bluuebunny/crossref_metadata_2025 huggingface dataset:
Targeted protein pullout from human tissue samples using competitive elution
Authors: Falk Ronny , Ramström Margareta , Eriksson Cecilia , Uhlén Mathias , Wernérus Henrik , Hober Sophia
Published: December 2010

One commonly used strategy to gain information on the proteins in a cell is to isolate the proteins of interest by specific binders, often antibodies. Not only the specificity of the capturing antibodies but also the washing and elution conditions are crucial to avoid false‐positive protein identifications. Eluting the target protein from the matrix, while avoiding the release of unrelated background proteins, should both provide more correct information on the target protein and its interaction partners, and minimize the effort to perform downstream analyses through the reduced number of eluted proteins. In this study, a novel approach for selective protein pullout is presented. Monospecific antibodies were used to selectively pullout target proteins from a complex biosample. Subsequently, the target proteins were competitively eluted from the affinity media with the recombinant antigen. To deplete the antigen from the eluted sample, IMAC spin columns were utilized to bind the N‐terminal His‐tag of the antigens. The competitive elution method was applied both to a model system, and for the extraction of a native human target protein. In the model system the recombinant target protein BBC7 was spiked into a protein extract of human liver, whereas an endogenously expressed target protein, cTAGE5, was extracted from the liver extract directly. SDS‐PAGE analysis and mass spectrometry confirmed affinity isolation of expected target proteins. More selective elution was obtained using the competitive procedure as compared to elution at low pH. Competitive elution has thus been shown to offer an effective approach for wide‐scale pullout experiments where proteins and their interaction partners are to be studied.
Prediction of activated sludge filamentous bulking using ATP data and neural networks
Authors: Brault Jean‐Martin , Labib Richard , Perrier Michel , Stuart Paul
Published: December 2010

Neural networks (NNs) were used to predict the onset of filamentous bulking, as described by trends in stirred sludge volume index, in a pulp and paper activated sludge treatment system. Variables related to activated sludge biomass viability, namely specific oxygen uptake rate (SOUR) and adenosine triphosphate (ATP), were used as inputs to the NN. ATP data were shown to improve NN performance in providing an early warning signal for bulking, both in terms of accuracy and prediction delay. A warning signal system was developed to provide operators with enough time to react and further investigate the causes of bulking.
Trace Elements in Sediments and Mussels – Spatial Distribution, Chemical Partitioning, and Risk Assessment
Authors: Khairy Mohammed A. , Kolb Marit , Schmidt Christiane , Zachmann Dieter W. , Mostafa Alaa R. , EL‐Fiky Anwar A. , Bahadir Müfit
Published: December 2010

Sediment samples were collected from 30 different locations in Abu Qir Bay (Mediterranean Sea), East Alexandria, Egypt and analyzed for trace elements. The highest concentrations of most of the elements were observed in the nearshore stations in the vicinity of the major anthropogenic activities as industrial settlements, wastewater discharges, and agricultural drainage. In addition, mussel samples of Mactra corallina and Tapes decussata were collected corresponding to the sediment samples. Concentrations of As, Cd, Cr, Mn, and Zn in the mussel tissues were higher than concentrations in sediments, thus indicating their relatively high bioavailability. Sequential extraction procedure was performed on selected sediment samples. Significant correlations were observed between the concentrations of Cu, Mn, Pb, and Zn in the exchangeable fraction of the sediments and the corresponding tissues of M. corallina. The output of the risk assessment applied on the sediments revealed that adverse ecological effects to benthic species could occur and that a higher level of risk is expected from the exposure to Cd, Cr, Hg, and Zn. No adverse carcinogenic or non‐carcinogenic human health effects are expected from the consumption of the two mussel species from Abu Qir Bay.
Metabolic factors and the risk of colorectal cancer in 580,000 men and women in the metabolic syndrome and cancer project (Me‐Can)
Authors: Stocks Tanja , Lukanova Annekatrin , Bjørge Tone , Ulmer Hanno , Manjer Jonas , Almquist Martin , Concin Hans , Engeland Anders , Hallmans Göran , Nagel Gabriele , Tretli Steinar , Veierød Marit B. , Jonsson Håkan , Stattin Pär ,   for the Metabolic Syndrome Cancer Project (Me‐Can) Group
Published: December 2010

BACKGROUND:

The metabolic syndrome (MetS) has been related to an increased risk of colorectal cancer, but the modest size of previous studies precluded detailed characterization of the role of individual MetS factors and their interaction on risk.

METHODS:

In the Metabolic Syndrome and Cancer Project (Me‐Can), data on body mass index (BMI), blood pressure, and blood levels of glucose, cholesterol, and triglycerides were available for 578,700 men and women. The mean age of participants at baseline was 44 years, and the mean follow‐up was 12 years. Relative risks (RR) of colorectal cancer per 1 standard deviation increment in Z score of factors and for a combined MetS score, were calculated from Cox regression models, including adjustment for potential confounders.

RESULTS:

During follow‐up, 2834 men and 1861 women were diagnosed with colorectal cancer. The RR of colorectal cancer for the MetS score was 1.25 (95% confidence interval [CI], 1.18‐1.32) in men, and 1.14 (95% CI, 1.06‐1.22) in women. Significant associations also were observed in men for BMI (RR, 1.07; 95% CI, 1.02‐1.13), blood pressure (RR, 1.10; 95% CI, 1.02‐1.18), and triglycerides (RR, 1.17; 95% CI, 1.06‐1.28) and, in women, for BMI (RR, 1.08; 95% CI, 1.01‐1.15). There was no significant positive interaction between the metabolic factors on risk.

CONCLUSIONS:

The combination of metabolic factors and some separate factors was related to an increased risk of colorectal cancer, but there was no interaction between metabolic factors. Cancer 2011;. © 2010 American Cancer Society.
Fine‐needle cytology of cutaneous juvenile xanthogranuloma and langerhans cell histiocytosis
Authors: Fassina Ambrogio , Olivotto Andrea , Cappellesso Rocco , Vendraminelli Roberto , Fassan Matteo
Published: December 2010

BACKGROUND:

In pediatric patients, a cutaneous nodule is usually diagnosed by performing an excisional biopsy, but fine‐needle cytology (FNC) is a safer and noninvasive diagnostic method widely used to obtain diagnostic specimens with little stress to the patient. The authors compared the ability of FNC and biopsy to differentiate Langerhans cell histiocytosis (LCH) from juvenile xanthogranuloma (JXG).

METHODS:

Correlating cytological results with histological findings, the authors reviewed 27 patients (15 males and 12 females; mean age, 37 months; range, 1 month to 14 years) admitted to the University of Padua Department of Pediatrics from 1998 to 2010.

RESULTS:

Cytology smears were adequate in all 27 (100%) patients: 14 (52%) were classified as having JXG, 12 (44%) as having LCH, and 1 (4%) as having a doubtful finding. A biopsy was also performed in 20 of these patients, and in all but 1, the 2 methods were completely concordant.

CONCLUSIONS:

FNC is safe and useful in the diagnostic workup of pediatric patients with cutaneous nodules and has no contraindications to its use as the initial diagnostic procedure. Cancer (Cancer Cytopathol) 2011;. © 2010 American Cancer Society.
Poly(2‐oxazoline)s based on fatty acids
Authors: Hoogenboom Richard
Published: December 2010

Poly(2‐oxazoline)s are an interesting class of synthetic poly(amide)s that can be prepared by living cationic ring‐opening polymerization. The properties of poly(2‐oxazoline)s can be tuned by variation of the 2‐substituent of the 2‐oxazoline monomer. In this contribution the utilization of fatty acids as side chains for poly(2‐oxazoline)s is highlighted. The incorporation of such long aliphatic side‐chains results in hydrophobic crystalline poly(2‐oxazoline)s that are often applied for the preparation of amphiphilic structures as well as for low surface energy and low adhesive coatings. The most popular fatty‐acid based poly(2‐oxazoline)s are the saturated poly(2‐nonyl‐2‐oxazoline) and poly(2‐undecyl‐2‐oxazoline) as well as the unsaturated poly(2‐decenyl‐2‐oxazoline) and poly(2‐“soy alkyl”‐2‐oxazoline).
Exploitation of Furanoid 5‐Azido‐3‐C‐Branched‐Chain Sugars Towards Highly Functionalized Nitrogen‐Containing Carbohydrate Derivatives
Authors: Xavier Nuno M. , Queneau Yves , Rauter Amélia P.
Published: December 2010

The ability of easily accessed 1,2‐O‐protected 5‐azido‐3‐C‐(ethoxycarbonyl)methylenefuranoses to serve as precursors for the generation of imino sugar derivatives containing an α,β‐unsaturated lactone or ketone functionality has been investigated. A key aspect was the propensity of the corresponding deprotected δ‐amino α,β‐unsaturated esters to undergo 5‐aminofuranose/iminopyranose isomerization. Acid hydrolysis of the δ‐amino (Z)‐α,β‐unsaturated ester followed by treatment with base led to a butenolide‐containing N‐ethylformamide arising from a rearrangement of the imino‐sugar‐fused butenolide intermediate induced by the conjugated system. When carrying out the ring expansion step under neutral conditions, a 2‐keto imino sugar was obtained that was readily converted into a 1,2‐dihydropyridin‐3‐one by acetylation. Furthermore, reduction of the δ‐azido (E)‐α,β‐unsaturated ester to the amine was followed by spontaneous intramolecular cyclization, providing the related furanose‐fused unsaturated δ‐lactam.
Synthesis and Complexation Studies between Trifluoromethylammonium Threads and Dibenzo[24]Crown‐8
Authors: Johnsen Carsten , Stein Paul C. , Nielsen Kent A. , Bond Andrew D. , Jeppesen Jan O.
Published: December 2010

Two new ammonium threads were synthesized and characterized. They are composed of either one or two bis‐alkylammonium sites that can act as recognition elements for dibenzo[24]crown‐8 (DB24C8) and are both appended with two electron‐withdrawing trifluoromethyl (CF3) groups. The pseudorotaxanes formed between the trifluoromethyl ammonium threads and DB24C8 were characterized by single‐crystal X‐ray diffraction analyses and studied by NMR spectroscopy. The NMR spectroscopic data reveal that attachment of two electron‐withdrawing trifluoromethyl groups to the single‐site ammonium thread enhances the binding strength between the DB24C8 ring and the ammonium thread. Investigations carried out between the double‐site ammonium thread and DB24C8 reveal that the relative amount between the [2]pseudorotaxane and the [3]pseudorotaxane can be controlled by changing the ratio between the double‐site ammonium thread and DB24C8. Quantitative studies carried out by NMR titrations indicate at weak(K2/K1 = 0.24) anticooperative effect in the formation of the [3]pseudorotaxane.
Ring Expansion of 2‐(1‐Hydroxyalkyl)azetidines to 4‐(2‐Chloroethyl)oxazolidinones
Authors: Couty François , Drouillat Bruno , Lemée Frédéric
Published: December 2010

2‐(1‐Hydroxyalkyl)azetidines react with bis(trichloromethyl) carbonate (BTC) after basic treatment to afford 4‐(2‐chloroethyl)oxazolidinones. The scope of this rearrangement was examined in detail and its efficiency was shown to depend on the class of the reacting alcohol and on the substitution pattern on the azetidine ring.
Continuous full filling capillary electrochromatography–electrospraying chromatographic nanoparticles
Authors: Malmström David , Axén Jakob , Bergquist Jonas , Viberg Peter , Spégel Peter
Published: December 2010

The influence of instrumental parameters affecting the ionization in continuous full filling capillary electrochromatography/electrospray ionization mass spectrometry (CFF‐CEC/ESI‐MS) was investigated. The investigated parameters were the BGE and sheath liquid ion strength and organic modifier content, the nebulizer gas pressure, and the concentration of nanoparticles in the BGE. It was found that the nebulizer pressure had the largest influence on the separation efficiency and apparent retention. It was shown that even the lowest pressure investigated was sufficient to guide the nanoparticle flow away from the mass spectrometer inlet. A nebulizer pressure of 5 psi was found to be optimal; increasing the pressure significantly decreased the separation efficiency due to the generation of a hydrodynamic flow. Generally, the ion strength of both the BGE and the sheath liquid were found to have very moderate effects on the separation of a homologous series of dialkyl phthalates, whereas the ionization efficiency was found to be unaffected by the nanoparticles and the separation efficiency was found to increase with increasing concentrations up to 3.8 mg/mL, whereafter it was observed to drop. The optimized method was linear over a wide concentration range and presented LOD and LOQ more than threefold lower than those previously reported using CFF‐CEC/ESI‐MS.
Determination of the epimerization rate constant of amygdalin by microemulsion electrokinetic chromatography
Authors: Yu Lishuang , Ye Hongzhi , Zheng Lili , Chen Lidian , Chu Kedan , Liu Xianxiang , Xu Xueqin , Chen Guonan
Published: December 2010

A new method for separation and determination of amygdalin and its epimer (neoamygdalin) in the epimerization of amygdalin by MEEKC is proposed. For the chiral separation of amygdalin and neoamygdalin, a running buffer composed of 80 mM sodium cholate, 5.0% v/v butan‐1‐ol, 0.5% v/v heptane and 94.5% v/v 30 mM Na2B4O7 buffer (pH 9.00) is proposed. Under optimum conditions, the basic separation of amygdalin and neoamygdalin can be achieved within 7 min. The calibration curve for amygdalin showed excellent linearity in the concentration range of 20–1000 μg/mL with a detection limit of 5.0 μg/mL (S/N=3). The epimerization rate constant of amygdalin in basic microemulsion was first determined by monitoring the concentration changes of amygdalin, and the epimerization rate constant of amygdalin was found to be 2×10−3 min−1 at 25°C under the above optimum microemulsion conditions.
Identification of immunoreactive secretory proteins from the stationary phase culture of Burkholderia pseudomallei
Authors: Vellasamy Kumutha Malar , Mariappan Vanitha , Hashim Onn H. , Vadivelu Jamuna
Published: December 2010

Bacterial secreted proteins are known to be involved in virulence and may mediate important host–pathogen interactions. In this study, when the stationary phase culture supernatant of Burkholderia pseudomallei was subjected to 2‐DE, 113 protein spots were detected. Fifty‐four of the secreted proteins, which included metabolic enzymes, transcription/translation regulators, potential virulence factors, chaperones, transport regulators, and hypothetical proteins, were identified using MS and database search. Twelve of these proteins were apparently reactive to antisera of mice that were immunised with B. pseudomallei secreted proteins. These proteins might be excellent candidates to be used as diagnostic markers or putative candidate vaccines against B. pseudomallei infections.
Localization of cerebral functional deficits in patients with non‐neuropsychiatric systemic lupus erythematosus
Authors: Lin Yun , Zou Qing‐Hua , Wang Jian , Wang Yong , Zhou Dai‐Quan , Zhang Rong‐Hua , Zhang Yan‐Wei , Lii Hai‐Tao , Fang Yong‐Fei
Published: December 2010

Neuropsychiatric systemic lupus erythematosus (NP‐SLE) is a common complication of systemic lupus erythematosus (SLE), and clinical interventions are of only limited efficacy despite relatively high prevalence. Such complications have been studied extensively, but the pathoetiology of NP‐SLE has not yet been elucidated. Diagnosis of NP‐SLE focuses primarily on psychological manifestations, and the underlying mechanisms leading to neuropsychiatric complications remain unknown. To address potential changes in brain function before NP‐SLE development, we used resting‐state functional magnetic resonance imaging (MRI) to compare regional brain activity in SLE patients versus matched controls. We report that regional activity in cerebellum and in areas of the default mode network are attenuated in patients with SLE, and moreover individual alterations in cerebellar activity correlated positively with the disease activity index. These findings provide direct evidence that significant alteration of brain function, resembling that observed in patients with NP‐SLE, is already present in SLE patients without neuropsychiatric complications, highlighting the need for early evaluation and intervention in SLE patients. Furthermore, the disease activity rating correlated with regional functional alterations in the cerebellum, suggesting that the cerebellum could play a role in the pathogenesis of NP‐SLE. Hum Brain Mapp, 2011. © 2010 Wiley‐Liss, Inc.
HepaRG Cells: A Human Model to Study Mechanisms of Acetaminophen Hepatotoxicity Δσ
Authors: McGill Mitchell R. , Yan Hui-Min , Ramachandran Anup , Murray Gordon J. , Rollins Douglas E. , Jaeschke Hartmut
Published: December 2010

Acetaminophen (APAP) overdose is the leading cause of acute liver failure in Western countries. In the last four decades much progress has been made in our understanding of APAP-induced liver injury through rodent studies. However, some differences exist in the time course of injury between rodents and humans. To study the mechanism of APAP hepatotoxicity in humans, a human-relevant

in vitro

system is needed. Here we present evidence that the cell line HepaRG is a useful human model for the study of APAP-induced liver injury. Exposure of HepaRG cells to APAP at several concentrations resulted in glutathione depletion, APAP-protein adduct formation, mitochondrial oxidant stress and peroxynitrite formation, mitochondrial dysfunction (assessed by JC-1 fluorescence), and lactate dehydrogenase (LDH) release. Importantly, the time course of LDH release resembled the increase in plasma aminotransferase activity seen in humans following APAP overdose. Based on propidium iodide uptake and cell morphology, the majority of the injury occurred within clusters of hepatocyte-like cells. The progression of injury in these cells involved mitochondrial reactive oxygen and reactive nitrogen formation. APAP did not increase caspase activity above untreated control values and a pancaspase inhibitor did not protect against APAP-induced cell injury.

Conclusion:

These data suggest that key mechanistic features of APAP-induced cell death are the same in human HepaRG cells, rodent

in vivo

models, and primary cultured mouse hepatocytes. Thus, HepaRG cells are a useful model to study mechanisms of APAP hepatotoxicity in humans. (Hepatology 2011)
Evolution of Genomic Instability in Diethylnitrosamine-Induced Hepatocarcinogenesis in Mice Δ
Authors: Aleksic Kristina , Lackner Carolin , Geigl Jochen B. , Schwarz Martina , Auer Martina , Ulz Peter , Fischer Maria , Trajanoski Zlatko , Otte Marcus , Speicher Michael R.
Published: December 2010

Diethylnitrosamine (DEN) is a hepatic procarcinogen which is frequently used as an inducer of hepatocellular carcinoma (HCC) in mice. Although mice after DEN exposure are among the most widely used models for liver tumorigenesis, a detailed, mechanistic characterization of the longitudinal changes in the respective tumor genomes has never been performed. Here we established the chronological order of genetic alterations during DEN carcinogenesis by examining mice at different points in time. Tumor samples were isolated by laser microdissection and subjected to array-comparative genomic hybridization (array-CGH) and sequencing analysis. Chromosomal gains and losses were observed in tumors by week 32 and increased significantly by week 56. Loss of distal chromosome 4q, including the tumor suppressors

Runx3

and

Nr0b2/Shp
, was a frequent early event and persisted during all tumor stages. Surprisingly, sequencing revealed that β-catenin mutations occurred late and were clearly preceded by chromosomal instability. Thus, contrary to common belief, β-catenin mutations and activation of the Wnt/β-catenin pathway are not involved in tumor initiation in this model of chemical hepatocarcinogenesis.

Conclusion:

Our study suggests that the majority of the current knowledge about genomic changes in HCC is based on advanced tumor lesions and that systematic analyses of the chronologic order including early lesions may reveal new, unexpected findings. (Hepatology 2011;)
Folic acid and prevention of colorectal adenomas: A combined analysis of randomized clinical trials
Authors: Figueiredo Jane C. , Mott Leila A. , Giovannucci Edward , Wu Kana , Cole Bernard , Grainge Matthew J. , Logan Richard F. , Baron John A.
Published: December 2010

Observational data suggest that lower folate status is associated with an increased risk of colorectal neoplasia, implying that folate may be useful as a chemopreventive agent. We conducted a combined analysis of three large randomized trials of folic acid supplementation for the prevention of metachronous adenomas in patients with an adenoma history. Participants included 2,632 men and women who had a history of adenomas randomized to either 0.5 or 1.0 mg/day of folic acid or placebo and who had a follow‐up endoscopy 6 to 42 months after randomization [mean = 30.6 (standard deviation = 8.1) months]. We used random‐effects meta‐analysis to estimate risk ratios (RRs) and 95% confidence intervals (CIs). The RR comparing folic acid versus placebo was 0.98 (95% CI = 0.82–1.17) for all adenomas and 1.06 (95% CI = 0.81–1.39) for advanced lesions. Folic acid was associated with a nonsignificant decreased risk of any adenoma among subjects in the lowest quartile of baseline plasma folate (≤11 nmol/L) and no effect among individuals in the highest quartile (>29 nmol/L, p for trend = 0.17). There was a nonsignificant trend of decreasing risk of any adenoma associated with folic acid supplements with increasing alcohol intake. During the early follow‐up reported here, more deaths occurred in the placebo group than in the folic acid group (1.7% vs. 0.5%, p = 0.002). In conclusion, after up to 3.5 years of folic acid use, there is no clear decrease or increase in the occurrence of new adenomas in patients with a history of adenoma.
Polo‐like kinase 1 regulates cell proliferation and is targeted by miR‐593* in esophageal cancer
Authors: Ito Tetsuo , Sato Fumiaki , Kan Takatsugu , Cheng Yulan , David Stefan , Agarwal Rachana , Paun Bogdan C. , Jin Zhe , Olaru Alexandru V. , Hamilton James P. , Selaru Florin M. , Yang Jian , Matsumura Nobutoshi , Shimizu Kazuharu , Abraham John M. , Shimada Yutaka , Mori Yuriko , Meltzer Stephen J.
Published: December 2010

Polo‐like kinase 1 (PLK1) is overexpressed in various human cancers. However, the biological functions and the post‐transcriptional regulations of PLK1 in esophageal cancer (EC) are still unknown. The purposes of our study are to determine whether PLK1 can be a molecular target of EC therapy and to identify a microRNA (miRNA) targeting PLK1. We performed loss‐of‐function and gain‐of‐function experiments regarding cell proliferation, cell cycle, apoptosis, in vivo tumor formation and luciferase reporter assays, using siRNAs against PLK1 and miRNA. PLK1 protein was expressed in all 11 EC cell lines, but not in normal esophageal epithelial cells (HEEpiC). Knockdown of PLK1 in EC cells induced G2/M arrest (p < 0.001) in cell cycle assay and reduced cell proliferation (p = 0.019) and tumor formation ability in vivo (p < 0.0001). MiR‐593*, identified as a miRNA targeting PLK1 by a database search, was less expressed especially in six EC cell lines than HEEpiC cells. Moreover, miR‐593* expression level was inversely correlated with PLK1 mRNA level in 48 clinical tissue specimens of EC (p = 0.006). Introduction of synthetic miR‐593* suppressed PLK1 expression by 69–73%, reduced cell proliferation (p = 0.008) and increased cell proportion of G2/M phase (p = 0.01) in HSA/c (an EC cells), whereas a miR‐593* inhibitor upregulated PLK1 expression by 11–55%. Additionally, luciferase assay demonstrated that miR‐593* interacted two binding sites in the PLK1 3′‐UTR and reduced 56.8–71.5% of luciferase activity by degrading luciferase mRNA in HSA/c cells. In conclusion, PLK1 is post‐transcriptionally regulated by miR‐593* and could be a promising molecular target for EC treatment.
The importance of longitudinal pretest‐posttest designs in estimating college impact
Authors: Seifert Tricia A. , Pascarella Ernest T. , Erkel Sherri I. , Goodman Kathleen M.
Published: December 2010

This chapter opens with a literature scan examining the use of longitudinal pretest‐posttest designs in college impact research. With that in mind, the authors present an example of how researchers can mis‐estimate college impact if pretest‐posttest designs are not used.
What incentives can teach us about missing data in longitudinal assessment
Authors: Martin Georgianna L. , Loes Chad N.
Published: December 2010

This chapter explores the use of incentives in reducing missing data in longitudinal research and offers practical suggestions for using incentives in institutional assessment.
Using longitudinal data to improve the experiences and engagement of first‐year students
Authors: Cole James S. , Korkmaz Ali
Published: December 2010

This chapter describes how campuses can use longitudinal data to investigate and improve the experiences and engagement patterns of their first‐year students.
The Morphological Radiation of Setae in the Cladocera (Crustacea) and Their Potential for Morphogenesis
Authors: Smirnov Nikolai N. , Kotov Alexey A.
Published: December 2010

The present review seeks to demonstrate the presence of an inherent biological tendency for the modification of form in cladoceran setae. We present a comparative description of the setal equipment of the cladoceran antenna I, antenna II, maxilla I, maxilla II, each thoracic limb, the carapace valves, and the postabdomen. We revealed significant differences between planktonic and benthic species of the Cladocera. Also our analysis stresses the great differences between the “daphniid” line (Daphniidae + Moinidae) and the “chydorid” line (all other families) of the order Anomopoda.

Comments on cladoceran limb evolution are made, and some general conclusions concerning the major tendencies of setal evolutionary transformations are drawn. The morphological range of homologous structures in different species is generally wide, from an undifferentiated seta to either its disappearance or to enlargement, heavy chitinization, and specialization. Special issues, such as parallelisms, oligomerization, asymmetry, abnormalities, and conjugated morphogenesis are discussed. It is assumed that, having been originated, if not eliminated, these modifications either find some adaptive use in the process of radiation at the next level – adaptive radiation – or restrict the niches of specialized groups, or just remain ecologically neutral and then give rise to a series of similar species. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Population Growth of Six Iranian Brachionus Rotifer Strains in Response to Salinity and Food Type
Authors: Malekzadeh Viayeh Reza , Mohammadi Habib , Shafiei Abbas Banj
Published: December 2010

Intrinsic rates of population increase (r) were evaluated as a measure of population dynamics of four strains of Brachionus plicatilis and two strains of B. urceolaris from Iran in response to different salinities and feeding algae. Each rotifer strain was cultured at four salinities: 5, 20, 25 and 30‰ and fed with two microalgal species: Chlorella vulgaris and Nannochloropsis oculata. Salinity of 5‰ was critical for all the examined strains, at which r was at minimum and was different from the other salinities (P < 0.05). For B. plicatilis strains, the maximum r was observed in those fed on Chlorella at salinities of 10 and 30‰ (64 ± 0.01 day−1). While, in B. urceolaris, maximum r was for Nannochloropsis fed rotifers at salinity of 20‰ (0.69 ± 0.01 day−1). Maximum final population density (FD) was obtained for a strain of B. urceolaris fed on Nannochloropsis at 20‰ (329.3 ± 10.9 ind.mL−1). FD was relatively lower in B. plicatilis strains among all examined salinities. ANOVA showed the significant effect of salinity and rotifer strain, and algae × rotifer strain on both r and FD, and salinity × rotifer × algae on FD (P < 0.05). (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Spatial and Temporal Diversity Patterns of Planktonic Rotifer Assemblages in Water Bodies of the Floodplain Gemenc (Duna‐Dráva National Park, Hungary)
Authors: Schöll Károly
Published: December 2010

The Gemenc floodplain of the Danube possesses numerous side arms and backwaters. The aim of my study was to explore connections between hydrological events and diversity patterns of the planktonic rotifer assemblages of these water bodies. During the study period (2002–2008) 75 taxa of rotifers were found. Generally, the water bodies of the floodplain had more diverse rotifer assemblages than the main arm. At low and medium water levels diversity was highest in the parapotamal water bodies. This result may be explained by the intermediate disturbance hypothesis. At high water levels the highest biodiversities shifted to the plesiopotamal. Biodiversity, dominance, and evenness correlated with water flow and temperature. Patterns of biodiversity seem to be determined by the water level of the main arm; therefore the water regime appears to provide pronounced temporal variability in the hydro‐ecology of the floodplain. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Gluconeogenesis in dairy cows: The secret of making sweet milk from sour dough
Authors: Aschenbach Jörg R. , Kristensen Niels B. , Donkin Shawn S. , Hammon Harald M. , Penner Gregory B.
Published: December 2010

Gluconeogenesis is a crucial process to support glucose homeostasis when nutritional supply with glucose is insufficient. Because ingested carbohydrates are efficiently fermented to short‐chain fatty acids in the rumen, ruminants are required to meet the largest part of their glucose demand by de novo genesis after weaning. The qualitative difference to nonruminant species is that propionate originating from ruminal metabolism is the major substrate for gluconeogenesis. Disposal of propionate into gluconeogenesis via propionyl‐CoA carboxylase, methylmalonyl‐CoA mutase, and the cytosolic form of phosphoenolpyruvate carboxykinase (PEPCK) has a high metabolic priority and continues even if glucose is exogenously supplied. Gluconeogenesis is regulated at the transcriptional and several posttranscriptional levels and is under hormonal control (primarily insulin, glucagon, and growth hormone). Transcriptional regulation is relevant for regulating precursor entry into gluconeogenesis (propionate, alanine and other amino acids, lactate, and glycerol). Promoters of the bovine pyruvate carboxylase (PC) and PEPCK genes are directly controlled by metabolic products. The final steps decisive for glucose release (fructose 1,6‐bisphosphatase and glucose 6‐phosphatase) appear to be highly dependent on posttranscriptional regulation according to actual glucose status. Glucogenic precursor entry, together with hepatic glycogen dynamics, is mostly sufficient to meet the needs for hepatic glucose output except in high‐producing dairy cows during the transition from the dry period to peak lactation. Lactating cows adapt to the increased glucose requirement for lactose production by mobilization of endogenous glucogenic substrates and increased hepatic PC expression. If these adaptations fail, lipid metabolism may be altered leading to fatty liver and ketosis. Increasing feed intake and provision of glucogenic precursors from the diet are important to ameliorate these disturbances. An improved understanding of the complex mechanisms underlying gluconeogenesis may further improve our options to enhance the postpartum health status of dairy cows. © 2010 IUBMB IUBMB Life, 62(12): 869–877
The effect of betacyclodextrin and hydroxypropyl betacyclodextrin incorporation into plasticized poly(vinyl chloride) on its compatibility with human U937 cells
Authors: George Susan M. , Gaylor John D. S. , Leadbitter Jason , Grant M. Helen
Published: December 2010

Di (2‐ethyl hexyl) phthalate (DEHP) is one of the main plasticizers used in poly(vinyl chloride) (PVC) medical devices and is currently the only one listed for use in the European Pharmacopoeia Monograph. It leaches out of PVC when the material is in contact with lipophilic media, for example, blood and certain nutritional feeds. Consequently, concerns have been expressed since in certain animal species, DEHP has been shown to exhibit both carcinogenic and reproductive toxic effects. Incorporation of beta cyclodextrin (BCD) and hydroxypropyl betacyclodectrin (HPBCD) into plasticized materials has been reported to decrease the leaching of DEHP. We have investigated whether this results in improved in vitro biocompatibility by measuring the responses of U937 cells to plasticized PVC in the presence and absence of added BCD or HPBCD. Growth and viability of the U937 cells, as well as tumor necrosis factor‐α (TNF‐α) production in contact with these materials revealed no significant difference between unmodified plasticized PVC materials and those containing BCD or HPBCD. Lipopolysaccharide (LPS) was used to elicit TNF‐α production, and the response of cells to LPS in the presence of the PVC materials was evaluated. When PVC was modified by addition of HPBCD there was a significant reduction in the TNF‐α production in response to LPS. Modification of plasticized PVC biomaterials by adding cyclodextrins did not significantly improve their biocompatibility. However, the HPBCD modified plasticized PVC materials caused a reduction in the production in TNF‐α induced by LPS which may have implications for the inflammatory potential of these biomaterials. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2011.
PaDEL‐descriptor: An open source software to calculate molecular descriptors and fingerprints
Authors: Yap Chun Wei
Published: December 2010

Introduction

PaDEL‐Descriptor is a software for calculating molecular descriptors and fingerprints. The software currently calculates 797 descriptors (663 1D, 2D descriptors, and 134 3D descriptors) and 10 types of fingerprints. These descriptors and fingerprints are calculated mainly using The Chemistry Development Kit. Some additional descriptors and fingerprints were added, which include atom type electrotopological state descriptors, McGowan volume, molecular linear free energy relation descriptors, ring counts, count of chemical substructures identified by Laggner, and binary fingerprints and count of chemical substructures identified by Klekota and Roth.

Methods

PaDEL‐Descriptor was developed using the Java language and consists of a library component and an interface component. The library component allows it to be easily integrated into quantitative structure activity relationship software to provide the descriptor calculation feature while the interface component allows it to be used as a standalone software. The software uses a Master/Worker pattern to take advantage of the multiple CPU cores that are present in most modern computers to speed up calculations of molecular descriptors.

Results

The software has several advantages over existing standalone molecular descriptor calculation software. It is free and open source, has both graphical user interface and command line interfaces, can work on all major platforms (Windows, Linux, MacOS), supports more than 90 different molecular file formats, and is multithreaded.

Conclusion

PaDEL‐Descriptor is a useful addition to the currently available molecular descriptor calculation software. The software can be downloaded at http://padel.nus.edu.sg/software/padeldescriptor. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
Creation of a panel of vectors based on ape adenovirus isolates
Authors: Roy Soumitra , Medina‐Jaszek Angelica , Wilson Matthew J. , Sandhu Arbansjit , Calcedo Roberto , Lin Jianping , Wilson James M.
Published: December 2010

Background

We recently reported the isolation and sequencing of 30 novel adenoviruses from chimpanzees, bonobos and gorillas. These adenoviruses are promising candidates for the purpose of expanding the repertoire of adenoviral serotypes that can be used to create vectors for circumventing pre‐existing neutralizing antibodies in human populations. We thus aimed to create vectors from 20 of the newly isolated adenoviruses.

Methods

Plasmid molecular clones were created that harbored the complete E1‐deleted genomes from 20 of the newly isolated ape adenoviruses belonging to species B, C and E. The plasmids were transfected into human embryonic kidney (HEK) 293 cells to rescue vectors. We also tested normal human sera to determine the extent of pre‐existing cross‐neutralizing anti‐adenovirus neutralizing antibodies.

Results

Twelve vectors could be rescued and expanded following transfection into HEK 293 cells with yields (from fifty 150‐mm culture dishes) that ranged from 3 × 1011 to 7 × 1013 viral particles. Sera from 50 normal human donors were tested for the presence of neutralizing activity against 21 of the newly isolated ape adenoviruses. Cross‐neutralizing activity was generally low, although outliers with high neutralizing activity were frequently detected. Species B ape adenoviruses generally showed the least cross‐neutralization with antibodies present in the human sera that were tested.

Conclusions

E1‐deleted adenovirus vectors can be created from a wide variety of ape adenoviruses that can be rescued and propagated in HEK 293 cells. The prevalence of pre‐existing antibodies that can neutralize these adenoviruses in human populations is low. Copyright © 2010 John Wiley & Sons, Ltd.
Hydrogen isotope labelling using iridium(I) dionates
Authors: Lockley W. J. S.
Published: December 2010

The cyclooctadienyliridium(I) dionates provide an alternative ortho‐labelling approach to the more conventional iridium catalysts reviewed elsewhere in this special issue. The catalysts are utilized in DMF or DMA, removing potential problems of substrate insolubility in the solvents conventionally used for exchange labelling. Moreover, while readily prepared in a single step, the catalysts are also commercially available. In most cases recoveries are high, while the labelling achieved is both efficient and regiospecific. In addition, the reaction conditions are simple, requiring only conventional laboratory facilities and equipment. Copyright © 2010 John Wiley & Sons, Ltd.
The development and use of iridium(I) phosphine systems for ortho‐directed hydrogen‐isotope exchange
Authors: Salter Rhys
Published: December 2010

Rapid and efficient iridium‐mediated hydrogen‐tritium exchange labeling of pharmaceutical compounds is a key methodology in the life sciences industry. A review of the development and use of iridium(I) phosphine systems for ortho‐directed isotopic exchange is described to provide the reader with a comprehensive introduction to the area and to serve as a starting point for experimental investigators. Examples of useful catalyst systems and their application to different substrates types as well as potential areas for further development are discussed. Copyright © 2010 John Wiley & Sons, Ltd.
Synthesis of deuterium‐labelled drugs by hydrogen–deuterium (H–D) exchange using heterogeneous catalysis
Authors: Modutlwa Nkaelang , Maegawa Tomohiro , Monguchi Yasunari , Sajiki Hironao
Published: December 2010

Multi‐deuterium incorporations into drugs, such as theophylline, caffeine, valpromide, phenytoin, and trimethoprim, were post‐synthetically achieved by Pd/C‐, Pt/C‐, or/and Rh/C‐catalyzed hydrogen–deuterium exchange reactions under neutral conditions using deuterium oxide as the deuterium source in the presence of hydrogen gas. The present study offers facile and convenient methods for the preparation of highly deuterated medicines, which are expected to be used as long‐lasting medicines as well as internal standards for metabolic studies and for the quantitative analyses of the parent drugs.
Tissue differentiation around a short stemmed metaphyseal loading implant employing a modified mechanoregulatory algorithm: A finite element study
Authors: Puthumanapully Pramod Kumar , Browne Martin
Published: December 2010

Short stemmed cementless implants are being used increasingly to avoid problems associated with their long stemmed counterparts such as size, stiffness, and bulky nature, which can contribute to stress shielding, fractures, and hence loosening. They are also thought to enhance physiological loading of the femur. We performed a computational investigation of the possible tissue differentiation and bone ingrowth processes for a specific type of stemless implant using a mechanoregulatory hypothesis, with modifications to simulate tissue differentiation, and simplified loading conditions. The peak forces during stair climbing and normal walking were investigated to evaluate their influence on the process. The results were compared to clinical studies for relevance and corroboration. The majority of the tissue type formed was fibrous, occupying the proximal regions of the implant. The lateral flare design feature of the implant was predicted to enhance bone and cartilage formation in regions beneath it compared to the same design without a flare. The percentage of bone formed increased through the iterations and accounted for nearly 35% of the tissue at the end of the iterations in Gruen zones 2 and 6, replacing cartilage tissue as differentiation progressed. This agreed well with clinical data showing similar regions of bone formation and suggests that the distal regions of the implant under the lateral flare, resting in the metaphyseal region of the bone, promoted implant stability. © 2010 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 29:787–794, 2011
Recent advances in linear and nonlinear Raman spectroscopy. Part IV
Authors: Nafie Laurence A.
Published: December 2010

The purpose of the review is to provide a concise overview of recent advances in the broadly defined field of Raman spectroscopy as reflected in part by the many articles published each year in the Journal of Raman Spectroscopy (JRS) as well as in trends across all related journals publishing in this research area. Context for the review is provided by considering statistical data on citations for the Thompson Reuters ISI Web of Science by year and by subfield of Raman spectroscopy. Additional statistics of number of papers and posters presented by category at the XXII International Conference on Raman Spectroscopy (ICORS 2010) is also provided. Papers published in JRS in 2009, as reviewed here, reflect trends at the cutting edge of Raman spectroscopy which is expanding rapidly as a sensitive photonic probe of matter at the molecular level with an ever widening sphere of novel applications. Copyright © 2010 John Wiley & Sons, Ltd.
Method development and validation for the analysis of a new anti‐cancer infusion solution via HPLC
Authors: Donnarumma Fabrizio , Schober Margot , Greilberger Joachim , Matzi Veronika , Lindenmann Jörg , Maier Alfred , Herwig Ralf , Wintersteiger Reinhold
Published: December 2010

A fast and simple HPLC method has been developed and validated for the quantification of a completely new anti‐cancer drug during the manufacturing process. The combination of four compounds including α‐ketoglutaric acid, hydroxymethylfurfural, N‐acetyl‐L‐methionine and N‐acetyl‐L‐selenomethionine, administered intravenously, is still in test phase but has already shown promising results in cancer therapy. HPLC separation was achieved on an RP‐18 column with a gradient system. However, the highly different concentrations of the compounds required a variation in the detection wavelength within one run. In order to produce a chromatogram where peaks were comparable on a similar range scale, detection at absorption maxima for the two most concentrated components was avoided. After optimization of the gradient program it was possible to detect all four substances within 14 min in spite of their strongly different chemical structure. The method developed was validated for accuracy, repeatability, reproducibility and robustness in relation to temperature and pH of buffer. Linearity as well as the limit of detection and quantification were determined. This HPLC method was found to be precise, accurate and reproducible and can be easily used for in‐line process control during the manufacture of the anti‐tumour infusion solution.
Bedouin wives on the home front: Living with men serving in the Israel Defense Forces
Authors: Caspi Yael , Slobodin Ortal , Kammerer Nina , Enosh Guy , Shorer Shai , Klein Ehud
Published: December 2010

This community‐based study examined emotional and somatic symptoms of 129 Bedouin women whose husbands serve in the Israel Defense Forces. Wives of men diagnosed with posttraumatic stress disorder (PTSD) reported more symptoms than wives of men diagnosed with other disorders and wives of men with no diagnosis. Findings indicate that not only was PTSD in Bedouin servicemen positively associated with their wives' symptoms of posttraumatic stress and depression and somatic complaints, but that this relationship was fully mediated by husbands' aggression. Unraveling the special circumstances of women from traditional backgrounds faced with the devastating effects of husbands' combat‐related posttraumatic pathology may inform an approach to the concept of vicarious trauma that is more specific to non‐Western societies.
An isogeometric approach to cohesive zone modeling
Authors: Verhoosel Clemens V. , Scott Michael A. , de Borst René , Hughes Thomas J. R.
Published: December 2010

The possibility of enhancing a B‐spline basis with discontinuities by means of knot insertion makes isogeometric finite elements a suitable candidate for modeling discrete cracks. In this contribution we use isogeometric finite elements to discretize the cohesive zone formulation for failure in materials. In the case of a pre‐defined interface, non‐uniform rational B‐splines are used to obtain an efficient discretization. In the case that propagating cracks are considered, T‐splines are found to be more suitable, due to their ability to generate localized discontinuities. Various numerical simulations demonstrate the suitability of the isogeometric approach to cohesive zone modeling. Copyright © 2010 John Wiley & Sons, Ltd.
Linear finite elements with orthogonal discontinuous basis functions for explicit earthquake ground motion modeling
Authors: Ichimura T. , Hori M. , Wijerathne M. L. L.
Published: December 2010

The dynamic explicit finite element method is commonly used in earthquake ground motion modeling. In this method, the element mass matrix is approximately lumped, which may lead to numerical dispersion. On the other hand, the orthogonal finite element method, based on orthogonal polynomial basis functions, naturally derives a lumped diagonal mass matrix and can be applied to dynamic explicit finite element analysis. In this paper, we propose finite elements based on orthogonal discontinuous basis functions, the element mass matrices of which are lumped without approximation. Orthogonal discontinuous basis functions are used to improve the accuracy and reduce the numerical dispersion in earthquake ground motion modeling. We present a detailed formulation of the 4‐node tetrahedral and 8‐node hexahedral elements. The relationship between the proposed finite elements and conventional finite elements is investigated, and the solutions obtained from the conventional explicit finite element method are compared with analytical solutions to verify the numerical dispersion caused by the lumping approximation. Comparison of solutions obtained with the proposed finite elements to analytical solutions demonstrates the usefulness of the technique. Examples are also presented to illustrate the effectiveness of the proposed method in earthquake ground motion modeling in the actual three‐dimensional crust structure. Copyright © 2010 John Wiley & Sons, Ltd.