Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure analysis of peptide deformylase from Bacillus cereus

Introduction. Peptide deformylases (PDF, EC 3.5.1.88) are metalloproteases (Fe ) that cleave the N-terminal formyl groups from newly synthesized proteins, therefore important in protein processing. Since the PDF activity is reported to be essential for bacterial survival, and PDF homologs in animal and human are not functional on deformylation, PDF has been considered as a potential target in antimicrobial chemotherapy. There have been a number of inhibitors reported targeting PDF including the ones mimic actinonin, a naturally occurring hydroxamic acid pseudo-peptide that is known to be highly potent (Ki 0.28 nM for E. coli PDF). Based on amino acid sequence similarity, PDFs have been classified into two subfamilies, type I being represented by the Escherichia coli enzyme and the type II by Staphylococcus aureus enzyme. Both biochemical and structural studies show that the two types share close enzymatic properties and overall structures in spite of rather low sequence homology. –13 Many bacteria possess only one gene coding PDF, but some are found with two, three or even four active PDF gene sequences. For example, recently reported genome of endospore-forming bacteria Bacillus cereus, an opportunistic pathogen causing food poisoning, diarrhea and emetic symptoms, and Bacillus anthracis, the causative agent of inhalational anthrax, show that they possess two def genes encoding PDF as in Bacillus subtilis. The two PDF proteins in B. cereus and B. anthracis as well as B. subtilis share about 30% amino acid sequence identities and one is about 25 residues longer than the other. In case of B. subtilis the longer PDF, that is, YkrB, is reported to be more active. The structure of PDF from B. Stearothermophilus is reported to be of type II. Here we report the crystal structures of the short PDF from B. cereus in both inhibitor free (denoted as BcPDF) and actinonin bound (denoted as BcPDF/Actinonin) forms.
Digital signal processing for compensating fiber nonlinearities

Successful compensation of nonlinear distortions due to fiber Kerr nonlinearities relies on the availability of an accurate channel model. Some models obtained by approximate solutions of the nonlinear Schrödinger equation and the back-propagation method are taken into account. It turns out that backpropagation is not the optimal processing technique and in some cases is outperformed by simpler processing techniques.
Cyclic AMP production in isolated colonic epithelial crypts: a highly sensitive model for the evaluation of vasoactive intestinal peptide action in human intestine

Abstract. Epithelial cells of human colon were isolated in the form of entire epithelial crypts devoid of vasoactive intestinal peptide (VIP) as measured by radioimmunoassay. This preparation allowed the demonstration, in any conditions tested, of the considerable sensitivity of cyclic AMP accumulation in colonic epithelium to VIP. The magnitude of cyclic AMP accumulation in this preparation was dependent on temperature, time of incubation and concentration of phosphodiesterase inhibitor. At 37 C, in the presence 0–2 mM 3‐isobutyl‐l‐methylxanthine, a 4‐fold increase of cyclic AMP above basal was observed 5 min after addition of 10‐10 M VIP and a 16‐fold increase (maximal response) was obtained after 20 min by 10‐8 M VIP. The dose‐response curve was studied in conditions of equilibrium, i.e. a 60 min incubation at 15CC in the presence of 0–2 mM 3‐isobutyl‐l‐methylxanthine, and appeared to be monophasic with a half‐maximal stimulation at l‐2 times 10‐9 M VIP. Synthetic secretin, porcine intestinal histidine isoleucine amide (PIHI) and the other active substances (prostaglandins E and isoproterenol) were 2500, 600, and at least 100 times less potent than VIP, respectively. Adenylate cyclase of membranes prepared from epithelial crypts was stimulated by concentrations of VIP identical to those acting on cyclic AMP level in intact crypts. Plasmas from patients with the watery diarrhoea syndrome were able to induce a significant rise of cyclic AMP production in human colonic epithelial crypts. This effect was suppressed by previous exposure of the plasmas to a specific anti‐VIP immunserum.
The Porphyrias: Clinic, Diagnostics, Novel Investigative Tools and Evolving Molecular Therapeutic Strategies

The porphyrias are clinically and genetically heterogeneous metabolic disorders resulting from a predominantly hereditary dysfunction of specific enzymes involved in heme biosynthesis. Today, the clinical, biochemical, and genetic characteristics of this fascinating group of diseases are well established. Recently, different in vitro and animal models have facilitated the investigation of etiopathologic mechanisms in the different types of porphyria and the development of causal treatment strategies such as pathway interference, enzyme replacement, and gene therapy. The continuous progress in basic science has made an invaluable contribution to the rapid translation of discoveries made in the laboratory into new diagnostics and therapeutics in the near future.
Kaolin‐induced hydrocephalus impairs CSF secretion by the choroid plexus

CSF volume flow and sodium (Na+)-influx rates in normal and kaolin-induced hydrocephalic cats were measured during ventricular perfusion with anisotonic sucrose solutions. When ventricular fluid osmolality was 120 mOsm, CSF volume flow ceased for both groups of cats. As ventricular fluid osmolality was increased, the CSF volume flow rate of normal cats increased to 70 μl per minute, and in hydrocephalic cats to 40 μl per minute. In normal cats, for ventricular fluid osmolality between 50 and 350 mOsm, Na+-influx was constant and thought to occur by diffusion; while for higher osmolalities, Na+-influx increased. In hydrocephalic cats, Na+-influx increased over the entire range of ventricular osmolality but was less than in normal cats. Acetazolamide decreased the CSF volume flow in normal cats by 40 percent, but was ineffective in hydrocephaiic cats. These results suggest that CSF secretion by the choroid plexus of cats with kaolin-induced hydrocephalus is impaired.
Bank Consolidation and the Dynamics of Consumer Loan Interest Rates

This paper analyzes interest rates quoted by individual banks for personal and automobile loans in 10 cities. Personal loan rates are higher in concentrated markets, and banks involved in mergers reduce personal rates relative to their competitors prior to the merger's completion. This is consistent with mergers changing the size structure of personal loan markets and merger participants' desire to gain regulatory approval. Auto rates are unaffected by local concentration and mergers, suggesting that their market is nationwide. Rates for both loan types respond asymmetrically to changes in Treasury rates, being more sensitive to a rise than a fall.
Metabolic availability of medium-chain triglycerides coingested with carbohydrates during prolonged exercise.

The present study examined the metabolic response to medium-chain triglycerides (MCTs) ingestion with or without carbohydrates (CHOs). Eight well-trained athletes cycled 4 x 180 min at 50% maximal work rate (57% maximal O2 consumption). Subjects drank a bolus of 4 ml/kg at the start and 2 ml/kg every 20 min during exercise of either a 15% (214 g) CHO solution (CHO trial), an equicaloric 149 g CHO-29 g MCT suspension (CHO+MCT trial), 214 g CHO [high CHO (HCHO)]-29 g MCT suspension (HCHO+MCT trial) or 29 g MCT solution (MCT trial). Exogenous MCT oxidation was measured by adding a [1,1,1-13C]trioctanoate tracer to the MCT oil. 13CO2 enrichment of breath samples were measured every 15 min. During the second hour (60- to 120-min period), the amount of MCT oxidized was 72% of the amount ingested during the CHO+MCT trial, whereas during the MCT trial only 33% was oxidized. The rate of MCT oxidation increased more rapidly during the HCHO+MCT and CHO+MCT trials compared with the MCT trial, yet in all three cases the oxidation rate stabilized at 0.12 g/min during 120-180 min of exercise. It is concluded that more MCTs are oxidized when ingested in combination with CHOs. Data do confirm the hypothesis that oral MCTs might serve as an energy source in addition to glucose during exercise because the metabolic availability of MCTs was high during the last hour of exercise, with oxidation rates being approximately 70% of the ingestion rate. (ABSTRACT TRUNCATED AT 250 WORDS)
On-line decision support for take-off runaway scheduling at London Heathrow Airport

The research problem considered in this thesis was presented by NATS, who are responsible for the take-off runway scheduling at London Heathrow airport. The sequence in which aircraft take off is very important and can have a huge effect upon the throughput of the runway and the consequent delay for aircraft awaiting take-off. Sequence-dependent separations apply between aircraft at take-off, some aircraft have time-slots within which they must take-off and all re-sequencing performed by the runway controller has to take place within restrictive areas of the airport surface called holding areas. Despite the complexity of the task and the short decision time available, take-off sequencing is performed manually by runway controllers. In such a rapidly changing environment, with much communication and observation demanded of the busy controller, it is hardly surprising that sub-optimal mental heuristics are currently used. The task presented by NATS was to develop the decision-making algorithms for a decision support tool to aid a runway controller to solve this complex real-world problem. A design for such a system is presented in this thesis. Although the decision support system presents only a take-off sequence to controllers, it is vitally important that the movement within the holding area that is required in order to achieve the re-sequencing is both easy to identify and acceptable to controllers. A key objective of the selected design is to ensure that this will always be the case. Both regulatory information and details of controller working methods and preferences were utilised to ensure that the presented sequences will not only be achievable but will also be acceptable to controllers. A simulation was developed to test the system and permit an evaluation of the potential benefits. Experiments showed that the decision support system found take-off sequences which significantly reduced the delay compared with those that the runway controllers actually used. These sequences had an equity of delay comparable with that in the sequences the controllers generated, and were achieved in a very similar way. Much of the benefit that was gained was a result of the decision support system having visibility of the taxiing aircraft in addition to those already queueing for the runway. The effects of uncertainty in taxi times and differing planning horizons are explicitly considered in this thesis. The limited decision time available ensures that it is not practical for a runway controller to consider as many aircraft as the decision support algorithms can. The results presented in this thesis indicate that huge benefits may be possible from the development of a system to simplify the sequencing task for the controllers while simultaneously giving them greater visibility of taxiing aircraft. Even beyond these benefits, however, the system described here will also be seen to have further potential benefits, such as for evaluating the effects of constraints upon the departure system or the flexibility of holding area structures.
A new family of space-time block codes based on the ZF and the MMSE receivers

The zero-forcing (ZF) and the minimum mean square error (MMSE) linear receivers, due to their simple decoding process are of great interest. This property of linear receivers has motivated research to design new space-time block codes (STBCs) based on them. In this paper, we propose a new family of STBCs, called O-OACs, by combining the orthogonal STBCs (OSTBCs) and the overlapped Alamouti codes (OACs). The OOACs employ the ZF and the MMSE receivers in their decoding processes, which benefit from lower complexity in comparison with the maximum likelihood (ML) decoder. The second advantage of the O-OACs is that they need less time slots to be constructed when compared with the recently proposed codes, namely the group orthogonal-Toeplitz codes (GOTCs) and the OACs. So this property of the O-OACs is in accordance with reality. And also simulation results demonstrate that the O-OACs outperform the GOTCs and the OACs.
Circadian variation in urine pH and uric acid nephrolithiasis risk.

The proportion of uric acid stones in paediatric stone formers is estimated at 3–4% in the United States [1], although reports from Armenia and Turkey indicate higher proportions of 7 and 15%, respectively [2,3]. Risk factors for uric acid stones include hyperuricosuria, low urinary volume and unduly acidic UpH (<5.5) [4]. Acidic UpH is a recognized risk factor in children consuming a ketogenic diet [5], or those with chronic diarrhoea. In adults, an acidic urine pH is the most common abnormality that predisposes to idiopathic uric acid nephrolithiasis [4]. Urinary alkalinization with potassium citrate is an effective treatment for uric acid kidney stones in adults [6]. We report the case of a 13-year-old boy who presented with recurrent uric acid stones that did not respond to a conventional regimen of potassium citrate therapy.
Applications of statistical assessment of power system security under uncertainty

A background of increasing uncertainties in all time horizons of power system planning and operation has prompted the development of a comprehensive methodology and an advanced new practical tool for assessing both the static and dynamic security of a real network facing a large number of uncertainties. This paper briefly describes the methodology and then focuses on various applications and perspectives.
The spectral characteristics of the excitation of cylindrical surface with nonlinear loads with a metamaterial layer

In this paper, a two-dimensional problem of excitation of the perfectly conducting cylindrical surface coated with the MM, by a filament of magnetic current is examined. On a cylindrical surface parallel to element of cylinder the narrow nonlinear loads (NLs) are placed. The problem is solved using nonlinear boundary conditions on the surface of NLs and is reduced to the system of nonlinear integral equations relatively frequency harmonics of surface currents on NLs. The homogenization of the MM layer of which provides a good transmission and weak reflection of waves at the fundamental frequency, and transmission of waves on the second and third harmonics is executed. An effect of MM coating on characterictics of excited field for loaded cylinder with MM is studied.
The Impact of Project Management in Virtual Environment: A Software Industry Perspective

Virtual team in a project within an Organization could achieve optimize project performance by acquiring appropriate human resources, coordination, communication and regular performance evaluation. According to the literature many ICT tools will collaborate to manage virtual teams, but still most of the projects lead to failure in the software industry. Aim of this research is to discover the most affected factors for virtual project human resource management.
Mobile Beacon-Based 3D-Localization with Multidimensional Scaling in Large Sensor Networks

Localization is essential in wireless sensor networks to handle the reporting of events from sensor nodes. For 3-D applications, we propose a mobile beacon-based localization using classical multidimensional scaling (MBL-MDS) by taking full advantage of MDS with connectivity and measurements. To further improve location performance, MBL-MDS adopts a selection rule to choose useful reference points, and a decision rule to prevent a failure case due to reference points placed on the same plane. Simulation results show improved performance of MBL-MDS in terms of location accuracy and computation complexity.
Cycling G1 CD34+/CD38+ Cells Potentiate the Motility and Engraftment of Quiescent G0 CD34+/CD38−/low Severe Combined Immunodeficiency Repopulating Cells

The mechanism of human stem cell expansion ex vivo is not fully understood. Furthermore, little is known about the mechanisms of human stem cell homing/repopulation and the role that differentiating progenitor cells may play in these processes. We report that 2‐ to 3‐day in vitro cytokine stimulation of human cord blood CD34+‐enriched cells induces the production of short‐term repopulating, cycling G1 CD34+/CD38+ cells with increased matrix metalloproteinase (MMP)‐9 secretion as well as increased migration capacity to the chemokine stromal cell–derived factor‐1 (SDF‐1) and homing to the bone marrow of irradiated nonobese diabetic severe/combined immunodeficiency (NOD/SCID) mice. These cycling G1 cells enhance SDF‐1–mediated in vitro migration and in vivo homing of quiescent G0 CD34+ cells, which is partially abrogated after inhibition of MMP‐2/‐9 activity. Moreover, the engraftment potential of quiescent G0 SCID repopulating cells (SRCs) is also increased by the cycling G1 CD34+/CD38+ cells. This effect is significantly abrogated after incubation of cycling G1 cells with a neutralizing anti‐CXCR4 antibody. Our data suggest synergistic interactions between accessory cycling G1 CD34+/CD38+ committed progenitor cells and quiescent, primitive G0 CD34+/CD38−/low SRC/stem cells, the former increasing the motility and engraftment potential of the latter, partly via secretion of MMP‐9.
CD9 Is a Surface Marker on Mouse and Rat Male Germline Stem Cells1

Abstract Spermatogenesis is dependent on a small population of stem cells. Despite the biological significance of spermatogonial stem cells, their analysis has been hampered by their scarcity. However, spermatogonial stem cells can be enriched by selection with an antibody against cell-surface molecules. In this investigation, we searched for new antigens expressed on spermatogonial stem cells. Using the spermatogonial transplantation technique, we examined expression of the CD9 molecule, which is commonly expressed on stem cells of other tissues. Selection of both mouse and rat testis cells with anti-CD9 antibody resulted in 5- to 7-fold enrichment of spermatogonial stem cells from intact testis cells, indicating that CD9 is commonly expressed on spermatogonial stem cells of both species. Therefore, CD9 may be involved in the common machinery in stem cells of many self-renewing tissues, and the identification of a common surface antigen on spermatogonial stem cells of different species has important implications for the development of a technique to enrich stem cells from other mammalian species.
The HOX genes are expressed, in vivo, in human tooth germs: In vitro cAMP exposure of dental pulp cells results in parallel HOX network activation and neuronal differentiation

Homeobox‐containing genes play a crucial role in odontogenesis. After the detection of Dlx and Msx genes in overlapping domains along maxillary and mandibular processes, a homeobox odontogenic code has been proposed to explain the interaction between different homeobox genes during dental lamina patterning. No role has so far been assigned to the Hox gene network in the homeobox odontogenic code due to studies on specific Hox genes and evolutionary considerations. Despite its involvement in early patterning during embryonal development, the HOX gene network, the most repeat‐poor regions of the human genome, controls the phenotype identity of adult eukaryotic cells. Here, according to our results, the HOX gene network appears to be active in human tooth germs between 18 and 24 weeks of development. The immunohistochemical localization of specific HOX proteins mostly concerns the epithelial tooth germ compartment. Furthermore, only a few genes of the network are active in embryonal retromolar tissues, as well as in ectomesenchymal dental pulp cells (DPC) grown in vitro from adult human molar. Exposure of DPCs to cAMP induces the expression of from three to nine total HOX genes of the network in parallel with phenotype modifications with traits of neuronal differentiation. Our observations suggest that: (i) by combining its component genes, the HOX gene network determines the phenotype identity of epithelial and ectomesenchymal cells interacting in the generation of human tooth germ; (ii) cAMP treatment activates the HOX network and induces, in parallel, a neuronal‐like phenotype in human primary ectomesenchymal dental pulp cells. J. Cell. Biochem. 97: 836–848, 2006. © 2005 Wiley‐Liss, Inc.
Rapid disuse and denervation atrophy involve transcriptional changes similar to those of muscle wasting during systemic diseases

We previously identified a common set of genes, termed atrogenes, whose expression is coordinately induced or suppressed in muscle during systemic wasting states (fasting, cancer cachexia, renal failure, diabetes). To determine whether this transcriptional program also functions during atrophy resulting from loss of contractile activity and whether atrogene expression correlates with the rate of muscle weight loss, we used cDNA microarrays and RT‐polymerase chain reaction to analyze changes in mRNA from rat gastrocnemius during disuse atrophy induced by denervation or spinal cord isolation. Three days after Den or SI, the rate of muscle weight loss was greatest, and 78% of the atrogenes identified during systemic catabolic states were induced or repressed. Of particular interest were the large inductions of key ubiquitin ligases, atrogin‐1 (35‐to 44‐fold) and MuRF1 (12‐to 22‐fold), and the suppression of PGC‐1α and PGC‐1ᵦ coactivators (15‐fold). When atrophy slowed (day 14), the expression of 92% of these atrogenes returned toward basal levels. At 28 days, the atrophy‐inducing transcription factor, FoxO1, was still induced and may be important in maintaining the “atrophied” state. Thus, 1) the atrophy associated with systemic catabolic states and following disuse involves similar transcriptional adaptations; and 2) disuse atrophy proceeds through multiple phases corresponding to rapidly atrophying and atrophied muscles that involve distinct transcriptional patterns. Sacheck, J. M. , Hyatt, J‐P. K. , Raffaello, A. , Jagoe, R. T. , Roy, R. R. , Edgerton, V. R. , Lecker, S. H. , Goldberg, A. L. Rapid disuse and denervation atrophy involve transcriptional changes similar to those of muscle wasting during systemic diseases. FASEB J. 21, 140–155 (2007)
Analysis and design for RCD clamped snubber used in output rectifier of phase-shift full-bridge ZVS converters

Detailed analysis and parameter design for a resistor-capacitor-diode (RCD) clamped snubber used in the output rectifier of phase-shift full-bridge zero-voltage-switching (PS-FB-ZVS) power converters are presented. Design equations and some properties of the clamped circuit are also highlighted.
Evaluation of anti-elastase and antioxidant activity in antiaging formulations containing terminalia extracts

Most in vitro efficacy studies of creams are based on estimation of active constituents as solubility is the limiting factor. Our aim was to establish a method for efficacy testing of both anti-elastase and antioxidant activity in final formulations and to compare the same with the activity of the active ingredients to ascertain whether the native activity remains unaffected, enhanced or is compromised in any way. The actives evaluated in the antiaging formulations included the crude extracts of Terminalia arjuna and Terminalia chebula, either alone or in combination on the activity of porcine pancreatic elastase and to reduce 2, 2-Diphenyl-1-picrylhydrazyl (DPPH). The results showed that the T. arjuna formulation had higher inhibitory activity of elastase (IC50 6.6 mg/ml) while T. chebula formulation depicted better antioxidant activity (IC50 0.032 mg/ml). The combination cream had excellent antielastase (IC50 2.8 mg/ml) and antioxidant properties (IC50 0.14 mg/ml). Further the cytotoxicity of the two extracts was tested on 3T3 cell line and both extracts were found to have negligible inhibition up to 80 µg/ml.