bluuebunny/crossref_metadata_2025_split huggingface dataset:
A modified root reinforcement technique for acute aortic dissection with a weakened aortic root: a modified Florida sleeve technique and two cases report
Authors: Heo Woon , Min Ho-Ki , Kang Do Kyun , Jun Hee Jae , Hwang Youn-Ho , Choi Jin Ho , Wi Jin Hong 
Published: October 2013

Abstract
Despite marvelous advances in repair for acute type A aortic dissection over past decades, it remains challenging to repair the aortic root when aortic dissection extended to the sinuses causes the fragile root because of its thinner layers, which are susceptible to suture trauma. Here, we describe a modified Florida sleeve technique to strengthen the weakened aortic root. After mobilization of the aortic root and the coronary arteries, a designed Dacron tube graft was wrapped outside the sinuses as neo-adventitia to reinforce the dissected weakened wall. During surgery for aortic dissection, our technique is easy and effective to reinforce a weakened root and avoid bleeding. Furthermore, this might be an alternative technique to restore and maintain the geometry of the aortic root.
Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti
Authors: Ponce-de-León Miguel , Montero Francisco , Peretó Juli 
Published: October 2013

Abstract

Background
Metabolic reconstruction is the computational-based process that aims to elucidate the network of metabolites interconnected through reactions catalyzed by activities assigned to one or more genes. Reconstructed models may contain inconsistencies that appear as gap metabolites and blocked reactions. Although automatic methods for solving this problem have been previously developed, there are many situations where manual curation is still needed.

Results
We introduce a general definition of gap metabolite that allows its detection in a straightforward manner. Moreover, a method for the detection of Unconnected Modules, defined as isolated sets of blocked reactions connected through gap metabolites, is proposed. The method has been successfully applied to the curation of iCG238, the genome-scale metabolic model for the bacterium Blattabacterium cuenoti, obligate endosymbiont of cockroaches.

Conclusion
We found the proposed approach to be a valuable tool for the curation of genome-scale metabolic models. The outcome of its application to the genome-scale model B. cuenoti iCG238 is a more accurate model version named as B. cuenoti iMP240.
Discrete control for ensuring consistency between multiple autonomic managers
Authors: karé Gueye Soguy Mak , Palma Noël De , Rutten Eric , Tchana Alain , Hagimont Daniel 
Published: October 2013

AbstractThe increasing complexity of computer systems has led to the automation of administration functions, in the form of autonomic managers. Today many autonomic managers are available but they mostly address a specific administration aspect which makes necessary their coexistence for a complete autonomic system management. However, coordinating them is necessary for proper and effective global administration. Such coordination can be considered as a problem of synchronization and logical control of managers actions. We therefore investigate the use of reactive models with events and states, and discrete control techniques to solve this problem. This paper presents an application of the latter approach for coordinating autonomic managers addressing resource optimization, in the perspective of green computing. The managers control server provisioning (self-sizing manager) and CPU frequency (Dvfs manager), and the coordination controller controls the managers actions so as to avoid incoherent management decisions. The coordination controller is designed using synchronous programming and Discrete controller synthesis (DCS) which are well-suited for the design of reactive systems. Experimental results are presented to evaluate the efficacy of the approach.
Magnetostatic surface waves propagation at dissipative ferrite-MTMs-metal structure
Authors: Al-Sahhar Zeyad I , Shabat Mohammed M , El-Khozondar Hala J 
Published: October 2013

AbstractThe magnetostatic surface waves (MSSW) propagation in a layered structure composed of ferrite film covered by air and on top of metamaterial (MTM) placed on metal is discussed. Dispersion equations which relate the parameters of different layers are derived and used to analyse propagation of MSSW. It is found that the MSSW excitation band depends on the thickness of the MTM layer and ferrite layer.
Molecular structure and modeling studies of azobenzene derivatives containing maleimide groups
Authors: Cojocaru Corneliu , Airinei Anton , Fifere Nicusor 
Published: October 2013

Abstract
The molecular orbital calculations have been carried out to investigate the structure and stability of (E) / (Z) isomers of some azobenzene derivatives containing maleimide groups. A special attention has been devoted to the compound (E)-1, (E)-1-(4-(phenyldiazenyl)phenyl)-1H-pyrrole-2,5-dione, for which the available crystallographic experimental data have been used to validate the modeling structures computed at the theoretical levels AM1, PM3, RHF/6-31+G(d,p) and B3LYP/6-31+G(d,p). To this end, the discrepancy between experimental and calculated structural parameters has been ascertained in terms of root-mean-square deviation (RMSD). The quantum calculations at the level RHF/6-31+G(d,p) yield the most accurate results on (E)-1 structure giving a deviation error from crystallographic data of about 5.00% for bond lengths and 0.97% for interatomic angles. The theoretical electronic absorption spectra of azobenzene derivatives of concern have been computed by means of configuration-interaction method (CI) at the level of semi-empirical Hamiltonians (AM1 and PM3). Likewise, the molecular energy spectra, electrostatic potential and some quantitative structure activity relationship (QSAR) properties of studied molecules have been computed and discussed in the paper.
Modeling precision treatment of breast cancer
Authors: Daemen Anneleen , Griffith Obi L , Heiser Laura M , Wang Nicholas J , Enache Oana M , Sanborn Zachary , Pepin Francois , Durinck Steffen , Korkola James E , Griffith Malachi , Hur Joe S , Huh Nam , Chung Jongsuk , Cope Leslie , Fackler Mary Jo , Umbricht Christopher , Sukumar Saraswati , Seth Pankaj , Sukhatme Vikas P , Jakkula Lakshmi R , Lu Yiling , Mills Gordon B , Cho Raymond J , Collisson Eric A , van’t Veer Laura J , Spellman Paul T , Gray Joe W 
Published: October 2013

Abstract
Background
First-generation molecular profiles for human breast cancers have enabled the identification of features that can predict therapeutic response; however, little is known about how the various data types can best be combined to yield optimal predictors. Collections of breast cancer cell lines mirror many aspects of breast cancer molecular pathobiology, and measurements of their omic and biological therapeutic responses are well-suited for development of strategies to identify the most predictive molecular feature sets.

Results
We used least squares-support vector machines and random forest algorithms to identify molecular features associated with responses of a collection of 70 breast cancer cell lines to 90 experimental or approved therapeutic agents. The datasets analyzed included measurements of copy number aberrations, mutations, gene and isoform expression, promoter methylation and protein expression. Transcriptional subtype contributed strongly to response predictors for 25% of compounds, and adding other molecular data types improved prediction for 65%. No single molecular dataset consistently out-performed the others, suggesting that therapeutic response is mediated at multiple levels in the genome. Response predictors were developed and applied to TCGA data, and were found to be present in subsets of those patient samples.

Conclusions
These results suggest that matching patients to treatments based on transcriptional subtype will improve response rates, and inclusion of additional features from other profiling data types may provide additional benefit. Further, we suggest a systems biology strategy for guiding clinical trials so that patient cohorts most likely to respond to new therapies may be more efficiently identified.
Blood flow dynamics in the snake spectacle
Authors: van Doorn Kevin , Sivak Jacob G. 
Published: October 2013

SUMMARYThe eyes of snakes are shielded beneath a layer of transparent integument referred to as the ‘reptilian spectacle’. Well adapted to vision by virtue of its optical transparency, it nevertheless retains one characteristic of the integument that would otherwise prove detrimental to vision: its vascularity. Given the potential consequence of spectacle blood vessels on visual clarity, one might expect adaptations to have evolved that mitigate their negative impact. Earlier research demonstrated an adaptation to their spatial layout in only one species to reduce the vessels' density in the region serving the foveal and binocular visual fields. Here, we present a study of spectacle blood flow dynamics and provide evidence of a mechanism to mitigate the spectacle blood vessels' deleterious effect on vision by regulation of blood flow through them. It was found that when snakes are at rest and undisturbed, spectacle vessels undergo cycles of dilation and constriction, such that the majority of the time the vessels are fully constricted, effectively removing them from the visual field. When snakes are presented with a visual threat, spectacle vessels constrict and remain constricted for longer periods than occur during the resting cycles, thus guaranteeing the best possible visual capabilities in times of need. Finally, during the snakes' renewal phase when they are generating a new stratum corneum, the resting cycle is abolished, spectacle vessels remain dilated and blood flow remains strong and continuous. The significance of these findings in terms of the visual capabilities and physiology of snakes is discussed.
Synthesis of Optically Active Thromboxane A2 and Leukotriene D4 Receptor Antagonists
Authors: Kawazoe Souichirou , Okamoto Yoshinori , Yokota Masaki , Kubota Hirokazu , Naito Ryo , Takeuchi Makoto , Ieda Shigeru , Okada Minoru , Oriyama Takeshi 
Published: October 2013

Abstract
Both (+)- and (−)-4-{[(2-{4-chlorophenylsulfonylamino}-1-{3-[(E)-2-(7-chloro-2-quinolyl)-vinyl]phenyl}ethyl)thio]methyl}benzoic acid (1), Thromboxane A2 and Leukotriene D4 receptor dual antagonist were synthesized. Racemic methyl 4-({[2-amino-1-(3-hydroxymethylphenyl)ethyl]thio}methyl)benzoate (2), and methyl 4-[({2-amino-1-[3-(1,3-dioxolan-2-yl)phenyl]ethyl}thio)methyl]benzoate (3) were derived from 2-(3-bromophenyl)-1,3-dioxolane (4). Compound 2 was resolved via di-p-toluoyl-d/l-tartaric acid salts to transform to (+)- and (−)-1, respectively. We also demonstrated that one optically active salt of compound 2 was converted to optically active (+)-1 without chromatography purification.
Design and Evaluation of Selective Recognition on Supramolecular Gel Using Soft Molecular Template Effect
Authors: Hashimoto Takeshi , Yamazaki Masafumi , Ishii Hiroyuki , Yamada Taiji , Hayashita Takashi 
Published: October 2013

Abstract
A supramolecular cyclodextrin (CyD) gel having selective monosaccharide recognition function was prepared by polymerization of γ-CyD containing a lipophilic phenylboronic acid azoprobe. The non-template gel exhibited galactose selectivity in adsorption, whereas the glucose-template gel exhibited glucose selectivity.
Tuning of Sol–Gel Transition Temperatures for Thermoreversible Ion Gels
Authors: Kitazawa Yuzo , Ueki Takeshi , Imaizumi Satoru , Lodge Timothy P , Watanabe Masayoshi 
Published: October 2013

Abstract
Thermoreversible gelation of ionic liquids (ILs) was demonstrated using a well-defined ABA triblock copolymer. The ABA triblock copolymer consisted of poly(phenylethyl methacrylate) terminal A blocks and a poly(methyl methacrylate) middle B block. Temperature-tunable thermosensitive sol–gel transition, i.e., low-temperature-sol–high-temperature-gel, can be realized because of the lower critical solution temperature aggregation behavior of the A blocks. The sol–gel transition behavior of polymer–IL composites can be precisely controlled not only by changing the chemical structure of the A blocks but also by changing that of the ILs.
Perioperative changes in cortical excitability, mood, and quality of life in patients with primary hyperparathyroidism: a pilot study using transcranial magnetic stimulation
Authors: Hermsen A , Eienbröker A , Haag A , Mylius V , Hamer H M , Menzler K , Karakas E , Rosenow F 
Published: October 2013

ObjectiveSerum calcium (Ca2+) and parathyroid hormone (PTH), amongst others, modify cortical excitability. Alterations in cortical excitability were shown in patients with epilepsy as well as hyper- or hypoparathyroidism. In patients with primary hyperparathyroidism (pHPT), preoperative elevated serum calcium and parathyroidectomy (PTx) may affect mood and quality of life. We hypothesized that perioperative changes in Ca2+ and PTH in pHPT will affect cortical excitability and improve subjective health.Design and methodsTranscranial magnetic stimulation (TMS) was performed before and after surgery in 15 pHPT patients. We measured resting motor threshold, cortical silent period (CSP), short intracortical inhibition, and intracortical facilitation. Health questionnaires were administered before, 1 day and 6 months after PTx, along with the disease-specific Pasieka's parathyroid assessment of symptoms (PAS), which was, to our knowledge, its first use in German.ResultsSurgery was successful in all patients. TMS-measurements remained unchanged when analyzing all patients in this pilot study. Postoperatively, depression declined (P=0.05) and quality of life improved significantly (P=0.001) in the SF-36-subscales: vitality, social functioning, mental health and subjective health transition (post-hoc analysis). The PAS proved early relief of disease-specific symptoms (P<0.001).ConclusionsWe found unchanged cortical excitability comparing pre- and post-PTx in this pilot study. Mood and quality of life improved postoperatively. The German PAS is valuable in detecting disease-specific changes early after PTx.
Carcinoid syndrome caused by a serotonin-secreting pituitary tumour
Authors: Lynggård Louise A , Nielsen Eigil Husted , Laurberg Peter 
Published: October 2013

BackgroundNeuroendocrine tumours are most frequently located in the gastrointestinal organ system or in the lungs, but they may occasionally be found in other organs.CaseWe describe a 56-year-old woman suffering from a carcinoid syndrome caused by a large serotonin-secreting pituitary tumour. She had suffered for years from episodes of palpitations, dyspnoea and flushing. Cardiac disease had been suspected, which delayed the diagnosis, until blood tests revealed elevated serotonin and chromogranin A in plasma. The somatostatin receptor (SSR) scintigraphy showed a single-positive focus in the region of the pituitary gland and MRI showed a corresponding intra- and suprasellar heterogeneous mass. After pre-treatment with octreotide leading to symptomatic improvement, the patient underwent trans-cranial surgery with removal of the tumour. This led to a clinical improvement and to a normalisation of SSR scintigraphy, as well as serotonin and chromogranin A levels.ConclusionTo our knowledge, this is the first reported case of a serotonin-secreting tumour with a primary location in the pituitary.
The Basis for Evolution of DNA-Binding Specificity of the Aft1 Transcription Factor in Yeasts
Authors: Gonçalves Isabelle R , Conde e Silva Natalia , Garay Cesar La Torre , Lesuisse Emmanuel , Camadro Jean Michel , Blaiseau Pierre Louis 
Published: October 2013

AbstractThe Saccharomyces cerevisiae Aft1 and Kluyveromyces lactis KlAft are orthologous yeast transcription activators that regulate the expression of the same group of iron-uptake genes but bind to the different DNA sites: TGCACCC for Aft1 and PuCACCC for KlAft. To establish whether the DNA-binding mechanisms of Aft1 and KlAft have diverged during the evolution of the Aft-type transcription factor, we examined the function of a nonconserved region in their DNA-binding domains. A large part of this region is composed of a sequence predicted to be disordered in structure and potentially phosphorylated. We show with deletion mutant analyses that this sequence is essential for the binding of Aft1 to its DNA site and for the iron uptake and growth of S. cerevisiae under iron-limited conditions. We constructed hybrid proteins by exchanging the nonconserved regions of Aft1 and KlAft. We show that the Aft1 region is necessary and sufficient for KlAft to bind efficiently to the Aft1 DNA site in S. cerevisiae and to complement the iron-dependent phenotype of the aft1Δaft2Δ mutant. This demonstrates that the changes in the nonconserved region of the Aft-type DNA-binding domain have led to changes in the DNA-binding specificity and have major consequences for the regulation of iron homeostasis. The combination of bioinformatic and experimental analyses indicates that the sequence TGCACCC is the most probable ancestral Aft-type element. Our findings suggest that the changes in the nonconserved region of the DNA-binding domain are responsible for the evolution of the TGCACCC sequence toward PuCACCC in the K. lactis species.
A Novel Role for Cet1p mRNA 5′-Triphosphatase in Promoter Proximal Accumulation of RNA Polymerase II in Saccharomyces cerevisiase
Authors: Lahudkar Shweta , Durairaj Geetha , Uprety Bhawana , Bhaumik Sukesh R 
Published: October 2013

Abstract
Yeast mRNA 5′-triphosphatase, Cet1p, recognizes phosphorylated-RNA polymerase II as a component of capping machinery via Ceg1p for cotranscriptional formation of mRNA cap structure that recruits cap-binding complex (CBC) and protects mRNA from exonucleases. Here, we show that the accumulation of RNA polymerase II at the promoter proximal site of ADH1 is significantly enhanced in the absence of Cet1p. Similar results are also found at other genes. Cet1p is recruited to the 5′ end of the coding sequence, and its absence impairs mRNA capping, and hence CBC recruitment. However, such an impaired recruitment of CBC does not enhance promoter proximal accumulation of RNA polymerase II. Thus, Cet1p specifically lowers the accumulation of RNA polymerase II at the promoter proximal site independently of mRNA cap structure or CBC. Further, we show that Cet1p’s N-terminal domain, which is not involved in mRNA capping, decreases promoter proximal accumulation of RNA polymerase II. An accumulation of RNA polymerase II at the promoter proximal site in the absence of Cet1p’s N-terminal domain is correlated with reduced transcription. Collectively, our results demonstrate a novel role of Cet1p in regulation of promoter proximal accumulation of RNA polymerase II independently of mRNA capping activity, and hence transcription in vivo.
Risk of posttransplant lymphoproliferative disorder associated with use of belatacept
Authors: Martin Spencer T. , Powell Jaclyn T. , Patel Monank , Tsapepas Demetra 
Published: October 2013

Abstract

Purpose
Published evidence on a rare but serious malignancy associated with use of the first biological agent approved for long-term maintenance immunosuppression in renal transplant recipients is reviewed.

Summary
Belatacept (Nulojix, Bristol-Myers Squibb) is approved by the Food and Drug Administration for use in combination therapy to prevent renal graft rejection in patients who are Epstein-Barr virus seropositive. Belatacept appears to offer some advantages over calcineurin inhibitor-based regimens (e.g., no need for therapeutic drug monitoring), but its use poses a risk of posttransplant lymphoproliferative disorder (PTLD), a rapidly progressing and often lethal malignancy. The efficacy and safety of more-intensive and less-intensive belatacept regimens were established in two Phase III clinical trials, which found that rates of patient and graft survival were comparable to those in cyclosporine users; belatacept was shown to be superior in preserving renal function. The occurrence of PTLD, particularly PTLD involving the central nervous system, in 0–4% of belatacept-treated patients in clinical trials prompted postmarketing initiatives: (1) implementation of a risk evaluation and mitigation strategy (REMS) program to help ensure the safe and proper use of belatacept, (2) longitudinal studies to better define the risks and outcomes of belatacept therapy, and (3) a manufacturer-created patient registry to track belatacept use and encourage voluntary reporting of associated adverse events.

Conclusion
Appropriate patient selection and adherence to REMS requirements, including patient counseling and facilitation of registry enrollment, are essential in mitigating the increased risk of PTLD associated with belatacept therapy.
Effect of Wildfires on Physicochemical Changes of Watershed Dissolved Organic Matter
Authors: Revchuk Alex D. , Suffet I. H. (Mel) 
Published: October 2013

ABSTRACTPhysicochemical characterization of dissolved organic carbon (DOC) provides essential data to describe watershed characteristics after drastic changes caused by wildfires. Post‐fire watershed behavior is important for water source selection, management, and drinking water treatment optimization. Using ash and other burned vegetation fragments, a leaching procedure was implemented to describe physicochemical changes to watershed DOC caused by wildfires. Samples were collected after the 2007 and 2009 wildfires near Santa Barbara, California. Substantial differences in size distribution (measured by ultrafiltration), polarity (measured by polarity rapid assessment method), and the origin of leached DOC (measured by fluorescence) were observed between burned and unburned sites. Recently burned ash had 10 times the DOC leaching potential, and was dominated by large size fragments, compared to weathered 2‐year‐old ash. Charged DOC fractions were found to positively correlate with DOC size, whereas hydrophobic and hydrophilic DOC fractions were not. Proteins were only observed in recently burned ash and were indicative of recent post‐fire biological activity.
Removal of Copper Ions From Water Using Epichlorohydrin Cross‐Linked β‐Cyclodextrin Polymer: Characterization, Isotherms and Kinetics
Authors: Sikder M. Tajuddin , Islam Md Shariful , Kikuchi Tohru , Suzuki Junichi , Saito Takeshi , Kurasaki Masaaki 
Published: October 2013

ABSTRACTβ‐cyclodextrin (β‐CD) cross‐linked with epichlorohydrin to form water insoluble β‐cyclodextrin polymer (β‐CDP) has been shown to be an effective sorbent for sorption of organic particles, but the sorption of copper (Cu2+) in aqueous solutions by β‐CDP has not been conducted. The objective of this study was to explore the sorption mechanism of β‐CDP for copper. The effects of different experimental conditions such as pH, ionic strength, contact time, and temperature were inspected using a batch method. In addition, binding scheme was estimated by using Fourier transform infrared (FTIR) spectroscopy, X‐ray photoelectron spectroscopy (XPS), a scanning electron microscope (SEM), and Brunauer‐Emmett‐Teller (BET) analysis. The adsorption of Cu2+ was observed to be higher at pH 6.0. The kinetic study revealed that the adsorption is fitted well by the pseudo‐second‐order kinetic model. The maximum binding of Cu2+ was estimated to be 111.11 mg/g through the Langmuir isotherm model — much higher than the existing sorption technologies. Hence, the adsorption‐desorption trends of epichlorohydrin cross‐linked with β‐CD, along with its good recyclability, establish an alternative, effective, and novel remediation technology for the removal of Cu2+ from aqueous solutions.