bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative metabolomics analysis of amino acid metabolism in recombinant Pichia pastoris under different oxygen availability conditions
Authors: Carnicer Marc , ten Pierick Angela , van Dam Jan , Heijnen Joseph J , Albiol Joan , van Gulik Walter , Ferrer Pau 
Published: January 2013

Abstract

Background
Environmental and intrinsic stress factors can result in the global alteration of yeast physiology, as evidenced by several transcriptional studies. Hypoxia has been shown to have a beneficial effect on the expression of recombinant proteins in Pichia pastoris growing on glucose. Furthermore, transcriptional profiling analyses revealed that oxygen availability was strongly affecting ergosterol biosynthesis, central carbon metabolism and stress responses, in particular the unfolded protein response. To contribute to the better understanding of the effect and interplay of oxygen availability and foreign protein secretion on central metabolism, a first quantitative metabolomic analysis of free amino acids pools in a recombinant P. pastoris strain growing under different oxygen availability conditions has been performed.

Results
The values obtained indicate significant variations in the intracellular amino acid pools due to different oxygen availability conditions, showing an overall increase of their size under oxygen limitation. Notably, even while foreign protein productivities were relatively low (about 40–80 μg Fab/gDCW·h), recombinant protein production was found to have a limited but significant impact on the intracellular amino acid pools, which were generally decreased in the producing strain compared with the reference strain. However, observed changes in individual amino acids pools were not correlated with their corresponding relative abundance in the recombinant protein sequence, but to the overall cell protein amino acid compositional variations.

Conclusions
Overall, the results obtained, combined with previous transcriptomic and proteomic analyses provide a systematic metabolic fingerprint of the oxygen availability impact on recombinant protein production in P. pastoris.
A new method of kidney biopsy using low dose CT-guidance with coaxial trocar and bard biopsy gun
Authors: Pi Xiao-ling , Tang Zhen , Fu Li-qian , Guo Mei-hua , Shi Mei-hua , Chen Lan , Wan Zheng-ying 
Published: January 2013

Abstract

Background
To explore a new method of kidney biopsy with coaxial trocar and bard biopsy gun under low dose computed tomography (CT)-guidance and evaluate its accuracy, safety, and efficacy.

Methods
Sixty patients underwent renal biopsy under CT-guidance. They were randomly divided into two groups: group I, low dose CT-guided (120 kV and 25 or 50 mAs) and group II, standard dose CT-guided (120 kV and 250 mAs). For group I, the coaxial trocar was accurately placed adjacent to the renal capsule of the lower pole, the needle core was removed, and samples were obtained with a bard biopsy gun. For group II, the coaxial trocar was not used. Total number of passes, mean biopsy diameter, mean glomeruli per specimen, mean operation time, mean scanning time, and mean radiation dose were noted. Dose-length product (DLP) was used to calculate the radiation doses. After 24 hours of the biopsy, ultrasound was repeated to identify any subcapsular hematoma.

Results
Success rate of biopsy in group I was 100% while using low dose CT-guidance along with coaxial trocar renal. There was no statistic differences bewteen group I and II in the total number of passes, mean biopsy diameter, mean glomeruli per specimen and mean time of operation and CT scanning. The average DLP of group I was lower as compared to the value of group II (p <0.05).

Conclusions
Kidney biopsy using coaxial trocar and bard biopsy gun under low dose CT was an accurate, simple and safe method for diagnosis and treatment of kidney diseases. It can be used for repeat and multiple biopsies, particularly suitable for obese and renal atrophy patients in whom the kidneys are difficult to image.
Facile synthesis of ultrathin magnetic iron oxide nanoplates by Schikorr reaction
Authors: Ma Ming , Zhang Yu , Guo Zhirui , Gu Ning 
Published: January 2013

Abstract
In this work, a very facile one-pot hydrothermal synthesis approach has been developed for the preparation of ultrathin magnetite nanoplates. The hydrothermal procedure was performed by aging ferrous hydroxide under anaerobic conditions, which is known as Schikorr reaction. Ethylene glycol (EG), which was introduced to the reaction as another solvent, played a critical role in the formation process of these nanoplates. Typically, hexagonal Fe3O4 nanoplates with a thickness of 10 to 15 nm and a side length of 150 to 200 nm have been synthesized with EG/H2O = 1:1 in experiments. Our data suggest that the thickness of Fe3O4 nanoplates decreases, and the shape of the nanoplate becomes more irregular when the concentration of EG increases. The as-prepared Fe3O4 nanoplates were highly crystallized single crystals and exhibited large coercivity and specific absorption rate coefficient.
Attenuation of multiple Nef functions in HIV-1 elite controllers
Authors: Mwimanzi Philip , Markle Tristan J , Martin Eric , Ogata Yoko , Kuang Xiaomei T , Tokunaga Michiyo , Mahiti Macdonald , Pereyra Florencia , Miura Toshiyuki , Walker Bruce D , Brumme Zabrina L , Brockman Mark A , Ueno Takamasa 
Published: January 2013

Abstract

Background
Impaired HIV-1 Gag, Pol, and Env function has been described in elite controllers (EC) who spontaneously suppress plasma viremia to < 50 RNA copies/mL; however, activity of the accessory protein Nef remains incompletely characterized. We examined the ability of 91 Nef clones, isolated from plasma of 45 EC and 46 chronic progressors (CP), to down-regulate HLA class I and CD4, up-regulate HLA class II invariant chain (CD74), enhance viral infectivity, and stimulate viral replication in PBMC.

Results
In general, EC Nef clones were functional; however, all five activities were significantly lower in EC compared to CP. Nef clones from HLA-B*57-expressing EC exhibited poorer CD4 down-regulation function compared to those from non-B*57 EC, and the number of EC-specific B*57-associated Nef polymorphisms correlated inversely with 4 of 5 Nef functions in these individuals.

Conclusion
Results indicate that decreased HIV-1 Nef function, due in part to host immune selection pressures, may be a hallmark of the EC phenotype.
Genetic and evolutionary characterization of RABVs from China using the phosphoprotein gene
Authors: Wang Lihua , Wu Hui , Tao Xiaoyan , Li Hao , Rayner Simon , Liang Guodong , Tang Qing 
Published: January 2013

Abstract

Background
While the function of the phosphoprotein (P) gene of the rabies virus (RABV) has been well studied in laboratory adapted RABVs, the genetic diversity and evolution characteristics of the P gene of street RABVs remain unclear. The objective of the present study was to investigate the mutation and evolution of P genes in Chinese street RABVs.

Results
The P gene of 77 RABVs from brain samples of dogs and wild animals collected in eight Chinese provinces through 2003 to 2008 were sequenced. The open reading frame (ORF) of the P genes was 894 nucleotides (nt) in length, with 85-99% (80-89%) amino acid (nucleotide) identity compared with the laboratory RABVs and vaccine strains. Phylogenetic analysis based on the P gene revealed that Chinese RABVs strains could be divided into two distinct clades, and several RABV variants were found to co circulating in the same province. Two conserved (CD1, 2) and two variable (VD1, 2) domains were identified by comparing the deduced primary sequences of the encoded P proteins. Two sequence motifs, one believed to confer binding to the cytoplasmic dynein light chain LC8 and a lysine-rich sequence were conserved throughout the Chinese RABVs. In contrast, the isolates exhibited lower conservation of one phosphate acceptor and one internal translation initiation site identified in the P protein of the rabies challenge virus standard (CVS) strain. Bayesian coalescent analysis showed that the P gene in Chinese RABVs have a substitution rate (3.305x10-4 substitutions per site per year) and evolution history (592 years ago) similar to values for the glycoprotein (G) and nucleoprotein (N) reported previously.

Conclusion
Several substitutions were found in the P gene of Chinese RABVs strains compared to the laboratory adapted and vaccine strains, whether these variations could affect the biological characteristics of Chinese RABVs need to be further investigated. The substitution rate and evolution history of P gene is similar to G and N gene, combine the topology of phylogenetic tree based on the P gene is similar to the G and N gene trees, indicate that the P, G and N genes are equally valid for examining the phylogenetics of RABVs.
Temporal changes in respiratory adenovirus serotypes circulating in the greater Toronto area, Ontario, during December 2008 to April 2010
Authors: Abbas Kaniza Zahra , Lombos Ernesto , Duvvuri Venkata R , Olsha Romy , Higgins Rachel R , Gubbay Jonathan B 
Published: January 2013

Abstract

Background
Certain adenovirus serotypes cause severe infections, especially in children. It is important to monitor temporal changes in serotypes causing clinical disease. The objective of this study was to document circulating respiratory adenovirus serotypes by sequencing adenovirus culture isolates from the Greater Toronto Area, Ontario, during December 2008 to April 2010.

Methods
Nucleic acid extraction was performed on 90 respiratory tract adenovirus culture isolates. PCR amplification was conducted with primers targeting the adenovirus hexon gene hypervariable region 7. Sanger sequencing and phylogenetic analyses were performed to determine serotype identities.

Results
Among 90 clinical respiratory isolates sequenced, eight different serotypes were identified. Serotype 3 (34, 38%), serotype 2 (30, 30%), and serotype 1 (14, 16%) isolates were most common; serotypes 5, 6, 11, 17 and 21 were also observed. Seventeen (50%) of the 34 HAdV-3 isolates were identified between December 2008 and February 2009, while none were identified from December 2009 to February 2010. Between December 2008 and April 2009, the two most common serotypes were HAdV-3 and HAdV-2, detected in 18 (53%) and 8 (24%) of the 34 cultures isolates, respectively. However, from December 2009 to April 2010, there was an increase in HAdV-2, which became the most prevalent serotype, detected in 10 (50%) of the 20 isolates identified (p = 0.05).

Conclusions
There was a gradual shift in prevailing adenovirus serotypes during the 17 month study period, from predominantly HAdV-3 to HAdV-2. If an adenovirus vaccine were to be broadly implemented, multiple serotypes should be included.
In vivo characterization of chimeric PCV DNA clones containing heterogeneous capsid protein nuclear localization signals (NLS)
Authors: Shuai Jiangbing , Zhang Xiaofeng , Chen Wujian , Li Ke , Wu Shan , He Yongqiang , Fang Weihuan 
Published: January 2013

Abstract

Background
PCV ORF2 capsid protein was predicted to contribute to the control of replication via an interaction between the Cap and Rep proteins in the nucleoplasm. We previously showed that the nuclear localization signal (NLS) on the capsid protein plays an accessory role in the replication of PCV in vitro. To further evaluate the in vivo characteristics of NLS-chimeric PCV DNA clones, BALB/C mice were inoculated intranasally and intraperitoneally with the DNA clones.

Results
As expected, no gross lesions were detected during the study of the inoculated animals. The chimeric PCV12-, PCV1-NLS2- and PCV2-NLS1-inoculated animals had significantly fewer and less severe histopathological lesions in lymphoid tissues than the PCV2-inoculated animals (P < 0.05). PCV12 induced a specific antibody response against PCV2 ORF2 comparable to that induced by wild-type PCV2 but demonstrated a shorter period of viremia and much lower level of virus loads in sera than those in PCV2-inoculated mice. Remarkably, the PCV2-NLS1 and PCV1-NLS2 chimeras replicated in inoculated mice and induced specific antibody responses but failed to produce viral antigens in the lymph nodes or a detectable viremia.

Conclusions
The chimeric PCV2-NLS1 and PCV1-NLS2 demonstrated a lower replication level as compared with wild type of PCV2 or PCV1 in vivo, suggesting that ORF2 NLSs played an accessory role in PCV replication. The chimeric PCV12 is a good candidate for vaccination against PCV2 infection.
Association between the GRM7 rs3792452 polymorphism and attention deficit hyperacitiveity disorder in a Korean sample
Authors: Park Subin , Jung Sun-Woo , Kim Boong-Nyun , Cho Soo-Churl , Shin Min-Sup , Kim Jae-Won , Yoo Hee Jeong , Cho Dae-Yeon , Chung Un-Sun , Son Jung-Woo , Kim Hyo-Won 
Published: January 2013

Abstract

Background
The purpose of this study was to investigate the association between the ionotropic and glutamate receptors, N-methyl D-asparate 2A (GRIN2A) and 2B (GRIN2B), and the metabotropic glutamate receptor mGluR7 (GRM7) gene polymorphisms and attention-deficit hyperactivity disorder (ADHD) in Korean population.

Methods
We conducted a case–control analysis of 202 ADHD subjects and 159 controls, performed a transmission disequilibrium test (TDT) on 149 trios, and compared scores from the continuous performance test (CPT), the Children’s Depression Inventory (CDI), and the State-Trait Anxiety Inventory for Children (STAIC) according to the genotype of the glutamate receptor genes.

Results
There were no significant differences in the genotype or allele frequencies of the GRIN2A rs8049651, GRIN2B rs2284411, or GRM7 rs37952452 polymorphisms between the ADHD and control groups. For 148 ADHD trios, the TDT analysis also showed no preferential transmission of the GRIN2A rs8049651 or GRIN2B rs2284411 polymorphisms. However, the TDT analysis of the GRM7 rs3792452 polymorphism showed biased transmission of the G allele (χ2 = 4.67, p = 0.031). In the ADHD probands, the subjects with GG genotype in the GRM7 rs37952452 polymorphism had higher mean T-scores for omission errors on the CPT than did those with the GA or AA genotype (t = 3.38, p = 0.001). In addition, the ADHD subjects who were homozygous for the G allele in the GRM7 rs37952452 polymorphism had higher STAIC-T (t = 5.52, p < 0.001) and STAIC-S (t = 2.74, p = 0.007) scores than did those with the GA or AA genotype.

Conclusions
These results provide preliminary evidence of an association between the GRM7 rs37952452 polymorphism and selective attention deficit and anxiety found within the Korean ADHD population.
Intraoperative laser angiography using the SPY system: review of the literature and recommendations for use
Authors: Gurtner Geoffrey C , Jones Glyn E , Neligan Peter C , Newman Martin I , Phillips Brett T , Sacks Justin M , Zenn Michael R 
Published: January 2013

Abstract
Inadequate tissue perfusion is a key contributor to early complications following reconstructive procedures. Accurate and reliable intraoperative evaluation of tissue perfusion is critical to reduce complications and improve clinical outcomes. Clinical judgment is the most commonly used method for evaluating blood supply, but when used alone, is not always completely reliable. A variety of other methodologies have been evaluated, including Doppler devices, tissue oximetry, and fluorescein, among others. However, none have achieved widespread acceptance. Recently, intraoperative laser angiography using indocyanine green was introduced to reconstructive surgery. This vascular imaging technology provides real-time assessment of tissue perfusion that correlates with clinical outcomes and can be used to guide surgical decision making. Although this technology has been used for decades in other areas, surgeons may not be aware of its utility for perfusion assessment in reconstructive surgery. A group of experts with extensive experience with intraoperative laser angiography convened to identify key issues in perfusion assessment, review available methodologies, and produce initial recommendations for the use of this technology in reconstructive procedures.
New phosphine-diamine and phosphine-amino-alcohol tridentate ligands for ruthenium catalysed enantioselective hydrogenation of ketones and a concise lactone synthesis enabled by asymmetric reduction of cyano-ketones
Authors: Fuentes José A , Phillips Scott D , Clarke Matthew L 
Published: January 2013

Abstract
Enantioselective hydrogenation of ketones is a key reaction in organic chemistry. In the past, we have attempted to deal with some unsolved challenges in this arena by introducing chiral tridentate phosphine-diamine/Ru catalysts. New catalysts and new applications are presented here, including the synthesis of phosphine-amino-alcohol P,N,OH ligands derived from (R,S)-1-amino-2-indanol, (S,S)-1-amino-2-indanol and a new chiral P,N,N ligand derived from (R,R)-1,2-diphenylethylenediamine. Ruthenium pre-catalysts of type [RuCl2(L)(DMSO)] were isolated and then examined in the hydrogenation of ketones. While the new P,N,OH ligand based catalysts are poor, the new P,N,N system gives up to 98% e.e. on substrates that do not react at all with most catalysts. A preliminary attempt at realising a new delta lactone synthesis by organocatalytic Michael addition between acetophenone and acrylonitrile, followed by asymmetric hydrogenation of the nitrile functionalised ketone is challenging in part due to the Michael addition chemistry, but also since Noyori pressure hydrogenation catalysts gave massively reduced reactivity relative to their performance for other acetophenone derivatives. The Ru phosphine-diamine system allowed quantitative conversion and around 50% e.e. The product can be converted into a delta lactone by treatment with KOH with complete retention of enantiomeric excess. This approach potentially offers access to this class of chiral molecules in three steps from the extremely cheap building blocks acrylonitrile and methyl-ketones; we encourage researchers to improve on our efforts in this potentially useful but currently flawed process.
Oxidation of benzoin catalyzed by oxovanadium (IV) schiff base complexes
Authors: Alsalim Tahseen A , Hadi Jabbar S , Ali Omar N , Abbo Hanna S , Titinchi Salam JJ 
Published: January 2013

Abstract

Background
The oxidative transformation of benzoin to benzil has been accomplished by the use of a wide variety of reagents or catalysts and different reaction procedures. The conventional oxidizing agents yielded mainly benzaldehyde or/and benzoic acid and only a trace amount of benzil. The limits of practical utilization of these reagents involves the use of stoichiometric amounts of corrosive acids or toxic metallic reagents, which in turn produce undesirable waste materials and required high reaction temperatures.
In recent years, vanadium complexes have attracted much attention for their potential utility as catalysts for various types of reactions.

Results
Active and selective catalytic systems of new unsymmetrical oxovanadium(IV) Schiff base complexes for the oxidation of benzoin is reported. The Schiff base ligands are derived between 2-aminoethanol and 2-hydroxy-1-naphthaldehyde (H2L1) or 3-ethoxy salicylaldehyde (H2L3); and 2-aminophenol and 3-ethoxysalicylaldehyde (H2L2) or 2-hydroxy-1-naphthaldehyde (H2L4). The unsymmetrical Schiff bases behave as tridentate dibasic ONO donor ligands. Reaction of these Schiff base ligands with oxovanadyl sulphate afforded the mononuclear oxovanadium(IV) complexes (VIVOLx.H2O), which are characterized by various physico-chemical techniques.
The catalytic oxidation activities of these complexes for benzoin were evaluated using H2O2 as an oxidant. The best reaction conditions are obtained by considering the effect of solvent, reaction time and temperature. Under the optimized reaction conditions, VOL4 catalyst showed high conversion (>99%) with excellent selectivity to benzil (~100%) in a shorter reaction time compared to the other catalysts considered.

Conclusion
Four tridentate ONO type Schiff base ligands were synthesized. Complexation of these ligands with vanadyl(IV) sulphate leads to the formation of new oxovanadium(IV) complexes of type VIVOL.H2O.
Elemental analyses and spectral data of the free ligands and their oxovanadium(IV) complexes were found to be in good agreement with their structures, indicating high purity of all the compounds.
Oxovanadium complexes were screened for the oxidation of benzoin to benzil using H2O2 as oxidant. The effect of time, solvent and temperature were optimized to obtain maximum yield. The catalytic activity results demonstrate that these catalytic systems are both highly active and selective for the oxidation of benzoin under mild reaction conditions.
PubChem3D: conformer ensemble accuracy
Authors: Kim Sunghwan , Bolton Evan E , Bryant Stephen H 
Published: January 2013

Abstract

Background
PubChem is a free and publicly available resource containing substance descriptions and their associated biological activity information. PubChem3D is an extension to PubChem containing computationally-derived three-dimensional (3-D) structures of small molecules. All the tools and services that are a part of PubChem3D rely upon the quality of the 3-D conformer models. Construction of the conformer models currently available in PubChem3D involves a clustering stage to sample the conformational space spanned by the molecule. While this stage allows one to downsize the conformer models to more manageable size, it may result in a loss of the ability to reproduce experimentally determined “bioactive” conformations, for example, found for PDB ligands. This study examines the extent of this accuracy loss and considers its effect on the 3-D similarity analysis of molecules.

Results
The conformer models consisting of up to 100,000 conformers per compound were generated for 47,123 small molecules whose structures were experimentally determined, and the conformers in each conformer model were clustered to reduce the size of the conformer model to a maximum of 500 conformers per molecule. The accuracy of the conformer models before and after clustering was evaluated using five different measures: root-mean-square distance (RMSD), shape-optimized shape-Tanimoto (ST

ST-opt
) and combo-Tanimoto (ComboT

ST-opt
), and color-optimized color-Tanimoto (CT

CT-opt
) and combo-Tanimoto (ComboT

CT-opt
). On average, the effect of clustering decreased the conformer model accuracy, increasing the conformer ensemble’s RMSD to the bioactive conformer (by 0.18 ± 0.12 Å), and decreasing the ST

ST-opt
, ComboT

ST-opt
, CT

CT-opt
, and ComboT

CT-opt
scores (by 0.04 ± 0.03, 0.16 ± 0.09, 0.09 ± 0.05, and 0.15 ± 0.09, respectively).

Conclusion
This study shows the RMSD accuracy performance of the PubChem3D conformer models is operating as designed. In addition, the effect of PubChem3D sampling on 3-D similarity measures shows that there is a linear degradation of average accuracy with respect to molecular size and flexibility. Generally speaking, one can likely expect the worst-case minimum accuracy of 90% or more of the PubChem3D ensembles to be 0.75, 1.09, 0.43, and 1.13, in terms of ST

ST-opt
, ComboT

ST-opt
, CT

CT-opt
, and ComboT

CT-opt
, respectively. This expected accuracy improves linearly as the molecule becomes smaller or less flexible.