. In this paper, we focus on classical composer identification, and propose a content-based feature set which addresses the limitations of current classifiers caused by the album effect.
Expression of functional CB1 cannabinoid receptors in retinoic acid‐differentiated P19 embryonal carcinoma cells

Although primary neuronal cell cultures, usually obtained from embryonic or early postnatal rodents, have been used in vitro to study the neural cannabinoid signalling system, development of cell lines with neural properties exhibiting native expression of cannabinoid receptors is desirable. This study was undertaken to investigate the expression of CB1 and CB2 cannabinoid receptors in neurons that develop from retinoic acid (RA)‐primed mouse P19 embryonal carcinoma cells. Both undifferentiated P19 cells and RA‐treated P19 neurons were positive, by using reverse transcription‐polymerase chain reaction (RT‐PCR), for CB1 (but not CB2) mRNA. Neuronal differentiation increased the CB1 mRNA expression, and Western blotting with a CB1 receptor antibody showed a strong immunoreactive band at approximately 62 kDa in membranes from P19‐derived neurons. The cannabinoid receptor agonists CP 55,940 and HU‐210 produced concentration‐dependent inhibition of forskolin‐induced (3 μM) cyclic AMP production in the P19‐derived neurons (29% at 1 μM CP 55,940 and 34% at 1 μM HU‐210), which could be blocked by the CB1‐selective receptor antagonist AM251, but not by the CB2‐selective antagonist AM630. Furthermore, glutamate (100 μM) induced a sustained increase in [Ca2+]i in P19‐derived neurons that could be concentration‐dependently blocked by the cannabinoid receptor agonists WIN 55,212‐2. Thus, the protocol used provides an in vitro model system expressing CB1 cannabinoid receptors at the level of mRNA, protein, and AM251‐sensitive agonist‐induced inhibition of intracellular cyclic AMP accumulation, which may be useful to investigate the developmental regulation, expression and function of neuronal cannabinoid receptors. © 2006 Wiley‐Liss, Inc.
Information rates of sampled Wiener processes

The minimal distortion attainable in recovering the waveform of a continuous-time Wiener process from an encoded version of its uniform samples is considered. We first introduce a combined sampling and source coding problem and prove an associated source coding theorem. We then derive an upper bound on the minimal distortion attainable under any sampling rate and a prescribed number of bits to encode the samples. We show that this bound is accurate to within a second order term in the sampling rate, and converges to the true distortion-rate function of the Wiener process as the sampling rate goes to infinity. For example, this bound implies that by providing a single bit per sample it is possible to achieve the optimal distortion-rate performance of the Wiener process, given by its distortion-rate function, to within a factor of 1.5. We conclude the distortion-rate function of the Wiener process is strictly smaller than the indirect distortion-rate function from its uniform samples obtained at any finite sampling rate. This is in contrast to stationary infinite bandwidth processes.
Identification of methicillin-resistant strains of staphylococci by polymerase chain reaction

A simple and reliable method using a polymerase chain reaction (PCR) was devised to identify methicillin-resistant staphylococci. By using lysates of the strain to be tested as templates and 22-mer oligonucleotides as primers, a 533-bp region of mecA, the structural gene of a low-affinity penicillin-binding protein (PBP 2'), was amplified by PCR and detected by agarose gel electrophoresis. Results obtained by this method were compared with those obtained by broth microdilution MIC determination for 210 and 100 clinical isolates of Staphylococcus aureus and coagulase-negative staphylococci, respectively. Of 99 mecA-negative S. aureus isolates, 100% of the strains were methicillin susceptible and 98% of the strains were oxacillin susceptible. Three strains (3%) of 111 mecA-positive S. aureus isolates exhibited almost the same susceptibility to beta-lactams as the mecA-negative ones and did not produce detectable amounts of PBP 2' despite the presence of the mecA gene. One of them yielded typically methicillin-resistant variants at a low frequency with concomitant recovery of PBP 2' production. The mecA gene was also found in coagulase-negative Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus sciuri, Staphylococcus saprophyticus, and Staphylococcus caprae and conferred resistance on most of the bacteria.
A Brief review of supersymmetric non-linear sigma models and generalized complex geometry

This is a review of the relation between supersymmetric non-linear sigma models and target space geometry. In particular, we report on the derivation of generalized Kahler geometry from sigma models with additional spinorial superfields. Some of the results reviewed are: Generalized complex geometry from sigma models in the Lagrangian formulation; Coordinatization of generalized Kahler geometry in terms of chiral, twisted chiral and semi-chiral superfields; Generalized Kahler geometry from sigma models in the Hamiltonian formulation.
Inhibition of Akt survival pathway by a small-molecule inhibitor in human glioblastoma

Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) and Akt are important regulators of the phosphatidylinositol 3-kinase (PI3K) pathway and thus are important to the regulation of a wide spectrum of tumor-related biological processes. Akt regulates several critical cellular functions, including cell cycle progression; cell migration, invasion, and survival; and angiogenesis. Decreased expression of PTEN and overexpression of the Akt proto-oncogene, which is located downstream of PI3K, have been shown in a variety of cancers, including glioblastoma. Novel small-molecule inhibitors of receptors and signaling pathways, including inhibitors of the PI3K pathway, have shown antitumor activity, but inhibitors of Akt have not been examined. In this study, we tested our hypothesis that the pharmacologic inhibition of Akt has an antiproliferative effect on gliomas. We showed that two newly developed Akt inhibitors, KP-372-1 and KP-372-2 (herein called KP-1 and KP-2), effectively inhibited the PI3K/Akt signaling cascade. KP-1 and KP-2 blocked both the basal and epidermal growth factor–induced phosphorylation of Akt Ser473 at 125 and 250 nmol/L, which, in turn, reduced the activation of intracellular downstream targets of Akt, including GSK-3β and p70s6k. Furthermore, the treatment of U87 and U251 glioma cells with 125 to 250 nmol/L KP-1 and KP2 for 48 hours inhibited cell growth by ∼50%. This decrease in cell growth stemmed from the induction of apoptosis. Collectively, these results provide a strong rationale for the pharmacologic targeting of Akt for the treatment of gliomas. [Mol Cancer Ther 2006;5(3):637–44]