bluuebunny/crossref_metadata_2025 huggingface dataset:
Forelimb to Hindlimb Shape Covariance in Extant Hominoids and Fossil Hominins
Authors: Tallman Melissa
Published: November 2012

Researchers often attempt to use limb proportions to ascertain the locomotor repertoires of fossil hominins. This can be problematic as there are few skeletons in the fossil record that preserve both a full forelimb and hindlimb; therefore, estimates of full limb lengths are typically associated with substantial error. In this study, two‐block partial least squares analyses were used to examine covariation between forelimb and hindlimb elements in extant hominoids and fossil hominins. This has the benefit of including both forelimb and hindlimb in a type of functional analysis without necessitating an accurate length estimate. There is a high degree of covariation between forelimb and hindlimb segments in the mixed species sample, particularly in the proximal ulna, distal humerus, and proximal/distal femur and that shape covariation is significantly correlated with intermembral indices in the extant taxa. Overall, the fossil hominins most closely resembled modern humans with the exception of analyses utilizing the distal femur where some occupied a unique morphological position; thus, some fossil hominins likely possessed locomotor capabilities similar to modern humans, whereas others likely represent a unique morphological compromise between terrestrial bipedality and other positional behaviors not present among extant hominoids. Anat Rec, 2013. © 2012 Wiley Periodicals, Inc.
BRCA1 Germ‐Line Mutations and Tumor Characteristics in Eastern Chinese Women with Familial Breast Cancer
Authors: Cao Wenming , Wang Xiaojia , Gao Yun , Yang Hongjian , Li Ji‐Cheng
Published: November 2012

Although several studies detected the BRCA1 germ‐line mutations in Chinese women with familial breast cancer, most of them did not employ conventional full gene sequencing, especially in eastern China. In addition, the clinicopathological features of BRCA1‐associated breast cancer in Chinese women were not well investigated. In this study, we screened the complete coding regions and exon‐intron boundaries of BRCA1 by polymerase chain reaction (PCR)‐sequencing assay. Immunohistochemistry analyses were performed on tumor samples to detect the expression of estrogen receptor (ER), progesterone receptor (PR), P53, and human epidermal growth factor receptor‐2 (HER‐2). Breast cancer patients having one or more affected relatives referred from the Zhejiang Cancer Hospital, eastern China during 2008–2011 were selected for the study. A total of 62 familial breast cancer patients received the BRCA1 germ‐line mutation screening. Five deleterious mutations were detected in this cohort. The mutation rate was 11.3% (7/62). We found two novel mutations (3414delC and 5,280 C > T) and two recurrent mutations (5,273 G > A and 5589del8). BRCA1 mutation tumors tended to be negative for ER, PR, and HER‐2, and exhibited high histological grade compared with tumors without BRCA1 mutations. Our study suggests that recurrent mutations may exist in eastern Chinese women with familial breast cancer and PCR‐sequencing assay is a useful tool to screen these mutations. It also suggests that BRCA1‐associated breast cancers in Chinese women exhibit an aggressive phenotype. Anat Rec, 2013. © 2012 Wiley Periodicals, Inc.
Modelling the cost-effectiveness of carotid endarterectomy for asymptomatic stenosis
Authors: Thapar A , Garcia Mochon L , Epstein D , Shalhoub J , Davies A H
Published: November 2012

Background

The aim of this study was to model the cost-effectiveness of carotid endarterectomy for asymptomatic stenosis versus medical therapy based on 10-year data from the Asymptomatic Carotid Surgery Trial (ACST).

Methods

This was a cost–utility analysis based on clinical effectiveness data from the ACST with UK-specific costs and stroke outcomes. A Markov model was used to calculate the incremental cost-effectiveness ratio (ICER, or cost per additional quality-of-life year) for a strategy of early endarterectomy versus medical therapy for the average patient and published subgroups. An exploratory analysis considered contemporary event rates.

Results

The ICER was £ 7584 per additional quality-adjusted life-year (QALY) for the average patient in the ACST. At thresholds of £ 20 000 and £ 30 000 there was a 74 and 84 per cent chance respectively of early endarterectomy being cost-effective. The ICER for men below 75 years of age was £ 3254, and that for men aged 75 years or above was £ 71 699. For women aged under 75 years endarterectomy was less costly and more effective than medical therapy; for women aged 75 years or more endarterectomy was less effective and more costly than medical therapy. At contemporary perioperative event rates of 2·7 per cent and background any-territory stroke rates of 1·6 per cent, early endarterectomy remained cost-effective.

Conclusion

In the ACST, early endarterectomy was predicted to be cost-effective in those below 75 years of age, using a threshold of £ 20 000 per QALY. If background any-territory stroke rates fell below 1 per cent per annum, early endarterectomy would cease to be cost-effective.
Lymphadenectomy around the left renal vein in Siewert type II adenocarcinoma of the oesophagogastric junction
Authors: Mine S , Sano T , Hiki N , Yamada K , Nunobe S , Yamaguchi T
Published: November 2012

Background

The extent of lymphadenectomy in patients with Siewert type II adenocarcinoma of the oesophagogastric junction is controversial. The aim of this study was to investigate lymph node involvement around the left renal vein.

Methods

Lymph node involvement and prognosis in patients with Siewert type II cancers treated by R0–1 surgical resection were investigated, with regard to lymphadenectomy around the left renal vein. Based on the incidence of involvement at each node, the node stations were divided into three tiers (first tier, more than 20 per cent involvement; second tier, 10–20 per cent involvement; third tier, less than 10 per cent involvement).

Results

Of 150 patients with type II oesophagogastric adenocarcinoma, 94 had left renal vein lymphadenectomy. The first lymph node tier included nodes along the lesser curvature, right cardia, left cardia and left gastric artery, with involvement of 28·0–46·0 per cent and a 5-year survival rate of 42–53 per cent in patients with positive nodes. The nodes around the lower mediastinum, left renal vein, splenic artery and coeliac axis constituted the second tier, with involvement of 12·7–18 per cent and a 5-year survival rate of 11–35 per cent. With regard to the left renal vein, the incidence of involvement was 17 per cent and the 5-year rate survival rate was 19 per cent. Multivariable analysis showed that left renal vein lymphadenectomy was an independent prognostic factor in patients with pathological tumour category pathological T3–4 disease (hazard ratio 0·51, 95 per cent confidence interval 0·26 to 0·99; P = 0·048).

Conclusion

Left renal vein nodal involvement is similar to that seen along the splenic artery, in the lower mediastinum and coeliac axis, with similar impact on patient survival.
S‐Adenosyl‐Methionine‐Dependent Methyltransferases: Highly Versatile Enzymes in Biocatalysis, Biosynthesis and Other Biotechnological Applications
Authors: Struck Anna‐Winona , Thompson Mark L. , Wong Lu Shin , Micklefield Jason
Published: November 2012

S‐adenosyl methionine (SAM) is a universal biological cofactor that is found in all branches of life where it plays a critical role in the transfer of methyl groups to various biomolecules, including DNA, proteins and small‐molecule secondary metabolites. The methylation process thus has important implications in various disease processes and applications in industrial chemical processing. This methyl transfer is catalysed by SAM‐dependent methyltransferases (MTases), which are by far the largest groups of SAM‐dependent enzymes. A significant amount is now known regarding the structural biology and enzymology of these enzymes, and, consequently, there is now significant scope for the development of new MTases and SAM analogues for applications from biomolecular imaging to biocatalytic industrial processes. This review will focus on current efforts in the manipulation of class I and V SAM‐dependent MTases and the use of synthetic SAM analogues, which together offer the best prospects for rational redesign towards biotechnological applications. Firstly, metabolic engineering of organisms incorporating small‐molecule MTases is discussed; this can be applied in a variety of areas from the industrial bioprocessing of flavourants and antibiotics to frontier research in biofuel production and bioremediation. Secondly, the application of MTases in combination with SAM analogues is reviewed; this allows the tagging of proteins and oligonucleotides with moieties other than the methyl group. Such tagging allows the isolation of the tagged biomolecule and aids its visualisation by a range of analytical methods. The review then summarises the potential advantages of MTase‐mediated chemistry and offers some future perspectives on downstream applications.
Host–Guest Interactions of Phosphorescent Molecular Tweezers Based on an Alkynylplatinum(II) Terpyridine System with Polyaromatic Hydrocarbons
Authors: Tanaka Yuya , Wong Keith Man‐Chung , Yam Vivian Wing‐Wah
Published: November 2012

Host–guest interactions of a molecular tweezer complex 1 with various planar organic molecules including polyaromatic hydrocarbons (PAHs) were investigated by 1D and 2D 1H NMR spectroscopy, UV/Vis absorption and emission titration studies. 2D and DOSY NMR spectroscopies support the sandwiched binding mode based on 1:1 host–guest interactions. The binding constants (KS) of complex 1 for various PAHs were determined by NMR titration studies and the values were found to span up to an order of 104 M−1 for coronene to no observable interaction for benzene, indicating that the π‐surface area is important for such host–guest interactions. The substituent effect on the host–guest interaction based on the guest series of 9‐substituted anthracenes was also studied. In general, a stronger interaction was observed for the anthracene guest with electron‐donating groups, although steric and π‐conjugation factors cannot be completely excluded. The photophysical responses of complex 1 upon addition of various PAHs were measured by UV/Vis and emission titration studies. The UV/Vis absorption spectra were found to show a drop in absorbance of the metal‐to‐ligand charge‐transfer (MLCT) and ligand‐to‐ligand charge‐transfer (LLCT) admixture band upon addition of various guest molecules to 1, whereas the emission behavior was found to change differently depending on the guest molecules, showing emission enhancement and/or quenching. It was found that emission quenching occurred either via energy transfer or electron transfer pathway or both, while emission enhancement was caused by the increase in rigidity of complex 1 as a result of host–guest interaction.
Low Catalyst Loading in Ring‐Closing Metathesis Reactions
Authors: Kadyrov Renat
Published: November 2012

An efficient procedure is described for ring‐closing metathesis reactions. A conversion of 95 % for diethyl diallylmalonate in dilute solution could be achieved within a few minutes, reaching TOF=4173 min−1, with very low loading of commercially available Ru catalysts that contained unsaturated NHC ligands. In general, only 50 to 250 ppm of the catalyst is required to achieve near‐quantitative conversion into a broad variety of 5–16‐membered heterocyclic compounds. The practicality of this procedure was illustrated in the synthesis of 5–8‐membered N‐tert‐butoxycarbonyl (N‐Boc)‐ and N‐para‐toluenesulfonyl (N‐Ts)‐protected cyclic amines and 9–16‐membered lactones. The synthesis of macrocyclic proline‐based lactams required slightly higher catalyst loadings. Along with monocyclic products, oligomeric byproducts, mostly cyclodimers, were isolated and characterized.
On the Solution Behaviour of Benzyllithium⋅(−)‐Sparteine Adducts and Related Lithium Organyls – A Case Study on Applying 7Li,15N{1H} HMQC and Further NMR Methods, Including Some Investigation into Asymmetric Synthesis
Authors: Casimiro María , Oña‐Burgos Pascual , Meyer Jens , Styra Steffen , Kuzu Istemi , Breher Frank , Fernández Ignacio
Published: November 2012

2D 7Li,15N heteronuclear shift correlation through scalar coupling has successfully been applied to several lithium organyls consisting of polydentate N ligands such as N,N,N′,N′‐tetramethylethylenediamine (tmeda), N,N,N′,N′,N′′‐pentamethyldiethylentriamine (pmdta) and (−)‐sparteine. Structural insights on the conformation of benzyllithium⋅pmdta (5) in a toluene solution and the strength of ion pairing in combination with PGSE NMR measurements, 1H,1H‐NOESY and 1H,7Li‐HOESY experiments are presented. By studying in detail the formation of 5 in solution, a transient species has been observed for the first time and assigned to a pre‐complex of nBuLi and pmdta. In addition, the solution behaviour of the complex formed between benzyllithium and (−)‐sparteine (8) has been studied by PGSE and multinuclear NMR spectroscopy. The straightforward synthesis and first applications in asymmetric lithiations are also reported, which show that the new system benzyllithium⋅(−)‐sparteine (8) provide poorer enantioselective induction than the classical nBuLi⋅(−)‐sparteine (6). The results were supported by deprotonation experiments confirming that the formation of 8 relies on two relevant factors, namely temperature and lithiating reagent. The existence of 8 may thus interfere with the asymmetric induction when the system nBuLi⋅ (−)‐sparteine is used in the enantioselective deprotonations of N‐Boc‐N‐(p‐methoxyphenyl)‐benzylamine conducted in toluene.
Synthesis, Structure, and Theoretical Study of Trifluoromethyl Derivatives of C84(22) Fullerene
Authors: Chang Kaichin , Fritz Maria A. , Tamm Nadezhda B. , Goryunkov Alexey A. , Sidorov Lev N. , Chen Chuanbao , Yang Shangfeng , Kemnitz Erhard , Troyanov Sergey I.
Published: November 2012

Trifluoromethylation of higher fullerene mixtures with CF3I was performed in ampoules at 400 to 420 and 550 to 560 °C. HPLC separation followed by crystal growth and X‐ray diffraction studies allowed the structure elucidation of nine CF3 derivatives of D2‐C84 (isomer 22). Molecular structures of two isomers of C84(22)(CF3)12, two isomers of C84(22)(CF3)14, four isomers of C84(22)(CF3)16, and one isomer of C84(22)(CF3)20 were discussed in terms of their addition patterns and relative formation energies. DFT calculations were also used to predict the most stable molecular structures of lower CF3 derivatives, C84(22)(CF3)2–10. It was found that the addition of CF3 groups to C84(22) is governed by two rules: additions can only occur at para positions of C6(CF3)2 hexagons and no additions can occur at triple‐hexagon‐junction positions on the fullerene cage.
Prompt and Slow Electron‐Detachment‐Dissociation/Electron‐Photodetachment‐Dissociation of a 21‐Mer Peptide
Authors: Pérot‐Taillandier Marie , Zirah Séverine , Enjalbert Quentin , Antoine Rodolphe , Lemoine Jérôme , Dugourd Philippe , Rebuffat Sylvie , Tabet Jean‐Claude , Afonso Carlos
Published: November 2012

Electron detachment dissociation (EDD) and electron photodetachment dissociation (EPD) are relatively new dissociation methods that involve electron detachment followed by radical‐driven dissociation from multiply deprotonated species. EDD yields prompt dissociation whereas only electron detachment is obtained by EPD; subsequent vibrational activation of the charge‐reduced radical anion is required to obtain the product ions. Herein, the fragmentation patterns that were obtained by EDD and by vibrational activation of the charge‐reduced radical anions that were produced through EDD or EPD (activated‐EDD and activated‐EPD) were compared. The observed differences were related to the dissociation kinetics and/or the contribution of electron‐induced dissociation (EID). Time‐resolved double‐resonance experiments were performed to measure the dissociation rate constants of the EDD product ions. Differences in the formation kinetics were revealed between the classical EDD/EPD ′a.i/′′xj complementary ions and some ′a.i/ci/′′′z.j product ions, which were produced with slower dissociation rate constants, owing to the presence of specific neighbouring side chains. A new fragmentation pathway is proposed for the formation of the slow‐kinetics ′a.i ions.
Coordinative Interactions between Porphyrins and C60, La@C82, and La2@C80
Authors: Tsuchiya Takahiro , Rudolf Marc , Wolfrum Silke , Radhakrishnan Shankara Gayathri , Aoyama Ryo , Yokosawa Yuya , Oshima Azusa , Akasaka Takeshi , Nagase Shigeru , Guldi Dirk M.
Published: November 2012

For the first time, a C60 derivative (1) and two different lanthanum metallofullerene derivatives, La@C82Py (2) and La2@C80Py (3), that feature a pyridyl group as a coordination site for transition‐metal ions have been synthesized and integrated as electron acceptors into coordinative electron‐donor/electron‐acceptor hybrids. Zinc tetraphenylporphyrin (ZnP) served as an excited‐state electron donor in this respect. Our investigations, by means of steady‐state and time‐resolved photophysical techniques found that electron transfer governs the excited‐state deactivation in all of these systems, namely 1/ZnP, 2/ZnP, and 3/ZnP, whereas, in the ground state, notable electronic interactions are lacking. Variation of the electron‐accepting fullerene or metallofullerene moieties provides the incentive for fine‐tuning the binding constants, the charge‐separation kinetics, and the charge‐recombination kinetics. To this end, the binding constants, which ranged from log Kassoc=3.94–4.38, are dominated by axial coordination, with minor contributions from the orbital overlap of the curved and planar π systems. The charge‐separation and charge‐recombination kinetics, which are in the order of 1010 and 108 s−1, relate to the reduction potential of the fullerene and metallofullerenes, respectively.
A Bioinorganic View of Alzheimer’s Disease: When Misplaced Metal Ions (Re)direct the Electrons to the Wrong Target
Authors: Faller Peter , Hureau Christelle
Published: November 2012

Metal ions Cu, Zn and Fe, seem to play a pivotal role in Alzheimer’s disease and other neurodegenerative diseases. In order to understand this in a broader sense, one has to considerer the peculiarities of metal metabolism in the brain compared to most other tissues, as well as the importance of the redox active metal ions, Fe and Cu, in oxygen metabolism and the connected oxidative stress.
Synthesis and Molecular Properties of Acceptor‐Substituted Squaraine Dyes
Authors: Mayerhöffer Ulrich , Gsänger Marcel , Stolte Matthias , Fimmel Benjamin , Würthner Frank
Published: November 2012

A broad series of more than 20 acceptor‐substituted squaraines was synthesized that feature different acceptor functionalities at the central squaraine four‐membered ring. The influence of these acceptor units on the reactivity of semisquaraine precursors and stability of the respective squaraines were explored. Thereby the dicyanovinyl group was found to be the most versatile acceptor group that enabled various modifications at the donor moiety of the squaraine scaffold, leading to an extended series of dicyanovinyl‐functionalized squaraines. The variation of donor units afforded a set of NIR fluorophores that cover a wavelength region from the visible at about 650 nm far into the NIR up to 920 nm with fluorescence quantum yields between 0.93 and 0.11 and outstanding optical brightness. This excellent optical property is related to a rigid molecular scaffold that is fixed in an all‐cis configuration by the additional dicyanovinyl acceptor unit. The change of the molecular symmetry from C2h to C2v upon functionalization of the squaraine core with dicyanovinyl acceptor group has been confirmed in solution by electro‐optical absorption (EOA) spectroscopy, revealing permanent ground‐state dipole moments μg in the range between 4.3 and 6.4 D. These dipole moments direct an antiparallel packing of the molecules in the solid state according to single‐crystal X‐ray analyses achieved for four dicyanovinyl‐functionalized squaraines. The structural properties, the EOA results, as well as the band shapes of the optical spectra indicate that these polymethine dyes are cyanine‐type chromophores. It is worth noting that the orientation of the dipole moment vectors is orthogonal to the orientation of the transition dipole moment vectors, which is an uncommon but characteristic feature of this rather novel class of polymethine dyes. With regard to applications of these dyes in organic solar cells, their redox properties were also studied by cyclic voltammetry.
Efficient Synthesis of Substituted 3‐Azabicyclo[3.1.0]hexan‐2‐ones from 2‐Iodocyclopropanecarboxamides Using a Copper‐Free Sonogashira Coupling
Authors: de Carné‐Carnavalet Benoît , Archambeau Alexis , Meyer Christophe , Cossy Janine , Folléas Benoît , Brayer Jean‐Louis , Demoute Jean‐Pierre
Published: November 2012

The copper‐free Sonogashira coupling between N‐substituted cis‐ 2‐iodocyclopropanecarboxamides and terminal aryl‐, heteroaryl‐alkynes or enynes, followed by 5‐exo‐dig cyclization of the nitrogen amide onto the carbon–carbon triple bond, provides a remarkably efficient access to a variety of substituted 4‐methylene‐3‐azabicyclo[3.1.0]hexan‐2‐ones in excellent yields. Protonation of these latter enamides generates bicyclic N‐acyliminium ions that can be involved in Pictet–Spengler cyclizations leading to new 3‐azabicyclo[3.1.0]hexan‐2‐ones, possessing a quaternary stereocenter at C4, with high diastereoselectivities. This strategy constitutes an attractive complementary alternative to the classical route that relies on the addition of organometallic reagents to cyclopropyl imides.
Synthesis of (−)‐Morphine: Application of Sequential Claisen/Claisen Rearrangement of an Allylic Vicinal Diol
Authors: Ichiki Masato , Tanimoto Hiroki , Miwa Shohei , Saito Ryosuke , Sato Takaaki , Chida Noritaka
Published: November 2012

A detailed exploration of the synthesis of (−)‐morphine based on sequential [3,3]‐sigmatropic rearrangements is described. The sequential Claisen/Claisen rearrangements of an allylic vicinal diol resulted in the stereoselective formation of the two contiguous carbon centers, including a sterically encumbered quaternary carbon, in a single operation. The two ethyl esters generated in this reaction were successfully differentiated during a subsequent Friedel–Crafts‐type cyclization. The (−)‐morphine double bond was introduced at a late stage in our first‐generation synthesis, but was formed at an earlier stage in the second‐generation synthesis, resulting in a more efficient route to the end product.
PtM (M=Cu, Co, Ni, Fe) Nanocrystals: From Small Nanoparticles to Wormlike Nanowires by Oriented Attachment
Authors: Yu Xiaofei , Wang Dingsheng , Peng Qing , Li Yadong
Published: November 2012

PtM (M=Cu, Co, Ni, Fe) wormlike nanowires with excellent catalytic activities were produced by a hydrothermal method. Based on the experiment results, PtM nanoparticles grew into nanowires through oriented attachment. The electrocatalytic activities of these nanowires toward methanol oxidation were also studied by cyclic voltammetry and chronoamperometry measurements. The synthesized PtM nanowires showed higher catalytic activity and stability for methanol oxidation than Pt nanowires and commercial Pt black.
Convergent Modulation of Singlet and Triplet Excited States of Phosphine‐Oxide Hosts through the Management of Molecular Structure and Functional‐Group Linkages for Low‐Voltage‐Driven Electrophosphorescence
Authors: Han Chunmiao , Zhang Zhensong , Xu Hui , Xie Guohua , Li Jing , Zhao Yi , Deng Zhaopeng , Liu Shiyong , Yan Pengfei
Published: November 2012

The controllable tuning of the excited states in a series of phosphine‐oxide hosts (DPExPOCzn) was realized through introducing carbazolyl and diphenylphosphine‐oxide (DPPO) moieties to adjust the frontier molecular orbitals, molecular rigidity, and the location of the triplet excited states by suppressing the intramolecular interplay of the combined multi‐insulating and meso linkage. On increasing the number of substituents, simultaneous lowering of the first singlet energy levels (S1) and raising of the first triplet energy levels (T1, about 3.0 eV) were achieved. The former change was mainly due to the contribution of the carbazolyl group to the HOMOs and the extended conjugation. The latter change was due to an enhanced molecular rigidity and the shift of the T1 states from the diphenylether group to the carbazolyl moieties. This kind of convergent modulation of excited states not only facilitates the exothermic energy transfer to the dopants in phosphorescent organic light‐emitting diodes (PHOLEDs), but also realizes the fine‐tuning of electrical properties to achieve the balanced carrier injection and transportation in the emitting layers. As the result, the favorable performance of blue‐light‐emitting PHOLEDs was demonstrated, including much‐lower driving voltages of 2.6 V for onset and 3.0 V at 100 cd m−2, as well as a remarkably improved E.Q.E. of 12.6 %.
Small‐Molecule APOBEC3G DNA Cytosine Deaminase Inhibitors Based on a 4‐Amino‐1,2,4‐triazole‐3‐thiol Scaffold
Authors: Olson Margaret E. , Li Ming , Harris Reuben S. , Harki Daniel A.
Published: November 2012

APOBEC3G (A3G) is a single‐stranded DNA cytosine deaminase that functions in innate immunity against retroviruses and retrotransposons. Although A3G can potently restrict Vif‐deficient HIV‐1 replication by catalyzing excessive levels of G→A hypermutation, sublethal levels of A3G‐catalyzed mutation may contribute to the high level of HIV‐1 fitness and its incurable prognosis. To chemically modulate A3G catalytic activity with the goal of decreasing the HIV‐1 genomic mutation rate, we synthesized and biochemically evaluated a class of 4‐amino‐1,2,4‐triazole‐3‐thiol small‐molecule inhibitors identified by high‐throughput screening. This class of compounds exhibits low‐micromolar (3.9–8.2 μM) inhibitory potency and remarkable specificity for A3G versus the related cytosine deaminase, APOBEC3A. Chemical modification of inhibitors, A3G mutational screening, and thiol reactivity studies implicate C321, a residue proximal to the active site, as the critical A3G target for this class of molecules.
Consciousness and the structuring property of typical data
Authors: Mason Jonathan W. D.
Published: November 2012

The theoretical base for consciousness, in particular, an explanation of how consciousness is defined by the brain, has long been sought by science. We propose a partial theory of consciousness as relations defined by typical data. The theory is based on the idea that a brain state on its own is almost meaningless but in the context of the typical brain states, defined by the brain's structure, a particular brain state is highly structured by relations. The proposed theory can be applied and tested both theoretically and experimentally. Precisely how typical data determines relations is fully established using discrete mathematics. © 2012 Wiley Periodicals, Inc. Complexity, 2012
Optimization of Hydrothermal Pretreatment of Lignocellulosic Biomass in the Bioethanol Production Process
Authors: Nitsos Christos K. , Matis Konstantinos A. , Triantafyllidis Kostas S.
Published: November 2012

The natural resistance to enzymatic deconstruction exhibited by lignocellulosic materials has designated pretreatment as a key step in the biological conversion of biomass to ethanol. Hydrothermal pretreatment in pure water represents a challenging approach because it is a method with low operational costs and does not involve the use of organic solvents, difficult to handle chemicals, and “external” liquid or solid catalysts. In the present work, a systematic study has been performed to optimize the hydrothermal treatment of lignocellulosic biomass (beech wood) with the aim of maximizing the enzymatic digestibility of cellulose in the treated solids and obtaining a liquid side product that could also be utilized for the production of ethanol or valuable chemicals. Hydrothermal treatment experiments were conducted in a batch‐mode, high‐pressure reactor under autogeneous pressure at varying temperature (130–220 °C) and time (15–180 min) regimes, and at a liquid‐to‐solid ratio (LSR) of 15. The intensification of the process was expressed by the severity factor, log Ro. The major changes induced in the solid biomass were the dissolution/removal of hemicellulose to the process liquid and the partial removal and relocation of lignin on the external surface of biomass particles in the form of recondensed droplets. The above structural changes led to a 2.5‐fold increase in surface area and total pore volume of the pretreated biomass solids. The enzymatic hydrolysis of cellulose to glucose increased from less than 7 wt % for the parent biomass to as high as 70 wt % for the treated solids. Maximum xylan recovery (60 wt %) in the hydrothermal process liquid was observed at about 80 wt % hemicellulose removal; this was accomplished by moderate treatment severities (log Ro=3.8–4.1). At higher severities (log Ro=4.7), xylose degradation products, mainly furfural and formic acid, were the predominant chemicals formed.
The metabolic deterioration that antedates diabetes: personal trajectories of HbA1c and fasting glucose as early indicators and possible triggers for intervention
Authors: Dankner Rachel , Bergman Michael , Danoff Ann , Qureshi Sana , Whitford Ian , Kaviani Nargess , Dynkevich Yevgeniya , Roth Jesse
Published: November 2012

HbA1c testing has become an accepted means of diagnosing diabetes as an alternative to blood glucose levels. However, population‐based norms of glucose and of HbA1c levels do not enable the detection of diabetes at an early enough stage to thwart complications. Personal trajectories of glucose levels show steep increases a number of years prior to diabetes diagnosis. Here, we hypothesize that a comparable time‐dependent deviation in an individual's HbA1c level may be an early manifestation of disease that should prompt lifestyle modifications. We predict that analysis of personal trajectories of glucose and of HbA1c will promote earlier intervention and a greater reduction in disease complications than current standards, which are based on population‐based norms. Copyright © 2012 John Wiley & Sons, Ltd.
Experimental approaches for gene regulatory network construction: The chick as a model system
Authors: Streit Andrea , Tambalo Monica , Chen Jingchen , Grocott Timothy , Anwar Maryam , Sosinsky Alona , Stern Claudio D.
Published: November 2012

Setting up the body plan during embryonic development requires the coordinated action of many signals and transcriptional regulators in a precise temporal sequence and spatial pattern. The last decades have seen an explosion of information describing the molecular control of many developmental processes. The next challenge is to integrate this information into logic “wiring diagrams” that visualize gene actions and outputs, have predictive power and point to key control nodes. Here, we provide an experimental workflow on how to construct gene regulatory networks using the chick as model system. genesis 51:296–310, 2012. © 2012 Wiley Periodicals, Inc.
Metabolic viability of Escherichia coli trapped by dielectrophoresis in microfluidics
Authors: Donato Sandra S. , Chu Virginia , Prazeres Duarte M. F. , Conde Joao P.
Published: November 2012

The spatial and temporal control of biological species is essential in complex microfluidic biosystems. In addition, if the biological species is a cell, microfluidic handling must ensure that the cell's metabolic viability is maintained. The use of DEP for cell manipulation in microfluidics has many advantages because it is remote and fast, and the voltages required for cell trapping scale well with miniaturization. In this paper, the conditions for bacterial cell (Escherichia coli) trapping using a quadrupole electrode configuration in a PDMS microfluidic channel were developed both for stagnant and for in‐flow fluidic situations. The effect of the electrical conductivity of the fluid, the applied electric field and frequency, and the fluid‐flow velocity were studied. A dynamic exchange between captured and free‐flowing cells during DEP trapping was demonstrated. The metabolic activity of trapped cells was confirmed by using E. coli cells genetically engineered to express green fluorescent protein under the control of an inducible promoter. Noninduced cells trapped by negative DEP and positive DEP were able to express green fluorescent protein minutes after the inducer was inserted in the microchannel system immediately after DEP trapping. Longer times of trapping prior to exposure to the inducer indicated first a degradation of the cell metabolic activity and finally cell death.
Low‐complexity high‐rate irregular QC‐LDPC codes with applications to PR2 and EPR2 channels
Authors: Imtawil Virasit , Kupimai Mongkol , Kruesubthaworn Anan , Siritaratiwat Apirat , Meesomboon Anupap
Published: November 2012

In this paper, we propose a modified high rate (3,L) quasi‐cyclic low‐density parity‐check (QC‐LDPC) code based on circulant permutation matrices for efficient encoder implementation. The structure of the code is modified from a (3,L) regular QC‐LDPC code to be an approximate lower triangular matrix and a linear independent form. We present two novel efficient encoding techniques for generating redundant parity bits. The complexity of the encoder implementation depends on the number of redundant parity bits of the code for one‐stage encoding and the length of the code for two‐stage encoding. The advantage of both encoding techniques is that few XOR gates are used in encoder implementation. The simulation results show that the proposed codes at code rate 0.884 and 0.953 have good bit error rate performance compared with other LDPC codes over PR2 and EPR2 channels. European Transactions on Telecommunications. Copyright © 2012 John Wiley & Sons, Ltd.
Adult sea lamprey tolerates biliary atresia by altering bile salt composition and renal excretion
Authors: Cai Shi-Ying , Lionarons Daniël A. , Hagey Lee , Soroka Carol J. , Mennone Albert , Boyer James L.
Published: November 2012

The sea lamprey (

Petromyzon marinus

) is a genetically programmed animal model for biliary atresia, as it loses its bile ducts and gallbladder during metamorphosis. However, in contrast to patients with biliary atresia or other forms of cholestasis who develop progressive disease, the postmetamorphosis lampreys grow normally to adult size. To understand how the adult lamprey thrives without the ability to secrete bile, we examined bile salt homeostasis in larval and adult lampreys. Adult livers were severely cholestatic, with levels of bile salts >1 mM, but no evidence of necrosis, fibrosis, or inflammation. Interestingly, both larvae and adults had normal plasma levels (˜10 μM) of bile salts. In larvae, petromyzonol sulfate (PZS) was the predominant bile salt, whereas the major bile salts in adult liver were sulfated C27 bile alcohols. Cytotoxicity assays revealed that PZS was highly toxic. Pharmacokinetic studies in free-swimming adults revealed that ˜35% of intravenously injected bromosulfophthalein (BSP) was eliminated over a 72-hour period. Collection of urine and feces demonstrated that both endogenous and exogenous organic anions, including biliverdin, bile salts, and BSP, were predominantly excreted by way of the kidney, with minor amounts also detected in feces. Gene expression analysis detected marked up-regulation of orthologs of known organic anion and bile salt transporters in the kidney, with lesser effects in the intestine and gills in adults compared to larvae. These findings indicate that adult lampreys tolerate cholestasis by altering hepatic bile salt composition, while maintaining normal plasma bile salt levels predominantly through renal excretion of bile products. Therefore, we conclude that strategies to accelerate renal excretion of bile salt and other toxins should be beneficial for patients with cholestasis.
Sexual transmission of hepatitis C virus among monogamous heterosexual couples: The HCV partners study
Authors: Terrault Norah A. , Dodge Jennifer L. , Murphy Edward L. , Tavis John E. , Kiss Alexi , Levin T. R. , Gish Robert G. , Busch Michael P. , Reingold Arthur L. , Alter Miriam J.
Published: November 2012

The efficiency of hepatitis C virus (HCV) transmission by sexual activity remains controversial. We conducted a cross-sectional study of HCV-positive subjects and their partners to estimate the risk for HCV infection among monogamous heterosexual couples. A total of 500 anti–HCV-positive, human immunodeficiency virus–negative index subjects and their long-term heterosexual partners were studied. Couples were interviewed separately for lifetime risk factors for HCV infection, within-couple sexual practices, and sharing of personal grooming items. Blood samples were tested for anti-HCV, HCV RNA, and HCV genotype and serotype. Sequencing and phylogenetic analysis determined the relatedness of virus isolates among genotype-concordant couples. The majority of HCV-positive index subjects were non-Hispanic white, with a median age of 49 years (range, 26–79 years) and median of 15 years (range, 2–52 years) of sexual activity with their partners. Overall, HCV prevalence among partners was 4% (n = 20), and nine couples had concordant genotype/serotype. Viral isolates in three couples (0.6%) were highly related, consistent with transmission of virus within the couple. Based on 8,377 person-years of follow-up, the maximum incidence rate of HCV transmission by sex was 0.07% per year (95% confidence interval, 0.01–0.13) or approximately one per 190,000 sexual contacts. No specific sexual practices were related to HCV positivity among couples.

Conclusion
: The results of this study provide quantifiable risk information for counseling long-term monogamous heterosexual couples in which one partner has chronic HCV infection. In addition to the extremely low estimated risk for HCV infection in sexual partners, the lack of association with specific sexual practices provides unambiguous and reassuring counseling messages. (Hepatology 2013)
A randomized trial comparing conventional cytology to liquid‐based cytology and computer assistance
Authors: Klug Stefanie J. , Neis Klaus J. , Harlfinger Werner , Malter Armin , König Jochem , Spieth Sibylle , Brinkmann‐Smetanay Friederike , Kommoss Friedrich , Weyer Veronika , Ikenberg Hans
Published: November 2012

Liquid‐based cytology (LBC) has replaced conventional cytology (CC) for cervical cancer screening in some countries. However, it remains unclear whether LBC is superior to CC. A randomized controlled trial was conducted between August 2007 and March 2009 in Germany to compare LBC, alone and in combination with computer‐assisted imaging technology (CAS), to CC in the detection of histologically confirmed cervical intraepithelial neoplasia (CIN). The main outcome measures were detection rates, relative sensitivities, positive predictive values (PPVs) and relative PPVs comparing LBC without and with CAS to CC. Primary histological outcome was CIN2 or higher. Included were 20,627 women participating in opportunistic cervical cancer screening at 20 gynecologic practices. The practices were randomized weekly to use LBC (n = 11,331) or CC (n = 9,296). Patients with positive findings were invited to expert colposcopy. The relative sensitivity of LBC versus CC using the CIN2+ cut‐off was 2.74 (95% confidence interval [CI] 1.66–4.53). The relative sensitivity of LBC/CAS versus CC for CIN2+ was 3.17 (95% CI 1.94–5.19). The PPV of LBC and CC for CIN2+ was 48% and 38%, respectively. The PPV ratio did not differ significantly from unity. Differences between LBC and CC were smaller in some sensitivity and subgroup analyses; however, relative sensitivity of LBC remained increased. LBC without and with CAS compared with CC under the field conditions of an opportunistic screening system had a significantly higher sensitivity for the detection of CIN without deterioration of PPVs. Additional use of CAS did not further improve sensitivity of LBC. © 2012 Wiley Periodicals, Inc.
Ag nanorod based surface‐enhanced Raman spectroscopy applied to bioanalytical sensing
Authors: Negri Pierre , Dluhy Richard A.
Published: November 2012

Recent progress in substrate nanofabrication has led to the development of Ag nanorod arrays as uniform, reproducible, large area SERS‐active substrates with high signal enhancement. These novel nanostructures fabricated by oblique angle vapor deposition (OAD) offer a robust platform for the rapid detection of biological agents and open new perspectives for the development and integration of biomedical diagnostic for clinical and therapeutic applications. Ag nanorod arrays have been investigated as SERS‐active substrates for the detection and identification of pathogens, including bacteria and viruses, as well as to evaluate the potential of this biosensing platform for bio‐recognition of high affinity events using oligonucleotide‐modified substrates. This review summarizes the various nanostructured substrates designed for SERS‐based applications, highlights the nanofabrication methodology used to produce Ag nanorod arrays, outlines their morphological and physical properties, and provides a summary of the most recent uses of these substrates for clinical diagnostic and biomedical applications. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
PICVib: An accurate, fast, and simple procedure to investigate selected vibrational modes at high theoretical levels
Authors: Santos Marcus V. P. dos , Aguiar Eduardo C. , Silva João Bosco P. da , Longo Ricardo L.
Published: November 2012

A new approach Procedure for Investigating Categories of Vibrations (PICVib) for estimating vibrational frequencies of selected modes using only the structure and energy calculations at a more demanding computational level is presented and explored. The PICVib has an excellent performance at only a small fraction of the computational demand required for a complete analytical calculation. The errors are smaller than ca. 0.5% when DFT functionals are combined with high level ab initio methods. The approach is general because it can use any quantum chemical program and electronic structure method. It is very robust because it was validated for a wide range of frequency values (ca. 20–4800 cm–1) and systems: XH3 (D3h) with X = B, Al, Ga, N, P, As, O, S, and Se, YH4 (D4h) with Y = C, Si, and Ge, conformers of RDX, SN2 and E2 reactions, [W(dppe)2(NNC5H10)] complex, carbon nanotubes, and hydrogen‐bonded complexes including guanine‐cytosine pair. © 2012 Wiley Periodicals, Inc.
Hardness potential derivatives and their relation to Fukui indices
Authors: Saha Soumen , Bhattacharjee Rituparna , Roy Ram Kinkar
Published: November 2012

A simple as well as easy to compute formalism of hardness potential (originally defined by Parr and Gazquez, J. Phys. Chem., 1993, 97, 3939) is presented. Use of hardness potential formally resolves the N‐dependence problem of local hardness. However, the hardness potential cannot describe the intra as well as intermolecular reactivity sequence satisfactorily of some chemical systems. The corresponding electrophilic [Δ+h(k)] and nucleophilic [Δ−h(k)] variants of the hardness potential are also developed, which measure the reactivity toward a nucleophilic (i.e., Nu−) and an electrophilic (i.e., El+) reagent, respectively. Interestingly, these two variants of the hardness potential lead to the right and left derivatives of Fukui potential. The proposed reactivity descriptors correctly predict the expected reactivity trends in the chosen systems. It has also been illustrated that the values of the variants of hardness potential (or Fukui potential) at the atomic nucleus have the ability to explain the intramolecular reactivity of biologically active indole derivatives. The future scope of applications as well as limitations of the proposed descriptors is also highlighted. © 2012 Wiley Periodicals, Inc.
Ab initio calculations of the Ar–ethane intermolecular potential energy surface using bond function basis sets
Authors: Zhang Jian‐Dong , Li Shu‐Jin , Tao Fu‐Ming
Published: November 2012

The intermolecular potential energy surface (PES) of argon with ethane has been studied by ab initio calculations at the levels of second‐order Møller–Plesset perturbation (MP2) theory and coupled‐cluster theory with single, double, and noniterative triple configurations (CCSD(T)) using a series of augmented correlation‐consistent basis sets. Two sets of bond functions, bf1 (3s3p2d) and bf2 (6s6p4d2f), have been added to the basis sets to show a dramatic and systematic improvement in the convergence of the entire PES. The PES of Ar–ethane is characterized by a global minimum at a near T‐shaped configuration with a well depth of 0.611 kcal mol−1, a second minimum at a collinear configuration with a well depth of 0.456 kcal mol−1, and a saddle point connecting the two minima. It is shown that an augmented correlation‐consistent basis set with a set of bond functions, either bf1 or bf2, can effectively produce results equivalent to the next larger augmented correlation‐consistent basis set, that is, aug‐cc‐pVDZ‐bf1 ≈ aug‐cc‐pVTZ, aug‐cc‐pVTZ‐bf1 ≈ aug‐cc‐pVQZ. Very importantly, the use of bond functions improves the PES globally, resulting accurate potential anisotropy. Finally, MP2 method is inadequate for accurate calculations, because it gives a potentially overestimated well depth and, more seriously, a poor potential anisotropy. © 2012 Wiley Periodicals, Inc.
SEM‐EDX, water absorption, and wetting capability studies on evaluation of the influence of nano‐zinc oxide as additive to paraloid B72 solutions used for wooden artifacts consolidation
Authors: Tuduce Trǎistaru Ana‐Adriana , Crina Anca Sandu Irina , Cristina Timar Maria , Lucia Dumitrescu Georgeta , Sandu Ion
Published: November 2012

Consolidation of frail, degraded wood is a key issue of wooden cultural heritage conservation. Paraloid B72 is one of the most often used consolidant in conservation practice. The present research aimed at formulating stable consolidation solutions of Paraloid B72 with ZnO nano‐additives and at determining the influence of these additives on the penetration pathways, retention of the consolidation material into wood and on the water behavior of the treated wood. The experiments were performed on sound samples of aspen (Populus tremula). The addition of nano‐ZnO slightly increased the uptake and retention of the consolidant within the wooden structure and led to hydrophobic surfaces. However, the influence of nano‐ZnO additives to the water absorption was not conclusive. Scanning Electron Microscope coupled with an EDX Detector investigation proved vessels, fibers, and interconnecting pits as main pathways of consolidant penetration into the wooden structure as well as the presence and distribution of nano‐ZnO. Microsc. Res. Tech., 2013. © 2012 Wiley Periodicals, Inc.
String mitochondria in mouse soleus muscle
Authors: Fujioka Hisashi , Tandler Bernard , Haldar Saptarsi M. , Jain Mukesh K. , Hoppel Charles L.
Published: November 2012

Red myofibers in mouse soleus muscle have two spatially distinct populations of mitochondria: one where these organelles are disposed in large clusters just inside the sarcolemma and the other situated between the myofibrils. In most cases, the interfibrillar mitochondria (IFM), which are much smaller than the subsarcolemmal ones (SSM), are arranged as pairs, with each member on opposite sides of the Z‐line. In some myofibers, the IFM have fused end‐to‐end to form greatly elongated organelles, which we call “string mitochondria.” Although narrow, these can be many sarcomeres in length. The SSM do not form string mitochondria. Most of the string mitochondria exhibit many instances of “pinching,” a process involved in mitochondrial division. Elements of sarcoplasmic reticulum are intimately involved with each mitochondrial membrane invagination. It appears as if the fusion:fission balance of IFM in the soleus muscle is slightly out of kilter, with end‐to‐end fusion predominating over fission. Microsc. Res. Tech. 76:237–241, 2013. © 2012 Wiley Periodicals, Inc.