Miracle-dz/UniFAR-FTUs huggingface dataset:
RHYTHM—a server to predict the orientation of transmembrane helices in channels and membrane-coils

RHYTHM is a web server that predicts buried versus exposed residues of helical membrane proteins. Starting from a given protein sequence, secondary and tertiary structure information is calculated by RHYTHM within only a few seconds. The prediction applies structural information from a growing data base of precalculated packing files and evolutionary information from sequence patterns conserved in a representative dataset of membrane proteins (‘Pfam-domains’). The program uses two types of position specific matrices to account for the different geometries of packing in channels and transporters (‘channels’) or other membrane proteins (‘membrane-coils’). The output provides information on the secondary structure and topology of the protein and specifically on the contact type of each residue and its conservation. This information can be downloaded as a graphical file for illustration, a text file for analysis and statistics and a PyMOL file for modeling purposes. The server can be freely accessed at: URL: http://proteinformatics.de/rhythm
Danish experience with the EDIP tool for environmental design of industrial products

Since its publication in, 1996, the Danish method and tools for the environmental design of industrial products (EDIP) have been used in companies in Denmark and abroad, and experience has been gained with a variety of product categories such as electronics, electromechanical products, furniture, foodstuffs, packaging, textiles, building equipment, energy systems and railway systems. The experience shows that large environmental improvement potentials can be found in all product categories. As a broad average, 30-50% environmental improvement of products have been implemented over few years by companies working with the EDIP tools. The paper presents examples from pumps, refrigerator, high pressure cleaners audio/video products, book shelves and moulded cardboards. A questionnaire investigation of the experience with life cycle assessment (LCA) and ecodesign within the Danish pioneer companies in the area was made in November 1997. A total of 39 companies, known to have worked more or less with LCA and ecodesign, were contacted, and 26 companies volunteered to participate. The investigation covered from small (8 employees) to large (>7000 employees) companies having from very little to several years of experience with LCA and ecodesign. The attitude towards the disciplines were mainly positive: 70% of the companies claim that the LCA work has resulted in new priorities in product development. More than 70% of the companies stated that they would continue to include LCA in their product development in the future. Abort 80% of these companies use the EDIP method and tools.
A Preliminary Investigation on Surface Roughness Assessment of Complex Additive Manufactured Parts Scanned by X-ray Computed Tomography

The additive manufacturing (AM) technologies bring in a number of benefits over traditional subtractive manufacturing technologies. However as-built surface finish of AM produced components is often not satisfactory and usually needs further post-process. Surface roughness is vitally important to the product’s functional performance. However, the measurement and characterization of the complex functional AM surfaces is difficult due to their complicated shape or intricate internal geometries. XCT is current the only valid method that can measure complete internal and external geometry without constraints of traditional tactile and optical techniques. Nonetheless, XCT measurement posts two obstacles to standard roughness characterisation: the measured surface form and the non-uniform sampled measurement data structure. Aiming for a holistic and reliable roughness assessment, it is proposed to use the linear diffusion equation to achieve a Gaussian filtering effect on complex surfaces and to extend the roughness areal parameters on a triangular mesh.
Familial Handedness and Access to Words, Meaning, and Syntax during Sentence Comprehension

We compared right-handed familial dextral (FS-) and familial sinistral (FS+) participants who were aged either 10-13 years (children) or 18-23 years (adults). In word probe and associative probe tasks, FS+ adults responded faster than all other groups and FS+ children responded more slowly than all other groups. In the word probe task, only the FS- adults showed a significant effect of the serial position of the target word. We interpret these differences to support an analysis-by-synthesis model of comprehension in which individuals who differ in familial handedness and age emphasize different linguistic representations during comprehension. In general, FS+ individuals focus on words and meaning, while FS- individuals focus on syntactic representations. In FS+ individuals, age-related experiences with language produce a shift in responding from compositional meaning to words and their associations. In FS- individuals, age-related experiences with language produce a shift toward responding based more on detailed syntactic representations, including the serial order of words and possibly the structural roles of clauses.
Dual N- and C-Terminal Helices Are Required for Endoplasmic Reticulum and Lipid Droplet Association of Alcohol Acetyltransferases in Saccharomyces cerevisiae

In the yeast Saccharomyces cerevisiae two alcohol acetyltransferases (AATases), Atf1 and Atf2, condense short chain alcohols with acetyl-CoA to produce volatile acetate esters. Such esters are, in large part, responsible for the distinctive flavors and aromas of fermented beverages including beer, wine, and sake. Atf1 and Atf2 localize to the endoplasmic reticulum (ER) and Atf1 is known to localize to lipid droplets (LDs). The mechanism and function of these localizations are unknown. Here, we investigate potential mechanisms of Atf1 and Atf2 membrane association. Segments of the N- and C-terminal domains of Atf1 (residues 24–41 and 508–525, respectively) are predicted to be amphipathic helices. Truncations of these helices revealed that the terminal domains are essential for ER and LD association. Moreover, mutations of the basic or hydrophobic residues in the N-terminal helix and hydrophobic residues in the C-terminal helix disrupted ER association and subsequent sorting from the ER to LDs. Similar amphipathic helices are found at both ends of Atf2, enabling ER and LD association. As was the case with Atf1, mutations to the N- and C-terminal helices of Atf2 prevented membrane association. Sequence comparison of the AATases from Saccharomyces, non-Saccharomyces yeast (K. lactis and P. anomala) and fruits species (C. melo and S. lycopersicum) showed that only AATases from Saccharomyces evolved terminal amphipathic helices. Heterologous expression of these orthologs in S. cerevisiae revealed that the absence of terminal amphipathic helices eliminates LD association. Combined, the results of this study suggest a common mechanism of membrane association for AATases via dual N- and C-terminal amphipathic helices.
Synthesis of β-Maltooligosaccharides of Glycitein and Daidzein and their Anti-Oxidant and Anti-Allergic Activities

The production of β-maltooligosaccharides of glycitein and daidzein using Lactobacillus delbrueckii and cyclodextrin glucanotransferase (CGTase) as biocatalysts was investigated. The cells of L. delbrueckii glucosylated glycitein and daidzein to give their corresponding 4'- and 7-O-β-glucosides. The β-glucosides of glycitein and daidzein were converted into the corresponding β-maltooligosides by CGTase. The 7-O-β-glucosides of glycitein and daidzein and 7-O-β-maltoside of glycitein showed inhibitory effects on IgE antibody production. On the other hand, β-glucosides of glycitein and daidzein exerted 2,2-diphenyl-1-picrylhydrazyl (DPPH) free-radical scavenging activity and supeoxide-radical scavenging activity.
A Tool Chain for UML-based Modeling and Simulation of VANET Scenarios with Realistic Mobility Models

We show the advantages of integrated tool support for evaluating Vehicular Ad Hoc Network (VANET) scenarios. This includes three primary aspects. First, we provide support for convenient graphical modeling using UML diagrams and automated model transformation into executable simulation code using the Syntony framework. Secondly, a bidirectional coupling of network simulation and road traﬃc microsimulation provides realistic mobility models. The Veins system supports manifold interactions between the Inter Vehicle Communication (IVC) protocols and the microsimulation based road traﬃc. Finally, the developed integrated simulation framework is based on the state-of-the-art network simulation core OMNeT++ which also provides a comprehensive library of well-tested simulation models for communication networks. We demonstrate the feasibility and the advantages of this integrated modeling and simulation based on a traﬃc information system that is investigated in the context of the CoCar research project.
RNA-RNA interaction prediction based on multiple sequence alignments

MOTIVATION Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, O(N(6)) time and O(N(4)) space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes. However, few of these methods incorporate the knowledge concerning related sequences, thus relevant evolutionary information is often neglected from the structure determination. Therefore, it is of considerable practical interest to introduce a method taking into consideration both: thermodynamic stability as well as sequence/structure covariation. RESULTS We present the a priori folding algorithm ripalign, whose input consists of two (given) multiple sequence alignments (MSA). ripalign outputs (i) the partition function, (ii) base pairing probabilities, (iii) hybrid probabilities and (iv) a set of Boltzmann-sampled suboptimal structures consisting of canonical joint structures that are compatible to the alignments. Compared to the single sequence-pair folding algorithm rip, ripalign requires negligible additional memory resource but offers much better sensitivity and specificity, once alignments of suitable quality are given. ripalign additionally allows to incorporate structure constraints as input parameters. AVAILABILITY The algorithm described here is implemented in C as part of the rip package.
Combating synchronization errors in cooperative relays

Cooperative relays have recently been proposed and studied for mobile ad hoc networks. It has been shown that under perfect symbol synchronization, parallel relays with space-time modulation can yield more than 10 dB power savings over conventional serial relays in a highly mobile environment. We analyze the effect of synchronization errors on the performance of parallel relays, and also study several effective methods to reduce the negative impact of synch errors. Our study shows that when the synch errors are much smaller than a symbol interval, the performance of parallel relays deteriorates gracefully. We have also found that well designed space-time coding techniques, such as TR-STC and ST-OFDM, can be highly effective in combating large synch errors with only marginal reduction of data rate.
ERTAPENEM RESISTANCE AMONG EXTENDED-SPECTRUM-Β-LACTAMASE-PRODUCING KLEBSIELLA PNEUMONIAE ISOLATES

Correct detection of carbapenemase-producing strains is of crucial importance. Carbapenem resistance in Klebsiella pneumoniae is rare. Aim: The purpose of our study was to analyze the resistance to carbapenems of Klebsiella pneumoniae strains isolated from different pathological products. Methods: The resistance mechanism of 58 Klebsiella pneumoniae isolates, with decreased susceptibility to carbapenems collected from 2007 to 2009 was investigated. Detection of the resistance mechanisms included a screening step, an optional phenotypic confirmatory step, followed by a genotypic step. Results: Hyper production of ESBL type enzymes combined with porin loss is regarded as the main mechanism of resistance. Analysis of β-lactamases showed that all isolates possessed ESBL genes. Other β-lactamases belonging to class A, including bla-KPC-1, class B or OXA-type carbapenemases, were not detected. Conclusions: The emergence of multiresistant Klebsiella pneumoniae isolates is of major concern and highlights the need for further surveillance.
The Myth of Dangerous Human-Caused Climate Change

Human-caused global warming has become the environmental cause celebre of the early 21st century. The strong warming alarmist camp currently includes the United Nations, most Western governments, most of the free press, many large corporations (including Enron, before it failed), the major churches, most scientific organisations and a large portion of general public opinion. This phalanx of support notwithstanding there is no scientific consensus as to the danger of human-induced climate change. There is, therefore, a strong conflict between the level of public alarm and its scientific justification. How can this be? In a democracy, the media serve to convey to the public the facts and hypotheses of climate change as provided by individual scientists, governmental and international research agencies, and NGO and other lobby groups. In general, the media have promulgated an alarmist cause for climate change; they have certainly failed to convey the degree of uncertainty that is characteristic of climate science, or a balanced summary of the many essential facts that are relevant to human causation. Climate change is as much a geological as it is a meteorological issue. Natural climate changes, both warmings and coolings, are indeed a societal hazard. We usually deal with geological hazards by providing civil defence authorities and the public with accurate, evidence-based, general information about events like earthquakes, volcanic eruptions, tsunamis and floods, and then by adapting to the effects when a damaging event occurs. As for other major natural disasters, the appropriate preparation for extreme climate events is to mitigate and manage the negative effects when they occur, and especially so for dangerous coolings. Attempting instead to ‘stop climate change’ by reducing human carbon dioxide emissions is a costly exercise of utter futility. Rational climate policies must be based on adaptation to dangerous change as and when it occurs, and irrespective of its sign or causation. The issue now is no longer climate change as such, the reality of which will always be with us. Rather, the issues are, first, the failure of the free press to inform the public about the true facts of human-caused climate change and of the dangers posed by natural climate change. And, second, the vested interests held by many of the groups of warming alarmists. These interests include not only the obvious commercial ones, but also the many scientists and science managers who have discounted or remained silent about the huge uncertainties of the human-caused global warming hypothesis because it suited them to do so. Public opinion will soon demand an explanation as to why experienced editors and hardened investigative journalists, worldwide, have melted before the blowtorch of self-induced guilt, political correctness and special interest expediency that marks the sophisms of global warming alarmists.
Research on Service Usage Pattern Mining Method in the Distributed Context

Composite service selection is a research difficulties in service-oriented computing domain. Most selection approaches are based on service QoS information which is difficult to acquire accurately. In this paper, a distributed web service usage pattern mining infrastructure based on services execution information is proposed. In order to meet the cross-organizational associated business requirement, a service registry federation mechanism is presented. Then, a distributed algorithm of composite service frequent sequential mining within registry federation is described. In the end, some simulation results are demonstrated to show the effectiveness of the proposed method.
Tempered anomalous diffusion in heterogeneous systems

Passive tracers in heterogeneous media experience preasymptotic transport with scale‐dependent anomalous diffusion, before eventually converging to the asymptotic diffusion limit. We propose a novel tempered model to capture the slow convergence of sub‐diffusion to a diffusion limit for passive tracers in heterogeneous media. Previous research used power‐law waiting times to capture the time‐nonlocal transport process. Here those waiting times are exponentially tempered, to capture the natural cutoff of retention times. The model is validated against particle concentrations from detailed numerical simulations and field measurements, at various scales and geological environments.
VHF-BAND SAR FOR FOREST STEM VOLUME APPLICATIONS

VHF-band SAR holds great promise for forest stem volume mapping. The paper describes a coherent scattering model and demonstrates that radar backscattering is mainly proportional to stem volume in coniferous forests. The model is also used to develop inverse methods. It is noted that a sloping ground may change the backscattering significantly and therefore needs compensation. Results of stem volume retrieval using the CARABAS-II SAR (20-90 MHz, HHpolarisation) are shown for several coniferous forests including both flat and topographic areas. The rms error is about 20% when compared with ground truth.
Suppression of experimental allergic encephalomyelitis in Lewis rats after elimination of macrophages

Almost 50% of the cells infiltrating the central nervous system (CNS) of animals with experimental allergic encephalomyelitis (EAE) are macrophages (M psi). To investigate the role of the M psi in the pathogenesis of EAE, we eliminated M psi by means of mannosylated liposomes containing dichloromethylene diphosphonate (Cl2MDP). Cl2MDP- containing liposomes injected intravenously eliminate M psi in spleen and liver. Incorporation of mannose into the lipid layers enables the liposomes to pass the blood-brain barrier (BBB). Injections of Cl2MDP- containing mannose liposomes intravenously shortly before the appearance of clinical signs, markedly suppressed the expression of clinical signs of EAE. This suppression was accompanied by a marked reduction of infiltrated M psi in the CNS. Cl2MDP-containing liposomes without mannose incorporated had no effect. Cl2MDP-containing mannosylated liposomes had no effect on plasma corticosterone levels compared with injections of saline; thus, the suppression of expression of EAE was not corticosterone mediated. These results show that the M psi within the CNS play an important role in the pathogenesis of EAE.
Growth of graphene on cylindrical copper conductors as an anticorrosion coating: a microscopic study

We have successfully grown graphene film on the surface of cylindrical copper conductors by chemical vapour deposition. The quality and number of graphene layers have been investigated using Raman spectroscopy, Raman mapping and scanning electron microscopy, as a function of methane gas flow rate and of growth temperature. Transmission electron microscopy analysis has been performed to verify the number of graphene layers, confirming the results obtained by Raman spectroscopy. The results open up the possibility of using graphene as an anticorrosion coating for copper cables and earth grids.
Titanium allergy or not? "Impurity" of titanium implant materials

For patients suffering from allergies to nickel, chrome and cobalt, titanium implants are the implants of choice. Nevertheless, titanium implant sensitivity has been reported in the form of “allergies” and an increasing number of patients are confused. This paper aims to use spectral analysis as a diagnostic tool for analyzing different titanium implant alloys in order to determine the percentage of the alloy components and additions that are known to cause allergies. Different materials, such as sponge titanium, TiAl6Nb7, Ti21SRx, TiAl6V4 [forged alloy], TiAl6V4 [cast alloy], TMZF, pure titanium [c. p. 1] and iodide titanium were analyzed for the presence of the elements that have been associated with allergic reactions using spectral analysis. All the implant material samples contained traceable amounts of Be, Cd, Co, up to a maximum of 0.001 percent by weight [wt. %], Cr up to 0.033 wt. %, Cu up to 0.007 wt. %, Hf up to 0.035 wt. %, Mn up to 0.007 wt. %, Ni up to 0.031 wt. %, and Pd up to 0.001 wt. %. This paper demonstrates that all the investigated implant material samples contained a low but consistent percentage of components that have been associated with allergies. For example, low nickel contents are related to the manufacturing pro- cess and are completely dissolved in the titanium grid. Therefore, they can virtually be classified as “impurities”. Under certain circumstances, these small amounts may be sufficient to trigger allergic reactions in patients suffering from the corresponding allergies, such as a nickel, palladium or chrome allergy.
The Erlang model with non-poisson call arrivals

The Erlang formula is known to be insensitive to the holding time distribution beyond the mean. While calls are generally assumed to arrive as a Poisson process, we prove that it is in fact sufficient that users generate sessions according to a Poisson process, each session being composed of a random, finite number of calls and idle periods. A key role is played by the retrial behavior in case of call blocking. We illustrate the results by a number of examples.
A Survey on the Computational Approaches to Identify Drug Targets in the Postgenomic Era

Identifying drug targets plays essential roles in designing new drugs and combating diseases. Unfortunately, our current knowledge about drug targets is far from comprehensive. Screening drug targets in the lab is an expensive and time-consuming procedure. In the past decade, the accumulation of various types of omics data makes it possible to develop computational approaches to predict drug targets. In this paper, we make a survey on the recent progress being made on computational methodologies that have been developed to predict drug targets based on different kinds of omics data and drug property data.
Computer-vision-based registration techniques for augmented reality

Augmented reality is a term used to describe systems in which computer-generated information is superimposed on top of the real world; for example, through the use of a see- through head-mounted display. A human user of such a system could still see and interact with the real world, but have valuable additional information, such as descriptions of important features or instructions for performing physical tasks, superimposed on the world. For example, the computer could identify and overlay them with graphic outlines, labels, and schematics. The graphics are registered to the real-world objects and appear to be 'painted' onto those objects. Augmented reality systems can be used to make productivity aids for tasks such as inspection, manufacturing, and navigation. One of the most critical requirements for augmented reality is to recognize and locate real-world objects with respect to the person's head. Accurate registration is necessary in order to overlay graphics accurately on top of the real-world objects. At the Colorado School of Mines, we have developed a prototype augmented reality system that uses head-mounted cameras and computer vision techniques to accurately register the head to the scene. The current system locates and tracks a set of pre-placed passive fiducial targets placed on the real-world objects. The system computes the pose of the objects and displays graphics overlays using a see-through head-mounted display. This paper describes the architecture of the system and outlines the computer vision techniques used.