bluuebunny/crossref_metadata_2025_split huggingface dataset:
The first hundred families diagnosed with familial hypercholesterolaemia in two lipid clinics in lothian
Authors: Finnie Robert M , Bell Christine , Bloomfield Peter , Ho Clement KM , Jenks Sara , Shand Nicola , Walker Simon W 
Published: November 2012

As in other areas of Western Europe, familial hypercholesterolaemia (FH) is one of the most frequent genetic disorders in the UK. Genetic testing for this condition is available in Scotland. This observational study describes the genetic variants found when the databases of the two principal designated lipid clinics in South East Scotland were amalgamated. The genetic mutations were identified by the Molecular Genetics Department in Aberdeen Royal Infirmary by sequencing all 18 exons of the LDLR gene and using multiplex ligation probe amplification (MLPA) to identify major deletions and duplications in the gene. Variants of the APOB gene at codon 3527 and the common PCSK9 mutations were also investigated. The first 100 genetically positive families (as opposed to individuals) were studied and unidentified variants included. Care was taken not to include patients who could be related. Sixty six different genetic mutations were found, including point mutations, major rearrangements, deletions or duplications or unidentified variants. No PCSK9 mutations were found. The frequency of mutations in different exons of the LDLR gene was explored. There was a higher frequency than expected of unclassified variants. Our results were compared with two commercial kits and analysed with the pick-up rate, in this population, disappointing.
RETRACTED ARTICLE: Proteomic analysis on N, N′-dinitrosopiperazine-mediated metastasis of nasopharyngeal carcinoma 6-10B cells
Authors: Li Yuejin , Liu Na , Huang Damao , Zhang Zhenlin , Peng Zhengke , Duan Chaojun , Tang Xiaowei , Tan Gongjun , Yan Guangrong , Mei Wenhua , Tang Faqing 
Published: November 2012

Abstract
Background
Nasopharyngeal carcinoma (NPC) has a high metastatic feature. N,N′-Dinitrosopiperazine (DNP) is involved in NPC metastasis, but its mechanism is not clear. The aim of this study is to reveal the pathogenesis of DNP-involved metastasis. 6-10B cells with low metastasis are from NPC cell line SUNE-1, were used to investigate the mechanism of DNP-mediated NPC metastasis.

Results
6-10B cells were grown in DMEM containing 2H4-L-lysine and 13C 6 15 N4-L-arginine or conventional L-lysine and L-arginine, and identified the incorporation of amino acid by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Labeled 6-10B cells were treated with DNP at 0 -18 μM to establish the non-cytotoxic concentration (NCC) range. NCC was 0 -10 μM. Following treatment with DNP at this range, the motility and invasion of cells were detected in vitro, and DNP-mediated metastasis was confirmed in the nude mice. DNP increased 6-10B cell metastasis in vitro and vivo. DNP-induced protein expression was investigated using a quantitative proteomic. The SILAC-based approach quantified 2698 proteins, 371 of which showed significant change after DNP treatment (172 up-regulated and 199 down-regulated proteins). DNP induced the change in abundance of mitochondrial proteins, mediated the status of oxidative stress and the imbalance of redox state, increased cytoskeletal protein, cathepsin, anterior gradient-2, and clusterin expression. DNP also increased the expression of secretory AKR1B10, cathepsin B and clusterin 6-10B cells. Gene Ontology and Ingenuity Pathway analysis showed that DNP may regulate protein synthesis, cellular movement, lipid metabolism, molecular transport, cellular growth and proliferation signaling pathways.

Conclusion
DNP may regulate cytoskeletal protein, cathepsin, anterior gradient-2, and clusterin expression, increase NPC cells motility and invasion, is involved NPC metastasis.
Estimating relative abundances of proteins from shotgun proteomics data
Authors: McIlwain Sean , Mathews Michael , Bereman Michael S , Rubel Edwin W , MacCoss Michael J , Noble William Stafford 
Published: November 2012

Abstract

Background
Spectral counting methods provide an easy means of identifying proteins with differing abundances between complex mixtures using shotgun proteomics data. The command, implemented as part of the Crux software toolkit, implements four previously reported spectral counting methods, the spectral index (SI
N
), the exponentially modified protein abundance index (emPAI), the normalized spectral abundance factor (NSAF), and the distributed normalized spectral abundance factor (dNSAF).

Results
We compared the reproducibility and the linearity relative to each protein’s abundance of the four spectral counting metrics. Our analysis suggests that NSAF yields the most reproducible counts across technical and biological replicates, and both SI
N
and NSAF achieve the best linearity.

Conclusions
With the command, Crux provides open-source modular methods to analyze mass spectrometry data for identifying and now quantifying peptides and proteins. The C++ source code, compiled binaries, spectra and sequence databases are available athttp://noble.gs.washington.edu/proj/crux-spectral-counts.
Identification and profiling of novel microRNAs in the Brassica rapagenome based on small RNA deep sequencing
Authors: Kim Bumjin , Yu Hee-Ju , Park Sin-Gi , Shin Ja Young , Oh Mijin , Kim Namshin , Mun Jeong-Hwan 
Published: November 2012

Abstract

Background
MicroRNAs (miRNAs) are one of the functional non-coding small RNAs involved in the epigenetic control of the plant genome. Although plants contain both evolutionary conserved miRNAs and species-specific miRNAs within their genomes, computational methods often only identify evolutionary conserved miRNAs. The recent sequencing of the Brassica rapa genome enables us to identify miRNAs and their putative target genes. In this study, we sought to provide a more comprehensive prediction of B. rapa miRNAs based on high throughput small RNA deep sequencing.

Results
We sequenced small RNAs from five types of tissue: seedlings, roots, petioles, leaves, and flowers. By analyzing 2.75 million unique reads that mapped to the B. rapa genome, we identified 216 novel and 196 conserved miRNAs that were predicted to target approximately 20% of the genome’s protein coding genes. Quantitative analysis of miRNAs from the five types of tissue revealed that novel miRNAs were expressed in diverse tissues but their expression levels were lower than those of the conserved miRNAs. Comparative analysis of the miRNAs between the B. rapa and Arabidopsis thaliana genomes demonstrated that redundant copies of conserved miRNAs in the B. rapa genome may have been deleted after whole genome triplication. Novel miRNA members seemed to have spontaneously arisen from the B. rapa and A. thaliana genomes, suggesting the species-specific expansion of miRNAs. We have made this data publicly available in a miRNA database of B. rapa called BraMRs. The database allows the user to retrieve miRNA sequences, their expression profiles, and a description of their target genes from the five tissue types investigated here.

Conclusions
This is the first report to identify novel miRNAs from Brassica crops using genome-wide high throughput techniques. The combination of computational methods and small RNA deep sequencing provides robust predictions of miRNAs in the genome. The finding of numerous novel miRNAs, many with few target genes and low expression levels, suggests the rapid evolution of miRNA genes. The development of a miRNA database, BraMRs, enables us to integrate miRNA identification, target prediction, and functional annotation of target genes. BraMRs will represent a valuable public resource with which to study the epigenetic control of B. rapa and other closely related Brassica species. The database is available at the following link: http://bramrs.rna.kr [1].
Optimal chroma-like channel design for passive color image splicing detection
Authors: Zhao Xudong , Li Shenghong , Wang Shilin , Li Jianhua , Yang Kongjin 
Published: November 2012

Abstract
Image splicing is one of the most common image forgeries in our daily life and due to the powerful image manipulation tools, image splicing is becoming easier and easier. Several methods have been proposed for image splicing detection and all of them worked on certain existing color channels. However, the splicing artifacts vary in different color channels and the selection of color model is important for image splicing detection. In this article, instead of finding an existing color model, we propose a color channel design method to find the most discriminative channel which is referred to as optimal chroma-like channel for a given feature extraction method. Experimental results show that both spatial and frequency features extracted from the designed channel achieve higher detection rate than those extracted from traditional color channels.
Inferred calcification rate of a Mediterranean azooxanthellate coral is uncoupled with sea surface temperature along an 8° latitudinal gradient
Authors: Caroselli Erik , Mattioli Guido , Levy Oren , Falini Giuseppe , Dubinsky Zvy , Goffredo Stefano 
Published: November 2012

Abstract

Introduction
Correlations between sea surface temperature (SST) and growth parameters of the solitary azooxanthellate Dendrophylliid Leptopsammia pruvoti were assessed along an 8° latitudinal gradient on western Italian coasts (Mediterranean Sea), to check for possible negative effects of increasing temperature as the ones reported for a closely related, sympatric but zooxanthellate species.

Results
Calcification rate was correlated with skeletal density but not with linear extension rate, indicating that calcium carbonate deposition was preferentially allocated to keep a constant skeletal density. Unlike most studies on both temperate and tropical zooxanthellate corals, where calcification rate is strongly related to environmental parameters such as SST, in the present study calcification rate was not correlated with SST.

Conclusions
The lower sensitivity of L. pruvoti to SST with respect to other sympatric zooxanthellate corals, such as Balanophyllia europaea, may rely on the absence of a temperature induced inhibition of photosynthesis, and thus the absence of an inhibition of the calcification process. This study is the first field investigation of the relationship between SST and the three growth parameters of an azooxanthellate coral. Increasing research effort on determining the effects of temperature on biological traits of the poorly studied azooxanthellate scleractinians may help to predict the possible species assemblage shifts that are likely to occur in the immediate future as a consequence of global climatic change.
Tick infestations in extensively grazed cattle and efficacy trial of high-cis cypermethrin pour-on preparation for control of ticks in Mvomero district in Tanzania
Authors: Hezron E Nonga , Adrian Muwonge , Robinson H Mdegela 
Published: November 2012

Abstract

Background
This study aimed at determining the extent of tick infestations in extensively grazed cattle and assess the efficacy of Ecotix® acaricide (2.5% high cis cypermethrin) in Mvomero district in Tanzania. A total of 1200 Tanzanian short horn Zebu (TSHZ) from two farms in two villages were qualitatively assessed for tick infestations and 40 animals (grouped in 10s from each farm) were separated in their herds and quantitatively examined to establish the tick load. The animals were grouped in treatment regime groups (TxRG 1, 2, 3, and 4), TxRG 1 being the control group was treated with water. Ecotix® was applied on day 0 for TxRG 2, days 0 and 7 for TxRG 3 and days 0, 7 and 14 for TxRG 4 and tick load was monitored for 28 days.

Results
All the animals examined were infested with ticks. The identified ticks were Rhipicephalus appendiculatus (55%), Amblyomma variegatum (18%), R. (Boophilus) microplus (12.9%), R. (B) decoloratus (7.1%), R. evertsi evertsi (4.4%) and R. composites (2.6%). The overall mean (mean ± SEM) tick density on day zero was 63 ± 30 ticks per animal (ranging from 20–160). The mean tick density on day zero was 44.6 ± 25.4, 74.6 ± 30.3, 55.0 ± 26.2 and 77 ± 33.5 for groups one, two, three and four respectively. Post-treatment quantitative assessment of tick burden revealed that the TxRG 1 animals maintained a tick load throughout the study period. A significant decrease in tick load in animals in groups TxRG 2, 3 and 4 (P=0.0001) with increasing frequency of Ecotix® application was recorded. There was however no significant difference in tick reduction between TxRG 3 and 4 (P=0.0986). Thus TxRG 3 would be sufficient for the monthly tick treatment and with this regime, the farmer would save up to 2.5 USD per animal during six months of dry season.

Conclusions
The study revealed a high tick infestation among the TSHZ kept in extensive grazing systems in Mvomero district and that when treated with Ecotix® as pour-on preparation using a two application regime per month, the tick control strategy was effective.
Relationship between beta-globin gene carrier state and insulin resistance
Authors: Bahar Adele , Kashi Zahra , Sohrab Mehrnoush , Kosaryan Mehrnoush , Janbabai Ghasem 
Published: November 2012

Abstract
Objective
To assess the relationship between being beta globin gene carrier and developing insulin resistance.

Methods
This study was conducted on 164 subjects including 82 healthy ones and 82 patients with beta thalassemia minor (microcytosis (MCV <80 fl) and hypochromia (MCH <25 pg) and HbA2 ≥ 3.5% using HPLC). Fasting blood glucose (FBS) values of 100–125 mg/dl were considered as impaired fasting glucose, and above
125 mg/dl as diabetes mellitus. Two hours After 75 gram glucose load(GTT), blood sugar level of 140–199 mg/dl was considered as impaired glucose tolerance and above 199 mg/dl as diabetes mellitus. Insulin resistance was diagnosed based on homeostasis model assessment method (HOMA).

Results
According to FBS and BS2hPG values, the percentages of diabetes mellitus, pre diabetes, and normal glucose tolerance in case group was 8.5%, 9.8% and 81.7%, respectively. There was no case of diabetes mellitus in control group and 6.1% of this group were pre diabetic and 93.9% of them had normal glucose tolerance test
(P = 0.02). Relative risk for diabetes mellitus and insulin resistance in the cases with minor thalassemia was
2 (95% CI: 1.8-2.5) and 2.02 (95% CI: 1.7-2.4), respectively.

Conclusion
The risk of developing diabetes and insulin resistance in patients with thalassemia minor is two times greater than the general population. Considering the high serum levels of CRP in these cases, the inflammation noted in liver cells could be considered as the underlying cause of insulin resistance, impaired glucose tolerance and diabetes in these patients.
Surgical Results of Patients With Unilateral Superior Oblique Palsy Presenting With Large Hypertropias
Authors: Nejad Mitra , Thacker Neepa , Velez Federico G. , Rosenbaum Arthur L. , Pineles Stacy L. 
Published: November 2012

Purpose:
Surgical management of superior oblique palsy (SOP) is challenging because of combined vertical, horizontal, and torsional misalignment. The authors report the surgical results of patients with large primary position hypertropias (> 20 prism diopters [PD]) due to unilateral SOP.

Methods:
Criteria for success included correction of the anomalous head posture, primary position alignment between orthotropia and 6 PD of undercorrection, and no reoperation required for residual deviations in any direction of gaze.

Results:

Forty-five patients met inclusion criteria. Mean preoperative alignment in primary gaze was 26.5 ± 6.5 PD compared to 3.0 ± 4.4 PD postoperatively (
P
< .001). Twenty-three (51%) cases met the criteria for success with one operation. Of the patients who had single muscle surgery, 14% had a successful outcome, with a mean 67% (17.3 PD) reduction in hypertropia. Of patients who underwent simultaneous multiple muscle surgery, 58% met the criteria for a successful result, with a mean 92% (24.6 PD) reduction in primary gaze hypertropia. Success was the highest in patients who underwent ipsilateral inferior oblique combined with contralateral inferior rectus recessions with (60% success) or without (65% success) a Harada–Ito procedure.

Conclusion:
Undercorrections are frequent following surgery for unilateral SOP with preoperative deviations greater than 20 PD in primary position, especially after single-muscle surgery. Simultaneous multiple muscle surgery rarely results in overcorrection and is recommended in patients with SOP and more than 20 PD of hypertropia in primary position.
Assessment of Breast Volume Change after Transverse Rectus Abdominis Myocutaneous Flap
Authors: Park Sang Uk , Shim Jeong Su 
Published: November 2012

Background The evaluation of a breast after breast reconstruction depends on a surgeon's subjective criteria. We used computed tomography (CT) scans to obtain an objective evaluation of the postoperative results by measuring the breast volume of patients who had undergone breast reconstruction using pedicled transverse rectus abdominis myocutaneous (TRAM) flaps. This research will help in the objective postoperative evaluation of reconstructed breasts, and also in the preoperative flap size designs.
Methods A total of 27 patients underwent breast reconstruction using pedicled TRAM flaps after mastectomy from September 2007 to July 2010. Of these, 10 patients who were followed up and underwent CT scans 2 or more times during the follow-up period were included in this study. We evaluated the change in breast volume over time using CT scans, and the interval breast volume change between CT scans.
Results All of the 10 patients' reconstructed breasts showed a volume decrease over time. The breast volume changes in the intervals between CT scans were as follows: 5.65% decrease between the first CT and second CT scan, 2.3% decrease between the second CT and third CT scan, (statistically significant) and 1.89% decrease between the third CT and forth CT scan. (not statistically significant).
Conclusions This research shows the possibility of objectively evaluating the postoperative breast volume changes. The findings will be helpful in designing the size of TRAM flaps to use on defects after mastectomy. Based on these results, we should also closely observe the reconstructed breast volume for at least 2 years.
Fluorescent Labeling of Specific Cysteine Residues Using CyMPL
Authors: Puljung Michael C. , Zagotta William N. 
Published: November 2012

AbstractThe unique reactivity and relative rarity of cysteine among amino acids makes it a convenient target for the site‐specific chemical modification of proteins. Commercially available fluorophores and modifiers react with cysteine through a variety of electrophilic functional groups. However, it can be difficult to achieve specific labeling of a particular cysteine residue in a protein containing multiple cysteines, in a mixture of proteins, or in a protein's native environment. This unit describes a procedure termed CyMPL (Cysteine Metal Protection and Labeling), which enables specific labeling by incorporating a cysteine of interest into a minimal binding site for group 12 metal ions (e.g., Cd2+ and Zn2+). These sites can be inserted into any region of known secondary structure in virtually any protein and cause minimal structural perturbation. Bound metal ions protect the cysteine from reaction while background cysteines are covalently blocked with non‐fluorescent modifiers. The metal ions are subsequently removed and the deprotected cysteine is labeled specifically. Curr. Protoc. Protein Sci. 70:14.14.1‐14.14.10. © 2012 by John Wiley & Sons, Inc.
Lithographic Resists
Authors: Hinsberg W. D. , Wallraff G. M. 
Published: November 2012

Abstract
This article provides an overview of the chemistry and processes used to form micro‐ and nanoscale patterns for the fabrication of semiconductors and other electronic devices. The basic functional attributes of lithographic resists and the physical principles of modern lithographic process technologies are addressed. The imaging chemistry of the major classes of resists in current use is described. A detailed discussion of chemically amplified resists, the most widely used class of resist, summarizes their evolutionary development, mechanisms of imaging chemistry, key processing characteristics, and factors that limit ultimate extendibility. A number of newly emerging techniques for lithographic patterning are described.
Relation of Cell Uniformity and Mechanical Property of a Close Cell Aluminum Foam
Authors: Deqing Wang 
Published: November 2012

AbstractSamples of closed‐cell aluminum foams are prepared by air‐foaming aluminum melt, and two techniques are employed to obtain uniform and non‐uniform aluminum foams under identical processing conditions. Experiment results show that the uniform‐celled aluminum foam presents an overall 25% improvement of the yield strength over the one for the non‐uniform cells with the same density, and a very precise relation between yield strength and density is obtained for the uniform‐celled aluminum foam. The cell size uniformization does not affect elastic modulus significantly, and the uniformity of the aluminum foam cells decreases the energy absorption ability.
SERS Active Surface in Two Steps, Patterning and Metallization
Authors: Acevedo Diego , Salavagione Horacio , Lasagni Andrés , Morallón Emilia , Mücklich Frank , Barbero César 
Published: November 2012

AbstractRobust and reproducible metallized nano/microstructured surfaces of polymeric surfaces have been successfully prepared by direct laser interference patterning (DLIP) of commercial polymeric films followed by sputtering of metallic thin films. The SERS spectra for 2‐thioaniline adsorbed on a structured polycarbonate surfaces covered with a gold or platinum film showed a ca. three order of magnitude enhancement over a flat surface with the same metal film. The method here reported is suitable for mass production of substrates for SERS since large areas (several cm2) can be structured in ca. 1–5 s.
Graphene‐Based Nanomaterials: Synthesis, Properties, and Optical and Optoelectronic Applications
Authors: Chang Haixin , Wu Hongkai 
Published: November 2012

AbstractGraphene, a two‐dimensional, single‐atom‐thick carbon crystal arranged in a honeycomb lattice, shows extraordinary electronic, mechanical, thermal, optical, and optoelectronic properties, and has great potential in next‐generation electronics, optics, and optoelectronics. Graphene and graphene‐based nanomaterials have witnessed a very fast development of both fundamental and practical aspects in optics and optoelectronics since 2008. In this Feature Article, the synthesis techniques and main electronic and optical properties of graphene‐based nanomaterials are introduced with a comprehensive view. Recent progress of graphene‐based nanomaterials in optical and optoelectronic applications is then reviewed, including transparent conductive electrodes, photodetectors and phototransistors, photovoltaics and light emitting devices, saturable absorbers for ultrafast lasers, and biological and photocatalytic applications. In the final section, perspectives are given and future challenges in optical and optoelectronic applications of graphene‐based nanomaterials are addressed.