bluuebunny/crossref_metadata_2025 huggingface dataset:
Stromal factors SDF1α, sFRP1, and VEGFD induce dopaminergic neuron differentiation of human pluripotent stem cells
Authors: Schwartz Catherine M. , Tavakoli Tahereh , Jamias Charmaine , Park Sung‐Soo , Maudsley Stuart , Martin Bronwen , Phillips Terry M. , Yao Pamela J. , Itoh Katsuhiko , Ma Wu , Rao Mahendra S. , Arenas Ernest , Mattson Mark P.
Published: April 2012

Human embryonic stem cell (hESC)‐derived dopaminergic (DA) neurons hold potential for treating Parkinson's disease (PD) through cell replacement therapy. Generation of DA neurons from hESCs has been achieved by coculture with the stromal cell line PA6, a source of stromal cell‐derived inducing activity (SDIA). However, the factors produced by stromal cells that result in SDIA are largely undefined. We previously reported that medium conditioned by PA6 cells can generate functional DA neurons from NTera2 human embryonal carcinoma stem cells. Here we show that PA6‐conditioned medium can induce DA neuronal differentiation in both NTera2 cells and the hESC I6 cell line. To identify the factor(s) responsible for SDIA, we used large‐scale microarray analysis of gene expression combined with mass spectrometric analysis of PA6‐conditioned medium (CM). The candidate factors, hepatocyte growth factor (HGF), stromal cell‐derived factor‐1 α (SDF1α), secreted frizzled‐related protein 1 (sFRP1), and vascular endothelial growth factor D (VEGFD) were identified, and their concentrations in PA6 CM were established by immunoaffinity capillary electrophoresis. Upon addition of SDF1α, sFRP1, and VEGFD to the culture medium, we observed an increase in the number of cells expressing tyrosine hydroxylase (a marker for DA neurons) and βIII‐tubulin (a marker for immature neurons) in both the NTera2 and I6 cell lines. These results indicate that SDF1α, sFRP1, and VEGFD are major components of SDIA and suggest the potential use of these defined factors to elicit DA differentiation of pluripotent human stem cells for therapeutic intervention in PD. © 2012 Wiley Periodicals, Inc.
m‐trifluoromethyl diphenyl diselenide attenuates glutaric acid‐induced seizures and oxidative stress in rat pups: Involvement of the γ‐aminobutyric acidergic system
Authors: Magni Danieli Valnes , Brüning César Augusto , Gai Bibiana Mozzaquatro , Quines Caroline Brandão , Rosa Suzan Gonçalves , Fighera Michele Rechia , Nogueira Cristina Wayne
Published: April 2012

Glutaric acidemia type I (GA‐I) is an inherited metabolic disease characterized by accumulation of glutaric acid (GA) and seizures. The intrastriatal GA administration in rats has been used as an animal model to mimic seizures presented by glutaric acidemic patients. m‐Trifluoromethyl diphenyl diselenide, (m‐CF3‐C6H4Se)2, is an organoselenium compound that protects against seizures induced by pentylenetetrazole in mice. Thus, the aim of this study was to investigate whether (m‐CF3‐C6H4Se)2 is effective against GA‐induced seizures and oxidative stress in rat pups 21 days of age. Our findings demonstrate that (m‐CF3‐C6H4Se)2 preadministration (50 mg/kg; p.o.) protected against the reduction in latency and the increased duration of GA (1.3 μmol/right striatum)‐induced seizures in rat pups. In addition, (m‐CF3‐C6H4Se)2 protected against the increase in reactive species generation and the reduction in antioxidant defenses glutathione peroxidase and glutathione S‐transferase activities induced by GA. By contrast, no change in glutathione reductase or catalase activities was found. In addition, (m‐CF3‐C6H4Se)2 was effective in protecting against inhibition of Na+,K+‐ATPase activity caused by GA in striatum of rat pups. This study showed for the first time that GA administration caused an increase in [3H]GABA uptake from striatum slices of rat pups and that (m‐CF3‐C6H4Se)2 preadministration protected against this increase. A positive correlation between duration of seizures and [3H]GABA uptake levels was demonstrated. The results indicate that (m‐CF3‐C6H4Se)2 protected against GA‐induced seizures. Moreover, these findings suggest that the protection against oxidative stress, the inhibition of Na+,K+‐ATPase activity, and the increase in [3H]GABA uptake are possible mechanisms for the potential anticonvulsant action of (m‐CF3‐C6H4Se)2. © 2012 Wiley Periodicals, Inc.
Workaholism and daily recovery: A day reconstruction study of leisure activities
Authors: Bakker Arnold B. , Demerouti Evangelia , Oerlemans Wido , Sonnentag Sabine
Published: April 2012

This study among 85 individuals used a day reconstruction approach to examine whether workaholism moderates the relationship between daily activities during non‐work time and daily well‐being in the evening (evening happiness, momentary vigor before bedtime, and momentary recovery before bedtime). Specifically, it was hypothesized that daily work‐related activities during the evening have a stronger negative relationship with daily well‐being for employees high (versus low) in workaholism and that daily physical and social activities have a stronger positive relationship with well‐being for employees high (versus low) in workaholism. The results of multilevel analyses largely supported the hypotheses for daily physical and work‐related activities but not for social activities during non‐work time. These findings imply that organizations should not encourage their employees and particularly those who score high on workaholism to work during non‐work time and instead promote physical exercise. Copyright © 2012 John Wiley & Sons, Ltd.
Predicting poor physical performance after total knee arthroplasty
Authors: Bade Michael J. , Wolfe Pamela , Zeni Joseph A. , Stevens‐Lapsley Jennifer E. , Snyder‐Mackler Lynn
Published: April 2012

The purpose of this study was to develop a preliminary decision algorithm predicting functional performance outcomes to aid in the decision of when to undergo total knee arthroplasty (TKA). One hundred and nineteen patients undergoing primary unilateral TKA were evaluated before and 6 months after TKA. A regression tree analysis using a recursive partitioning function was performed with the Timed Up and Go (TUG) time, Six‐Minute Walk (6MW) distance, and Stair Climbing Test (SCT) time as measured 6 months after TKA as the primary outcomes. Preoperative measures of functional performance, joint performance, anthropometrics, demographics, and self‐reported status were evaluated as predictors of the primary outcomes 6 months after surgery. Individuals taking ≥10.1 s on the TUG and aged 72 years or older before surgery had the poorest performance on the TUG 6 months after surgery. Individuals walking <314 meters on the 6MW before surgery had the poorest performance on the 6MW test 6 months after surgery. Individuals taking ≥17 s to complete the SCT and scoring <40 on the SF‐36 mental component score before surgery had the poorest performance on the SCT 6 months after surgery. Poorer performance preoperatively on the 6MW, SCT, and TUG, was related to poorer performance in the same measure after TKA. Age and decreased mental health were secondary predictors of poorer performance at 6 months on the TUG and SCT, respectively. These measures may help further develop models predicting thresholds for poor outcomes after TKA. © 2012 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 30:1805–1810, 2012
Corruption in sub‐Saharan Africa: A phenomenological study
Authors: Odemba Alexander S.
Published: April 2012

The author conducted a qualitative phenomenological study to identify and describe the challenges of government leaders with regard to addressing corrupt practices in sub‐Saharan Africa, particularly Tanzania. The author interviewed 12 senior government leaders to explore their perceptions on corrupt practices in sub‐Saharan Africa. Interview data collected resulted in five themes encompassing the need for change in education and behaviors among citizens, media freedom, government transparency, election reform, and global sanctions. The study findings provide a fresh perspective on the challenges of corrupt practices particularly facing leaders in sub‐Saharan Africa, which extend beyond the prevailing theories of corruption.
Photokinetics of two novel photochromic diarylethenes derived from benzothiophene
Authors: Vázquez A. , Nudelman N. Sbarbati
Published: April 2012

Two new unsymmetrically substituted photochromic diarylethenes, namely 3‐[3, 3,4,4,5,5‐hexafluoro‐2‐(2‐methylbenzothien‐3‐yl)cyclopent‐1‐en‐1‐yl]‐2‐methyl‐6‐methoxy‐1‐ benzothiophene and 3‐[3,3,4,4,5,5‐hexafluoro‐2‐(2‐methylbenzothien‐3‐yl)cyclopent‐1‐en‐1‐yl]‐2‐methyl‐6‐methoxy‐7‐nitro‐1‐benzothiophene, were synthesized. Their optical properties and kinetics of cyclization and cycloreversion were determined in four solvents and compared with the symmetrical diarylethene (3,3,4,4,5,5‐hexafluorocyclopent‐1‐en‐1,2‐diyl)bis(2‐methyl‐1‐benzothiophene). While the UV spectra of the three compounds are almost insensitive to solvent changes, the rates of the ring‐opening and ring‐closure reactions exhibit interesting kinetic behavior that differs from other diarylethenes reported in the literature. The cycloreversion for the three compounds follows first‐order kinetics, whereas the cyclization cannot be described by a simple kinetic law. Different approaches were tested, and a complex exponential equation could be derived that fits the experimental data. The unusual presence of two ring‐opened conformational isomers, one of them nonphotochromic, is proposed for the ring‐opened compounds to explain the derived kinetic law and observed solvent effects. These results are of interest in relation to the application of the novel diarylethenes as potential optical materials. © 2012 Wiley Periodicals, Inc. Int J Chem Kinet 44: 736–744, 2012
The role of extraesophageal reflux in medically and surgically refractory rhinosinusitis
Authors: Loehrl Todd A. , Samuels Tina L. , Poetker David M. , Toohill Robert J. , Blumin Joel H. , Johnston Nikki
Published: April 2012

Objectives/Hypothesis:

To clarify the relationship between chronic rhinosinusitis (CRS) and extraesophageal reflux (EER) using state‐of‐the‐art technology. We hypothesized that patients with medically and surgically refractory CRS would have a greater prevalence of EER. We also hypothesized that there would be evidence of gastric refluxate reaching the nasopharynx and paranasal sinuses.

Study Design:

Case‐control analysis.

Methods:

Twenty‐two patients with medically and surgically refractory rhinosinusitis were enrolled in the study. Subjects all underwent comprehensive testing for EER including 24‐hour pharyngeal pH probe, aerosolized nasopharyngeal pH testing, and nasopharyngeal tissue biopsy for pepsin analysis. In addition, the last five subjects underwent nasal lavage pepsin analysis. A control group of healthy subjects underwent the same nasal secretion pepsin analysis.

Results:

Twenty subjects completed the study. The pharyngeal pH probe results were positive in 19/20 (95%), where the DeMeester score was positive in 9/19 (47%). The nasopharyngeal pH probe data were available in 17/20 patients and correlated poorly with the pharyngeal pH probe testing. In all 20 subjects, nasopharyngeal tissue biopsies were negative for pepsin. However, in the five subjects who underwent nasal lavage pepsin analysis, all were pepsin positive while five healthy control nasal lavage pepsin analysis were negative.

Conclusions:

This study supports an association of EER with medically and surgically refractory CRS. The finding of pepsin in nasal lavages suggests that direct contact of the refluxate with the paranasal sinus mucosa may play a role in the pathophysiology of CRS in this patient population. Finally, evaluation for pepsin in nasal fluid may be a viable method for determining the presence of refluxate in the nose and paranasal sinuses.
Inferior turbinate surgery in children: A survey of practice patterns
Authors: Jiang Zi Yang , Pereira Kevin D. , Friedman Norman R. , Mitchell Ron B.
Published: April 2012

Objectives/Hypothesis:

A variety of techniques for inferior turbinate reduction have been used in children, but to date practice patterns have not been studied. The purpose of this survey was to study the practice of inferior turbinate surgery among pediatric otolaryngologists.

Study Design:

Cross‐sectional survey study.

Methods:

A questionnaire was sent electronically to American Society of Pediatric Otolaryngologists members.

Results:

A total of 249 questionnaires were sent, and 103 (41%) were completed. Six questionnaires were eliminated due to incompleteness. Seventy‐nine (81%) respondents performed inferior turbinate surgery. The most common reason for not performing the procedure was lack of outcomes data. Coblation was the most common technique used in 51% of respondents. A change in surgical technique in the last 2 to 5 years, most commonly to coblation or microdebridement, was reported by 53% of respondents. Nasal obstruction was the primary indication for turbinate reduction (81%), followed by sleep‐disordered breathing (16%). Respondents reported that 20% of turbinate reductions were sole procedures, and 80% were with other procedures: adenotonsillectomy, septoplasty, and sinus surgery. Fifty‐six (71%) responders were either satisfied or very satisfied with the results of pediatric turbinate surgery. Failure of the procedure, epistaxis, and nasal crusting were commonly reported complications, and 9% reported major complications.

Conclusions:

A high proportion of pediatric otolaryngologists perform inferior turbinate surgery, most commonly for nasal obstruction. Coblation is the most common technique used, and complications are mostly minor. Physician satisfaction rates are high despite a paucity of outcomes data on the procedure.
Microencapsulation of Alkaline Salt Hydrate Melts for Phase Change Applications by Surface Thiol‐Michael Addition Polymerization
Authors: Platte Daniela , Helbig Uta , Houbertz Ruth , Sextl Gerhard
Published: April 2012

The microencapsulation of alkaline salt hydrates suitable as inorganic phase change materials (PCMs) via surface Michael‐type addition polymerization of thiols and acrylates is reported. The encapsulation performance depending on the resins' acrylate‐to‐thiol ratio and monomer functionality is investigated, and the best encapsulation performance is found for resin compositions with considerable acrylate excess ratios. The step‐growth nature of the reaction can be substantiated via comparative bulk polymerizations. A multistage encapsulation mechanism is proposed in order to explain the different dependencies on the acrylate to thiol ratio observed in PCM encapsulations in comparison to bulk polymerizations.

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Ultrashort TE T1ρ magic angle imaging
Authors: Du Jiang , Statum Sheronda , Znamirowski Richard , Bydder Graeme M. , Chung Christine B.
Published: April 2012

An ultrashort TE T1ρ sequence was used to measure T1ρ of the goat posterior cruciate ligament (n = 1) and human Achilles tendon specimens (n = 6) at a series of angles relative to the B0 field and spin‐lock field strengths to investigate the contribution of dipole–dipole interaction to T1ρ relaxation. Preliminary results showed a significant magic angle effect. T1ρ of the posterior cruciate ligament increased from 6.9 ± 1.3 ms at 0° to 36 ± 5 ms at 55° and then gradually reduced to 12 ± 3 ms at 90°. Mean T1ρ of the Achilles tendon increased from 5.5 ± 2.2 ms at 0° to 40 ± 5 ms at 55°. T1ρ dispersion study showed a significant T1ρ increase from 2.3 ± 0.9 ms to 11 ± 3 ms at 0° as the spin‐lock field strength increased from 150 Hz to 1 kHz, and from 30 ± 3 ms to 42 ± 4 ms at 55° as the spin‐lock field strength increased from 100 to 500 Hz. These results suggest that dipolar interaction is the dominant T1ρ relaxation mechanism in tendons and ligaments. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.
Oblivious OSPF routing with weight optimization under polyhedral demand uncertainty
Authors: Altin Ayşegül , Fortz B. , Ümit Hakan
Published: April 2012

The desire for configuring well‐managed open shortest path first (OSPF) routes to handle the communication needs in the contemporary business world with larger networks and changing service requirements has opened the way to use traffic engineering tools with the OSPF protocol. Moreover, anticipating possible shifts in expected traffic demands while using network resources efficiently has started to gain more attention. We take these two crucial issues into consideration and study the weight setting problem for OSPF routing problem with polyhedral demands. Our motivation is to optimize the link weight metric such that the minimum cost routing uses shortest paths with equal cost multipath splitting and the routing decisions are robust to possible fluctuations in demands. In addition to a compact mixed integer programming model, we provide an algorithmic approach with two variations to tackle the problem. We present several test results for these two strategies and discuss whether we could make our weight‐managed OSPF comparable to unconstrained routing under polyhedral demand uncertainty. © 2012 Wiley Periodicals, Inc. NETWORKS, 2012
Conceptual design of reinforced concrete structures using topology optimization with elastoplastic material modeling
Authors: Bogomolny Michael , Amir Oded
Published: April 2012

Design of reinforced concrete structures is governed by the nonlinear behavior of concrete and by its different strengths in tension and compression. The purpose of this article is to present a computational procedure for optimal conceptual design of reinforced concrete structures on the basis of topology optimization with elastoplastic material modeling. Concrete and steel are both considered as elastoplastic materials, including the appropriate yield criteria and post‐yielding response. The same approach can be applied also for topology optimization of other material compositions where nonlinear response must be considered. Optimized distribution of materials is achieved by introducing interpolation rules for both elastic and plastic material properties. Several numerical examples illustrate the capability and potential of the proposed procedure. Copyright © 2012 John Wiley & Sons, Ltd.
Can Nonexperimental Estimates Replicate Estimates Based on Random Assignment in Evaluations of School Choice? A Within‐Study Comparison
Authors: Bifulco Robert
Published: April 2012

The ability of nonexperimental estimators to match impact estimates derived from random assignment is examined using data from the evaluation of two interdistrict magnet schools. As in previous within‐study comparisons, nonexperimental estimates differ from estimates based on random assignment when nonexperimental estimators are implemented without pretreatment measures of academic performance. With comparison groups consisting of students drawn from the same districts or districts with similar student body characteristics as the districts where treatment group students reside, using pretreatment test scores reduces the bias in nonexperimental methods between 64 and 96 percent. Adding pretreatment test scores does not achieve as much bias reduction when the comparison group consists of students drawn from districts with different student body characteristics than the treatment group students’ districts. The results suggest that using pretreatment outcome measures and comparison groups that are geographically aligned with the treatment group greatly improves the performance of nonexperimental estimators.
Recrystallization behavior of β‐isotactic polypropylene in homogeneous and heterogeneous matrix–fiber composites
Authors: Liu Qi , Li Huihui , Qiu Zhaobin , Yan Shouke
Published: April 2012

β‐isotactic polypropylene (β‐iPP) cylindritic crystals were produced in homogeneous iPP fiber–matrix composites and heterogeneous polyamide (PA)–iPP fiber–matrix composites under different sample preparation conditions. The melt recrystallization behaviors of the β‐iPP crystals obtained in the homogeneous and heterogeneous composites were studied by optical microscopy. The experimental results show that, by heating the sample to 180 °C, the birefringence contributed by the iPP crystals in both α‐ and β‐forms disappears completely. During the cooling process, the β‐iPP crystals in the homogeneous composite appear again, while the iPP in the heterogeneous composite crystallizes in its α‐form. This demonstrates the different origins of the β‐iPP cylindrites in the homogeneous and heterogeneous composites. While the β‐iPP cylindrites in the heterogeneous composite are associated with the sample preparation procedure, the β‐iPP cylindrites in the homogeneous composite are produced by recrystallization of the molten but incompletely relaxed iPP fibers. In situ observation of the melt recrystallization process shows that the molten iPP oriented fibers crystallize first during the cooling process at relatively higher temperature in the α‐form. Abundant randomly dispersed β‐iPP nuclei formed at the surface of the recrystallized iPP fibers, which generate the β‐iPP cylindrites. Copyright © 2012 Society of Chemical Industry
Influence of Average Photon Energy index on solar irradiance characteristics and outdoor performance of photovoltaic modules
Authors: Cornaro Cristina , Andreotti Angelo
Published: April 2012

Solar spectral irradiance measurements on a routinely basis are relevant to study the influence of solar spectrum on the photovoltaic (PV) module performance, especially for thin film and third generation PV. Two spectroradiometers from EKO were added to the instrumentation available at the ESTER outdoor station of the University of Rome Tor Vergata. A detailed characterisation of the spectral irradiance at the site was carried on during more than 6 months of monitoring activity measuring spectral solar irradiance in the range 350–1700 nm with a time interval of 10 min on a horizontal plane. A wide variety of spectra were acquired in various weather conditions, and indications about the spectra behaviour on a daily and seasonal basis were obtained. Moreover, information about the effect of the weather conditions on the solar radiation spectral distribution were identified. The Average Photon Energy index was used as an indicator of the spectra characteristics. The same index was also used to evidence the solar spectrum influence on polycrystalline and double junction amorphous silicon PV modules. Copyright © 2012 John Wiley & Sons, Ltd.
Laser processing of Al2O3/a‐SiCx:H stacks: a feasible solution for the rear surface of high‐efficiency p‐type c‐Si solar cells
Authors: Martín I. , Ortega P. , Colina M. , Orpella A. , López G. , Alcubilla R.
Published: April 2012

We explore the potential of laser processing aluminium oxide (Al2O3)/amorphous silicon carbide (a‐SiCx:H) stacks to be used at the rear surface of p‐type crystalline silicon (c‐Si) solar cells. For this stack, excellent quality surface passivation is measured with effective surface recombination velocities as low as 2 cm/s. By means of an infrared laser, the dielectric film is locally opened. Simultaneously, part of the aluminium in the Al2O3 film is introduced into the c‐Si, creating p+ regions that allow ohmic contacts with low‐surface recombination velocities. At optimum pitch, high‐efficiency solar cells are achievable for substrates of 0.5–2.5 Ω cm. Copyright © 2012 John Wiley & Sons, Ltd.
Performance analysis of a reflective 3D crossed compound parabolic concentrating photovoltaic system for building façade integration
Authors: Mammo Eliyas Debebe , Sellami Nazmi , Mallick Tapas Kumar
Published: April 2012

A reflective 3D crossed compound parabolic‐based photovoltaic module (3D CCPC PV) was designed and its electrical and optical performance was analyzed for building integrated photovoltaic applications. A maximum power concentration of 3.0× was achieved compared to similar type of non‐concentrating module. The reduction of the concentration factor from the geometrical concentration of 3.61× for the designed 3D CCPC were due to manufacturing errors, mismatch losses, series resistance losses, and thermal loses. The experimental output was validated by developing a MATLAB simulation code for its electrical performance. Good agreements were observed between experimental and electrical simulation with maximum electrical conversion efficiency of the concentrating system of 14%. The experimental characterization of the optical efficiency was found to show a deviation of 19.4% from the 3D ray tracing simulation efficiency of 94.6% for direct incidence. This deviation is mainly due to the fact that 3D ray tracing simulation does not take the non‐uniform illumination distribution into account. Copyright © 2012 John Wiley & Sons, Ltd.
Secretome analysis of Magnaporthe oryzae using in vitro systems
Authors: Jung Young‐Ho , Jeong Seung‐Hee , Kim So Hee , Singh Raksha , Lee Jae‐eun , Cho Yoon‐Seong , Agrawal Ganesh Kumar , Rakwal Randeep , Jwa Nam‐Soo
Published: April 2012

Magnaporthe oryzae is a devastating blast fungal pathogen of rice (Oryza sativa L.) that causes dramatic decreases in seed yield and quality. During the early stages of infection by this pathogen, the fungal spore senses the rice leaf surface, germinates, and penetrates the cell via an infectious structure known as an appressorium. During this process, M. oryzae secretes several proteins; however, these proteins are largely unknown mainly due to the lack of a suitable method for isolating secreted proteins during germination and appressoria formation. We examined the secretome of M. oryzae by mimicking the early stages of infection in vitro using a glass plate (GP), PVDF membrane, and liquid culture medium (LCM). Microscopic observation of M. oryzae growth revealed appressorium formation on the GP and PVDF membrane resembling natural M. oryzae–rice interactions; however, appresorium formation was not observed in the LCM. Secreted proteins were collected from the GP (3, 8, and 24 h), PVDF membrane (24 h), and LCM (48 h) and identified by two‐dimensional gel electrophoresis (2DE) followed by tandem mass spectrometry. The GP, PVDF membrane, and LCM‐derived 2D gels showed distinct protein patterns, indicating that they are complementary approaches. Collectively, 53 nonredundant proteins including previously known and novel secreted proteins were identified. Six biological functions were assigned to the proteins, with the predominant functional classes being cell wall modification, reactive oxygen species detoxification, lipid modification, metabolism, and protein modification. The in vitro system using GPs and PVDF membranes applied in this study to survey the M. oryzae secretome, can be used to further our understanding of the early interactions between M. oryzae and rice leaves.
Proteome characterization of the unsequenced psychrophile Pedobacter cryoconitis using 15N metabolic labeling, tandem mass spectrometry, and a new bioinformatic workflow
Authors: Pereira‐Medrano Ana G. , Margesin Rosa , Wright Phillip C.
Published: April 2012

Organisms without a sequenced genome and lacking a complete protein database encounter an added level of complexity to protein identification and quantitation. De novo sequencing, new bioinformatics tools, and mass spectrometry (MS) techniques allow for advances in this area. Here, the proteomic characterization of an unsequenced psychrophilic bacterium, Pedobacter cryoconitis, is presented employing a novel workflow based on 15N metabolic labelling, 2DE, MS/MS, and bioinformatics tools. Two bioinformatics pipelines, based on nitrogen constraint (N‐constraint), ortholog searching, and de novo peptide sequencing with N‐constraint similarity database search, are compared based on proteome coverage and throughput. Results demonstrate the effect of different growth temperatures (1°C, 20°C) and different carbon sources (glucose, maltose) on the proteome. Seventy‐six and 69 proteins were identified and validated from the glucose‐ and maltose‐grown bacterium, respectively, from which 21 and 22 were differentially expressed at different growth temperatures. Differentially expressed proteins are involved in stress response and carbohydrate metabolism, with higher expression at 20°C than at 1°C, while antioxidants were upregulated at 1°C. This study provides an alternative workflow to identify, validate, and quantify proteins from unsequenced organisms distantly related to other species in the protein database. Furthermore, it provides further understanding on bacterial adaptation mechanisms to cold environments, and a comparative proteomic analyses with other psychrophilic microorganisms.
Enabling proteomic studies with RNA‐Seq: The proteome of tomato pollen as a test case
Authors: Lopez‐Casado Gloria , Covey Paul A. , Bedinger Patricia A. , Mueller Lukas A. , Thannhauser Theodore W. , Zhang Sheng , Fei Zhangjun , Giovannoni James J. , Rose Jocelyn K. C.
Published: April 2012

Effective proteome profiling is generally considered to depend heavily on the availability of a high‐quality DNA reference database. As such, proteomics has long been taxonomically restricted, with limited inroads being made into the proteomes of “non‐model” organisms. However, next generation sequencing (NGS), and particularly RNA‐Seq, now allows deep coverage detection of expressed genes at low cost, which in turn potentially facilitates the matching of peptide mass spectra with cognate gene sequence. To test this, we performed a quantitative analysis of the proteomes of pollen from domesticated tomato (Solanum lycopersicum) and two wild relatives that exhibit differences in mating systems and in interspecific reproductive barriers. Using a custom tomato RNA‐Seq database created through 454 pyrosequencing, more than 1200 proteins were identified, with subsets showing expression differences between genotypes or in the accumulation of the corresponding transcripts. Importantly, no major qualitative or quantitative differences were observed in the characterized proteomes when mass spectra were used to interrogate either a highly curated community database of tomato sequences generated through traditional sequencing technologies, or the RNA‐Seq database. We conclude that RNA‐Seq provides a cost‐effective and robust platform for protein identification and will be increasingly valuable to the field of proteomics.
Proteomic analysis of the effects of baicalein on colorectal cancer cells
Authors: Huang Wen‐Shih , Kuo Yi‐Hung , Chin Chih‐Chien , Wang Jeng‐Yi , Yu Hong‐Ren , Sheen Jiunn‐Ming , Tung Shui‐Yi , Shen Chien‐Heng , Chen Te‐Chuan , Sung Mei‐Lan , Liang Hwey‐Fang , Kuo Hsing‐Chun
Published: April 2012

Baicalein is the flavonoids with multiple pharmacological activities. The aim of our study was to investigate the effects of baicalein on colorectal cancer (CRC) and to recognize the targets of baicalein treatment. To better understand baicalein's target, proteomic approaches were used to purify and identify the protein substrates using 2D difference gel electrophoresis (2D SDS‐PAGE) to elucidate proteins differential display. Results from this study investigate that baicalein treatment of CRC cells results in reduced cell proliferation. As a result, differential protein displays between baicalein‐treated and untreated CRC were determined and validated. There were 11 differentially expressed proteins between baicalein‐treated and untreated CRC. Furthermore, we demonstrate that baicalein inhibits cancer cell proliferation and reduced reactive oxygen species (ROS) by up‐regulating the levels of peroxiredoxin‐6 (PRDX6). Knockdown of PRDX6 in baicalein‐treated CRC cells by specific small interfering RNA resulted in ROS production and proliferation, opposite of the baicalein treatment scenario as indicated by cell cycle distribution. These results illustrate that baicalein up‐regulates the expression of PRDX6, which attenuates the generation of ROS and inhibits the growth of CRC cells, whereas baicalein treatment have no effect on normal epithelial cells.
Differential regulation of aquaporins, small GTPases and V‐ATPases proteins in rice leaves subjected to drought stress and recovery
Authors: Mirzaei Mehdi , Pascovici Dana , Atwell Brian J. , Haynes Paul A.
Published: April 2012

Mechanisms of drought tolerance are complex, interacting, and polygenic. This paper describes patterns of gene expression at precise physiological stages of drought in 35‐day‐old seedlings of Oryza sativa cv. Nipponbare. Drought was imposed gradually for up to 15 days, causing abscisic acid levels to rise and growth to cease, and plants were then re‐watered. Proteins were identified from leaf samples after moderate drought, extreme drought, and 3 and 6 days of re‐watering. Label‐free quantitative shotgun proteomics resulted in identification of 1548 non‐redundant proteins. More proteins were down‐regulated in early stages of drought but more were up‐regulated as severe drought developed. After re‐watering, there was notable down regulation, suggesting that stress‐related proteins were being degraded. Proteins involved in signalling and transport became dominant as severe drought took hold but decreased again on re‐watering. Most of the nine aquaporins identified were responsive to drought, with six decreasing rapidly in abundance as plants were re‐watered. Nine G‐proteins appeared in large amounts during severe drought and dramatically degraded once plants were re‐watered. We speculate that water transport and drought signalling are critical elements of the overall response to drought in rice and might be the key to biotechnological approaches to drought tolerance.
Two‐dimensional proteome reference map of Rhizobium tropici PRF 81 reveals several symbiotic determinants and strong resemblance with agrobacteria
Authors: Gomes Douglas Fabiano , da Silva Batista Jesiane Stefania , Torres Adalgisa Ribeiro , de Souza Andrade Diva , Galli‐Terasawa Lygia Vitoria , Hungria Mariangela
Published: April 2012

Rhizobium tropici strain PRF 81 is used in commercial inoculants for common‐bean crops in Brazil because of its high efficiency in nitrogen fixation and, as in other strains belonging to this species, its tolerance of environmental stresses, representing a useful biological alternative to chemical nitrogen fertilizers. In this study, a proteomic reference map of PRF 81 was obtained by two‐dimensional gel electrophoresis and MALDI‐TOF/TOF‐TOF mass spectrometry. In total, 115 spots representing 109 different proteins were successfully identified, contributing to a better understanding of the rhizobia‐legume symbiosis and supporting, at proteomics level, a strong resemblance with agrobacteria.
Quantitative proteomics of heavy metal stress responses in Sydney rock oysters
Authors: Muralidharan Sridevi , Thompson Emma , Raftos David , Birch Gavin , Haynes Paul A.
Published: April 2012

Currently, there are few predictive biomarkers in key biomonitoring species, such as oysters, that can detect heavy metal pollution in coastal waterways. Several attributes make oysters superior to other organisms for positive biomonitoring of heavy metal pollution. In particular, they are filter feeders with a high capacity for bioaccumulation. In this study, we used two proteomics approaches, namely label‐free shotgun proteomics based on SDS‐PAGE gel separation and gas phase fractionation, to investigate the heavy metal stress responses of Sydney rock oysters. Protein samples were prepared from haemolymph of oysters exposed to 100 μg/L of PbCl2, CuCl2, or ZnCl2 for 4 days in closed aquaria. Peptides were identified using a Bivalvia protein sequence database, due to the unavailability of a complete oyster genome sequence. Statistical analysis revealed 56 potential biomarker proteins, as well as several protein biosynthetic pathways to be greatly impacted by metal stress. These have the potential to be incorporated into bioassays for prevention and monitoring of heavy metal pollution in Australian oyster beds. The study confirms that proteomic analysis of biomonitoring species is a promising approach for assessing the effects of environmental pollution, and our experiments have provided insights into the molecular mechanisms underlying oyster stress responses.
jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data
Authors: Reisinger Florian , Krishna Ritesh , Ghali Fawaz , Ríos Daniel , Hermjakob Henning , Antonio Vizcaíno Juan , Jones Andrew R.
Published: April 2012

We present a Java application programming interface (API), jmzIdentML, for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. The API combines the power of Java Architecture of XML Binding (JAXB) and an XPath‐based random‐access indexer to allow a fast and efficient mapping of extensible markup language (XML) elements to Java objects. The internal references in the mzIdentML files are resolved in an on‐demand manner, where the whole file is accessed as a random‐access swap file, and only the relevant piece of XMLis selected for mapping to its corresponding Java object. The APIis highly efficient in its memory usage and can handle files of arbitrary sizes. The APIfollows the official release of the mzIdentML (version 1.1) specifications and is available in the public domain under a permissive licence at http://www.code.google.com/p/jmzidentml/.
HUPO 2011: The New Cardiovascular Initiative ‐ Integrating Proteomics and Cardiovascular Biology in Health and Disease
Authors: Lam Maggie P. Y. , Vivanco Fernando , Scholten Arjen , Hermjakob Henning , Van Eyk Jennifer , Ping Peipei
Published: April 2012

A newly reorganized HUPO Cardiovascular Initiative was announced at the HUPO 2011 Cardiovascular Initiative Workshop at Geneva. The new initiative is now part of the biology‐ and disease‐driven component of the HUPO Human Proteome Project (B/D‐HPP). Here we report the recent achievements and future directions of the initiative, and offer a perspective on the present challenges of cardiovascular proteomics and its integration with the cardiovascular biology community at large.
Multidisciplinary care of patients with Parkinson's disease
Authors: Skelly Rob , Lindop Fiona , Johnson Claire
Published: April 2012

There is increasing evidence that the effective care of patients with Parkinson's disease should involve a multidisciplinary team of health professionals, including the neurologist or geriatrician, Parkinson's disease nurse specialist, physiotherapist, occupational therapist, speech and language therapist, dietitian, clinical psychologist and social worker, among others. Here, the authors review the evidence for the efficacy of multi‐disciplinary working and describe their own model of care in Derby.
Synthesis of sterically hindered antipyrines for intramolecularcharge transfer facilitated sensing
Authors: Bian Linyi , Sun Gang , Sun Yuxi , Tang Weihua
Published: April 2012

A new series of sterically hindered antipyrine derivatives have been synthesized by Schiff base condensation for potential fluorescence sensing applications. Their optical, thermal, and electrochemical properties were fully characterized. Broad absorption spectra were observed as a result of the strong intramolecular charge transfer between antipyrine and sterically hindered conjugated moiety. Reversible one electron oxidation couple was observed for most compounds, with carbazole, phenothiazine, and bithiophene functionalized derivatives exhibiting extra reversible one one‐electron oxidation process at higher positive potentials. Cabazole functionalized antipyrine derivative APCZ presents good fluorescence sensing for Co2+ and Cu2+, with 3.41‐fold enhancement in fluorescence intensity and 2‐fold enhancement in fluorescence quantum yield observed. Copyright © 2012 John Wiley & Sons, Ltd.
High‐performance amorphous donor–acceptor conjugated polymers containing x‐shaped anthracene‐based monomer and 2,5‐bis(2‐octyldodecyl)pyrrolo[3,4‐c]pyrrole‐1,4(2H,5H)‐dione for organic thin‐film transistors
Authors: Lee Joo Bin , Kim Kyung Hwan , Hong Chang Seop , Choi Dong Hoon
Published: April 2012

New diketopyrrolopyrrole (DPP)‐containing amorphous conjugated polymers, such as poly(3‐(5‐((9,10‐bis((4‐hexylphenyl)ethynyl)‐6‐(prop‐1‐ynyl)anthracen‐2‐yl)ethynyl) thiophen‐2‐yl)‐5‐(2‐hexyldecyl)‐2‐(2‐octyldodecyl)‐6‐(thiophen‐2‐yl)pyrrolo[3,4‐c]pyrrole‐1,4(2H,5H)‐dione) (4), and poly(3‐(5‐((2,6‐bis((4‐hexylphenyl)ethynyl)‐10‐(prop‐1‐ynyl)anthracen‐9‐yl)ethynyl)thiophen‐2‐yl)‐2,5‐bis(2‐octyldodecyl)‐6‐(thio phen‐2‐yl)pyrrolo[3,4‐c]pyrrole‐1,4(2H,5H)‐dione) (7), were successfully synthesized via Sonogashira coupling reactions under microwave conditions. Copolymer 7, incorporating a DPP moiety at the 9,10‐position of the anthracene ring through a triple bond, showed a much lower bandgap energy (Eg = 1.81 eV) than copolymer 4 (Eg = 2.13 eV). Tuning of the molecular frontier orbital energies was achieved by only changing the anchoring position of dithiophenyl‐DPP from the 2,6‐ to the 9,10‐position in the anthracene ring. Because of the donor–acceptor (D–A) interaction and the two‐dimensional planar structure of the X‐shaped donor monomer, the resulting polymers showed good interchain π−π stacking in the thin‐film state, despite being amorphous polymers. When the newly synthesized polymer 7 was used as a semiconductor material in an organic thin‐film transistor, the best mobility of up to 0.12 cm2 V−1 s−1 (Ion/off = ∼ 4.4 × 106) was observed, which is one of the highest values recorded for amorphous polymer films reported to date. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Synthesis of NMP/RAFT inifers and preparation of block copolymers
Authors: St. Thomas Claude , Maldonado‐Textle Hortensia , Rockenbauer Antal , Korecz Laszlo , Nagy Nora , Guerrero‐Santos Ramiro
Published: April 2012

Two different initiator/transfer agents (inifers) containing an alkoxyamine and a dithiobenzoate were synthetized and used to trigger out either reversible addition‐fragmentation chain transfer (RAFT) polymerization or nitroxide‐mediated polymerization (NMP). α‐Dithiobenzoate‐ω‐alkoxyamine‐difunctional polymers were produced in both cases which were subsequently used as precursors in the formation of block copolymers. This synthetic approach was applied to N‐isopropylacrylamide (NIPAM) or polyethylene oxide methacrylate (EOMA) to form α,ω‐heterodifunctional homopolymers via RAFT at 60°C which were chain extended with styrene by activating the alkoxyamine moiety at 120°C. Under such temperature conditions, it is proposed that a tandem NMP/RAFT polymerization is initiated producing a simultaneous growth of polystyrene blocks at both chain‐ends. Self‐assembled nanostructures of these amphiphilic block copolymers were evidenced by scanning electron microscopy. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Synthesis and properties of monocleavable amphiphilic comblike copolymers with alternating PEG and PCL grafts
Authors: Li Shixian , Ye Chunnuan , Zhao Guangdong , Zhang Meijing , Zhao Youliang
Published: April 2012

Symmetric reduction‐responsive amphiphilic comblike copolymers mid‐disulfide‐functionalized comblike copolymers with alternating copolymer comprised of styrenic unit and N‐(2‐hydroxyethyl) maleimide (HEMI) unit (poly(St‐alt‐HEMI)) backbones and alternating PEG and PCL side chains (S‐CP(PEG‐alt‐PCL)) with poly(St‐alt‐HEMI) backbones and alternating poly(ε‐caprolactone) (PCL) and poly(ethylene glycol) (PEG) side chains were synthesized and used as nanocarriers for in vitro release of doxorubicin. The target copolymers with predetermined molecular weight and narrow molecular weight distribution (Mw/Mn = 1.15–1.20) were synthesized by reversible addition‐fragmentation chain transfer (RAFT) copolymerization of vinylbenzyl‐terminated PEG and N‐(2‐hydroxyethyl) maleimide mediated by a disulfide‐functionalized RAFT agent S‐CPDB, and followed by ring‐opening polymerization of ε‐caprolactone. When compared with linear block copolymer comprised of poly(ethylene glycol) (PEG) and poly(ϵ‐caprolactone) (PCL) segments (PEG‐b‐PCL) copolymers, comblike copolymers with similar PCL contents usually exhibited decreased crystallization temperature, melting temperature, and degree of crystallinity, indicating the significant influence of copolymer architecture on physicochemical properties. Dynamic light scattering measurements revealed that comblike copolymers were liable to self‐assemble into aggregates involving vesicles and micelles with average diameter in the range of 56–226 nm and particle size distribution ranging between 0.07 and 0.20. In contrast to linear copolymer aggregates, comblike copolymer aggregates with similar compositions were of improved storage stability and enhanced drug‐loading efficiency. In vitro drug release confirmed the disulfide‐linked comblike copolymer aggregates could rapidly release the encapsulated drug when triggered by 10 mM DL‐dithiothreitol. These reduction‐sensitive, biocompatible, and biodegradable aggregates have a potential as controlled delivery vehicles. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Activation of silenced tumor suppressor genes in prostate cancer cells by a novel energy restriction‐mimetic agent
Authors: Lin Hsiang‐Yu , Kuo Yi‐Chiu , Weng Yu‐I , Lai I‐Lu , Huang Tim H.‐M. , Lin Shuan‐Pei , Niu Dau‐Ming , Chen Ching‐Shih
Published: April 2012

BACKGROUND

Targeting tumor metabolism by energy restriction‐mimetic agents (ERMAs) has emerged as a strategy for cancer therapy/prevention. Evidence suggests a mechanistic link between ERMA‐mediated antitumor effects and epigenetic gene regulation.

METHODS

Microarray analysis showed that a novel thiazolidinedione‐derived ERMA, CG‐12, and glucose deprivation could suppress DNA methyltransferase (DNMT)1 expression and reactivate DNA methylation‐silenced tumor suppressor genes in LNCaP prostate cancer cells. Thus, we investigated the effects of a potent CG‐12 derivative, CG‐5, vis‐à‐vis 2‐deoxyglucose, glucose deprivation and/or 5‐aza‐deoxycytidine, on DNMT isoform expression (Western blotting, RT‐PCR), DNMT1 transcriptional activation (luciferase reporter assay), and expression of genes frequently hypermethylated in prostate cancer (quantitative real‐time PCR). Promoter methylation was assessed by pyrosequencing analysis. SiRNA‐mediated knockdown and ectopic expression of DNMT1 were used to validate DNMT1 as a target of CG‐5.

RESULTS

CG‐5 and glucose deprivation upregulated the expression of DNA methylation‐silenced tumor suppressor genes, including GADD45a, GADD45b, IGFBP3, LAMB3, BASP1, GPX3, and GSTP1, but also downregulated methylated tumor/invasion‐promoting genes, including CD44, S100A4, and TACSTD2. In contrast, 5‐aza‐deoxycytidine induced global reactivation of these genes. CG‐5 mediated these epigenetic effects by transcriptional repression of DNMT1, which was associated with reduced expression of Sp1 and E2F1. SiRNA‐mediated knockdown and ectopic expression of DNMT1 corroborated DNMT1's role in the modulation of gene expression by CG‐5. Pyrosequencing revealed differential effects of CG‐5 versus 5‐aza‐deoxycytidine on promoter methylation in these genes.

CONCLUSIONS

These findings reveal a previously uncharacterized epigenetic effect of ERMAs on DNA methylation‐silenced tumor suppressor genes, which may foster novel strategies for prostate cancer therapy. Prostate 72:1767–1778, 2012. © 2012 Wiley Periodicals, Inc.