bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct vs 2-stage approaches to structured motif finding
Authors: Federico Maria , Leoncini Mauro , Montangero Manuela , Valente Paolo 
Published: August 2012

Abstract

Background
The notion of DNA motif is a mathematical abstraction used to model regions of the DNA (known as Transcription Factor Binding Sites, or TFBSs) that are bound by a given Transcription Factor to regulate gene expression or repression. In turn, DNA structured motifs are a mathematical counterpart that models sets of TFBSs that work in concert in the gene regulations processes of higher eukaryotic organisms. Typically, a structured motif is composed of an ordered set of isolated (or simple) motifs, separated by a variable, but somewhat constrained number of “irrelevant” base-pairs. Discovering structured motifs in a set of DNA sequences is a computationally hard problem that has been addressed by a number of authors using either a direct approach, or via the preliminary identification and successive combination of simple motifs.

Results
We describe a computational tool, named SISMA, for the de-novo discovery of structured motifs in a set of DNA sequences. SISMA is an exact, enumerative algorithm, meaning that it finds all the motifs conforming to the specifications. It does so in two stages: first it discovers all the possible component simple motifs, then combines them in a way that respects the given constraints. We developed SISMA mainly with the aim of understanding the potential benefits of such a 2-stage approach w.r.t. direct methods. In fact, no 2-stage software was available for the general problem of structured motif discovery, but only a few tools that solved restricted versions of the problem. We evaluated SISMA against other published tools on a comprehensive benchmark made of both synthetic and real biological datasets. In a significant number of cases, SISMA outperformed the competitors, exhibiting a good performance also in most of the cases in which it was inferior.

Conclusions
A reflection on the results obtained lead us to conclude that a 2-stage approach can be implemented with many advantages over direct approaches. Some of these have to do with greater modularity, ease of parallelization, and the possibility to perform adaptive searches of structured motifs. As another consideration, we noted that most hard instances for SISMA were easy to detect in advance. In these cases one may initially opt for a direct method; or, as a viable alternative in most laboratories, one could run both direct and 2-stage tools in parallel, halting the computations when the first halts.
The labial gene is required to terminate proliferation of identified neuroblasts in postembryonic development of the Drosophila brain
Authors: Kuert Philipp A. , Bello Bruno C. , Reichert Heinrich 
Published: August 2012

Summary
The developing brain of Drosophila has become a useful model for studying the molecular genetic mechanisms that give rise to the complex neuronal arrays that characterize higher brains in other animals including mammals. Brain development in Drosophila begins during embryogenesis and continues during a subsequent postembryonic phase. During embryogenesis, the Hox gene labial is expressed in the developing tritocerebrum, and labial loss-of-function has been shown to be associated with a loss of regional neuronal identity and severe patterning defects in this part of the brain. However, nothing is known about the expression and function of labial, or any other Hox gene, during the postembryonic phase of brain development, when the majority of the neurons in the adult brain are generated. Here we report the first analysis of Hox gene action during postembryonic brain development in Drosophila. We show that labial is expressed initially in six larval brain neuroblasts, of which only four give rise to the labial expressing neuroblast lineages present in the late larval brain. Although MARCM-based clonal mutation of labial in these four neuroblast lineages does not result in an obvious phenotype, a striking and unexpected effect of clonal labial loss-of-function does occur during postembryonic brain development, namely the formation of two ectopic neuroblast lineages that are not present in wildtype brains. The same two ectopic neuroblast lineages are also observed following cell death blockage and, significantly, in this case the resulting ectopic lineages are Labial-positive. These findings imply that labial is required in two specific neuroblast lineages of the wildtype brain for the appropriate termination of proliferation through programmed cell death. Our analysis of labial function reveals a novel cell autonomous role of this Hox gene in shaping the lineage architecture of the brain during postembryonic development.
Optimal Paths for a Light-Driven Engine with [A]=[B] Reacting System and Generalized Radiative Heat Transfer Law
Authors: Chen Lingen , Ma Kang , Sun Fengrui 
Published: August 2012

Abstract
A generalized radiative heat transfer law is introduced into an irreversible light-driven engine with a working fluid composed of the bimolecular reacting system [A]=[B], and the effects of heat transfer laws on the optimal paths of the engine are investigated in this paper. Piston paths for maximizing work output and minimizing entropy generation are determined for such an engine with rate-dependent loss mechanisms of friction and heat leakage by applying the optimal control theory. Numerical examples for the optimal configurations with three special heat transfer laws ( n=-1, n=1 and n=4 ) are provided, and the obtained results are compared with each other. The research on the optimal paths of a light-driven engine from Newton’s heat transfer law to the generalized radiative heat transfer law enriches the finite time thermodynamics. The results presented herein can provide some guidelines for optimal design and operation of real light-driven engines.
Effect of Chitosan Addition on NiMo/Al2O3 Catalysts for Dibenzothiophene Hydrodesulfurization
Authors: Ríos-Caloch Guillermina , Santes Víctor , Escobar José , Valle-Orta Maiby , Barrera María C. , Hernández-Barrera Melissa 
Published: August 2012

Abstract
A series of supported NiMo catalysts were prepared by impregnating ammonium heptamolybdate and nickel nitrate (at 12 and 3 wt% of Mo and Ni, respectively) over chitosan (Chi) modified Al2O3 carrier. Alumina substrate was first impregnated with the organic additive (in acidic aqueous HNO3 solution, given the insolubility of chitosan at neutral pH) at concentrations corresponding to Chi/Ni mol ratios of 0.5, 1 and 2. Lower Mo dispersion in materials prepared over Chi-modified alumina was observed by Raman spectroscopy. Also, in those samples formation of hardly reducible aluminum molybdates (due to acidic conditions used during chitosan deposition) was evidenced by thermal analysis. Sulfided (under H2S/H2 flow, at 400 °C) catalysts were tested in dibenzothiophene hydrodesulfurization (HDS, at 72.4 kg/cm2, 320 °C, batch reactor, n-hexadecane as solvent) where no improved activity (in pseudo first order kinetic constant basis) was registered for chitosan-modified samples. However, increased selectivity to the product from direct desulfurization route (biphenyl) suggested enhanced promotion of MoS2 phase (by Ni) in catalysts prepared with organic additive. CO adsorption at -173 °C (followed by infrared spectroscopy) showed lower concentration of NiMoS active sites over catalysts prepared over chitosan-impregnated alumina carrier pointing out to the existence of highly efficient sites, in spite of their lower surface concentration. The present investigation opens the possibility of using chitosan, a sub-product from seafood industry, as efficient HDS catalyst additive.
Role of extracellular matrix in regulating embryonic epithelial-mesenchymal transition
Authors: Zito Francesca 
Published: August 2012

AbstractEmbryogenesis and morphogenesis are characterized by complex cell rearrangements and movements which require appropriate interactions of cells with the surrounding extracellular matrix (ECM) by means of specific membrane receptors. Interest in the identification and purification of ECM components, as well as in conducting functional studies of them, including their ligands and other molecules involved in cell-matrix adhesion, has intensified in recent years, increasing our knowledge of developmental machinery. Cellular movements play an important role during the epithelial-mesenchymal transition (EMT) events, which are key processes in normal embryogenesis as well as in pathological conditions, such as fibrotic diseases and cancer. Thus, to more fully understand mechanisms underlying the EMT process, and for better knowledge of the embryonic defects related to this process, it would be useful to study the substrates on which EMT cells move during embryo development. This review focuses on a few different embryonic systems, taking into account the cell migration that occurs during EMT and highlighting, in particular, studies describing the direct involvement of ECM molecules.
Floristic macroalgal diversity in selected submarine caves located within two marine protected areas off Lampedusa Island and Sicily (Italy)
Authors: Alongi Giuseppina , Cormaci Mario , Furnari Giovanni , Catra Marcello 
Published: August 2012

Abstract
We investigated phytobenthos in submerged marine caves. Underwater caves have rarely been examined for floristic composition. The study was carried out in two Mediterranean marine protected areas (MPAs) [Plemmirio (Maddalena Peninsula, Syracuse, Ionian Sea) and Pelagean Islands (Straits of Sicily)] and the caves were chosen on the basis of their geomorphology, exposure, and bathymetry. From our comparative study of cave floras, we demonstrated that the macroalgal flora of each cave is influenced by the floristic composition of the adjacent area that is a natural source of recruits and by the light environment. Caves that are “visited” (i.e., those situated on one of the underwater routes for scuba divers visiting the MPAs) had floristic richnesses higher than those of “scarcely” or “not visited” ones (i.e., not on tourist routed). This is likely because the visited caves, due to their large entrance and shallow location, have good lighting that favors high macroalgal biodiversity.
Molecular systematic reassessment of Sargassum (Fucales, Phaeophyceae) in Korea using four gene regions
Authors: Cho Sung Mi , Lee Sang Mook , Ko Yong Deok , Mattio Lydiane , Boo Sung Min 
Published: August 2012

Abstract

Sargassum is an ecologically and economically important brown alga in East Asia. A total of 28 species are listed in the available literature for South Korea. To identify the species and evaluate the phylogenetic relationships of Korean Sargassum, we analyzed ITS2, rbcL, psaA, and cox3 sequences from a subset of 50 specimens assigned to 22 Sargassum species; sequences of Korean-collected Myagropsis myagroides and Coccophora langsdorfii were also included. We reconstructed the phylogeny of Sargassum using the concatenated dataset. The Korean Sargassum species fell into two subgenera: 19 species were assigned to S. subgen. Bactrophycus and three species to S. subgen. Sargassum. The species in the S. subgen. Bactrophycus represented the sections Halochloa, Hizikia, Spongocarpus, and Teretia, whereas those of S. subgen. Sargassum represented the sections Binderiana and Sargassum. All Korean Sargassum species identified in the present study are part of the East Asiatic complex of species co-occurring in Japan and surrounding areas. Our four-gene dataset was highly resolved at the sectional level and confirmed recently proposed revisions within the genus. The present study is the first comprehensive phylogenetic analysis of Sargassum using four molecular markers.
Pregnancy-associated plasma protein A: spotlight on kidney diseases
Authors: Kalousová Marta , Tesaíř Vladimír , Muravská Alexandra , Zima Tomáš 
Published: August 2012

Abstract
Pregnancy-associated plasma protein A (PAPP-A) is a biomarker routinely used in screening for Down syndrome in the first trimester of pregnancy. It is also present in very small amounts in men and non-pregnant women. PAPP-A is a key regulator of local insulin-like growth factor (IGF) bioavailability – IGFs are essential for normal body size during fetal development, but they are associated with aging and age-related diseases. Measurement of circulating PAPP-A can provide valuable information not only in pregnant women (chromosomal anomalies and adverse pregnancy outcomes) but also in patients with coronary artery disease (contribution to diagnosis, prognostic value) and in patients with kidney diseases. PAPP-A is associated with renal function and proteinuria, is increased mainly in dialysis patients and decreases after kidney transplantation. It is an independent mortality predictor of hemodialysis patients and indicator of adverse outcome of transplanted patients. PAPP-A levels can be influenced by various chemicals and drugs, among them mainly heparin. Various assays for PAPP-A exist and the type of assay used in a study should be considered. This article reviews the data summarizing basic information about PAPP-A with a particular focus on the significance of PAPP-A in renal diseases.
Update on multiple sclerosis, its diagnosis and treatments
Authors: Cross Anne H. , Cross Kevin A. , Piccio Laura 
Published: August 2012

Abstract
Multiple sclerosis (MS) is a central nervous system disorder, characterized by mononuclear cell inflammation, demyelination and often with extensive axonal injury. It was first described neuropathologically in the late 1800s. MS has an interesting geographical epidemiology, with a higher rate at latitudes further from the equator in both directions. Women outnumber males by about 2:1; this ratio has been increasing in recent years. Genome wide association studies have thus far identified over 50 genetic susceptibility loci, and these are rapidly expanding. Several environmental risk factors have been identified, including low serum vitamin D levels, exposure to Epstein-Barr virus and cigarette smoking. MS displays a heterogeneous disease course; most patients with the disease begin with a relapsing-remitting course, but often eventually develop steady disability progression. A small percentage of MS patients have a progressive course without clinical relapses. Several treatments are now available to decrease relapse rate and slow the accumulation of disability in patients with relapsing MS, but there is currently no effective treatment to slow the progressive forms of MS.
Contribution of procoagulant phospholipids, thrombomodulin activity and thrombin generation assays as prognostic factors in intensive care patients with septic and non-septic organ failure
Authors: Van Dreden Patrick , Woodhams Barry , Rousseau Aurélie , Dreyfus Jean-François , Vasse Marc 
Published: August 2012

AbstractBackground:Multiple organ dysfunction syndrome (MODS) observed in patients with sepsis and in non-septic patients organ failure (OF) is associated with a high mortality rate. We investigated whether new coagulation assays [quantification of procoagulant phospholipids (PPL) activity, functional assays measuring the activity of thrombomodulin (TMa) or tissue factor (TFa) and thrombin generation using calibrated automated thrombography (CAT)] could constitute new tools to better understand the physiopathology of MODS and have any prognostic value.Methods:We measured TMa, TFa, PPL and CAT in 32 healthy controls, 24 patients with sepsis and 26 patients with non-septic OF. We compared these parameters with usual coagulation assays [prothrombin time, activated partial thromboplastin time, protein C (PC), protein S, D-Dimers (D-Di), soluble thrombomodulin (sTM)] and markers of inflammation (IL-6, CRP). Samples were collected within 24 h of the diagnosis.Results:TMa, TFa, PPL, the lag time and time to thrombin peak levels were increased in both groups of patients. For both groups D-Di, IL-6, CRP and endogenous thrombin potential (ETP) were higher in non-survivors than in survivors, while PC and PPL were lower in non-survivors than in survivors. TMa increase was more marked in non-survivors patients with OF, while the ratio TMa/sTM was low in non-survivors with sepsis. Received operating characteristic (ROC) curve analysis indicated that thrombin peak and ETP were the more powerful discriminating factors in patients with sepsis or non-septic OF, respectively.Conclusions:PPL, TMa and CAT assays could represent promising tools to identify patients with increased risk of mortality in MODS and could procure insights into pathogenesis of MODS.
Implementation of new recommendations for the diagnosis of gestational diabetes: a 5-month audit
Authors: Szoke Dominika , Valente Cristina , Dolci Alberto , Panteghini Mauro 
Published: August 2012

Abstract

Background: Recent international recommendations for the diagnosis of gestational diabetes (GD) were implemented in a university hospital. The aim was to audit the appropriateness of use of the new diagnostic approach.

Methods: The same 5-month period, one before [2009, traditional two-step oral glucose tolerance test (OGTT) approach, S1] and one after the implementation of new criteria (2010, S2) were compared.

Results: In the two periods, 256 (S1) and 245 (S2) pregnant women were examined and 298 (50 g, n=195; 100 g, n=103) and 252 (75 g) OGTTs were, respectively, executed. In S1, 54 (27.7%) 50 g OGTTs resulted positive and 36 (66.7%) of those performed the 100 g OGTT. In addition, three (1.5% of total) 50 g OGTT negative women were submitted to 100 g OGTT. Sixty-three women did 100 g OGTT only. In total, 14 (13.6%) 100 g OGTTs were positive. In S2, 38 (15.1%) 75 g OGTTs were positive. In women who did the complete protocol in the hospital, 98.3% in S1 and 77.0% in S2 performed the correct protocol (p<0.0001).

Conclusions: In this hospital new recommendations for GD diagnosis are not correctly applied in 23% of cases. The main issue seems to be the lack of consideration of the new threshold for fasting glycemia (5.1 mmol/L) as a main decisional driver for performing OGTT.
Free products and wild nearfields
à la B. H. Neumann and Hans Zassenhaus
Authors: Grundhöfer Theo 
Published: August 2012

Abstract
The modular group PSL
2
ℤ contains many subgroups that
are sharply transitive on the rational projective line ℚ ∪ ∞. If the field E is a purely transcendental extension
of transcendency degree |E|, then PSL
2

E contains free
subgroups that are sharply transitive on the projective line
E ∪ ∞. This yields wild infinite
nearfields and sharply two-transitive permutation groups.
Effects of systematic variation of wood adherend bending stiffness on fracture properties. Part 2. Revisiting traditional DCB analysis methods
Authors: Nicoli Edoardo , Dillard David A. , Frazier Charles E. 
Published: August 2012

Abstract
Part 1 of the paper evaluated how the orientation and stiffness of the layers in layered beams of constant cross section used in double cantilever beams (DCB) specimens influence the stiffness variation of individual adherends along their length. The behavior of bonded DCB specimens made with such materials, of which wood is a common example, are analyzed in this part 2 of the paper to determine errors associated with common data analysis methods for mode I fracture testing: simple beam theory (SBT), corrected beam theory (CBT), experimental compliance method (ECM or Berry method), and area method (AM). In particular, the first three methods are described in British Standards (BS) 7991 (1991) or the American Society for Testing and Materials (ASTM) D 3433 (1999/2005), while the AM is not suggested by the mentioned standards. SBT, CBT, and ECM, although initially developed for characterizing bonds between uniform and isotropic adherends, have also been commonly applied to other materials including wood. Nevertheless, these three standardized methods may lack precision for determining the critical strain energy release rate, , when applied to bonded wood adherends, due to the elastic stiffness variability that can occur along the length of the bonded beams. The AM yields more coherent results in the developed analytical procedure, although practical issues can limit its reliability with experimental results. Another physical problem that arises with the adherend stiffness variation is the onset of a slight mode II loading component that is not anticipated, nor accounted for, in the traditional data analysis methods.
Properties of molding plates made with albizia wood particles impregnated with alcohol-soluble PF resins prepared from phenol-liquefied lignins
Authors: Lee Wen-Jau , Chang Kuo-Chun , Hsu Ling-Ying , Tseng I-Min 
Published: August 2012

Abstract
Alkaline lignin and de-alkaline lignin were liquefied in phenol with H2SO4 or HCl as catalysts. Liquefied lignins were reacted with formalin under weakly alkaline condition, and in this manner, alcohol-soluble resol-type phenol-formaldehyde (PF) resins (PFlignin) were prepared. Small particles of albizia [Albizia falcataria (L.) Fosberg] passing 100-mesh sieve were impregnated with these resins, and the resulting molded test plates (MTPlignin) with the dimensions of 10×10×0.4 cm3 were analyzed. Differential scanning calorimeter revealed that the PFlignin resins need higher temperatures for curing than those of industrial PF resin (control). MTPlignin has higher internal bonding and bending strengths than those of the MTPcontrol. Thermogravimetric analysis of MTPs shows three distinct degradation rates, and the following heat resistance was found: MTPcontrol>MTPAL>MTPDAL. MTPs have, after carbonization at 800°C, a uniform internal structure as revealed by dimension shrinkage analysis.
Chaperones for proper androgen action – a plethora of assistance to androgen receptor function
Authors: Hessenkemper Wiebke , Baniahmad Aria 
Published: August 2012

AbstractThe androgen receptor (AR) plays a major role for normal prostate growth and also promotes the development and progression of prostate cancer (PCa). PCa, an important age-related disease, is one of the most commonly diagnosed cancers and the second leading cause of cancer mortality for men in Western countries. AR function and activity are regulated by molecular chaperones. The AR belongs to the steroid hormone receptor (SHR) family and can be activated by androgens such as dihydrotestosterone. SHRs are ligand-dependent transcription factors that are predominantly localized in the cytoplasm in the absence of their appropriate ligand. Upon hormone binding, translocation to the nucleus occurs as shown for glucocorticoid receptors, mineralocorticoid receptors, or the AR, while others, such as estrogen and progesterone receptors, are mainly nuclear. Importantly, the newly synthesized and unliganded receptors bind stepwise with chaperones then being associated in a dynamic chaperone heterocomplex, including heat shock proteins. It emerges that chaperones are very important, not only in the proper folding of the AR but they are also involved in receptor stability, intracellular localization and androgen-controlled transcription. Accordingly, chaperones may be interesting future targets for PCa treatment. In this review we will summarize the involvement of chaperones controlling AR activity.