bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kelvin‐Helmholtz vortices observed by THEMIS at the duskside of the magnetopause under southward interplanetary magnetic field
Authors: Yan G. Q. , Mozer F. S. , Shen C. , Chen T. , Parks G. K. , Cai C. L. , McFadden J. P. 
Published: June 2014

AbstractThe Time History of Events and Macroscale Interactions during Substorms (THEMIS) observed several magnetopause crossings periodically at the duskside of magnetopause under southward interplanetary magnetic field (IMF), with significant sunward returning flows inside the magnetopause. The vortex features of the flows and the periodic enhancements in the calculated vorticity normal to the spacecraft plane could be found in the observation. The distortion of the magnetopause, the periodic features of vortex flows, the tailward propagation, and the evaluation of Kelvin‐Helmholtz instability (KHI) condition support the evidence of the Kelvin‐Helmholtz vortices produced by the velocity shear at the duskside of magnetopause. Based on three‐point simultaneous observations of the flow, the vorticity was calculated to be about 0.15 s−1, similar to previous results. The tailward propagation of the vortices along the flank magnetopause was estimated to be about 292 km/s. The circular‐induced electric field of several mV/m was deduced perpendicular to the magnetic field when the magnetic field compression occurred at the edges of the vortices.
Transient modulation of Kuroshio upper layer flow by directly impinging typhoon Morakot in east of Taiwan in 2009
Authors: Zheng Zhe‐Wen , Zheng Quanan , Lee Chia‐Ying , Gopalakrishnan Ganesh 
Published: June 2014

AbstractThis study deals with the modulation of the Kuroshio upper layer flow (KULF) in response to the passage of Typhoon Morakot in 2009, using Regional Oceanic Modeling System (ROMS) and in situ measurements from Argos drifters and Argo floats. The analysis of the simulated current fields near the typhoon track revealed an intermittency phenomenon of the KULF, which was almost shut down for at least 6 hours. The process begun 2 days prior to the approach of typhoon center due to blockage of the KULF by the steadily northerly winds, and lasted for more than 2 days, simultaneously shifting the Kuroshio main stream (KMS) path. When the Morakot gradually moved closely to the Kuroshio, the KMS shifted vertically from the surface layer to deeper layer of 50 – 100 m depth, and the maximum current speed in the KMS decreased from more than 1.3 m s−1to less than 1.1 m s−1. When the Morakot center approached about 100 km to the original position of the Kuroshio, the KULF spread eastward for 1.5 degrees at 24°N. When the Morakot center moved to the original position of the KMS, the Kuroshio abruptly rushed with a maximum speed near 1.4 m s−1. Meanwhile, an offshore cool jet originating from southeastern tip of Taiwan was generated and extended northward along the Kuroshio. In the cool jet, the lowest temperature reached about 5°C lower than the ambient waters. Modeled current variations and the cool jet during the Morakot passage were validated by in situ measurements.
Glycerophospholipids
Authors: Farooqui Akhlaq A 
Published: June 2014

Abstract

Glycerophospholipids are derivatives of
sn
‐glycero‐3‐phosphoric acid. They contain an
O
‐acyl or
O
‐alkyl or
O
‐alk‐1′‐enyl residue at the
sn
‐1 position and an
O
‐acyl residue at the
sn
‐2 position of the glycerol moiety and are defined on the basis of the substituents on the phosphoric acid at the
sn
‐3 position. Glycerophospholipids are asymmetrically distributed between the two bilayers membranes, which also contain cholesterol and proteins. Glycerophospholipids not only constitute the backbone of cellular membranes, but also provide the membrane with a suitable environment, fluidity and ion permeability. They are synthesised at the endoplasmic reticulum and are transported to other membranous structures by phospholipid exchange and transfer proteins. Once glycerophospholipids are laid down in a biomembrane, they undergo interconversion reactions. These reactions and activities of phospholipases may be responsible for the turnover, compositional maintenance and rearrangements of glycerophospholipids in membranes. This process results in the modulation of membrane function. Glycerophospholipids are precursors for lipid mediators, which play important roles in internal and external communication and modulate cellular responses. In addition, glycerophospholipids and their lipid mediators may be involved in membrane fusion, apoptosis and regulation of the activities of membrane‐bound enzymes and ion channels.

Key Concepts:

Lipid bilayers provide the fundamental architecture of biological membranes, which are made up of lipids (phospholipids, cholesterol and sphingolipids) and proteins.

The role of lipids is to provide membranes with integrity and flexibility, whereas embedded proteins in biomembrane are associated with the maintenance of cellular chemical climate.

Phospholipids are reservoir for lipid mediators, cholesterol provides flexibility, and sphingolipids and cholesterol are involved in formation of lipid rafts.

Lipid mediators not only transduce signals from the cell surface to the interior, but also modulate gene expression, growth, differentiation, adhesion, migration and apoptosis.

Arachidonic acid‐derived lipid mediators induce oxidative stress and inflammatory effects.

Docosahexaenoic acid‐derived lipid mediators produce antioxidative and anti‐inflammatory effects.
Nuclear Protein Import: Methods
Authors: Wagstaff Kylie M , Jans David A 
Published: June 2014

AbstractProtein synthesis takes place predominantly in the cytoplasm, meaning that proteins that are needed in the nuclear compartment, such as those that control gene transcription, have to be transported from the cytoplasm to the nucleus. Analysis of the regulation of nuclear import, which is central to cell responses to signalling pathways, and stress responses such as viral infection, requires dynamic experimental systems able to provide quantitative kinetic information. This article describes anin vitroreconstituted system as well as quantitative live cell imaging approaches, including the technique of fluorescence recovery after photobleaching, that enable the rate and extent of nuclear import to be quantitatively determined, and assist mechanistic studies with respect to the nuclear transporters and targeting signals involved. This is critical to a full understanding of the importance of nuclear trafficking in biological systems.Key Concepts:The regulation of nuclear transport is critical to transcriptional control in response to cellular and developmental signals, viral infection, etc.Using quantitative confocal laser scanning microscopy (CLSM) can enable small changes in nuclear localisation to be identified.Systems to reconstitute nuclear transportin vitrocan enable the delineation of nuclear transport mechanisms.The technique of fluorescence recovery after photobleaching can be used to determine nuclear transport kinetics in the living cell.Quantitative techniques to examine nuclear transport allow for sequences and mechanisms underpinning regulated nucleocytoplasmic protein transport to be dissected.
Molecular Genetics of Holt–Oram Syndrome
Authors: Barnett Phil , Postma Alex V 
Published: June 2014

Abstract

The Holt–Oram syndrome (HOS) is an autosomal‐dominant hand–heart syndrome characterised by malformations of the upper limbs, mainly involving the preaxial (radial) ray, and variable cardiac defects. Mutations in
TBX5,
a transcription factor that regulates a wide variety of developmental processes, underlie HOS. Thus far, more than a hundred
TBX5
mutations have been identified in patients with HOS. However, only the application of stringent diagnostic criteria will lead to a high sensitivity and specificity in
TBX5
mutation screening. Various pathogenic mechanisms that lead to HOS have been uncovered, ranging from loss‐of‐function to gain‐of‐function. Nonetheless, in a significant minority of HOS patients, who do fulfil the strict diagnostic criteria, no
TBX5
mutation is identified. This suggests that mutations in regulatory parts of
TBX5
could cause disease, or mutations in genes other than
TBX5
could underlie HOS. Application of exome sequencing or even whole‐genome sequencing should be pursued in those cases.

Key Concepts:

Holt–Oram syndrome is caused by
TBX5
mutations.

The majority of
TBX5
mutations lead to loss‐of‐function.

Application of stringent diagnostic criteria increases the yield of TBX5 mutation screening in HOS patients.

In a minority of HOS patients, who fulfil the stringent diagnostic criteria, no
TBX5
mutation is identified.

TBX5 is involved in the specification of the mesoderm and development of the heart, vasculature and limbs.
Autosomal Mutations and Spermatogenic Failure
Authors: Lima Ana C , Lopes Alexandra M 
Published: June 2014

Abstract

Male infertility is commonly due to an impairment in the production of viable sperm, capable of fertilisation. Spermatogenic failure can manifest in its most severe form by an absence of mature sperm or, more often, by a reduction in sperm counts, as an isolated phenotype or in combination with abnormalities in sperm motility and morphology. In only a fraction of patients with primary spermatogenic failure can an underlying genetic cause be identified, such as karyotype abnormalities and Y chromosome microdeletions. However, a small number of autosomal genes harbour rare variants/mutations with strong evidence of their impact in primary spermatogenic failure in otherwise healthy men (
SYCP3
,
NR5A1
,
DMRT1
,
CATSPER
,
DNAI1
,
DNAH5
,
DNAH11
,
SLC26A8
,
AURKC
,
SPATA16
,
DPY19L2
,
KLHL10
and
SEPT12
). Even though the clinical relevance of the majority of these variants is still uncertain, they represent promising markers for spermatogenesis deficits.

Key Concepts:

Spermatogenesis is an intricate process and a large number of genes on the autosomes are involved.

The etiopathogenesis of severe spermatogenic failure in otherwise healthy men is complex and still largely unknown.

A highly penetrant genetic variant resulting in male infertility should be rare in a population.

Validation of potentially deleterious variants must rely on the analysis of a large number of patients, replication in cohorts of different ethnicity, familial data and functional assays.

Spermatogenic failure may result from the disturbance of many different processes (gonadal formation and maintenance, meiosis and morphological differentiation of gametes).
Development and Role of the Human Reference Sequence in Personal Genomics
Authors: Smith Todd M , Porter Sandra G 
Published: June 2014

Abstract

Genome maps, like geographical maps, need to be interpreted carefully. Although maps are essential to exploration and navigation they cannot be completely accurate. Humans have been mapping the world for several millennia, but genomes have been mapped and explored for just a single century with the greatest advancements in making a sequence reference map of the human genome possible in the past 30 years. After the
deoxyribonucleic acid (DNA)
sequence of the human genome was completed in 2003, the reference sequence underwent several improvements and today provides the underlying comparative resource for a multitude genetic assays and biochemical measurements. However, the ability to simplify genetic analysis through a single comprehensive map remains an elusive goal.

Key Concepts:

Maps are incomplete and contain errors.

DNA sequence data are interpreted through biochemical experiments or comparisons to other DNA sequences.

A reference genome sequence is a map that provides the essential coordinate system for annotating the functional regions of the genome and comparing differences between individuals' genomes.

The reference genome sequence is always product of understanding at a set point in time and continues to evolve.

DNA sequences evolve through duplication and mutation and, as a result, contain many repeated sequences of different sizes, which complicates data analysis.

DNA sequence variation happens on large and small scales with respect to the lengths of the DNA differences to include single base changes, insertions, deletions, duplications and rearrangements.

DNA sequences within the human population undergo continual change and vary highly between individuals.

The current reference genome sequence is a collection of sequences, an assembly, that include sequences assembled into chromosomes, sequences that are part of structurally complex regions that cannot be assembled, patches (fixes) that cannot be included in the primary sequence, and high variability sequences that are organised into alternate loci.

Genetic analysis is error prone and the data require validation because the methods for collecting DNA sequences create artifacts and the reference sequence used for comparative analyses is incomplete.
Anthropometric and lifestyle characteristics of active and inactive saudi and british adolescents
Authors: Duncan Michael J. , Al‐hazzaa Hazzaa M. , Al‐Nakeeb Yahya , Al‐Sobayel Hana I. , Abahussain Nada A. , Musaiger Abdulrahman O. , Lyons Mark , Collins Peter , Nevill Alan 
Published: June 2014

ObjectivesTo compare the anthropometric and lifestyle characteristics of active and inactive adolescents in Saudi Arabia and Britain.MethodsA school‐based cross‐sectional study was conducted at four cities in Saudi Arabia (Riyadh and Al‐Khobar; N = 1,648) and Britain (Birmingham and Coventry; N = 1,158). The participants (14‐ to 18‐year‐olds) were randomly selected using a multistage stratified cluster sampling. Measurements included anthropometric [BMI, Waist circumference (WC), Waist to height ratio], screen time, validated physical activity questionnaire and dietary habits.ResultsBritish males were lighter (P = 0.04, 64.4 vs. 68.2 kg), and had lower values for WC (P = 0.003, 77.1 vs. 78.7 cm) than Saudi males. Males (P = 0.0001) were significantly more active than females but the difference between inactive Saudi and British females was greater than that between inactive Saudi and British males. Being female was significantly (P < 0.001) associated with lower activity levels in both the Saudi and British adolescents. Having lower frequency of fruit intake was significantly (P < 0.001) associated with lower activity levels, whereas increased frequency of consumption of French fries/potato chips was significantly (P = 0.008) associated with increased activity levels in Saudi adolescents. Among British adolescents, lower frequency of breakfast was (P = 0.045) associated with lower activity levels, increased frequency of consumption of sweetened beverages was significantly (P = 0.005) associated with higher activity levels. Higher energy drinks intake frequency was significantly (P = 0.007) associated with higher activity levels.ConclusionThe present study identifies crosscultural differences and similarities in lifestyle habits in adolescents from Britain and Saudi Arabia. Activity status (active vs. inactive) appears to play an important role in other lifestyle related behaviors, with active adolescent more likely to engage in healthy dietary behavior than their inactive peers, irrespective of country of origin. Am. J. Hum. Biol. 26:635–642, 2014. © 2014 Wiley Periodicals, Inc.
Adsorption‐based immobilization of Caldicellulosiruptor saccharolyticus cellobiose 2‐epimerase on Bacillus subtilis spores
Authors: Gu Junyan , Yang Ruijin , Hua Xiao , Zhang Wenbin , Zhao Wei 
Published: June 2014

AbstractNonrecombinant spore was examined as a novel immobilization support to adsorb enzymes. Caldicellulosiruptor saccharolyticus cellobiose 2‐epimerase (CsCE), efficiently producing lactulose using lactose as a single substrate, was immobilized on Bacillus subtilis spores via adsorption. The immobilization process was optimized, and the properties of immobilized CsCE and the interactions between the enzyme and spores were also investigated. Under the optimized conditions (pH 4.5, temperature 4 °C, reaction time 2 H, and initial enzyme concentration 2.4 mg/mL), the maximum adsorbed amount of CsCE was 1.47 mg/1011 spores, and the enzyme activity recovery was 79.4%. The spore‐immobilized CsCE presented a higher pH and thermal stability than a free enzyme. Total desorption of the immobilized enzyme was only achieved by treatment with 1.0 M NaCl at pH 1.0, indicating a strong adsorption between CsCE and B. subtilis spores. Efficient binding may require a potent combination of electrostatic and hydrophobic interactions between spores and an enzyme. The immobilized CsCE was applied to produce 395 g/L lactulose after 4 H. Moreover, the spores could be regenerated and the spore‐immobilized enzyme showed good reusability as it retained approximately 70% of its initial activity after eight recycles.
A Rational Designed Dual‐channel Chemosensor for Mercury Ions Based on Hydrolysis of Schiff Base
Authors: Wu Guiyuan , Shi Bingbing , Hu Bing , Zhang Youming , Lin Qi , Yao Hong , Wei Taibao 
Published: June 2014

AbstractA bilateral Schiff base is reported for the colorimetric and fluorometric dual‐channel sensing of Hg2+ ions by taking advantage of the hydrolysis of carbon‐nitrogen double bond, altering an ICT state mechanism and then Hg2+ ions coordinating with amino moieties of 1,5‐DAN and leading to the aggregation of 1,5‐DAN. Meanwhile, it formed a stable neutral complex of amino‐Hg‐amino. In addition, test strips based on L were fabricated, which also exhibited a good selectivity to Hg2+ as in solution. This work provides a novel approach for the selective recognition of mercury ions. Notably, the color changes are very significant and all the recognition processes can be observed by the naked eyes. We believe the test strips can act as a convenient and efficient Hg2+ test kit.
Facile Fabrication of Polymeric Ionic Liquid Grafted Porous Polymer Monolith for Mixed‐Mode High Performance Liquid Chromatography
Authors: Li Yaping , Qi Li , Shen Ying , Zhang Haizhi , Ma Huimin 
Published: June 2014

AbstractA novel polymeric ionic liquid grafted porous polymer monolith has been facilely fabricated for mixed‐mode chromatography. The column is prepared from poly (glycidyl methacrylate‐co‐ethylene dimethacrylate) monolith through hydrolyzation of the epoxy moieties into hydroxyl groups, followed by "grafting from" polymerization of ionic liquid of 1‐vinyl‐3‐butylimidazolium chloride. Successful modification is characterized by scanning electron microscope, infrared spectroscopy, elemental analysis and mercury intrusion porosimetry. The HPLC performance of developed column is evaluated by separating acidic vitamin B analytes, neutral steroids and basic aromatic amines in mixed‐mode chromatography on a single column, respectively. The ionic liquid affords the monolith with both enhanced separation ability and improved column efficiency.
Spectroscopic and Computational Characterizations of Alkaline‐Earth‐ and Heavy‐Metal‐Exchanged Natrolites
Authors: Liu Dan , Chen Xin , Ma Yanming , Liu Zhenxian , Vogt Thomas , Lee Yongjae 
Published: June 2014

AbstractSynchrotron infrared (IR) and micro‐Raman spectra of natrolites containing alkaline‐earth ions (Ca2+, Sr2+, and Ba2+) and heavy metals (Cd2+, Pb2+, and Ag+) as extra‐framework cations (EFCs) were measured under ambient conditions. Complementing our previous spectroscopic investigations of natrolites with monovalent alkali metal (Li+, Na+, K+, Rb+, and Cs+) EFCs, we establish a correlation between the redshifts of the frequencies of the 4‐ring and helical 8‐ring units and the size of the EFCs in natrolite. Through ab initio calculations we have derived structural models of Ca2+‐ and Ag+‐exchanged natrolites with hydrogen atoms, and found that the frequency shifts in the HOH bending mode and the differences in the OH stretching vibration modes can be correlated with the orientations of the water molecules along the natrolite channel. Assuming that the members of a solid solution series behave as an ideal mixture, we will be able to use spectroscopy to probe compositions. Deviation from ideal behavior might indicate the occurrence of phase separation on various length scales.
Catalytic Conversion of γ‐Valerolactone to ε‐Caprolactam: Towards Nylon from Renewable Feedstock
Authors: Raoufmoghaddam Saeed , Rood Marcus T. M. , Buijze Florine K. W. , Drent Eite , Bouwman Elisabeth 
Published: June 2014

AbstractThe conversion of γ‐valerolactone (GVL) in three atom‐efficient steps to the important polymer precursor ε‐caprolactam is reported. The bio‐based GVL can be converted to a mixture of isomeric methyl pentenoates (MP) via trans‐esterification with methanol with 94 % yield (ratio of 3‐MP/4‐MP=3:1); subsequent aminolysis with ammonia leads to a mixture of pentenamides (PA) almost quantitatively (99 % conversion). The resulting pentenamides are ultimately converted into ε‐caprolactam via a rhodium‐catalyzed intramolecular hydroamidomethylation reaction, comprising an initial hydroformylation of the alkene moiety of PA and subsequent ring‐closing reductive amidation of the resulting aldehyde with the amide functionality. A promising yield of caprolactam of about 90 % can be obtained with a Rh/xantphos catalyst system in a two‐stage hydroformylation–reductive amidation using pure 4‐PA as feedstock. The use of 3‐PA as a substrate not only results in a significantly lower regioselectivity for the 7‐membered lactam, but also in the formation of high amounts of valeramide (VA). Consequently, a best overall yield of caprolactam of nearly 40 % could be demonstrated with a Rh/POP‐xantphos [POP‐xantphos=4,5‐bis(2,8‐dimethyl‐10‐phenoxaphosphino)‐9,9,‐dimethylxanthene] catalyst system based on the 3:1 mixture of 3‐PA/4‐PA directly obtainable from GVL.
Small sample sorting of primary adherent cells by automated micropallet imaging and release
Authors: Shah Pavak K. , Herrera‐Loeza Silvia Gabriela , Sims Christopher E. , Yeh Jen Jen , Allbritton Nancy L. 
Published: June 2014

AbstractPrimary patient samples are the gold standard for molecular investigations of tumor biology yet are difficult to acquire, heterogeneous in nature and variable in size. Patient‐derived xenografts (PDXs) comprised of primary tumor tissue cultured in host organisms such as nude mice permit the propagation of human tumor samples in an in vivo environment and closely mimic the phenotype and gene expression profile of the primary tumor. Although PDX models reduce the cost and complexity of acquiring sample tissue and permit repeated sampling of the primary tumor, these samples are typically contaminated by immune, blood, and vascular tissues from the host organism while also being limited in size. For very small tissue samples (on the order of 103 cells) purification by fluorescence‐activated cell sorting (FACS) is not feasible while magnetic activated cell sorting (MACS) of small samples results in very low purity, low yield, and poor viability. We developed a platform for imaging cytometry integrated with micropallet array technology to perform automated cell sorting on very small samples obtained from PDX models of pancreatic and colorectal cancer using antibody staining of EpCAM (CD326) as a selection criteria. These data demonstrate the ability to automate and efficiently separate samples with very low number of cells. © 2014 International Society for Advancement of Cytometry