Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative modeling and protein‐like features of hydrophobic–polar models on a two‐dimensional lattice

Lattice models of proteins have been extensively used to study protein thermodynamics, folding dynamics, and evolution. Our study considers two different hydrophobic–polar (HP) models on the 2D square lattice: the purely HP model and a model where a compactness‐favoring term is added. We exhaustively enumerate all the possible structures in our models and perform the study of their corresponding folds, HP arrangements in space and shapes. The two models considered differ greatly in their numbers of structures, folds, arrangements, and shapes. Despite their differences, both lattice models have distinctive protein‐like features: (1) Shapes are compact in both models, especially when a compactness‐favoring energy term is added. (2) The residue composition is independent of the chain length and is very close to 50% hydrophobic in both models, as we observe in real proteins. (3) Comparative modeling works well in both models, particularly in the more compact one. The fact that our models show protein‐like features suggests that lattice models incorporate the fundamental physical principles of proteins. Our study supports the use of lattice models to study questions about proteins that require exactness and extensive calculations, such as protein design and evolution, which are often too complex and computationally demanding to be addressed with more detailed models. Proteins 2012; © 2012 Wiley Periodicals, Inc.
Inter and intra-document contexts applied in polyrepresentation

The principle of polyrepresentation offers a theoretical framework for handling multiple contexts in Information Retrieval (IR). This paper presents an empirical study of polyrepresentation of the information space with focus on inter and intra-document features. The Cystic Fibrosis test collection indexed in a best match system constitutes the experimental setting. Overlaps between four functionally and/or cognitively different representations are identified. Supporting the principle of polyrepresentation, results show that in general overlaps generated by three or four representations have higher precision than those generated from one or two overlaps both in structured and unstructured search mode. It is concluded that a highly structured query language is necessary when implementing the principle of polyrepresentation in a best match IR system because the principle is inherently Boolean. Finally a re-ranking test shows promising results when search results are re-ranked according to precision obtained in the overlaps.
Alpine: Efficient In-Situ Data Exploration in the Presence of Updates

The ever growing data collections create the need for brief explorations of the available data to extract relevant information before decision making becomes necessary. In this context of data exploration, current data analysis solutions struggle to quickly pinpoint useful information in data collections. One major reason is that loading data in a DBMS without knowing which part of it will actually be useful is a major bottleneck. To remove this bottleneck, state-of-the art approaches perform queries in situ, thus avoiding the loading overhead. In situ query engines, however, are index-oblivious, and lack sophisticated techniques to reduce the amount of data to be accessed. Furthermore, applications constantly generate fresh data and update the existing raw data files whereas state-of-the art in situ approaches support only append-like workloads. In this demonstration, we showcase the efficiency of adaptive indexing and partitioning techniques for analytical queries in the presence of updates. We demonstrate an online partitioning and indexing tuner for in situ querying which plugs to a query engine and offers support for fast queries over raw data files. We present Alpine, our prototype implementation, which combines the tuner with a query executor incorporating in situ query techniques to provide efficient raw data access. We will visually demonstrate how Alpine incrementally and adaptively builds auxiliary data structures and indexes over raw data files and how it adapts its behavior as a side-effect of updates in the raw data files.
FRACTIONAL VEGETATION COVER ESTIMATION FROM PROBA / CHRIS DATA : METHODS , ANALYSIS OF ANGULAR EFFECTS AND APPLICATION TO THE LAND SURFACE EMISSIVITY RETRIEVAL

RESUME In this paper, two different methods for fractional vegetation cover (FVC) retrieval from CHRIS (Compact High Resolution Imaging Spectrometer) data based on vegetation indices have been analyzed. The first method uses NDVI (Normalized Difference Vegetation Index) values, as suggested, among others, by Carlson and Ripley (1997) and Gutman and Ignatov (1998), and the second method uses VARI (Variable Atmospherically Resistant Index) values as suggested by Gitelson et al. (2002). In addition, a simple Spectral Mixture Analysis has been also carried out in order to obtain the fractional vegetation cover. The different methods have been tested using vegetation cover values obtained from hemispherical photographs. All methods provide differences with in situ values lower than 15%. The methods based on the VARI and the spectral mixture analysis show the best results, with differences lower than 10%. Substantial angular effects for the different view zenith angles of CHRIS acquisitions have not been found. The fractional vegetation cover has been used in order to obtain land surface emissivity maps with a very simplified approximation, which is only valid for flat surfaces because it does not take into account the cavity effect. In this way, land surface emissivity, which is a parameter used when working with thermal infrared data, can be retrieved from sensors with no available thermal bands.
Alternative Splicing Switches the Divalent Cation Selectivity of TRPM3 Channels*

TRPM3 is a poorly understood member of the large family of transient receptor potential (TRP) ion channels. Here we describe five novel splice variants of TRPM3, TRPM3α1–5. These variants are characterized by a previously unknown amino terminus of 61 residues. The differences between the five variants arise through splice events at three different sites. One of these splice sites might be located in the pore region of the channel as indicated by sequence alignment with other, better-characterized TRP channels. We selected two splice variants, TRPM3α1 and TRPM3α2, that differ only in this presumed pore region and analyzed their biophysical characteristics after heterologous expression in human embryonic kidney 293 cells. TRPM3α1 as well as TRPM3α2 induced a novel, outwardly rectifying cationic conductance that was tightly regulated by intracellular Mg2+. However, these two variants are highly different in their ionic selectivity. Whereas TRPM3α1-encoded channels are poorly permeable for divalent cations, TRPM3α2-encoded channels are well permeated by Ca2+ and Mg2+. Additionally, we found that currents through TRPM3α2 are blocked by extracellular monovalent cations, whereas currents through TRPM3α1 are not. These differences unambiguously show that TRPM3 proteins constitute a pore-forming channel subunit and localize the position of the ion-conducting pore within the TRPM3 protein. Although the ionic selectivity of ion channels has traditionally been regarded as rather constant for a given channel-encoding gene, our results show that alternative splicing can be a mechanism to produce channels with very different selectivity profiles.
Anatomy of the auditory thalamocortical system of the guinea pig

We investigated the projection from the medial geniculate body (MG) to the tonotopic fields (the anterior field A, the dorsocaudal field DC, the small field S) and to the nontonotopic ventrocaudal belt in the auditory cortex of the guinea pig. The auditory fields were first delimited in electrophysiological experiments with microelectrode mapping techniques. Then, small quantities of horseradish peroxidase (HRP) and/or fluorescent retrograde tracers were injected into the sites of interest, and the thalamus was checked for labeled cells.
Context Model Automata for Text Compression

Department of Information Technology, Lappeenranta University of Technology, PO Box 20,FIN-53851 Lappeenranta, FinlandEmail: franti@cs.joensuu. ﬁFinite-state automata offer an alternative approach in the implementation of context models wherethe states in the automata cannot in general be assigned by a single context. Despite the potential ofthis approach, it makes the design of the modelling more problematic because the exact behaviourof themodel is not known. Here we propose a simple formalism—context model automata (CMA)—that gives an exact interpretation for the minimumcontext belonging to each state in the automaton.The formalism is general enough to simulate context models such as PPM and GDMC. Using theCMA formalism as our tool, we study the behaviour of the above two context models.Received April 28, 1997; revised August 7, 1998
Response of body weight and clearance and secretion rates of growth hormone to photoperiod in Holstein heifers.

Effects of photoperiod on growth, eating patterns and clearance rate, secretion rate and half-life of growth hormone in serum were assessed in Holstein heifers. Sixty-four prepubertal heifers (avg body wt 102 kg) were blocked by weight into four groups of 16. Within block, each animal was randomly assigned to one of four photoperiod treatments: 16 h of cool-white fluorescent light:8 h dark (CW-16L:8D), CW-8L:16D, CW-6L:8D:2L:8D or 16 h of VitaLite fluorescent light:8D (V-16L:8D). Animals were fed ad libitum a complete mixed diet formulated for heifers to gain approximately . 9 kg/d. Average daily body weight gains were . 93, . 96, . 98 and 1.0 kg/d during 112 d of exposure to CW-8L:16D, CW-6L:8D:2L:8D, CW-16L:8D and V-16L:8D, respectively. Heifers exposed to V16L:8D and CW-16L:8D gained more weight (112 and 110 kg; P less than .05 and P less than .08, respectively) than heifers exposed to CW-8L:16D (104 kg). Body weight gain was not different (P greater than .10) between heifers exposed to CW-6L:8D:2L:8D (108 kg) or CW-8L:16D, or between heifers exposed to CW-16L:8D or V-16L:8D. Total number of eating events in 30 h and percentage of total events in the lighted period were 549 and 96% and 523 and 50% in heifers exposed to CW-16L:8D and CW-8L:16D, respectively. Clearance rates (620 vs 636 ml/min), secretion rates (3.0 vs 3.8 micrograms/min) and half lives (17.2 vs 17.9 min) of growth hormone in serum were similar in heifers exposed to CW-16L:8D and CW-8L:16D. (ABSTRACT TRUNCATED AT 250 WORDS)
Perceived Increase in Mortality After Process and Policy Changes Implemented With Computerized Physician Order Entry

done before or after the study period ended. The authors also describe 2 critical deficiencies that are reflective of inadequate preparation for implementation of an electronic medical chart, not of CPOE per se. First was the lack of bandwidth capacity on their wireless network. This infrastructure deficiency likely contributed to decreased face-to-face interactions between the nurse and the physician when orders were being entered and highlights the important concept that CPOE is not a replacement for verbal communication. Second, the authors state in their methods section that “no ICU-specific order sets had been programmed at the time of CPOE implementation but instead were developed over time after CPOE implementation. ” In a consensus statement on successful CPOE implementation, Ash et al wrote that “order sets . must be developed, reviewed, and maintained for personal and/or departmental usage. ”4 In fact, the authors later acknowledge in their discussion section that “ongoing development of preprogrammed order sets has helped to reduce some of the upfront time cost of order entry,” but again, it is not clear whether this effort was made before or after the study period ended. In summary, we believe that inadequate preparation for CPOE implementation, highlighted by inappropriate policy and process changes, insufficient infrastructure, and lack of critical care order sets, contributed substantially to the increased mortality rate reported by Han et al. We applaud the authors for highlighting the importance of careful workflow redesign in CPOE implementation, particularly in the intensive care environment, but we caution other readers not to dismiss the importance of CPOE as a tool to help prevent medical errors and enhance patient safety. Indeed, other authors from the same institution have demonstrated a hospital-wide decrease in harmful adverse drug events,5 and other studies have described decreased medical errors in both a PICU6 and an NICU7 with successful CPOE implementation.
Is there a need to improve asthma diagnosis in young athletes?

Since the late 1990s, many studies have highlighted that, compared to the general population, the prevalence of respiratory disorders is markedly increased in elite sport [1]. Notwithstanding other frequent respiratory ailments (e.g. exercise-induced laryngeal obstruction or dysfunctional breathing), asthma/airway hyperresponsiveness (AHR) is the most common chronic medical condition in elite athletes; the prevalence in Olympians being 8% [2]. While the majority of data have been obtained in athletes aged 18 or over, it has been recognized that up to 50% of young elite athletes could suffer from asthma/AHR [3]. Athletes the most at risk for asthma/AHR are the ones competing in endurance and winter sports, and in swimming [2]. The AHR is thought to reflect injury to the epithelium of the lower airways, as a result of the need to condition large volumes of air repetitively during training [4]. Inhalation of cold air or of noxious airborne agents (allergens, pollutants, or chlorination by-products) could contribute and/or amplify the damage, and add to the chronicity of the airway inflammation [4]. In the sporting field, AHR often expresses itself in the form of exercise-induced bronchoconstriction (EIB) – i.e. a transient narrowing of the airways that occurs during and/or shortly after strenuous exercise – [5]. As such, serial measurements of forced expiratory volume in 1 s (FEV1) – an index of airway caliber – are recommended for objective assessment of EIB [6]. The use of respiratory symptoms alone is strongly discouraged for diagnostic purpose, in that symptoms are neither sufficient, nor essential to confirm the presence of asthma/EIB in young athletes [3,7–9]. Further, resting spirometry measurements are poor predictors of variable airflow obstruction in athletes [10].
Spectrin Domain of Eukaryotic Initiation Factor 3a Is the Docking Site for Formation of the a:b:i:g Subcomplex*

Background: eIF3a (eukaryotic initiation factor 3a), the largest subunit of eIF3, contains three putative protein-binding domains. Results: The spectrin domain of eIF3a binds directly to eIF3i and eIF3b concurrently and indirectly to eIF3g via eIF3b. Conclusion: The spectrin domain of eIF3a is responsible for eIF3(a:b:i:g) subcomplex formation. Significance: Identification of the binding sites helps therapeutic discovery targeting protein-protein interactions in eIF3. eIF3a (eukaryotic translation initiation factor 3a), one of the core subunits of the eIF3 complex, has been implicated in regulating translation of different mRNAs and in tumorigenesis. A subcomplex consisting of eIF3a, eIF3b, eIF3g, and eIF3i (eIF3(a:b:i:g)) has also been identified. However, how eIF3a participates in translational regulation and in formation of the eIF3(a:b:i:g) subcomplex remain to be solved. In this study, we used the tandem affinity purification approach in combination with tandem MS/MS and identified the spectrin domain of eIF3a as the docking site for the formation of eIF3(a:b:i:g) subcomplex. Although eIF3b and eIF3i bind concurrently to the spectrin domain of eIF3a within ∼10–15 amino acids apart, eIF3g binds to eIF3a indirectly via binding to the carboxyl-terminal domain of eIF3b. The binding of eIF3b to the spectrin domain of eIF3a occurs in its RNA recognition motif domain where eIF3j also binds in a mutually exclusive manner. Together, we conclude that the spectrin domain of eIF3a is responsible for the formation of eIF3(a:b:i:g) subcomplex and, because of mutually exclusive nature of bindings of eIF3a and eIF3j to eIF3b, different subcomplexes of eIF3 likely exist and may perform noncanonical functions in translational regulation.
Oxidative stress response: a proteomic view

The oxidative stress response is characterized by various effects on a range of biologic molecules. When examined at the protein level, both expression levels and protein modifications are altered by oxidative stress. While these effects have been studied in the past by classic biochemical methods, the recent onset of proteomics methods has allowed the oxidative stress response to be studied on a much wider scale. The input of proteomics in the study of oxidative stress response and in the evidence of an oxidative stress component in biologic phenomena is reviewed in this paper.
Optimization-Tool for local renewable energy usage in the connected system : “ Building-eMobility ”

Renewable energy production and decentralized energy storage as well as optimized usage of existing energy resources are matters of rapidly growing importance. Even today in building architecture as well as modern mobility concepts these technologies are major cost drivers. Staying abreast to these changes, EA EnergieArchitektur GmbH together with IAD TU Dresden are developing a simulation tool to identify and optimize the potentials for building specific energy storage and production as well as optimized usage strategies on the consumer side. Furthermore the simulation tool allows analyzing the smart integration of new eMobility concepts. In this it works as a test bench for system wide energy management with priority on charging strategies for such vehicles from the decentralized power supply.
Cadherin expression delineates the divisions of the postnatal and adult mouse amygdala

The amygdaloid complex represents a group of telencephalic nuclei and cortical areas that control emotional and social behavior. Amygdalar development is poorly understood. It is generally accepted that the structures of the amygdala originate from the neuroepithelium at both sides of the pallial–subpallial boundary. In the present study, we mapped the expression of 13 members of the cadherin superfamily of cell adhesion molecules, which provide an adhesive code for the development and maintenance of functional structures in the central nervous system (CNS). Five classic cadherins (Cdh4, Cdh6, Cdh7, Cdh8, Cdh11) and eight delta‐protocadherins (Pcdh1, Pcdh7, Pcdh8, Pcdh9, Pcdh10, Pcdh11, PCdh17, PCdh19) were studied by in situ hybridization in the postnatal (P5) and adult mouse amygdala. In the different parts of the amygdala, each of these (proto‐) cadherins shows a distinct and spatially restricted expression pattern that is highly similar at postnatal and adult stages. The combinatorial expression of (proto‐) cadherins allows the distinction of multiple molecular subdivisions within the amygdala that partially coincide with previously described morphological divisions. Beyond these expected results, a number of novel molecular subdivisions and subpopulations of cells were identified; for example, additional molecular subdomains, patches, or cell aggregates with distinct (proto‐) cadherin expression in several nuclei/areas of the amygdala. We also show that several cadherins are molecular markers for particular functional subsystems within the amygdala, such as in the olfactory projections. In summary, (proto‐) cadherins provide a code of potentially adhesive cues that can aid the understanding of functional organization in the amygdala. J. Comp. Neurol. 520:3982–4012, 2012. © 2012 Wiley Periodicals, Inc.
Distributed collaborative key agreement and authentication protocols for dynamic peer Groups

We consider several distributed collaborative key agreement and authentication protocols for dynamic peer groups. There are several important characteristics which make this problem different from traditional secure group communication. They are: 1) distributed nature in which there is no centralized key server; 2) collaborative nature in which the group key is contributory (i.e., each group member will collaboratively contribute its part to the global group key); and 3) dynamic nature in which existing members may leave the group while new members may join. Instead of performing individual rekeying operations, i.e., recomputing the group key after every join or leave request, we discuss an interval-based approach of rekeying. We consider three interval-based distributed rekeying algorithms, or interval-based algorithms for short, for updating the group key: 1) the Rebuild algorithm; 2) the Batch algorithm; and 3) the Queue-batch algorithm. Performance of these three interval-based algorithms under different settings, such as different join and leave probabilities,is analyzed. We show that the interval-based algorithms significantly outperform the individual rekeying approach and that the Queue-batch algorithm performs the best among the three interval-based algorithms. More importantly, the Queue-batch algorithm can substantially reduce the computation and communication workload in a highly dynamic environment. We further enhance the interval-based algorithms in two aspects: authentication and implementation. Authentication focuses on the security improvement, while implementation realizes the interval-based algorithms in real network settings. Our work provides a fundamental understanding about establishing a group key via a distributed and collaborative approach for a dynamic peer group.
'Children and obesity: a pan-European project examining the role of food marketing'.

BACKGROUND Rising levels of obesity in school-age children across Europe are causing increasing concern. The 'Children, Obesity and associated avoidable Chronic Diseases' project sought to examine the effects of promotion within food marketing, given the influential role it plays in children's diets. METHOD A questionnaire and data-collection protocol was designed for the national co-ordinators, facilitating standardized responses. Co-ordinators collected data from within 20 European Union countries relating to food promotion to children. RESULTS Results showed that unhealthy foods such as savoury snacks and confectionary were the most commonly marketed and consumed by children across all countries. Television was found to be the prime promotional medium, with in-school and internet marketing seen as growth areas. Media literacy programmes designed specifically to counterbalance the effects of food marketing to children were reported by only a few of the 20 countries. An ineffective and incoherent pattern of regulation was observed across the countries as few governments imposed tough restrictions with most preferring to persuade industry to voluntarily act with responsibly. Most health, consumer and public interest groups supported food marketing restrictions whilst industry and media groups advocated self-regulation. CONCLUSION Recommendations include the amendment of the European Union's Television Without Frontiers Directive to ban all TV advertising of unhealthy food to children, the adoption of a commonly agreed European Union definition of an 'unhealthy' food, and the establishment of a mechanism for pan-European monitoring of the nature and extent of food marketing to children and its regulation.