Miracle-dz/UniFAR-FTUs huggingface dataset:
Proposal for a peptidoglycan‐associating alpha‐helical motif in the C‐terminal regions of some bacterial cell‐surface proteins

In a recent MicroCorrespondence (De Mot and Vanderleyden, 1994, Mol Microbiol 12; 333-334) an interaction of the C-terminal regions of a number of bacterial cellsurface proteins with the peptidoglycan was suggested, among them the enterobacterial OmpA proteins, pseudomonad OprF proteins, some PAL proteins, neisserial Rmp proteins, and flageliar MotB proteins. Here I wish to point out some additional facts supporting this hypothesis. First, if the C-terminal (presumably periplasmic) part of the Escherichia coli OmpA protein (amino acid residues 188-325) is analysed by a new method for secondarystructure prediction (Rost and Sander, 1993, J Moi Biol 232: 584-599), there are two a-helices strongly (Gln250-Ser-266, Glu-212-Asn-226) and one weakly (Lys294-Asp-30i) predicted. The first one represents the most conserved part of these C-terminal regions. A corresponding a-helical content comprising about 42 residues (versus 40 residues 'in this prediction) has been demonstrated for the C-terminal part of OmpA by Raman spectroscopy (Vogel and Jahnig, 1986, J Mol Bioi 190:191 -199). Both strongly predicted a-helices are identified by the same prediction algorithm in all OmpA-related proteins which are contained in the SWISSPROT database (Release 30.0). A multiple alignment together with the predicted secondary structure of all these proteins is available on request. Second, a helical wheel plot (Fig. 1) shows that all highly conserved amino acid residues would be located at one face of a putative a-helix. Hence, this consensus motif (NX2LSX2RAX2VX3L) could provide a molecular explanation for the hypothetical interaction with the peptidoglycan. Third, two E coli PAL-PhoA fusion proteins have been described (Lazzaroni and Portalier, 1992, Mol Microbioi 6i 735-742). One Is fused at Gly-116, corresponding to the C-termina! end of the predicted and conserved a-helix of PAL, and mediates a strong association with the peptidoglycan. The other is only 15 amino acid residues shorter and lacks this strong association. These results may be interpreted as indicating that a major determinant of peptidoglycan-association is located in this region. Finally, during isolation of dominant, non-functional mofS alleles of E. co//(Blair ef a/., 1991, J Bacteriol ^73: 4049-4055) a surprising clustering of mutations was observed, resulting in changes near or within the proposed cc-heiical motif. The disnjption of the interaction with the peptidoglycan provides an explanation for the observed phenotypes, as already suggested by De Mo! and Vanderleyden in their MicroCorrespondence. Database searches (GenBank Release 86.0: TFASTA) revealed additional homoiogues of this OmpA-related protein family (Gentry-Weeks ef a/. , 1992, J Bacterioi 174: 7729-7742; Hardham and Stamm, 1994, Infect Immun
Nutritional Value Determination of Different Varieties of Oats and Barley Using Near-Infrared Spectroscopy Method for the Horses Nutrition

In horse nutrition, the most suitable cereal for their rations composition could be defined as oats and barley. Oats have high nutritive value because it provides more protein, fiber, iron and zinc than other whole grains, has good taste, and an activity of stimulating metabolic changes in the body. Another cereal – barley is very similar to oats as a feed except for some characteristics that affect how it is used; however, barley is lower in fiber than oats and is classified as a "heavy" feed. The value of oats and barley grain, first of all is dependent on its composition. Near-infrared spectroscopy (NIRS) has long been considered and used as a significant method in component and quality analysis and as an emerging technology for authenticity applications for cereal quality control. This paper presents the chemical and amino acid composition of different varieties of barley and oats, also digestible energy of different cereals for horses. Ten different spring barley (n = 5) and oats (n = 5) varieties, grown in one location in Lithuania, were assayed for their chemical composition (dry matter, crude protein, crude fat, crude ash, crude fiber, starch) and amino acids content, digestible amino acids and amino acids digestibility. Also, the grains digestible energy for horses was calculated. The oats and barley samples reflectance spectra were measured by means of NIRS using Foss-Tecator DS2500 equipment. The chemical components: fat, crude protein, starch and fiber differed statistically (P<0.05) between the oats and barley varieties. The highest total amino acid content between oats was determined in variety Flamingsprofi (4.56 g/kg) and the lowest – variety Circle (3.57 g/kg), and between barley respectively in varieties Publican (3.50 g/kg) and Sebastian (3.11 g/kg). The different varieties of oats digestible amino acid content varied from 3.11 g/kg to 4.07 g/kg; barley different varieties varied from 2.59 g/kg to 2.94 g/kg. The average amino acids digestibility of oats varied from 74.4% (Liz) to 95.6% (Fen) and in barley from 75.8 % (Tre) to 89.6% (Fen). The amount of digestible energy in the analyzed varieties of oats and barley was an average compound 13.74 MJ/kg DM and 14.85 MJ/kg DM, respectively. An analysis of the results showed that different varieties of oats compared with barley are preferable for horse nutrition according to the crude fat, crude fiber, ash and separate amino acids content, but the analyzed barley varieties dominated the higher amounts of crude protein, the digestible Liz amount and higher DE content, and thus, could be
Referral Letter with an Attached Structured Reply Form: Is it A Solution for Not Getting Replies

Background: Communication between primary care doctors and specialists/hospital doctors is vital for smooth functioning of a health care system. In many instances referral and reply letters are the sole means of communication between general practitioners and hospital doctors/specialists. Despite the obvious benefits to patient care, answers to referral letters are the exception worldwide. In Sri Lanka hand written conventional letters are used to refer patients and replies are scarce. Materials and Methods: This interventional study was designed to assess if attaching a structured reply form with the referral letter would increase the rate of replies/back-referrals. It was conducted at the Family Medicine Clinic of the Faculty of Medicine, University of Kelaniya. A structured referral letter (form) was designed based on guide lines and literature and it was used for referral of patients for a period of six months. Similarly a structured reply form was also designed and both the referral letter and the reply letter were printed on A4 papers side by side and these were used for the next six months for referrals. Both letters had headings and space underneath to write details pertaining to the patient. A register was maintained to document the number of referrals and replies received during both phases. Patents were asked to return the reply letters if specialists/hospital doctors obliged to reply. Results: Total of 90 patients were referred using the structured referral form during 1st phase. 80 letters (with reply form attached) were issued during the next six months. Patients were referred to eight different specialties. Not a single reply during the 1st phase and there were six 6 (7.5%) replies during the 2nd phase. Discussion: This was an attempt to improve communication between specialists/hospital doctors and primary care doctors. Even though there was some improvement it was not satisfactory. A multicenter island wide study should be conducted to assess the acceptability of the format to primary care doctors and specialists and its impact on reply rate.
Pafhogenesis of Laser-Induced Choroidal Subrefinal Neovascularization

The early stages (1 day to 3 weeks) in the development of laser-induced choroidal subretinal neovascularization were studied in the monkey eye. Histopathology revealed that the intense laser beam disrupted the choroid/Bruch's membrane/retinal pigment epithelium (RPE) complex and initiated a repair process. Although all lesions received the same energy density, the initial choroidal wound varied among the lesions: in some, the necrotic choroid was surrounded by hemorrhagic retinal detachment with RPE denudation; in others, the necrotic choroid was surrounded only by minimal damage to the RPE monolayer. Formation of the choroidal wound was followed by an inflammatory response. Later, newly formed choroidal tissue filled the wound and continued to proliferate towards the subretinal space. RPE cells from the edges of the wound proliferated over the newly formed subretinal tissue and closed the wound. In lesions with a large area of damaged RPE, coverage of the wound was slow; fluid accumulated in the subretinal space, and the lesions demonstrated pooling of fluorescein on angiography (leaky lesions). In lesions with minimal damage to the RPE monolayer, closure of the wound was rapid, and the proliferating choroidal tissue did not reach the subretinal space. There was no subretinal fluid accumulation and no pooling of fluorescein on angiography (nonleaky lesions). Our results indicate that both the amount of damage of the choroid/Bruch's membrane/RPE complex and the ability of RPE cells around the damaged area to proliferate and restore the continuity of the RPE layer determine the evolution of newly formed choroidal fibrovascular tissue into a subretinal membrane with or without pooling. Invest Ophthalmol Vis Sci 31:899908, 1990
Sir Charles Bell on Visual Direction

Helmholtz is usually credited with demonstrating the relationship between the perception of visual direction and eye muscle activity: he said that directional judgements resulted from the effort of will involved in altering the position of the eyes. However, Bell reached the same conclusion many years earlier, primarily on the basis of experiments with afterimages: an afterimage appeared to move with voluntary movement of the eye, but it appeared stationary when the eye was moved passively.
A putative two‐component signal transduction system regulates σE, a sigma factor required for normal cell wall integrity in Streptomyces coelicolor A3(2)

The extracytoplasmic function (ECF) sigma factor, σE, is required for normal cell wall integrity in Streptomyces coelicolor. We have investigated the regulation of σE through a transcriptional and mutational analysis of sigE and the surrounding genes. Nucleotide sequencing identified three genes located downstream of sigE ; orf202, cseB and cseC (cse, control of sigE ). cseB and cseC encode a putative response regulator and a putative transmembrane sensor histidine protein kinase respectively. Although most sigE transcription appeared to be monocistronic, sigE was also transcribed as part of a larger operon, including at least orf202. sigE null mutants are sensitive to cell wall lytic enzymes, have an altered peptidoglycan muropeptide profile, and on medium deficient in Mg2+ they overproduce actinorhodin, sporulate poorly and form crenellated colonies. A constructed cseB null mutant appeared to have the same phenotype as a sigE null mutant, which was accounted for by the observed absolute dependence of the sigE promoter on cseB. It is likely that the major role of cseB is to regulate sigE transcription because expression of sigE alone from a heterologous promoter suppressed the cseB mutation. Mg2+ suppresses the CseB/SigE phenotype, probably by stabilizing the cell envelope, and sigE transcript levels were consistently higher in Mg2+‐deficient cultures than in high Mg2+‐grown cultures. We propose a model in which the CseB/CseC two‐component system modulates activity of the sigE promoter in response to signals from the cell envelope.
PDZ-containing 1 acts as a suppressor of pancreatic cancer by regulating PTEN phosphorylation

Phosphorylation is a recently established cause of phosphatase and tensin homolog (PTEN) gene inactivation, which leads to defect tumour-suppressor function. In pancreatic cancer, this phenomenon has not been reported. Based on database and clinical sample analyses, we found that PTEN phosphorylation occurs in pancreatic ductal adenocarcinoma patient tissues and cell lines, and we aimed to find a method for dephosphorylation. PDZ-containing 1 (PDZK1), a tumour-associated protein that shares its PDZ-binding sequence with the carboxyl-terminal domain of PTEN, was significantly down-regulated in pancreatic cancer as compared to adjacent non-tumour tissues. In vitro, PDZK1 overexpression reversed the proliferation and migration abilities of pancreatic cancer cells and led to significantly decreased PTEN phosphorylation and AKT phosphorylation by interacting with wild-type PTEN. In addition, a transcription factor-activation assay supported that PDZK1 overexpression enhanced the anti-oncogene function of PTEN by regulating the activities of its downstream transcription factors, including p53, NF-κB, and FOXO1. In vivo, nude mice stably over-expressing PDZK1 had lower tumour weights and volumes and showed significantly down-regulated PTEN phosphorylation in xenograft tumour tissues as compared to the control group. Moreover, low PDZK1 expression strongly correlated with advanced stage and poor prognosis of patients with pancreatic ductal adenocarcinoma. In conclusion, our study elucidated the tumour-suppressor role of PDZK1 in pancreatic cancer through down-regulating PTEN phosphorylation, and established PDZK1 as a potential novel prognostic marker for pancreatic cancer.
A tool for teaching interactions between design patterns

We describe the Patterns+UML tool that has been designed to help students of a first year object-oriented programming (OOP) course to apply design patterns to UML class diagrams, to analyze the code generated after their application, and especially to learn how different design patterns interact each other when they share some classes that play a different role in each pattern.
Interference of hepatitis C virus RNA replication by short interfering RNAs

Hepatitis C virus (HCV) infection is a major cause of chronic liver disease, which can lead to the development of liver cirrhosis and hepatocellular carcinoma. Current therapy of patients with chronic HCV infection includes treatment with IFNα in combination with ribavirin. Because most treated patients do not resolve the infection, alternative treatment is essential. RNA interference (RNAi) is a recently discovered antiviral mechanism present in plants and animals that induces double-stranded RNA degradation. Using a selectable subgenomic HCV replicon cell culture system, we have shown that RNAi can specifically inhibit HCV RNA replication and protein expression in Huh-7 cells that stably replicate the HCV genome, and that this antiviral effect is independent of IFN. These results suggest that RNAi may represent a new approach for the treatment of persistent HCV infection.
The Use of Aztreonam in Pediatric Patients: A Review

Aztreonam is the first monobactam available for use in this country. A parenteral antibiotic, its antibacterial spectrum is limited to gram‐negative aerobic pathogens. The drug's pharmacologic, pharmacokinetic, and toxicologic properties are reviewed. Based on early experience in pediatric patients, certain recommendations can be made for the use of aztreonam.
BIOCHEMICAL HETEROGENEITY OF THE CYTOPLASMIC PARTICLES ISOLATED FROM RAT LIVER HOMOGENATE

By separating the cytoplasmic granules of 0.88 M sucrose homogenates of rat liver into eight fractions it has been possible to demonstrate marked chemical and enzymatic heterogeneity among the isolated microsomes and less pronounced heterogeneity among the isolated mitochondria. The more readily sedimented microsomes are rich in ribose nucleic acid and show high esterase, adenosine-5’-phosphatase, acid phosphatase and uricase activities, while the less readily sedimented microsomes, although rich in ribose nucleic acid esterase and adenosine-5’-phosphatase have low levels of acid phosphatase and uricase activities. The very small mitochondria differ from the larger ones in the levels of activities of all enzymes studied, with the exception of adenosine-5’-phosphatase; the most striking differences were found in the cases of acid phosphatase and uricase. A centrifugation schedule is given to isolate a "nuclear fraction," a mitochondrial fraction, a mixed fraction of smallest mitochondria and microsomes (of two types differing in optical density), a fraction of optically less dense microsomes, and a "supernatant fluid. "
Osteopontin Modulates Myocardial Hypertrophy in Response to Chronic Pressure Overload in Mice

Osteopontin (OPN) expression increases in the heart during hypertrophy and heart failure. Here, we studied the role of OPN in pressure overload–induced hypertrophy and analyzed the signaling pathways involved in hypertrophy. Aortic banding (AB) was performed in a group of wild-type (WT) and OPN knockout (KO) mice to induce pressure overload. Left ventricular (LV) structural and functional remodeling was studied 1 month after AB. AB increased OPN and &bgr;1 integrin (a receptor for OPN) protein expression in WT-AB group. Hypertrophic response as measured by increased heart weight-to-body weight ratio and myocyte cross-sectional area was significantly increased in WT-AB and KO-AB groups when compared with their respective shams. However, the increase was significantly higher in WT-AB. Re-expression of atrial natriuretic factor was only detected in WT-AB group. LV end-diastolic pressure-volume curve obtained using Langendorff perfusion analysis exhibited a leftward shift in WT-AB group, not in KO-AB. LV-developed pressures measured over a range of LV volumes were significantly increased in WT-AB, not in KO-AB mice. Increased phosphorylation of c-Jun N-terminal kinases, p38 kinase, Akt, and glycogen synthase kinase-3&bgr; was significantly higher in WT-AB when compared with KO-AB group. Increased OPN expression may play an essential role in modulating compensatory cardiac hypertrophy in response to chronic pressure overload.
RANDOMIZED, CONTROLLED TRIAL OF TELCAGEPANT FOR THE ACUTE TREATMENT OF MIGRAINE

Reply from the Author: We thank Dr. Savolainen for the comments on our article. Diabetes is associated with peripheral polyneuropathy but this manifestation is usually a late complication. The sample we studied was free of problems associated with metabolic syndrome. We also limited our study to assess the silent manifestation of metabolic syndrome in CNS but not the peripheral nervous system. In future studies, the determination of D-lactate in our sample and the correlation analysis with white matter change indicators will be valuable. M. Angeles Jurado, Barcelona, Spain
IDENTIFYING CAUSAL MECHANISMS (PRIMARILY) BASED ON INVERSE PROBABILITY WEIGHTING

SUMMARY This paper demonstrates the identification of causal mechanisms of a binary treatment under selection on observables, (primarily) based on inverse probability weighting; i.e. we consider the average indirect effect of the treatment, which operates through an intermediate variable (or mediator) that is situated on the causal path between the treatment and the outcome, as well as the (unmediated) direct effect. Even under random treatment assignment, subsequent selection into the mediator is generally non‐random such that causal mechanisms are only identified when controlling for confounders of the mediator and the outcome. To tackle this issue, units are weighted by the inverse of their conditional treatment propensity given the mediator and observed confounders. We show that the form and applicability of weighting depend on whether some confounders are themselves influenced by the treatment or not. A simulation study gives the intuition for these results and an empirical application to the direct and indirect health effects (through employment) of the US Job Corps program is also provided. Copyright © 2013 John Wiley & Sons, Ltd.
Force and Stiffness of Passive Magnetic Bearings Using Permanent Magnets. Part 1: Axial Magnetization

This paper deals with the calculation of the force and the stiffness between two ring permanent magnets whose polarization is axial. Such a configuration corresponds to a passive magnetic bearing. All the calculations are determined by using the Coulombian model. The paper also discusses the optimal ring dimensions that provide a large force or stiffness between the rings. Such properties are commonly sought in passive magnetic bearings. We propose a three-dimensional method for optimizing these parameters. An important result is established in this paper: the exact relative position of the rings for which the force is the strongest depends on the air gap dimension. As the expressions in this paper give this exact relative position, manufacturers can easily optimize their passive magnetic bearings. This result is new because the curvature effect is taken into account. Such semianalytical expressions are more precise than the numerical evaluation of the magnetic forces obtained with the finite-element method. In addition, semianalytical expressions have a low computational cost whereas the finite-element method is computation-intensive. Such calculations make it easy to optimize quadripolar lenses and other devices utilizing permanent magnets.
Modeling and efficient mining of intentional knowledge of outliers

In this paper, we study in a general setting the notion of outliered patterns as intentional knowledge of outliers and algorithms to mine those patterns. Our contributions consist of a model for defining outliered patterns with the help of categorical and behavioral similarities of outliers, and efficient algorithms for mining knowledge sets of distance-based outliers and outliered patterns. Our algorithms require only very limited domain knowledge, and no classified information. We also present an empirical study to show the feasibility of our algorithms.
Treatment efficacy of DNA lipid nanocapsules and DNA multimodular systems after systemic administration in a human glioma model

We previously developed different types of DNA nanocarriers for systemic administration. Recently, the biodistribution profiles of these intravenously administered nanocarriers, DNA lipid nanocapsules (LNCs) and different multimodular systems (MMS), were analysed in healthy mice using in vivo biofluorescence imaging.
Quantizer design in LSP speech analysis-synthesis

The performance of several algorithms for the quantization of the LSP (line spectrum polar) parameters is studied. An adaptive method that utilizes the ordering property of the LSP parameters is introduced. A combination of this adaptive algorithm with nonuniform-step-size quantization is shown to be very effective for encoding the LSP parameters. The performance of the different quantization schemes is studied on several sequences of speech samples. For the spectra distortion measure, appropriate performance comparisons between the different quantization schemes are rendered. >
Decentralized Sliding Mode Load Frequency Control for Multi-Area Power Systems

Based on the decentralized sliding mode control, a load frequency controller is designed in this paper for multi-area interconnected power systems with matching and unmatched uncertainties. The proportional and integral switching surface is constructed for each area to improve system dynamic performance in reaching intervals. The robust controller is proposed by the reaching law method to assure that frequency fluctuation converges to zero after a load and operation point variation. A three-area interconnected power system is studied to illustrate the effectiveness of the proposed decentralized sliding mode control scheme.