bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of protein folding rates from primary sequences using hybrid sequence representation
Authors: Jiang Yingfu , Iglinski Paul , Kurgan Lukasz 
Published: August 2008

AbstractThe ability to predict protein folding rates constitutes an important step in understanding the overall folding mechanisms. Although many of the prediction methods are structure based, successful predictions can also be obtained from the sequence. We developed a novel method called prediction of protein folding rates (PPFR), for the prediction of protein folding rates from protein sequences. PPFR implements a linear regression model for each of the mainstream folding dynamics including two‐, multi‐, and mixed‐state proteins. The proposed method provides predictions characterized by strong correlations with the experimental folding rates, which equal 0.87 for the two‐ and multistate proteins and 0.82 for the mixed‐state proteins, when evaluated with out‐of‐sample jackknife test. Based on in‐sample and out‐of‐sample tests, the PPFR's predictions are shown to be better than most of other sequence only and structure‐based predictors and complementary to the predictions of the most recent sequence‐based QRSM method. We show that simultaneous incorporation of several characteristics, including the sequence, physiochemical properties of residues, and predicted secondary structure provides improved quality. This hybridized prediction model was analyzed to reveal the complementary factors that can be used in tandem to predict folding rates. We show that bigger proteins require more time for folding, higher helical and coil content and the presence of Phe, Asn, and Gln may accelerate the folding process, the inclusion of Ile, Val, Thr, and Ser may slow down the folding process, and for the two‐state proteins increased β‐strand content may decelerate the folding process. Finally, PPFR provides strong correlation when predicting sequences with low similarity. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Evidence for the involvement of prothymosin α in the spermatogenesis of the frog Rana esculenta
Authors: Ferrara Diana , Izzo Gaia , Liguori Lucia , d'Istria Michela , Aniello Francesco , Minucci Sergio 
Published: August 2008

AbstractProthymosin α (PTMA) is a small acidic protein abundantly and ubiquitously expressed in mammals and involved in different biological activities. Until now, its specific function in spermatogenesis has never been properly investigated. Recently, the isolation of a cDNA encoding for PTMA from the testis of the frog Rana esculenta has been reported: ptma transcript is highly expressed throughout the frog reproductive cycle, peaking in September/October, in concomitance with the germ cell maturation; it is specifically localized in the cytoplasm of primary and secondary spermatocytes and, at a lower level, in the interstitial compartment, in Leydig cells.In this article we support the involvement of PTMA in the meiotic phases of frog spermatogenesis. The expression of ptma mRNA increases in the testis of frogs treated with the antiandrogen cyproterone acetate, which blocks the II meiotic division and induces an increase in SPC cysts; on the contrary, it highly decreases in the testis of animals kept at 4°C and treated with human corionic gonadotropin, in concomitance with the induced block of spermatogenesis and the disappearance of meiotic cells in the tubules. Furthermore, for the first time we have also evidenced by immunohistochemistry the expression of PTMA in the nuclei of secondary spermatocytes, spermatids, and spermatozoa, as well as in the cytoplasm of interstitial Leydig cells. Taken together our data suggest for an important role of PTMA in germ cell maturation and/or differentiation during R. esculenta spermatogenesis. J. Exp. Zool. 311A:1–10, 2009. © 2008 Wiley‐Liss, Inc.
Brain‐derived neurotrophic factor effects on oligodendrocyte progenitors of the basal forebrain are mediated through trkB and the MAP kinase pathway
Authors: Van't Veer Ashlee , Du Yangzhou , Fischer Tanya Z. , Boetig Deborah R. , Wood Melissa R. , Dreyfus Cheryl F. 
Published: August 2008

AbstractPrevious work has indicated that BDNF increases the differentiation of basal forebrain (BF) oligodendrocytes (OLGs) in culture through the mediation of trkB and the MAPK pathway (Du et al. [ 2006a, b] Mol. Cell. Neurosci. 31:366–375; J. Neurosci. Res. 84:1692–1702). In the present work, effects of BDNF on BF OLG progenitor cells (OPCs) were examined. BDNF increased DNA synthesis of OPCs, as assessed by thymidine and bromodeoxyuridine incorporation. Effects of BDNF on DNA synthesis were mediated through the trkB receptor and not the p75 receptor, as shown by inhibitors that block neurotrophin binding to the receptors and by the phosphorylation of trkB. TrkB can activate the mitogen‐ activated protein kinase (MAPK), phosphatidylinositol‐3 kinase (PI3‐K), and phospholipase C‐γ (PLC‐γ) pathways. BDNF elicited the phosphorylation of MAPK and Akt, a kinase downstream of PI3K, but not PLC‐γ in OPCs. Through the use of specific inhibitors to the MAPK and PI3‐K pathways, it was found that the MAPK pathway was responsible for the effect of BDNF on DNA synthesis. These data indicate that BDNF affects OPC proliferation and development through the mediation of trkB and the MAPK pathway. © 2008 Wiley‐Liss, Inc.
Regulation of the phosphoinositide‐3 kinase and mitogen‐activated protein kinase signaling pathways by progesterone and its reduced metabolites in the rat brain
Authors: Guerra‐Araiza Christian , Amorim Miguel A.R. , Pinto‐Almazán Rodolfo , González‐Arenas Aliesha , Campos Maria G. , Garcia‐Segura Luis M. 
Published: August 2008

AbstractSeveral growth factors, such as vascular endothelial growth factor, brain‐derived neurotrophic factor, and insulin‐like growth factor‐I are involved in the actions of progesterone in the central nervous system. Previous studies in neuronal and glial cultures have shown that progesterone may regulate growth factor signaling, increasing the phosphorylation of extracellular‐signal regulated kinase (ERK) and the phosphorylation of Akt, components of the mitogen‐activated protein kinase (MAPK) and the phosphoinositide‐3 kinase (PI3K) signaling pathways, respectively. In this study, we have evaluated whether progesterone and its reduced metabolites, dihydroprogesterone and tetrahydroprogesterone, regulate PI3K and MAPK signaling in the brain of ovariectomized rats in vivo. Significant increases in the phosphorylation of ERK, in the expression of the catalytic (p110) and the regulatory (p85) subunits of PI3K and in the phosphorylation of Akt were observed in the hypothalamus, the hippocampus, and the cerebellum 24 hr after progesterone administration. Progesterone metabolites partially mimicked the effect of progesterone and had a stronger effect on MAPK and PI3K signaling in the hypothalamus than in the other brain regions. These findings suggest that progesterone regulates MAPK and PI3K signaling pathways in the central nervous system in vivo by direct hormonal actions and by mechanisms involving progesterone metabolites. © 2008 Wiley‐Liss, Inc.
Variability of extreme temperature and precipitation in Iran during recent decades
Authors: Rahimzadeh Fatemeh , Asgari Ahmad , Fattahi Ebrahim 
Published: August 2008

AbstractWe examined extreme temperature and precipitation as indicative climatic variables to determine recent climatic changes over Iran. We present the results from 27 synoptic stations which have been quality controlled, tested for homogeneity and have less missing data. For each station, 27 indicative climatic indices recommended by the joint World Meteorological Organization CCL/CLIVAR/JCOMM Expert Team on Climate Change Detection and Indices (ETCCDI) were calculated.Marked negative trends for indices like frost days (FD), ice days (ID), cool days (TX10p), cool nights (TN10p) and diurnal temperature range (DTR) were found over most regions of Iran. Conversely, positive trends were found for summer days (SU25), warm days (TX90p) and tropical nights (TR20) over most regions of the country. For indices such as Cold Spell Duration Index (CSDI) and Warm Spell Duration Index (WSDI), both positive and negative trends were obtained.We found negative trends in consecutive dry days (CDD) over most of the country. A negative trend was observed for about two‐thirds of the country for annual total wet days precipitation (PRCPTOT). Positive trends in the Simple Daily Intensity Index (SDII) were found for the northern half of the country, and concurrently negative trends in total wet days for many places within the same region. We observed a negative trend in very wet days exceeding the 95th percentile (R95p) over the eastern and western regions, and a positive trend over the central region of the country, although a clear negative trend was observed for extremely wet days exceeding the 99th percentile (R99p) over most of the country. No similar trends in either the maximum 1‐day precipitation (Rx1DAY) or maximum 5‐day precipitation (Rx5DAY) were found over the country. Copyright © 2008 Royal Meteorological Society
Modes of periacetabular load transfer to cortical and cancellous bone after cemented versus uncemented total hip arthroplasty: A prospective study using computed tomography‐assisted osteodensitometry
Authors: Mueller Lutz Arne , Schmidt Rainer , Ehrmann Cornelia , Nowak Tobias Eckhard , Kress Alexander , Forst Raimund , Pfander David 
Published: August 2008

AbstractStress‐shielding and periprosthetic bone loss after total hip arthroplasty (THA) may be clinically relevant for high‐demand patients. Analysis of cortical and cancellous bone density (BD) changes in vivo after THA is of interest to basic science researchers and joint reconstruction surgeons. An insufficient periprosthetic bone stock may predispose to migration, early mechanical failure, and major problems in revision surgery. We used computed tomography (CT)‐assisted osteodensitometry in two prospectively analyzed cohorts after cemented (n = 21) versus noncemented (n = 23) cup fixation. Periacetabular BD (mgCaHa/mL) was determined in five CT scans cranial and five CT scans at the level of the cup 10 days and 26 months postoperatively. For press‐fit cups BD decreased significantly in all CT cans except in four out of the five scans of cortical bone cranial to the cup. The decrease was highest for cancellous bone ventral to the cup (−45 to −53%). After cemented cup fixation, significant cortical BD decrease was seen ventral to the cup (−11 to −20%). Cancellous BD decrased only ventral (−21 to −31%) and in two scans cranial (−11 and −12%) to the cup. The modes of load transfer between cemented and uncemented cups differ fundamentally. Cemented cups especially prevent the loss of cancellous bone of the acetabulum while also cortical BD loss was significantly lower in most CT scans surrounding the cemented cup compared to the press‐fit component. Long‐term results are required to prove whether third‐generation cementing technique protects periprosthetic BD and thereby improve implant survival. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27:176–182, 2009
Coccolithophores as palaeoecological indicators for shifts of the ITCZ in the Cariaco Basin during the late Quaternary
Authors: Mertens Kenneth N. J. M. , Lynn Matt , Aycard Mylene , Lin Hui‐Ling , Louwye Stephen 
Published: August 2008

AbstractCoccoliths were studied from the ODP Hole 1002C and core PL07‐39PC in the Cariaco Basin. Increases in Emiliania huxleyi are synchronous with decreases of Gephyrocapsa oceanica and vice versa. A new index (GEX) based on the relative abundances of these two taxa is proposed, and correlates with various other proxies. It is shown that GEX can serve as upwelling proxy. This confirms that the Intertropical Convergence Zone shifted north during the Bølling/Allerød, south during the Younger Dryas and back north during the Preboreal. The upwelling proxy shows few discrepancies with the terrigenous record. Copyright © 2008 John Wiley & Sons, Ltd.
Sequential real number computation and recursive relations
Authors: Marcial‐Romero J. Raymundo , Moshier M. Andrew 
Published: August 2008

AbstractIn the first author's thesis [10], a sequential language, LRT, for real number computation is investigated. That thesis includes a proof that all polynomials are programmable, but that work comes short of giving a complete characterization of the expressive power of the language even for first‐order functions. The technical problem is that LRT is non‐deterministic. So a natural characterization of its expressive power should be in terms of relations rather than in terms of functions. In [2], Brattka examines a formalization of recursive relations in the style of Kleene's recursive functions on the natural numbers. This paper is an expanded version of [13] which establishes the expressive power of LRTp, a variant of LRT, in terms of Brattka's recursive relations. Because Brattka already did the work of establishing the precise connection between his recursive relations and Type 2 Theory of Effectivity, we thus obtain a complete characterization of first‐order definability in LRTp. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Entwicklung von Tyrosinkinase‐Inhibitoren bei hämatologischen Neoplasien. FLT3 und JAK2 als therapeutische Targets
Authors: Lipka Daniel , Heidel Florian , Huber Christoph , Fischer Thomas 
Published: August 2008

AbstractTyrosinkinase‐Inhibitoren stellen einen wichtigen Beitrag zur Weiterentwicklung und Verbesserung der Therapie von hämatologischen Neoplasien dar. Zahlreiche Inhibitoren befinden sich bereits in fortgeschrittener klinischer Testung. Während bei einem Teil der Erkrankungen (CML) die Inhibitor‐Therapie bereits als Standard etabliert ist, befinden sich die “small molecules” bei Akuter Myeloischer Leukämie und chronisch‐myeloproliferativen Syndromen noch in der Etablierungsphase. Die Entwicklung von neuen zielgerichteten Substanzen zählt zu den großen präklinischen und klinischen Herausforderungen der nächsten Jahre.
Innovationen mit systemsprengendem Potenzial? Neue Wirkstoffe mit hohen Preisen
Authors: Pfannkuche Matthias S. , Glaeske Gerd 
Published: August 2008

AbstractDie innovativen Tyrosinkinase‐Inhibitoren haben den therapeutischen “Wirkstoffschatz” sinnvoll erweitert, sind allerdings auch mit Preisen verbunden, die ein systemsprengendes Potenzial aufweisen. Für die zukünftige Finanzierbarkeit solcher Innovationen sind geeignete Strategien zu diskutieren.
Neue Therapieansätze bei Cystischer Fibrose
Authors: Vestner Anne , Schrepfer Barbara , Kockler Jutta , Mohr Franziska , Zündorf Ilse , Dingermann Theo 
Published: August 2008

AbstractCystische Fibrose ist mit einer Inzidenz von 1/2.500 bis 1/1.600 die häufigste autosomal‐rezessive Erbkrankheit in Mittel‐ und Nord‐Europa. Ungefähr jeder Zwanzigste ist Träger eines defekten Allels. Mutiert ist dabei das CFTR‐Gen (Cystic Fibrosis Conductance Transmembrane Regulator), das sich auf Chromosom 7 befindet.
Design of new polypropylene–woodflour composites: Processing and physical characterization
Authors: Bouza R. , Pardo S.‐G. , Barral L. , Abad M.J. 
Published: August 2008

AbstractWoodflour/polypropylene composites were prepared with 10 and 20% in weight of woodflour (WF). The influence of the WF, the compatibilizer, and processing aid (WP) in the crystalline structure of the polypropylene was studied by thermal analysis. The results showed that the WF acts as a nucleating agent, increasing the crystallization rate of the PP at the cooling rates studied. The morphological study by SEM proved that the WP increased the dispersion of the filler into the PP matrix, and the ionomer, used like compatibilized improved the adhesion between the PP and the filler obtaining a more uniform morphology. The mechanical properties indicated that the incorporation of the ionomer and the WP enhanced the ductility of the composites at the same time that the materials reached a more uniform morphology. The amount of additives (compatibilizer and WP) included in the woodflour‐plastic composite (WPC) formulations was small, for this, the formulations are suitable to use in a possible industrial application. POLYM. COMPOS., 2009. © 2008 Society of Plastics Engineers
Vitreous proteomic analysis of proliferative vitreoretinopathy
Authors: Yu Jing , Liu Feng , Cui Shu‐Jian , Liu Yan , Song Zheng‐Yu , Cao Hui , Chen Feng‐E , Wang Wei‐Jun , Sun Tao , Wang Fang 
Published: August 2008

AbstractProliferative vitreoretinopathy (PVR) is the most common cause of anatomic failure in retinal detachment surgery. To understand the molecular mechanisms, vitreous proteomes of patients with PVR were investigated by two‐dimensional‐nano‐liquid chromatography coupled with tandem mass spectrometry. Vitreous samples of moderate PVR (grade B), and severe PVR (grade C or D) were aspirated during pars plana vitrectomy before infusion. In the current study, 129, 97 and 137 proteins were identified in vitreous of normal control, moderate and severe PVR, respectively. In PVR vitreous samples, complement components, serine proteinase inhibitors, and extracellular proteins were up‐regulated or appeared, while normal cytoskeleton and metabolism proteins were down‐regulated or disappeared. It was noteworthy that the proteins involved in transcription and translation regulation increased in vitreous with PVR. Among 102 PVR‐specific proteins, kininogen 1 was specifically detected in both vitreous and the corresponding serum. Therefore, it can be concluded that PVR is a complicated pathology process with great amount of proteins involved in metabolism dysfunction, immune reactions, and cytoskeleton remolding. Kininogen 1 may be a candidate biomarker of PVR. Further investigations of these special proteins will provide additional targets for treatment or prevention of ocular proliferative diseases.
Comparative proteomic study of arsenic‐induced differentially expressed proteins in rice roots reveals glutathione plays a central role during As stress
Authors: Ahsan Nagib , Lee Dong‐Gi , Alam Iftekhar , Kim Pil Joo , Lee Jeung Joo , Ahn Young‐Ock , Kwak Sang‐Soo , Lee In‐Jung , Bahk Jeong Dong , Kang Kyu Young , Renaut Jenny , Komatsu Setsuko , Lee Byung‐Hyun 
Published: August 2008

AbstractWhile the phytotoxic responses of arsenic (As) on plants have been studied extensively, based on physiological and biochemical aspects, very little is known about As stress‐elicited changes in plants at the proteome level. Hydroponically grown 2‐wk‐old rice seedlings were exposed to different doses of arsenate, and roots were collected after 4 days of treatment, as well as after a recovery period. To gain a comprehensive understanding of the precise mechanisms underlying As toxicity, metabolism, and the defense reactions in plants, a comparative proteomic analysis of rice roots has been conducted in combination with physiological and biochemical analyses. Arsenic treatment resulted in increases of As accumulation, lipid peroxidation, andin vivoH2O2contents in roots. A total of 23 As‐regulated proteins including predicted and novel ones were identified using 2‐DE coupled with MS analyses. The expression levels ofS‐adenosylmethionine synthetase (SAMS), GSTs, cysteine synthase (CS), GST‐tau, and tyrosine‐specific protein phosphatase proteins (TSPP) were markedly up‐regulated in response to arsenate, whereas treatment by H2O2also regulated the levels of CS suggesting that its expression was certainly regulated by As or As‐induced oxidative stress. In addition, an omega domain containing GST was induced only by arsenate. However, it was not altered by treatment of arsenite, copper, or aluminum, suggesting that it may play a particular role in arsenate stress. Analysis of the total glutathione (GSH) content and enzymatic activity of glutathione reductase (GR) in rice roots during As stress revealed that their activities respond in a dose‐dependent manner of As. These results suggest that SAMS, CS, GSTs, and GR presumably work synchronously wherein GSH plays a central role in protecting cells against As stress.
Combining “click” chemistry and step‐growth polymerization for the generation of highly functionalized polyesters
Authors: Billiet Leen , Fournier David , Du Prez Filip 
Published: August 2008

AbstractAliphatic polyesters bearing pendant alkyne groups were successfully prepared by step‐growth polymerization of different building blocks such as adipic acid and succinic acid in combination with an acetylene‐based diol, 2‐methyl‐2‐propargyl‐1,3‐propanediol, besides 1,4‐butanediol and ethylene glycol. It was demonstrated that the alkyne groups survive the high reaction temperatures (200 °C) in the presence of a radical inhibitor. The alkyne loading has been tuned by the ratio of the different monomers used, up to 25 mol % of alkyne groups. Subsequently, the alkyne groups have been reacted with azides by the copper‐catalyzed Huisgen 1,3‐dipolar cycloaddition reaction, a popular type of “click” chemistry. “Click” reactions have been performed quantitatively in the presence of benzyl azide and azide‐terminated poly(ethylene glycol), yielding brush copolymers in the latter case. Kinetic investigations about this click reaction have been performed by means of on‐line Fourier transform mid‐infrared spectroscopy, which was reported for the first time in the field of the click chemistry research. A whole range of functionalized polyesters, based on poly(ethylene succinate) and poly(butylene adipate), is available, the properties of which can be tailored by choosing the appropriate azide compound. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 6552–6564, 2008
Unexpected reactions associated with the xanthate‐mediated polymerization of N‐vinylpyrrolidone
Authors: Pound Gwenaelle , Eksteen Zaskia , Pfukwa Rueben , McKenzie Jean M. , Lange Ronald F. M. , Klumperman Bert 
Published: August 2008

AbstractThe monomer N‐vinylpyrrolidone (NVP) undergoes side reactions in the presence of R group functional xanthates and impurities. The fate of the monomer NVP and a selection of six O‐ethyl xanthates during xanthate‐mediated polymerization were studied via NMR spectroscopy. A high number of by‐products were identified. Significant side reactions affecting NVP include the formation of an unsaturated dimer and hydration products in bulk or in solution in C6D6. In addition, the xanthate adjacent to a NVP unit was found to undergo elimination at moderate temperature (60–70 °C), resulting in unsaturated species and the formation of new xanthate species. The presence of the chlorinated compound α‐chlorophenyl acetic acid, ethyl ester, a precursor in the synthesis of the xanthate S‐(2‐ethyl phenylacetate) O‐ethyl xanthate, resulted in a dramatic increase in the rate of side reactions such as unsaturated dimer formation and a high ratio of unsaturated chain ends. The conditions for the occurrence of such side reactions are discussed in this article, with relevance to increasing the control over the polymerization kinetics, endgroup functionality, and control over the molar mass distribution. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 6575–6593, 2008