Miracle-dz/UniFAR-FTUs huggingface dataset:
Discrimination of native loop conformations in membrane proteins: Decoy library design and evaluation of effective energy scoring functions

The recent determination of crystal structures for several important membrane proteins opens the way for comparative modeling of their membrane‐spanning regions. However, the ability to predict correctly the structures of loop regions, which may be critical, for example, in ligand binding, remains a considerable challenge. To meet this challenge, accurate scoring methods have to discriminate between candidate conformations of an unknown loop structure. Some success in loop prediction has been reported for globular proteins; however, the proximity of membrane protein loops to the lipid bilayer casts doubt on the applicability of the same scoring methods to this problem. In this work, we develop “decoy libraries” of non‐native folds generated, using the structures of two membrane proteins, with molecular dynamics and Monte Carlo techniques over a range of temperatures. We introduce a new approach for decoy library generation by constructing a flat distribution of conformations covering a wide range of Cα–root‐mean‐square deviation (RMSD) from the native structure; this removes possible bias in subsequent scoring stages. We then score these decoy conformations with effective energy functions, using increasingly more cpu‐intensive implicit solvent models, including (1) simple Coulombic electrostatics with constant or distance‐dependent dielectrics; (2) atomic solvation parameters; (3) the effective energy function (EEF1) of Lazaridis and Karplus; (4) generalized Born/Analytical Continuum Solvent; and (5) finite‐difference Poisson–Boltzmann energy functions. We show that distinction of native‐like membrane protein loops may be achieved using effective energies with the assumption of a homogenous environment; thus, the absence of the adjacent lipid bilayer does not affect the scoring ability. In particular, the Analytical Continuum Solvent and finite‐difference Poisson–Boltzmann energy functions are seen to be the most powerful scoring functions. Interestingly, the use of the uncharged states of ionizable sidechains is shown to aid prediction, particularly for the simplest energy functions. Proteins 2003;52:492–509. © 2003 Wiley‐Liss, Inc.
Diuretics in obstructive sleep apnea with diastolic heart failure.

BACKGROUND Upper airway edema might contribute to pharyngeal collapsibility and account for the high prevalence of obstructive sleep apnea (OSA) in patients with heart disease. The aim of this study was to evaluate if intensive unloading with diuretics improves sleep-disordered breathing and increases pharyngeal caliber in patients with severe OSA and diastolic heart failure. METHODS Fifteen patients with severe OSA, hypertension, and diastolic heart failure were hospitalized to receive IV furosemide, 20 mg, and spironolactone, 100 mg, bid for 3 days. Polysomnography was performed for assessment of apnea-hypopnea index (AHI), acoustic pharyngometry was performed for assessment of the oropharyngeal junction (OPJ) area, and forced midinspiratory flow (FIF(50)), forced midexpiratory flow (FEF(50))/FIF(50) percentage, and exhaled nitric oxide (FeNO) were measured before and after diuretic treatment. RESULTS Diuretic treatment produced a significant decrease in body weight, BP, and AHI (from 74.89 +/- 6.95 to 57.17 +/- 5.40/h, p < 0.001), associated with an improvement in OPJ area (from 1.33 +/- 0.10 to 1.78 +/- 0.16 cm(2), p = 0.007), FIF(50) (from 3.16 +/- 0.4 to 3.94 +/- 0.4 L/s, p = 0.006), and FEF(50)/FIF(50) percentage (from 117.9 +/- 11.8 to 93.15 +/- 10.1%, p = 0.002). Weight loss was significantly related to the decrease of AHI (R = 0.602; p = 0.018), to the increase of FIF(50) (R = 0.68; p = 0.005), and to the decrease of FEF(50)/FIF(50) (R = 0.635; p = 0.011). CONCLUSIONS These findings suggest that pharyngeal edema contributes to sleep-disordered breathing in obese patients with severe OSA, hypertension, and diastolic heart failure. Upper airway edema may contribute to the frequent occurrence of OSA in patients with heart disease.
Understanding Plasma Fluid Dynamics Inside Plasma Torches Through Advanced Modeling

The aim of this paper is to investigate the behavior of different types of transferred-arc dual-gas plasma torches used for the cutting of metallic materials by means of a 2-D FLUENT-based numerical model, putting into evidence the physical reasons for the industrial success of various design and process solutions appeared over the last years, such as the following: vented-nozzle technology, various different approaches for the geometry of the plasma chamber, the effect of externally superimposed magnetic fields, and secondary-gas-swirl injections with different directions. Flow and heat-transfer equations are solved with coupled electromagnetic ones for local-thermodynamic-equilibrium optically thin plasma, whereas turbulence phenomena are taken into account by means of a K-epsiv realizable model. The simulations include a prediction of the thermal behavior of the solid components of the torch head, including electrode and hafnium insert, and the efficiency of nozzle- and electrode-cooling systems in various operating conditions, including gas mixtures (O2/air, H35/N2, and N2/N2). Radiation is included in the calculation of heat transfer to the surfaces of the components, using a customized discrete-ordinate model. Results have been analyzed with respect to plasma behavior, and conclusions have been drawn, concerning the powerfulness of numerical simulation as a tool for cutting torch design.
Iron Sources Used by the Nonpathogenic Lactic Acid Bacterium Lactobacillus sakei as Revealed by Electron Energy Loss Spectroscopy and Secondary-Ion Mass Spectrometry

ABSTRACT Lactobacillus sakei is a lactic acid bacterium naturally found on meat. Although it is generally acknowledged that lactic acid bacteria are rare species in the microbial world which do not have iron requirements, the genome sequence of L. sakei 23K has revealed quite complete genetic equipment dedicated to transport and use of this metal. Here, we aimed to investigate which iron sources could be used by this species as well as their role in the bacterium's physiology. Therefore, we developed a microscopy approach based on electron energy loss spectroscopy (EELS) analysis and nano-scale secondary-ion mass spectrometry (SIMS) in order to analyze the iron content of L. sakei cells. This revealed that L. sakei can use iron sources found in its natural ecosystem, myoglobin, hemoglobin, hematin, and transferrin, to ensure long-term survival during stationary phase. This study reveals that analytical image methods (EELS and SIMS) are powerful complementary tools for investigation of metal utilization by bacteria.
Multiscale penalized weighted least-squares image-domain decomposition for dual-energy CT

Image-domain dual-energy CT (DECT) is practical and critical for medical diagnosis and treatment evaluation. The bottleneck of DECT imaging is the significantly magnified noise after a direct inversion decomposition. A good balance is not readily achievable between noise suppression and spatial resolution maintenance. Noise suppression is conventionally included in DECT decomposition implicitly or explicitly and results in the spatial resolution loss. To tackle this problem, we propose a multiscale framework for DECT imaging. High- and low-energy CT images are decomposed into the scale space to fully explore the flexibility of signal processing in each scale. The scale images are then decomposed into two material-specific images using penalized weighted least-squares (PWLS) algorithm with adjustable penalty parameters in different scales using the statistical information in the DECT decomposition process. The final material-specific images are generated by accumulating the decomposed images throughout all scales. The proposed algorithm is evaluated on two physical phantoms: Catphan©600 evaluation phantom and an anthropomorphic head phantom. Noise standard deviation (STD) is reduced by 93% and 98% using the proposed strategy for bone and soft-tissue images as compared with the one using direct inversion for Catphan©600 evaluation phantom, and by 96% and 98% for the anthropomorphic head phantom. Compared with its single-scale counterpart, the proposed multiscale PWLS-based method increases the spatial resolution of soft-tissue images by 28% using a lower scaling factor (k = 20), and by 51% with a higher scaling factor (k = 80). The noise STDs of the decomposed material images remain at the similar level using single- and multi-scale schemes. The proposed multiscale PWLS-based decomposition method is thus attractive for low-dose DECT imaging and clinical practice.
Error Separation Method of Inductosyn

In order to implement the inductosyn error analysis with no higher precise angle measuring device, the error separation technique is studied. The data separation theory of the combination intercomparsion is analyzed and this method is applied to two inductosyns. Through intercomparsive measurement of two inductosyns, the inductosyn error datas are isolated by using the combination intercomparsion. The error data model of the inductosyn angle measuring system is established for error compensation. Through two inductosyns actual experiment, it proves the correctness of the error separation algorithm and error compensation model. Through reasonable error separation and compensation, high-accuracy inductosyn measurement can be achieved with no higher precise measuring equipment.
Differentially-fed microstrip patch antenna for omni-directional GPS applications

A novel omni-directional circularly-polarised GPS antenna suitable for differential feed is presented. The antenna covers the GPS L1 frequency band. The antenna provides an input impedance of 300 Ω and an axial-ratio bandwidth of 10 MHz from 1.570 GHz to 1.580 GHz. The cross polarization is better than 20 dB.
Searching a pattern in compressed DNA sequences

This paper introduces a novel algorithm for DNA sequence compression that makes use of a transformation and statistical properties within the transformed sequence. A word based tagged code is used for identification of end of code. The word based encoder uses frequency distribution for assigning the code of words. The designed compression algorithm is efficient and effective for DNA sequence compression. As a statistical compression method, it is able to search the pattern inside the compressed text which is useful in knowledge discovery. Experiments show that our algorithm is shown to outperform existing compressors on typical DNA sequence datasets.
Separating News from Opinion in Social Media using Machine learning

Recent growth in social media platforms has produced huge amount of user-generated content. This huge commingled data set is a collection of both “factual information” like breaking-news posted by a user, as well as individual “user’s opinion”. For information extraction applications like news media, factual data are more relevant rather than user opinions and conversely for many opinion-mining applications, user’s perceptions are more important than “factual information”. Hence, separating news from opinion offers distinct advantage for both information extraction systems and opinion mining applications. In this study, we have identified limitation of existing lexicon based, subjectivity detection techniques in noisy microblog domain. We present a novel algorithm that automatically separate news from opinions from the mixed social media corpus. We used “Twitter” as our data corpus and evaluated our algorithm with eight machine-learning classifiers against the baseline. Our algorithm demonstrates significant improvement in classification accuracy over the existing baseline.
Central Tolerance to Myogenic Cell Transplants Does Not Include Muscle Neoantigens

Background. Duchenne muscular dystrophy is a fatal genetic disease caused by lack of dystrophin. Myogenic cell transplantation (MT), a potential therapy for Duchenne muscular dystrophy, can restore dystrophin expression in muscles. Because allogeneic MT is highly resistant to peripheral tolerance, we proposed to induce central tolerance. However, given its immunogenicity, we asked whether central tolerance to donor major histocompatibility complex would allow long-term expression of dystrophin, a tissue-specific neoantigen in dystrophic recipients. Methods. Central tolerance was induced in C57BL/10J mdx (dystrophic) mice by allogeneic bone marrow transplantation (BMT) after conditioning with either lethal total body irradiation (TBI) or an established nonmyeloablative protocol (anti-CD154, anti-CD8 mAbs, and low-dose TBI). Recipients subsequently received donor-strain MT or skin grafts. Results. Long-term hematopoietic chimeras generated using either lethal TBI or the nonmyeloablative regimen were tolerant to donor skin grafts and both primary and secondary donor MT (>90 days). Myogenic cell transplantation survival was decreased when chimerism was transient, which was most common with nonmyeloablative conditioning and fully rather than haplo-mismatched donors. Interestingly, regardless of conditioning, MT was associated with localized muscle infiltration with Foxp3+CD4+, CD25+CD4+, and Perforin+CD8+ cells, whereas skin grafts lacked infiltration. Conclusions. Central tolerance achieved using regimens that eliminate nearly all endogenous peripheral lymphocytes (i.e., lethal irradiation) or a nonmyeloablative protocol that depleted peripheral CD8 cells, results in lymphocytic infiltration in muscles that received MT but not in skin allografts. This suggests that muscle-specific infiltration may result from lack of negative selection for peripheral neoantigens in the thymus after BMT and that tolerance after MT may rely on peripheral regulatory mechanisms.
Conceptualizing IT Self-Service Engagement: A Grounded Theory Approach

The phenomenon of solving one’s own technological problem without seeking the help of the IT department is increasing. Up to 54% of organizations are predicted to use IT self-service as an alternative way to provide services to its employees. The concept gained little attention in IS discipline despite its emerging role in modern IT departments. To explore IT self-service engagement, this paper follows an exploratory approach. Interviews are being collected from users and IT professionals working in the domain of IT service delivery. Applying grounded theory principles, particular that of open, axial and selective coding, the study will allow the concept of IT self-service engagement to emerge from the data, along with its causal conditions, intervening conditions, contextual conditions, strategies and outcomes. This study will also place the phenomenon of IT self-service within the stream of IT service research as well as identify strategies that promote IT self-service engagement within the organization.
Bicortical Biodegradable Screws for Rigid Fixation of Traumatic Sagittal Split Mandibular Fracture

Rigid fixation is the most important issue in the bone healing process. Although internal metallic bone fixation has become increasingly popular over the past 10 years, the presence of several potential problems of metallic bone implants with the popularity of the use of biodegradable plates and screws for craniomaxillofacial fixation have increased in the last 10 years. Rigid fixation of bony fragments was achieved by bicortical applied biodegradable screws in a patient with a sagittal oblique mandibular fracture. Precise bone reduction was maintained with bicortical applied biodegradable screws in the postoperative period. The postoperative period was uneventful and the patient retained the intraoperatively achieved perfect occlusion within a 9-month follow-up period. In this particular case, the advantages of use of resorbable fixation systems are combined with the advantages of bicortical screw fixation of split osteotomy without sacrificing the stability of rigid fixation.
Performance evaluation of social networking application with different Load balancing policy across virtual machine in a single Data Center using CloudAnalyst

To improve the IT resource utilization using Internet base computing we use virtualization technology. Virtualization put the foundation of cloud computing. To deploy the Cloudlet in Cloud computing environment we need to select the Load balancing policy across virtual machine. Virtual machine is hosted on physical hardware inside the Data Center. Hence we want to test the comparative performance of cloud based application. We use different load balancing policy across the virtual machine. Using cloud test bed we identify the performance for different simulation configuration scenario. It includes the variable load balancing policy across the virtual machine deployed on host inside the data center.
Exploring nurse learner wastage/persistence using a discursive approach: towards a theoretical understanding of the subject.

RATIONALE AND AIMS OF THE STUDY This article summarizes the findings of an exploratory study of nurse learner wastage/persistence conducted in England between 1996 and 2000. Given the lack of theorizing in much of the literature on nurse learner wastage/persistence, this study sought to generate a theoretical standpoint from which to explore voluntary nurse learner wastage. DESIGN/METHODS The theoretical standpoint developed drew together the theme of integration, derived from the work of Tinto, with the themes of identity and discourses, as conceptualized by Foucault. Accordingly, integration was defined in terms of how well the learner was able to subscribe to the subjectivities made available by the institutional discourses. One of the chief strengths of this approach was that it facilitated an understanding of the interaction between the individual and the institution in relation to wastage/persistence. A multiple case study strategy was used which focused on learners in the first year of a Project 2000 course. The case study strategy utilized a range of qualitative research methods. FINDINGS AND CONCLUSION The findings indicated that the institution was constituted by two major discourses: the 'apprentice' discourse and the 'autonomous' discourse. It was found that the stayers were much more integrated into the institution, hence they were able to persist on the course, by virtue of being able to manage the contradictions in their identity as a nurse and a learner that these two discourses engendered.
Removing Negative Country Images: Effects of Decomposition, Branding, and Product Experience

This article reports two studies on how negative country images can be removed by investigating the effects of decomposing country image into component and assembly origins, as well as the effects of global branding and product experience. Study 1 examines the psychological mechanism consumers use when a country image is decomposed into component and assembly origins. Study 2 extends the effect of decomposing country image to the context of global brands and product experience. It was found that subjects do not seem to differ either in the psychological mechanism they use or in their confidence in evaluating a product which is “made in “ a country versus a product which has its “components from” and “is assembled in” the same country. As hypothesized, the effect of country image was weakened when it was decomposed. A strong positive brand was found to override negative assembly origin effect. After the product experience, the component origin effect was also removed. These findings suggest that when manufacturers lower their production costs by globalizing their production lines, they may simultaneously benefit from having a positive product image.
Impact of heavy metals on the oil products biodegradation process

Oil products continue to be used as a principal source of energy. Wide-scale production, transport, global use and disposal of petroleum have made them major contaminants in prevalence and quantity in the environment. In accidental spills, actions are taken to remove or remediate or recover the contaminants immediately, especially if they occur in environmentally sensitive areas, for example, in coastal zones. Traditional methods to cope with oil spills are confined to physical containment. Biological methods can have an advantage over the physical—chemical treatment regimes in removing spills in situ as they offer biodegradation of oil fractions by the micro-organisms. Recently, biological methods have been known to play a significant role in bioremediation of oil-polluted coastal areas. Such systems are likely to be of significance in the effective management of sensitive coastal ecosystems chronically subjected to oil spillage. For this reason the aim of this paper is to present an impact of Mn, Cu, Co and Mo quantities on oil biodegradation effectiveness in coastal soil and to determine the relationship between metal concentrations and degradation of two oil products (black oil and diesel fuel). Soil was collected in the Baltic Sea coastal zone oil products degradation area (Klaipeda, Lithuania). The experiment consisted of two parts: study on the influence of micro-elements on the oil product biodegradation process; and analysis of the influence of metal concentration on the number of HDMs. The analysis performed and results obtained address the following areas: impact of metal on a population of hydrocarbon degrading micro-organisms, impact of metals on residual concentrations of oil products, influence of metals on the growth of micro-organisms, inter-relation of metal concentrations with degradation rates. Statistical analysis was made using `Statgraphics plus' software. The influence of metals on the growth of micro-organisms, the biodegradation process rate and the oil product concentrations were evaluated with analysis of variance. The impact has been investigated separately and synergetically.
Cooling Effects and Regulating Ecosystem Services Provided by Urban Trees—Novel Analysis Approaches Using Urban Tree Cadastre Data

The provision of ecosystem services by urban trees is not yet routinely integrated in city administrations’ planting scenarios because the quantification of these services is often time-consuming and expensive. Accounting for these welfare functions can enhance life quality for city dwellers. We present innovative approaches that may appeal to the numerous city administrations that keep tree inventory or cadastre databases of all trees growing on city property for civil law liability reasons. Mining these ubiquitous data can be a feasible alternative to field surveys and improve cost–benefit ratios for ecosystem service assessment. We present methods showing how data gaps (in particular tree height and crown light exposure) in the cadastre data can be filled to estimate ecosystem services with i-Tree Eco. Furthermore, we used the i-Tree Eco output for a noval approach which focus on predicting energy reduction as a proxy for cooling benefits provided by trees. The results for the total publicly owned and managed street trees in our study site of Duisburg (Germany) show that the most important ecosystem services are the removal of particulate matter by 16% of the city emissions and the reduction of 58% of the direct and thermal radiation in the effective range of the trees in the cadastre.