bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein lysine‐Nζ alkylation and O‐phosphorylation mediated by DTT‐generated reactive oxygen species
Authors: Kumar Nigam , Ippel Hans , Weber Christian , Hackeng Tilman , Mayo Kevin H. 
Published: January 2013

AbstractReactive oxygen species (ROS) play crucial roles in physiology and pathology. In this report, we use NMR spectroscopy and mass spectrometry (MS) to demonstrate that proteins (galectin‐1, ubiquitin, RNase, cytochrome c, myoglobin, and lysozyme) under reducing conditions with dithiothreitol (DTT) become alkylated at lysine‐Nζ groups and O‐phosphorylated at serine and threonine residues. These adduction reactions only occur in the presence of monophosphate, potassium, trace metals Fe/Cu, and oxygen, and are promoted by reactive oxygen species (ROS) generated via DTT oxidation. Superoxide mediates the chemistry, because superoxide dismutase inhibits the reaction, and hydroxyl and phosphoryl radicals are also likely involved. While lysine alkylation accounts for most of the adduction, low levels of phosphorylation are also observed at some serine and threonine residues, as determined by western blotting and MS fingerprinting. The adducted alkyl group is found to be a fragment of DTT that forms a Schiff base at lysine Nζ groups. Although its exact chemical structure remains unknown, the DTT fragment includes a SH group and a CHOHCH2 group. Chemical adduction appears to be promoted in the context of a well‐folded protein, because some adducted sites in the proteins studied are considerably more reactive than others and the reaction occurs to a lesser extent with shorter, unfolded peptides and not at all with small organic molecules. A structural signature involving clusters of positively charged and other polar groups appears to facilitate the reaction. Overall, our findings demonstrate a novel reaction for DTT‐mediated ROS chemistry with proteins.
DFT, CBS‐Q, W1BD and G4MP2 calculation of the proton and electron affinities, gas phase basicities and ionization energies of saturated and unsaturated carboxylic acids (C1–C4)
Authors: Valadbeigi Younes , Farrokhpour Hossein 
Published: January 2013

AbstractThe proton affinities, gas phase basicities and ionization energies of formic acid, acetic acid, propanoic acid, 2‐propenoic acid, propiolic acid, butanoic acid, 2‐butenoic acid, 3‐botenoic acid, 2‐methyl‐propanoic acid and 2‐methyl‐2‐propenoic acid were calculated using the computational methods including B3LYP/6‐311++G(2df,p), CBS‐Q and G4MP2. Also, the considered properties were calculated using W1BD method only for formic and acetic acids. In addition, the electron affinities of the acids were calculated using B3LYP, CBS‐Q, G4MP2 and G2MP2 methods, separately. The calculations showed that the PA and gas phase basicity increase with the increase in the number of carbon atoms. The calculated Ionization energies of the unsaturated carboxylic acids are less than the corresponding saturated acids, which are in good agreement with the experimental results. © 2013 Wiley Periodicals, Inc.
Individual Hematopoietic Stem Cells in Human Bone Marrow of Patients with Aplastic Anemia or Myelodysplastic Syndrome Stably Give Rise to Limited Cell Lineages
Authors: Katagiri Takamasa , Kawamoto Hiroshi , Nakakuki Takashi , Ishiyama Ken , Okada-Hatakeyama Mariko , Ohtake Shigeki , Seiki Yu , Hosokawa Kohei , Nakao Shinji 
Published: January 2013

Abstract
Mutation of the phosphatidylinositol N-acetylglucosaminyltransferase subunit A (PIG-A) gene in hematopoietic stem cells (HSCs) results in the loss of glycosylphosphatidylinositol-anchored proteins (GPI-APs) on HSCs, but minimally affects their development, and thus can be used as a clonal maker of HSCs. We analyzed GPI-APs expression on six major lineage cells in a total of 574 patients with bone marrow (BM) failure in which microenvironment itself is thought to be unaffected, including aplastic anemia (AA) or myelodysplastic syndrome (MDS). GPI-APs-deficient (GPI-APs−) cells were detected in 250 patients. Whereas the GPI-APs− cells were seen in all six lineages in a majority of patients who had higher proportion ([dbmtequ]3%) of GPI-APs− cells, they were detected in only limited lineages in 92.9% of cases in the lower proportion (&lt;3%) group. In all 250 cases, the same lineages of GPI-APs− cells were detected even after 6–18-month intervals, indicating that the GPI-APs− cells reflect hematopoiesis maintained by a self-renewing HSC in most of cases. The frequency of clones with limited lineages seen in mild cases of AA was similar to that in severe cases, and clones with limited lineages were seen even in two health volunteer cases. These results strongly suggest most individual HSCs produce only restricted lineages even in a steady state. While this restriction could reflect heterogeneity in the developmental potential of HSCs, we propose an alternative model in which the BM microenvironment is mosaic in supporting commitment of progenitors toward distinct lineages. Our computer simulation based on this model successfully recapitulated the observed clinical data.
Decrease in Abundance of Apurinic/Apyrimidinic Endonuclease Causes Failure of Base Excision Repair in Culture-Adapted Human Embryonic Stem Cells
Authors: Krutá Miriama , Bálek Lukáš , Hejnová Renata , Dobšáková Zuzana , Eiselleová Livia , Matulka Kamil , Bárta Tomáš , Fojtík Petr , Fajkus Jiří , Hampl Aleš , Dvořák Petr , Rotrekl Vladimír 
Published: January 2013

Abstract
The inevitable accumulation of chromosomal abnormalities in human embryonic stem cells (hESCs) during in vitro expansion represents a considerable obstacle for cell replacement therapies. To determine the source of chromosomal abnormalities, we examined hESCs maintained in culture for over 55 months for defects in telomere maintenance and DNA repair. Although prolonged culture affected neither telomerase activity nor nonhomologous end joining, the efficiency of base excision repair (BER) was significantly decreased and correlated with reduced expression of apurinic/apyrimidinic endonuclease 1 (APE1), the major nuclease required for BER. Interestingly, the expression of other BER enzymes was unchanged. Addition of human recombinant APE1 protein to nuclear extracts from late passage hESCs increased BER efficiency to the level typical of early passage hESCs. The link between BER and double-strand breaks (DSB) was demonstrated by decreased DSB release after downregulation of APE1 in early passage hESCs via siRNA. Correspondingly lower APE1 level in late passage hESC resulted in slower and less intensive but long lasting DSB release upon ionizing radiation (IR). Downregulation of APE1 in early passage hESCs also led to approximately 30% decrease in γ-H2AX signaling following IR, similar to that in late passage hESCs. We suggest that downregulation of APE1 significantly contributes to the failure of BER during long-term culture of hESCs, and further that BER failure is one of the factors affecting the genomic instability of hESCs by altering BER-dependent DSB release and cell cycle/checkpoint signaling.
Inhibition Performance of Novel Dissymmetric Bisquaternary Ammonium Salt with an Imidazoline Ring and an Ester Group
Authors: Zhang Jing , Shi Dali , Gong Xuliang , Zhu Fengmin , Du Min 
Published: January 2013

AbstractIn this paper, the inhibition performance of a novel dissymmetric bis‐quaternary ammonium salt with an imidazoline ring and an ester group (DBAS) for Q235 steel in 2 % NaCl solution saturated with CO2 was investigated using weight loss, the polarization curve, electrochemical impedance spectroscopy methods and the quantum chemistry calculation. The results show that DBAS, which is good for the environment and have many activated centers and low ELUMO, has a high inhibition performance for Q235 steel in 2 % NaCl solution saturated with CO2. The inhibition efficiency of the studied corrosion inhibitor increased with increasing inhibitor concentrations. The inhibitor is a mixed‐type inhibitor which inhibits both anodic and cathodic reactions.
On decay of periodic entropy solutions to a scalar conservation law
Authors: Panov E.Yu. 
Published: January 2013

We establish a necessary and sufficient condition for decay of periodic entropy solutions to a multidimensional conservation law with merely continuous flux vector.

Résumé
Nous considérons les lois de conservation [hyperboliques] en plusieurs dimensions dʼespace avec la fonction de flux seulement continue. Nous établissons une condition nécessaire et suffisante pour la décroissance des solutions entropiques périodiques de ce problème.
Low‐intensity physical training recovers object recognition memory impairment in rats after early‐life induced Status epilepticus
Authors: Córdova Sandro Daniel , Loss Cássio Morais , de Oliveira Diogo Losch 
Published: January 2013

AbstractWhen it occurs early in life, Status epilepticus (SE) can cause behavioural and cognitive impairments in adulthood. Here, we evaluated the putative benefits of low‐intensity treadmill training on long‐standing cognitive impairment in rats submitted to SE early in life. Wistar rats were submitted to LiCl‐pilocarpine‐induced SE at P16. Animals from the trained group underwent a low‐intensity treadmill protocol for 5 days per week for 4 weeks. At adulthood, rats subjected to early‐life SE displayed impairment in long‐term memory in an object recognition task, while the training protocol completely reversed this deficit. This result was associated with neither locomotor alterations nor changes in emotional behaviour; there were no differences between groups in the distance travelled, grooming or rearing in the open field test; there were also no differences between groups in the number of risk assessment, time spent in open arms in an elevated plus maze and number of entries into the open arms. These data suggest that physical exercise can ameliorate the long‐standing recognition memory deficit induced by early‐life SE, suggesting that it may be useful as a putative intervention for patients who suffered SE during infancy.
Errors in the treatment of hypertensive disorders of pregnancy and their impact on maternal mortality
Authors: Zuleta‐Tobón John J. , Pandales‐Pérez Heleodora , Sánchez Sandra , Vélez‐Álvarez Gladis A. , Velásquez‐Penagos Jesús A. 
Published: January 2013

AbstractObjectiveTo describe the patients' characteristics and the factors that contributed to the maternal deaths associated with hypertensive disorders of pregnancy that occurred in the department of Antioquia, Colombia, from 2004 through 2011.MethodsA committee of experts conducted a retrospective descriptive study to analyze the information obtained from both mandatory reports of health facilities to the Public Health Surveillance System and interviews with family members.ResultsFrom 2004 through 2011, there were 720 170 births and 389 maternal deaths in the Department of Antioquia, and 70 of the deaths were due to hypertensive disorder of pregnancy. The factors that most contributed to the deaths were a lack of emergency administration of antihypertensive drugs (64.6%); the inadequate administration of antihypertensive drugs (58.8%); retaining the patient at a health facility ill equipped to treat her appropriately for her clinical state (54.7%); untimely referral or inadequate conditions for transfer (50.8%); and an error in classifying the severity of the disorder, which prevented appropriate management (49.1%).ConclusionA substandard quality of care was the determining factor in the deaths of women who presented with hypertensive disorders of pregnancy.
An experimental model of Stanford type B aortic dissection with intravenous epinephrine injection
Authors: Wang Li‐Xin , Wang Yu‐Qi , Guo Da‐Qiao , Jiang Jun‐Hao , Zhang Jing , Cui Jia‐Sen , Fu Wei‐Guo 
Published: January 2013

AbstractThe aim of this study was to create an experimental model of aortic dissection (AD) with a long‐term patent false lumen to develop new treatments for Stanford type B aortic dissection. Sixteen adult beagle dogs (weight 14–18 kg) were used. After exposure and partially clamping, the descending aorta was cut through the adventitia to one‐third of the depth of the tunica media. The aortic wall was divided into two layers by raspatory. Then half the circumference of the inner layer was cut transversely. All of the proximal layers and the distal outer layers were anastomosed together. Epinephrine was immediately used to expand the false lumen, and the effect was terminated using nitroglycerin when necessary. All dogs underwent both digital subtraction angiography (DSA) and computed tomography angiography (CTA) immediately after and 1 week and 1 month after surgery. The dogs were followed up at 1 day, 3 months, 1 year, and 2 years. The surgery was successful in 12 dogs. Dissection formation was observed immediately after epinephrine administration and confirmed by DSA and CTA. Our results showed typical characteristics of AD, such as a tear, septum, and true and false lumens. This is an easy and feasible way of developing a Stanford type B AD model by intravenous injection of epinephrine. In this canine model of AD, the false lumen has excellent long‐term patency and the dissection plane is histologically similar to that in human AD. This model may contribute to the development of new treatments for Stanford type B AD.
Outcome assessment in acute pancreatitis patients
Authors: Lee Wei‐Sin , Huang Jee‐Fu , Chuang Wan‐Long 
Published: January 2013

AbstractEarly diagnosis and severity evaluation in patients with acute pancreatitis (AP) are very important due to its potential morbidity and mortality. Several clinical, laboratory, and radiologic factors, and many scoring systems have been proposed for outcome prediction. Although the Ranson and Acute Physiology and Chronic Health Evaluation II scoring systems have been widely used for decades, the cumbersome components partly limit their predictability. Recently, the Bedside Index for Severity in AP scoring system and series blood urea nitrogen changes, which are simple and convenient to evaluate within 24 hours after admission, have been validated for accuracy by several large‐cohort studies. The presence of organ failure and systemic inflammatory response syndrome are also helpful to evaluate the severity of AP. Herein we review recent advances of the predictive methods for AP to provide an up‐to‐date perspective on outcome assessment of AP.
Comparisons of noninvasive indices based on daily practice parameters for predicting liver cirrhosis in chronic hepatitis B and hepatitis C patients in hospital and community populations
Authors: Tseng Po‐Lin , Wang Jing‐Houng , Hung Chao‐Hung , Tung Hung‐Da , Chen Tsung‐Ming , Huang Wu‐Shiung , Liu Shiann‐Long , Hu Tsung‐Hui , Lee Chuan‐Mo , Lu Sheng‐Nan 
Published: January 2013

AbstractSeveral noninvasive indices have been proposed for predicting liver cirrhosis (LC), particularly in chronic hepatitis C (CHC). In this study, noninvasive indices for predicting LC and hepatocellular carcinoma (HCC) were compared. A total of 119 chronic hepatitis B (CHB) patients and 240 CHC patients were evaluated in a hospital‐based setting using various predictors for pathologic LC such as aspartate aminotransferase/alanine aminotransferase (AST/ALT) ratio (AAR), AAR‐to‐platelet ratio index (AARPRI), AST‐to‐platelet ratio index (APRI), age‐platelet (AP) index, and platelet counts. In addition, these indices were used to predict LC [based on ultrasound (US)] in a community‐based population of 201 patients with endemic hepatitis C virus (HCV). These indices were evaluated for their ability to predict HCC in CHB and CHC patients (n = 200). In CHB patients, the diagnostic performance of all indices was inadequate for predicting LC (areas under receiver operating characteristic curves < 0.7). Thrombocytopenia consistently demonstrated comparable accuracy to AARPRI ≥ 0.7 in CHB and AP index ≥ 7.0 in CHC patients. The best cut‐off values for APRI, AARPRI, and AP index in predicting LC in CHC were 1.3, 0.8, and 7.0, respectively. The best cut‐off values for APRI, AARPRI, and AP index in predicting LC (based on US) were 1.0, 1.2, and 8.0, respectively, in a HCV endemic community. An AAR > 1.4 might be a useful tool to identify candidates at high risk for HCC. In conclusion, platelet count was both consistent and accurate in predicting LC. An AAR > 1.4 is proposed as a possible surrogate marker for identifying patients at high risk for developing HCC.
Profiling pathway‐specific novel therapeutics in preclinical assessment for central nervous system atypical teratoid rhabdoid tumors (CNS ATRT): Favorable activity of targeting EGFR‐ ErbB2 signaling with lapatinib
Authors: Singh Anjali , Lun Xueqing , Jayanthan Aarthi , Obaid Halah , Ruan Yibing , Strother Douglas , Chi Susan N. , Smith Amy , Forsyth Peter , Narendran Aru 
Published: January 2013

Despite intensifying multimodal treatments, children with central nervous system atypical teratoid/rhabdoid tumor (CNS ATRT) continue to endure unacceptably high mortality rates. At present, concerted efforts are focusing on understanding the characteristic INI1 mutation and its implications for the growth and survival of these tumors. Additionally, pharmaceutical pipeline libraries constitute a significant source of potential agents that can be taken to clinical trials in a timely manner. However, this process requires efficient target validation and relevant preclinical studies. As an initial screening approach, a panel of 129 small molecule inhibitors from multiple pharmaceutical pipeline libraries was tested against three ATRT cell lines by in vitro cytotoxicity assays. Based on these data, agents that have strong activity and corresponding susceptible cellular pathways were identified. Target modulation, antibody array analysis, drug combination and in vivo xenograft studies were performed on one of the pathway inhibitors found in this screening. Approximately 20% of agents in the library showed activity with IC50 values of 1 μM or less and many showed IC50 values less than 0.05 μM. Intra cell line variability was also noted among some of the drugs. However, it was determined that agents capable of affecting pathways constituting ErbB2, mTOR, proteasomes, Hsp90, Polo like kinases and Aurora kinases were universally effective against the three ATRT cell lines. The first target selected for further analysis, the inhibition of ErbB2‐EGFR pathway by the small molecule inhibitor lapatinib, indicated inhibition of cell migration properties and the initiation of apoptosis. Synergy between lapatinib and IGF‐IR inhibition was also demonstrated by combination index (CI) values. Xenograft studies showed effective antitumor activity of lapatinib in vivo. We present an experimental approach to identifying agents and drug combinations for future clinical trials and provide evidence for the potential of lapatinib as an effective agent in the context of the biology and heterogeneity of its targets in ATRT.
CePa: an R package for finding significant pathways weighted by multiple network centralities
Authors: Gu Zuguang , Wang Jin 
Published: January 2013

Abstract
Summary: CePa is an R package aiming to find significant pathways through network topology information. The package has several advantages compared with current pathway enrichment tools. First, pathway node instead of single gene is taken as the basic unit when analysing networks to meet the fact that genes must be constructed into complexes to hold normal functions. Second, multiple network centralities are applied simultaneously to measure importance of nodes from different aspects to make a full view on the biological system. CePa extends standard pathway enrichment methods, which include both over-representation analysis procedure and gene-set analysis procedure. CePa has been evaluated with high performance on real-world data, and it can provide more information directly related to current biological problems.
Availability: CePa is available at the Comprehensive R Archive Network (CRAN): http://cran.r-project.org/web/packages/CePa/
Contact: jwang@nju.edu.cn
Supplementary information: Supplementary Data are available at Bioinformatics online.
Common genetic variants of the natriuretic peptide gene locus are not associated with heart failure risk in participants in the EPIC‐Norfolk study
Authors: Pfister Roman , Luben Robert N. , Khaw Kay‐Tee , Wareham Nick J. 
Published: January 2013

AimsBNP has important effects on haemodynamics and myocardial remodelling which are protective from development and progression of heart failure. The aim of this study was to examine whether three common genetic variants (rs198389, rs5068, and rs198358) within or adjacent to the BNP gene locus which were shown to be associated with BNP blood levels are associated with risk of heart failure in the pospective population‐based EPIC‐Norfolk cohort.Methods and resultsThe hazard ratio on heart failure was calculated in 23 192 participants in the EPIC‐Norfolk study with Cox proportional regression analyses. During a mean follow‐up of 12.6 years, 1673 (7.2%) participants had a heart failure event. There was no significant association between genotypes of rs198389, rs5068, and rs198358 and heart failure risk. Results did not differ materially in analyses stratified by hypertension, obesity, and coronary heart disease.ConclusionsCommon genetic variants reported to be associated with BNP levels were not associated with a relevant risk of heart failure in our population‐based cohort. However, we cannot exclude a small association with risk of heart failure or an association with individual subtypes of the heart failure syndrome.
Long-term changes in coastal zoobenthos in the northern Baltic Sea: the role of abiotic environmental factors
Authors: Rousi Heta , Laine Ari O. , Peltonen Heikki , Kangas Pentti , Andersin Ann-Britt , Rissanen Jouko , Sandberg-Kilpi Eva , Bonsdorff Erik 
Published: January 2013

AbstractRousi, H., Laine, A. O., Peltonen, H., Kangas, P., Andersin, A-B., Rissanen, J., Sandberg-Kilpi, E., and Bonsdorff, E. 2013. Long-term changes in coastal zoobenthos in the northern Baltic Sea: the role of abiotic environmental factors – ICES Journal of Marine Science, 70: 440–451. We investigated site-specific changes in a coastal zoobenthic community during 1964–2007 in the northern Baltic Sea. Multivariate analysis indicated that the community structure had changed. The amphipods Monoporeia affinis and Pontoporeia femorata decreased drastically in the late 1970s–early 1980s, and by the early 1990s P. femorata vanished and M. affinis abundance was low. The decline of M. affinis and P. femorata was followed by an increase of the bivalve Macoma balthica and the arrival of the polychaete genus Marenzelleria in the 1990s. Trend analyses showed a rising trend for near-bottom temperature from the late 1960s. There was a significant decline in salinity during the early 1980s, which stabilized during the early 1990s. A negative trend was observed for oxygen concentration during the entire study period. There were interannual variations in the phosphorus and nitrogen concentrations, and a step-like increase in phosphorus concentration at the beginning of the 21st century. The correlations of temperature, salinity, oxygen, total phosphorus and nitrogen with zoobenthic communities were examined using Constrained Correspondence Analysis. Temperature was the most highly correlated explanatory variable for the benthic species. The study highlights the importance of long-term data sets in assessing the state and ecological processes of zoobenthic systems.