julilili42/papers huggingface dataset:
Evaluation of enantioselective gas chromatography for the determination of minute deviations from racemic composition of α‐amino acids with emphasis on tyrosine: Accuracy and precision of the method
2007-03-26

Abstract Whereas the determination of high enantiomeric fractions (EF) of chiral compounds is very well established, the accurate determination of small deviations from racemic compositions has not yet received much attention despite its relevance to studies dealing with the origin of homochirality, where only small initial enantiomeric bias is expected. Racemic samples of representative α‐amino acids were derivatized as N ‐( O,S )‐trifluoroacetyl/ethylesters and analyzed by enantioselective gas chromatography (GC) on fused silica capillaries coated with the chiral stationary phases (CSPs) Chirasil‐ D ‐Val, Chirasil‐ L ‐Val, and Lipodex E with GC/FID and GC/MS detection. The validation (accuracy and precision) of the determination of the enantiomeric fraction EF of the D ‐enantiomer in racemic or near‐racemic compositions for 10 DL ‐α‐amino acids obtained from commercial sources has been carried out. Emphasis is given to DL ‐tyrosine, the enantiomers of which have recently been claimed to show different crystallization properties. Values of EF obtained from GC measurements using CSPs were compared with those from CE using chiral mobile phase additives. While the precision of the GC method is generally better than 0.08% for all DL ‐α‐amino acids studied, accuracy (trueness) of determination of amino acids with polar side chains is poorer than expected from the precision as a result of systematic errors. The accuracy determined relied on measurements on two oppositely configurated CSPs. Chirality, 2007. © 2007 Wiley‐Liss, Inc.
Biodegradable magnesium scaffolds: Part 1: Appropriate inflammatory response
2007-03-27

Abstract Current tissue engineering strategies focus on the replacement of pathologically altered tissues by the transplantation of cells in combination with supportive biocompatible scaffolds. Scaffolds for tissue engineering strategies in musculoskeletal research require an appropriate mechanical stability. In recent studies, considerable attention has thus been given to magnesium alloys as biodegradable implants. The aim of this study was to characterize the biocompatibility of magnesium scaffolds by the inflammatory host response. Open porous scaffolds made of the magnesium alloy AZ91D were implanted into the distal femur condyle of rabbits and were compared to autologous bone, which was transplanted into the contralateral condyle in a 3 and 6 months follow‐up group. After 3 months, magnesium scaffolds were already largely degraded and most of the original magnesium alloy has disappeared. Concomitantly, a fibrous capsule enclosed the operation site. Histological analysis revealed that the magnesium scaffolds caused no significant harm to their neighboring tissues. This study shows that even fast degrading magnesium scaffolds show a good biocompatibility and react in vivo with an appropriate inflammatory host response. Magnesium alloy based implants are therefore a very promising approach in the development of mechanically suitable and open porous scaffolds for the replacement of subchondral bone in cartilage tissue engineering. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res 2007
Sedimentary architecture and 3D ground‐penetrating radar analysis of gravelly meandering river deposits (Neckar Valley, SW Germany)
2007-03-27

Abstract Sedimentological outcrop analysis and sub‐surface ground‐penetrating radar (GPR) surveys are combined to characterize the three‐dimensional sedimentary architecture of Quaternary coarse‐grained fluvial deposits in the Neckar Valley (SW Germany). Two units characterized by different architectural styles are distinguished within the upper part of the gravel body, separated by an erosional unconformity: (i) a lower unit dominated by trough‐shaped depositional elements with erosional, concave‐up bounding surfaces that are filled by cross‐bedded sets of mainly openwork and filled framework gravel; and (ii) an upper unit characterized by gently inclined sheets of massive and openwork gravels with thin, sandy interlayers that show lateral accretion on a lower erosional unconformity. The former is interpreted as confluence scour pool elements formed in a multi‐channel, possibly braided river system, the latter as extensive point bar deposits formed by the lateral migration of a meandering river channel. The lateral accretion elements are locally cut by chute channels mainly filled by gravels rich in fines, and by fine‐grained abandoned channel fills. The lateral accretion elements are associated with gravel dune deposits characterized by steeply inclined cross‐beds of alternating open and filled framework gravel. Floodplain fines with a cutbank and point bar morphology cover the gravel deposits. The GPR images, revealing the three‐dimensional geometries of the depositional elements and their stacking patterns, confirm a change in sedimentary style between the two stratigraphic units. The change occurred at the onset of the Holocene, as indicated by 14 C‐dating of wood fragments, and is related to a re‐organization of the fluvial system that probably was driven by climatic changes. The integration of sedimentological and GPR results highlights the heterogeneity of the fluvial deposits, a factor that is important for modelling groundwater flow in valley‐fill aquifers.
SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data
2007-03-28

Abstract Motivation: Knowing the localization of a protein within the cell helps elucidate its role in biological processes, its function and its potential as a drug target. Thus, subcellular localization prediction is an active research area. Numerous localization prediction systems are described in the literature; some focus on specific localizations or organisms, while others attempt to cover a wide range of localizations. Results: We introduce SherLoc, a new comprehensive system for predicting the localization of eukaryotic proteins. It integrates several types of sequence and text-based features. While applying the widely used support vector machines (SVMs), SherLoc’s main novelty lies in the way in which it selects its text sources and features, and integrates those with sequence-based features. We test SherLoc on previously used datasets, as well as on a new set devised specifically to test its predictive power, and show that SherLoc consistently improves on previous reported results. We also report the results of applying SherLoc to a large set of yet-unlocalized proteins. Availability: SherLoc, along with Supplementary Information, is available at: http://www-bs.informatik.uni-tuebingen.de/Services/SherLoc/ Contact: shatkay@cs.queensu.ca Supplementary information: Supplementary data are available at Bioinformatics online.
A confusing world: what to call histology of three‐dimensional tumour margins?
2007-03-28

Abstract Complete three‐dimensional histology of excised skin tumour margins has a long tradition and, unfortunately, a multitude of names as well. Mohs, who introduced it, called it ‘microscopically controlled surgery’. Others have described it as ‘micrographic surgery’, ‘Mohs’ micrographic surgery’, or simply ‘Mohs’ surgery’. Semantic confusion became truly rampant when variant forms, each useful in its own way for detecting subclinical outgrowths of malignant skin tumours, were later introduced under such names as histographic surgery, systematic histologic control of the tumour bed, histological control of excised tissue margins, the square procedure, the perimeter technique, etc. All of these methods are basically identical in concept. All involve complete, three‐dimensional histological visualization and evaluation of excision margins. Their common goal is to detect unseen tumour outgrowths. For greater clarity, the authors of this paper recommend general adoption of ‘3D histology’ as a collective designation for all the above methods. As an added advantage, 3D histology can also be used in other medical disciplines to confirm true R0 resection of, for example, breast cancer or intestinal cancer.
Discovery of a point-like very-high-energy γ-ray source in Monoceros
2007-03-29

Aims.The complex Monoceros Loop SNR/Rosette Nebula region contains several potential sources of very-high-energy (VHE) -ray emission and two as yet unidentified high-energy EGRET sources. Sensitive VHE observations are required to probe acceleration processes in this region.\\nMethods.The HESS telescope array has been used to search for very high-energy -ray sources in this region. CO data from the NANTEN telescope were used to map the molecular clouds in the region, which could act as target material for -ray production via hadronic interactions.\\nResults.We announce the discovery of a new -ray source, HESS J0632+057, located close to the rim of the Monoceros SNR. This source is unresolved by HESS and has no clear counterpart at other wavelengths but is possibly associated with the weak X-ray source 1RXS J063258.3+054857, the Be-star MWC 148 and/or the lower energy -ray source 3EG J0634+0521. No evidence for an associated molecular cloud was found in the CO data.
Antitumor effects of arsenic trioxide alone and in combination with pro-oxidants, Akt-inhibitors and sirolimus on transformed thyroid cells in vitro
2007-03-29

Objectives: For a higher efficacy of radioiodine treatment of metastasized differentiated thyroid carcinomas substances that increase iodide uptake are needed. Since not all tumors respond well to retinoic acid the action of arsenic trioxide, effective in promyelocytic leukemia patients relapsed after retinoic acid treatment, alone and in various combinations was evaluated in follicular and papillary thyroid carcinoma cell lines (FTC 238, CGTH-W-1, ONCO-DG-1).
Plant proton pumps
2007-03-30

Chemiosmotic circuits of plant cells are driven by proton (H + ) gradients that mediate secondary active transport of compounds across plasma and endosomal membranes. Furthermore, regulation of endosomal acidification is critical for endocytic and secretory pathways. For plants to react to their constantly changing environments and at the same time maintain optimal metabolic conditions, the expression, activity and interplay of the pumps generating these H + gradients have to be tightly regulated. In this review, we will highlight results on the regulation, localization and physiological roles of these H + ‐ pumps, namely the plasma membrane H + ‐ATPase, the vacuolar H + ‐ATPase and the vacuolar H + ‐PPase.
Coordination of three and four Cu(I) to the α− and β‐domain of vertebrate Zn‐metallothionein‐1, respectively, induces significant structural changes
2007-03-30

Vertebrate metallothioneins are found to contain Zn(II) and variable amounts of Cu(I), in vivo, and are believed to be important for d 10 ‐metal control. To date, structural information is available for the Zn(II) and Cd(II) forms, but not for the Cu(I) or mixed metal forms. Cu(I) binding to metallothionein‐1 has been investigated by circular dichroism, luminescence and 1 H NMR using two synthetic fragments representing the α‐ and the β‐domain. The 1 H NMR data and thus the structures of Zn 4 α metallothionein (MT)‐1 and Zn 3 βMT‐1 were essentially the same as those already published for the corresponding domains of native Cd 7 MT‐1. Cu(I) titration of the Zn(II)‐reconstituted domains provided clear evidence of stable polypeptide folds of the three Cu(I)‐containing α‐ and the four Cu(I)‐containing β‐domains. The solution structures of these two species are grossly different from the structures of the starting Zn(II) complexes. Further addition of Cu(I) to the two single domains led to the loss of defined domain structures. Upon mixing of the separately prepared aqueous three and four Cu(I) loaded α‐ and β‐domains, no interaction was seen between the two species. There was neither any indication for a net transfer of Cu(I) between the two domains nor for the formation of one large single Cu(I) cluster involving both domains.
Hypomethylation in the 11p15 telomeric imprinting domain in a patient with Silver–Russell syndrome with a CSH1 deletion (17q24) renders a functional role of this alteration unlikely
2007-03-30

Silver–Russell syndrome (SRS) is a clinical and genetic heterogeneous malformation syndrome. Patients show intrauterine and postnatal growth retardation (<3rd centile), and numerous additional dysmorphisms such as a relative macrocephaly, a small triangular face, a prominent forehead, clinodactyly V and asymmetry of head, limbs and trunk (for a review, see Hitchins et al 1). Several genetic disturbances have meanwhile been described, among them cytogenetic aberrations affecting different chromosomes and maternal uniparental disomy of chromosome 7 in 7–10% of cases. Epimutations of the telomeric imprinting centre region 1 (ICR1) in 11p15 can be detected in at least 30% of cases (for a review, see Eggermann ...
The DELLA Domain of GA INSENSITIVE Mediates the Interaction with the GA INSENSITIVE DWARF1A Gibberellin Receptor ofArabidopsis
2007-04-01

Abstract Gibberellic acid (GA) promotes seed germination, elongation growth, and flowering time in plants. GA responses are repressed by DELLA proteins, which contain an N-terminal DELLA domain essential for GA-dependent proteasomal degradation of DELLA repressors. Mutations of or within the DELLA domain of DELLA repressors have been described for species including Arabidopsis thaliana, wheat (Triticum aestivum), maize (Zea mays), and barley (Hordeum vulgare), and we show that these mutations confer GA insensitivity when introduced into the Arabidopsis GA INSENSITIVE (GAI) DELLA repressor. We also demonstrate that Arabidopsis mutants lacking the three GA INSENSITIVE DWARF1 (GID1) GA receptor genes are GA insensitive with respect to GA-promoted growth responses, GA-promoted DELLA repressor degradation, and GA-regulated gene expression. Our genetic interaction studies indicate that GAI and its close homolog REPRESSOR OF ga1-3 are the major growth repressors in a GA receptor mutant background. We further demonstrate that the GA insensitivity of the GAI DELLA domain mutants is explained in all cases by the inability of the mutant proteins to interact with the GID1A GA receptor. Since we found that the GAI DELLA domain alone can mediate GA-dependent GID1A interactions, we propose that the DELLA domain functions as a receiver domain for activated GA receptors.
The Etiopathogenesis of Parkinson Disease and Suggestions for Future Research. Part I
2007-04-01

We are at a critical juncture in our knowledge of the etiology and pathogenesis of Parkinson disease (PD). It is clear that PD is not a single entity simply resulting from a dopaminergic deficit; rather it is most likely caused by a combination of genetic and environmental factors. Although there is extensive new information on the etiology and pathogenesis of PD, which may advance its treatment, new syntheses of this information are needed. The second part of this two-part, state-of-the-art review by leaders in PD research critically examines the research field to identify areas for which new knowledge and ideas might be helpful for treatment purposes. Topics reviewed in Part II are genetics, animal models, and oxidative stress.
MAXIMUM SPECIES RICHNESS AT INTERMEDIATE FREQUENCIES OF DISTURBANCE: CONSISTENCY AMONG LEVELS OF PRODUCTIVITY
2007-04-01

Development of a mechanistic understanding and predictions of patterns of biodiversity is a central theme in ecology. One of the most influential theories, the intermediate disturbance hypothesis (IDH), predicts maximum diversity at intermediate levels of disturbance frequency. The dynamic equilibrium model (DEM), an extension of the IDH, predicts that the level of productivity determines at what frequency of disturbance maximum diversity occurs. To test, and contrast, the predictions of these two models, a field experiment on marine hard-substratum assemblages was conducted with seven levels of disturbance frequency and three levels of nutrient availability. Consistent with the IDH, maximum diversity, measured as species richness, was observed at an intermediate frequency of disturbance. Despite documented effects on productivity, the relationship between disturbance and diversity was not altered by the nutrient treatments. Thus, in this system the DEM did not improve the understanding of patterns of diversity compared to the IDH. Furthermore, it is suggested that careful consideration of measurements and practical definitions of productivity in natural assemblages is necessary for a rigorous test of the DEM.
In vitro susceptibility of Staphylococcus aureus to thrombin-induced platelet microbicidal protein-1 (tPMP-1) is influenced by cell membrane phospholipid composition and asymmetry
2007-04-01

Thrombin-induced platelet microbicidal proteins (e.g. tPMP-1) are small cationic peptides released from mammalian platelets. As the cytoplasmic membrane (CM) is a primary target of tPMPs, distinct CM characteristics are likely to affect the cells' susceptibility profiles. In Staphylococcus aureus, CM surface charge and hydrophobicity are principally determined by the content and distribution of its three major phospholipid (PL) constituents: negatively charged phosphatidylglycerol (PG) and cardiolipin (CL) and positively charged lysyl-PG (LPG). PL composition profiles, and inner vs outer CM leaflet PL distributions, were compared in an isogenic tPMP-susceptible (tPMP(S)) and -resistant (tPMP(R)) S. aureus strain pair (ISP479C vs ISP479R respectively). All PLs were asymmetrically distributed between the outer and inner CM leaflets in both strains. However, in ISP479R, the outer CM leaflet content of LPG was significantly increased vs ISP479C (27.3+/-11.0 % vs 18.6+/-7.0 % respectively; P=0.05). This observation correlated with reduced binding of the cationic proteins cytochrome c, poly-L-lysine, tPMP-1 and the tPMP-1-mimetic peptide, RP1, to tPMP-1(R) whole cells and to model liposomal CMs with LPG content and distribution similar to that of tPMP-1(R) strains. Collectively, selected CM parameters correlated with reduced staphylocidal capacities of tPMP-1 against certain S. aureus strains, including relative increases in outer CM leaflet positive charge and reduced surface binding of cationic molecules. These findings offer new insights into mechanisms of antimicrobial peptide susceptibility and resistance in S. aureus.
Assessing intraindividual variability in sustained attention: reliability, relation to speed and accuracy, and practice effects
2007-04-01

We investigated the psychometric properties of competing measures of sustained attention. 179 subjects were assessed twice within seven day&amp;apos;s time with a test designed to measure sustained atten-tion, or concentration, respectively. In addition to traditional performance indices [i.e., speed (MRT) and accuracy (E%)], we evaluated two intraindividual response time (RT) variability measures: standard deviation (SDRT) and coefficient of variation (CVRT). For the overall test, both indices were reliable. SDRT showed good to acceptable retest reliability for all subtests. For CVRT, retest reliability coeffi-cients ranged from very good to not satisfactory. While the reversed-word recognition test proved highly reliable, the mental calculation test and the arrows test were not sufficiently reliable. CVRT was only slightly correlated but SDRT was highly correlated with MRT. In contrast to substantial practice gains for MRT, SDRT and E%, only CVRT proved to be stable. In conclusion, CVRT appears to be a poten-tial index for assessing performance variability: it is reliable for the overall test, only moderately corre-lated with speed, and virtually not affected by practice. However, before applying CVRT in practical assessment settings, additional research is required to elucidate the impact of task-specific factors on the reliability of this performance measure. Key words: concentration; sustained attention; intraindividual variability; coefficient of variation; reliability; response time
Review of sitagliptin phosphate: a novel treatment for type 2 diabetes
2007-04-01

Sitagliptin (Januvia, Merck Pharmaceuticals) is a dipeptidyl-peptidase inhibitor (DPP-4 inhibitor) that has recently been approved for the therapy of type 2 diabetes. Like other DPP-4 inhibitors its action is mediated by increasing levels of the incretin hormones glucagon-like peptide-1 (GLP-1) and gastric inhibitory polypeptide (GIP). Sitagliptin is effective in lowering HbA1c, and fasting as well as postprandial glucose in monotherapy and in combination with other oral antidiabetic agents. It stimulates insulin secretion when hyperglycemia is present and inhibits glucagon secretion. In clinical studies it is weight neutral. This article gives an overview of the mechanism of action, the pharmacology, and the clinical efficacy and safety of sitagliptin in type 2 diabetes therapy.
Cosmetic Permanent Fillers for Soft Tissue Augmentation
2007-04-01

The normal host response to a cosmetic filler is a weak granulomatous reaction. Interferon and other immunostimulatory medications can lead to an exacerbation of this preexisting low-grade chronic inflammation that is quite similar to interferon-triggered sarcoidosis. This potential long-term risk has medicolegal implications for informed consent and for the potential use of both permanent fillers and interferon.
Gradient-Based Optimization of Kernel-Target Alignment for Sequence Kernels Applied to Bacterial Gene Start Detection
2007-04-01

Biological data mining using kernel methods can be improved by a task-specific choice of the kernel function. Oligo kernels for genomic sequence analysis have proven to have a high discriminative power and to provide interpretable results. Oligo kernels that consider subsequences of different lengths can be combined and parameterized to increase their flexibility. For adapting these parameters efficiently, gradient-based optimization of the kernel-target alignment is proposed. The power of this new, general model selection procedure and the benefits of fitting kernels to problem classes are demonstrated by adapting oligo kernels for bacterial gene start detection.
Characterization of theVIER F-BOX PROTEINEGenes fromArabidopsisReveals Their Importance for Plant Growth and Development
2007-04-01

Abstract E3 ubiquitin ligases (E3s) target proteins for degradation by the 26S proteasome. In SKP1/CDC53/F-box protein–type E3s, substrate specificity is conferred by the interchangeable F-box protein subunit. The vast majority of the 694 F-box proteins encoded by the Arabidopsis thaliana genome remain to be understood. We characterize the VIER F-BOX PROTEINE (VFB; German for FOUR F-BOX PROTEINS) genes from Arabidopsis that belong to subfamily C of the Arabidopsis F-box protein superfamily. This subfamily also includes the F-box proteins TRANSPORT INHIBITOR RESPONSE1 (TIR1)/AUXIN SIGNALING F-BOX (AFB) proteins and EIN3 BINDING F-BOX proteins, which regulate auxin and ethylene responses, respectively. We show that loss of VFB function causes delayed plant growth and reduced lateral root formation. We find that the expression of a number of auxin-responsive genes and the activity of DR5:β-glucuronidase, a reporter for auxin reponse, are reduced in the vfb mutants. This finding correlates with an increase in the abundance of an AUXIN/INDOLE-3-ACETIC ACID repressor. However, we also find that auxin responses are not affected in the vfb mutants and that a representative VFB family member, VFB2, cannot functionally complement the tir1-1 mutant. We therefore exclude the possibility that VFBs are functional orthologs of TIR1/AFB proteins.