bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpretation of the Nano-Electron-Diffraction Patterns along the Five-Fold Axis of Decahedral Gold Nanoparticles
Authors: Romeu L.D. , Reyes-Gasga J. 
Published: March 2011

AbstractThe transition from 10-fold to 5-fold symmetry was observed during the analysis of nanodiffraction patterns of a gold decahedral multiple twinned nanoparticle of 15 nm in diameter. The analysis shows that as the convergence of the beam is increased, the rotational symmetry of the diffraction pattern shifts from 10- to 5-fold. The 10-fold symmetry predicted by Friedel's law is lost by the asymmetric shift of the diffraction spots, an effect that becomes more noticeable as the electron beam convergence increases. Dynamical and kinematical diffraction calculations indicate this decrease in symmetry is the result of a double refraction effect coupled with the variation of the dynamical diffraction conditions arising from a varying electron beam convergence.
Quantum vibrational analysis and infrared spectra of microhydrated sodium ions using an ab initio potential
Authors: Kamarchik Eugene , Wang Yimin , Bowman Joel M. 
Published: March 2011

We present a full-dimensional potential energy surface and a dipole moment surface (DMS) for hydrated sodium ion. These surfaces are based on an n-body expansion for both the potential energy and the dipole moment, truncated at the two-body level for the H2O–Na+ interaction and also for the DMS. The water–water interaction is truncated at the three-body level. The new full-dimensional two-body H2O–Na+ potential is a fit to roughly 20 000 coupled-cluster single double (triple)/aug-cc-pVTZ energies. Properties of this two-body potential and the potential describing (H2O)nNa+ clusters, with n up to 4 are given. We then report anharmonic, coupled vibrational calculations with the “local-monomer model” to obtain infrared spectra and also 0 K radial distribution functions for these clusters. Some comparisons are made with the recent infrared predissociation spectroscopy experiments of Miller and Lisy [J. Am. Chem. Soc. 130, 15381 (2008).]
Unsuspected pathway of the allosteric transition in hemoglobin
Authors: Fischer Stefan , Olsen Kenneth W. , Nam Kwangho , Karplus Martin 
Published: March 2011

Large conformational transitions play an essential role in the function of many proteins, but experiments do not provide the atomic details of the path followed in going from one end structure to the other. For the hemoglobin tetramer, the transition path between the unliganded (T) and tetraoxygenated (R) structures is not known, which limits our understanding of the cooperative mechanism in this classic allosteric system, where both tertiary and quaternary changes are involved. The conjugate peak refinement algorithm is used to compute an unbiased minimum energy path at atomic detail between the two end states. Although the results confirm some of the proposals of Perutz [Perutz MF (1970) Stereochemistry of cooperative effects in haemoglobin.
Nature
228:726–734], the subunit motions do not follow the textbook description of a simple rotation of one αβ-dimer relative to the other. Instead, the path consists of two sequential quaternary rotations, each involving different subdomains and axes. The quaternary transitions are preceded and followed by phases of tertiary structural changes. The results explain the recent photodissociation measurements, which suggest that the quaternary transition has a fast (2 μs) as well as a slow (20 μs) component and provide a testable model for single molecule FRET experiments.
Ectopic B-cell clusters that infiltrate transplanted human kidneys are clonal
Authors: Cheng Julong , Torkamani Ali , Grover Rajesh K. , Jones Teresa M. , Ruiz Diana I. , Schork Nicholas J. , Quigley Michael M. , Hall F. Wesley , Salomon Daniel R. , Lerner Richard A. 
Published: March 2011

B cells and their immunoglobulin products participate in allograft rejection of transplanted human kidneys in which an interesting feature is the presence of a germinal center like B-cell clusters in the allograft. We report here that the immunoglobulin repertoires of these infiltrating B cells are highly restricted and the B cells within a cluster are clonal. Antibody libraries made from the infiltrating B cells of individual patients unexpectedly revealed that each patient utilizes a particular set of dominant germ line genes as well as dominant complementarity determining region 3. Comparison of kidney and peripheral blood from the same patient showed that the immunoglobulin genes from both compartments had dominant clones, but they differed. The lymphocytes that infiltrate the kidneys express the immunoglobulin gene somatic recombination machinery usually restricted to highly activated lymphocytes in germinal centers and lymphomas. An analogy can be made between the inescapable antigenic drive in chronic infection versus that in an allograft, both of which may lead to emergence of dominant B-cell clones and even lymphoid malignancy.
High genetic diversity in a world-wide collection ofLathyrus sativusL. revealed by isozymatic analysis
Authors: Gutiérrez-Marcos José Francisco , Vaquero Francisca , Sáenz de Miera Luis Enrique , Vences Francisco Javier 
Published: March 2011

AbstractGrasspea (Lathyrus sativusL.) is an annual, herbaceous, drought-resistant legume and staple crop in Asian and African countries. Little is known about the nature and the amount of genetic diversity present in existing grasspea seed collections, yet this information is pivotal for future breeding programmes, such as those striving to reduce high neurotoxin levels present in seeds. Here we report on the level of genetic diversity within a world-wide collection ofL. sativus, determined by isozymatic analysis. Although grasspea is generally considered a predominantly self-pollinating species, we found that the population genetic structure of these accessions showed a considerable outcrossing rate of 36%. The identification of a mixed mating system inL. sativushas significant implications for collecting and multiplying genetic resources for conservation and for future breeding purposes. In addition, we determined the genetic closeness of grasspea accessions from different geographical regions around the world. While we noticed an allelic richness in this species that was conserved across the regions, we did not find any evidence of high genetic identity between accessions, even when originating from the same geographical location. Instead, we found that greater genetic variability existed at the intra-regional level than at the inter-regional level.
A DNA fingerprinting-based taxonomic allocation of Kamut wheat
Authors: Khlestkina Elena K. , Röder Marion S. , Grausgruber Heinrich , Börner Andreas 
Published: March 2011

AbstractKamut wheat, said to have been derived from seed found in the Egyptian pyramids, appeared on the market about 25 years ago. We have investigated its taxonomic placement using microsatellite genotyping. In all, 89 accessions of 13 tetraploid wheat species, along with samples of Kamut wheat, were genotyped using two A and B genome wheat microsatellite markers per chromosome, generating 453 alleles (8–33 alleles per locus), and a mean allelic polymorphic information content (PIC) of 0.80. A diversity analysis showed that nine major accession groups could be defined, and these were inconsistent with formal taxonomic classifications of about 10% of the material. Most of these misclassifications are due to either species introgression or seed admixture. Some accessions appear to be duplicates. The Kamut wheats grouped together in a cluster containing three accessions ofTriticum polonicumand three ofT. durum, originating from Turkey, Iraq, Iran and Israel. We suggest that Kamut perhaps derived from a natural hybrid betweenT. durumandT. polonicum, which occurred in the Fertile Crescent.
AFLP marker diversity in water yam (Dioscorea alataL.)
Authors: Egesi C. N. , Asiedu R. , Ude G. , Ogunyemi S. , Egunjobi J. K. 
Published: March 2011

AbstractAmplified fragment length polymorphism (AFLP) markers were employed to assess intraspecific variability in water yam (Dioscorea alataL.). Fifty-three accessions of diverse geographic origins in West and Central Africa (Benin, Côte d'Ivoire, Ghana, Nigeria and Chad) and Puerto Rico were analysed using three AFLP primer combinations. Of the 342 amplification products generated, a mean of 53.4% were polymorphic. Genetic similarity coefficients ranged from 0.29 to 0.95. The accessions could be clustered into three major genetic groups with one outlier. Each group was a mixture of accessions of different geographical origin indicating that geography has not played a major role in the differentiation of the species. A few accessions clustered very tightly suggesting that there may be duplicate accessions in the collection. The wide genetic variation observed constitutes a good basis for genetic improvement of yam.
Structure-based de novo prediction of zinc-binding sites in proteins of unknown function
Authors: Zhao Wei , Xu Meng , Liang Zhi , Ding Bo , Niu Liwen , Liu Haiyan , Teng Maikun 
Published: March 2011

Abstract
Motivation: Zinc-binding proteins are the most abundant metallo-proteins in Protein Data Bank (PDB). Accurate prediction of zinc-binding sites in proteins of unknown function may provide important clues for the inference of protein function. As zinc binding is often associated with characteristic 3D arrangements of zinc ligand residues, its prediction may benefit from using not only the sequence information but also the structure information of proteins.
Results: In this work, we present a structure-based method, TEMSP (3D TEmplate-based Metal Site Prediction), to predict zinc-binding sites. TEMSP significantly improves over previously reported best methods in predicting as many as possible true ligand residues for zinc with minimum overpredictions: if only those results in which all zinc ligand residues have been correctly predicted are defined as true positives, our method improves sensitivity from less than 30% to above 60%, and selectivity from around 25% to 80%. These results are for predictions based on apo state structures. In addition, the method can predict the zinc-bound local structures reliably, generating predictions useful for function inference. We applied TEMSP to 1888 protein structures of the ‘Unknown Function’ class in the PDB database. A number of zinc-binding sites have been discovered de novo, i.e. based solely on the protein structures. Using the predicted local structures of these sites, possible functional roles were analyzed.
Availability: TEMSP is freely available from http://netalign.ustc.edu.cn/temsp/.
Contact: hyliu@ustc.edu.cn; mkteng@ustc.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
A wholly defined Agilent microarray spike-in dataset
Authors: Zhu Qianqian , Miecznikowski Jeffrey C. , Halfon Marc S. 
Published: March 2011

Abstract
Motivation: Spike-in datasets provide a valuable resource for assessing and comparing among competing microarray analysis strategies. Our previous wholly defined spike-in datasets, the Golden and Platinum Spikes, have provided insights for the analysis of Affymetrix GeneChips. However, a similar dataset, in which all cRNA identities and relative levels are known prospectively, has not been available for two-color platforms.
Results: We have generated a wholly defined spike-in dataset for Agilent microarrays consisting of 12 arrays with more than 2000 differentially expressed, and approximately 3600 background, cRNAs. The composition of this ‘Ag Spike’ dataset is identical to that of our previous Platinum Spike dataset and therefore allows direct cross-platform comparison. We demonstrate here the utility of the Ag Spike dataset for evaluating different analysis methods designed for two-color arrays. Comparison between the Ag Spike and Platinum Spike studies shows high agreement between results obtained using the Affymetrix and Agilent platforms.
Availability: The Ag Spike raw data can be accessed at http://www.ccr.buffalo.edu/halfon/spike/index.html and through NCBI's Gene Expression Omnibus (GEO; accession GSE24866).
Contact: qzhu@buffalo.edu; mshalfon@buffalo.edu.
Supplementary information: Supplementary data are available at Bioinformatics online.
Nonspecific Proctitis: Association with Human Immunodeficiency Virus Infection in Homosexual Men
Authors: Law Carmella L. H. , Qassim Mohammed , Cunningham Anthony L. , Mulhall Brian , Grierson Jean M. 
Published: March 2011

Abstract
In a cross-sectional study of 140 homosexual men attending a sexually transmissible diseases clinic, the association between the presence of antibody to the human immunodeficiency virus (HIV) and the presence of proctitis, as determined by histologic examination, as well as past or present exposure to other pathogens and details of sexual practices was analyzed. Significant associations with HIV seropositivity were found with the number of lifetime partners, positive treponemal serology, and evidence of previous infection with herpes simplex virus. However the major and unique finding was the strong and independent association between proctitis diagnosed by histologic criteria and seropositivity for HIV. Whether this is cause or effect awaits further elucidation.
Comprehensive Sequence Analysis of 24,783 Barley Full-Length cDNAs Derived from 12 Clone Libraries
Authors: Matsumoto Takashi , Tanaka Tsuyoshi , Sakai Hiroaki , Amano Naoki , Kanamori Hiroyuki , Kurita Kanako , Kikuta Ari , Kamiya Kozue , Yamamoto Mayu , Ikawa Hiroshi , Fujii Nobuyuki , Hori Kiyosumi , Itoh Takeshi , Sato Kazuhiro 
Published: March 2011

Abstract
Full-length cDNA (FLcDNA) libraries consisting of 172,000 clones were constructed from a two-row malting barley cultivar (Hordeum vulgare ‘Haruna Nijo’) under normal and stressed conditions. After sequencing the clones from both ends and clustering the sequences, a total of 24,783 complete sequences were produced. By removing duplicates between these and publicly available sequences, 22,651 representative sequences were obtained: 17,773 were novel barley FLcDNAs, and 1,699 were barley specific. Highly conserved genes were found in the barley FLcDNA sequences for 721 of 881 rice (Oryza sativa) trait genes with 50% or greater identity. These FLcDNA resources from our Haruna Nijo cDNA libraries and the full-length sequences of representative clones will improve our understanding of the biological functions of genes in barley, which is the cereal crop with the fourth highest production in the world, and will provide a powerful tool for annotating the barley genome sequences that will become available in the near future.
Defining intra‐operative hypotension – a pilot comparison of blood pressure during sleep and general anaesthesia*
Authors: Soo J. C. L. , Lacey S. , Kluger R. , Silbert B. S. 
Published: March 2011

SummaryThe scientific justification for particular values of intra‐operative hypotension is poorly substantiated. To provide a rationale for appropriate values we recorded blood pressure measurements at home for 24 h using an automated non‐invasive ambulatory blood pressure measurement device. These blood pressures were compared with blood pressure measured before and during general anaesthesia in 18 subjects undergoing elective day surgery. We confirmed that a pre‐operative reading taken upon admission to hospital is significantly elevated compared to a usual daytime blood pressure in the same patient. The median (IQR [range]) increases in systolic and mean arterial pressures were 10 (2–15 [−5 to 59]) mmHg, p = 0.003 and 10 (5–14 [−5 to 35]) mmHg, p = 0.002, respectively. When using this admission blood pressure measurement as a ‘baseline’, systolic and mean arterial pressures decreased during sleep by 41 (30–46 [6–83]) mmHg and 34 (26–36 [6–58]) mmHg, respectively (p = 0.001). This decreased even further intra‐operatively: systolic blood pressure by 49 (36–64 [15–96]) mmHg and mean arterial pressure by 36 (26–46 [8–66]) mmHg (p = 0.001).
Epidural volume extension in combined spinal epidural anaesthesia for elective caesarean section: a randomised controlled trial
Authors: Loubert C. , O’Brien P. J. , Fernando R. , Walton N. , Philip S. , Addei T , Columb M. O. , Hallworth S. 
Published: March 2011

SummaryWe investigated the effect of epidural volume extension on spinal blockade in pregnant women undergoing elective caesarean section with a combined spinal‐epidural technique. We randomly allocated 90 healthy subjects to three groups to receive spinal hyperbaric bupivacaine 7.5 mg (group B7.5), spinal hyperbaric bupivacaine 7.5 mg immediately followed by epidural volume extension with saline 5 ml (group B7.5‐EVE) or spinal hyperbaric bupivacaine 10 mg without epidural volume extension (group B10). We evaluated the height of the block every 5 min for 15 min following the spinal injection. The overall sensory block level increased with time (p < 0.001), regardless of the group studied, and there were significantly fewer failures of block in the group B10 compared with both B7.5 and B7.5‐EVE groups (p = 0.001). In conclusion, we could not demonstrate a benefit in using epidural volume extension with 5 ml saline as part of a combined spinal epidural technique in term parturients undergoing elective caesarean section.
Efficacy and safety of high‐dose peanut oral immunotherapy with factors predicting outcome
Authors: Anagnostou K. , Clark A. , King Y. , Islam S. , Deighton J. , Ewan P. 
Published: March 2011

SummaryBackground
Peanut allergy is severe and rarely resolves.Objective
To test the efficacy and safety of a new oral immunotherapy (OIT) protocol for peanut allergy.Method
Twenty‐two peanut‐allergic children underwent oral challenge. OIT was administered by gradual updosing with 2‐weekly increments (8–38 weeks) to 800 mg of protein (5 peanuts/day) followed by 30‐week maintenance. Oral challenge was repeated after 6 and 30 weeks maintenance.Results
Twenty‐two children (median 11 years) had positive challenges (threshold 1–110 mg). Nineteen of 22 (86%) tolerated updosing and maintenance at 800 mg protein/day. One of 22 dropped out; 2/22 tolerated updosing and maintenance at 200–400 mg protein. Reactions, mostly mild, occurred in 86% during immunotherapy, adrenaline was not required. Eight of 8 with pre‐immunotherapy peanut IgE<27.3 kU/L required no dose adjustment compared with 5/13 with pre‐immunotherapy peanut IgE27.3 kU/L. Twelve of 22 (54%) required a transient dose reduction because of reactions possibly related to extrinsic factors: tiredness, infection and exercise. After 6 weeks, 12/22 (54%) had no reaction to a 2.6 g protein challenge. After 30 weeks, 14/22 (64%) tolerated 6.6 g protein. The median tolerated peanut dose increased 1000‐fold following immunotherapy, from 6 to 6459 mg of protein.Conclusions and Clinical Relevance
We used a novel protocol using gradual updosing, and higher maintenance dose resulting in a better outcome compared with rush protocols. There was a 1000‐fold increase in the amount of peanut tolerated with a good safety profile. No serious adverse events occurred. Most subjects tolerated five peanuts and all were protected against amounts likely during accidental ingestion. New information is provided on ‘extrinsic factors’, updosing method and factors associated with success (trial registration http://ClinicalTrials.gov– ID number NCT01259804). Cite this as: K. Anagnostou, A. Clark, Y. King, S. Islam, J. Deighton and P. Ewan, Clinical & Experimental Allergy, 2011 (41) 1273–1281.
An investigation of NCRC11 immunoreactivity in normal and neoplastic epithelia of the female genital tract and ovary
Authors: Hitchcock A. , Ellis I. O. , Bell J. , Robins A. 
Published: March 2011

An investigation of NCRC11 immunoreactivity in normal and neoplastic epithelia of the female genital tract and ovaryNCRC11 is a monoclonal antibody raised against human mammary carcinoma cells. The prognostic value of tumour cell immunoreactivity to NCRC11 in breast cancer has been shown previously. This study describes NCRC11 immunoreactivity in a wide range of normal and neoplastic epithelial types from the female genital tract and ovary. In the tumours examined, a wide range of staining patterns was seen. The implications of these findings are discussed in relation to the potential uses of this antibody in diagnosis and monitoring of gynaecological diseases.
S‐100 protein: Is it useful as a tumour marker in diagnostic immunocytochemistry?
Authors: Schmitt F. C. , Bacchi C. E. 
Published: March 2011

S‐100 protein: Is it useful as a tumour marker in diagnostic immunocytochemistry?A heterogeneous group of 159 tumours was studied for the presence of S‐100 protein by the immunoperoxidase technique in order to determine whether this marker may be of value in facilitating immunocytochemical diagnosis. Among cases of melanocytic and pigmented lesions, S‐100 was widely distributed and demonstrated the strongest degrees of reactivity. S‐100 protein was identified in virtually all nerve sheath tumours such as schwannomas, neurofibromas, myxoid sheath nerve tumour and also in some tumours of controversial histogenesis such as granular cell tumours. The great majority of carcinomas did not express S‐100, with only two cases of breast carcinoma displaying focal S‐100 staining. In a miscellaneous group of tumours S‐100 was demonstrated in chordomas, myoepitheliomas and Wilms” tumour with Schwann cell differentiation. Despite its presence in a wide array of cell types, S‐100 protein continues to be an extremely useful marker especially for soft tissue and peripheral nervous system tumours.
Is discharge knee range of motion a useful and relevant clinical indicator after total knee replacement? Part 2
Authors: Naylor Justine M. , Ko Victoria , Rougellis Steve , Green Nick , Mittal Rajat , Heard Rob , Yeo Anthony E. T. , Barnett Anne , Hackett Danella , Saliba Chris , Smith Nicole , Mackey Martin , Harmer Alison , Harris Ian A. , Adie Sam , McEvoy Lynette 
Published: March 2011

AbstractObjective  Knee range of motion (ROM) at discharge from acute care is used as a clinical indicator following total knee replacement (TKR) surgery. This study aimed to assess the clinical relevance of this indicator by determining whether discharge knee ROM predicts longer‐term knee ROM and patient‐reported knee pain and function.Methods  A total of 176 TKR recipients were prospectively followed after discharge from acute care. Outcomes assessed included knee ROM and Oxford knee score post rehabilitation and 1 year post surgery. Discharge ROM and other patient factors were identified a priori as potential predictors in multiple linear regression modelling.Results  A total of 133 (76%) and 141 (80%) patients were available for follow‐up post rehabilitation [mean postoperative week 8.1 (SD 2.7)] and at 1 year [mean postoperative month 12.1 (SD 1.4)], respectively. Greater discharge knee flexion was a significant (P < 0.001) predictor of greater post‐rehabilitation flexion but not 1‐year knee flexion (P < 0.083). Better discharge knee extension was a significant predictor of better post‐rehabilitation (P = 0.001) and 1‐year knee extension (P = 0.013). Preoperative Oxford score and post‐rehabilitation knee flexion independently predicted post‐rehabilitation Oxford score, and gender predicted 1‐year Oxford score. Discharge ROM did not significantly predict Oxford score in either model.Conclusion  The finding that early knee range predicts longer‐term range provides clinical evidence favouring the relevance of discharge knee ROM as a clinical indicator. Although longer‐term patient‐reported knee pain and function were not directly associated with discharge knee ROM, they were associated with ROM when measured concurrently in the sub‐acute phase. No causal effect has been demonstrated, but the findings suggest it may be important for physiotherapists to maximize range in the early and sub‐acute periods.