bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physicochemical, crystalline, and thermal properties of native, oxidized, acid, and enzyme hydrolyzed Chinese yam (Dioscorea opposite Thunb) starch
Authors: Xia Li , Wenyuan Gao , Qianqian Jiang , Yanli Wang , Xinhua Guo , Luqi Huang 
Published: June 2011

AbstractNative yam starch was modified by oxidation (with sodium hypochlorite), acid, and enzyme (with gluco‐amylase), respectively. Ash content, fat content, protein, and AM contents were reduced following modifications. All the modifications reduced swelling capacity whereas improved the solubility. The SEM of the native starch showed the presence of large oval or spherical to small irregular‐shaped granules, however, oxidation and hydrolysis caused collapse of the granules. From the XRD, the typical C‐type XRD pattern of the native starch changed to the typical A‐type XRD pattern of the three modified starches. The above results also demonstrated that amorphous region of yam starch granules was preferentially degraded than crystalline region of granules. DSC showed that oxidation and acid/enzyme hydrolysis reduced peak temperature of gelatinization (Tp) of native starch significantly. Enthalpy of gelatinization (ΔH) of oxidation and enzyme starch was reduced but it has no obviously change following acid modification.
Brief Report: Benchmarking Human Pluripotent Stem Cell Markers During Differentiation Into the Three Germ Layers Unveils a Striking Heterogeneity: All Markers Are Not Equal
Authors: Ramirez Jean-Marie , Gerbal-Chaloin Sabine , Milhavet Ollivier , Qiang Bai , Becker Fabienne , Assou Said , Lemaître Jean-Marc , Hamamah Samir , De Vos John 
Published: June 2011

Abstract
Pluripotent stem cells (PSC) are functionally characterized by their capacity to differentiate into all the cell types from the three germ layers. A wide range of markers, the expression of which is associated with pluripotency, has been used as surrogate evidence of PSC pluripotency, but their respective relevance is poorly documented. Here, we compared by polychromatic flow cytometry the kinetics of loss of expression of eight widely used pluripotency markers (SSEA3, SSEA4, TRA-1-60, TRA-1-81, CD24, OCT4, NANOG, and alkaline phosphatase [AP]) at days 0, 5, 7, and 9 after induction of PSC differentiation into cells representative of the three germ layers. Strikingly, each marker showed a different and specific kinetics of disappearance that was similar in all the PSC lines used and for all the induced differentiation pathways. OCT4, SSEA3, and TRA-1-60 were repeatedly the first markers to be downregulated, and their expression was completely lost at day 9. By contrast, AP activity, CD24, and NANOG proteins were still detectable at day 9. In addition, we show that differentiation markers are coexpressed with pluripotency markers before the latter begin to disappear. These results suggest that OCT4, SSEA3, and TRA-1-60 might be better to trace in vitro the emergence of pluripotent cells during reprogramming.
Expression of Tlx in Both Stem Cells and Transit Amplifying Progenitors Regulates Stem Cell Activation and Differentiation in the Neonatal Lateral Subependymal Zone
Authors: Obernier Kirsten , Simeonova Ina , Fila Tatiana , Mandl Claudia , Hölzl-Wenig Gabriele , Monaghan-Nichols Paula , Ciccolini Francesca 
Published: June 2011

Abstract
Niche homeostasis in the postnatal subependymal zone of the lateral ventricle (lSEZ) requires coordinated proliferation and differentiation of neural progenitor cells. The mechanisms regulating this balance are scarcely known. Recent observations indicate that the orphan nuclear receptor Tlx is an intrinsic factor essential in maintaining this balance. However, the effect of Tlx on gene expression depends on age and cell-type cues. Therefore, it is essential to establish its expression pattern at different developmental ages. Here, we show for the first time that in the neonatal lSEZ activated neural stem cells (NSCs) and especially transit-amplifying progenitors (TAPs) express Tlx and that its expression may be regulated at the posttranscriptional level. We also provide evidence that in both cell types Tlx affects gene expression in a positive and negative manner. In activated NSCs, but not in TAPs, absence of Tlx leads to overexpression of negative cell cycle regulators and impairment of proliferation. Moreover, in both cell types, the homeobox transcription factor Dlx2 is downregulated in the absence of Tlx. This is paralleled by increased expression of Olig2 in activated NSCs and glial fibrillary acidic protein in TAPs, indicating that in both populations Tlx decreases gliogenesis. Consistent with this, we found a higher proportion of cells expressing glial makers in the neonatal lSEZ of mutant mice than in the wild type counterpart. Thus, Tlx playing a dual role affects the expression of distinct genes in these two lSEZ cell types.
Zebrafish neurotoxicity from aphantoxins—cyanobacterial paralytic shellfish poisons (PSPs) from Aphanizomenon flos‐aquae DC‐1
Authors: Zhang Delu , Hu Chunxiang , Wang Gaohong , Li Dunhai , Li Genbao , Liu Yongding 
Published: June 2011

AbstractAphanizomenon flos‐aquae (A. flos‐aquae), a cyanobacterium frequently encountered in water blooms worldwide, is source of neurotoxins known as PSPs or aphantoxins that present a major threat to the environment and to human health. Although the molecular mechanism of PSP action is well known, many unresolved questions remain concerning its mechanisms of toxicity. Aphantoxins purified from a natural isolate of A. flos‐aquae DC‐1 were analyzed by high‐performance liquid chromatography (HPLC), the major component toxins were the gonyautoxins1 and 5 (GTX1 and GTX5, 34.04% and 21.28%, respectively) and the neosaxitoxin (neoSTX, 12.77%). The LD50 of the aphantoxin preparation was determined to be 11.33 μg/kg (7.75 μg saxitoxin equivalents (STXeq) per kg) following intraperitoneal injection of zebrafish (Danio rerio). To address the neurotoxicology of the aphantoxin preparation, zebrafish were injected with low and high sublethal doses of A. flos‐aquae DC‐1 toxins 7.73 and 9.28 μg /kg (5.3 and 6.4 μg STXeq/kg, respectively) and brain tissues were analyzed by electron microscopy and RT‐PCR at different timepoints postinjection. Low‐dose aphantoxin exposure was associated with chromatin condensation, cell‐membrane blebbing, and the appearance of apoptotic bodies. High‐dose exposure was associated with cytoplasmic vacuolization, mitochondrial swelling, and expansion of the endoplasmic reticulum. At early timepoints (3 h) many cells exhibited characteristic features of both apoptosis and necrosis. At later timepoints apoptosis appeared to predominate in the low‐dose group, whereas necrosis predominated in the high‐dose group. RT‐PCR revealed that mRNA levels of the apoptosis‐related genes encoding p53, Bax, caspase‐3, and c‐Jun were upregulated after aphantoxin exposure, but there was no evidence of DNA laddering; apoptosis could take place by pathways independent of DNA fragmentation. These results demonstrate that aphantoxin exposure can cause cell death in zebrafish brain tissue, with low doses inducing apoptosis and higher doses inducing necrosis. © 2011 Wiley Periodicals, Inc. Environ Toxicol, 2013.
Recent developments and applications of the CHARMM force fields
Authors: Zhu Xiao , Lopes Pedro E. M. , MacKerell Alexander D. 
Published: June 2011

AbstractEmpirical force fields (FFs) commonly used to describe the condensed‐phase properties of complex systems such as biological macromolecules are continuously being updated. Improvements in quantum mechanical methods used to generate target data, availability of new experimental target data, incorporation of new classes of compounds, and new theoretical developments (e.g., polarizable methods) make FF development a dynamic domain of research. Accordingly, a number of improvements and extensions of the Chemistry at HARvard Molecular Mechanics (CHARMM) FFs have occurred over the years. The objective of the present review is to provide an up‐to‐date overview of the CHARMM FFs. A limited presentation on the historical aspects of FFs will be given, including underlying methodologies and principles, along with a brief description of the strategies used for parameter development. This is followed by information on the CHARMM additive and polarizable FFs, including examples of recent applications of those FFs. © 2011 John Wiley & Sons, Ltd.This article is categorized under:

Molecular and Statistical Mechanics > Molecular Mechanics
Transfer RNA‐derived fragments: origins, processing, and functions
Authors: Sobala Andrew , Hutvagner Gyorgy 
Published: June 2011

AbstractDeep sequencing approaches have revealed multiple types of small RNAs with known and unknown functions. In this review we focus on a recently identified group of small RNAs that are derived from transfer RNAs (tRNAs), tRNA fragments (tRFs). We review the mechanism of their processing and their functions in mammalian cells, and highlight points of possible cross‐talk between tRFs and the canonical small RNA pathway characterized by small interfering RNAs (siRNAs), microRNAs (miRNAs), and Piwi‐interacting RNAs (piRNAs). We also propose a nomenclature that is based on their processing characteristics. WIREs RNA 2011 2 853–862 DOI: 10.1002/wrna.96This article is categorized under:

RNA Processing > tRNA Processing
Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
Metal Complexes of Biologically Important Ligands, CLXXVI.[1] Formation of Peptides within the Coordination Sphere of Metal Ions and of Classical and Organometallic Complexes and Some Aspects of Prebiotic Chemistry
Authors: Beck Wolfgang 
Published: June 2011

AbstractThe formation of peptide bonds in the neighborhood of metal ions is reviewed. The metal ions can function as activating and catalytic groups; they can act as templates. Metal ions can play a role as stabilizing spectators when peptides are formed within their ligands and they are able to protect the amino or carboxylate group of amino acids during peptide synthesis. Some related chemistry of metal‐peptide conjugates is included. This survey represents an attractive combination of coordination, organic, organometallic chemistry and biochemistry and reveals some interesting aspects of prebiotic chemistry.
Two Manganese(II) Complexes with a Bulky Fluorene‐Based Carboxylate Ligand: Syntheses, Crystal Structures, and Luminescent Properties
Authors: Wang Junjie , Shi Yunfeng , Li Sujuan 
Published: June 2011

AbstractTo explore the coordination possibilities of fluorene‐based ligands, two manganese(II) complexes with the ligand 9,9‐dibutyl‐9H‐fluorene‐2,7‐carboxylate (L) were synthesized and characterized: [Mn2(L)2(DMF)3]∞ (1) and [Mn2(L)2(DMF)]∞ (2). X‐ray single‐crystal diffraction analyses show that complex 1 has a two‐dimensional (2D) (4,4) structure, whereas complex 2 consits of a three‐dimensional (3D) (4,5)‐connected topology framework. The results indicate that the steric bulk of the fluorene ring in H2L plays an important role in the formations of 1 and 2. Additional pyridine‐based ligands govern the formation of the final frameworks of 2. Moreover, the luminescent properties of these complexes were briefly investigated.
Carbon Halide Bond Activation of Benzyl Chloride and Benzyl Bromide Using An NHC‐Stabilized Nickel(0) Complex
Authors: Zell Thomas , Radius Udo 
Published: June 2011

AbstractA first example of the application of an NHC‐stabilized nickel complex as a catalyst in Suzuki–Miyaura cross‐coupling reactions of alkyl halides is reported. The complexes trans‐[Ni(iPr2Im)2(X)(CH2Ph)] (X = Cl 2 and Br 3) were prepared from the reactions of benzyl chloride and benzyl bromide and the dinuclear complex [Ni2(iPr2Im)4(COD)] (1). These compounds were fully characterized by elemental analysis, IR spectroscopy, multinuclear NMR spectroscopy, and X‐ray crystallography. Based on these stoichiometric oxidative addition reactions catalytic Suzuki–Miyaura cross‐coupling reactions have been performed. Complex 1 is an effective catalyst for the Suzuki–Miyaura cross‐coupling reaction of benzyl chloride and phenylboronic acid. Quantitative conversion of benzyl chloride with a high selectivity to the cross‐coupling product diphenylmethane was achieved after two hours reaction time using three equivalents phenylboronic acid, three equivalents cesium fluoride and 1.22 mol‐% [Ni2(iPr2Im)4(COD)] (1) as a catalyst.
Syntheses and Molecular Structure of Dinuclear Transition Metal Complexes Bridged by Dipyridylamine Derivative Ligands
Authors: Gupta Gajendra , Park Sunhong , Lee Shim Sung , Kim Jinkwon 
Published: June 2011

AbstractStable dinuclear transition metal complexes,[(η6‐C6H6)2Ru2(L1)Cl2]2+ (1), [(η6‐p‐iPrC6H4Me)2Ru2(L1)Cl2]2+ (2), [(η6‐C6Me6)2Ru2(L1)Cl2]2+ (3), [(η6‐C6H6)2Ru2(L2)Cl2]2+ (4),[(η6‐p‐iPrC6H4Me)2Ru2(L2)Cl2]2+ (5), [(η6‐C6Me6)2Ru2(L2)Cl2]2+ (6), [(η5‐C5Me5)2Rh2(L1)Cl2]2+ (7), [(η5‐C5Me5)2Ir2(L1)Cl2]2+ (8),[(η5‐C5Me5)2Rh2(L2)Cl2]2+ (9), and [(η5‐C5Me5)2Rh2(L2)Cl2]2+ (10), with the bis‐bidentate ligands 1,3‐bis(di‐2‐pyridylaminomethyl)benzene (L1) and 1,4‐bis(di‐2‐pyridylaminomethyl)benzene (L2), which contain two chelating dipyridylamine units connected by an aromatic spacer, were synthesized. The cationic dinuclear complexes were isolated as their hexafluorophosphate salts and characterized by using a combination of NMR, IR, and UV/Vis spectroscopic methods and mass spectrometry. The solid‐state structure of complex 8 as a representative was determined by X‐ray structure analysis.
Effect of Metal Ions on the Structures of Coordination Polymers Based on Biphenyl‐2,2′,4,4′‐Tetracarboxylate
Authors: Wang Ji‐Jiang , Lv Jun‐Fang , Cao Pei‐Xiang , Zhang Mei‐Li , Gao Lou‐Jun , Lv Lei , Ren Yi‐Xia , Hou Xiang‐Yang 
Published: June 2011

AbstractTwo new coordination polymers, {[Cd2(btc)(2,2′‐bpy)2]·H2O}n (1) and [Zn2(btc)(2,2′‐bpy)(H2O)]n (2) (H4btc = biphenyl‐2,2′,4,4′‐tetracarboxylic acid, 2,2′‐bpy = 2,2′‐bipyridine), were synthesized hydrothermally under similar conditions and characterized by elemental analysis, IR spectra, TGA, and single‐crystal X‐ray diffraction analysis. In complexes 1 and 2, the (btc)4– ligand acts as connectors to link metal ions to give a 2D bilayer network of 1 and a 3D metal‐organic framework of 2, respectively. The differences in the structures are induced by diverging coordination modes of the (btc)4– ligand, which can be attributed to the difference metal ions in sizes. The results indicate that metal ions have significant effects on the formation and structures of the final complexes. Additionally, the fluorescent properties of the two complexes were also studied in the solid state at room temperature.
Li35Ln9Si30N59O2F with Ln = Ce, Pr – Highly Condensed Nitridosilicates
Authors: Lupart Saskia , Durach Dajana , Schnick Wolfgang 
Published: June 2011

AbstractThe isotypic nitridosilicates Li35Ln9Si30N59O2F (Ln = Ce, Pr) were synthesized by reaction of LnF3 and LiN3 with Si(NH)2 in liquid lithium flux in weld shut tantalum ampoules. The crystal structures of the isotypic compounds were solved and refined on the basis of single‐crystal X‐ray diffraction (P$\bar{3}$c1 (no. 165), Z = 2; Li35Ce9Si30N59O2F:, a = 1479.9(2), c = 1538.3(3) pm, R1 = 0.0526, 1671 data, 175 parameters; Li35Pr9Si30N59O2F: a = 1477.3(2), c = 1533.9(3) pm, R1 = 0.0441, 1331 data, 175 parameters). The silicate substructure represents a 3D network of all side corner sharing SiN4 tetrahedra. At one discrete and not condensed mixed anion position an atomic ratio O:F = 2:1 is assumed in order to achieve charge neutrality. With an atomic ratio Si:N = 30:59, the degree of condensation of the silicate substructure is slightly above κ = 1/2. Accordingly, there are triply crosslinking N[3] atoms in the silicate substructure. The obtained structures prove that by employing the lithium flux technique not only nitridosilicates with a low degree of condensation can be obtained by using rather mild reaction conditions at low temperatures. Lattice energy calculations (MAPLE) and EDX measurements confirmed the electrostatic bonding interactions and the chemical composition.
Risk Factors for Stroke During Surgery for Carotid Body Tumors
Authors: Gwon Jun Gyo , Kwon Tae‐Won , Kim Hyangkyoung , Cho Yong‐Pil 
Published: June 2011

AbstractBackgroundRemoving carotid body tumors (CBTs) carry the risk of operative morbidity including stroke. We evaluated the risk factors for stroke related to resection of CBTs.MethodsWe retrospectively reviewed the records of 17 procedures performed on 16 patients with CBT between March 1998 and September 2008.ResultsThe study population consisted of 5 men and 11 women, of mean age 41.7 years (range: 23–62 years). At surgery, 8 cases (47%) were localized and classified as Shamblin class I, 4 cases (23.5%) as class II, and 5 cases (29.4%) as class III. Four patients had postoperative stroke (23.5%), with Shamblin classification related to the incidence of stroke (P = 0.041). In contrast, neither tumor size (P = 0.412) nor heparin injection before internal carotid artery (ICA) manipulation (P = 0.538) was associated with stroke. Although preoperative embolization of the tumor feeder did not significantly reduce the stroke rate (P = 0.579), early external carotid artery (ECA) division in patients with class II and III tumors was effective (P = 0.008). Internal carotid artery (ICA) manipulation, including reconstruction, ligation, and repair of injury, significantly increased the incidence of stroke (P = 0.029), as did ICA ligation without reconstruction (P = 0.044).ConclusionsInternal carotid artery manipulation, including reconstruction, ligation, and repair of injury, significantly increased the incidence of stroke. For uncomplicated CBT resection, careful preoperative planning, especially for patients with class II and III tumors, is mandatory to avoid inadvertent ICA manipulation necessitated by bleeding. Early ECA division during the operation rather than preoperative percutaneous embolization in patients with class II and III tumors was significantly effective in reducing the stroke rate
Liver Resection of Colorectal Liver Metastases in Elderly Patients
Authors: Kulik U. , Framke T. , Großhennig A. , Ceylan A. , Bektas H. , Klempnauer J. , Lehner F. 
Published: June 2011

AbstractBackgroundThe percentage of elderly patients with colorectal liver metastases (CLM) has increased. Liver resection remains the only curative therapy; data evaluating the outcome in this age group is limited. Aim of the present study was to determine if postoperative morbidity, mortality, and other independent predictors influence survival in patients ≥70 years undergoing liver resection for CLM.MethodsClinical data on primary tumor and metastases of 939 patients after liver resection for CLM between 1994 and 2008 were retrospectively collected and subdivided in three age‐groups (≥70, 40–69, <40). Independent predictors of survival were evaluated with overall and age‐specific univariate and multivariate Cox regression models.ResultsA total of 939 patients underwent liver resection for CLM, 20.3% aged ≥70 years. Overall postoperative mortality and morbidity were 1.08 and 14.82%, revealing no age‐related differences. With 5‐year survival of 31.8% in the elderly and 37.5% in the mid‐age population, age ≥70 years was linked with decreased survival (Hazard Ratio [HR] = 1.305; P = 0.0186). Multivariate overall analyses showed size of CLM > 50 mm (HR = 1.376; P = 0.0060), a high amount of transfusion during surgery (HR = 1.676; P = 0.0110), duration of surgery >210 min (HR = 1.241; P = 0.0322), primary UICC (International Union Against Cancer) stage IV (HR = 2.297; P < 0.0001), and performance of repeat resections (HR = 0.652; P = 0.0107) as independent predictors of survival. In the elderly group, effects of UICC IV (HR = 3.260; P = 0.0148) and high numbers of transfusions (HR = 3.647; P = 0.0129) were confirmed; the others did not show statistical significance.ConclusionsResection of CLM at older age is feasible with morbidity and mortality rates similar to those in younger patients. Although age ≥70 was shown to be associated with poorer overall outcome, reasonable 5‐year survival was observed.
Multidisciplinary Discussion and Management of Rectal Cancer: A Population‐based Study
Authors: Swellengrebel H. A. M. , Peters E. G. , Cats A. , Visser O. , Blaauwgeers H. G. T. , Verwaal V. J. , van Velthuysen M. L. , Cense H. A. , Bruin S. C. , Marijnen C. A. M. 
Published: June 2011

AbstractBackgroundThe purpose of the present study was to evaluate the value of discussing rectal cancer patients in a multidisciplinary team (MDT).MethodsAll treated rectal cancer patients (>T1M0) diagnosed in 2006–2008 were included. According to the national guidelines, neoadjuvant (chemo)radiotherapy should be given to all rectal cancer patients. Patients were scored as “discussed” (MDT+) only if documented proof was available. The primary endpoint was the number of positive circumferential resection margins (CRM ≤1 mm).ResultsOf the 275 patients included, 210 were analyzed (exclusions: (recto)sigmoid tumor, acute laparotomy, and inoperability). Neoadjuvant treatment was applied in 174 (83%) patients and followed by total mesorectal excision in 171 (81%) patients. Patients considered not to require downstaging, received short‐course radiotherapy (SCRT) (n = 116) or no radiotherapy (no RT) (n = 36), whereas 58 more advanced patients received chemoradiotherapy (CRT). The MDT discussion took place in 116 cases (55%). In the MDT+ group an MRI was used more often (p = 0.001) and TNM staging was more complete (p < 0.001). The proportion of patients with advanced disease was higher in the MDT+ group (88% ≥T3/N+ versus 68%; p = 0.001). The overall CRM+ rate was 13% and did not differ between the MDT+ and the MDT− group (p = 0.392). In patients receiving SCRT or no RT, the CRM+ rate was 10%, whereas the rate was 20% for patients receiving CRT.ConclusionsAlthough no difference in CRM+ rate was found for those patients who were discussed and those who were not, our results demonstrate room for improvement, especially in the selection of patients for SCRT or no RT. We advocate standardized documentation of treatment decisions and pathology reports.
Facilitation of plant species richness and endangered species by a tussock grass in a moist tall grassland revealed using hierarchical Bayesian analysis
Authors: Wang Zhe , Nishihiro Jun , Washitani Izumi 
Published: June 2011

AbstractUsing hierarchical Bayesian analysis, we tested the hypothesis that a perennial tussock grass, Ischaemum aristatum var. glaucum, facilitates the species diversity of vegetation and the regeneration of individual native vascular plants in Ukishima Marsh, a moist tall grassland of eastern Japan. We analyzed microscale distribution patterns of sympatric plant species in response to ground height. Both the species richness of the whole plant assemblage and the occurrence of many native vascular plants, including two endangered species, were positively correlated with ground elevation, which was directly mediated by I. aristatum var. glaucum tussocks and/or the occurrence of mosses on tussocks. Susceptibility to late spring inundation of microsites on the tussocks was significantly lower than that on bare ground. These results suggest that the facilitation by I. aristatum var. glaucum contributes to maintaining the high species richness of the marsh. Consideration of the facilitation among native vascular plants is necessary for establishing sound conservation plans of wetland vegetation.